Mock Version: 2.15 Mock Version: 2.15 Mock Version: 2.15 ENTER ['do_with_status'](['bash', '--login', '-c', '/usr/bin/rpmbuild -bs --target riscv64 --nodeps /builddir/build/SPECS/python-pysam.spec'], chrootPath='/var/lib/mock/f40-build-764741-123116/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=432000uid=991gid=135user='mockbuild'nspawn_args=[]unshare_net=TrueprintOutput=False) Executing command: ['bash', '--login', '-c', '/usr/bin/rpmbuild -bs --target riscv64 --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'} and shell False Building target platforms: riscv64 Building for target riscv64 setting SOURCE_DATE_EPOCH=1701302400 Wrote: /builddir/build/SRPMS/python-pysam-0.22.0-2.fc40.src.rpm Child return code was: 0 ENTER ['do_with_status'](['bash', '--login', '-c', '/usr/bin/rpmbuild -bb --target riscv64 --nodeps /builddir/build/SPECS/python-pysam.spec'], chrootPath='/var/lib/mock/f40-build-764741-123116/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=432000uid=991gid=135user='mockbuild'nspawn_args=[]unshare_net=TrueprintOutput=False) Executing command: ['bash', '--login', '-c', '/usr/bin/rpmbuild -bb --target riscv64 --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'} and shell False Building target platforms: riscv64 Building for target riscv64 setting SOURCE_DATE_EPOCH=1701302400 Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.SEtMWX + 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/libcvcf.c pysam/libcfaidx.c pysam/libcalignedsegment.c pysam/libcbcftools.c pysam/libcsamfile.c pysam/libcutils.c pysam/libcsamtools.c pysam/libcalignmentfile.c pysam/libchtslib.c pysam/libctabix.c pysam/libcbgzf.c pysam/libctabixproxies.c pysam/libcbcf.c + RPM_EC=0 ++ jobs -p + exit 0 Executing(%build): /bin/sh -e /var/tmp/rpm-tmp.CBRoDD + umask 022 + cd /builddir/build/BUILD + CFLAGS='-O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -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 -fasynchronous-unwind-tables -fno-omit-frame-pointer ' + export CFLAGS + CXXFLAGS='-O2 -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 -fasynchronous-unwind-tables -fno-omit-frame-pointer ' + export CXXFLAGS + FFLAGS='-O2 -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 -fasynchronous-unwind-tables -fno-omit-frame-pointer -I/usr/lib64/gfortran/modules ' + export FFLAGS + FCFLAGS='-O2 -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 -fasynchronous-unwind-tables -fno-omit-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=-Wl,-z,relro -Clink-arg=-Wl,-z,now -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 -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 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -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 -fasynchronous-unwind-tables -fno-omit-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -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 -fasynchronous-unwind-tables -fno-omit-frame-pointer -fPIC # pysam: (env) LDFLAGS=-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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-riscv64-cpython-312 creating build/lib.linux-riscv64-cpython-312/pysam copying pysam/version.py -> build/lib.linux-riscv64-cpython-312/pysam copying pysam/__init__.py -> build/lib.linux-riscv64-cpython-312/pysam copying pysam/config.py -> build/lib.linux-riscv64-cpython-312/pysam copying pysam/bcftools.py -> build/lib.linux-riscv64-cpython-312/pysam copying pysam/samtools.py -> build/lib.linux-riscv64-cpython-312/pysam copying pysam/utils.py -> build/lib.linux-riscv64-cpython-312/pysam copying pysam/Pileup.py -> build/lib.linux-riscv64-cpython-312/pysam creating build/lib.linux-riscv64-cpython-312/pysam/include copying pysam/include/__init__.py -> build/lib.linux-riscv64-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:204: _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:204: _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:204: _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:204: _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:204: _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-riscv64-cpython-312/pysam copying pysam/csamtools_util.h -> build/lib.linux-riscv64-cpython-312/pysam copying pysam/htslib_util.c -> build/lib.linux-riscv64-cpython-312/pysam copying pysam/htslib_util.h -> build/lib.linux-riscv64-cpython-312/pysam copying pysam/libcalignedsegment.pxd -> build/lib.linux-riscv64-cpython-312/pysam copying pysam/libcalignedsegment.pyi -> build/lib.linux-riscv64-cpython-312/pysam copying pysam/libcalignedsegment.pyx -> build/lib.linux-riscv64-cpython-312/pysam copying pysam/libcalignmentfile.pxd -> build/lib.linux-riscv64-cpython-312/pysam copying pysam/libcalignmentfile.pyi -> build/lib.linux-riscv64-cpython-312/pysam copying pysam/libcalignmentfile.pyx -> build/lib.linux-riscv64-cpython-312/pysam copying pysam/libcbcf.pxd -> build/lib.linux-riscv64-cpython-312/pysam copying pysam/libcbcf.pyi -> build/lib.linux-riscv64-cpython-312/pysam copying pysam/libcbcf.pyx -> build/lib.linux-riscv64-cpython-312/pysam copying pysam/libcbcftools.pxd -> build/lib.linux-riscv64-cpython-312/pysam copying pysam/libcbcftools.pyi -> build/lib.linux-riscv64-cpython-312/pysam copying pysam/libcbcftools.pyx -> build/lib.linux-riscv64-cpython-312/pysam copying pysam/libcbgzf.pyi -> build/lib.linux-riscv64-cpython-312/pysam copying pysam/libcbgzf.pyx -> build/lib.linux-riscv64-cpython-312/pysam copying pysam/libcfaidx.pxd -> build/lib.linux-riscv64-cpython-312/pysam copying pysam/libcfaidx.pyi -> build/lib.linux-riscv64-cpython-312/pysam copying pysam/libcfaidx.pyx -> build/lib.linux-riscv64-cpython-312/pysam copying pysam/libchtslib.pxd -> build/lib.linux-riscv64-cpython-312/pysam copying pysam/libchtslib.pyi -> build/lib.linux-riscv64-cpython-312/pysam copying pysam/libchtslib.pyx -> build/lib.linux-riscv64-cpython-312/pysam copying pysam/libcsamfile.pxd -> build/lib.linux-riscv64-cpython-312/pysam copying pysam/libcsamfile.pyi -> build/lib.linux-riscv64-cpython-312/pysam copying pysam/libcsamfile.pyx -> build/lib.linux-riscv64-cpython-312/pysam copying pysam/libcsamtools.pxd -> build/lib.linux-riscv64-cpython-312/pysam copying pysam/libcsamtools.pyi -> build/lib.linux-riscv64-cpython-312/pysam copying pysam/libcsamtools.pyx -> build/lib.linux-riscv64-cpython-312/pysam copying pysam/libctabix.pxd -> build/lib.linux-riscv64-cpython-312/pysam copying pysam/libctabix.pyi -> build/lib.linux-riscv64-cpython-312/pysam copying pysam/libctabix.pyx -> build/lib.linux-riscv64-cpython-312/pysam copying pysam/libctabixproxies.pxd -> build/lib.linux-riscv64-cpython-312/pysam copying pysam/libctabixproxies.pyi -> build/lib.linux-riscv64-cpython-312/pysam copying pysam/libctabixproxies.pyx -> build/lib.linux-riscv64-cpython-312/pysam copying pysam/libcutils.pxd -> build/lib.linux-riscv64-cpython-312/pysam copying pysam/libcutils.pyi -> build/lib.linux-riscv64-cpython-312/pysam copying pysam/libcutils.pyx -> build/lib.linux-riscv64-cpython-312/pysam copying pysam/libcvcf.pxd -> build/lib.linux-riscv64-cpython-312/pysam copying pysam/libcvcf.pyi -> build/lib.linux-riscv64-cpython-312/pysam copying pysam/libcvcf.pyx -> build/lib.linux-riscv64-cpython-312/pysam copying pysam/py.typed -> build/lib.linux-riscv64-cpython-312/pysam copying pysam/pysam_stream.h -> build/lib.linux-riscv64-cpython-312/pysam copying pysam/pysam_util.c -> build/lib.linux-riscv64-cpython-312/pysam copying pysam/pysam_util.h -> build/lib.linux-riscv64-cpython-312/pysam copying pysam/version.h -> build/lib.linux-riscv64-cpython-312/pysam copying pysam/version.pyi -> build/lib.linux-riscv64-cpython-312/pysam creating build/lib.linux-riscv64-cpython-312/pysam/include/samtools copying samtools/LICENSE -> build/lib.linux-riscv64-cpython-312/pysam/include/samtools copying samtools/README -> build/lib.linux-riscv64-cpython-312/pysam/include/samtools copying samtools/amplicon_stats.c -> build/lib.linux-riscv64-cpython-312/pysam/include/samtools copying samtools/amplicon_stats.c.pysam.c -> build/lib.linux-riscv64-cpython-312/pysam/include/samtools copying samtools/bam.c -> build/lib.linux-riscv64-cpython-312/pysam/include/samtools copying samtools/bam.c.pysam.c -> build/lib.linux-riscv64-cpython-312/pysam/include/samtools copying samtools/bam.h -> build/lib.linux-riscv64-cpython-312/pysam/include/samtools copying samtools/bam2depth.c -> build/lib.linux-riscv64-cpython-312/pysam/include/samtools copying samtools/bam2depth.c.pysam.c -> build/lib.linux-riscv64-cpython-312/pysam/include/samtools copying samtools/bam_addrprg.c -> build/lib.linux-riscv64-cpython-312/pysam/include/samtools copying samtools/bam_addrprg.c.pysam.c -> build/lib.linux-riscv64-cpython-312/pysam/include/samtools copying samtools/bam_ampliconclip.c -> build/lib.linux-riscv64-cpython-312/pysam/include/samtools copying samtools/bam_ampliconclip.c.pysam.c -> build/lib.linux-riscv64-cpython-312/pysam/include/samtools copying samtools/bam_ampliconclip.h -> build/lib.linux-riscv64-cpython-312/pysam/include/samtools copying samtools/bam_aux.c -> build/lib.linux-riscv64-cpython-312/pysam/include/samtools copying samtools/bam_aux.c.pysam.c -> build/lib.linux-riscv64-cpython-312/pysam/include/samtools copying samtools/bam_cat.c -> build/lib.linux-riscv64-cpython-312/pysam/include/samtools copying samtools/bam_cat.c.pysam.c -> build/lib.linux-riscv64-cpython-312/pysam/include/samtools copying samtools/bam_color.c -> build/lib.linux-riscv64-cpython-312/pysam/include/samtools copying samtools/bam_color.c.pysam.c -> build/lib.linux-riscv64-cpython-312/pysam/include/samtools copying samtools/bam_consensus.c -> build/lib.linux-riscv64-cpython-312/pysam/include/samtools copying samtools/bam_consensus.c.pysam.c -> build/lib.linux-riscv64-cpython-312/pysam/include/samtools copying samtools/bam_fastq.c -> build/lib.linux-riscv64-cpython-312/pysam/include/samtools copying samtools/bam_fastq.c.pysam.c -> build/lib.linux-riscv64-cpython-312/pysam/include/samtools copying samtools/bam_flags.c -> build/lib.linux-riscv64-cpython-312/pysam/include/samtools copying samtools/bam_flags.c.pysam.c -> build/lib.linux-riscv64-cpython-312/pysam/include/samtools copying samtools/bam_import.c -> build/lib.linux-riscv64-cpython-312/pysam/include/samtools copying samtools/bam_import.c.pysam.c -> build/lib.linux-riscv64-cpython-312/pysam/include/samtools copying samtools/bam_index.c -> build/lib.linux-riscv64-cpython-312/pysam/include/samtools copying samtools/bam_index.c.pysam.c -> build/lib.linux-riscv64-cpython-312/pysam/include/samtools copying samtools/bam_lpileup.c -> build/lib.linux-riscv64-cpython-312/pysam/include/samtools copying samtools/bam_lpileup.c.pysam.c -> build/lib.linux-riscv64-cpython-312/pysam/include/samtools copying samtools/bam_lpileup.h -> build/lib.linux-riscv64-cpython-312/pysam/include/samtools copying samtools/bam_markdup.c -> build/lib.linux-riscv64-cpython-312/pysam/include/samtools copying samtools/bam_markdup.c.pysam.c -> build/lib.linux-riscv64-cpython-312/pysam/include/samtools copying samtools/bam_mate.c -> build/lib.linux-riscv64-cpython-312/pysam/include/samtools copying samtools/bam_mate.c.pysam.c -> build/lib.linux-riscv64-cpython-312/pysam/include/samtools copying samtools/bam_md.c -> build/lib.linux-riscv64-cpython-312/pysam/include/samtools copying samtools/bam_md.c.pysam.c -> build/lib.linux-riscv64-cpython-312/pysam/include/samtools copying samtools/bam_plbuf.c -> build/lib.linux-riscv64-cpython-312/pysam/include/samtools copying samtools/bam_plbuf.c.pysam.c -> build/lib.linux-riscv64-cpython-312/pysam/include/samtools copying samtools/bam_plbuf.h -> build/lib.linux-riscv64-cpython-312/pysam/include/samtools copying samtools/bam_plcmd.c -> build/lib.linux-riscv64-cpython-312/pysam/include/samtools copying samtools/bam_plcmd.c.pysam.c -> build/lib.linux-riscv64-cpython-312/pysam/include/samtools copying samtools/bam_quickcheck.c -> build/lib.linux-riscv64-cpython-312/pysam/include/samtools copying samtools/bam_quickcheck.c.pysam.c -> build/lib.linux-riscv64-cpython-312/pysam/include/samtools copying samtools/bam_reheader.c -> build/lib.linux-riscv64-cpython-312/pysam/include/samtools copying samtools/bam_reheader.c.pysam.c -> build/lib.linux-riscv64-cpython-312/pysam/include/samtools copying samtools/bam_rmdup.c -> build/lib.linux-riscv64-cpython-312/pysam/include/samtools copying samtools/bam_rmdup.c.pysam.c -> build/lib.linux-riscv64-cpython-312/pysam/include/samtools copying samtools/bam_rmdupse.c -> build/lib.linux-riscv64-cpython-312/pysam/include/samtools copying samtools/bam_rmdupse.c.pysam.c -> build/lib.linux-riscv64-cpython-312/pysam/include/samtools copying samtools/bam_samples.c -> build/lib.linux-riscv64-cpython-312/pysam/include/samtools copying samtools/bam_samples.c.pysam.c -> build/lib.linux-riscv64-cpython-312/pysam/include/samtools copying samtools/bam_sort.c -> build/lib.linux-riscv64-cpython-312/pysam/include/samtools copying samtools/bam_sort.c.pysam.c -> build/lib.linux-riscv64-cpython-312/pysam/include/samtools copying samtools/bam_split.c -> build/lib.linux-riscv64-cpython-312/pysam/include/samtools copying samtools/bam_split.c.pysam.c -> build/lib.linux-riscv64-cpython-312/pysam/include/samtools copying samtools/bam_stat.c -> build/lib.linux-riscv64-cpython-312/pysam/include/samtools copying samtools/bam_stat.c.pysam.c -> build/lib.linux-riscv64-cpython-312/pysam/include/samtools copying samtools/bamshuf.c -> build/lib.linux-riscv64-cpython-312/pysam/include/samtools copying samtools/bamshuf.c.pysam.c -> build/lib.linux-riscv64-cpython-312/pysam/include/samtools copying samtools/bamtk.c -> build/lib.linux-riscv64-cpython-312/pysam/include/samtools copying samtools/bamtk.c.pysam.c -> build/lib.linux-riscv64-cpython-312/pysam/include/samtools copying samtools/bedcov.c -> build/lib.linux-riscv64-cpython-312/pysam/include/samtools copying samtools/bedcov.c.pysam.c -> build/lib.linux-riscv64-cpython-312/pysam/include/samtools copying samtools/bedidx.c -> build/lib.linux-riscv64-cpython-312/pysam/include/samtools copying samtools/bedidx.c.pysam.c -> build/lib.linux-riscv64-cpython-312/pysam/include/samtools copying samtools/bedidx.h -> build/lib.linux-riscv64-cpython-312/pysam/include/samtools copying samtools/consensus_pileup.c -> build/lib.linux-riscv64-cpython-312/pysam/include/samtools copying samtools/consensus_pileup.c.pysam.c -> build/lib.linux-riscv64-cpython-312/pysam/include/samtools copying samtools/consensus_pileup.h -> build/lib.linux-riscv64-cpython-312/pysam/include/samtools copying samtools/coverage.c -> build/lib.linux-riscv64-cpython-312/pysam/include/samtools copying samtools/coverage.c.pysam.c -> build/lib.linux-riscv64-cpython-312/pysam/include/samtools copying samtools/cram_size.c -> build/lib.linux-riscv64-cpython-312/pysam/include/samtools copying samtools/cram_size.c.pysam.c -> build/lib.linux-riscv64-cpython-312/pysam/include/samtools copying samtools/cut_target.c -> build/lib.linux-riscv64-cpython-312/pysam/include/samtools copying samtools/cut_target.c.pysam.c -> build/lib.linux-riscv64-cpython-312/pysam/include/samtools copying samtools/dict.c -> build/lib.linux-riscv64-cpython-312/pysam/include/samtools copying samtools/dict.c.pysam.c -> build/lib.linux-riscv64-cpython-312/pysam/include/samtools copying samtools/faidx.c -> build/lib.linux-riscv64-cpython-312/pysam/include/samtools copying samtools/faidx.c.pysam.c -> build/lib.linux-riscv64-cpython-312/pysam/include/samtools copying samtools/padding.c -> build/lib.linux-riscv64-cpython-312/pysam/include/samtools copying samtools/padding.c.pysam.c -> build/lib.linux-riscv64-cpython-312/pysam/include/samtools copying samtools/phase.c -> build/lib.linux-riscv64-cpython-312/pysam/include/samtools copying samtools/phase.c.pysam.c -> build/lib.linux-riscv64-cpython-312/pysam/include/samtools copying samtools/reference.c -> build/lib.linux-riscv64-cpython-312/pysam/include/samtools copying samtools/reference.c.pysam.c -> build/lib.linux-riscv64-cpython-312/pysam/include/samtools copying samtools/reset.c -> build/lib.linux-riscv64-cpython-312/pysam/include/samtools copying samtools/reset.c.pysam.c -> build/lib.linux-riscv64-cpython-312/pysam/include/samtools copying samtools/sam_opts.c -> build/lib.linux-riscv64-cpython-312/pysam/include/samtools copying samtools/sam_opts.c.pysam.c -> build/lib.linux-riscv64-cpython-312/pysam/include/samtools copying samtools/sam_opts.h -> build/lib.linux-riscv64-cpython-312/pysam/include/samtools copying samtools/sam_utils.c -> build/lib.linux-riscv64-cpython-312/pysam/include/samtools copying samtools/sam_utils.c.pysam.c -> build/lib.linux-riscv64-cpython-312/pysam/include/samtools copying samtools/sam_utils.h -> build/lib.linux-riscv64-cpython-312/pysam/include/samtools copying samtools/sam_view.c -> build/lib.linux-riscv64-cpython-312/pysam/include/samtools copying samtools/sam_view.c.pysam.c -> build/lib.linux-riscv64-cpython-312/pysam/include/samtools copying samtools/sample.c -> build/lib.linux-riscv64-cpython-312/pysam/include/samtools copying samtools/sample.c.pysam.c -> build/lib.linux-riscv64-cpython-312/pysam/include/samtools copying samtools/sample.h -> build/lib.linux-riscv64-cpython-312/pysam/include/samtools copying samtools/samtools.h -> build/lib.linux-riscv64-cpython-312/pysam/include/samtools copying samtools/samtools.pysam.c -> build/lib.linux-riscv64-cpython-312/pysam/include/samtools copying samtools/samtools.pysam.h -> build/lib.linux-riscv64-cpython-312/pysam/include/samtools copying samtools/splaysort.h -> build/lib.linux-riscv64-cpython-312/pysam/include/samtools copying samtools/stats.c -> build/lib.linux-riscv64-cpython-312/pysam/include/samtools copying samtools/stats.c.pysam.c -> build/lib.linux-riscv64-cpython-312/pysam/include/samtools copying samtools/stats_isize.c -> build/lib.linux-riscv64-cpython-312/pysam/include/samtools copying samtools/stats_isize.c.pysam.c -> build/lib.linux-riscv64-cpython-312/pysam/include/samtools copying samtools/stats_isize.h -> build/lib.linux-riscv64-cpython-312/pysam/include/samtools copying samtools/tmp_file.c -> build/lib.linux-riscv64-cpython-312/pysam/include/samtools copying samtools/tmp_file.c.pysam.c -> build/lib.linux-riscv64-cpython-312/pysam/include/samtools copying samtools/tmp_file.h -> build/lib.linux-riscv64-cpython-312/pysam/include/samtools copying samtools/version.sh -> build/lib.linux-riscv64-cpython-312/pysam/include/samtools creating build/lib.linux-riscv64-cpython-312/pysam/include/samtools/lz4 copying samtools/lz4/LICENSE -> build/lib.linux-riscv64-cpython-312/pysam/include/samtools/lz4 copying samtools/lz4/lz4.c -> build/lib.linux-riscv64-cpython-312/pysam/include/samtools/lz4 copying samtools/lz4/lz4.c.pysam.c -> build/lib.linux-riscv64-cpython-312/pysam/include/samtools/lz4 copying samtools/lz4/lz4.h -> build/lib.linux-riscv64-cpython-312/pysam/include/samtools/lz4 copying samtools/config.h -> build/lib.linux-riscv64-cpython-312/pysam/include/samtools creating build/lib.linux-riscv64-cpython-312/pysam/include/bcftools copying bcftools/HMM.c -> build/lib.linux-riscv64-cpython-312/pysam/include/bcftools copying bcftools/HMM.c.pysam.c -> build/lib.linux-riscv64-cpython-312/pysam/include/bcftools copying bcftools/HMM.h -> build/lib.linux-riscv64-cpython-312/pysam/include/bcftools copying bcftools/LICENSE -> build/lib.linux-riscv64-cpython-312/pysam/include/bcftools copying bcftools/README -> build/lib.linux-riscv64-cpython-312/pysam/include/bcftools copying bcftools/abuf.c -> build/lib.linux-riscv64-cpython-312/pysam/include/bcftools copying bcftools/abuf.c.pysam.c -> build/lib.linux-riscv64-cpython-312/pysam/include/bcftools copying bcftools/abuf.h -> build/lib.linux-riscv64-cpython-312/pysam/include/bcftools copying bcftools/bam2bcf.c -> build/lib.linux-riscv64-cpython-312/pysam/include/bcftools copying bcftools/bam2bcf.c.pysam.c -> build/lib.linux-riscv64-cpython-312/pysam/include/bcftools copying bcftools/bam2bcf.h -> build/lib.linux-riscv64-cpython-312/pysam/include/bcftools copying bcftools/bam2bcf_iaux.c -> build/lib.linux-riscv64-cpython-312/pysam/include/bcftools copying bcftools/bam2bcf_iaux.c.pysam.c -> build/lib.linux-riscv64-cpython-312/pysam/include/bcftools copying bcftools/bam2bcf_indel.c -> build/lib.linux-riscv64-cpython-312/pysam/include/bcftools copying bcftools/bam2bcf_indel.c.pysam.c -> build/lib.linux-riscv64-cpython-312/pysam/include/bcftools copying bcftools/bam_sample.c -> build/lib.linux-riscv64-cpython-312/pysam/include/bcftools copying bcftools/bam_sample.c.pysam.c -> build/lib.linux-riscv64-cpython-312/pysam/include/bcftools copying bcftools/bam_sample.h -> build/lib.linux-riscv64-cpython-312/pysam/include/bcftools copying bcftools/bcftools.h -> build/lib.linux-riscv64-cpython-312/pysam/include/bcftools copying bcftools/bcftools.pysam.c -> build/lib.linux-riscv64-cpython-312/pysam/include/bcftools copying bcftools/bcftools.pysam.h -> build/lib.linux-riscv64-cpython-312/pysam/include/bcftools copying bcftools/bin.c -> build/lib.linux-riscv64-cpython-312/pysam/include/bcftools copying bcftools/bin.c.pysam.c -> build/lib.linux-riscv64-cpython-312/pysam/include/bcftools copying bcftools/bin.h -> build/lib.linux-riscv64-cpython-312/pysam/include/bcftools copying bcftools/call.h -> build/lib.linux-riscv64-cpython-312/pysam/include/bcftools copying bcftools/ccall.c -> build/lib.linux-riscv64-cpython-312/pysam/include/bcftools copying bcftools/ccall.c.pysam.c -> build/lib.linux-riscv64-cpython-312/pysam/include/bcftools copying bcftools/cigar_state.h -> build/lib.linux-riscv64-cpython-312/pysam/include/bcftools copying bcftools/cols.c -> build/lib.linux-riscv64-cpython-312/pysam/include/bcftools copying bcftools/cols.c.pysam.c -> build/lib.linux-riscv64-cpython-312/pysam/include/bcftools copying bcftools/cols.h -> build/lib.linux-riscv64-cpython-312/pysam/include/bcftools copying bcftools/consensus.c -> build/lib.linux-riscv64-cpython-312/pysam/include/bcftools copying bcftools/consensus.c.pysam.c -> build/lib.linux-riscv64-cpython-312/pysam/include/bcftools copying bcftools/convert.c -> build/lib.linux-riscv64-cpython-312/pysam/include/bcftools copying bcftools/convert.c.pysam.c -> build/lib.linux-riscv64-cpython-312/pysam/include/bcftools copying bcftools/convert.h -> build/lib.linux-riscv64-cpython-312/pysam/include/bcftools copying bcftools/csq.c -> build/lib.linux-riscv64-cpython-312/pysam/include/bcftools copying bcftools/csq.c.pysam.c -> build/lib.linux-riscv64-cpython-312/pysam/include/bcftools copying bcftools/dbuf.h -> build/lib.linux-riscv64-cpython-312/pysam/include/bcftools copying bcftools/dist.c -> build/lib.linux-riscv64-cpython-312/pysam/include/bcftools copying bcftools/dist.c.pysam.c -> build/lib.linux-riscv64-cpython-312/pysam/include/bcftools copying bcftools/dist.h -> build/lib.linux-riscv64-cpython-312/pysam/include/bcftools copying bcftools/em.c -> build/lib.linux-riscv64-cpython-312/pysam/include/bcftools copying bcftools/em.c.pysam.c -> build/lib.linux-riscv64-cpython-312/pysam/include/bcftools copying bcftools/extsort.c -> build/lib.linux-riscv64-cpython-312/pysam/include/bcftools copying bcftools/extsort.c.pysam.c -> build/lib.linux-riscv64-cpython-312/pysam/include/bcftools copying bcftools/extsort.h -> build/lib.linux-riscv64-cpython-312/pysam/include/bcftools copying bcftools/filter.c -> build/lib.linux-riscv64-cpython-312/pysam/include/bcftools copying bcftools/filter.c.pysam.c -> build/lib.linux-riscv64-cpython-312/pysam/include/bcftools copying bcftools/filter.h -> build/lib.linux-riscv64-cpython-312/pysam/include/bcftools copying bcftools/gff.c -> build/lib.linux-riscv64-cpython-312/pysam/include/bcftools copying bcftools/gff.c.pysam.c -> build/lib.linux-riscv64-cpython-312/pysam/include/bcftools copying bcftools/gff.h -> build/lib.linux-riscv64-cpython-312/pysam/include/bcftools copying bcftools/gvcf.c -> build/lib.linux-riscv64-cpython-312/pysam/include/bcftools copying bcftools/gvcf.c.pysam.c -> build/lib.linux-riscv64-cpython-312/pysam/include/bcftools copying bcftools/gvcf.h -> build/lib.linux-riscv64-cpython-312/pysam/include/bcftools copying bcftools/hclust.c -> build/lib.linux-riscv64-cpython-312/pysam/include/bcftools copying bcftools/hclust.c.pysam.c -> build/lib.linux-riscv64-cpython-312/pysam/include/bcftools copying bcftools/hclust.h -> build/lib.linux-riscv64-cpython-312/pysam/include/bcftools copying bcftools/hex.h -> build/lib.linux-riscv64-cpython-312/pysam/include/bcftools copying bcftools/khash_str2str.h -> build/lib.linux-riscv64-cpython-312/pysam/include/bcftools copying bcftools/kheap.h -> build/lib.linux-riscv64-cpython-312/pysam/include/bcftools copying bcftools/kmin.c -> build/lib.linux-riscv64-cpython-312/pysam/include/bcftools copying bcftools/kmin.c.pysam.c -> build/lib.linux-riscv64-cpython-312/pysam/include/bcftools copying bcftools/kmin.h -> build/lib.linux-riscv64-cpython-312/pysam/include/bcftools copying bcftools/main.c -> build/lib.linux-riscv64-cpython-312/pysam/include/bcftools copying bcftools/main.c.pysam.c -> build/lib.linux-riscv64-cpython-312/pysam/include/bcftools copying bcftools/mcall.c -> build/lib.linux-riscv64-cpython-312/pysam/include/bcftools copying bcftools/mcall.c.pysam.c -> build/lib.linux-riscv64-cpython-312/pysam/include/bcftools copying bcftools/mpileup.c -> build/lib.linux-riscv64-cpython-312/pysam/include/bcftools copying bcftools/mpileup.c.pysam.c -> build/lib.linux-riscv64-cpython-312/pysam/include/bcftools copying bcftools/mw.h -> build/lib.linux-riscv64-cpython-312/pysam/include/bcftools copying bcftools/ploidy.c -> build/lib.linux-riscv64-cpython-312/pysam/include/bcftools copying bcftools/ploidy.c.pysam.c -> build/lib.linux-riscv64-cpython-312/pysam/include/bcftools copying bcftools/ploidy.h -> build/lib.linux-riscv64-cpython-312/pysam/include/bcftools copying bcftools/prob1.c -> build/lib.linux-riscv64-cpython-312/pysam/include/bcftools copying bcftools/prob1.c.pysam.c -> build/lib.linux-riscv64-cpython-312/pysam/include/bcftools copying bcftools/prob1.h -> build/lib.linux-riscv64-cpython-312/pysam/include/bcftools copying bcftools/rbuf.h -> build/lib.linux-riscv64-cpython-312/pysam/include/bcftools copying bcftools/read_consensus.c -> build/lib.linux-riscv64-cpython-312/pysam/include/bcftools copying bcftools/read_consensus.c.pysam.c -> build/lib.linux-riscv64-cpython-312/pysam/include/bcftools copying bcftools/read_consensus.h -> build/lib.linux-riscv64-cpython-312/pysam/include/bcftools copying bcftools/regidx.c -> build/lib.linux-riscv64-cpython-312/pysam/include/bcftools copying bcftools/regidx.c.pysam.c -> build/lib.linux-riscv64-cpython-312/pysam/include/bcftools copying bcftools/regidx.h -> build/lib.linux-riscv64-cpython-312/pysam/include/bcftools copying bcftools/reheader.c -> build/lib.linux-riscv64-cpython-312/pysam/include/bcftools copying bcftools/reheader.c.pysam.c -> build/lib.linux-riscv64-cpython-312/pysam/include/bcftools copying bcftools/smpl_ilist.c -> build/lib.linux-riscv64-cpython-312/pysam/include/bcftools copying bcftools/smpl_ilist.c.pysam.c -> build/lib.linux-riscv64-cpython-312/pysam/include/bcftools copying bcftools/smpl_ilist.h -> build/lib.linux-riscv64-cpython-312/pysam/include/bcftools copying bcftools/str_finder.c -> build/lib.linux-riscv64-cpython-312/pysam/include/bcftools copying bcftools/str_finder.c.pysam.c -> build/lib.linux-riscv64-cpython-312/pysam/include/bcftools copying bcftools/str_finder.h -> build/lib.linux-riscv64-cpython-312/pysam/include/bcftools copying bcftools/tabix.c -> build/lib.linux-riscv64-cpython-312/pysam/include/bcftools copying bcftools/tabix.c.pysam.c -> build/lib.linux-riscv64-cpython-312/pysam/include/bcftools copying bcftools/tsv2vcf.c -> build/lib.linux-riscv64-cpython-312/pysam/include/bcftools copying bcftools/tsv2vcf.c.pysam.c -> build/lib.linux-riscv64-cpython-312/pysam/include/bcftools copying bcftools/tsv2vcf.h -> build/lib.linux-riscv64-cpython-312/pysam/include/bcftools copying bcftools/utlist.h -> build/lib.linux-riscv64-cpython-312/pysam/include/bcftools copying bcftools/variantkey.h -> build/lib.linux-riscv64-cpython-312/pysam/include/bcftools copying bcftools/vcfannotate.c -> build/lib.linux-riscv64-cpython-312/pysam/include/bcftools copying bcftools/vcfannotate.c.pysam.c -> build/lib.linux-riscv64-cpython-312/pysam/include/bcftools copying bcftools/vcfbuf.c -> build/lib.linux-riscv64-cpython-312/pysam/include/bcftools copying bcftools/vcfbuf.c.pysam.c -> build/lib.linux-riscv64-cpython-312/pysam/include/bcftools copying bcftools/vcfbuf.h -> build/lib.linux-riscv64-cpython-312/pysam/include/bcftools copying bcftools/vcfcall.c -> build/lib.linux-riscv64-cpython-312/pysam/include/bcftools copying bcftools/vcfcall.c.pysam.c -> build/lib.linux-riscv64-cpython-312/pysam/include/bcftools copying bcftools/vcfcnv.c -> build/lib.linux-riscv64-cpython-312/pysam/include/bcftools copying bcftools/vcfcnv.c.pysam.c -> build/lib.linux-riscv64-cpython-312/pysam/include/bcftools copying bcftools/vcfconcat.c -> build/lib.linux-riscv64-cpython-312/pysam/include/bcftools copying bcftools/vcfconcat.c.pysam.c -> build/lib.linux-riscv64-cpython-312/pysam/include/bcftools copying bcftools/vcfconvert.c -> build/lib.linux-riscv64-cpython-312/pysam/include/bcftools copying bcftools/vcfconvert.c.pysam.c -> build/lib.linux-riscv64-cpython-312/pysam/include/bcftools copying bcftools/vcffilter.c -> build/lib.linux-riscv64-cpython-312/pysam/include/bcftools copying bcftools/vcffilter.c.pysam.c -> build/lib.linux-riscv64-cpython-312/pysam/include/bcftools copying bcftools/vcfgtcheck.c -> build/lib.linux-riscv64-cpython-312/pysam/include/bcftools copying bcftools/vcfgtcheck.c.pysam.c -> build/lib.linux-riscv64-cpython-312/pysam/include/bcftools copying bcftools/vcfhead.c -> build/lib.linux-riscv64-cpython-312/pysam/include/bcftools copying bcftools/vcfhead.c.pysam.c -> build/lib.linux-riscv64-cpython-312/pysam/include/bcftools copying bcftools/vcfindex.c -> build/lib.linux-riscv64-cpython-312/pysam/include/bcftools copying bcftools/vcfindex.c.pysam.c -> build/lib.linux-riscv64-cpython-312/pysam/include/bcftools copying bcftools/vcfisec.c -> build/lib.linux-riscv64-cpython-312/pysam/include/bcftools copying bcftools/vcfisec.c.pysam.c -> build/lib.linux-riscv64-cpython-312/pysam/include/bcftools copying bcftools/vcfmerge.c -> build/lib.linux-riscv64-cpython-312/pysam/include/bcftools copying bcftools/vcfmerge.c.pysam.c -> build/lib.linux-riscv64-cpython-312/pysam/include/bcftools copying bcftools/vcfnorm.c -> build/lib.linux-riscv64-cpython-312/pysam/include/bcftools copying bcftools/vcfnorm.c.pysam.c -> build/lib.linux-riscv64-cpython-312/pysam/include/bcftools copying bcftools/vcfplugin.c -> build/lib.linux-riscv64-cpython-312/pysam/include/bcftools copying bcftools/vcfplugin.c.pysam.c -> build/lib.linux-riscv64-cpython-312/pysam/include/bcftools copying bcftools/vcfquery.c -> build/lib.linux-riscv64-cpython-312/pysam/include/bcftools copying bcftools/vcfquery.c.pysam.c -> build/lib.linux-riscv64-cpython-312/pysam/include/bcftools copying bcftools/vcfroh.c -> build/lib.linux-riscv64-cpython-312/pysam/include/bcftools copying bcftools/vcfroh.c.pysam.c -> build/lib.linux-riscv64-cpython-312/pysam/include/bcftools copying bcftools/vcfsom.c -> build/lib.linux-riscv64-cpython-312/pysam/include/bcftools copying bcftools/vcfsom.c.pysam.c -> build/lib.linux-riscv64-cpython-312/pysam/include/bcftools copying bcftools/vcfsort.c -> build/lib.linux-riscv64-cpython-312/pysam/include/bcftools copying bcftools/vcfsort.c.pysam.c -> build/lib.linux-riscv64-cpython-312/pysam/include/bcftools copying bcftools/vcfstats.c -> build/lib.linux-riscv64-cpython-312/pysam/include/bcftools copying bcftools/vcfstats.c.pysam.c -> build/lib.linux-riscv64-cpython-312/pysam/include/bcftools copying bcftools/vcfview.c -> build/lib.linux-riscv64-cpython-312/pysam/include/bcftools copying bcftools/vcfview.c.pysam.c -> build/lib.linux-riscv64-cpython-312/pysam/include/bcftools copying bcftools/vcmp.c -> build/lib.linux-riscv64-cpython-312/pysam/include/bcftools copying bcftools/vcmp.c.pysam.c -> build/lib.linux-riscv64-cpython-312/pysam/include/bcftools copying bcftools/vcmp.h -> build/lib.linux-riscv64-cpython-312/pysam/include/bcftools copying bcftools/version.c -> build/lib.linux-riscv64-cpython-312/pysam/include/bcftools copying bcftools/version.c.pysam.c -> build/lib.linux-riscv64-cpython-312/pysam/include/bcftools copying bcftools/version.sh -> build/lib.linux-riscv64-cpython-312/pysam/include/bcftools copying bcftools/config.h -> build/lib.linux-riscv64-cpython-312/pysam/include/bcftools creating build/lib.linux-riscv64-cpython-312/pysam/include/htslib copying htslib/LICENSE -> build/lib.linux-riscv64-cpython-312/pysam/include/htslib copying htslib/Makefile -> build/lib.linux-riscv64-cpython-312/pysam/include/htslib copying htslib/README -> build/lib.linux-riscv64-cpython-312/pysam/include/htslib copying htslib/bcf_sr_sort.c -> build/lib.linux-riscv64-cpython-312/pysam/include/htslib copying htslib/bcf_sr_sort.h -> build/lib.linux-riscv64-cpython-312/pysam/include/htslib copying htslib/bgzf.c -> build/lib.linux-riscv64-cpython-312/pysam/include/htslib copying htslib/bgzip.c -> build/lib.linux-riscv64-cpython-312/pysam/include/htslib copying htslib/builddir_vars.mk.in -> build/lib.linux-riscv64-cpython-312/pysam/include/htslib copying htslib/config.h.in -> build/lib.linux-riscv64-cpython-312/pysam/include/htslib copying htslib/config.mk.in -> build/lib.linux-riscv64-cpython-312/pysam/include/htslib copying htslib/configure -> build/lib.linux-riscv64-cpython-312/pysam/include/htslib copying htslib/configure.ac -> build/lib.linux-riscv64-cpython-312/pysam/include/htslib copying htslib/errmod.c -> build/lib.linux-riscv64-cpython-312/pysam/include/htslib copying htslib/faidx.c -> build/lib.linux-riscv64-cpython-312/pysam/include/htslib copying htslib/header.c -> build/lib.linux-riscv64-cpython-312/pysam/include/htslib copying htslib/header.h -> build/lib.linux-riscv64-cpython-312/pysam/include/htslib copying htslib/hfile.c -> build/lib.linux-riscv64-cpython-312/pysam/include/htslib copying htslib/hfile_gcs.c -> build/lib.linux-riscv64-cpython-312/pysam/include/htslib copying htslib/hfile_internal.h -> build/lib.linux-riscv64-cpython-312/pysam/include/htslib copying htslib/hfile_libcurl.c -> build/lib.linux-riscv64-cpython-312/pysam/include/htslib copying htslib/hfile_s3.c -> build/lib.linux-riscv64-cpython-312/pysam/include/htslib copying htslib/hfile_s3_write.c -> build/lib.linux-riscv64-cpython-312/pysam/include/htslib copying htslib/hts.c -> build/lib.linux-riscv64-cpython-312/pysam/include/htslib copying htslib/hts_expr.c -> build/lib.linux-riscv64-cpython-312/pysam/include/htslib copying htslib/hts_internal.h -> build/lib.linux-riscv64-cpython-312/pysam/include/htslib copying htslib/hts_os.c -> build/lib.linux-riscv64-cpython-312/pysam/include/htslib copying htslib/hts_time_funcs.h -> build/lib.linux-riscv64-cpython-312/pysam/include/htslib copying htslib/htscodecs_bundled.mk -> build/lib.linux-riscv64-cpython-312/pysam/include/htslib copying htslib/htscodecs_external.mk -> build/lib.linux-riscv64-cpython-312/pysam/include/htslib copying htslib/htsfile.c -> build/lib.linux-riscv64-cpython-312/pysam/include/htslib copying htslib/htslib.mk -> build/lib.linux-riscv64-cpython-312/pysam/include/htslib copying htslib/htslib.pc.in -> build/lib.linux-riscv64-cpython-312/pysam/include/htslib copying htslib/htslib_vars.mk -> build/lib.linux-riscv64-cpython-312/pysam/include/htslib copying htslib/kfunc.c -> build/lib.linux-riscv64-cpython-312/pysam/include/htslib copying htslib/kstring.c -> build/lib.linux-riscv64-cpython-312/pysam/include/htslib copying htslib/md5.c -> build/lib.linux-riscv64-cpython-312/pysam/include/htslib copying htslib/multipart.c -> build/lib.linux-riscv64-cpython-312/pysam/include/htslib copying htslib/plugin.c -> build/lib.linux-riscv64-cpython-312/pysam/include/htslib copying htslib/probaln.c -> build/lib.linux-riscv64-cpython-312/pysam/include/htslib copying htslib/realn.c -> build/lib.linux-riscv64-cpython-312/pysam/include/htslib copying htslib/regidx.c -> build/lib.linux-riscv64-cpython-312/pysam/include/htslib copying htslib/region.c -> build/lib.linux-riscv64-cpython-312/pysam/include/htslib copying htslib/sam.c -> build/lib.linux-riscv64-cpython-312/pysam/include/htslib copying htslib/sam_internal.h -> build/lib.linux-riscv64-cpython-312/pysam/include/htslib copying htslib/sam_mods.c -> build/lib.linux-riscv64-cpython-312/pysam/include/htslib copying htslib/synced_bcf_reader.c -> build/lib.linux-riscv64-cpython-312/pysam/include/htslib copying htslib/tabix.c -> build/lib.linux-riscv64-cpython-312/pysam/include/htslib copying htslib/tbx.c -> build/lib.linux-riscv64-cpython-312/pysam/include/htslib copying htslib/textutils.c -> build/lib.linux-riscv64-cpython-312/pysam/include/htslib copying htslib/textutils_internal.h -> build/lib.linux-riscv64-cpython-312/pysam/include/htslib copying htslib/thread_pool.c -> build/lib.linux-riscv64-cpython-312/pysam/include/htslib copying htslib/thread_pool_internal.h -> build/lib.linux-riscv64-cpython-312/pysam/include/htslib copying htslib/vcf.c -> build/lib.linux-riscv64-cpython-312/pysam/include/htslib copying htslib/vcf_sweep.c -> build/lib.linux-riscv64-cpython-312/pysam/include/htslib copying htslib/vcfutils.c -> build/lib.linux-riscv64-cpython-312/pysam/include/htslib copying htslib/version.sh -> build/lib.linux-riscv64-cpython-312/pysam/include/htslib creating build/lib.linux-riscv64-cpython-312/pysam/include/htslib/cram copying htslib/cram/cram.h -> build/lib.linux-riscv64-cpython-312/pysam/include/htslib/cram copying htslib/cram/cram_codecs.c -> build/lib.linux-riscv64-cpython-312/pysam/include/htslib/cram copying htslib/cram/cram_codecs.h -> build/lib.linux-riscv64-cpython-312/pysam/include/htslib/cram copying htslib/cram/cram_decode.c -> build/lib.linux-riscv64-cpython-312/pysam/include/htslib/cram copying htslib/cram/cram_decode.h -> build/lib.linux-riscv64-cpython-312/pysam/include/htslib/cram copying htslib/cram/cram_encode.c -> build/lib.linux-riscv64-cpython-312/pysam/include/htslib/cram copying htslib/cram/cram_encode.h -> build/lib.linux-riscv64-cpython-312/pysam/include/htslib/cram copying htslib/cram/cram_external.c -> build/lib.linux-riscv64-cpython-312/pysam/include/htslib/cram copying htslib/cram/cram_index.c -> build/lib.linux-riscv64-cpython-312/pysam/include/htslib/cram copying htslib/cram/cram_index.h -> build/lib.linux-riscv64-cpython-312/pysam/include/htslib/cram copying htslib/cram/cram_io.c -> build/lib.linux-riscv64-cpython-312/pysam/include/htslib/cram copying htslib/cram/cram_io.h -> build/lib.linux-riscv64-cpython-312/pysam/include/htslib/cram copying htslib/cram/cram_samtools.h -> build/lib.linux-riscv64-cpython-312/pysam/include/htslib/cram copying htslib/cram/cram_stats.c -> build/lib.linux-riscv64-cpython-312/pysam/include/htslib/cram copying htslib/cram/cram_stats.h -> build/lib.linux-riscv64-cpython-312/pysam/include/htslib/cram copying htslib/cram/cram_structs.h -> build/lib.linux-riscv64-cpython-312/pysam/include/htslib/cram copying htslib/cram/mFILE.c -> build/lib.linux-riscv64-cpython-312/pysam/include/htslib/cram copying htslib/cram/mFILE.h -> build/lib.linux-riscv64-cpython-312/pysam/include/htslib/cram copying htslib/cram/misc.h -> build/lib.linux-riscv64-cpython-312/pysam/include/htslib/cram copying htslib/cram/open_trace_file.c -> build/lib.linux-riscv64-cpython-312/pysam/include/htslib/cram copying htslib/cram/open_trace_file.h -> build/lib.linux-riscv64-cpython-312/pysam/include/htslib/cram copying htslib/cram/os.h -> build/lib.linux-riscv64-cpython-312/pysam/include/htslib/cram copying htslib/cram/pooled_alloc.c -> build/lib.linux-riscv64-cpython-312/pysam/include/htslib/cram copying htslib/cram/pooled_alloc.h -> build/lib.linux-riscv64-cpython-312/pysam/include/htslib/cram copying htslib/cram/string_alloc.c -> build/lib.linux-riscv64-cpython-312/pysam/include/htslib/cram copying htslib/cram/string_alloc.h -> build/lib.linux-riscv64-cpython-312/pysam/include/htslib/cram creating build/lib.linux-riscv64-cpython-312/pysam/include/htslib/htscodecs creating build/lib.linux-riscv64-cpython-312/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/arith_dynamic.c -> build/lib.linux-riscv64-cpython-312/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/arith_dynamic.h -> build/lib.linux-riscv64-cpython-312/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/c_range_coder.h -> build/lib.linux-riscv64-cpython-312/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/c_simple_model.h -> build/lib.linux-riscv64-cpython-312/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/fqzcomp_qual.c -> build/lib.linux-riscv64-cpython-312/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/fqzcomp_qual.h -> build/lib.linux-riscv64-cpython-312/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/htscodecs.c -> build/lib.linux-riscv64-cpython-312/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/htscodecs.h -> build/lib.linux-riscv64-cpython-312/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/htscodecs_endian.h -> build/lib.linux-riscv64-cpython-312/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/pack.c -> build/lib.linux-riscv64-cpython-312/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/pack.h -> build/lib.linux-riscv64-cpython-312/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/permute.h -> build/lib.linux-riscv64-cpython-312/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/pooled_alloc.h -> build/lib.linux-riscv64-cpython-312/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/rANS_byte.h -> build/lib.linux-riscv64-cpython-312/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/rANS_static.c -> build/lib.linux-riscv64-cpython-312/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/rANS_static.h -> build/lib.linux-riscv64-cpython-312/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/rANS_static16_int.h -> build/lib.linux-riscv64-cpython-312/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/rANS_static32x16pr.c -> build/lib.linux-riscv64-cpython-312/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/rANS_static32x16pr.h -> build/lib.linux-riscv64-cpython-312/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/rANS_static32x16pr_avx2.c -> build/lib.linux-riscv64-cpython-312/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/rANS_static32x16pr_avx512.c -> build/lib.linux-riscv64-cpython-312/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/rANS_static32x16pr_neon.c -> build/lib.linux-riscv64-cpython-312/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/rANS_static32x16pr_sse4.c -> build/lib.linux-riscv64-cpython-312/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/rANS_static4x16.h -> build/lib.linux-riscv64-cpython-312/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/rANS_static4x16pr.c -> build/lib.linux-riscv64-cpython-312/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/rANS_word.h -> build/lib.linux-riscv64-cpython-312/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/rle.c -> build/lib.linux-riscv64-cpython-312/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/rle.h -> build/lib.linux-riscv64-cpython-312/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/tokenise_name3.c -> build/lib.linux-riscv64-cpython-312/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/tokenise_name3.h -> build/lib.linux-riscv64-cpython-312/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/utils.c -> build/lib.linux-riscv64-cpython-312/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/utils.h -> build/lib.linux-riscv64-cpython-312/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/varint.h -> build/lib.linux-riscv64-cpython-312/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/varint2.h -> build/lib.linux-riscv64-cpython-312/pysam/include/htslib/htscodecs/htscodecs copying htslib/htscodecs/htscodecs/version.h -> build/lib.linux-riscv64-cpython-312/pysam/include/htslib/htscodecs/htscodecs creating build/lib.linux-riscv64-cpython-312/pysam/include/htslib/m4 copying htslib/m4/hts_check_compile_flags_needed.m4 -> build/lib.linux-riscv64-cpython-312/pysam/include/htslib/m4 copying htslib/m4/hts_hide_dynamic_syms.m4 -> build/lib.linux-riscv64-cpython-312/pysam/include/htslib/m4 