Mock Version: 2.9 ENTER ['do_with_status'](['bash', '--login', '-c', '/usr/bin/rpmbuild -bs --target x86_64 --nodeps /builddir/build/SPECS/python-pysam.spec'], chrootPath='/var/lib/mock/fedora-rawhide-x86_64-1611945235.291798/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=0uid=1001gid=135user='mockbuild'nspawn_args=['--capability=cap_ipc_lock', '--rlimit=RLIMIT_NOFILE=10240', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.aa3k2ktq:/etc/resolv.conf', '--bind=/dev/btrfs-control', '--bind=/dev/loop-control', '--bind=/dev/loop0', '--bind=/dev/loop1', '--bind=/dev/loop2', '--bind=/dev/loop3', '--bind=/dev/loop4', '--bind=/dev/loop5', '--bind=/dev/loop6', '--bind=/dev/loop7', '--bind=/dev/loop8', '--bind=/dev/loop9', '--bind=/dev/loop10', '--bind=/dev/loop11']unshare_net=TrueprintOutput=True) Using nspawn with args ['--capability=cap_ipc_lock', '--rlimit=RLIMIT_NOFILE=10240', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.aa3k2ktq:/etc/resolv.conf', '--bind=/dev/btrfs-control', '--bind=/dev/loop-control', '--bind=/dev/loop0', '--bind=/dev/loop1', '--bind=/dev/loop2', '--bind=/dev/loop3', '--bind=/dev/loop4', '--bind=/dev/loop5', '--bind=/dev/loop6', '--bind=/dev/loop7', '--bind=/dev/loop8', '--bind=/dev/loop9', '--bind=/dev/loop10', '--bind=/dev/loop11'] Executing command: ['/usr/bin/systemd-nspawn', '-q', '-M', '45ba22866650403193603f48369751e5', '-D', '/var/lib/mock/fedora-rawhide-x86_64-1611945235.291798/root', '-a', '-u', 'mockbuild', '--capability=cap_ipc_lock', '--rlimit=RLIMIT_NOFILE=10240', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.aa3k2ktq:/etc/resolv.conf', '--bind=/dev/btrfs-control', '--bind=/dev/loop-control', '--bind=/dev/loop0', '--bind=/dev/loop1', '--bind=/dev/loop2', '--bind=/dev/loop3', '--bind=/dev/loop4', '--bind=/dev/loop5', '--bind=/dev/loop6', '--bind=/dev/loop7', '--bind=/dev/loop8', '--bind=/dev/loop9', '--bind=/dev/loop10', '--bind=/dev/loop11', '--console=pipe', '--setenv=TERM=vt100', '--setenv=SHELL=/bin/bash', '--setenv=HOME=/builddir', '--setenv=HOSTNAME=mock', '--setenv=PATH=/usr/bin:/bin:/usr/sbin:/sbin', '--setenv=PROMPT_COMMAND=printf "\\033]0;\\007"', '--setenv=PS1= \\s-\\v\\$ ', '--setenv=LANG=C.UTF-8', '--resolv-conf=off', 'bash', '--login', '-c', '/usr/bin/rpmbuild -bs --target x86_64 --nodeps /builddir/build/SPECS/python-pysam.spec'] with env {'TERM': 'vt100', 'SHELL': '/bin/bash', 'HOME': '/builddir', 'HOSTNAME': 'mock', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'PROMPT_COMMAND': 'printf "\\033]0;\\007"', 'PS1': ' \\s-\\v\\$ ', 'LANG': 'C.UTF-8', 'SYSTEMD_NSPAWN_TMPFS_TMP': '0'} and shell False Building target platforms: x86_64 Building for target x86_64 setting SOURCE_DATE_EPOCH=1604188800 Wrote: /builddir/build/SRPMS/python-pysam-0.16.0.1-1.fc34.src.rpm Child return code was: 0 ENTER ['do_with_status'](['bash', '--login', '-c', '/usr/bin/rpmbuild -bb --target x86_64 --nodeps /builddir/build/SPECS/python-pysam.spec'], chrootPath='/var/lib/mock/fedora-rawhide-x86_64-1611945235.291798/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=0uid=1001gid=135user='mockbuild'nspawn_args=['--capability=cap_ipc_lock', '--rlimit=RLIMIT_NOFILE=10240', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.aa3k2ktq:/etc/resolv.conf', '--bind=/dev/btrfs-control', '--bind=/dev/loop-control', '--bind=/dev/loop0', '--bind=/dev/loop1', '--bind=/dev/loop2', '--bind=/dev/loop3', '--bind=/dev/loop4', '--bind=/dev/loop5', '--bind=/dev/loop6', '--bind=/dev/loop7', '--bind=/dev/loop8', '--bind=/dev/loop9', '--bind=/dev/loop10', '--bind=/dev/loop11']unshare_net=TrueprintOutput=True) Using nspawn with args ['--capability=cap_ipc_lock', '--rlimit=RLIMIT_NOFILE=10240', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.aa3k2ktq:/etc/resolv.conf', '--bind=/dev/btrfs-control', '--bind=/dev/loop-control', '--bind=/dev/loop0', '--bind=/dev/loop1', '--bind=/dev/loop2', '--bind=/dev/loop3', '--bind=/dev/loop4', '--bind=/dev/loop5', '--bind=/dev/loop6', '--bind=/dev/loop7', '--bind=/dev/loop8', '--bind=/dev/loop9', '--bind=/dev/loop10', '--bind=/dev/loop11'] Executing command: ['/usr/bin/systemd-nspawn', '-q', '-M', '98849c26914d442ab2cafe30100627ab', '-D', '/var/lib/mock/fedora-rawhide-x86_64-1611945235.291798/root', '-a', '-u', 'mockbuild', '--capability=cap_ipc_lock', '--rlimit=RLIMIT_NOFILE=10240', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.aa3k2ktq:/etc/resolv.conf', '--bind=/dev/btrfs-control', '--bind=/dev/loop-control', '--bind=/dev/loop0', '--bind=/dev/loop1', '--bind=/dev/loop2', '--bind=/dev/loop3', '--bind=/dev/loop4', '--bind=/dev/loop5', '--bind=/dev/loop6', '--bind=/dev/loop7', '--bind=/dev/loop8', '--bind=/dev/loop9', '--bind=/dev/loop10', '--bind=/dev/loop11', '--console=pipe', '--setenv=TERM=vt100', '--setenv=SHELL=/bin/bash', '--setenv=HOME=/builddir', '--setenv=HOSTNAME=mock', '--setenv=PATH=/usr/bin:/bin:/usr/sbin:/sbin', '--setenv=PROMPT_COMMAND=printf "\\033]0;\\007"', '--setenv=PS1= \\s-\\v\\$ ', '--setenv=LANG=C.UTF-8', '--resolv-conf=off', 'bash', '--login', '-c', '/usr/bin/rpmbuild -bb --target x86_64 --nodeps /builddir/build/SPECS/python-pysam.spec'] with env {'TERM': 'vt100', 'SHELL': '/bin/bash', 'HOME': '/builddir', 'HOSTNAME': 'mock', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'PROMPT_COMMAND': 'printf "\\033]0;\\007"', 'PS1': ' \\s-\\v\\$ ', 'LANG': 'C.UTF-8', 'SYSTEMD_NSPAWN_TMPFS_TMP': '0'} and shell False Building target platforms: x86_64 Building for target x86_64 setting SOURCE_DATE_EPOCH=1604188800 Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.rfQxzw + umask 022 + cd /builddir/build/BUILD + cd /builddir/build/BUILD + rm -rf pysam-0.16.0.1 + /usr/bin/gzip -dc /builddir/build/SOURCES/pysam-0.16.0.1.tar.gz + /usr/bin/tar -xof - + STATUS=0 + '[' 0 -ne 0 ']' + cd pysam-0.16.0.1 + /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w . + rm -rf pysam.egg-info + RPM_EC=0 ++ jobs -p + exit 0 Executing(%build): /bin/sh -e /var/tmp/rpm-tmp.6zs3lY + umask 022 + cd /builddir/build/BUILD + cd pysam-0.16.0.1 + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld ' + /usr/bin/python3 setup.py build '--executable=/usr/bin/python3 -s' # pysam: cython is available - using cythonize if necessary # pysam: htslib mode is shared # pysam: HTSLIB_CONFIGURE_OPTIONS=None # pysam: (sysconfig) CC=gcc -pthread # pysam: (env) CFLAGS=-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection # pysam: (env) LDFLAGS=-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld checking for gcc... gcc -pthread 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 -pthread accepts -g... yes checking for gcc -pthread 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... unknown 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 compiler accepts -fvisibility=hidden... yes checking how to run the C preprocessor... gcc -pthread -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 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 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 for libdeflate.h... no checking for libdeflate_deflate_compress in -ldeflate... 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 -pthread 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 -pthread accepts -g... yes checking for gcc -pthread 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... unknown 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 compiler accepts -fvisibility=hidden... yes checking how to run the C preprocessor... gcc -pthread -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 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 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 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 whether PTHREAD_MUTEX_RECURSIVE is declared... yes configure: creating ./config.status config.status: creating config.mk config.status: creating htslib.pc.tmp config.status: creating config.h make: ./version.sh: No such file or directory make: ./version.sh: No such file or directory # pysam: htslib configure options: --disable-libcurl # pysam: htslib_config LIBHTS_OBJS=kfunc.o knetfile.o kstring.o bcf_sr_sort.o bgzf.o errmod.o faidx.o header.o hfile.o hfile_net.o hts.o hts_os.o md5.o multipart.o probaln.o realn.o regidx.o region.o sam.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_samtools.o cram/cram_stats.o cram/mFILE.o cram/open_trace_file.o cram/pooled_alloc.o cram/rANS_static.o cram/string_alloc.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-x86_64-3.9 creating build/lib.linux-x86_64-3.9/pysam copying pysam/bcftools.py -> build/lib.linux-x86_64-3.9/pysam copying pysam/Pileup.py -> build/lib.linux-x86_64-3.9/pysam copying pysam/__init__.py -> build/lib.linux-x86_64-3.9/pysam copying pysam/version.py -> build/lib.linux-x86_64-3.9/pysam copying pysam/config.py -> build/lib.linux-x86_64-3.9/pysam copying pysam/utils.py -> build/lib.linux-x86_64-3.9/pysam copying pysam/samtools.py -> build/lib.linux-x86_64-3.9/pysam creating build/lib.linux-x86_64-3.9/pysam/include copying pysam/include/__init__.py -> build/lib.linux-x86_64-3.9/pysam/include package init file 'samtools/__init__.py' not found (or not a regular file) package init file 'bcftools/__init__.py' not found (or not a regular file) package init file 'htslib/__init__.py' not found (or not a regular file) package init file 'htslib/htslib/__init__.py' not found (or not a regular file) copying pysam/libcbcftools.pxd -> build/lib.linux-x86_64-3.9/pysam copying pysam/libcvcf.pxd -> build/lib.linux-x86_64-3.9/pysam copying pysam/libcalignmentfile.pxd -> build/lib.linux-x86_64-3.9/pysam copying pysam/libcsamfile.pxd -> build/lib.linux-x86_64-3.9/pysam copying pysam/libcalignedsegment.pxd -> build/lib.linux-x86_64-3.9/pysam copying pysam/libctabix.pxd -> build/lib.linux-x86_64-3.9/pysam copying pysam/libcbcf.pxd -> build/lib.linux-x86_64-3.9/pysam copying pysam/libcfaidx.pxd -> build/lib.linux-x86_64-3.9/pysam copying pysam/libcutils.pxd -> build/lib.linux-x86_64-3.9/pysam copying pysam/libcsamtools.pxd -> build/lib.linux-x86_64-3.9/pysam copying pysam/libchtslib.pxd -> build/lib.linux-x86_64-3.9/pysam copying pysam/libctabixproxies.pxd -> build/lib.linux-x86_64-3.9/pysam copying pysam/htslib_util.h -> build/lib.linux-x86_64-3.9/pysam copying pysam/cbcftools_util.h -> build/lib.linux-x86_64-3.9/pysam copying pysam/pysam_util.h -> build/lib.linux-x86_64-3.9/pysam copying pysam/version.h -> build/lib.linux-x86_64-3.9/pysam copying pysam/pysam_stream.h -> build/lib.linux-x86_64-3.9/pysam copying pysam/csamtools_util.h -> build/lib.linux-x86_64-3.9/pysam creating build/lib.linux-x86_64-3.9/pysam/include/samtools copying samtools/config.h -> build/lib.linux-x86_64-3.9/pysam/include/samtools copying samtools/bam_plbuf.h -> build/lib.linux-x86_64-3.9/pysam/include/samtools copying samtools/bam2bcf.h -> build/lib.linux-x86_64-3.9/pysam/include/samtools copying samtools/bam_lpileup.h -> build/lib.linux-x86_64-3.9/pysam/include/samtools copying samtools/tmp_file.h -> build/lib.linux-x86_64-3.9/pysam/include/samtools copying samtools/sam_opts.h -> build/lib.linux-x86_64-3.9/pysam/include/samtools copying samtools/stats_isize.h -> build/lib.linux-x86_64-3.9/pysam/include/samtools copying samtools/samtools.pysam.h -> build/lib.linux-x86_64-3.9/pysam/include/samtools copying samtools/sample.h -> build/lib.linux-x86_64-3.9/pysam/include/samtools copying samtools/bam_endian.h -> build/lib.linux-x86_64-3.9/pysam/include/samtools copying samtools/samtools.h -> build/lib.linux-x86_64-3.9/pysam/include/samtools copying samtools/sam.h -> build/lib.linux-x86_64-3.9/pysam/include/samtools copying samtools/bedidx.h -> build/lib.linux-x86_64-3.9/pysam/include/samtools copying samtools/bam.h -> build/lib.linux-x86_64-3.9/pysam/include/samtools creating build/lib.linux-x86_64-3.9/pysam/include/bcftools copying bcftools/config.h -> build/lib.linux-x86_64-3.9/pysam/include/bcftools copying bcftools/variantkey.h -> build/lib.linux-x86_64-3.9/pysam/include/bcftools copying bcftools/bam2bcf.h -> build/lib.linux-x86_64-3.9/pysam/include/bcftools copying bcftools/ploidy.h -> build/lib.linux-x86_64-3.9/pysam/include/bcftools copying bcftools/rbuf.h -> build/lib.linux-x86_64-3.9/pysam/include/bcftools copying bcftools/khash_str2str.h -> build/lib.linux-x86_64-3.9/pysam/include/bcftools copying bcftools/bin.h -> build/lib.linux-x86_64-3.9/pysam/include/bcftools copying bcftools/kheap.h -> build/lib.linux-x86_64-3.9/pysam/include/bcftools copying bcftools/kmin.h -> build/lib.linux-x86_64-3.9/pysam/include/bcftools copying bcftools/gvcf.h -> build/lib.linux-x86_64-3.9/pysam/include/bcftools copying bcftools/hex.h -> build/lib.linux-x86_64-3.9/pysam/include/bcftools copying bcftools/smpl_ilist.h -> build/lib.linux-x86_64-3.9/pysam/include/bcftools copying bcftools/cols.h -> build/lib.linux-x86_64-3.9/pysam/include/bcftools copying bcftools/filter.h -> build/lib.linux-x86_64-3.9/pysam/include/bcftools copying bcftools/vcfbuf.h -> build/lib.linux-x86_64-3.9/pysam/include/bcftools copying bcftools/prob1.h -> build/lib.linux-x86_64-3.9/pysam/include/bcftools copying bcftools/mw.h -> build/lib.linux-x86_64-3.9/pysam/include/bcftools copying bcftools/call.h -> build/lib.linux-x86_64-3.9/pysam/include/bcftools copying bcftools/vcmp.h -> build/lib.linux-x86_64-3.9/pysam/include/bcftools copying bcftools/regidx.h -> build/lib.linux-x86_64-3.9/pysam/include/bcftools copying bcftools/HMM.h -> build/lib.linux-x86_64-3.9/pysam/include/bcftools copying bcftools/tsv2vcf.h -> build/lib.linux-x86_64-3.9/pysam/include/bcftools copying bcftools/bam_sample.h -> build/lib.linux-x86_64-3.9/pysam/include/bcftools copying bcftools/convert.h -> build/lib.linux-x86_64-3.9/pysam/include/bcftools copying bcftools/bcftools.pysam.h -> build/lib.linux-x86_64-3.9/pysam/include/bcftools copying bcftools/hclust.h -> build/lib.linux-x86_64-3.9/pysam/include/bcftools copying bcftools/bcftools.h -> build/lib.linux-x86_64-3.9/pysam/include/bcftools creating build/lib.linux-x86_64-3.9/pysam/include/htslib copying htslib/config.h -> build/lib.linux-x86_64-3.9/pysam/include/htslib copying htslib/textutils_internal.h -> build/lib.linux-x86_64-3.9/pysam/include/htslib copying htslib/bcf_sr_sort.h -> build/lib.linux-x86_64-3.9/pysam/include/htslib copying htslib/sam_internal.h -> build/lib.linux-x86_64-3.9/pysam/include/htslib copying htslib/header.h -> build/lib.linux-x86_64-3.9/pysam/include/htslib copying htslib/hfile_internal.h -> build/lib.linux-x86_64-3.9/pysam/include/htslib copying htslib/thread_pool_internal.h -> build/lib.linux-x86_64-3.9/pysam/include/htslib copying htslib/hts_internal.h -> build/lib.linux-x86_64-3.9/pysam/include/htslib creating build/lib.linux-x86_64-3.9/pysam/include/htslib/htslib copying htslib/htslib/vcf.h -> build/lib.linux-x86_64-3.9/pysam/include/htslib/htslib copying htslib/htslib/cram.h -> build/lib.linux-x86_64-3.9/pysam/include/htslib/htslib copying htslib/htslib/bgzf.h -> build/lib.linux-x86_64-3.9/pysam/include/htslib/htslib copying htslib/htslib/hts_endian.h -> build/lib.linux-x86_64-3.9/pysam/include/htslib/htslib copying htslib/htslib/vcfutils.h -> build/lib.linux-x86_64-3.9/pysam/include/htslib/htslib copying htslib/htslib/hts_os.h -> build/lib.linux-x86_64-3.9/pysam/include/htslib/htslib copying htslib/htslib/khash_str2int.h -> build/lib.linux-x86_64-3.9/pysam/include/htslib/htslib copying htslib/htslib/kbitset.h -> build/lib.linux-x86_64-3.9/pysam/include/htslib/htslib copying htslib/htslib/tbx.h -> build/lib.linux-x86_64-3.9/pysam/include/htslib/htslib copying htslib/htslib/hts_log.h -> build/lib.linux-x86_64-3.9/pysam/include/htslib/htslib copying htslib/htslib/regidx.h -> build/lib.linux-x86_64-3.9/pysam/include/htslib/htslib copying htslib/htslib/hts_defs.h -> build/lib.linux-x86_64-3.9/pysam/include/htslib/htslib copying htslib/htslib/kseq.h -> build/lib.linux-x86_64-3.9/pysam/include/htslib/htslib copying htslib/htslib/kstring.h -> build/lib.linux-x86_64-3.9/pysam/include/htslib/htslib copying htslib/htslib/knetfile.h -> build/lib.linux-x86_64-3.9/pysam/include/htslib/htslib copying htslib/htslib/klist.h -> build/lib.linux-x86_64-3.9/pysam/include/htslib/htslib copying htslib/htslib/khash.h -> build/lib.linux-x86_64-3.9/pysam/include/htslib/htslib copying htslib/htslib/sam.h -> build/lib.linux-x86_64-3.9/pysam/include/htslib/htslib copying htslib/htslib/thread_pool.h -> build/lib.linux-x86_64-3.9/pysam/include/htslib/htslib copying htslib/htslib/ksort.h -> build/lib.linux-x86_64-3.9/pysam/include/htslib/htslib copying htslib/htslib/vcf_sweep.h -> build/lib.linux-x86_64-3.9/pysam/include/htslib/htslib copying htslib/htslib/faidx.h -> build/lib.linux-x86_64-3.9/pysam/include/htslib/htslib copying htslib/htslib/synced_bcf_reader.h -> build/lib.linux-x86_64-3.9/pysam/include/htslib/htslib copying htslib/htslib/kfunc.h -> build/lib.linux-x86_64-3.9/pysam/include/htslib/htslib copying htslib/htslib/hfile.h -> build/lib.linux-x86_64-3.9/pysam/include/htslib/htslib copying htslib/htslib/hts.h -> build/lib.linux-x86_64-3.9/pysam/include/htslib/htslib Fixing build/lib.linux-x86_64-3.9/pysam/bcftools.py build/lib.linux-x86_64-3.9/pysam/Pileup.py build/lib.linux-x86_64-3.9/pysam/__init__.py build/lib.linux-x86_64-3.9/pysam/version.py build/lib.linux-x86_64-3.9/pysam/config.py build/lib.linux-x86_64-3.9/pysam/utils.py build/lib.linux-x86_64-3.9/pysam/samtools.py build/lib.linux-x86_64-3.9/pysam/include/__init__.py /usr/lib/python3.9/site-packages/setuptools/lib2to3_ex.py:36: SetuptoolsDeprecationWarning: 2to3 support is deprecated. If the project still requires Python 2 support, please migrate to a single-codebase solution or employ an independent conversion process. warnings.warn( Skipping optional fixer: buffer Skipping optional fixer: idioms Skipping optional fixer: set_literal Skipping optional fixer: ws_comma Fixing build/lib.linux-x86_64-3.9/pysam/bcftools.py build/lib.linux-x86_64-3.9/pysam/Pileup.py build/lib.linux-x86_64-3.9/pysam/__init__.py build/lib.linux-x86_64-3.9/pysam/version.py build/lib.linux-x86_64-3.9/pysam/config.py build/lib.linux-x86_64-3.9/pysam/utils.py build/lib.linux-x86_64-3.9/pysam/samtools.py build/lib.linux-x86_64-3.9/pysam/include/__init__.py Skipping optional fixer: buffer Skipping optional fixer: idioms Skipping optional fixer: set_literal Skipping optional fixer: ws_comma running build_ext skipping 'pysam/libchtslib.c' Cython extension (up-to-date) skipping 'pysam/libcsamtools.c' Cython extension (up-to-date) skipping 'pysam/libcbcftools.c' Cython extension (up-to-date) skipping 'pysam/libcutils.c' Cython extension (up-to-date) skipping 'pysam/libcalignmentfile.c' Cython extension (up-to-date) skipping 'pysam/libcsamfile.c' Cython extension (up-to-date) skipping 'pysam/libcalignedsegment.c' Cython extension (up-to-date) skipping 'pysam/libctabix.c' Cython extension (up-to-date) skipping 'pysam/libcfaidx.c' Cython extension (up-to-date) skipping 'pysam/libcbcf.c' Cython extension (up-to-date) skipping 'pysam/libcbgzf.c' Cython extension (up-to-date) skipping 'pysam/libctabixproxies.c' Cython extension (up-to-date) skipping 'pysam/libcvcf.c' Cython extension (up-to-date) building 'pysam.libchtslib' extension creating build/temp.linux-x86_64-3.9 creating build/temp.linux-x86_64-3.9/htslib creating build/temp.linux-x86_64-3.9/htslib/cram creating build/temp.linux-x86_64-3.9/pysam gcc -pthread -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.16.0.1/htslib -I/builddir/build/BUILD/pysam-0.16.0.1/samtools -I/builddir/build/BUILD/pysam-0.16.0.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.16.0.1/bcftools -I/builddir/build/BUILD/pysam-0.16.0.1/pysam -I/builddir/build/BUILD/pysam-0.16.0.1 -I/usr/include/python3.9 -c htslib/bcf_sr_sort.c -o build/temp.linux-x86_64-3.9/htslib/bcf_sr_sort.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -pthread -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.16.0.1/htslib -I/builddir/build/BUILD/pysam-0.16.0.1/samtools -I/builddir/build/BUILD/pysam-0.16.0.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.16.0.1/bcftools -I/builddir/build/BUILD/pysam-0.16.0.1/pysam -I/builddir/build/BUILD/pysam-0.16.0.1 -I/usr/include/python3.9 -c htslib/bgzf.c -o build/temp.linux-x86_64-3.9/htslib/bgzf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -pthread -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.16.0.1/htslib -I/builddir/build/BUILD/pysam-0.16.0.1/samtools -I/builddir/build/BUILD/pysam-0.16.0.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.16.0.1/bcftools -I/builddir/build/BUILD/pysam-0.16.0.1/pysam -I/builddir/build/BUILD/pysam-0.16.0.1 -I/usr/include/python3.9 -c htslib/cram/cram_codecs.c -o build/temp.linux-x86_64-3.9/htslib/cram/cram_codecs.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -pthread -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.16.0.1/htslib -I/builddir/build/BUILD/pysam-0.16.0.1/samtools -I/builddir/build/BUILD/pysam-0.16.0.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.16.0.1/bcftools -I/builddir/build/BUILD/pysam-0.16.0.1/pysam -I/builddir/build/BUILD/pysam-0.16.0.1 -I/usr/include/python3.9 -c htslib/cram/cram_decode.c -o build/temp.linux-x86_64-3.9/htslib/cram/cram_decode.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -pthread -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.16.0.1/htslib -I/builddir/build/BUILD/pysam-0.16.0.1/samtools -I/builddir/build/BUILD/pysam-0.16.0.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.16.0.1/bcftools -I/builddir/build/BUILD/pysam-0.16.0.1/pysam -I/builddir/build/BUILD/pysam-0.16.0.1 -I/usr/include/python3.9 -c htslib/cram/cram_encode.c -o build/temp.linux-x86_64-3.9/htslib/cram/cram_encode.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -pthread -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.16.0.1/htslib -I/builddir/build/BUILD/pysam-0.16.0.1/samtools -I/builddir/build/BUILD/pysam-0.16.0.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.16.0.1/bcftools -I/builddir/build/BUILD/pysam-0.16.0.1/pysam -I/builddir/build/BUILD/pysam-0.16.0.1 -I/usr/include/python3.9 -c htslib/cram/cram_external.c -o build/temp.linux-x86_64-3.9/htslib/cram/cram_external.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -pthread -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.16.0.1/htslib -I/builddir/build/BUILD/pysam-0.16.0.1/samtools -I/builddir/build/BUILD/pysam-0.16.0.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.16.0.1/bcftools -I/builddir/build/BUILD/pysam-0.16.0.1/pysam -I/builddir/build/BUILD/pysam-0.16.0.1 -I/usr/include/python3.9 -c htslib/cram/cram_index.c -o build/temp.linux-x86_64-3.9/htslib/cram/cram_index.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -pthread -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.16.0.1/htslib -I/builddir/build/BUILD/pysam-0.16.0.1/samtools -I/builddir/build/BUILD/pysam-0.16.0.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.16.0.1/bcftools -I/builddir/build/BUILD/pysam-0.16.0.1/pysam -I/builddir/build/BUILD/pysam-0.16.0.1 -I/usr/include/python3.9 -c htslib/cram/cram_io.c -o build/temp.linux-x86_64-3.9/htslib/cram/cram_io.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement In file included from /usr/include/string.h:519, from htslib/cram/cram_io.c:49: In function ‘strncpy’, inlined from ‘cram_dopen’ at htslib/cram/cram_io.c:4304:9: /usr/include/bits/string_fortified.h:95:10: warning: ‘strncpy’ specified bound 20 equals destination size [-Wstringop-truncation] 95 | return __builtin___strncpy_chk (__dest, __src, __len, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 96 | __glibc_objsize (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -pthread -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.16.0.1/htslib -I/builddir/build/BUILD/pysam-0.16.0.1/samtools -I/builddir/build/BUILD/pysam-0.16.0.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.16.0.1/bcftools -I/builddir/build/BUILD/pysam-0.16.0.1/pysam -I/builddir/build/BUILD/pysam-0.16.0.1 -I/usr/include/python3.9 -c htslib/cram/cram_samtools.c -o build/temp.linux-x86_64-3.9/htslib/cram/cram_samtools.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -pthread -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.16.0.1/htslib -I/builddir/build/BUILD/pysam-0.16.0.1/samtools -I/builddir/build/BUILD/pysam-0.16.0.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.16.0.1/bcftools -I/builddir/build/BUILD/pysam-0.16.0.1/pysam -I/builddir/build/BUILD/pysam-0.16.0.1 -I/usr/include/python3.9 -c htslib/cram/cram_stats.c -o build/temp.linux-x86_64-3.9/htslib/cram/cram_stats.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -pthread -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.16.0.1/htslib -I/builddir/build/BUILD/pysam-0.16.0.1/samtools -I/builddir/build/BUILD/pysam-0.16.0.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.16.0.1/bcftools -I/builddir/build/BUILD/pysam-0.16.0.1/pysam -I/builddir/build/BUILD/pysam-0.16.0.1 -I/usr/include/python3.9 -c htslib/cram/mFILE.c -o build/temp.linux-x86_64-3.9/htslib/cram/mFILE.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -pthread -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.16.0.1/htslib -I/builddir/build/BUILD/pysam-0.16.0.1/samtools -I/builddir/build/BUILD/pysam-0.16.0.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.16.0.1/bcftools -I/builddir/build/BUILD/pysam-0.16.0.1/pysam -I/builddir/build/BUILD/pysam-0.16.0.1 -I/usr/include/python3.9 -c htslib/cram/open_trace_file.c -o build/temp.linux-x86_64-3.9/htslib/cram/open_trace_file.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -pthread -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.16.0.1/htslib -I/builddir/build/BUILD/pysam-0.16.0.1/samtools -I/builddir/build/BUILD/pysam-0.16.0.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.16.0.1/bcftools -I/builddir/build/BUILD/pysam-0.16.0.1/pysam -I/builddir/build/BUILD/pysam-0.16.0.1 -I/usr/include/python3.9 -c htslib/cram/pooled_alloc.c -o build/temp.linux-x86_64-3.9/htslib/cram/pooled_alloc.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -pthread -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.16.0.1/htslib -I/builddir/build/BUILD/pysam-0.16.0.1/samtools -I/builddir/build/BUILD/pysam-0.16.0.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.16.0.1/bcftools -I/builddir/build/BUILD/pysam-0.16.0.1/pysam -I/builddir/build/BUILD/pysam-0.16.0.1 -I/usr/include/python3.9 -c htslib/cram/rANS_static.c -o build/temp.linux-x86_64-3.9/htslib/cram/rANS_static.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -pthread -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.16.0.1/htslib -I/builddir/build/BUILD/pysam-0.16.0.1/samtools -I/builddir/build/BUILD/pysam-0.16.0.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.16.0.1/bcftools -I/builddir/build/BUILD/pysam-0.16.0.1/pysam -I/builddir/build/BUILD/pysam-0.16.0.1 -I/usr/include/python3.9 -c htslib/cram/string_alloc.c -o build/temp.linux-x86_64-3.9/htslib/cram/string_alloc.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -pthread -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.16.0.1/htslib -I/builddir/build/BUILD/pysam-0.16.0.1/samtools -I/builddir/build/BUILD/pysam-0.16.0.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.16.0.1/bcftools -I/builddir/build/BUILD/pysam-0.16.0.1/pysam -I/builddir/build/BUILD/pysam-0.16.0.1 -I/usr/include/python3.9 -c htslib/errmod.c -o build/temp.linux-x86_64-3.9/htslib/errmod.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -pthread -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.16.0.1/htslib -I/builddir/build/BUILD/pysam-0.16.0.1/samtools -I/builddir/build/BUILD/pysam-0.16.0.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.16.0.1/bcftools -I/builddir/build/BUILD/pysam-0.16.0.1/pysam -I/builddir/build/BUILD/pysam-0.16.0.1 -I/usr/include/python3.9 -c htslib/faidx.c -o build/temp.linux-x86_64-3.9/htslib/faidx.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -pthread -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.16.0.1/htslib -I/builddir/build/BUILD/pysam-0.16.0.1/samtools -I/builddir/build/BUILD/pysam-0.16.0.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.16.0.1/bcftools -I/builddir/build/BUILD/pysam-0.16.0.1/pysam -I/builddir/build/BUILD/pysam-0.16.0.1 -I/usr/include/python3.9 -c htslib/header.c -o build/temp.linux-x86_64-3.9/htslib/header.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -pthread -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.16.0.1/htslib -I/builddir/build/BUILD/pysam-0.16.0.1/samtools -I/builddir/build/BUILD/pysam-0.16.0.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.16.0.1/bcftools -I/builddir/build/BUILD/pysam-0.16.0.1/pysam -I/builddir/build/BUILD/pysam-0.16.0.1 -I/usr/include/python3.9 -c htslib/hfile.c -o build/temp.linux-x86_64-3.9/htslib/hfile.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -pthread -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.16.0.1/htslib -I/builddir/build/BUILD/pysam-0.16.0.1/samtools -I/builddir/build/BUILD/pysam-0.16.0.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.16.0.1/bcftools -I/builddir/build/BUILD/pysam-0.16.0.1/pysam -I/builddir/build/BUILD/pysam-0.16.0.1 -I/usr/include/python3.9 -c htslib/hfile_net.c -o build/temp.linux-x86_64-3.9/htslib/hfile_net.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -pthread -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.16.0.1/htslib -I/builddir/build/BUILD/pysam-0.16.0.1/samtools -I/builddir/build/BUILD/pysam-0.16.0.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.16.0.1/bcftools -I/builddir/build/BUILD/pysam-0.16.0.1/pysam -I/builddir/build/BUILD/pysam-0.16.0.1 -I/usr/include/python3.9 -c htslib/hts.c -o build/temp.linux-x86_64-3.9/htslib/hts.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement htslib/hts.c: In function ‘hts_idx_init’: htslib/hts.c:1631:59: warning: overflow in conversion from ‘uint32_t’ {aka ‘unsigned int’} to ‘int’ changes value from ‘idx->z.last_bin = 4294967295’ to ‘-1’ [-Woverflow] 1631 | idx->z.save_bin = idx->z.save_tid = idx->z.last_tid = idx->z.last_bin = 0xffffffffu; | ^~~ gcc -pthread -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.16.0.1/htslib -I/builddir/build/BUILD/pysam-0.16.0.1/samtools -I/builddir/build/BUILD/pysam-0.16.0.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.16.0.1/bcftools -I/builddir/build/BUILD/pysam-0.16.0.1/pysam -I/builddir/build/BUILD/pysam-0.16.0.1 -I/usr/include/python3.9 -c htslib/hts_os.c -o build/temp.linux-x86_64-3.9/htslib/hts_os.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -pthread -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.16.0.1/htslib -I/builddir/build/BUILD/pysam-0.16.0.1/samtools -I/builddir/build/BUILD/pysam-0.16.0.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.16.0.1/bcftools -I/builddir/build/BUILD/pysam-0.16.0.1/pysam -I/builddir/build/BUILD/pysam-0.16.0.1 -I/usr/include/python3.9 -c htslib/kfunc.c -o build/temp.linux-x86_64-3.9/htslib/kfunc.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -pthread -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.16.0.1/htslib -I/builddir/build/BUILD/pysam-0.16.0.1/samtools -I/builddir/build/BUILD/pysam-0.16.0.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.16.0.1/bcftools -I/builddir/build/BUILD/pysam-0.16.0.1/pysam -I/builddir/build/BUILD/pysam-0.16.0.1 -I/usr/include/python3.9 -c htslib/knetfile.c -o build/temp.linux-x86_64-3.9/htslib/knetfile.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -pthread -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.16.0.1/htslib -I/builddir/build/BUILD/pysam-0.16.0.1/samtools -I/builddir/build/BUILD/pysam-0.16.0.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.16.0.1/bcftools -I/builddir/build/BUILD/pysam-0.16.0.1/pysam -I/builddir/build/BUILD/pysam-0.16.0.1 -I/usr/include/python3.9 -c htslib/kstring.c -o build/temp.linux-x86_64-3.9/htslib/kstring.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -pthread -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.16.0.1/htslib -I/builddir/build/BUILD/pysam-0.16.0.1/samtools -I/builddir/build/BUILD/pysam-0.16.0.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.16.0.1/bcftools -I/builddir/build/BUILD/pysam-0.16.0.1/pysam -I/builddir/build/BUILD/pysam-0.16.0.1 -I/usr/include/python3.9 -c htslib/md5.c -o build/temp.linux-x86_64-3.9/htslib/md5.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -pthread -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.16.0.1/htslib -I/builddir/build/BUILD/pysam-0.16.0.1/samtools -I/builddir/build/BUILD/pysam-0.16.0.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.16.0.1/bcftools -I/builddir/build/BUILD/pysam-0.16.0.1/pysam -I/builddir/build/BUILD/pysam-0.16.0.1 -I/usr/include/python3.9 -c htslib/multipart.c -o build/temp.linux-x86_64-3.9/htslib/multipart.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -pthread -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.16.0.1/htslib -I/builddir/build/BUILD/pysam-0.16.0.1/samtools -I/builddir/build/BUILD/pysam-0.16.0.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.16.0.1/bcftools -I/builddir/build/BUILD/pysam-0.16.0.1/pysam -I/builddir/build/BUILD/pysam-0.16.0.1 -I/usr/include/python3.9 -c htslib/probaln.c -o build/temp.linux-x86_64-3.9/htslib/probaln.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -pthread -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.16.0.1/htslib -I/builddir/build/BUILD/pysam-0.16.0.1/samtools -I/builddir/build/BUILD/pysam-0.16.0.