copying htslib/m4/hts_prog_cc_warnings.m4 -> build/lib.linux-riscv64-cpython-312/pysam/include/htslib/m4 copying htslib/m4/pkg.m4 -> build/lib.linux-riscv64-cpython-312/pysam/include/htslib/m4 creating build/lib.linux-riscv64-cpython-312/pysam/include/htslib/os copying htslib/os/lzma_stub.h -> build/lib.linux-riscv64-cpython-312/pysam/include/htslib/os copying htslib/os/rand.c -> build/lib.linux-riscv64-cpython-312/pysam/include/htslib/os copying htslib/config.h -> build/lib.linux-riscv64-cpython-312/pysam/include/htslib creating build/lib.linux-riscv64-cpython-312/pysam/include/htslib/htslib copying htslib/htslib/bgzf.h -> build/lib.linux-riscv64-cpython-312/pysam/include/htslib/htslib copying htslib/htslib/cram.h -> build/lib.linux-riscv64-cpython-312/pysam/include/htslib/htslib copying htslib/htslib/faidx.h -> build/lib.linux-riscv64-cpython-312/pysam/include/htslib/htslib copying htslib/htslib/hfile.h -> build/lib.linux-riscv64-cpython-312/pysam/include/htslib/htslib copying htslib/htslib/hts.h -> build/lib.linux-riscv64-cpython-312/pysam/include/htslib/htslib copying htslib/htslib/hts_defs.h -> build/lib.linux-riscv64-cpython-312/pysam/include/htslib/htslib copying htslib/htslib/hts_endian.h -> build/lib.linux-riscv64-cpython-312/pysam/include/htslib/htslib copying htslib/htslib/hts_expr.h -> build/lib.linux-riscv64-cpython-312/pysam/include/htslib/htslib copying htslib/htslib/hts_log.h -> build/lib.linux-riscv64-cpython-312/pysam/include/htslib/htslib copying htslib/htslib/hts_os.h -> build/lib.linux-riscv64-cpython-312/pysam/include/htslib/htslib copying htslib/htslib/kbitset.h -> build/lib.linux-riscv64-cpython-312/pysam/include/htslib/htslib copying htslib/htslib/kfunc.h -> build/lib.linux-riscv64-cpython-312/pysam/include/htslib/htslib copying htslib/htslib/khash.h -> build/lib.linux-riscv64-cpython-312/pysam/include/htslib/htslib copying htslib/htslib/khash_str2int.h -> build/lib.linux-riscv64-cpython-312/pysam/include/htslib/htslib copying htslib/htslib/klist.h -> build/lib.linux-riscv64-cpython-312/pysam/include/htslib/htslib copying htslib/htslib/knetfile.h -> build/lib.linux-riscv64-cpython-312/pysam/include/htslib/htslib copying htslib/htslib/kroundup.h -> build/lib.linux-riscv64-cpython-312/pysam/include/htslib/htslib copying htslib/htslib/kseq.h -> build/lib.linux-riscv64-cpython-312/pysam/include/htslib/htslib copying htslib/htslib/ksort.h -> build/lib.linux-riscv64-cpython-312/pysam/include/htslib/htslib copying htslib/htslib/kstring.h -> build/lib.linux-riscv64-cpython-312/pysam/include/htslib/htslib copying htslib/htslib/regidx.h -> build/lib.linux-riscv64-cpython-312/pysam/include/htslib/htslib copying htslib/htslib/sam.h -> build/lib.linux-riscv64-cpython-312/pysam/include/htslib/htslib copying htslib/htslib/synced_bcf_reader.h -> build/lib.linux-riscv64-cpython-312/pysam/include/htslib/htslib copying htslib/htslib/tbx.h -> build/lib.linux-riscv64-cpython-312/pysam/include/htslib/htslib copying htslib/htslib/thread_pool.h -> build/lib.linux-riscv64-cpython-312/pysam/include/htslib/htslib copying htslib/htslib/vcf.h -> build/lib.linux-riscv64-cpython-312/pysam/include/htslib/htslib copying htslib/htslib/vcf_sweep.h -> build/lib.linux-riscv64-cpython-312/pysam/include/htslib/htslib copying htslib/htslib/vcfutils.h -> build/lib.linux-riscv64-cpython-312/pysam/include/htslib/htslib running build_ext creating htslib/config_vars.h for 'pysam.libchtslib' extension building 'libhts.a' gcc -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -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 -fasynchronous-unwind-tables -fno-omit-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 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -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 -fasynchronous-unwind-tables -fno-omit-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 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -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 -fasynchronous-unwind-tables -fno-omit-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 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -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 -fasynchronous-unwind-tables -fno-omit-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 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -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 -fasynchronous-unwind-tables -fno-omit-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 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -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 -fasynchronous-unwind-tables -fno-omit-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 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -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 -fasynchronous-unwind-tables -fno-omit-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 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -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 -fasynchronous-unwind-tables -fno-omit-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 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -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 -fasynchronous-unwind-tables -fno-omit-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 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -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 -fasynchronous-unwind-tables -fno-omit-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 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -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 -fasynchronous-unwind-tables -fno-omit-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 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -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 -fasynchronous-unwind-tables -fno-omit-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 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -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 -fasynchronous-unwind-tables -fno-omit-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 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -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 -fasynchronous-unwind-tables -fno-omit-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 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -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 -fasynchronous-unwind-tables -fno-omit-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 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -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 -fasynchronous-unwind-tables -fno-omit-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 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -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 -fasynchronous-unwind-tables -fno-omit-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 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -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 -fasynchronous-unwind-tables -fno-omit-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 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -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 -fasynchronous-unwind-tables -fno-omit-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 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -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 -fasynchronous-unwind-tables -fno-omit-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 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -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 -fasynchronous-unwind-tables -fno-omit-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 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -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 -fasynchronous-unwind-tables -fno-omit-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 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -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 -fasynchronous-unwind-tables -fno-omit-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 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -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 -fasynchronous-unwind-tables -fno-omit-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 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -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 -fasynchronous-unwind-tables -fno-omit-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 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -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 -fasynchronous-unwind-tables -fno-omit-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 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -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 -fasynchronous-unwind-tables -fno-omit-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 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -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 -fasynchronous-unwind-tables -fno-omit-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 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -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 -fasynchronous-unwind-tables -fno-omit-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 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -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 -fasynchronous-unwind-tables -fno-omit-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 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -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 -fasynchronous-unwind-tables -fno-omit-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 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -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 -fasynchronous-unwind-tables -fno-omit-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 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -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 -fasynchronous-unwind-tables -fno-omit-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 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -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 -fasynchronous-unwind-tables -fno-omit-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 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -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 -fasynchronous-unwind-tables -fno-omit-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 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -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 -fasynchronous-unwind-tables -fno-omit-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 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -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 -fasynchronous-unwind-tables -fno-omit-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 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -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 -fasynchronous-unwind-tables -fno-omit-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 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -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 -fasynchronous-unwind-tables -fno-omit-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 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -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 -fasynchronous-unwind-tables -fno-omit-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 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -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 -fasynchronous-unwind-tables -fno-omit-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 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -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 -fasynchronous-unwind-tables -fno-omit-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 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -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 -fasynchronous-unwind-tables -fno-omit-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 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -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 -fasynchronous-unwind-tables -fno-omit-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 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -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 -fasynchronous-unwind-tables -fno-omit-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 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -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 -fasynchronous-unwind-tables -fno-omit-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 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -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 -fasynchronous-unwind-tables -fno-omit-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 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -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 -fasynchronous-unwind-tables -fno-omit-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 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -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 -fasynchronous-unwind-tables -fno-omit-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 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -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 -fasynchronous-unwind-tables -fno-omit-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 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -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 -fasynchronous-unwind-tables -fno-omit-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-riscv64-cpython-312 creating build/temp.linux-riscv64-cpython-312/pysam gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -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 -fasynchronous-unwind-tables -fno-omit-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-riscv64-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 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -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 -fasynchronous-unwind-tables -fno-omit-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-riscv64-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 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -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 -fasynchronous-unwind-tables -fno-omit-frame-pointer -fPIC build/temp.linux-riscv64-cpython-312/pysam/htslib_util.o build/temp.linux-riscv64-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-riscv64-cpython-312/pysam -L/usr/lib64 -lz -llzma -lbz2 -lz -lm -o build/lib.linux-riscv64-cpython-312/pysam/libchtslib.cpython-312-riscv64-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-riscv64-cpython-312/samtools creating build/temp.linux-riscv64-cpython-312/samtools/lz4 gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -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 -fasynchronous-unwind-tables -fno-omit-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-riscv64-cpython-312/pysam/libcsamtools.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -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 -fasynchronous-unwind-tables -fno-omit-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-riscv64-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 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -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 -fasynchronous-unwind-tables -fno-omit-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-riscv64-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 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -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 -fasynchronous-unwind-tables -fno-omit-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-riscv64-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 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -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 -fasynchronous-unwind-tables -fno-omit-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-riscv64-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 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -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 -fasynchronous-unwind-tables -fno-omit-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-riscv64-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 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -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 -fasynchronous-unwind-tables -fno-omit-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-riscv64-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 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -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 -fasynchronous-unwind-tables -fno-omit-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-riscv64-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 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -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 -fasynchronous-unwind-tables -fno-omit-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-riscv64-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 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -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 -fasynchronous-unwind-tables -fno-omit-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-riscv64-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 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -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 -fasynchronous-unwind-tables -fno-omit-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-riscv64-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 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -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 -fasynchronous-unwind-tables -fno-omit-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-riscv64-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 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -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 -fasynchronous-unwind-tables -fno-omit-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-riscv64-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 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -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 -fasynchronous-unwind-tables -fno-omit-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-riscv64-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 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -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 -fasynchronous-unwind-tables -fno-omit-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-riscv64-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 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -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 -fasynchronous-unwind-tables -fno-omit-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-riscv64-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 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -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 -fasynchronous-unwind-tables -fno-omit-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-riscv64-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 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -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 -fasynchronous-unwind-tables -fno-omit-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-riscv64-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 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -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 -fasynchronous-unwind-tables -fno-omit-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-riscv64-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 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -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 -fasynchronous-unwind-tables -fno-omit-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-riscv64-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 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -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 -fasynchronous-unwind-tables -fno-omit-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-riscv64-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 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -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 -fasynchronous-unwind-tables -fno-omit-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-riscv64-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 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -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 -fasynchronous-unwind-tables -fno-omit-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-riscv64-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 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -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 -fasynchronous-unwind-tables -fno-omit-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-riscv64-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 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -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 -fasynchronous-unwind-tables -fno-omit-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-riscv64-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 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -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 -fasynchronous-unwind-tables -fno-omit-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-riscv64-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’: 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 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -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 -fasynchronous-unwind-tables -fno-omit-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-riscv64-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 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -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 -fasynchronous-unwind-tables -fno-omit-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-riscv64-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 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -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 -fasynchronous-unwind-tables -fno-omit-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-riscv64-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 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -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 -fasynchronous-unwind-tables -fno-omit-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-riscv64-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 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -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 -fasynchronous-unwind-tables -fno-omit-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-riscv64-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 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -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 -fasynchronous-unwind-tables -fno-omit-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-riscv64-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 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -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 -fasynchronous-unwind-tables -fno-omit-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-riscv64-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 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -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 -fasynchronous-unwind-tables -fno-omit-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-riscv64-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 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -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 -fasynchronous-unwind-tables -fno-omit-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-riscv64-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 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -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 -fasynchronous-unwind-tables -fno-omit-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-riscv64-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 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -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 -fasynchronous-unwind-tables -fno-omit-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-riscv64-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 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -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 -fasynchronous-unwind-tables -fno-omit-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-riscv64-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 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -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 -fasynchronous-unwind-tables -fno-omit-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-riscv64-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 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -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 -fasynchronous-unwind-tables -fno-omit-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-riscv64-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 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -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 -fasynchronous-unwind-tables -fno-omit-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-riscv64-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 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -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 -fasynchronous-unwind-tables -fno-omit-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-riscv64-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 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -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 -fasynchronous-unwind-tables -fno-omit-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-riscv64-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 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -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 -fasynchronous-unwind-tables -fno-omit-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-riscv64-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 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -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 -fasynchronous-unwind-tables -fno-omit-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-riscv64-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 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -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 -fasynchronous-unwind-tables -fno-omit-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-riscv64-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 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -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 -fasynchronous-unwind-tables -fno-omit-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-riscv64-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 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -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 -fasynchronous-unwind-tables -fno-omit-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-riscv64-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 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -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 -fasynchronous-unwind-tables -fno-omit-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-riscv64-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 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -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 -fasynchronous-unwind-tables -fno-omit-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-riscv64-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 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -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 -fasynchronous-unwind-tables -fno-omit-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-riscv64-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 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -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 -fasynchronous-unwind-tables -fno-omit-frame-pointer -fPIC build/temp.linux-riscv64-cpython-312/pysam/libcsamtools.o build/temp.linux-riscv64-cpython-312/samtools/amplicon_stats.c.pysam.o build/temp.linux-riscv64-cpython-312/samtools/bam.c.pysam.o build/temp.linux-riscv64-cpython-312/samtools/bam2depth.c.pysam.o build/temp.linux-riscv64-cpython-312/samtools/bam_addrprg.c.pysam.o build/temp.linux-riscv64-cpython-312/samtools/bam_ampliconclip.c.pysam.o build/temp.linux-riscv64-cpython-312/samtools/bam_aux.c.pysam.o build/temp.linux-riscv64-cpython-312/samtools/bam_cat.c.pysam.o build/temp.linux-riscv64-cpython-312/samtools/bam_color.c.pysam.o build/temp.linux-riscv64-cpython-312/samtools/bam_consensus.c.pysam.o build/temp.linux-riscv64-cpython-312/samtools/bam_fastq.c.pysam.o build/temp.linux-riscv64-cpython-312/samtools/bam_flags.c.pysam.o build/temp.linux-riscv64-cpython-312/samtools/bam_import.c.pysam.o build/temp.linux-riscv64-cpython-312/samtools/bam_index.c.pysam.o build/temp.linux-riscv64-cpython-312/samtools/bam_lpileup.c.pysam.o build/temp.linux-riscv64-cpython-312/samtools/bam_markdup.c.pysam.o build/temp.linux-riscv64-cpython-312/samtools/bam_mate.c.pysam.o build/temp.linux-riscv64-cpython-312/samtools/bam_md.c.pysam.o build/temp.linux-riscv64-cpython-312/samtools/bam_plbuf.c.pysam.o build/temp.linux-riscv64-cpython-312/samtools/bam_plcmd.c.pysam.o build/temp.linux-riscv64-cpython-312/samtools/bam_quickcheck.c.pysam.o build/temp.linux-riscv64-cpython-312/samtools/bam_reheader.c.pysam.o build/temp.linux-riscv64-cpython-312/samtools/bam_rmdup.c.pysam.o build/temp.linux-riscv64-cpython-312/samtools/bam_rmdupse.c.pysam.o build/temp.linux-riscv64-cpython-312/samtools/bam_samples.c.pysam.o build/temp.linux-riscv64-cpython-312/samtools/bam_sort.c.pysam.o build/temp.linux-riscv64-cpython-312/samtools/bam_split.c.pysam.o build/temp.linux-riscv64-cpython-312/samtools/bam_stat.c.pysam.o build/temp.linux-riscv64-cpython-312/samtools/bamshuf.c.pysam.o build/temp.linux-riscv64-cpython-312/samtools/bamtk.c.pysam.o build/temp.linux-riscv64-cpython-312/samtools/bedcov.c.pysam.o build/temp.linux-riscv64-cpython-312/samtools/bedidx.c.pysam.o build/temp.linux-riscv64-cpython-312/samtools/consensus_pileup.c.pysam.o build/temp.linux-riscv64-cpython-312/samtools/coverage.c.pysam.o build/temp.linux-riscv64-cpython-312/samtools/cram_size.c.pysam.o build/temp.linux-riscv64-cpython-312/samtools/cut_target.c.pysam.o build/temp.linux-riscv64-cpython-312/samtools/dict.c.pysam.o build/temp.linux-riscv64-cpython-312/samtools/faidx.c.pysam.o build/temp.linux-riscv64-cpython-312/samtools/lz4/lz4.o build/temp.linux-riscv64-cpython-312/samtools/padding.c.pysam.o build/temp.linux-riscv64-cpython-312/samtools/phase.c.pysam.o build/temp.linux-riscv64-cpython-312/samtools/reference.c.pysam.o build/temp.linux-riscv64-cpython-312/samtools/reset.c.pysam.o build/temp.linux-riscv64-cpython-312/samtools/sam_opts.c.pysam.o build/temp.linux-riscv64-cpython-312/samtools/sam_utils.c.pysam.o build/temp.linux-riscv64-cpython-312/samtools/sam_view.c.pysam.o build/temp.linux-riscv64-cpython-312/samtools/sample.c.pysam.o build/temp.linux-riscv64-cpython-312/samtools/samtools.pysam.o build/temp.linux-riscv64-cpython-312/samtools/stats.c.pysam.o build/temp.linux-riscv64-cpython-312/samtools/stats_isize.c.pysam.o build/temp.linux-riscv64-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-riscv64-cpython-312/pysam -Lbuild/lib.linux-riscv64-cpython-312/pysam -L/usr/lib64 -lz -llzma -lbz2 -lz -lm -lchtslib.cpython-312-riscv64-linux-gnu -o build/lib.linux-riscv64-cpython-312/pysam/libcsamtools.cpython-312-riscv64-linux-gnu.so -Wl,-rpath,$ORIGIN Compiling pysam/libcbcftools.pyx because it changed. [1/1] Cythonizing pysam/libcbcftools.pyx building 'pysam.libcbcftools' extension creating build/temp.linux-riscv64-cpython-312/bcftools gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -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 -fasynchronous-unwind-tables -fno-omit-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-riscv64-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 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -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 -fasynchronous-unwind-tables -fno-omit-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-riscv64-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 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -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 -fasynchronous-unwind-tables -fno-omit-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-riscv64-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 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -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 -fasynchronous-unwind-tables -fno-omit-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-riscv64-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 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -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 -fasynchronous-unwind-tables -fno-omit-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-riscv64-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 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -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 -fasynchronous-unwind-tables -fno-omit-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-riscv64-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 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -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 -fasynchronous-unwind-tables -fno-omit-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-riscv64-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 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -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 -fasynchronous-unwind-tables -fno-omit-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-riscv64-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 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -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 -fasynchronous-unwind-tables -fno-omit-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-riscv64-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 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -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 -fasynchronous-unwind-tables -fno-omit-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-riscv64-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 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -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 -fasynchronous-unwind-tables -fno-omit-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-riscv64-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 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -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 -fasynchronous-unwind-tables -fno-omit-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-riscv64-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 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -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 -fasynchronous-unwind-tables -fno-omit-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-riscv64-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 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -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 -fasynchronous-unwind-tables -fno-omit-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-riscv64-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 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -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 -fasynchronous-unwind-tables -fno-omit-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-riscv64-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 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -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 -fasynchronous-unwind-tables -fno-omit-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-riscv64-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 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -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 -fasynchronous-unwind-tables -fno-omit-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-riscv64-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 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -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 -fasynchronous-unwind-tables -fno-omit-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-riscv64-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 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -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 -fasynchronous-unwind-tables -fno-omit-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-riscv64-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 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -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 -fasynchronous-unwind-tables -fno-omit-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-riscv64-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 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -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 -fasynchronous-unwind-tables -fno-omit-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-riscv64-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 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -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 -fasynchronous-unwind-tables -fno-omit-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-riscv64-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 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -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 -fasynchronous-unwind-tables -fno-omit-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-riscv64-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 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -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 -fasynchronous-unwind-tables -fno-omit-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-riscv64-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 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -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 -fasynchronous-unwind-tables -fno-omit-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-riscv64-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 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -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 -fasynchronous-unwind-tables -fno-omit-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-riscv64-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 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -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 -fasynchronous-unwind-tables -fno-omit-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-riscv64-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 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -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 -fasynchronous-unwind-tables -fno-omit-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-riscv64-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 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -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 -fasynchronous-unwind-tables -fno-omit-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-riscv64-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 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -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 -fasynchronous-unwind-tables -fno-omit-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-riscv64-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 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -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 -fasynchronous-unwind-tables -fno-omit-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-riscv64-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 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -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 -fasynchronous-unwind-tables -fno-omit-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-riscv64-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 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -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 -fasynchronous-unwind-tables -fno-omit-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-riscv64-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 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -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 -fasynchronous-unwind-tables -fno-omit-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-riscv64-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 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -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 -fasynchronous-unwind-tables -fno-omit-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-riscv64-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 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -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 -fasynchronous-unwind-tables -fno-omit-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-riscv64-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 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -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 -fasynchronous-unwind-tables -fno-omit-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-riscv64-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 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -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 -fasynchronous-unwind-tables -fno-omit-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-riscv64-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 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -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 -fasynchronous-unwind-tables -fno-omit-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-riscv64-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 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -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 -fasynchronous-unwind-tables -fno-omit-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-riscv64-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 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -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 -fasynchronous-unwind-tables -fno-omit-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-riscv64-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 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -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 -fasynchronous-unwind-tables -fno-omit-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-riscv64-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 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -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 -fasynchronous-unwind-tables -fno-omit-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-riscv64-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 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -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 -fasynchronous-unwind-tables -fno-omit-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-riscv64-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 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -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 -fasynchronous-unwind-tables -fno-omit-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-riscv64-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) | ^~~~~~ gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -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 -fasynchronous-unwind-tables -fno-omit-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-riscv64-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 