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.16.0.1/bcftools -I/builddir/build/BUILD/pysam-0.16.0.1/pysam -I/builddir/build/BUILD/pysam-0.16.0.1 -I/usr/include/python3.9 -c htslib/realn.c -o build/temp.linux-x86_64-3.9/htslib/realn.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement htslib/realn.c: In function ‘sam_prob_realn’: htslib/realn.c:155:23: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] 155 | *(zq - 3) = 'B'; | ~~~~~~~~~~^~~~~ htslib/realn.c:151:23: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] 151 | *(bq - 3) = 'Z'; | ~~~~~~~~~~^~~~~ gcc -pthread -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.16.0.1/htslib -I/builddir/build/BUILD/pysam-0.16.0.1/samtools -I/builddir/build/BUILD/pysam-0.16.0.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.16.0.1/bcftools -I/builddir/build/BUILD/pysam-0.16.0.1/pysam -I/builddir/build/BUILD/pysam-0.16.0.1 -I/usr/include/python3.9 -c htslib/regidx.c -o build/temp.linux-x86_64-3.9/htslib/regidx.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -pthread -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.16.0.1/htslib -I/builddir/build/BUILD/pysam-0.16.0.1/samtools -I/builddir/build/BUILD/pysam-0.16.0.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.16.0.1/bcftools -I/builddir/build/BUILD/pysam-0.16.0.1/pysam -I/builddir/build/BUILD/pysam-0.16.0.1 -I/usr/include/python3.9 -c htslib/region.c -o build/temp.linux-x86_64-3.9/htslib/region.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -pthread -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.16.0.1/htslib -I/builddir/build/BUILD/pysam-0.16.0.1/samtools -I/builddir/build/BUILD/pysam-0.16.0.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.16.0.1/bcftools -I/builddir/build/BUILD/pysam-0.16.0.1/pysam -I/builddir/build/BUILD/pysam-0.16.0.1 -I/usr/include/python3.9 -c htslib/sam.c -o build/temp.linux-x86_64-3.9/htslib/sam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -pthread -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.16.0.1/htslib -I/builddir/build/BUILD/pysam-0.16.0.1/samtools -I/builddir/build/BUILD/pysam-0.16.0.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.16.0.1/bcftools -I/builddir/build/BUILD/pysam-0.16.0.1/pysam -I/builddir/build/BUILD/pysam-0.16.0.1 -I/usr/include/python3.9 -c htslib/synced_bcf_reader.c -o build/temp.linux-x86_64-3.9/htslib/synced_bcf_reader.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -pthread -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.16.0.1/htslib -I/builddir/build/BUILD/pysam-0.16.0.1/samtools -I/builddir/build/BUILD/pysam-0.16.0.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.16.0.1/bcftools -I/builddir/build/BUILD/pysam-0.16.0.1/pysam -I/builddir/build/BUILD/pysam-0.16.0.1 -I/usr/include/python3.9 -c htslib/tbx.c -o build/temp.linux-x86_64-3.9/htslib/tbx.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -pthread -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.16.0.1/htslib -I/builddir/build/BUILD/pysam-0.16.0.1/samtools -I/builddir/build/BUILD/pysam-0.16.0.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.16.0.1/bcftools -I/builddir/build/BUILD/pysam-0.16.0.1/pysam -I/builddir/build/BUILD/pysam-0.16.0.1 -I/usr/include/python3.9 -c htslib/textutils.c -o build/temp.linux-x86_64-3.9/htslib/textutils.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -pthread -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.16.0.1/htslib -I/builddir/build/BUILD/pysam-0.16.0.1/samtools -I/builddir/build/BUILD/pysam-0.16.0.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.16.0.1/bcftools -I/builddir/build/BUILD/pysam-0.16.0.1/pysam -I/builddir/build/BUILD/pysam-0.16.0.1 -I/usr/include/python3.9 -c htslib/thread_pool.c -o build/temp.linux-x86_64-3.9/htslib/thread_pool.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -pthread -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.16.0.1/htslib -I/builddir/build/BUILD/pysam-0.16.0.1/samtools -I/builddir/build/BUILD/pysam-0.16.0.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.16.0.1/bcftools -I/builddir/build/BUILD/pysam-0.16.0.1/pysam -I/builddir/build/BUILD/pysam-0.16.0.1 -I/usr/include/python3.9 -c htslib/vcf.c -o build/temp.linux-x86_64-3.9/htslib/vcf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -pthread -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.16.0.1/htslib -I/builddir/build/BUILD/pysam-0.16.0.1/samtools -I/builddir/build/BUILD/pysam-0.16.0.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.16.0.1/bcftools -I/builddir/build/BUILD/pysam-0.16.0.1/pysam -I/builddir/build/BUILD/pysam-0.16.0.1 -I/usr/include/python3.9 -c htslib/vcf_sweep.c -o build/temp.linux-x86_64-3.9/htslib/vcf_sweep.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -pthread -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.16.0.1/htslib -I/builddir/build/BUILD/pysam-0.16.0.1/samtools -I/builddir/build/BUILD/pysam-0.16.0.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.16.0.1/bcftools -I/builddir/build/BUILD/pysam-0.16.0.1/pysam -I/builddir/build/BUILD/pysam-0.16.0.1 -I/usr/include/python3.9 -c htslib/vcfutils.c -o build/temp.linux-x86_64-3.9/htslib/vcfutils.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -pthread -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.16.0.1/htslib -I/builddir/build/BUILD/pysam-0.16.0.1/samtools -I/builddir/build/BUILD/pysam-0.16.0.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.16.0.1/bcftools -I/builddir/build/BUILD/pysam-0.16.0.1/pysam -I/builddir/build/BUILD/pysam-0.16.0.1 -I/usr/include/python3.9 -c pysam/htslib_util.c -o build/temp.linux-x86_64-3.9/pysam/htslib_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -pthread -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.16.0.1/htslib -I/builddir/build/BUILD/pysam-0.16.0.1/samtools -I/builddir/build/BUILD/pysam-0.16.0.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.16.0.1/bcftools -I/builddir/build/BUILD/pysam-0.16.0.1/pysam -I/builddir/build/BUILD/pysam-0.16.0.1 -I/usr/include/python3.9 -c pysam/libchtslib.c -o build/temp.linux-x86_64-3.9/pysam/libchtslib.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -pthread -shared -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -g -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -g -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection build/temp.linux-x86_64-3.9/htslib/bcf_sr_sort.o build/temp.linux-x86_64-3.9/htslib/bgzf.o build/temp.linux-x86_64-3.9/htslib/cram/cram_codecs.o build/temp.linux-x86_64-3.9/htslib/cram/cram_decode.o build/temp.linux-x86_64-3.9/htslib/cram/cram_encode.o build/temp.linux-x86_64-3.9/htslib/cram/cram_external.o build/temp.linux-x86_64-3.9/htslib/cram/cram_index.o build/temp.linux-x86_64-3.9/htslib/cram/cram_io.o build/temp.linux-x86_64-3.9/htslib/cram/cram_samtools.o build/temp.linux-x86_64-3.9/htslib/cram/cram_stats.o build/temp.linux-x86_64-3.9/htslib/cram/mFILE.o build/temp.linux-x86_64-3.9/htslib/cram/open_trace_file.o build/temp.linux-x86_64-3.9/htslib/cram/pooled_alloc.o build/temp.linux-x86_64-3.9/htslib/cram/rANS_static.o build/temp.linux-x86_64-3.9/htslib/cram/string_alloc.o build/temp.linux-x86_64-3.9/htslib/errmod.o build/temp.linux-x86_64-3.9/htslib/faidx.o build/temp.linux-x86_64-3.9/htslib/header.o build/temp.linux-x86_64-3.9/htslib/hfile.o build/temp.linux-x86_64-3.9/htslib/hfile_net.o build/temp.linux-x86_64-3.9/htslib/hts.o build/temp.linux-x86_64-3.9/htslib/hts_os.o build/temp.linux-x86_64-3.9/htslib/kfunc.o build/temp.linux-x86_64-3.9/htslib/knetfile.o build/temp.linux-x86_64-3.9/htslib/kstring.o build/temp.linux-x86_64-3.9/htslib/md5.o build/temp.linux-x86_64-3.9/htslib/multipart.o build/temp.linux-x86_64-3.9/htslib/probaln.o build/temp.linux-x86_64-3.9/htslib/realn.o build/temp.linux-x86_64-3.9/htslib/regidx.o build/temp.linux-x86_64-3.9/htslib/region.o build/temp.linux-x86_64-3.9/htslib/sam.o build/temp.linux-x86_64-3.9/htslib/synced_bcf_reader.o build/temp.linux-x86_64-3.9/htslib/tbx.o build/temp.linux-x86_64-3.9/htslib/textutils.o build/temp.linux-x86_64-3.9/htslib/thread_pool.o build/temp.linux-x86_64-3.9/htslib/vcf.o build/temp.linux-x86_64-3.9/htslib/vcf_sweep.o build/temp.linux-x86_64-3.9/htslib/vcfutils.o build/temp.linux-x86_64-3.9/pysam/htslib_util.o build/temp.linux-x86_64-3.9/pysam/libchtslib.o -L/builddir/build/BUILD/pysam-0.16.0.1/pysam -L/builddir/build/BUILD/pysam-0.16.0.1/pysam -L/builddir/build/BUILD/pysam-0.16.0.1 -L/builddir/build/BUILD/pysam-0.16.0.1/build/lib.linux-x86_64-3.9/pysam -Lbuild/lib.linux-x86_64-3.9/pysam -L/usr/lib64 -lz -llzma -lbz2 -lz -lm -o build/lib.linux-x86_64-3.9/pysam/libchtslib.cpython-39-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN htslib/realn.c: In function ‘sam_prob_realn’: htslib/realn.c:155:23: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] 155 | *(zq - 3) = 'B'; | ^ htslib/realn.c:151:23: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] 151 | *(bq - 3) = 'Z'; | ^ building 'pysam.libcsamtools' extension creating build/temp.linux-x86_64-3.9/samtools creating build/temp.linux-x86_64-3.9/samtools/lz4 gcc -pthread -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.16.0.1/htslib -I/builddir/build/BUILD/pysam-0.16.0.1/samtools -I/builddir/build/BUILD/pysam-0.16.0.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.16.0.1/bcftools -I/builddir/build/BUILD/pysam-0.16.0.1/pysam -I/builddir/build/BUILD/pysam-0.16.0.1 -I/usr/include/python3.9 -c pysam/libcsamtools.c -o build/temp.linux-x86_64-3.9/pysam/libcsamtools.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -pthread -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.16.0.1/htslib -I/builddir/build/BUILD/pysam-0.16.0.1/samtools -I/builddir/build/BUILD/pysam-0.16.0.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.16.0.1/bcftools -I/builddir/build/BUILD/pysam-0.16.0.1/pysam -I/builddir/build/BUILD/pysam-0.16.0.1 -I/usr/include/python3.9 -c samtools/bam.c.pysam.c -o build/temp.linux-x86_64-3.9/samtools/bam.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -pthread -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.16.0.1/htslib -I/builddir/build/BUILD/pysam-0.16.0.1/samtools -I/builddir/build/BUILD/pysam-0.16.0.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.16.0.1/bcftools -I/builddir/build/BUILD/pysam-0.16.0.1/pysam -I/builddir/build/BUILD/pysam-0.16.0.1 -I/usr/include/python3.9 -c samtools/bam2bcf.c.pysam.c -o build/temp.linux-x86_64-3.9/samtools/bam2bcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -pthread -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.16.0.1/htslib -I/builddir/build/BUILD/pysam-0.16.0.1/samtools -I/builddir/build/BUILD/pysam-0.16.0.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.16.0.1/bcftools -I/builddir/build/BUILD/pysam-0.16.0.1/pysam -I/builddir/build/BUILD/pysam-0.16.0.1 -I/usr/include/python3.9 -c samtools/bam2bcf_indel.c.pysam.c -o build/temp.linux-x86_64-3.9/samtools/bam2bcf_indel.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -pthread -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.16.0.1/htslib -I/builddir/build/BUILD/pysam-0.16.0.1/samtools -I/builddir/build/BUILD/pysam-0.16.0.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.16.0.1/bcftools -I/builddir/build/BUILD/pysam-0.16.0.1/pysam -I/builddir/build/BUILD/pysam-0.16.0.1 -I/usr/include/python3.9 -c samtools/bam2depth.c.pysam.c -o build/temp.linux-x86_64-3.9/samtools/bam2depth.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -pthread -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.16.0.1/htslib -I/builddir/build/BUILD/pysam-0.16.0.1/samtools -I/builddir/build/BUILD/pysam-0.16.0.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.16.0.1/bcftools -I/builddir/build/BUILD/pysam-0.16.0.1/pysam -I/builddir/build/BUILD/pysam-0.16.0.1 -I/usr/include/python3.9 -c samtools/bam_addrprg.c.pysam.c -o build/temp.linux-x86_64-3.9/samtools/bam_addrprg.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -pthread -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.16.0.1/htslib -I/builddir/build/BUILD/pysam-0.16.0.1/samtools -I/builddir/build/BUILD/pysam-0.16.0.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.16.0.1/bcftools -I/builddir/build/BUILD/pysam-0.16.0.1/pysam -I/builddir/build/BUILD/pysam-0.16.0.1 -I/usr/include/python3.9 -c samtools/bam_aux.c.pysam.c -o build/temp.linux-x86_64-3.9/samtools/bam_aux.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -pthread -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.16.0.1/htslib -I/builddir/build/BUILD/pysam-0.16.0.1/samtools -I/builddir/build/BUILD/pysam-0.16.0.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.16.0.1/bcftools -I/builddir/build/BUILD/pysam-0.16.0.1/pysam -I/builddir/build/BUILD/pysam-0.16.0.1 -I/usr/include/python3.9 -c samtools/bam_cat.c.pysam.c -o build/temp.linux-x86_64-3.9/samtools/bam_cat.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -pthread -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.16.0.1/htslib -I/builddir/build/BUILD/pysam-0.16.0.1/samtools -I/builddir/build/BUILD/pysam-0.16.0.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.16.0.1/bcftools -I/builddir/build/BUILD/pysam-0.16.0.1/pysam -I/builddir/build/BUILD/pysam-0.16.0.1 -I/usr/include/python3.9 -c samtools/bam_color.c.pysam.c -o build/temp.linux-x86_64-3.9/samtools/bam_color.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -pthread -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.16.0.1/htslib -I/builddir/build/BUILD/pysam-0.16.0.1/samtools -I/builddir/build/BUILD/pysam-0.16.0.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.16.0.1/bcftools -I/builddir/build/BUILD/pysam-0.16.0.1/pysam -I/builddir/build/BUILD/pysam-0.16.0.1 -I/usr/include/python3.9 -c samtools/bam_fastq.c.pysam.c -o build/temp.linux-x86_64-3.9/samtools/bam_fastq.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -pthread -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.16.0.1/htslib -I/builddir/build/BUILD/pysam-0.16.0.1/samtools -I/builddir/build/BUILD/pysam-0.16.0.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.16.0.1/bcftools -I/builddir/build/BUILD/pysam-0.16.0.1/pysam -I/builddir/build/BUILD/pysam-0.16.0.1 -I/usr/include/python3.9 -c samtools/bam_flags.c.pysam.c -o build/temp.linux-x86_64-3.9/samtools/bam_flags.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -pthread -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.16.0.1/htslib -I/builddir/build/BUILD/pysam-0.16.0.1/samtools -I/builddir/build/BUILD/pysam-0.16.0.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.16.0.1/bcftools -I/builddir/build/BUILD/pysam-0.16.0.1/pysam -I/builddir/build/BUILD/pysam-0.16.0.1 -I/usr/include/python3.9 -c samtools/bam_index.c.pysam.c -o build/temp.linux-x86_64-3.9/samtools/bam_index.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -pthread -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.16.0.1/htslib -I/builddir/build/BUILD/pysam-0.16.0.1/samtools -I/builddir/build/BUILD/pysam-0.16.0.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.16.0.1/bcftools -I/builddir/build/BUILD/pysam-0.16.0.1/pysam -I/builddir/build/BUILD/pysam-0.16.0.1 -I/usr/include/python3.9 -c samtools/bam_lpileup.c.pysam.c -o build/temp.linux-x86_64-3.9/samtools/bam_lpileup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -pthread -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.16.0.1/htslib -I/builddir/build/BUILD/pysam-0.16.0.1/samtools -I/builddir/build/BUILD/pysam-0.16.0.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.16.0.1/bcftools -I/builddir/build/BUILD/pysam-0.16.0.1/pysam -I/builddir/build/BUILD/pysam-0.16.0.1 -I/usr/include/python3.9 -c samtools/bam_markdup.c.pysam.c -o build/temp.linux-x86_64-3.9/samtools/bam_markdup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -pthread -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.16.0.1/htslib -I/builddir/build/BUILD/pysam-0.16.0.1/samtools -I/builddir/build/BUILD/pysam-0.16.0.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.16.0.1/bcftools -I/builddir/build/BUILD/pysam-0.16.0.1/pysam -I/builddir/build/BUILD/pysam-0.16.0.1 -I/usr/include/python3.9 -c samtools/bam_mate.c.pysam.c -o build/temp.linux-x86_64-3.9/samtools/bam_mate.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -pthread -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.16.0.1/htslib -I/builddir/build/BUILD/pysam-0.16.0.1/samtools -I/builddir/build/BUILD/pysam-0.16.0.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.16.0.1/bcftools -I/builddir/build/BUILD/pysam-0.16.0.1/pysam -I/builddir/build/BUILD/pysam-0.16.0.1 -I/usr/include/python3.9 -c samtools/bam_md.c.pysam.c -o build/temp.linux-x86_64-3.9/samtools/bam_md.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -pthread -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.16.0.1/htslib -I/builddir/build/BUILD/pysam-0.16.0.1/samtools -I/builddir/build/BUILD/pysam-0.16.0.