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -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 -fasynchronous-unwind-tables -fno-omit-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-riscv64-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 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -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 -fasynchronous-unwind-tables -fno-omit-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-riscv64-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 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -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 -fasynchronous-unwind-tables -fno-omit-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-riscv64-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 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -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 -fasynchronous-unwind-tables -fno-omit-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-riscv64-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 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -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 -fasynchronous-unwind-tables -fno-omit-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-riscv64-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 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -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 -fasynchronous-unwind-tables -fno-omit-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-riscv64-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 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -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 -fasynchronous-unwind-tables -fno-omit-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-riscv64-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 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -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 -fasynchronous-unwind-tables -fno-omit-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-riscv64-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 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -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 -fasynchronous-unwind-tables -fno-omit-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-riscv64-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 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -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 -fasynchronous-unwind-tables -fno-omit-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-riscv64-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 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -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 -fasynchronous-unwind-tables -fno-omit-frame-pointer -fPIC build/temp.linux-riscv64-cpython-312/bcftools/HMM.c.pysam.o build/temp.linux-riscv64-cpython-312/bcftools/abuf.c.pysam.o build/temp.linux-riscv64-cpython-312/bcftools/bam2bcf.c.pysam.o build/temp.linux-riscv64-cpython-312/bcftools/bam2bcf_iaux.c.pysam.o build/temp.linux-riscv64-cpython-312/bcftools/bam2bcf_indel.c.pysam.o build/temp.linux-riscv64-cpython-312/bcftools/bam_sample.c.pysam.o build/temp.linux-riscv64-cpython-312/bcftools/bcftools.pysam.o build/temp.linux-riscv64-cpython-312/bcftools/bin.c.pysam.o build/temp.linux-riscv64-cpython-312/bcftools/ccall.c.pysam.o build/temp.linux-riscv64-cpython-312/bcftools/cols.c.pysam.o build/temp.linux-riscv64-cpython-312/bcftools/consensus.c.pysam.o build/temp.linux-riscv64-cpython-312/bcftools/convert.c.pysam.o build/temp.linux-riscv64-cpython-312/bcftools/csq.c.pysam.o build/temp.linux-riscv64-cpython-312/bcftools/dist.c.pysam.o build/temp.linux-riscv64-cpython-312/bcftools/em.c.pysam.o build/temp.linux-riscv64-cpython-312/bcftools/extsort.c.pysam.o build/temp.linux-riscv64-cpython-312/bcftools/filter.c.pysam.o build/temp.linux-riscv64-cpython-312/bcftools/gff.c.pysam.o build/temp.linux-riscv64-cpython-312/bcftools/gvcf.c.pysam.o build/temp.linux-riscv64-cpython-312/bcftools/hclust.c.pysam.o build/temp.linux-riscv64-cpython-312/bcftools/kmin.c.pysam.o build/temp.linux-riscv64-cpython-312/bcftools/main.c.pysam.o build/temp.linux-riscv64-cpython-312/bcftools/mcall.c.pysam.o build/temp.linux-riscv64-cpython-312/bcftools/mpileup.c.pysam.o build/temp.linux-riscv64-cpython-312/bcftools/ploidy.c.pysam.o build/temp.linux-riscv64-cpython-312/bcftools/prob1.c.pysam.o build/temp.linux-riscv64-cpython-312/bcftools/read_consensus.c.pysam.o build/temp.linux-riscv64-cpython-312/bcftools/regidx.c.pysam.o build/temp.linux-riscv64-cpython-312/bcftools/reheader.c.pysam.o build/temp.linux-riscv64-cpython-312/bcftools/smpl_ilist.c.pysam.o build/temp.linux-riscv64-cpython-312/bcftools/str_finder.c.pysam.o build/temp.linux-riscv64-cpython-312/bcftools/tabix.c.pysam.o build/temp.linux-riscv64-cpython-312/bcftools/tsv2vcf.c.pysam.o build/temp.linux-riscv64-cpython-312/bcftools/vcfannotate.c.pysam.o build/temp.linux-riscv64-cpython-312/bcftools/vcfbuf.c.pysam.o build/temp.linux-riscv64-cpython-312/bcftools/vcfcall.c.pysam.o build/temp.linux-riscv64-cpython-312/bcftools/vcfcnv.c.pysam.o build/temp.linux-riscv64-cpython-312/bcftools/vcfconcat.c.pysam.o build/temp.linux-riscv64-cpython-312/bcftools/vcfconvert.c.pysam.o build/temp.linux-riscv64-cpython-312/bcftools/vcffilter.c.pysam.o build/temp.linux-riscv64-cpython-312/bcftools/vcfgtcheck.c.pysam.o build/temp.linux-riscv64-cpython-312/bcftools/vcfhead.c.pysam.o build/temp.linux-riscv64-cpython-312/bcftools/vcfindex.c.pysam.o build/temp.linux-riscv64-cpython-312/bcftools/vcfisec.c.pysam.o build/temp.linux-riscv64-cpython-312/bcftools/vcfmerge.c.pysam.o build/temp.linux-riscv64-cpython-312/bcftools/vcfnorm.c.pysam.o build/temp.linux-riscv64-cpython-312/bcftools/vcfplugin.c.pysam.o build/temp.linux-riscv64-cpython-312/bcftools/vcfquery.c.pysam.o build/temp.linux-riscv64-cpython-312/bcftools/vcfroh.c.pysam.o build/temp.linux-riscv64-cpython-312/bcftools/vcfsom.c.pysam.o build/temp.linux-riscv64-cpython-312/bcftools/vcfsort.c.pysam.o build/temp.linux-riscv64-cpython-312/bcftools/vcfstats.c.pysam.o build/temp.linux-riscv64-cpython-312/bcftools/vcfview.c.pysam.o build/temp.linux-riscv64-cpython-312/bcftools/vcmp.c.pysam.o build/temp.linux-riscv64-cpython-312/bcftools/version.c.pysam.o build/temp.linux-riscv64-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-riscv64-cpython-312/pysam -Lbuild/lib.linux-riscv64-cpython-312/pysam -Lbuild/lib.linux-riscv64-cpython-312/pysam -L/usr/lib64 -lz -llzma -lbz2 -lz -lm -lchtslib.cpython-312-riscv64-linux-gnu -o build/lib.linux-riscv64-cpython-312/pysam/libcbcftools.cpython-312-riscv64-linux-gnu.so -Wl,-rpath,$ORIGIN Compiling pysam/libcutils.pyx because it changed. [1/1] Cythonizing pysam/libcutils.pyx building 'pysam.libcutils' extension gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -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 -fasynchronous-unwind-tables -fno-omit-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-riscv64-cpython-312/pysam/libcutils.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -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 -fasynchronous-unwind-tables -fno-omit-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-riscv64-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 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -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 -fasynchronous-unwind-tables -fno-omit-frame-pointer -fPIC build/temp.linux-riscv64-cpython-312/pysam/libcutils.o build/temp.linux-riscv64-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-riscv64-cpython-312/pysam -Lbuild/lib.linux-riscv64-cpython-312/pysam -Lbuild/lib.linux-riscv64-cpython-312/pysam -Lbuild/lib.linux-riscv64-cpython-312/pysam -L/usr/lib64 -lz -llzma -lbz2 -lz -lm -lchtslib.cpython-312-riscv64-linux-gnu -lcsamtools.cpython-312-riscv64-linux-gnu -lcbcftools.cpython-312-riscv64-linux-gnu -o build/lib.linux-riscv64-cpython-312/pysam/libcutils.cpython-312-riscv64-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 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -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 -fasynchronous-unwind-tables -fno-omit-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-riscv64-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:20477:20: warning: ignoring return value of ‘sam_hdr_write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 20477 | (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:37154:16: warning: ignoring return value of ‘bgzf_seek’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37154 | (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 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -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 -fasynchronous-unwind-tables -fno-omit-frame-pointer -fPIC build/temp.linux-riscv64-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-riscv64-cpython-312/pysam -Lbuild/lib.linux-riscv64-cpython-312/pysam -Lbuild/lib.linux-riscv64-cpython-312/pysam -Lbuild/lib.linux-riscv64-cpython-312/pysam -Lbuild/lib.linux-riscv64-cpython-312/pysam -L/usr/lib64 -lz -llzma -lbz2 -lz -lm -lchtslib.cpython-312-riscv64-linux-gnu -lcutils.cpython-312-riscv64-linux-gnu -o build/lib.linux-riscv64-cpython-312/pysam/libcalignmentfile.cpython-312-riscv64-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 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -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 -fasynchronous-unwind-tables -fno-omit-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-riscv64-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 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -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 -fasynchronous-unwind-tables -fno-omit-frame-pointer -fPIC build/temp.linux-riscv64-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-riscv64-cpython-312/pysam -Lbuild/lib.linux-riscv64-cpython-312/pysam -Lbuild/lib.linux-riscv64-cpython-312/pysam -Lbuild/lib.linux-riscv64-cpython-312/pysam -Lbuild/lib.linux-riscv64-cpython-312/pysam -Lbuild/lib.linux-riscv64-cpython-312/pysam -L/usr/lib64 -lz -llzma -lbz2 -lz -lm -lchtslib.cpython-312-riscv64-linux-gnu -lcutils.cpython-312-riscv64-linux-gnu -o build/lib.linux-riscv64-cpython-312/pysam/libcsamfile.cpython-312-riscv64-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 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -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 -fasynchronous-unwind-tables -fno-omit-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-riscv64-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 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -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 -fasynchronous-unwind-tables -fno-omit-frame-pointer -fPIC build/temp.linux-riscv64-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-riscv64-cpython-312/pysam -Lbuild/lib.linux-riscv64-cpython-312/pysam -Lbuild/lib.linux-riscv64-cpython-312/pysam -Lbuild/lib.linux-riscv64-cpython-312/pysam -Lbuild/lib.linux-riscv64-cpython-312/pysam -Lbuild/lib.linux-riscv64-cpython-312/pysam -Lbuild/lib.linux-riscv64-cpython-312/pysam -L/usr/lib64 -lz -llzma -lbz2 -lz -lm -lchtslib.cpython-312-riscv64-linux-gnu -lcutils.cpython-312-riscv64-linux-gnu -o build/lib.linux-riscv64-cpython-312/pysam/libcalignedsegment.cpython-312-riscv64-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 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -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 -fasynchronous-unwind-tables -fno-omit-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-riscv64-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 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -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 -fasynchronous-unwind-tables -fno-omit-frame-pointer -fPIC build/temp.linux-riscv64-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-riscv64-cpython-312/pysam -Lbuild/lib.linux-riscv64-cpython-312/pysam -Lbuild/lib.linux-riscv64-cpython-312/pysam -Lbuild/lib.linux-riscv64-cpython-312/pysam -Lbuild/lib.linux-riscv64-cpython-312/pysam -Lbuild/lib.linux-riscv64-cpython-312/pysam -Lbuild/lib.linux-riscv64-cpython-312/pysam -Lbuild/lib.linux-riscv64-cpython-312/pysam -L/usr/lib64 -lz -llzma -lbz2 -lz -lm -lchtslib.cpython-312-riscv64-linux-gnu -lcutils.cpython-312-riscv64-linux-gnu -o build/lib.linux-riscv64-cpython-312/pysam/libctabix.cpython-312-riscv64-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 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -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 -fasynchronous-unwind-tables -fno-omit-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-riscv64-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 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -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 -fasynchronous-unwind-tables -fno-omit-frame-pointer -fPIC build/temp.linux-riscv64-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-riscv64-cpython-312/pysam -Lbuild/lib.linux-riscv64-cpython-312/pysam -Lbuild/lib.linux-riscv64-cpython-312/pysam -Lbuild/lib.linux-riscv64-cpython-312/pysam -Lbuild/lib.linux-riscv64-cpython-312/pysam -Lbuild/lib.linux-riscv64-cpython-312/pysam -Lbuild/lib.linux-riscv64-cpython-312/pysam -Lbuild/lib.linux-riscv64-cpython-312/pysam -Lbuild/lib.linux-riscv64-cpython-312/pysam -L/usr/lib64 -lz -llzma -lbz2 -lz -lm -lchtslib.cpython-312-riscv64-linux-gnu -lcutils.cpython-312-riscv64-linux-gnu -o build/lib.linux-riscv64-cpython-312/pysam/libcfaidx.cpython-312-riscv64-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 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -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 -fasynchronous-unwind-tables -fno-omit-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-riscv64-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:85885:18: warning: ignoring return value of ‘bcf_hdr_write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 85885 | (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:80563:18: warning: ignoring return value of ‘bcf_hdr_write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 80563 | (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:44281:11: warning: ignoring return value of ‘bcf_hrec_add_key’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 44281 | bcf_hrec_add_key(__pyx_v_hrec, __pyx_t_17, ((int)__pyx_t_18)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pysam/libcbcf.c:44307:11: warning: ignoring return value of ‘bcf_hrec_set_val’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 44307 | 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:80258:18: warning: ignoring return value of ‘bcf_hdr_write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 80258 | (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 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -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 -fasynchronous-unwind-tables -fno-omit-frame-pointer -fPIC build/temp.linux-riscv64-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-riscv64-cpython-312/pysam -Lbuild/lib.linux-riscv64-cpython-312/pysam -Lbuild/lib.linux-riscv64-cpython-312/pysam -Lbuild/lib.linux-riscv64-cpython-312/pysam -Lbuild/lib.linux-riscv64-cpython-312/pysam -Lbuild/lib.linux-riscv64-cpython-312/pysam -Lbuild/lib.linux-riscv64-cpython-312/pysam -Lbuild/lib.linux-riscv64-cpython-312/pysam -Lbuild/lib.linux-riscv64-cpython-312/pysam -Lbuild/lib.linux-riscv64-cpython-312/pysam -L/usr/lib64 -lz -llzma -lbz2 -lz -lm -lchtslib.cpython-312-riscv64-linux-gnu -lcutils.cpython-312-riscv64-linux-gnu -o build/lib.linux-riscv64-cpython-312/pysam/libcbcf.cpython-312-riscv64-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 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -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 -fasynchronous-unwind-tables -fno-omit-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-riscv64-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 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -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 -fasynchronous-unwind-tables -fno-omit-frame-pointer -fPIC build/temp.linux-riscv64-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-riscv64-cpython-312/pysam -Lbuild/lib.linux-riscv64-cpython-312/pysam -Lbuild/lib.linux-riscv64-cpython-312/pysam -Lbuild/lib.linux-riscv64-cpython-312/pysam -Lbuild/lib.linux-riscv64-cpython-312/pysam -Lbuild/lib.linux-riscv64-cpython-312/pysam -Lbuild/lib.linux-riscv64-cpython-312/pysam -Lbuild/lib.linux-riscv64-cpython-312/pysam -Lbuild/lib.linux-riscv64-cpython-312/pysam -Lbuild/lib.linux-riscv64-cpython-312/pysam -Lbuild/lib.linux-riscv64-cpython-312/pysam -L/usr/lib64 -lz -llzma -lbz2 -lz -lm -lchtslib.cpython-312-riscv64-linux-gnu -lcutils.cpython-312-riscv64-linux-gnu -o build/lib.linux-riscv64-cpython-312/pysam/libcbgzf.cpython-312-riscv64-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 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -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 -fasynchronous-unwind-tables -fno-omit-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-riscv64-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 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -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 -fasynchronous-unwind-tables -fno-omit-frame-pointer -fPIC build/temp.linux-riscv64-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-riscv64-cpython-312/pysam -Lbuild/lib.linux-riscv64-cpython-312/pysam -Lbuild/lib.linux-riscv64-cpython-312/pysam -Lbuild/lib.linux-riscv64-cpython-312/pysam -Lbuild/lib.linux-riscv64-cpython-312/pysam -Lbuild/lib.linux-riscv64-cpython-312/pysam -Lbuild/lib.linux-riscv64-cpython-312/pysam -Lbuild/lib.linux-riscv64-cpython-312/pysam -Lbuild/lib.linux-riscv64-cpython-312/pysam -Lbuild/lib.linux-riscv64-cpython-312/pysam -Lbuild/lib.linux-riscv64-cpython-312/pysam -Lbuild/lib.linux-riscv64-cpython-312/pysam -L/usr/lib64 -lz -llzma -lbz2 -lz -lm -lchtslib.cpython-312-riscv64-linux-gnu -lcutils.cpython-312-riscv64-linux-gnu -o build/lib.linux-riscv64-cpython-312/pysam/libctabixproxies.cpython-312-riscv64-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 -DNDEBUG -fexceptions -fexceptions -fexceptions -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -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 -fasynchronous-unwind-tables -fno-omit-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-riscv64-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’: pysam/libcvcf.c:29986:16: warning: ‘__pyx_v_qual’ may be used uninitialized [-Wmaybe-uninitialized] 29986 | __pyx_t_11 = PyFloat_FromDouble(__pyx_v_qual); if (unlikely(!__pyx_t_11)) __PYX_ERR(0, 873, __pyx_L1_error) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pysam/libcvcf.c:24939:10: note: ‘__pyx_v_qual’ was declared here 24939 | double __pyx_v_qual; | ^~~~~~~~~~~~ gcc -shared -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -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 -fasynchronous-unwind-tables -fno-omit-frame-pointer -fPIC build/temp.linux-riscv64-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-riscv64-cpython-312/pysam -Lbuild/lib.linux-riscv64-cpython-312/pysam -Lbuild/lib.linux-riscv64-cpython-312/pysam -Lbuild/lib.linux-riscv64-cpython-312/pysam -Lbuild/lib.linux-riscv64-cpython-312/pysam -Lbuild/lib.linux-riscv64-cpython-312/pysam -Lbuild/lib.linux-riscv64-cpython-312/pysam -Lbuild/lib.linux-riscv64-cpython-312/pysam -Lbuild/lib.linux-riscv64-cpython-312/pysam -Lbuild/lib.linux-riscv64-cpython-312/pysam -Lbuild/lib.linux-riscv64-cpython-312/pysam -Lbuild/lib.linux-riscv64-cpython-312/pysam -Lbuild/lib.linux-riscv64-cpython-312/pysam -L/usr/lib64 -lz -llzma -lbz2 -lz -lm -lchtslib.cpython-312-riscv64-linux-gnu -lcutils.cpython-312-riscv64-linux-gnu -o build/lib.linux-riscv64-cpython-312/pysam/libcvcf.cpython-312-riscv64-linux-gnu.so -Wl,-rpath,$ORIGIN ++ echo /builddir/build/BUILD/pysam-0.22.0/build/lib.linux-riscv64-cpython-312 + PYTHONPATH=/builddir/build/BUILD/pysam-0.22.0/build/lib.linux-riscv64-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.RvnvcM + umask 022 + cd /builddir/build/BUILD + '[' /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64 '!=' / ']' + rm -rf /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64 ++ dirname /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64 + mkdir -p /builddir/build/BUILDROOT + mkdir /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64 + CFLAGS='-O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -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 -fasynchronous-unwind-tables -fno-omit-frame-pointer ' + export CFLAGS + CXXFLAGS='-O2 -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 -fasynchronous-unwind-tables -fno-omit-frame-pointer ' + export CXXFLAGS + FFLAGS='-O2 -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 -fasynchronous-unwind-tables -fno-omit-frame-pointer -I/usr/lib64/gfortran/modules ' + export FFLAGS + FCFLAGS='-O2 -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 -fasynchronous-unwind-tables -fno-omit-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=-Wl,-z,relro -Clink-arg=-Wl,-z,now -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 -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 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -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 -fasynchronous-unwind-tables -fno-omit-frame-pointer ' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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-0.22.0-2.fc40.riscv64 --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 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -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 -fasynchronous-unwind-tables -fno-omit-frame-pointer -fPIC # pysam: (env) LDFLAGS=-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -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: 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-0.22.0-2.fc40.riscv64/usr creating /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64 creating /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12 creating /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages creating /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-riscv64-cpython-312/pysam/libcutils.pyx -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-riscv64-cpython-312/pysam/version.py -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-riscv64-cpython-312/pysam/libcutils.pyi -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-riscv64-cpython-312/pysam/pysam_util.