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.16.0.1/bcftools -I/builddir/build/BUILD/pysam-0.16.0.1/pysam -I/builddir/build/BUILD/pysam-0.16.0.1 -I/usr/include/python3.9 -c samtools/bam_plbuf.c.pysam.c -o build/temp.linux-x86_64-3.9/samtools/bam_plbuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -pthread -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.16.0.1/htslib -I/builddir/build/BUILD/pysam-0.16.0.1/samtools -I/builddir/build/BUILD/pysam-0.16.0.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.16.0.1/bcftools -I/builddir/build/BUILD/pysam-0.16.0.1/pysam -I/builddir/build/BUILD/pysam-0.16.0.1 -I/usr/include/python3.9 -c samtools/bam_plcmd.c.pysam.c -o build/temp.linux-x86_64-3.9/samtools/bam_plcmd.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -pthread -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.16.0.1/htslib -I/builddir/build/BUILD/pysam-0.16.0.1/samtools -I/builddir/build/BUILD/pysam-0.16.0.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.16.0.1/bcftools -I/builddir/build/BUILD/pysam-0.16.0.1/pysam -I/builddir/build/BUILD/pysam-0.16.0.1 -I/usr/include/python3.9 -c samtools/bam_quickcheck.c.pysam.c -o build/temp.linux-x86_64-3.9/samtools/bam_quickcheck.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -pthread -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.16.0.1/htslib -I/builddir/build/BUILD/pysam-0.16.0.1/samtools -I/builddir/build/BUILD/pysam-0.16.0.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.16.0.1/bcftools -I/builddir/build/BUILD/pysam-0.16.0.1/pysam -I/builddir/build/BUILD/pysam-0.16.0.1 -I/usr/include/python3.9 -c samtools/bam_reheader.c.pysam.c -o build/temp.linux-x86_64-3.9/samtools/bam_reheader.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -pthread -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.16.0.1/htslib -I/builddir/build/BUILD/pysam-0.16.0.1/samtools -I/builddir/build/BUILD/pysam-0.16.0.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.16.0.1/bcftools -I/builddir/build/BUILD/pysam-0.16.0.1/pysam -I/builddir/build/BUILD/pysam-0.16.0.1 -I/usr/include/python3.9 -c samtools/bam_rmdup.c.pysam.c -o build/temp.linux-x86_64-3.9/samtools/bam_rmdup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -pthread -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.16.0.1/htslib -I/builddir/build/BUILD/pysam-0.16.0.1/samtools -I/builddir/build/BUILD/pysam-0.16.0.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.16.0.1/bcftools -I/builddir/build/BUILD/pysam-0.16.0.1/pysam -I/builddir/build/BUILD/pysam-0.16.0.1 -I/usr/include/python3.9 -c samtools/bam_rmdupse.c.pysam.c -o build/temp.linux-x86_64-3.9/samtools/bam_rmdupse.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -pthread -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.16.0.1/htslib -I/builddir/build/BUILD/pysam-0.16.0.1/samtools -I/builddir/build/BUILD/pysam-0.16.0.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.16.0.1/bcftools -I/builddir/build/BUILD/pysam-0.16.0.1/pysam -I/builddir/build/BUILD/pysam-0.16.0.1 -I/usr/include/python3.9 -c samtools/bam_sort.c.pysam.c -o build/temp.linux-x86_64-3.9/samtools/bam_sort.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -pthread -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.16.0.1/htslib -I/builddir/build/BUILD/pysam-0.16.0.1/samtools -I/builddir/build/BUILD/pysam-0.16.0.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.16.0.1/bcftools -I/builddir/build/BUILD/pysam-0.16.0.1/pysam -I/builddir/build/BUILD/pysam-0.16.0.1 -I/usr/include/python3.9 -c samtools/bam_split.c.pysam.c -o build/temp.linux-x86_64-3.9/samtools/bam_split.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -pthread -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.16.0.1/htslib -I/builddir/build/BUILD/pysam-0.16.0.1/samtools -I/builddir/build/BUILD/pysam-0.16.0.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.16.0.1/bcftools -I/builddir/build/BUILD/pysam-0.16.0.1/pysam -I/builddir/build/BUILD/pysam-0.16.0.1 -I/usr/include/python3.9 -c samtools/bam_stat.c.pysam.c -o build/temp.linux-x86_64-3.9/samtools/bam_stat.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -pthread -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.16.0.1/htslib -I/builddir/build/BUILD/pysam-0.16.0.1/samtools -I/builddir/build/BUILD/pysam-0.16.0.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.16.0.1/bcftools -I/builddir/build/BUILD/pysam-0.16.0.1/pysam -I/builddir/build/BUILD/pysam-0.16.0.1 -I/usr/include/python3.9 -c samtools/bamshuf.c.pysam.c -o build/temp.linux-x86_64-3.9/samtools/bamshuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -pthread -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.16.0.1/htslib -I/builddir/build/BUILD/pysam-0.16.0.1/samtools -I/builddir/build/BUILD/pysam-0.16.0.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.16.0.1/bcftools -I/builddir/build/BUILD/pysam-0.16.0.1/pysam -I/builddir/build/BUILD/pysam-0.16.0.1 -I/usr/include/python3.9 -c samtools/bamtk.c.pysam.c -o build/temp.linux-x86_64-3.9/samtools/bamtk.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -pthread -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.16.0.1/htslib -I/builddir/build/BUILD/pysam-0.16.0.1/samtools -I/builddir/build/BUILD/pysam-0.16.0.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.16.0.1/bcftools -I/builddir/build/BUILD/pysam-0.16.0.1/pysam -I/builddir/build/BUILD/pysam-0.16.0.1 -I/usr/include/python3.9 -c samtools/bedcov.c.pysam.c -o build/temp.linux-x86_64-3.9/samtools/bedcov.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -pthread -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.16.0.1/htslib -I/builddir/build/BUILD/pysam-0.16.0.1/samtools -I/builddir/build/BUILD/pysam-0.16.0.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.16.0.1/bcftools -I/builddir/build/BUILD/pysam-0.16.0.1/pysam -I/builddir/build/BUILD/pysam-0.16.0.1 -I/usr/include/python3.9 -c samtools/bedidx.c.pysam.c -o build/temp.linux-x86_64-3.9/samtools/bedidx.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -pthread -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.16.0.1/htslib -I/builddir/build/BUILD/pysam-0.16.0.1/samtools -I/builddir/build/BUILD/pysam-0.16.0.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.16.0.1/bcftools -I/builddir/build/BUILD/pysam-0.16.0.1/pysam -I/builddir/build/BUILD/pysam-0.16.0.1 -I/usr/include/python3.9 -c samtools/coverage.c.pysam.c -o build/temp.linux-x86_64-3.9/samtools/coverage.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -pthread -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.16.0.1/htslib -I/builddir/build/BUILD/pysam-0.16.0.1/samtools -I/builddir/build/BUILD/pysam-0.16.0.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.16.0.1/bcftools -I/builddir/build/BUILD/pysam-0.16.0.1/pysam -I/builddir/build/BUILD/pysam-0.16.0.1 -I/usr/include/python3.9 -c samtools/cut_target.c.pysam.c -o build/temp.linux-x86_64-3.9/samtools/cut_target.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -pthread -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.16.0.1/htslib -I/builddir/build/BUILD/pysam-0.16.0.1/samtools -I/builddir/build/BUILD/pysam-0.16.0.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.16.0.1/bcftools -I/builddir/build/BUILD/pysam-0.16.0.1/pysam -I/builddir/build/BUILD/pysam-0.16.0.1 -I/usr/include/python3.9 -c samtools/dict.c.pysam.c -o build/temp.linux-x86_64-3.9/samtools/dict.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -pthread -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.16.0.1/htslib -I/builddir/build/BUILD/pysam-0.16.0.1/samtools -I/builddir/build/BUILD/pysam-0.16.0.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.16.0.1/bcftools -I/builddir/build/BUILD/pysam-0.16.0.1/pysam -I/builddir/build/BUILD/pysam-0.16.0.1 -I/usr/include/python3.9 -c samtools/faidx.c.pysam.c -o build/temp.linux-x86_64-3.9/samtools/faidx.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -pthread -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.16.0.1/htslib -I/builddir/build/BUILD/pysam-0.16.0.1/samtools -I/builddir/build/BUILD/pysam-0.16.0.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.16.0.1/bcftools -I/builddir/build/BUILD/pysam-0.16.0.1/pysam -I/builddir/build/BUILD/pysam-0.16.0.1 -I/usr/include/python3.9 -c samtools/lz4/lz4.c -o build/temp.linux-x86_64-3.9/samtools/lz4/lz4.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -pthread -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.16.0.1/htslib -I/builddir/build/BUILD/pysam-0.16.0.1/samtools -I/builddir/build/BUILD/pysam-0.16.0.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.16.0.1/bcftools -I/builddir/build/BUILD/pysam-0.16.0.1/pysam -I/builddir/build/BUILD/pysam-0.16.0.1 -I/usr/include/python3.9 -c samtools/padding.c.pysam.c -o build/temp.linux-x86_64-3.9/samtools/padding.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -pthread -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.16.0.1/htslib -I/builddir/build/BUILD/pysam-0.16.0.1/samtools -I/builddir/build/BUILD/pysam-0.16.0.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.16.0.1/bcftools -I/builddir/build/BUILD/pysam-0.16.0.1/pysam -I/builddir/build/BUILD/pysam-0.16.0.1 -I/usr/include/python3.9 -c samtools/phase.c.pysam.c -o build/temp.linux-x86_64-3.9/samtools/phase.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -pthread -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.16.0.1/htslib -I/builddir/build/BUILD/pysam-0.16.0.1/samtools -I/builddir/build/BUILD/pysam-0.16.0.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.16.0.1/bcftools -I/builddir/build/BUILD/pysam-0.16.0.1/pysam -I/builddir/build/BUILD/pysam-0.16.0.1 -I/usr/include/python3.9 -c samtools/sam.c.pysam.c -o build/temp.linux-x86_64-3.9/samtools/sam.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -pthread -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.16.0.1/htslib -I/builddir/build/BUILD/pysam-0.16.0.1/samtools -I/builddir/build/BUILD/pysam-0.16.0.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.16.0.1/bcftools -I/builddir/build/BUILD/pysam-0.16.0.1/pysam -I/builddir/build/BUILD/pysam-0.16.0.1 -I/usr/include/python3.9 -c samtools/sam_opts.c.pysam.c -o build/temp.linux-x86_64-3.9/samtools/sam_opts.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -pthread -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.16.0.1/htslib -I/builddir/build/BUILD/pysam-0.16.0.1/samtools -I/builddir/build/BUILD/pysam-0.16.0.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.16.0.1/bcftools -I/builddir/build/BUILD/pysam-0.16.0.1/pysam -I/builddir/build/BUILD/pysam-0.16.0.1 -I/usr/include/python3.9 -c samtools/sam_utils.c.pysam.c -o build/temp.linux-x86_64-3.9/samtools/sam_utils.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -pthread -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.16.0.1/htslib -I/builddir/build/BUILD/pysam-0.16.0.1/samtools -I/builddir/build/BUILD/pysam-0.16.0.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.16.0.1/bcftools -I/builddir/build/BUILD/pysam-0.16.0.1/pysam -I/builddir/build/BUILD/pysam-0.16.0.1 -I/usr/include/python3.9 -c samtools/sam_view.c.pysam.c -o build/temp.linux-x86_64-3.9/samtools/sam_view.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -pthread -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.16.0.1/htslib -I/builddir/build/BUILD/pysam-0.16.0.1/samtools -I/builddir/build/BUILD/pysam-0.16.0.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.16.0.1/bcftools -I/builddir/build/BUILD/pysam-0.16.0.1/pysam -I/builddir/build/BUILD/pysam-0.16.0.1 -I/usr/include/python3.9 -c samtools/sample.c.pysam.c -o build/temp.linux-x86_64-3.9/samtools/sample.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -pthread -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.16.0.1/htslib -I/builddir/build/BUILD/pysam-0.16.0.1/samtools -I/builddir/build/BUILD/pysam-0.16.0.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.16.0.1/bcftools -I/builddir/build/BUILD/pysam-0.16.0.1/pysam -I/builddir/build/BUILD/pysam-0.16.0.1 -I/usr/include/python3.9 -c samtools/samtools.pysam.c -o build/temp.linux-x86_64-3.9/samtools/samtools.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -pthread -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.16.0.1/htslib -I/builddir/build/BUILD/pysam-0.16.0.1/samtools -I/builddir/build/BUILD/pysam-0.16.0.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.16.0.1/bcftools -I/builddir/build/BUILD/pysam-0.16.0.1/pysam -I/builddir/build/BUILD/pysam-0.16.0.1 -I/usr/include/python3.9 -c samtools/stats.c.pysam.c -o build/temp.linux-x86_64-3.9/samtools/stats.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -pthread -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.16.0.1/htslib -I/builddir/build/BUILD/pysam-0.16.0.1/samtools -I/builddir/build/BUILD/pysam-0.16.0.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.16.0.1/bcftools -I/builddir/build/BUILD/pysam-0.16.0.1/pysam -I/builddir/build/BUILD/pysam-0.16.0.1 -I/usr/include/python3.9 -c samtools/stats_isize.c.pysam.c -o build/temp.linux-x86_64-3.9/samtools/stats_isize.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -pthread -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.16.0.1/htslib -I/builddir/build/BUILD/pysam-0.16.0.1/samtools -I/builddir/build/BUILD/pysam-0.16.0.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.16.0.1/bcftools -I/builddir/build/BUILD/pysam-0.16.0.1/pysam -I/builddir/build/BUILD/pysam-0.16.0.1 -I/usr/include/python3.9 -c samtools/tmp_file.c.pysam.c -o build/temp.linux-x86_64-3.9/samtools/tmp_file.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -pthread -shared -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -g -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -g -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection build/temp.linux-x86_64-3.9/pysam/libcsamtools.o build/temp.linux-x86_64-3.9/samtools/bam.c.pysam.o build/temp.linux-x86_64-3.9/samtools/bam2bcf.c.pysam.o build/temp.linux-x86_64-3.9/samtools/bam2bcf_indel.c.pysam.o build/temp.linux-x86_64-3.9/samtools/bam2depth.c.pysam.o build/temp.linux-x86_64-3.9/samtools/bam_addrprg.c.pysam.o build/temp.linux-x86_64-3.9/samtools/bam_aux.c.pysam.o build/temp.linux-x86_64-3.9/samtools/bam_cat.c.pysam.o build/temp.linux-x86_64-3.9/samtools/bam_color.c.pysam.o build/temp.linux-x86_64-3.9/samtools/bam_fastq.c.pysam.o build/temp.linux-x86_64-3.9/samtools/bam_flags.c.pysam.o build/temp.linux-x86_64-3.9/samtools/bam_index.c.pysam.o build/temp.linux-x86_64-3.9/samtools/bam_lpileup.c.pysam.o build/temp.linux-x86_64-3.9/samtools/bam_markdup.c.pysam.o build/temp.linux-x86_64-3.9/samtools/bam_mate.c.pysam.o build/temp.linux-x86_64-3.9/samtools/bam_md.c.pysam.o build/temp.linux-x86_64-3.9/samtools/bam_plbuf.c.pysam.o build/temp.linux-x86_64-3.9/samtools/bam_plcmd.c.pysam.o build/temp.linux-x86_64-3.9/samtools/bam_quickcheck.c.pysam.o build/temp.linux-x86_64-3.9/samtools/bam_reheader.c.pysam.o build/temp.linux-x86_64-3.9/samtools/bam_rmdup.c.pysam.o build/temp.linux-x86_64-3.9/samtools/bam_rmdupse.c.pysam.o build/temp.linux-x86_64-3.9/samtools/bam_sort.c.pysam.o build/temp.linux-x86_64-3.9/samtools/bam_split.c.pysam.o build/temp.linux-x86_64-3.9/samtools/bam_stat.c.pysam.o build/temp.linux-x86_64-3.9/samtools/bamshuf.c.pysam.o build/temp.linux-x86_64-3.9/samtools/bamtk.c.pysam.o build/temp.linux-x86_64-3.9/samtools/bedcov.c.pysam.o build/temp.linux-x86_64-3.9/samtools/bedidx.c.pysam.o build/temp.linux-x86_64-3.9/samtools/coverage.c.pysam.o build/temp.linux-x86_64-3.9/samtools/cut_target.c.pysam.o build/temp.linux-x86_64-3.9/samtools/dict.c.pysam.o build/temp.linux-x86_64-3.9/samtools/faidx.c.pysam.o build/temp.linux-x86_64-3.9/samtools/lz4/lz4.o build/temp.linux-x86_64-3.9/samtools/padding.c.pysam.o build/temp.linux-x86_64-3.9/samtools/phase.c.pysam.o build/temp.linux-x86_64-3.9/samtools/sam.c.pysam.o build/temp.linux-x86_64-3.9/samtools/sam_opts.c.pysam.o build/temp.linux-x86_64-3.9/samtools/sam_utils.c.pysam.o build/temp.linux-x86_64-3.9/samtools/sam_view.c.pysam.o build/temp.linux-x86_64-3.9/samtools/sample.c.pysam.o build/temp.linux-x86_64-3.9/samtools/samtools.pysam.o build/temp.linux-x86_64-3.9/samtools/stats.c.pysam.o build/temp.linux-x86_64-3.9/samtools/stats_isize.c.pysam.o build/temp.linux-x86_64-3.9/samtools/tmp_file.c.pysam.o -L/builddir/build/BUILD/pysam-0.16.0.1/pysam -L/builddir/build/BUILD/pysam-0.16.0.1/pysam -L/builddir/build/BUILD/pysam-0.16.0.1 -L/builddir/build/BUILD/pysam-0.16.0.1/build/lib.linux-x86_64-3.9/pysam -Lbuild/lib.linux-x86_64-3.9/pysam -Lbuild/lib.linux-x86_64-3.9/pysam -L/usr/lib64 -lz -llzma -lbz2 -lz -lm -lchtslib.cpython-39-x86_64-linux-gnu -o build/lib.linux-x86_64-3.9/pysam/libcsamtools.cpython-39-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN building 'pysam.libcbcftools' extension creating build/temp.linux-x86_64-3.9/bcftools gcc -pthread -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.16.0.1/htslib -I/builddir/build/BUILD/pysam-0.16.0.1/samtools -I/builddir/build/BUILD/pysam-0.16.0.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.16.0.1/bcftools -I/builddir/build/BUILD/pysam-0.16.0.1/pysam -I/builddir/build/BUILD/pysam-0.16.0.1 -I/usr/include/python3.9 -c bcftools/HMM.c.pysam.c -o build/temp.linux-x86_64-3.9/bcftools/HMM.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -pthread -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.16.0.1/htslib -I/builddir/build/BUILD/pysam-0.16.0.1/samtools -I/builddir/build/BUILD/pysam-0.16.0.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.16.0.1/bcftools -I/builddir/build/BUILD/pysam-0.16.0.1/pysam -I/builddir/build/BUILD/pysam-0.16.0.1 -I/usr/include/python3.9 -c bcftools/bam2bcf.c.pysam.c -o build/temp.linux-x86_64-3.9/bcftools/bam2bcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -pthread -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.16.0.1/htslib -I/builddir/build/BUILD/pysam-0.16.0.1/samtools -I/builddir/build/BUILD/pysam-0.16.0.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.16.0.1/bcftools -I/builddir/build/BUILD/pysam-0.16.0.1/pysam -I/builddir/build/BUILD/pysam-0.16.0.1 -I/usr/include/python3.9 -c bcftools/bam2bcf_indel.c.pysam.c -o build/temp.linux-x86_64-3.9/bcftools/bam2bcf_indel.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -pthread -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.16.0.1/htslib -I/builddir/build/BUILD/pysam-0.16.0.1/samtools -I/builddir/build/BUILD/pysam-0.16.0.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.16.0.1/bcftools -I/builddir/build/BUILD/pysam-0.16.0.1/pysam -I/builddir/build/BUILD/pysam-0.16.0.1 -I/usr/include/python3.9 -c bcftools/bam_sample.c.pysam.c -o build/temp.linux-x86_64-3.9/bcftools/bam_sample.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -pthread -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.16.0.1/htslib -I/builddir/build/BUILD/pysam-0.16.0.1/samtools -I/builddir/build/BUILD/pysam-0.16.0.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.16.0.1/bcftools -I/builddir/build/BUILD/pysam-0.16.0.1/pysam -I/builddir/build/BUILD/pysam-0.16.0.1 -I/usr/include/python3.9 -c bcftools/bcftools.pysam.c -o build/temp.linux-x86_64-3.9/bcftools/bcftools.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -pthread -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.16.0.1/htslib -I/builddir/build/BUILD/pysam-0.16.0.1/samtools -I/builddir/build/BUILD/pysam-0.16.0.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.16.0.1/bcftools -I/builddir/build/BUILD/pysam-0.16.0.1/pysam -I/builddir/build/BUILD/pysam-0.16.0.1 -I/usr/include/python3.9 -c bcftools/bin.c.pysam.c -o build/temp.linux-x86_64-3.9/bcftools/bin.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -pthread -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.16.0.1/htslib -I/builddir/build/BUILD/pysam-0.16.0.1/samtools -I/builddir/build/BUILD/pysam-0.16.0.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.16.0.1/bcftools -I/builddir/build/BUILD/pysam-0.16.0.1/pysam -I/builddir/build/BUILD/pysam-0.16.0.1 -I/usr/include/python3.9 -c bcftools/ccall.c.pysam.c -o build/temp.linux-x86_64-3.9/bcftools/ccall.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -pthread -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.16.0.1/htslib -I/builddir/build/BUILD/pysam-0.16.0.1/samtools -I/builddir/build/BUILD/pysam-0.16.0.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.16.0.1/bcftools -I/builddir/build/BUILD/pysam-0.16.0.1/pysam -I/builddir/build/BUILD/pysam-0.16.0.1 -I/usr/include/python3.9 -c bcftools/cols.c.pysam.c -o build/temp.linux-x86_64-3.9/bcftools/cols.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -pthread -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.16.0.1/htslib -I/builddir/build/BUILD/pysam-0.16.0.1/samtools -I/builddir/build/BUILD/pysam-0.16.0.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.16.0.1/bcftools -I/builddir/build/BUILD/pysam-0.16.0.1/pysam -I/builddir/build/BUILD/pysam-0.16.0.1 -I/usr/include/python3.9 -c bcftools/consensus.c.pysam.c -o build/temp.linux-x86_64-3.9/bcftools/consensus.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -pthread -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.16.0.1/htslib -I/builddir/build/BUILD/pysam-0.16.0.1/samtools -I/builddir/build/BUILD/pysam-0.16.0.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.16.0.1/bcftools -I/builddir/build/BUILD/pysam-0.16.0.1/pysam -I/builddir/build/BUILD/pysam-0.16.0.1 -I/usr/include/python3.9 -c bcftools/convert.c.pysam.c -o build/temp.linux-x86_64-3.9/bcftools/convert.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -pthread -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.16.0.1/htslib -I/builddir/build/BUILD/pysam-0.16.0.1/samtools -I/builddir/build/BUILD/pysam-0.16.0.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.16.0.1/bcftools -I/builddir/build/BUILD/pysam-0.16.0.1/pysam -I/builddir/build/BUILD/pysam-0.16.0.1 -I/usr/include/python3.9 -c bcftools/csq.c.pysam.c -o build/temp.linux-x86_64-3.9/bcftools/csq.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -pthread -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.16.0.1/htslib -I/builddir/build/BUILD/pysam-0.16.0.1/samtools -I/builddir/build/BUILD/pysam-0.16.0.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.16.0.1/bcftools -I/builddir/build/BUILD/pysam-0.16.0.1/pysam -I/builddir/build/BUILD/pysam-0.16.0.1 -I/usr/include/python3.9 -c bcftools/em.c.pysam.c -o build/temp.linux-x86_64-3.9/bcftools/em.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -pthread -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.16.0.1/htslib -I/builddir/build/BUILD/pysam-0.16.0.1/samtools -I/builddir/build/BUILD/pysam-0.16.0.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.16.0.1/bcftools -I/builddir/build/BUILD/pysam-0.16.0.1/pysam -I/builddir/build/BUILD/pysam-0.16.0.1 -I/usr/include/python3.9 -c bcftools/filter.c.pysam.c -o build/temp.linux-x86_64-3.9/bcftools/filter.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -pthread -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.16.0.1/htslib -I/builddir/build/BUILD/pysam-0.16.0.1/samtools -I/builddir/build/BUILD/pysam-0.16.0.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.16.0.1/bcftools -I/builddir/build/BUILD/pysam-0.16.0.1/pysam -I/builddir/build/BUILD/pysam-0.16.0.1 -I/usr/include/python3.9 -c bcftools/gvcf.c.pysam.c -o build/temp.linux-x86_64-3.9/bcftools/gvcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -pthread -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.16.0.1/htslib -I/builddir/build/BUILD/pysam-0.16.0.1/samtools -I/builddir/build/BUILD/pysam-0.16.0.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.16.0.1/bcftools -I/builddir/build/BUILD/pysam-0.16.0.1/pysam -I/builddir/build/BUILD/pysam-0.16.0.1 -I/usr/include/python3.9 -c bcftools/hclust.c.pysam.c -o build/temp.linux-x86_64-3.9/bcftools/hclust.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -pthread -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.16.0.1/htslib -I/builddir/build/BUILD/pysam-0.16.0.1/samtools -I/builddir/build/BUILD/pysam-0.16.0.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.16.0.1/bcftools -I/builddir/build/BUILD/pysam-0.16.0.1/pysam -I/builddir/build/BUILD/pysam-0.16.0.1 -I/usr/include/python3.9 -c bcftools/kmin.c.pysam.c -o build/temp.linux-x86_64-3.9/bcftools/kmin.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -pthread -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.16.0.1/htslib -I/builddir/build/BUILD/pysam-0.16.0.1/samtools -I/builddir/build/BUILD/pysam-0.16.0.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.16.0.1/bcftools -I/builddir/build/BUILD/pysam-0.16.0.1/pysam -I/builddir/build/BUILD/pysam-0.16.0.1 -I/usr/include/python3.9 -c bcftools/main.c.pysam.c -o build/temp.linux-x86_64-3.9/bcftools/main.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -pthread -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.16.0.1/htslib -I/builddir/build/BUILD/pysam-0.16.0.1/samtools -I/builddir/build/BUILD/pysam-0.16.0.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.16.0.1/bcftools -I/builddir/build/BUILD/pysam-0.16.0.1/pysam -I/builddir/build/BUILD/pysam-0.16.0.1 -I/usr/include/python3.9 -c bcftools/mcall.c.pysam.c -o build/temp.linux-x86_64-3.9/bcftools/mcall.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -pthread -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.16.0.1/htslib -I/builddir/build/BUILD/pysam-0.16.0.1/samtools -I/builddir/build/BUILD/pysam-0.16.0.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.16.0.1/bcftools -I/builddir/build/BUILD/pysam-0.16.0.1/pysam -I/builddir/build/BUILD/pysam-0.16.0.1 -I/usr/include/python3.9 -c bcftools/mpileup.c.pysam.c -o build/temp.linux-x86_64-3.9/bcftools/mpileup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -pthread -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.16.0.1/htslib -I/builddir/build/BUILD/pysam-0.16.0.1/samtools -I/builddir/build/BUILD/pysam-0.16.0.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.16.0.1/bcftools -I/builddir/build/BUILD/pysam-0.16.0.1/pysam -I/builddir/build/BUILD/pysam-0.16.0.1 -I/usr/include/python3.9 -c bcftools/ploidy.c.pysam.c -o build/temp.linux-x86_64-3.9/bcftools/ploidy.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -pthread -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.16.0.1/htslib -I/builddir/build/BUILD/pysam-0.16.0.1/samtools -I/builddir/build/BUILD/pysam-0.16.0.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.16.0.1/bcftools -I/builddir/build/BUILD/pysam-0.16.0.1/pysam -I/builddir/build/BUILD/pysam-0.16.0.1 -I/usr/include/python3.9 -c bcftools/prob1.c.pysam.c -o build/temp.linux-x86_64-3.9/bcftools/prob1.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -pthread -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.16.0.1/htslib -I/builddir/build/BUILD/pysam-0.16.0.1/samtools -I/builddir/build/BUILD/pysam-0.16.0.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.16.0.1/bcftools -I/builddir/build/BUILD/pysam-0.16.0.1/pysam -I/builddir/build/BUILD/pysam-0.16.0.1 -I/usr/include/python3.9 -c bcftools/regidx.c.pysam.c -o build/temp.linux-x86_64-3.9/bcftools/regidx.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -pthread -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.16.0.1/htslib -I/builddir/build/BUILD/pysam-0.16.0.1/samtools -I/builddir/build/BUILD/pysam-0.16.0.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.16.0.1/bcftools -I/builddir/build/BUILD/pysam-0.16.0.1/pysam -I/builddir/build/BUILD/pysam-0.16.0.1 -I/usr/include/python3.9 -c bcftools/reheader.c.pysam.c -o build/temp.linux-x86_64-3.9/bcftools/reheader.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -pthread -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.16.0.1/htslib -I/builddir/build/BUILD/pysam-0.16.0.1/samtools -I/builddir/build/BUILD/pysam-0.16.0.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.16.0.1/bcftools -I/builddir/build/BUILD/pysam-0.16.0.1/pysam -I/builddir/build/BUILD/pysam-0.16.0.1 -I/usr/include/python3.9 -c bcftools/smpl_ilist.c.pysam.c -o build/temp.linux-x86_64-3.9/bcftools/smpl_ilist.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -pthread -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.16.0.1/htslib -I/builddir/build/BUILD/pysam-0.16.0.1/samtools -I/builddir/build/BUILD/pysam-0.16.0.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.16.0.1/bcftools -I/builddir/build/BUILD/pysam-0.16.0.1/pysam -I/builddir/build/BUILD/pysam-0.16.0.1 -I/usr/include/python3.9 -c bcftools/tabix.c.pysam.c -o build/temp.linux-x86_64-3.9/bcftools/tabix.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -pthread -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.16.0.1/htslib -I/builddir/build/BUILD/pysam-0.16.0.1/samtools -I/builddir/build/BUILD/pysam-0.16.0.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.16.0.1/bcftools -I/builddir/build/BUILD/pysam-0.16.0.1/pysam -I/builddir/build/BUILD/pysam-0.16.0.1 -I/usr/include/python3.9 -c bcftools/tsv2vcf.c.pysam.c -o build/temp.linux-x86_64-3.9/bcftools/tsv2vcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -pthread -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.16.0.1/htslib -I/builddir/build/BUILD/pysam-0.16.0.1/samtools -I/builddir/build/BUILD/pysam-0.16.0.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.16.0.1/bcftools -I/builddir/build/BUILD/pysam-0.16.0.1/pysam -I/builddir/build/BUILD/pysam-0.16.0.1 -I/usr/include/python3.9 -c bcftools/vcfannotate.c.pysam.c -o build/temp.linux-x86_64-3.9/bcftools/vcfannotate.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -pthread -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.16.0.1/htslib -I/builddir/build/BUILD/pysam-0.16.0.1/samtools -I/builddir/build/BUILD/pysam-0.16.0.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.16.0.1/bcftools -I/builddir/build/BUILD/pysam-0.16.0.1/pysam -I/builddir/build/BUILD/pysam-0.16.0.1 -I/usr/include/python3.9 -c bcftools/vcfbuf.c.pysam.c -o build/temp.linux-x86_64-3.9/bcftools/vcfbuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -pthread -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.16.0.1/htslib -I/builddir/build/BUILD/pysam-0.16.0.1/samtools -I/builddir/build/BUILD/pysam-0.16.0.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.16.0.1/bcftools -I/builddir/build/BUILD/pysam-0.16.0.1/pysam -I/builddir/build/BUILD/pysam-0.16.0.1 -I/usr/include/python3.9 -c bcftools/vcfcall.c.pysam.c -o build/temp.linux-x86_64-3.9/bcftools/vcfcall.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -pthread -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.16.0.1/htslib -I/builddir/build/BUILD/pysam-0.16.0.1/samtools -I/builddir/build/BUILD/pysam-0.16.0.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.16.0.1/bcftools -I/builddir/build/BUILD/pysam-0.16.0.1/pysam -I/builddir/build/BUILD/pysam-0.16.0.1 -I/usr/include/python3.9 -c bcftools/vcfcnv.c.pysam.c -o build/temp.linux-x86_64-3.9/bcftools/vcfcnv.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -pthread -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.16.0.1/htslib -I/builddir/build/BUILD/pysam-0.16.0.1/samtools -I/builddir/build/BUILD/pysam-0.16.0.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.16.0.1/bcftools -I/builddir/build/BUILD/pysam-0.16.0.1/pysam -I/builddir/build/BUILD/pysam-0.16.0.1 -I/usr/include/python3.9 -c bcftools/vcfconcat.c.pysam.c -o build/temp.linux-x86_64-3.9/bcftools/vcfconcat.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -pthread -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.16.0.1/htslib -I/builddir/build/BUILD/pysam-0.16.0.1/samtools -I/builddir/build/BUILD/pysam-0.16.0.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.16.0.1/bcftools -I/builddir/build/BUILD/pysam-0.16.0.1/pysam -I/builddir/build/BUILD/pysam-0.16.0.1 -I/usr/include/python3.9 -c bcftools/vcfconvert.c.pysam.c -o build/temp.linux-x86_64-3.9/bcftools/vcfconvert.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -pthread -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.16.0.1/htslib -I/builddir/build/BUILD/pysam-0.16.0.1/samtools -I/builddir/build/BUILD/pysam-0.16.0.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.16.0.1/bcftools -I/builddir/build/BUILD/pysam-0.16.0.1/pysam -I/builddir/build/BUILD/pysam-0.16.0.1 -I/usr/include/python3.9 -c bcftools/vcffilter.c.pysam.c -o build/temp.linux-x86_64-3.9/bcftools/vcffilter.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -pthread -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.16.0.1/htslib -I/builddir/build/BUILD/pysam-0.16.0.1/samtools -I/builddir/build/BUILD/pysam-0.16.0.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.16.0.1/bcftools -I/builddir/build/BUILD/pysam-0.16.0.1/pysam -I/builddir/build/BUILD/pysam-0.16.0.1 -I/usr/include/python3.9 -c bcftools/vcfgtcheck.c.pysam.c -o build/temp.linux-x86_64-3.9/bcftools/vcfgtcheck.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -pthread -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.16.0.1/htslib -I/builddir/build/BUILD/pysam-0.16.0.1/samtools -I/builddir/build/BUILD/pysam-0.16.0.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.16.0.1/bcftools -I/builddir/build/BUILD/pysam-0.16.0.1/pysam -I/builddir/build/BUILD/pysam-0.16.0.1 -I/usr/include/python3.9 -c bcftools/vcfindex.c.pysam.c -o build/temp.linux-x86_64-3.9/bcftools/vcfindex.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -pthread -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.16.0.1/htslib -I/builddir/build/BUILD/pysam-0.16.0.1/samtools -I/builddir/build/BUILD/pysam-0.16.0.