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-riscv64-cpython-312/pysam/libcvcf.pyx -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-riscv64-cpython-312/pysam/libcalignedsegment.pxd -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-riscv64-cpython-312/pysam/libchtslib.pyx -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-riscv64-cpython-312/pysam/libcsamfile.pyi -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-riscv64-cpython-312/pysam/libctabixproxies.pyx -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-riscv64-cpython-312/pysam/libcsamfile.pxd -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-riscv64-cpython-312/pysam/version.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-riscv64-cpython-312/pysam/htslib_util.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-riscv64-cpython-312/pysam/libctabixproxies.pxd -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-riscv64-cpython-312/pysam/libcbcf.pxd -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-riscv64-cpython-312/pysam/libcfaidx.pyi -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-riscv64-cpython-312/pysam/libcbcftools.pxd -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-riscv64-cpython-312/pysam/libcbgzf.cpython-312-riscv64-linux-gnu.so -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-riscv64-cpython-312/pysam/libchtslib.cpython-312-riscv64-linux-gnu.so -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-riscv64-cpython-312/pysam/__init__.py -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-riscv64-cpython-312/pysam/py.typed -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-riscv64-cpython-312/pysam/libcsamtools.pxd -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-riscv64-cpython-312/pysam/libcvcf.cpython-312-riscv64-linux-gnu.so -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-riscv64-cpython-312/pysam/libcfaidx.cpython-312-riscv64-linux-gnu.so -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-riscv64-cpython-312/pysam/libcsamtools.pyx -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-riscv64-cpython-312/pysam/libcsamtools.cpython-312-riscv64-linux-gnu.so -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-riscv64-cpython-312/pysam/libctabix.cpython-312-riscv64-linux-gnu.so -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-riscv64-cpython-312/pysam/libctabix.pyx -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-riscv64-cpython-312/pysam/libcsamtools.pyi -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-riscv64-cpython-312/pysam/config.py -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-riscv64-cpython-312/pysam/libchtslib.pxd -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-riscv64-cpython-312/pysam/libcalignedsegment.cpython-312-riscv64-linux-gnu.so -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-riscv64-cpython-312/pysam/libcbgzf.pyx -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-riscv64-cpython-312/pysam/libcalignmentfile.cpython-312-riscv64-linux-gnu.so -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-riscv64-cpython-312/pysam/libcsamfile.cpython-312-riscv64-linux-gnu.so -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-riscv64-cpython-312/pysam/libcvcf.pxd -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-riscv64-cpython-312/pysam/cbcftools_util.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-riscv64-cpython-312/pysam/bcftools.py -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-riscv64-cpython-312/pysam/htslib_util.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-riscv64-cpython-312/pysam/libcalignmentfile.pxd -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-riscv64-cpython-312/pysam/libcbcftools.cpython-312-riscv64-linux-gnu.so -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-riscv64-cpython-312/pysam/pysam_util.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-riscv64-cpython-312/pysam/libcutils.cpython-312-riscv64-linux-gnu.so -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-riscv64-cpython-312/pysam/libcbgzf.pyi -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-riscv64-cpython-312/pysam/libcbcf.pyx -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-riscv64-cpython-312/pysam/samtools.py -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-riscv64-cpython-312/pysam/libcvcf.pyi -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-riscv64-cpython-312/pysam/pysam_stream.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-riscv64-cpython-312/pysam/libcalignmentfile.pyx -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-riscv64-cpython-312/pysam/libcalignedsegment.pyi -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-riscv64-cpython-312/pysam/csamtools_util.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam creating /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include creating /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-riscv64-cpython-312/pysam/include/bcftools/hclust.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-riscv64-cpython-312/pysam/include/bcftools/prob1.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-riscv64-cpython-312/pysam/include/bcftools/kmin.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-riscv64-cpython-312/pysam/include/bcftools/vcfnorm.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-riscv64-cpython-312/pysam/include/bcftools/vcfgtcheck.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-riscv64-cpython-312/pysam/include/bcftools/vcfquery.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-riscv64-cpython-312/pysam/include/bcftools/version.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-riscv64-cpython-312/pysam/include/bcftools/str_finder.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-riscv64-cpython-312/pysam/include/bcftools/call.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-riscv64-cpython-312/pysam/include/bcftools/consensus.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-riscv64-cpython-312/pysam/include/bcftools/smpl_ilist.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-riscv64-cpython-312/pysam/include/bcftools/utlist.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-riscv64-cpython-312/pysam/include/bcftools/vcfsom.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-riscv64-cpython-312/pysam/include/bcftools/vcfindex.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-riscv64-cpython-312/pysam/include/bcftools/prob1.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-riscv64-cpython-312/pysam/include/bcftools/tsv2vcf.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-riscv64-cpython-312/pysam/include/bcftools/HMM.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-riscv64-cpython-312/pysam/include/bcftools/bam2bcf.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-riscv64-cpython-312/pysam/include/bcftools/extsort.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-riscv64-cpython-312/pysam/include/bcftools/dbuf.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-riscv64-cpython-312/pysam/include/bcftools/vcfview.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-riscv64-cpython-312/pysam/include/bcftools/abuf.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-riscv64-cpython-312/pysam/include/bcftools/vcfannotate.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-riscv64-cpython-312/pysam/include/bcftools/gvcf.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-riscv64-cpython-312/pysam/include/bcftools/hclust.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-riscv64-cpython-312/pysam/include/bcftools/bam2bcf.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-riscv64-cpython-312/pysam/include/bcftools/vcfbuf.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-riscv64-cpython-312/pysam/include/bcftools/vcfstats.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-riscv64-cpython-312/pysam/include/bcftools/abuf.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-riscv64-cpython-312/pysam/include/bcftools/hex.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-riscv64-cpython-312/pysam/include/bcftools/vcfsom.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-riscv64-cpython-312/pysam/include/bcftools/kmin.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-riscv64-cpython-312/pysam/include/bcftools/config.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-riscv64-cpython-312/pysam/include/bcftools/HMM.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-riscv64-cpython-312/pysam/include/bcftools/smpl_ilist.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-riscv64-cpython-312/pysam/include/bcftools/rbuf.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-riscv64-cpython-312/pysam/include/bcftools/mcall.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-riscv64-cpython-312/pysam/include/bcftools/mpileup.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-riscv64-cpython-312/pysam/include/bcftools/vcfisec.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-riscv64-cpython-312/pysam/include/bcftools/mw.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-riscv64-cpython-312/pysam/include/bcftools/vcfcnv.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-riscv64-cpython-312/pysam/include/bcftools/vcfroh.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-riscv64-cpython-312/pysam/include/bcftools/vcfcall.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-riscv64-cpython-312/pysam/include/bcftools/extsort.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-riscv64-cpython-312/pysam/include/bcftools/dist.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-riscv64-cpython-312/pysam/include/bcftools/HMM.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-riscv64-cpython-312/pysam/include/bcftools/vcfbuf.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-riscv64-cpython-312/pysam/include/bcftools/extsort.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-riscv64-cpython-312/pysam/include/bcftools/filter.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-riscv64-cpython-312/pysam/include/bcftools/vcmp.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-riscv64-cpython-312/pysam/include/bcftools/bcftools.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-riscv64-cpython-312/pysam/include/bcftools/bam2bcf_indel.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-riscv64-cpython-312/pysam/include/bcftools/regidx.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-riscv64-cpython-312/pysam/include/bcftools/filter.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-riscv64-cpython-312/pysam/include/bcftools/convert.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-riscv64-cpython-312/pysam/include/bcftools/vcfbuf.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-riscv64-cpython-312/pysam/include/bcftools/ccall.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-riscv64-cpython-312/pysam/include/bcftools/bam_sample.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-riscv64-cpython-312/pysam/include/bcftools/vcfisec.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-riscv64-cpython-312/pysam/include/bcftools/ploidy.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-riscv64-cpython-312/pysam/include/bcftools/main.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-riscv64-cpython-312/pysam/include/bcftools/abuf.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-riscv64-cpython-312/pysam/include/bcftools/read_consensus.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-riscv64-cpython-312/pysam/include/bcftools/vcfconcat.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-riscv64-cpython-312/pysam/include/bcftools/variantkey.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-riscv64-cpython-312/pysam/include/bcftools/bam_sample.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-riscv64-cpython-312/pysam/include/bcftools/vcfconvert.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-riscv64-cpython-312/pysam/include/bcftools/vcfmerge.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-riscv64-cpython-312/pysam/include/bcftools/vcfquery.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-riscv64-cpython-312/pysam/include/bcftools/gvcf.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-riscv64-cpython-312/pysam/include/bcftools/em.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-riscv64-cpython-312/pysam/include/bcftools/vcffilter.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-riscv64-cpython-312/pysam/include/bcftools/tabix.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-riscv64-cpython-312/pysam/include/bcftools/tsv2vcf.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-riscv64-cpython-312/pysam/include/bcftools/vcfconvert.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-riscv64-cpython-312/pysam/include/bcftools/vcfconcat.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-riscv64-cpython-312/pysam/include/bcftools/bin.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-riscv64-cpython-312/pysam/include/bcftools/vcfsort.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-riscv64-cpython-312/pysam/include/bcftools/gvcf.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-riscv64-cpython-312/pysam/include/bcftools/reheader.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-riscv64-cpython-312/pysam/include/bcftools/bcftools.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-riscv64-cpython-312/pysam/include/bcftools/em.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-riscv64-cpython-312/pysam/include/bcftools/reheader.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-riscv64-cpython-312/pysam/include/bcftools/ploidy.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-riscv64-cpython-312/pysam/include/bcftools/regidx.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-riscv64-cpython-312/pysam/include/bcftools/vcfsort.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-riscv64-cpython-312/pysam/include/bcftools/cols.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-riscv64-cpython-312/pysam/include/bcftools/cigar_state.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-riscv64-cpython-312/pysam/include/bcftools/vcfmerge.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-riscv64-cpython-312/pysam/include/bcftools/tabix.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-riscv64-cpython-312/pysam/include/bcftools/csq.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-riscv64-cpython-312/pysam/include/bcftools/vcfroh.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-riscv64-cpython-312/pysam/include/bcftools/vcffilter.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-riscv64-cpython-312/pysam/include/bcftools/vcfcnv.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-riscv64-cpython-312/pysam/include/bcftools/ccall.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-riscv64-cpython-312/pysam/include/bcftools/kmin.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-riscv64-cpython-312/pysam/include/bcftools/khash_str2str.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-riscv64-cpython-312/pysam/include/bcftools/bam2bcf.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-riscv64-cpython-312/pysam/include/bcftools/gff.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-riscv64-cpython-312/pysam/include/bcftools/read_consensus.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-riscv64-cpython-312/pysam/include/bcftools/version.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-riscv64-cpython-312/pysam/include/bcftools/gff.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-riscv64-cpython-312/pysam/include/bcftools/README -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-riscv64-cpython-312/pysam/include/bcftools/mcall.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-riscv64-cpython-312/pysam/include/bcftools/LICENSE -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-riscv64-cpython-312/pysam/include/bcftools/vcfplugin.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-riscv64-cpython-312/pysam/include/bcftools/convert.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-riscv64-cpython-312/pysam/include/bcftools/tsv2vcf.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-riscv64-cpython-312/pysam/include/bcftools/smpl_ilist.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-riscv64-cpython-312/pysam/include/bcftools/bam2bcf_iaux.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-riscv64-cpython-312/pysam/include/bcftools/consensus.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-riscv64-cpython-312/pysam/include/bcftools/vcmp.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-riscv64-cpython-312/pysam/include/bcftools/hclust.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-riscv64-cpython-312/pysam/include/bcftools/cols.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-riscv64-cpython-312/pysam/include/bcftools/bam_sample.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-riscv64-cpython-312/pysam/include/bcftools/ploidy.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-riscv64-cpython-312/pysam/include/bcftools/bam2bcf_indel.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-riscv64-cpython-312/pysam/include/bcftools/str_finder.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-riscv64-cpython-312/pysam/include/bcftools/version.sh -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-riscv64-cpython-312/pysam/include/bcftools/vcfplugin.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-riscv64-cpython-312/pysam/include/bcftools/regidx.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-riscv64-cpython-312/pysam/include/bcftools/str_finder.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-riscv64-cpython-312/pysam/include/bcftools/bam2bcf_iaux.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-riscv64-cpython-312/pysam/include/bcftools/cols.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-riscv64-cpython-312/pysam/include/bcftools/convert.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-riscv64-cpython-312/pysam/include/bcftools/dist.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-riscv64-cpython-312/pysam/include/bcftools/prob1.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-riscv64-cpython-312/pysam/include/bcftools/vcfhead.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-riscv64-cpython-312/pysam/include/bcftools/vcfgtcheck.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-riscv64-cpython-312/pysam/include/bcftools/main.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-riscv64-cpython-312/pysam/include/bcftools/read_consensus.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-riscv64-cpython-312/pysam/include/bcftools/vcfstats.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-riscv64-cpython-312/pysam/include/bcftools/bin.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-riscv64-cpython-312/pysam/include/bcftools/vcfnorm.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-riscv64-cpython-312/pysam/include/bcftools/vcfindex.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-riscv64-cpython-312/pysam/include/bcftools/vcmp.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-riscv64-cpython-312/pysam/include/bcftools/vcfannotate.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-riscv64-cpython-312/pysam/include/bcftools/dist.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-riscv64-cpython-312/pysam/include/bcftools/gff.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-riscv64-cpython-312/pysam/include/bcftools/bin.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-riscv64-cpython-312/pysam/include/bcftools/vcfhead.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-riscv64-cpython-312/pysam/include/bcftools/kheap.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-riscv64-cpython-312/pysam/include/bcftools/vcfview.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-riscv64-cpython-312/pysam/include/bcftools/vcfcall.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-riscv64-cpython-312/pysam/include/bcftools/mpileup.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-riscv64-cpython-312/pysam/include/bcftools/filter.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-riscv64-cpython-312/pysam/include/bcftools/bcftools.pysam.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/bcftools copying build/lib.linux-riscv64-cpython-312/pysam/include/bcftools/csq.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/bcftools creating /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/htslib creating /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/htslib/m4 copying build/lib.linux-riscv64-cpython-312/pysam/include/htslib/m4/pkg.m4 -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/htslib/m4 copying build/lib.linux-riscv64-cpython-312/pysam/include/htslib/m4/hts_check_compile_flags_needed.m4 -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/htslib/m4 copying build/lib.linux-riscv64-cpython-312/pysam/include/htslib/m4/hts_hide_dynamic_syms.m4 -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/htslib/m4 copying build/lib.linux-riscv64-cpython-312/pysam/include/htslib/m4/hts_prog_cc_warnings.m4 -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/htslib/m4 copying build/lib.linux-riscv64-cpython-312/pysam/include/htslib/vcfutils.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-riscv64-cpython-312/pysam/include/htslib/hts_os.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-riscv64-cpython-312/pysam/include/htslib/config.mk.in -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-riscv64-cpython-312/pysam/include/htslib/kfunc.