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.16.0.1/bcftools -I/builddir/build/BUILD/pysam-0.16.0.1/pysam -I/builddir/build/BUILD/pysam-0.16.0.1 -I/usr/include/python3.9 -c bcftools/vcfisec.c.pysam.c -o build/temp.linux-x86_64-3.9/bcftools/vcfisec.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -pthread -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.16.0.1/htslib -I/builddir/build/BUILD/pysam-0.16.0.1/samtools -I/builddir/build/BUILD/pysam-0.16.0.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.16.0.1/bcftools -I/builddir/build/BUILD/pysam-0.16.0.1/pysam -I/builddir/build/BUILD/pysam-0.16.0.1 -I/usr/include/python3.9 -c bcftools/vcfmerge.c.pysam.c -o build/temp.linux-x86_64-3.9/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:694:34: warning: argument 1 range [18446744071562067968, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 694 | ma->gvcf = (gvcf_aux_t*) calloc(ma->n,sizeof(gvcf_aux_t)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/pysam-0.16.0.1/htslib/htslib/kstring.h:30, from /builddir/build/BUILD/pysam-0.16.0.1/htslib/htslib/vcf.h:41, from bcftools/vcfmerge.c.pysam.c:34: /usr/include/stdlib.h:542:14: note: in a call to allocation function ‘calloc’ declared here 542 | extern void *calloc (size_t __nmemb, size_t __size) | ^~~~~~ gcc -pthread -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.16.0.1/htslib -I/builddir/build/BUILD/pysam-0.16.0.1/samtools -I/builddir/build/BUILD/pysam-0.16.0.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.16.0.1/bcftools -I/builddir/build/BUILD/pysam-0.16.0.1/pysam -I/builddir/build/BUILD/pysam-0.16.0.1 -I/usr/include/python3.9 -c bcftools/vcfnorm.c.pysam.c -o build/temp.linux-x86_64-3.9/bcftools/vcfnorm.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -pthread -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.16.0.1/htslib -I/builddir/build/BUILD/pysam-0.16.0.1/samtools -I/builddir/build/BUILD/pysam-0.16.0.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.16.0.1/bcftools -I/builddir/build/BUILD/pysam-0.16.0.1/pysam -I/builddir/build/BUILD/pysam-0.16.0.1 -I/usr/include/python3.9 -c bcftools/vcfplugin.c.pysam.c -o build/temp.linux-x86_64-3.9/bcftools/vcfplugin.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -pthread -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.16.0.1/htslib -I/builddir/build/BUILD/pysam-0.16.0.1/samtools -I/builddir/build/BUILD/pysam-0.16.0.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.16.0.1/bcftools -I/builddir/build/BUILD/pysam-0.16.0.1/pysam -I/builddir/build/BUILD/pysam-0.16.0.1 -I/usr/include/python3.9 -c bcftools/vcfquery.c.pysam.c -o build/temp.linux-x86_64-3.9/bcftools/vcfquery.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -pthread -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.16.0.1/htslib -I/builddir/build/BUILD/pysam-0.16.0.1/samtools -I/builddir/build/BUILD/pysam-0.16.0.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.16.0.1/bcftools -I/builddir/build/BUILD/pysam-0.16.0.1/pysam -I/builddir/build/BUILD/pysam-0.16.0.1 -I/usr/include/python3.9 -c bcftools/vcfroh.c.pysam.c -o build/temp.linux-x86_64-3.9/bcftools/vcfroh.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -pthread -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.16.0.1/htslib -I/builddir/build/BUILD/pysam-0.16.0.1/samtools -I/builddir/build/BUILD/pysam-0.16.0.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.16.0.1/bcftools -I/builddir/build/BUILD/pysam-0.16.0.1/pysam -I/builddir/build/BUILD/pysam-0.16.0.1 -I/usr/include/python3.9 -c bcftools/vcfsom.c.pysam.c -o build/temp.linux-x86_64-3.9/bcftools/vcfsom.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -pthread -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.16.0.1/htslib -I/builddir/build/BUILD/pysam-0.16.0.1/samtools -I/builddir/build/BUILD/pysam-0.16.0.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.16.0.1/bcftools -I/builddir/build/BUILD/pysam-0.16.0.1/pysam -I/builddir/build/BUILD/pysam-0.16.0.1 -I/usr/include/python3.9 -c bcftools/vcfsort.c.pysam.c -o build/temp.linux-x86_64-3.9/bcftools/vcfsort.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -pthread -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.16.0.1/htslib -I/builddir/build/BUILD/pysam-0.16.0.1/samtools -I/builddir/build/BUILD/pysam-0.16.0.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.16.0.1/bcftools -I/builddir/build/BUILD/pysam-0.16.0.1/pysam -I/builddir/build/BUILD/pysam-0.16.0.1 -I/usr/include/python3.9 -c bcftools/vcfstats.c.pysam.c -o build/temp.linux-x86_64-3.9/bcftools/vcfstats.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -pthread -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.16.0.1/htslib -I/builddir/build/BUILD/pysam-0.16.0.1/samtools -I/builddir/build/BUILD/pysam-0.16.0.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.16.0.1/bcftools -I/builddir/build/BUILD/pysam-0.16.0.1/pysam -I/builddir/build/BUILD/pysam-0.16.0.1 -I/usr/include/python3.9 -c bcftools/vcfview.c.pysam.c -o build/temp.linux-x86_64-3.9/bcftools/vcfview.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -pthread -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.16.0.1/htslib -I/builddir/build/BUILD/pysam-0.16.0.1/samtools -I/builddir/build/BUILD/pysam-0.16.0.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.16.0.1/bcftools -I/builddir/build/BUILD/pysam-0.16.0.1/pysam -I/builddir/build/BUILD/pysam-0.16.0.1 -I/usr/include/python3.9 -c bcftools/vcmp.c.pysam.c -o build/temp.linux-x86_64-3.9/bcftools/vcmp.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -pthread -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.16.0.1/htslib -I/builddir/build/BUILD/pysam-0.16.0.1/samtools -I/builddir/build/BUILD/pysam-0.16.0.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.16.0.1/bcftools -I/builddir/build/BUILD/pysam-0.16.0.1/pysam -I/builddir/build/BUILD/pysam-0.16.0.1 -I/usr/include/python3.9 -c bcftools/version.c.pysam.c -o build/temp.linux-x86_64-3.9/bcftools/version.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -pthread -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.16.0.1/htslib -I/builddir/build/BUILD/pysam-0.16.0.1/samtools -I/builddir/build/BUILD/pysam-0.16.0.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.16.0.1/bcftools -I/builddir/build/BUILD/pysam-0.16.0.1/pysam -I/builddir/build/BUILD/pysam-0.16.0.1 -I/usr/include/python3.9 -c pysam/libcbcftools.c -o build/temp.linux-x86_64-3.9/pysam/libcbcftools.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -pthread -shared -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -g -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -g -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection build/temp.linux-x86_64-3.9/bcftools/HMM.c.pysam.o build/temp.linux-x86_64-3.9/bcftools/bam2bcf.c.pysam.o build/temp.linux-x86_64-3.9/bcftools/bam2bcf_indel.c.pysam.o build/temp.linux-x86_64-3.9/bcftools/bam_sample.c.pysam.o build/temp.linux-x86_64-3.9/bcftools/bcftools.pysam.o build/temp.linux-x86_64-3.9/bcftools/bin.c.pysam.o build/temp.linux-x86_64-3.9/bcftools/ccall.c.pysam.o build/temp.linux-x86_64-3.9/bcftools/cols.c.pysam.o build/temp.linux-x86_64-3.9/bcftools/consensus.c.pysam.o build/temp.linux-x86_64-3.9/bcftools/convert.c.pysam.o build/temp.linux-x86_64-3.9/bcftools/csq.c.pysam.o build/temp.linux-x86_64-3.9/bcftools/em.c.pysam.o build/temp.linux-x86_64-3.9/bcftools/filter.c.pysam.o build/temp.linux-x86_64-3.9/bcftools/gvcf.c.pysam.o build/temp.linux-x86_64-3.9/bcftools/hclust.c.pysam.o build/temp.linux-x86_64-3.9/bcftools/kmin.c.pysam.o build/temp.linux-x86_64-3.9/bcftools/main.c.pysam.o build/temp.linux-x86_64-3.9/bcftools/mcall.c.pysam.o build/temp.linux-x86_64-3.9/bcftools/mpileup.c.pysam.o build/temp.linux-x86_64-3.9/bcftools/ploidy.c.pysam.o build/temp.linux-x86_64-3.9/bcftools/prob1.c.pysam.o build/temp.linux-x86_64-3.9/bcftools/regidx.c.pysam.o build/temp.linux-x86_64-3.9/bcftools/reheader.c.pysam.o build/temp.linux-x86_64-3.9/bcftools/smpl_ilist.c.pysam.o build/temp.linux-x86_64-3.9/bcftools/tabix.c.pysam.o build/temp.linux-x86_64-3.9/bcftools/tsv2vcf.c.pysam.o build/temp.linux-x86_64-3.9/bcftools/vcfannotate.c.pysam.o build/temp.linux-x86_64-3.9/bcftools/vcfbuf.c.pysam.o build/temp.linux-x86_64-3.9/bcftools/vcfcall.c.pysam.o build/temp.linux-x86_64-3.9/bcftools/vcfcnv.c.pysam.o build/temp.linux-x86_64-3.9/bcftools/vcfconcat.c.pysam.o build/temp.linux-x86_64-3.9/bcftools/vcfconvert.c.pysam.o build/temp.linux-x86_64-3.9/bcftools/vcffilter.c.pysam.o build/temp.linux-x86_64-3.9/bcftools/vcfgtcheck.c.pysam.o build/temp.linux-x86_64-3.9/bcftools/vcfindex.c.pysam.o build/temp.linux-x86_64-3.9/bcftools/vcfisec.c.pysam.o build/temp.linux-x86_64-3.9/bcftools/vcfmerge.c.pysam.o build/temp.linux-x86_64-3.9/bcftools/vcfnorm.c.pysam.o build/temp.linux-x86_64-3.9/bcftools/vcfplugin.c.pysam.o build/temp.linux-x86_64-3.9/bcftools/vcfquery.c.pysam.o build/temp.linux-x86_64-3.9/bcftools/vcfroh.c.pysam.o build/temp.linux-x86_64-3.9/bcftools/vcfsom.c.pysam.o build/temp.linux-x86_64-3.9/bcftools/vcfsort.c.pysam.o build/temp.linux-x86_64-3.9/bcftools/vcfstats.c.pysam.o build/temp.linux-x86_64-3.9/bcftools/vcfview.c.pysam.o build/temp.linux-x86_64-3.9/bcftools/vcmp.c.pysam.o build/temp.linux-x86_64-3.9/bcftools/version.c.pysam.o build/temp.linux-x86_64-3.9/pysam/libcbcftools.o -L/builddir/build/BUILD/pysam-0.16.0.1/pysam -L/builddir/build/BUILD/pysam-0.16.0.1/pysam -L/builddir/build/BUILD/pysam-0.16.0.1 -L/builddir/build/BUILD/pysam-0.16.0.1/build/lib.linux-x86_64-3.9/pysam -Lbuild/lib.linux-x86_64-3.9/pysam -Lbuild/lib.linux-x86_64-3.9/pysam -Lbuild/lib.linux-x86_64-3.9/pysam -L/usr/lib64 -lz -llzma -lbz2 -lz -lm -lchtslib.cpython-39-x86_64-linux-gnu -o build/lib.linux-x86_64-3.9/pysam/libcbcftools.cpython-39-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN bcftools/vcfmerge.c.pysam.c: In function ‘maux_init’: bcftools/vcfmerge.c.pysam.c:694:34: warning: argument 1 range [18446744071562067968, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 694 | ma->gvcf = (gvcf_aux_t*) calloc(ma->n,sizeof(gvcf_aux_t)); | ^ /usr/include/stdlib.h:542:14: note: in a call to allocation function ‘calloc’ declared here 542 | extern void *calloc (size_t __nmemb, size_t __size) | ^ building 'pysam.libcutils' extension gcc -pthread -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.16.0.1/htslib -I/builddir/build/BUILD/pysam-0.16.0.1/samtools -I/builddir/build/BUILD/pysam-0.16.0.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.16.0.1/bcftools -I/builddir/build/BUILD/pysam-0.16.0.1/pysam -I/builddir/build/BUILD/pysam-0.16.0.1 -I/usr/include/python3.9 -c pysam/libcutils.c -o build/temp.linux-x86_64-3.9/pysam/libcutils.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement pysam/libcutils.c: In function ‘__Pyx_decode_c_string’: pysam/libcutils.c:9991:9: warning: ‘PyUnicode_FromUnicode’ is deprecated [-Wdeprecated-declarations] 9991 | return PyUnicode_FromUnicode(NULL, 0); | ^~~~~~ In file included from /usr/include/python3.9/unicodeobject.h:1026, from /usr/include/python3.9/Python.h:97, from pysam/libcutils.c:4: /usr/include/python3.9/cpython/unicodeobject.h:551:42: note: declared here 551 | Py_DEPRECATED(3.3) PyAPI_FUNC(PyObject*) PyUnicode_FromUnicode( | ^~~~~~~~~~~~~~~~~~~~~ pysam/libcutils.c: In function ‘__pyx_pw_5pysam_9libcutils_9_pysam_dispatch’: pysam/libcutils.c:520:40: warning: ‘__pyx_v_retval’ may be used uninitialized in this function [-Wmaybe-uninitialized] 520 | #define PyInt_FromLong PyLong_FromLong | ^~~~~~~~~~~~~~~ pysam/libcutils.c:5967:7: note: ‘__pyx_v_retval’ was declared here 5967 | int __pyx_v_retval; | ^~~~~~~~~~~~~~ gcc -pthread -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.16.0.1/htslib -I/builddir/build/BUILD/pysam-0.16.0.1/samtools -I/builddir/build/BUILD/pysam-0.16.0.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.16.0.1/bcftools -I/builddir/build/BUILD/pysam-0.16.0.1/pysam -I/builddir/build/BUILD/pysam-0.16.0.1 -I/usr/include/python3.9 -c pysam/pysam_util.c -o build/temp.linux-x86_64-3.9/pysam/pysam_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -pthread -shared -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -g -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -g -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection build/temp.linux-x86_64-3.9/pysam/libcutils.o build/temp.linux-x86_64-3.9/pysam/pysam_util.o -L/builddir/build/BUILD/pysam-0.16.0.1/pysam -L/builddir/build/BUILD/pysam-0.16.0.1/pysam -L/builddir/build/BUILD/pysam-0.16.0.1 -L/builddir/build/BUILD/pysam-0.16.0.1/build/lib.linux-x86_64-3.9/pysam -Lbuild/lib.linux-x86_64-3.9/pysam -Lbuild/lib.linux-x86_64-3.9/pysam -Lbuild/lib.linux-x86_64-3.9/pysam -Lbuild/lib.linux-x86_64-3.9/pysam -L/usr/lib64 -lz -llzma -lbz2 -lz -lm -lchtslib.cpython-39-x86_64-linux-gnu -lcsamtools.cpython-39-x86_64-linux-gnu -lcbcftools.cpython-39-x86_64-linux-gnu -o build/lib.linux-x86_64-3.9/pysam/libcutils.cpython-39-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN building 'pysam.libcalignmentfile' extension gcc -pthread -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.16.0.1/htslib -I/builddir/build/BUILD/pysam-0.16.0.1/samtools -I/builddir/build/BUILD/pysam-0.16.0.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.16.0.1/bcftools -I/builddir/build/BUILD/pysam-0.16.0.1/pysam -I/builddir/build/BUILD/pysam-0.16.0.1 -I/usr/include/python3.9 -c pysam/libcalignmentfile.c -o build/temp.linux-x86_64-3.9/pysam/libcalignmentfile.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement pysam/libcalignmentfile.c: In function ‘__pyx_f_5pysam_17libcalignmentfile_14IteratorColumn_cnext’: pysam/libcalignmentfile.c:30108:127: warning: passing argument 5 of ‘bam_mplp_auto’ from incompatible pointer type [-Wincompatible-pointer-types] 30108 | __pyx_v_ret = bam_mplp_auto(__pyx_v_self->pileup_iter, (&__pyx_v_self->tid), (&__pyx_v_self->pos), (&__pyx_v_self->n_plp), (&__pyx_v_self->plp)); | ~^~~~~~~~~~~~~~~~~~~ | | | bam_pileup1_t ** In file included from pysam/htslib_util.h:4, from pysam/libcalignmentfile.c:612: /builddir/build/BUILD/pysam-0.16.0.1/htslib/htslib/sam.h:1709:96: note: expected ‘const bam_pileup1_t **’ but argument is of type ‘bam_pileup1_t **’ 1709 | int bam_mplp_auto(bam_mplp_t iter, int *_tid, int *_pos, int *n_plp, const bam_pileup1_t **plp); | ~~~~~~~~~~~~~~~~~~~~~~^~~ gcc -pthread -shared -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -g -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -g -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection build/temp.linux-x86_64-3.9/pysam/libcalignmentfile.o -L/builddir/build/BUILD/pysam-0.16.0.1/pysam -L/builddir/build/BUILD/pysam-0.16.0.1/pysam -L/builddir/build/BUILD/pysam-0.16.0.1 -L/builddir/build/BUILD/pysam-0.16.0.1/build/lib.linux-x86_64-3.9/pysam -Lbuild/lib.linux-x86_64-3.9/pysam -Lbuild/lib.linux-x86_64-3.9/pysam -Lbuild/lib.linux-x86_64-3.9/pysam -Lbuild/lib.linux-x86_64-3.9/pysam -Lbuild/lib.linux-x86_64-3.9/pysam -L/usr/lib64 -lz -llzma -lbz2 -lz -lm -lchtslib.cpython-39-x86_64-linux-gnu -lcutils.cpython-39-x86_64-linux-gnu -o build/lib.linux-x86_64-3.9/pysam/libcalignmentfile.cpython-39-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN building 'pysam.libcsamfile' extension gcc -pthread -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.16.0.1/htslib -I/builddir/build/BUILD/pysam-0.16.0.1/samtools -I/builddir/build/BUILD/pysam-0.16.0.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.16.0.1/bcftools -I/builddir/build/BUILD/pysam-0.16.0.1/pysam -I/builddir/build/BUILD/pysam-0.16.0.1 -I/usr/include/python3.9 -c pysam/libcsamfile.c -o build/temp.linux-x86_64-3.9/pysam/libcsamfile.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -pthread -shared -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -g -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -g -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection build/temp.linux-x86_64-3.9/pysam/libcsamfile.o -L/builddir/build/BUILD/pysam-0.16.0.1/pysam -L/builddir/build/BUILD/pysam-0.16.0.1/pysam -L/builddir/build/BUILD/pysam-0.16.0.1 -L/builddir/build/BUILD/pysam-0.16.0.1/build/lib.linux-x86_64-3.9/pysam -Lbuild/lib.linux-x86_64-3.9/pysam -Lbuild/lib.linux-x86_64-3.9/pysam -Lbuild/lib.linux-x86_64-3.9/pysam -Lbuild/lib.linux-x86_64-3.9/pysam -Lbuild/lib.linux-x86_64-3.9/pysam -Lbuild/lib.linux-x86_64-3.9/pysam -L/usr/lib64 -lz -llzma -lbz2 -lz -lm -lchtslib.cpython-39-x86_64-linux-gnu -lcutils.cpython-39-x86_64-linux-gnu -o build/lib.linux-x86_64-3.9/pysam/libcsamfile.cpython-39-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN building 'pysam.libcalignedsegment' extension gcc -pthread -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.16.0.1/htslib -I/builddir/build/BUILD/pysam-0.16.0.1/samtools -I/builddir/build/BUILD/pysam-0.16.0.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.16.0.1/bcftools -I/builddir/build/BUILD/pysam-0.16.0.1/pysam -I/builddir/build/BUILD/pysam-0.16.0.1 -I/usr/include/python3.9 -c pysam/libcalignedsegment.c -o build/temp.linux-x86_64-3.9/pysam/libcalignedsegment.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement pysam/libcalignedsegment.c: In function ‘__Pyx_decode_c_string’: pysam/libcalignedsegment.c:63099:9: warning: ‘PyUnicode_FromUnicode’ is deprecated [-Wdeprecated-declarations] 63099 | return PyUnicode_FromUnicode(NULL, 0); | ^~~~~~ In file included from /usr/include/python3.9/unicodeobject.h:1026, from /usr/include/python3.9/Python.h:97, from pysam/libcalignedsegment.c:4: /usr/include/python3.9/cpython/unicodeobject.h:551:42: note: declared here 551 | Py_DEPRECATED(3.3) PyAPI_FUNC(PyObject*) PyUnicode_FromUnicode( | ^~~~~~~~~~~~~~~~~~~~~ gcc -pthread -shared -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -g -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -g -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection build/temp.linux-x86_64-3.9/pysam/libcalignedsegment.o -L/builddir/build/BUILD/pysam-0.16.0.1/pysam -L/builddir/build/BUILD/pysam-0.16.0.1/pysam -L/builddir/build/BUILD/pysam-0.16.0.1 -L/builddir/build/BUILD/pysam-0.16.0.1/build/lib.linux-x86_64-3.9/pysam -Lbuild/lib.linux-x86_64-3.9/pysam -Lbuild/lib.linux-x86_64-3.9/pysam -Lbuild/lib.linux-x86_64-3.9/pysam -Lbuild/lib.linux-x86_64-3.9/pysam -Lbuild/lib.linux-x86_64-3.9/pysam -Lbuild/lib.linux-x86_64-3.9/pysam -Lbuild/lib.linux-x86_64-3.9/pysam -L/usr/lib64 -lz -llzma -lbz2 -lz -lm -lchtslib.cpython-39-x86_64-linux-gnu -lcutils.cpython-39-x86_64-linux-gnu -o build/lib.linux-x86_64-3.9/pysam/libcalignedsegment.cpython-39-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN building 'pysam.libctabix' extension gcc -pthread -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.16.0.1/htslib -I/builddir/build/BUILD/pysam-0.16.0.1/samtools -I/builddir/build/BUILD/pysam-0.16.0.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.16.0.1/bcftools -I/builddir/build/BUILD/pysam-0.16.0.1/pysam -I/builddir/build/BUILD/pysam-0.16.0.1 -I/usr/include/python3.9 -c pysam/libctabix.c -o build/temp.linux-x86_64-3.9/pysam/libctabix.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement pysam/libctabix.c: In function ‘__pyx_pf_5pysam_9libctabix_9TabixFile_7contigs___get__’: pysam/libctabix.c:8759:27: warning: assignment to ‘char **’ from incompatible pointer type ‘const char **’ [-Wincompatible-pointer-types] 8759 | __pyx_v_sequences = tbx_seqnames(__pyx_v_self->index, (&__pyx_v_nsequences)); | ^ In file included from pysam/libctabix.c:619: pysam/libctabix.c: In function ‘__pyx_pf_5pysam_9libctabix_4tabix_index’: /builddir/build/BUILD/pysam-0.16.0.1/htslib/htslib/tbx.h:41:21: warning: overflow in conversion from ‘int’ to ‘int8_t’ {aka ‘signed char’} changes value from ‘65536’ to ‘0’ [-Woverflow] 41 | #define TBX_UCSC 0x10000 | ^~~~~~~ pysam/libctabix.c:13954:39: note: in expansion of macro ‘TBX_UCSC’ 13954 | __pyx_t_1 = __Pyx_PyInt_From_int8_t(TBX_UCSC); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 975, __pyx_L1_error) | ^~~~~~~~ /builddir/build/BUILD/pysam-0.16.0.1/htslib/htslib/tbx.h:41:21: warning: overflow in conversion from ‘int’ to ‘int8_t’ {aka ‘signed char’} changes value from ‘65536’ to ‘0’ [-Woverflow] 41 | #define TBX_UCSC 0x10000 | ^~~~~~~ pysam/libctabix.c:13986:39: note: in expansion of macro ‘TBX_UCSC’ 13986 | __pyx_t_3 = __Pyx_PyInt_From_int8_t(TBX_UCSC); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 976, __pyx_L1_error) | ^~~~~~~~ /builddir/build/BUILD/pysam-0.16.0.1/htslib/htslib/tbx.h:41:21: warning: overflow in conversion from ‘int’ to ‘int8_t’ {aka ‘signed char’} changes value from ‘65536’ to ‘0’ [-Woverflow] 41 | #define TBX_UCSC 0x10000 | ^~~~~~~ pysam/libctabix.c:14356:43: note: in expansion of macro ‘TBX_UCSC’ 14356 | __pyx_t_3 = __Pyx_PyInt_From_int8_t(TBX_UCSC); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 1005, __pyx_L1_error) | ^~~~~~~~ gcc -pthread -shared -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -g -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -g -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection build/temp.linux-x86_64-3.9/pysam/libctabix.o -L/builddir/build/BUILD/pysam-0.16.0.1/pysam -L/builddir/build/BUILD/pysam-0.16.0.1/pysam -L/builddir/build/BUILD/pysam-0.16.0.1 -L/builddir/build/BUILD/pysam-0.16.0.1/build/lib.linux-x86_64-3.9/pysam -Lbuild/lib.linux-x86_64-3.9/pysam -Lbuild/lib.linux-x86_64-3.9/pysam -Lbuild/lib.linux-x86_64-3.9/pysam -Lbuild/lib.linux-x86_64-3.9/pysam -Lbuild/lib.linux-x86_64-3.9/pysam -Lbuild/lib.linux-x86_64-3.9/pysam -Lbuild/lib.linux-x86_64-3.9/pysam -Lbuild/lib.linux-x86_64-3.9/pysam -L/usr/lib64 -lz -llzma -lbz2 -lz -lm -lchtslib.cpython-39-x86_64-linux-gnu -lcutils.cpython-39-x86_64-linux-gnu -o build/lib.linux-x86_64-3.9/pysam/libctabix.cpython-39-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN building 'pysam.libcfaidx' extension gcc -pthread -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.16.0.1/htslib -I/builddir/build/BUILD/pysam-0.16.0.1/samtools -I/builddir/build/BUILD/pysam-0.16.0.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.16.0.1/bcftools -I/builddir/build/BUILD/pysam-0.16.0.1/pysam -I/builddir/build/BUILD/pysam-0.16.0.1 -I/usr/include/python3.9 -c pysam/libcfaidx.c -o build/temp.linux-x86_64-3.9/pysam/libcfaidx.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -pthread -shared -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -g -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -g -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection build/temp.linux-x86_64-3.9/pysam/libcfaidx.o -L/builddir/build/BUILD/pysam-0.16.0.1/pysam -L/builddir/build/BUILD/pysam-0.16.0.1/pysam -L/builddir/build/BUILD/pysam-0.16.0.1 -L/builddir/build/BUILD/pysam-0.16.0.1/build/lib.linux-x86_64-3.9/pysam -Lbuild/lib.linux-x86_64-3.9/pysam -Lbuild/lib.linux-x86_64-3.9/pysam -Lbuild/lib.linux-x86_64-3.9/pysam -Lbuild/lib.linux-x86_64-3.9/pysam -Lbuild/lib.linux-x86_64-3.9/pysam -Lbuild/lib.linux-x86_64-3.9/pysam -Lbuild/lib.linux-x86_64-3.9/pysam -Lbuild/lib.linux-x86_64-3.9/pysam -Lbuild/lib.linux-x86_64-3.9/pysam -L/usr/lib64 -lz -llzma -lbz2 -lz -lm -lchtslib.cpython-39-x86_64-linux-gnu -lcutils.cpython-39-x86_64-linux-gnu -o build/lib.linux-x86_64-3.9/pysam/libcfaidx.cpython-39-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN building 'pysam.libcbcf' extension gcc -pthread -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.16.0.1/htslib -I/builddir/build/BUILD/pysam-0.16.0.1/samtools -I/builddir/build/BUILD/pysam-0.16.0.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.16.0.1/bcftools -I/builddir/build/BUILD/pysam-0.16.0.1/pysam -I/builddir/build/BUILD/pysam-0.16.0.1 -I/usr/include/python3.9 -c pysam/libcbcf.c -o build/temp.linux-x86_64-3.9/pysam/libcbcf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -pthread -shared -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -g -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -g -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection build/temp.linux-x86_64-3.9/pysam/libcbcf.o -L/builddir/build/BUILD/pysam-0.16.0.1/pysam -L/builddir/build/BUILD/pysam-0.16.0.1/pysam -L/builddir/build/BUILD/pysam-0.16.0.1 -L/builddir/build/BUILD/pysam-0.16.0.1/build/lib.linux-x86_64-3.9/pysam -Lbuild/lib.linux-x86_64-3.9/pysam -Lbuild/lib.linux-x86_64-3.9/pysam -Lbuild/lib.linux-x86_64-3.9/pysam -Lbuild/lib.linux-x86_64-3.9/pysam -Lbuild/lib.linux-x86_64-3.9/pysam -Lbuild/lib.linux-x86_64-3.9/pysam -Lbuild/lib.linux-x86_64-3.9/pysam -Lbuild/lib.linux-x86_64-3.9/pysam -Lbuild/lib.linux-x86_64-3.9/pysam -Lbuild/lib.linux-x86_64-3.9/pysam -L/usr/lib64 -lz -llzma -lbz2 -lz -lm -lchtslib.cpython-39-x86_64-linux-gnu -lcutils.cpython-39-x86_64-linux-gnu -o build/lib.linux-x86_64-3.9/pysam/libcbcf.cpython-39-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN building 'pysam.libcbgzf' extension gcc -pthread -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.16.0.1/htslib -I/builddir/build/BUILD/pysam-0.16.0.1/samtools -I/builddir/build/BUILD/pysam-0.16.0.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.16.0.1/bcftools -I/builddir/build/BUILD/pysam-0.16.0.1/pysam -I/builddir/build/BUILD/pysam-0.16.0.1 -I/usr/include/python3.9 -c pysam/libcbgzf.c -o build/temp.linux-x86_64-3.9/pysam/libcbgzf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -pthread -shared -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -g -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -g -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection build/temp.linux-x86_64-3.9/pysam/libcbgzf.o -L/builddir/build/BUILD/pysam-0.16.0.1/pysam -L/builddir/build/BUILD/pysam-0.16.0.1/pysam -L/builddir/build/BUILD/pysam-0.16.0.1 -L/builddir/build/BUILD/pysam-0.16.0.1/build/lib.linux-x86_64-3.9/pysam -Lbuild/lib.linux-x86_64-3.9/pysam -Lbuild/lib.linux-x86_64-3.9/pysam -Lbuild/lib.linux-x86_64-3.9/pysam -Lbuild/lib.linux-x86_64-3.9/pysam -Lbuild/lib.linux-x86_64-3.9/pysam -Lbuild/lib.linux-x86_64-3.9/pysam -Lbuild/lib.linux-x86_64-3.9/pysam -Lbuild/lib.linux-x86_64-3.9/pysam -Lbuild/lib.linux-x86_64-3.9/pysam -Lbuild/lib.linux-x86_64-3.9/pysam -Lbuild/lib.linux-x86_64-3.9/pysam -L/usr/lib64 -lz -llzma -lbz2 -lz -lm -lchtslib.cpython-39-x86_64-linux-gnu -lcutils.cpython-39-x86_64-linux-gnu -o build/lib.linux-x86_64-3.9/pysam/libcbgzf.cpython-39-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN building 'pysam.libctabixproxies' extension gcc -pthread -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.16.0.1/htslib -I/builddir/build/BUILD/pysam-0.16.0.1/samtools -I/builddir/build/BUILD/pysam-0.16.0.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.16.0.1/bcftools -I/builddir/build/BUILD/pysam-0.16.0.1/pysam -I/builddir/build/BUILD/pysam-0.16.0.1 -I/usr/include/python3.9 -c pysam/libctabixproxies.c -o build/temp.linux-x86_64-3.9/pysam/libctabixproxies.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -pthread -shared -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -g -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -g -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection build/temp.linux-x86_64-3.9/pysam/libctabixproxies.o -L/builddir/build/BUILD/pysam-0.16.0.1/pysam -L/builddir/build/BUILD/pysam-0.16.0.1/pysam -L/builddir/build/BUILD/pysam-0.16.0.1 -L/builddir/build/BUILD/pysam-0.16.0.1/build/lib.linux-x86_64-3.9/pysam -Lbuild/lib.linux-x86_64-3.9/pysam -Lbuild/lib.linux-x86_64-3.9/pysam -Lbuild/lib.linux-x86_64-3.9/pysam -Lbuild/lib.linux-x86_64-3.9/pysam -Lbuild/lib.linux-x86_64-3.9/pysam -Lbuild/lib.linux-x86_64-3.9/pysam -Lbuild/lib.linux-x86_64-3.9/pysam -Lbuild/lib.linux-x86_64-3.9/pysam -Lbuild/lib.linux-x86_64-3.9/pysam -Lbuild/lib.linux-x86_64-3.9/pysam -Lbuild/lib.linux-x86_64-3.9/pysam -Lbuild/lib.linux-x86_64-3.9/pysam -L/usr/lib64 -lz -llzma -lbz2 -lz -lm -lchtslib.cpython-39-x86_64-linux-gnu -lcutils.cpython-39-x86_64-linux-gnu -o build/lib.linux-x86_64-3.9/pysam/libctabixproxies.cpython-39-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN building 'pysam.libcvcf' extension gcc -pthread -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.16.0.1/htslib -I/builddir/build/BUILD/pysam-0.16.0.1/samtools -I/builddir/build/BUILD/pysam-0.16.0.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.16.0.1/bcftools -I/builddir/build/BUILD/pysam-0.16.0.1/pysam -I/builddir/build/BUILD/pysam-0.16.0.1 -I/usr/include/python3.9 -c pysam/libcvcf.c -o build/temp.linux-x86_64-3.9/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.constprop.0’: pysam/libcvcf.c:25037:16: warning: ‘__pyx_v_qual’ may be used uninitialized in this function [-Wmaybe-uninitialized] 25037 | __pyx_t_12 = PyFloat_FromDouble(__pyx_v_qual); if (unlikely(!__pyx_t_12)) __PYX_ERR(0, 873, __pyx_L1_error) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -pthread -shared -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -g -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -g -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection build/temp.linux-x86_64-3.9/pysam/libcvcf.o -L/builddir/build/BUILD/pysam-0.16.0.1/pysam -L/builddir/build/BUILD/pysam-0.16.0.1/pysam -L/builddir/build/BUILD/pysam-0.16.0.1 -L/builddir/build/BUILD/pysam-0.16.0.1/build/lib.linux-x86_64-3.9/pysam -Lbuild/lib.linux-x86_64-3.9/pysam -Lbuild/lib.linux-x86_64-3.9/pysam -Lbuild/lib.linux-x86_64-3.9/pysam -Lbuild/lib.linux-x86_64-3.9/pysam -Lbuild/lib.linux-x86_64-3.9/pysam -Lbuild/lib.linux-x86_64-3.9/pysam -Lbuild/lib.linux-x86_64-3.9/pysam -Lbuild/lib.linux-x86_64-3.9/pysam -Lbuild/lib.linux-x86_64-3.9/pysam -Lbuild/lib.linux-x86_64-3.9/pysam -Lbuild/lib.linux-x86_64-3.9/pysam -Lbuild/lib.linux-x86_64-3.9/pysam -Lbuild/lib.linux-x86_64-3.9/pysam -L/usr/lib64 -lz -llzma -lbz2 -lz -lm -lchtslib.cpython-39-x86_64-linux-gnu -lcutils.cpython-39-x86_64-linux-gnu -o build/lib.linux-x86_64-3.9/pysam/libcvcf.cpython-39-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN + PYTHONPATH=/builddir/build/BUILD/pysam-0.16.0.1 + sphinx-build-3 doc html Running Sphinx v3.4.3 WARNING: Support for evaluating Python 2 syntax is deprecated and will be removed in Sphinx 4.0. Convert /builddir/build/BUILD/pysam-0.16.0.1/doc/conf.py to Python 3 syntax. 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 http://docs.python.org/3.5/objects.inv... WARNING: failed to reach any of the inventories with the following issues: intersphinx inventory 'http://docs.python.org/3.5/objects.inv' not fetchable due to : HTTPConnectionPool(host='docs.python.org', port=80): Max retries exceeded with url: /3.5/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 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... [ 55%] glossary reading sources... [ 66%] index reading sources... [ 77%] installation reading sources... [ 88%] release reading sources... [100%] usage docstring of pysam.libcalignmentfile.IndexedReads:1: WARNING: Inline emphasis start-string without end-string. docstring of pysam.libctabix.TabixFile:10: WARNING: Inline literal start-string without end-string. /builddir/build/BUILD/pysam-0.16.0.1/doc/faq.rst:142: WARNING: Inline literal start-string without end-string. looking for now-outdated files... none found pickling environment... /builddir/build/BUILD/pysam-0.16.0.1/doc/faq.rst:16: WARNING: Unknown target name: "gil". /builddir/build/BUILD/pysam-0.16.0.1/doc/installation.rst:7: WARNING: Unknown target name: "pypi". /builddir/build/BUILD/pysam-0.16.0.1/doc/installation.rst:34: WARNING: Unknown target name: "pypi". /builddir/build/BUILD/pysam-0.16.0.1/doc/installation.rst:95: WARNING: Unknown target name: "pip". /builddir/build/BUILD/pysam-0.16.0.1/doc/release.rst:194: WARNING: Unexpected indentation. /builddir/build/BUILD/pysam-0.16.0.1/doc/release.rst:195: WARNING: Block quote ends without a blank line; unexpected unindent. /builddir/build/BUILD/pysam-0.16.0.1/doc/release.rst:443: WARNING: Unexpected indentation. /builddir/build/BUILD/pysam-0.16.0.1/doc/release.rst:449: WARNING: Unexpected indentation. done checking consistency... /builddir/build/BUILD/pysam-0.16.0.1/doc/index.rst:57: WARNING: Citation [Li2009] is not referenced. done preparing documents... done writing output... [ 11%] api writing output... [ 22%] benchmarking writing output... [ 33%] developer writing output... [ 44%] faq writing output... [ 55%] glossary writing output... [ 66%] index writing output... [ 77%] installation writing output... [ 88%] release writing output... [100%] usage docstring of pysam.libcalignmentfile.AlignmentFile:8: WARNING: term not in glossary: CRAM docstring of pysam.libcalignmentfile.AlignmentFile:46: WARNING: term not in glossary: CRAM docstring of pysam.AlignmentFile.count:3: WARNING: term reference not found in case sensitive match.made a reference to Reference instead. docstring of pysam.AlignmentFile.count_coverage:3: WARNING: term reference not found in case sensitive match.made a reference to Reference instead. docstring of pysam.AlignmentFile.fetch:3: WARNING: term reference not found in case sensitive match.made a reference to Reference instead. docstring of pysam.AlignmentFile.get_reference_length:1: WARNING: term reference not found in case sensitive match.made a reference to Reference instead. docstring of pysam.AlignmentFile.get_reference_name:1: WARNING: term reference not found in case sensitive match.made a reference to Reference instead. docstring of pysam.AlignmentFile.get_tid:1: WARNING: term reference not found in case sensitive match.made a reference to Reference instead. docstring of pysam.AlignmentFile.lengths:1: WARNING: term reference not found in case sensitive