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-riscv64-cpython-312/pysam/include/htslib/plugin.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-riscv64-cpython-312/pysam/include/htslib/hfile_s3_write.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-riscv64-cpython-312/pysam/include/htslib/sam_mods.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-riscv64-cpython-312/pysam/include/htslib/configure -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-riscv64-cpython-312/pysam/include/htslib/thread_pool.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-riscv64-cpython-312/pysam/include/htslib/tbx.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-riscv64-cpython-312/pysam/include/htslib/hts_internal.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-riscv64-cpython-312/pysam/include/htslib/realn.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-riscv64-cpython-312/pysam/include/htslib/hts_time_funcs.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/htslib creating /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htslib copying build/lib.linux-riscv64-cpython-312/pysam/include/htslib/htslib/kstring.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htslib copying build/lib.linux-riscv64-cpython-312/pysam/include/htslib/htslib/hts_defs.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htslib copying build/lib.linux-riscv64-cpython-312/pysam/include/htslib/htslib/kbitset.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htslib copying build/lib.linux-riscv64-cpython-312/pysam/include/htslib/htslib/faidx.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htslib copying build/lib.linux-riscv64-cpython-312/pysam/include/htslib/htslib/hts_endian.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htslib copying build/lib.linux-riscv64-cpython-312/pysam/include/htslib/htslib/vcf.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htslib copying build/lib.linux-riscv64-cpython-312/pysam/include/htslib/htslib/synced_bcf_reader.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htslib copying build/lib.linux-riscv64-cpython-312/pysam/include/htslib/htslib/vcf_sweep.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htslib copying build/lib.linux-riscv64-cpython-312/pysam/include/htslib/htslib/khash.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htslib copying build/lib.linux-riscv64-cpython-312/pysam/include/htslib/htslib/kfunc.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htslib copying build/lib.linux-riscv64-cpython-312/pysam/include/htslib/htslib/hts.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htslib copying build/lib.linux-riscv64-cpython-312/pysam/include/htslib/htslib/vcfutils.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htslib copying build/lib.linux-riscv64-cpython-312/pysam/include/htslib/htslib/bgzf.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htslib copying build/lib.linux-riscv64-cpython-312/pysam/include/htslib/htslib/klist.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htslib copying build/lib.linux-riscv64-cpython-312/pysam/include/htslib/htslib/khash_str2int.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htslib copying build/lib.linux-riscv64-cpython-312/pysam/include/htslib/htslib/hfile.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htslib copying build/lib.linux-riscv64-cpython-312/pysam/include/htslib/htslib/ksort.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htslib copying build/lib.linux-riscv64-cpython-312/pysam/include/htslib/htslib/hts_log.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htslib copying build/lib.linux-riscv64-cpython-312/pysam/include/htslib/htslib/kseq.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htslib copying build/lib.linux-riscv64-cpython-312/pysam/include/htslib/htslib/regidx.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htslib copying build/lib.linux-riscv64-cpython-312/pysam/include/htslib/htslib/knetfile.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htslib copying build/lib.linux-riscv64-cpython-312/pysam/include/htslib/htslib/cram.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htslib copying build/lib.linux-riscv64-cpython-312/pysam/include/htslib/htslib/hts_expr.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htslib copying build/lib.linux-riscv64-cpython-312/pysam/include/htslib/htslib/tbx.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htslib copying build/lib.linux-riscv64-cpython-312/pysam/include/htslib/htslib/sam.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htslib copying build/lib.linux-riscv64-cpython-312/pysam/include/htslib/htslib/hts_os.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htslib copying build/lib.linux-riscv64-cpython-312/pysam/include/htslib/htslib/kroundup.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htslib copying build/lib.linux-riscv64-cpython-312/pysam/include/htslib/htslib/thread_pool.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htslib copying build/lib.linux-riscv64-cpython-312/pysam/include/htslib/hfile_gcs.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-riscv64-cpython-312/pysam/include/htslib/vcf_sweep.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-riscv64-cpython-312/pysam/include/htslib/config.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-riscv64-cpython-312/pysam/include/htslib/bgzf.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-riscv64-cpython-312/pysam/include/htslib/header.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-riscv64-cpython-312/pysam/include/htslib/bcf_sr_sort.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-riscv64-cpython-312/pysam/include/htslib/config.h.in -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-riscv64-cpython-312/pysam/include/htslib/htslib.mk -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/htslib creating /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htscodecs creating /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-riscv64-cpython-312/pysam/include/htslib/htscodecs/htscodecs/htscodecs.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-riscv64-cpython-312/pysam/include/htslib/htscodecs/htscodecs/pooled_alloc.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-riscv64-cpython-312/pysam/include/htslib/htscodecs/htscodecs/fqzcomp_qual.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-riscv64-cpython-312/pysam/include/htslib/htscodecs/htscodecs/permute.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-riscv64-cpython-312/pysam/include/htslib/htscodecs/htscodecs/pack.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-riscv64-cpython-312/pysam/include/htslib/htscodecs/htscodecs/rle.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-riscv64-cpython-312/pysam/include/htslib/htscodecs/htscodecs/version.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-riscv64-cpython-312/pysam/include/htslib/htscodecs/htscodecs/c_range_coder.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-riscv64-cpython-312/pysam/include/htslib/htscodecs/htscodecs/htscodecs.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-riscv64-cpython-312/pysam/include/htslib/htscodecs/htscodecs/fqzcomp_qual.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-riscv64-cpython-312/pysam/include/htslib/htscodecs/htscodecs/utils.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-riscv64-cpython-312/pysam/include/htslib/htscodecs/htscodecs/htscodecs_endian.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-riscv64-cpython-312/pysam/include/htslib/htscodecs/htscodecs/rANS_static4x16pr.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-riscv64-cpython-312/pysam/include/htslib/htscodecs/htscodecs/tokenise_name3.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-riscv64-cpython-312/pysam/include/htslib/htscodecs/htscodecs/rANS_static4x16.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-riscv64-cpython-312/pysam/include/htslib/htscodecs/htscodecs/rANS_word.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-riscv64-cpython-312/pysam/include/htslib/htscodecs/htscodecs/utils.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-riscv64-cpython-312/pysam/include/htslib/htscodecs/htscodecs/rANS_static32x16pr.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-riscv64-cpython-312/pysam/include/htslib/htscodecs/htscodecs/rANS_static32x16pr.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-riscv64-cpython-312/pysam/include/htslib/htscodecs/htscodecs/tokenise_name3.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-riscv64-cpython-312/pysam/include/htslib/htscodecs/htscodecs/rANS_byte.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-riscv64-cpython-312/pysam/include/htslib/htscodecs/htscodecs/varint2.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-riscv64-cpython-312/pysam/include/htslib/htscodecs/htscodecs/arith_dynamic.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-riscv64-cpython-312/pysam/include/htslib/htscodecs/htscodecs/rANS_static32x16pr_avx2.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-riscv64-cpython-312/pysam/include/htslib/htscodecs/htscodecs/rANS_static32x16pr_neon.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-riscv64-cpython-312/pysam/include/htslib/htscodecs/htscodecs/rANS_static32x16pr_sse4.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-riscv64-cpython-312/pysam/include/htslib/htscodecs/htscodecs/rANS_static.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-riscv64-cpython-312/pysam/include/htslib/htscodecs/htscodecs/arith_dynamic.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-riscv64-cpython-312/pysam/include/htslib/htscodecs/htscodecs/varint.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-riscv64-cpython-312/pysam/include/htslib/htscodecs/htscodecs/pack.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-riscv64-cpython-312/pysam/include/htslib/htscodecs/htscodecs/rANS_static32x16pr_avx512.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-riscv64-cpython-312/pysam/include/htslib/htscodecs/htscodecs/rANS_static.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-riscv64-cpython-312/pysam/include/htslib/htscodecs/htscodecs/rANS_static16_int.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-riscv64-cpython-312/pysam/include/htslib/htscodecs/htscodecs/rle.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-riscv64-cpython-312/pysam/include/htslib/htscodecs/htscodecs/c_simple_model.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/htslib/htscodecs/htscodecs copying build/lib.linux-riscv64-cpython-312/pysam/include/htslib/regidx.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-riscv64-cpython-312/pysam/include/htslib/sam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-riscv64-cpython-312/pysam/include/htslib/hfile_s3.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-riscv64-cpython-312/pysam/include/htslib/textutils_internal.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-riscv64-cpython-312/pysam/include/htslib/hfile.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-riscv64-cpython-312/pysam/include/htslib/vcf.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-riscv64-cpython-312/pysam/include/htslib/kstring.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-riscv64-cpython-312/pysam/include/htslib/htslib.pc.in -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-riscv64-cpython-312/pysam/include/htslib/hfile_internal.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-riscv64-cpython-312/pysam/include/htslib/configure.ac -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-riscv64-cpython-312/pysam/include/htslib/Makefile -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-riscv64-cpython-312/pysam/include/htslib/faidx.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-riscv64-cpython-312/pysam/include/htslib/synced_bcf_reader.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-riscv64-cpython-312/pysam/include/htslib/htslib_vars.mk -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-riscv64-cpython-312/pysam/include/htslib/builddir_vars.mk.in -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-riscv64-cpython-312/pysam/include/htslib/header.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-riscv64-cpython-312/pysam/include/htslib/tabix.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-riscv64-cpython-312/pysam/include/htslib/htscodecs_bundled.mk -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-riscv64-cpython-312/pysam/include/htslib/multipart.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-riscv64-cpython-312/pysam/include/htslib/region.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-riscv64-cpython-312/pysam/include/htslib/htscodecs_external.mk -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/htslib creating /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/htslib/cram copying build/lib.linux-riscv64-cpython-312/pysam/include/htslib/cram/pooled_alloc.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/htslib/cram copying build/lib.linux-riscv64-cpython-312/pysam/include/htslib/cram/cram_stats.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/htslib/cram copying build/lib.linux-riscv64-cpython-312/pysam/include/htslib/cram/mFILE.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/htslib/cram copying build/lib.linux-riscv64-cpython-312/pysam/include/htslib/cram/cram_index.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/htslib/cram copying build/lib.linux-riscv64-cpython-312/pysam/include/htslib/cram/cram_io.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/htslib/cram copying build/lib.linux-riscv64-cpython-312/pysam/include/htslib/cram/cram_decode.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/htslib/cram copying build/lib.linux-riscv64-cpython-312/pysam/include/htslib/cram/cram_codecs.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/htslib/cram copying build/lib.linux-riscv64-cpython-312/pysam/include/htslib/cram/cram_io.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/htslib/cram copying build/lib.linux-riscv64-cpython-312/pysam/include/htslib/cram/cram_encode.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/htslib/cram copying build/lib.linux-riscv64-cpython-312/pysam/include/htslib/cram/cram_structs.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/htslib/cram copying build/lib.linux-riscv64-cpython-312/pysam/include/htslib/cram/os.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/htslib/cram copying build/lib.linux-riscv64-cpython-312/pysam/include/htslib/cram/cram_decode.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/htslib/cram copying build/lib.linux-riscv64-cpython-312/pysam/include/htslib/cram/cram_samtools.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/htslib/cram copying build/lib.linux-riscv64-cpython-312/pysam/include/htslib/cram/cram.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/htslib/cram copying build/lib.linux-riscv64-cpython-312/pysam/include/htslib/cram/cram_external.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/htslib/cram copying build/lib.linux-riscv64-cpython-312/pysam/include/htslib/cram/string_alloc.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/htslib/cram copying build/lib.linux-riscv64-cpython-312/pysam/include/htslib/cram/cram_encode.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/htslib/cram copying build/lib.linux-riscv64-cpython-312/pysam/include/htslib/cram/open_trace_file.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/htslib/cram copying build/lib.linux-riscv64-cpython-312/pysam/include/htslib/cram/open_trace_file.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/htslib/cram copying build/lib.linux-riscv64-cpython-312/pysam/include/htslib/cram/string_alloc.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/htslib/cram copying build/lib.linux-riscv64-cpython-312/pysam/include/htslib/cram/misc.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/htslib/cram copying build/lib.linux-riscv64-cpython-312/pysam/include/htslib/cram/cram_stats.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/htslib/cram copying build/lib.linux-riscv64-cpython-312/pysam/include/htslib/cram/mFILE.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/htslib/cram copying build/lib.linux-riscv64-cpython-312/pysam/include/htslib/cram/pooled_alloc.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/htslib/cram copying build/lib.linux-riscv64-cpython-312/pysam/include/htslib/cram/cram_codecs.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/htslib/cram copying build/lib.linux-riscv64-cpython-312/pysam/include/htslib/cram/cram_index.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/htslib/cram copying build/lib.linux-riscv64-cpython-312/pysam/include/htslib/hts_expr.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-riscv64-cpython-312/pysam/include/htslib/README -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-riscv64-cpython-312/pysam/include/htslib/hts.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-riscv64-cpython-312/pysam/include/htslib/LICENSE -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/htslib creating /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/htslib/os copying build/lib.linux-riscv64-cpython-312/pysam/include/htslib/os/lzma_stub.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/htslib/os copying build/lib.linux-riscv64-cpython-312/pysam/include/htslib/os/rand.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/htslib/os copying build/lib.linux-riscv64-cpython-312/pysam/include/htslib/textutils.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-riscv64-cpython-312/pysam/include/htslib/sam_internal.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-riscv64-cpython-312/pysam/include/htslib/md5.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-riscv64-cpython-312/pysam/include/htslib/htsfile.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-riscv64-cpython-312/pysam/include/htslib/version.sh -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-riscv64-cpython-312/pysam/include/htslib/probaln.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-riscv64-cpython-312/pysam/include/htslib/bgzip.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-riscv64-cpython-312/pysam/include/htslib/errmod.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-riscv64-cpython-312/pysam/include/htslib/hfile_libcurl.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-riscv64-cpython-312/pysam/include/htslib/bcf_sr_sort.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-riscv64-cpython-312/pysam/include/htslib/thread_pool_internal.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/htslib copying build/lib.linux-riscv64-cpython-312/pysam/include/__init__.py -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include creating /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-riscv64-cpython-312/pysam/include/samtools/samtools.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-riscv64-cpython-312/pysam/include/samtools/cram_size.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-riscv64-cpython-312/pysam/include/samtools/bam_rmdup.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-riscv64-cpython-312/pysam/include/samtools/tmp_file.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-riscv64-cpython-312/pysam/include/samtools/bam2depth.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-riscv64-cpython-312/pysam/include/samtools/bam_cat.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-riscv64-cpython-312/pysam/include/samtools/bam_samples.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-riscv64-cpython-312/pysam/include/samtools/bam_color.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-riscv64-cpython-312/pysam/include/samtools/bam_flags.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-riscv64-cpython-312/pysam/include/samtools/sample.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-riscv64-cpython-312/pysam/include/samtools/bam_index.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-riscv64-cpython-312/pysam/include/samtools/cut_target.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-riscv64-cpython-312/pysam/include/samtools/bam_quickcheck.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-riscv64-cpython-312/pysam/include/samtools/bedidx.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-riscv64-cpython-312/pysam/include/samtools/bam_plbuf.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-riscv64-cpython-312/pysam/include/samtools/bam_markdup.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-riscv64-cpython-312/pysam/include/samtools/bedidx.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-riscv64-cpython-312/pysam/include/samtools/bam_plcmd.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-riscv64-cpython-312/pysam/include/samtools/bedcov.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-riscv64-cpython-312/pysam/include/samtools/stats_isize.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-riscv64-cpython-312/pysam/include/samtools/bam_plbuf.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-riscv64-cpython-312/pysam/include/samtools/config.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-riscv64-cpython-312/pysam/include/samtools/sample.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-riscv64-cpython-312/pysam/include/samtools/bam_rmdupse.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-riscv64-cpython-312/pysam/include/samtools/reference.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-riscv64-cpython-312/pysam/include/samtools/bam_mate.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-riscv64-cpython-312/pysam/include/samtools/bam_rmdupse.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-riscv64-cpython-312/pysam/include/samtools/faidx.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-riscv64-cpython-312/pysam/include/samtools/phase.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-riscv64-cpython-312/pysam/include/samtools/amplicon_stats.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-riscv64-cpython-312/pysam/include/samtools/bamshuf.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-riscv64-cpython-312/pysam/include/samtools/bam_lpileup.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-riscv64-cpython-312/pysam/include/samtools/samtools.pysam.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-riscv64-cpython-312/pysam/include/samtools/bam_color.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-riscv64-cpython-312/pysam/include/samtools/bam_reheader.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-riscv64-cpython-312/pysam/include/samtools/bedidx.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-riscv64-cpython-312/pysam/include/samtools/cram_size.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-riscv64-cpython-312/pysam/include/samtools/bamtk.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-riscv64-cpython-312/pysam/include/samtools/bam_consensus.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-riscv64-cpython-312/pysam/include/samtools/bam_flags.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-riscv64-cpython-312/pysam/include/samtools/bam_rmdup.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-riscv64-cpython-312/pysam/include/samtools/padding.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-riscv64-cpython-312/pysam/include/samtools/sam_opts.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-riscv64-cpython-312/pysam/include/samtools/samtools.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-riscv64-cpython-312/pysam/include/samtools/sam_opts.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-riscv64-cpython-312/pysam/include/samtools/bam_plcmd.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-riscv64-cpython-312/pysam/include/samtools/bam.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-riscv64-cpython-312/pysam/include/samtools/tmp_file.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-riscv64-cpython-312/pysam/include/samtools/bam_samples.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-riscv64-cpython-312/pysam/include/samtools/coverage.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-riscv64-cpython-312/pysam/include/samtools/bam2depth.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-riscv64-cpython-312/pysam/include/samtools/bam_markdup.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-riscv64-cpython-312/pysam/include/samtools/phase.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-riscv64-cpython-312/pysam/include/samtools/bam_plbuf.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-riscv64-cpython-312/pysam/include/samtools/bam_stat.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-riscv64-cpython-312/pysam/include/samtools/bam_reheader.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-riscv64-cpython-312/pysam/include/samtools/stats_isize.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-riscv64-cpython-312/pysam/include/samtools/bam_addrprg.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-riscv64-cpython-312/pysam/include/samtools/consensus_pileup.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-riscv64-cpython-312/pysam/include/samtools/bam_ampliconclip.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-riscv64-cpython-312/pysam/include/samtools/bamtk.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-riscv64-cpython-312/pysam/include/samtools/bamshuf.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-riscv64-cpython-312/pysam/include/samtools/bam_lpileup.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-riscv64-cpython-312/pysam/include/samtools/bam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-riscv64-cpython-312/pysam/include/samtools/bam_mate.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-riscv64-cpython-312/pysam/include/samtools/bam_lpileup.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-riscv64-cpython-312/pysam/include/samtools/sam_utils.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-riscv64-cpython-312/pysam/include/samtools/faidx.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-riscv64-cpython-312/pysam/include/samtools/bam_md.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/samtools creating /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/samtools/lz4 copying build/lib.linux-riscv64-cpython-312/pysam/include/samtools/lz4/lz4.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/samtools/lz4 copying build/lib.linux-riscv64-cpython-312/pysam/include/samtools/lz4/lz4.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/samtools/lz4 copying build/lib.linux-riscv64-cpython-312/pysam/include/samtools/lz4/LICENSE -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/samtools/lz4 copying build/lib.linux-riscv64-cpython-312/pysam/include/samtools/lz4/lz4.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/samtools/lz4 copying build/lib.linux-riscv64-cpython-312/pysam/include/samtools/bam_consensus.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-riscv64-cpython-312/pysam/include/samtools/sam_utils.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-riscv64-cpython-312/pysam/include/samtools/bam_sort.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-riscv64-cpython-312/pysam/include/samtools/sample.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-riscv64-cpython-312/pysam/include/samtools/dict.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-riscv64-cpython-312/pysam/include/samtools/bam_ampliconclip.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-riscv64-cpython-312/pysam/include/samtools/amplicon_stats.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-riscv64-cpython-312/pysam/include/samtools/padding.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-riscv64-cpython-312/pysam/include/samtools/cut_target.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-riscv64-cpython-312/pysam/include/samtools/consensus_pileup.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-riscv64-cpython-312/pysam/include/samtools/sam_opts.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-riscv64-cpython-312/pysam/include/samtools/README -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-riscv64-cpython-312/pysam/include/samtools/splaysort.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-riscv64-cpython-312/pysam/include/samtools/LICENSE -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-riscv64-cpython-312/pysam/include/samtools/bam_sort.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-riscv64-cpython-312/pysam/include/samtools/bam_split.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-riscv64-cpython-312/pysam/include/samtools/consensus_pileup.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-riscv64-cpython-312/pysam/include/samtools/bam_aux.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-riscv64-cpython-312/pysam/include/samtools/coverage.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-riscv64-cpython-312/pysam/include/samtools/bam_ampliconclip.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-riscv64-cpython-312/pysam/include/samtools/reset.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-riscv64-cpython-312/pysam/include/samtools/bedcov.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-riscv64-cpython-312/pysam/include/samtools/bam_stat.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-riscv64-cpython-312/pysam/include/samtools/sam_utils.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-riscv64-cpython-312/pysam/include/samtools/tmp_file.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-riscv64-cpython-312/pysam/include/samtools/sam_view.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-riscv64-cpython-312/pysam/include/samtools/reset.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-riscv64-cpython-312/pysam/include/samtools/version.sh -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-riscv64-cpython-312/pysam/include/samtools/bam_import.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-riscv64-cpython-312/pysam/include/samtools/bam_addrprg.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-riscv64-cpython-312/pysam/include/samtools/reference.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-riscv64-cpython-312/pysam/include/samtools/bam_fastq.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-riscv64-cpython-312/pysam/include/samtools/stats_isize.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-riscv64-cpython-312/pysam/include/samtools/bam_md.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-riscv64-cpython-312/pysam/include/samtools/dict.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-riscv64-cpython-312/pysam/include/samtools/bam_index.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-riscv64-cpython-312/pysam/include/samtools/bam.h -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-riscv64-cpython-312/pysam/include/samtools/bam_import.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-riscv64-cpython-312/pysam/include/samtools/bam_cat.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-riscv64-cpython-312/pysam/include/samtools/bam_quickcheck.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-riscv64-cpython-312/pysam/include/samtools/bam_aux.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-riscv64-cpython-312/pysam/include/samtools/bam_split.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-riscv64-cpython-312/pysam/include/samtools/stats.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-riscv64-cpython-312/pysam/include/samtools/stats.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-riscv64-cpython-312/pysam/include/samtools/sam_view.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-riscv64-cpython-312/pysam/include/samtools/bam_fastq.c.pysam.c -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/samtools copying build/lib.linux-riscv64-cpython-312/pysam/libcfaidx.pyx -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-riscv64-cpython-312/pysam/libcsamfile.pyx -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-riscv64-cpython-312/pysam/libctabixproxies.pyi -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-riscv64-cpython-312/pysam/libcbcf.cpython-312-riscv64-linux-gnu.so -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-riscv64-cpython-312/pysam/libchtslib.pyi -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-riscv64-cpython-312/pysam/libcalignmentfile.pyi -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-riscv64-cpython-312/pysam/utils.py -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-riscv64-cpython-312/pysam/libcfaidx.pxd -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-riscv64-cpython-312/pysam/libcbcftools.pyi -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-riscv64-cpython-312/pysam/libcutils.pxd -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-riscv64-cpython-312/pysam/libctabix.pxd -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-riscv64-cpython-312/pysam/libctabixproxies.cpython-312-riscv64-linux-gnu.so -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-riscv64-cpython-312/pysam/libcbcftools.pyx -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-riscv64-cpython-312/pysam/libcbcf.pyi -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-riscv64-cpython-312/pysam/libctabix.pyi -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-riscv64-cpython-312/pysam/Pileup.py -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-riscv64-cpython-312/pysam/version.pyi -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam copying build/lib.linux-riscv64-cpython-312/pysam/libcalignedsegment.pyx -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam creating /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/__pycache__ copying build/lib.linux-riscv64-cpython-312/pysam/__pycache__/utils.cpython-312.pyc -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/__pycache__ copying build/lib.linux-riscv64-cpython-312/pysam/__pycache__/config.cpython-312.pyc -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/__pycache__ copying build/lib.linux-riscv64-cpython-312/pysam/__pycache__/version.cpython-312.pyc -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/__pycache__ copying build/lib.linux-riscv64-cpython-312/pysam/__pycache__/samtools.cpython-312.pyc -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/__pycache__ copying build/lib.linux-riscv64-cpython-312/pysam/__pycache__/__init__.cpython-312.pyc -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/__pycache__ copying build/lib.linux-riscv64-cpython-312/pysam/__pycache__/Pileup.cpython-312.pyc -> /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/__pycache__ byte-compiling /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/bcftools.py to bcftools.cpython-312.pyc byte-compiling /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/include/__init__.py to __init__.cpython-312.pyc writing byte-compilation script '/tmp/tmpu8gzvn70.py' /usr/bin/python3 /tmp/tmpu8gzvn70.py removing /tmp/tmpu8gzvn70.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-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam-0.22.0-py3.12.egg-info running install_scripts + rm -rfv /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/bin/__pycache__ + rm /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/libcalignedsegment.pyx /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/libcalignmentfile.pyx /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/libcbcf.pyx /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/libcbcftools.pyx /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/libcbgzf.pyx /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/libcfaidx.pyx /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/libchtslib.pyx /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/libcsamfile.pyx /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/libcsamtools.pyx /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/libctabix.pyx /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/libctabixproxies.pyx /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/libcutils.pyx /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/libcvcf.pyx + rm /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/htslib_util.c /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12/site-packages/pysam/pysam_util.c + /usr/bin/find-debuginfo -j4 --strict-build-id -m -i --build-id-seed 0.22.0-2.fc40 --unique-debug-suffix -0.22.0-2.fc40.riscv64 --unique-debug-src-base python-pysam-0.22.0-2.fc40.riscv64 --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-0.22.0-2.fc40.riscv64 53730 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/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 mangling shebang in /usr/lib64/python3.12/site-packages/pysam/include/samtools/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 -j4 Bytecompiling .py files below /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib64/python3.12 using python3.12 Bytecompiling .py files below /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/lib/debug/usr/lib64/python3.12 using python3.12 + /usr/lib/rpm/redhat/brp-python-hardlink Processing files: python3-pysam-0.22.0-2.fc40.riscv64 Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.rblPsE + umask 022 + cd /builddir/build/BUILD + cd pysam-0.22.0 + DOCDIR=/builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/share/doc/python3-pysam + export LC_ALL= + LC_ALL= + export DOCDIR + /usr/bin/mkdir -p /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/share/doc/python3-pysam + cp -pr /builddir/build/BUILD/pysam-0.22.0/README.rst /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/share/doc/python3-pysam + RPM_EC=0 ++ jobs -p + exit 0 Executing(%license): /bin/sh -e /var/tmp/rpm-tmp.GCUZC3 + umask 022 + cd /builddir/build/BUILD + cd pysam-0.22.0 + LICENSEDIR=/builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/share/licenses/python3-pysam + export LC_ALL= + LC_ALL= + export LICENSEDIR + /usr/bin/mkdir -p /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/share/licenses/python3-pysam + cp -pr /builddir/build/BUILD/pysam-0.22.0/COPYING /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/share/licenses/python3-pysam + cp -pr /builddir/build/BUILD/pysam-0.22.0/bcftools/LICENSE /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/share/licenses/python3-pysam + cp -pr /builddir/build/BUILD/pysam-0.22.0/htslib/LICENSE /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/share/licenses/python3-pysam + cp -pr /builddir/build/BUILD/pysam-0.22.0/samtools/LICENSE /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/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-riscv64-linux-gnu.so()(64bit) libcalignmentfile.cpython-312-riscv64-linux-gnu.so()(64bit) libcbcf.cpython-312-riscv64-linux-gnu.so()(64bit) libcbcftools.cpython-312-riscv64-linux-gnu.so()(64bit) libcbgzf.cpython-312-riscv64-linux-gnu.so()(64bit) libcfaidx.cpython-312-riscv64-linux-gnu.so()(64bit) libchtslib.cpython-312-riscv64-linux-gnu.so()(64bit) libcsamfile.cpython-312-riscv64-linux-gnu.so()(64bit) libcsamtools.cpython-312-riscv64-linux-gnu.so()(64bit) libctabix.cpython-312-riscv64-linux-gnu.so()(64bit) libctabixproxies.cpython-312-riscv64-linux-gnu.so()(64bit) libcutils.cpython-312-riscv64-linux-gnu.so()(64bit) libcvcf.cpython-312-riscv64-linux-gnu.so()(64bit) python-pysam = 0.22.0-2.fc40 python3-pysam = 0.22.0-2.fc40 python3-pysam(riscv-64) = 0.22.0-2.fc40 python3.12-pysam = 0.22.0-2.fc40 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-riscv64-lp64d.so.1()(64bit) ld-linux-riscv64-lp64d.so.1(GLIBC_2.27)(64bit) libbz2.so.1()(64bit) libc.so.6()(64bit) libc.so.6(GLIBC_2.27)(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-riscv64-linux-gnu.so()(64bit) libchtslib.cpython-312-riscv64-linux-gnu.so()(64bit) libcsamtools.cpython-312-riscv64-linux-gnu.so()(64bit) liblzma.so.5()(64bit) liblzma.so.5(XZ_5.0)(64bit) libm.so.6()(64bit) libm.so.6(GLIBC_2.27)(64bit) libz.so.1()(64bit) python(abi) = 3.12 rtld(GNU_HASH) Obsoletes: python-pysam < 0.22.0-2.fc40 Processing files: python3-pysam-devel-0.22.0-2.fc40.riscv64 Provides: python-pysam-devel = 0.22.0-2.fc40 python3-pysam-devel = 0.22.0-2.fc40 python3-pysam-devel(riscv-64) = 0.22.0-2.fc40 python3.12-pysam-devel = 0.22.0-2.fc40 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-0.22.0-2.fc40.noarch Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.ynWd26 + umask 022 + cd /builddir/build/BUILD + cd pysam-0.22.0 + DOCDIR=/builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/share/doc/python-pysam-doc + export LC_ALL= + LC_ALL= + export DOCDIR + /usr/bin/mkdir -p /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/share/doc/python-pysam-doc + cp -pr /builddir/build/BUILD/pysam-0.22.0/html /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64/usr/share/doc/python-pysam-doc + RPM_EC=0 ++ jobs -p + exit 0 Provides: python-pysam-doc = 0.22.0-2.fc40 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Processing files: python-pysam-debugsource-0.22.0-2.fc40.riscv64 Provides: python-pysam-debugsource = 0.22.0-2.fc40 python-pysam-debugsource(riscv-64) = 0.22.0-2.fc40 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Processing files: python3-pysam-debuginfo-0.22.0-2.fc40.riscv64 Provides: debuginfo(build-id) = 136d02bfe5bcf16e970edbd5a47de84f7b9b60be debuginfo(build-id) = 18059eb9bf3ad4f7fd4de907cb7b87ea013fc3e8 debuginfo(build-id) = 234290b3161b20ddf12afee91d8ba3aaf8104c86 debuginfo(build-id) = 5163e3533bf80b709d6c0f612b473dbded2dd0fb debuginfo(build-id) = 524de720c8d504fd26369827b01ae825cb08dd81 debuginfo(build-id) = 55432efdd070e5c2f824cdcb54296598b89e6714 debuginfo(build-id) = 6de4aa1e5da3a36c79c877385e3a35989c7fd289 debuginfo(build-id) = 72f6bea5b39c5055efd70649ff6c4fc8eebd4dc7 debuginfo(build-id) = 7666bb820edad9e8f655cf983d1b01dce29ed835 debuginfo(build-id) = cf4488c7ab1e65ed17dd50fd31e339781e2b2c1b debuginfo(build-id) = d9525aa733a0a9d15465794cadbd30877ee39dca debuginfo(build-id) = dec5d3f16cc05958f675227041576f5b8b32f85d debuginfo(build-id) = f20c3ad305a609204fa13fa7fa487de68c6f678d libcalignedsegment.cpython-312-riscv64-linux-gnu.so-0.22.0-2.fc40.riscv64.debug()(64bit) libcalignmentfile.cpython-312-riscv64-linux-gnu.so-0.22.0-2.fc40.riscv64.debug()(64bit) libcbcf.cpython-312-riscv64-linux-gnu.so-0.22.0-2.fc40.riscv64.debug()(64bit) libcbcftools.cpython-312-riscv64-linux-gnu.so-0.22.0-2.fc40.riscv64.debug()(64bit) libcbgzf.cpython-312-riscv64-linux-gnu.so-0.22.0-2.fc40.riscv64.debug()(64bit) libcfaidx.cpython-312-riscv64-linux-gnu.so-0.22.0-2.fc40.riscv64.debug()(64bit) libchtslib.cpython-312-riscv64-linux-gnu.so-0.22.0-2.fc40.riscv64.debug()(64bit) libcsamfile.cpython-312-riscv64-linux-gnu.so-0.22.0-2.fc40.riscv64.debug()(64bit) libcsamtools.cpython-312-riscv64-linux-gnu.so-0.22.0-2.fc40.riscv64.debug()(64bit) libctabix.cpython-312-riscv64-linux-gnu.so-0.22.0-2.fc40.riscv64.debug()(64bit) libctabixproxies.cpython-312-riscv64-linux-gnu.so-0.22.0-2.fc40.riscv64.debug()(64bit) libcutils.cpython-312-riscv64-linux-gnu.so-0.22.0-2.fc40.riscv64.debug()(64bit) libcvcf.cpython-312-riscv64-linux-gnu.so-0.22.0-2.fc40.riscv64.debug()(64bit) python-pysam-debuginfo = 0.22.0-2.fc40 python3-pysam-debuginfo = 0.22.0-2.fc40 python3-pysam-debuginfo(riscv-64) = 0.22.0-2.fc40 python3.12-pysam-debuginfo = 0.22.0-2.fc40 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Recommends: python-pysam-debugsource(riscv-64) = 0.22.0-2.fc40 Checking for unpackaged file(s): /usr/lib/rpm/check-files /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64 Wrote: /builddir/build/RPMS/python3-pysam-0.22.0-2.fc40.riscv64.rpm Wrote: /builddir/build/RPMS/python-pysam-doc-0.22.0-2.fc40.noarch.rpm Wrote: /builddir/build/RPMS/python3-pysam-devel-0.22.0-2.fc40.riscv64.rpm Wrote: /builddir/build/RPMS/python3-pysam-debuginfo-0.22.0-2.fc40.riscv64.rpm Wrote: /builddir/build/RPMS/python-pysam-debugsource-0.22.0-2.fc40.riscv64.rpm Executing(%clean): /bin/sh -e /var/tmp/rpm-tmp.Cc51dh + umask 022 + cd /builddir/build/BUILD + cd pysam-0.22.0 + /usr/bin/rm -rf /builddir/build/BUILDROOT/python-pysam-0.22.0-2.fc40.riscv64 + RPM_EC=0 ++ jobs -p + exit 0 Executing(rmbuild): /bin/sh -e /var/tmp/rpm-tmp.U42j6J + umask 022 + cd /builddir/build/BUILD + rm -rf /builddir/build/BUILD/pysam-0.22.0-SPECPARTS + rm -rf pysam-0.22.0 pysam-0.22.0.gemspec + RPM_EC=0 ++ jobs -p + exit 0 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