match.made a reference to Reference instead. docstring of pysam.AlignmentFile.nreferences:1: WARNING: term reference not found in case sensitive match.made a reference to Reference instead. docstring of pysam.AlignmentFile.pileup:1: WARNING: term reference not found in case sensitive match.made a reference to Reference instead. docstring of pysam.AlignmentFile.references:1: WARNING: term reference not found in case sensitive match.made a reference to Reference instead. docstring of pysam.AlignmentHeader.get_tid:1: WARNING: term reference not found in case sensitive match.made a reference to Reference instead. docstring of pysam.AlignmentHeader.lengths:1: WARNING: term reference not found in case sensitive match.made a reference to Reference instead. docstring of pysam.AlignmentHeader.nreferences:1: WARNING: term reference not found in case sensitive match.made a reference to Reference instead. docstring of pysam.AlignmentHeader.references:1: WARNING: term reference not found in case sensitive match.made a reference to Reference instead. docstring of pysam.AlignedSegment.next_reference_id:1: WARNING: term reference not found in case sensitive match.made a reference to Reference instead. docstring of pysam.AlignedSegment.next_reference_name:1: WARNING: term reference not found in case sensitive match.made a reference to Reference instead. docstring of pysam.AlignedSegment.reference_id:1: WARNING: term reference not found in case sensitive match.made a reference to Reference instead. docstring of pysam.AlignedSegment.reference_name:1: WARNING: term reference not found in case sensitive match.made a reference to Reference instead. docstring of pysam.AlignedSegment.set_tags:4: WARNING: term not in glossary: value type docstring of pysam.PileupColumn.reference_name:1: WARNING: term reference not found in case sensitive match.made a reference to Reference instead. docstring of pysam.TabixFile.fetch:1: WARNING: term reference not found in case sensitive match.made a reference to Reference instead. docstring of pysam.FastaFile.fetch:3: WARNING: term reference not found in case sensitive match.made a reference to Reference instead. docstring of pysam.FastaFile.fetch:14: WARNING: term reference not found in case sensitive match.made a reference to Reference instead. docstring of pysam.FastaFile.lengths:1: WARNING: term reference not found in case sensitive match.made a reference to Reference instead. generating indices... docstring of pysam.FastaFile.nreferences:1: WARNING: term reference not found in case sensitive match.made a reference to Reference instead. docstring of pysam.FastaFile.references:1: WARNING: term reference not found in case sensitive match.made a reference to Reference instead. docstring of pysam.libcfaidx.FastxFile:1: WARNING: term not in glossary: fasta docstring of pysam.libcfaidx.FastxFile:1: WARNING: term not in glossary: fastq docstring of pysam.VariantFile.get_reference_name:1: WARNING: term reference not found in case sensitive match.made a reference to Reference instead. docstring of pysam.VariantFile.get_tid:1: WARNING: term reference not found in case sensitive match.made a reference to Reference instead. docstring of pysam.HTSFile.parse_region:1: WARNING: term reference not found in case sensitive match.made a reference to Reference instead. /builddir/build/BUILD/pysam-0.16.0.1/doc/developer.rst:31: WARNING: term not in glossary: cbcftools /builddir/build/BUILD/pysam-0.16.0.1/doc/developer.rst:58: WARNING: undefined label: benchmarking /builddir/build/BUILD/pysam-0.16.0.1/doc/glossary.rst:31: WARNING: term reference not found in case sensitive match.made a reference to Reference instead. /builddir/build/BUILD/pysam-0.16.0.1/doc/glossary.rst:114: WARNING: term not in glossary: fasta /builddir/build/BUILD/pysam-0.16.0.1/doc/release.rst:386: WARNING: term vcf not found in case sensitive match.made a reference to VCF instead. /builddir/build/BUILD/pysam-0.16.0.1/doc/release.rst:386: WARNING: term bcf not found in case sensitive match.made a reference to BCF instead. /builddir/build/BUILD/pysam-0.16.0.1/doc/usage.rst:23: WARNING: term not in glossary: CRAM /builddir/build/BUILD/pysam-0.16.0.1/doc/usage.rst:40: WARNING: term reference not found in case sensitive match.made a reference to Reference instead. /builddir/build/BUILD/pysam-0.16.0.1/doc/usage.rst:49: WARNING: term reference not found in case sensitive match.made a reference to Reference instead. /builddir/build/BUILD/pysam-0.16.0.1/doc/usage.rst:49: WARNING: term not in glossary: columns /builddir/build/BUILD/pysam-0.16.0.1/doc/usage.rst:205: WARNING: term not in glossary: bed /builddir/build/BUILD/pysam-0.16.0.1/doc/usage.rst:205: WARNING: term not in glossary: gtf /builddir/build/BUILD/pysam-0.16.0.1/doc/usage.rst:271: WARNING: term not in glossary: info /builddir/build/BUILD/pysam-0.16.0.1/doc/usage.rst:271: WARNING: term not in glossary: format /builddir/build/BUILD/pysam-0.16.0.1/doc/usage.rst:271: WARNING: term not in glossary: genotype /builddir/build/BUILD/pysam-0.16.0.1/doc/usage.rst:281: WARNING: term vcf not found in case sensitive match.made a reference to VCF instead. genindex done writing additional pages... search done copying static files... done copying extra files... done dumping search index in English (code: en)... done dumping object inventory... done build succeeded, 63 warnings. 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.a77v95 + umask 022 + cd /builddir/build/BUILD + '[' /builddir/build/BUILDROOT/python-pysam-0.16.0.1-1.fc34.x86_64 '!=' / ']' + rm -rf /builddir/build/BUILDROOT/python-pysam-0.16.0.1-1.fc34.x86_64 ++ dirname /builddir/build/BUILDROOT/python-pysam-0.16.0.1-1.fc34.x86_64 + mkdir -p /builddir/build/BUILDROOT + mkdir /builddir/build/BUILDROOT/python-pysam-0.16.0.1-1.fc34.x86_64 + cd pysam-0.16.0.1 + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection' + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld ' + /usr/bin/python3 setup.py install -O1 --skip-build --root /builddir/build/BUILDROOT/python-pysam-0.16.0.1-1.fc34.x86_64 # pysam: cython is available - using cythonize if necessary # pysam: htslib mode is shared # pysam: HTSLIB_CONFIGURE_OPTIONS=None # pysam: (sysconfig) CC=gcc -pthread # pysam: (env) CFLAGS=-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection # pysam: (env) LDFLAGS=-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld checking for gcc... gcc -pthread 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 -pthread accepts -g... yes checking for gcc -pthread 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... unknown 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 compiler accepts -fvisibility=hidden... yes checking how to run the C preprocessor... gcc -pthread -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 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 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 for libdeflate.h... no checking for libdeflate_deflate_compress in -ldeflate... 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 -pthread 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 -pthread accepts -g... yes checking for gcc -pthread 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... unknown 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 compiler accepts -fvisibility=hidden... yes checking how to run the C preprocessor... gcc -pthread -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 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 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 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 whether PTHREAD_MUTEX_RECURSIVE is declared... yes 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 make: ./version.sh: No such file or directory make: ./version.sh: No such file or directory # pysam: htslib configure options: --disable-libcurl # pysam: htslib_config LIBHTS_OBJS=kfunc.o knetfile.o kstring.o bcf_sr_sort.o bgzf.o errmod.o faidx.o header.o hfile.o hfile_net.o hts.o hts_os.o md5.o multipart.o probaln.o realn.o regidx.o region.o sam.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_samtools.o cram/cram_stats.o cram/mFILE.o cram/open_trace_file.o cram/pooled_alloc.o cram/rANS_static.o cram/string_alloc.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 running install_lib creating /builddir/build/BUILDROOT/python-pysam-0.16.0.1-1.fc34.x86_64/usr creating /builddir/build/BUILDROOT/python-pysam-0.16.0.1-1.fc34.x86_64/usr/lib64 creating /builddir/build/BUILDROOT/python-pysam-0.16.0.1-1.fc34.x86_64/usr/lib64/python3.9 creating /builddir/build/BUILDROOT/python-pysam-0.16.0.1-1.fc34.x86_64/usr/lib64/python3.9/site-packages creating /builddir/build/BUILDROOT/python-pysam-0.16.0.1-1.fc34.x86_64/usr/lib64/python3.9/site-packages/pysam creating /builddir/build/BUILDROOT/python-pysam-0.16.0.1-1.fc34.x86_64/usr/lib64/python3.9/site-packages/pysam/__pycache__ copying build/lib.linux-x86_64-3.9/pysam/__pycache__/version.cpython-39.pyc -> /builddir/build/BUILDROOT/python-pysam-0.16.0.1-1.fc34.x86_64/usr/lib64/python3.9/site-packages/pysam/__pycache__ copying build/lib.linux-x86_64-3.9/pysam/__pycache__/config.cpython-39.pyc -> /builddir/build/BUILDROOT/python-pysam-0.16.0.1-1.fc34.x86_64/usr/lib64/python3.9/site-packages/pysam/__pycache__ copying build/lib.linux-x86_64-3.9/pysam/__pycache__/samtools.cpython-39.pyc -> /builddir/build/BUILDROOT/python-pysam-0.16.0.1-1.fc34.x86_64/usr/lib64/python3.9/site-packages/pysam/__pycache__ copying build/lib.linux-x86_64-3.9/pysam/__pycache__/Pileup.cpython-39.pyc -> /builddir/build/BUILDROOT/python-pysam-0.16.0.1-1.fc34.x86_64/usr/lib64/python3.9/site-packages/pysam/__pycache__ copying build/lib.linux-x86_64-3.9/pysam/__pycache__/utils.cpython-39.pyc -> /builddir/build/BUILDROOT/python-pysam-0.16.0.1-1.fc34.x86_64/usr/lib64/python3.9/site-packages/pysam/__pycache__ copying build/lib.linux-x86_64-3.9/pysam/__pycache__/__init__.cpython-39.pyc -> /builddir/build/BUILDROOT/python-pysam-0.16.0.1-1.fc34.x86_64/usr/lib64/python3.9/site-packages/pysam/__pycache__ copying build/lib.linux-x86_64-3.9/pysam/libcvcf.cpython-39-x86_64-linux-gnu.so -> /builddir/build/BUILDROOT/python-pysam-0.16.0.1-1.fc34.x86_64/usr/lib64/python3.9/site-packages/pysam copying build/lib.linux-x86_64-3.9/pysam/libctabixproxies.cpython-39-x86_64-linux-gnu.so -> /builddir/build/BUILDROOT/python-pysam-0.16.0.1-1.fc34.x86_64/usr/lib64/python3.9/site-packages/pysam copying build/lib.linux-x86_64-3.9/pysam/libcbgzf.cpython-39-x86_64-linux-gnu.so -> /builddir/build/BUILDROOT/python-pysam-0.16.0.1-1.fc34.x86_64/usr/lib64/python3.9/site-packages/pysam copying build/lib.linux-x86_64-3.9/pysam/libcbcf.cpython-39-x86_64-linux-gnu.so -> /builddir/build/BUILDROOT/python-pysam-0.16.0.1-1.fc34.x86_64/usr/lib64/python3.9/site-packages/pysam copying build/lib.linux-x86_64-3.9/pysam/libcfaidx.cpython-39-x86_64-linux-gnu.so -> /builddir/build/BUILDROOT/python-pysam-0.16.0.1-1.fc34.x86_64/usr/lib64/python3.9/site-packages/pysam copying build/lib.linux-x86_64-3.9/pysam/libctabix.cpython-39-x86_64-linux-gnu.so -> /builddir/build/BUILDROOT/python-pysam-0.16.0.1-1.fc34.x86_64/usr/lib64/python3.9/site-packages/pysam copying build/lib.linux-x86_64-3.9/pysam/libcalignedsegment.cpython-39-x86_64-linux-gnu.so -> /builddir/build/BUILDROOT/python-pysam-0.16.0.1-1.fc34.x86_64/usr/lib64/python3.9/site-packages/pysam copying build/lib.linux-x86_64-3.9/pysam/libcsamfile.cpython-39-x86_64-linux-gnu.so -> /builddir/build/BUILDROOT/python-pysam-0.16.0.1-1.fc34.x86_64/usr/lib64/python3.9/site-packages/pysam copying build/lib.linux-x86_64-3.9/pysam/libcalignmentfile.cpython-39-x86_64-linux-gnu.so -> /builddir/build/BUILDROOT/python-pysam-0.16.0.1-1.fc34.x86_64/usr/lib64/python3.9/site-packages/pysam copying build/lib.linux-x86_64-3.9/pysam/libcutils.cpython-39-x86_64-linux-gnu.so -> /builddir/build/BUILDROOT/python-pysam-0.16.0.1-1.fc34.x86_64/usr/lib64/python3.9/site-packages/pysam copying build/lib.linux-x86_64-3.9/pysam/libcbcftools.cpython-39-x86_64-linux-gnu.so -> /builddir/build/BUILDROOT/python-pysam-0.16.0.1-1.fc34.x86_64/usr/lib64/python3.9/site-packages/pysam copying build/lib.linux-x86_64-3.9/pysam/libcsamtools.cpython-39-x86_64-linux-gnu.so -> /builddir/build/BUILDROOT/python-pysam-0.16.0.1-1.fc34.x86_64/usr/lib64/python3.9/site-packages/pysam copying build/lib.linux-x86_64-3.9/pysam/libchtslib.cpython-39-x86_64-linux-gnu.so -> /builddir/build/BUILDROOT/python-pysam-0.16.0.1-1.fc34.x86_64/usr/lib64/python3.9/site-packages/pysam copying build/lib.linux-x86_64-3.9/pysam/csamtools_util.h -> /builddir/build/BUILDROOT/python-pysam-0.16.0.1-1.fc34.x86_64/usr/lib64/python3.9/site-packages/pysam copying build/lib.linux-x86_64-3.9/pysam/pysam_stream.h -> /builddir/build/BUILDROOT/python-pysam-0.16.0.1-1.fc34.x86_64/usr/lib64/python3.9/site-packages/pysam copying build/lib.linux-x86_64-3.9/pysam/version.h -> /builddir/build/BUILDROOT/python-pysam-0.16.0.1-1.fc34.x86_64/usr/lib64/python3.9/site-packages/pysam copying build/lib.linux-x86_64-3.9/pysam/pysam_util.h -> /builddir/build/BUILDROOT/python-pysam-0.16.0.1-1.fc34.x86_64/usr/lib64/python3.9/site-packages/pysam copying build/lib.linux-x86_64-3.9/pysam/cbcftools_util.h -> /builddir/build/BUILDROOT/python-pysam-0.16.0.1-1.fc34.x86_64/usr/lib64/python3.9/site-packages/pysam copying build/lib.linux-x86_64-3.9/pysam/htslib_util.h -> /builddir/build/BUILDROOT/python-pysam-0.16.0.1-1.fc34.x86_64/usr/lib64/python3.9/site-packages/pysam copying build/lib.linux-x86_64-3.9/pysam/libctabixproxies.pxd -> /builddir/build/BUILDROOT/python-pysam-0.16.0.1-1.fc34.x86_64/usr/lib64/python3.9/site-packages/pysam copying build/lib.linux-x86_64-3.9/pysam/libchtslib.pxd -> /builddir/build/BUILDROOT/python-pysam-0.16.0.1-1.fc34.x86_64/usr/lib64/python3.9/site-packages/pysam copying build/lib.linux-x86_64-3.9/pysam/libcsamtools.pxd -> /builddir/build/BUILDROOT/python-pysam-0.16.0.1-1.fc34.x86_64/usr/lib64/python3.9/site-packages/pysam copying build/lib.linux-x86_64-3.9/pysam/libcutils.pxd -> /builddir/build/BUILDROOT/python-pysam-0.16.0.1-1.fc34.x86_64/usr/lib64/python3.9/site-packages/pysam copying build/lib.linux-x86_64-3.9/pysam/libcfaidx.pxd -> /builddir/build/BUILDROOT/python-pysam-0.16.0.1-1.fc34.x86_64/usr/lib64/python3.9/site-packages/pysam copying build/lib.linux-x86_64-3.9/pysam/libcbcf.pxd -> /builddir/build/BUILDROOT/python-pysam-0.16.0.1-1.fc34.x86_64/usr/lib64/python3.9/site-packages/pysam copying build/lib.linux-x86_64-3.9/pysam/libctabix.pxd -> /builddir/build/BUILDROOT/python-pysam-0.16.0.1-1.fc34.x86_64/usr/lib64/python3.9/site-packages/pysam copying build/lib.linux-x86_64-3.9/pysam/libcalignedsegment.pxd -> /builddir/build/BUILDROOT/python-pysam-0.16.0.1-1.fc34.x86_64/usr/lib64/python3.9/site-packages/pysam copying build/lib.linux-x86_64-3.9/pysam/libcsamfile.pxd -> /builddir/build/BUILDROOT/python-pysam-0.16.0.1-1.fc34.x86_64/usr/lib64/python3.9/site-packages/pysam copying build/lib.linux-x86_64-3.9/pysam/libcalignmentfile.pxd -> /builddir/build/BUILDROOT/python-pysam-0.16.0.1-1.fc34.x86_64/usr/lib64/python3.9/site-packages/pysam copying build/lib.linux-x86_64-3.9/pysam/libcvcf.pxd -> /builddir/build/BUILDROOT/python-pysam-0.16.0.1-1.fc34.x86_64/usr/lib64/python3.9/site-packages/pysam copying build/lib.linux-x86_64-3.9/pysam/libcbcftools.pxd -> /builddir/build/BUILDROOT/python-pysam-0.16.0.1-1.fc34.x86_64/usr/lib64/python3.9/site-packages/pysam creating /builddir/build/BUILDROOT/python-pysam-0.16.0.1-1.fc34.x86_64/usr/lib64/python3.9/site-packages/pysam/include creating /builddir/build/BUILDROOT/python-pysam-0.16.0.1-1.fc34.x86_64/usr/lib64/python3.9/site-packages/pysam/include/htslib creating /builddir/build/BUILDROOT/python-pysam-0.16.0.1-1.fc34.x86_64/usr/lib64/python3.9/site-packages/pysam/include/htslib/htslib copying build/lib.linux-x86_64-3.9/pysam/include/htslib/htslib/hts.h -> /builddir/build/BUILDROOT/python-pysam-0.16.0.1-1.fc34.x86_64/usr/lib64/python3.9/site-packages/pysam/include/htslib/htslib copying build/lib.linux-x86_64-3.9/pysam/include/htslib/htslib/hfile.h -> /builddir/build/BUILDROOT/python-pysam-0.16.0.1-1.fc34.x86_64/usr/lib64/python3.9/site-packages/pysam/include/htslib/htslib copying build/lib.linux-x86_64-3.9/pysam/include/htslib/htslib/kfunc.h -> /builddir/build/BUILDROOT/python-pysam-0.16.0.1-1.fc34.x86_64/usr/lib64/python3.9/site-packages/pysam/include/htslib/htslib copying build/lib.linux-x86_64-3.9/pysam/include/htslib/htslib/synced_bcf_reader.h -> /builddir/build/BUILDROOT/python-pysam-0.16.0.1-1.fc34.x86_64/usr/lib64/python3.9/site-packages/pysam/include/htslib/htslib copying build/lib.linux-x86_64-3.9/pysam/include/htslib/htslib/faidx.h -> /builddir/build/BUILDROOT/python-pysam-0.16.0.1-1.fc34.x86_64/usr/lib64/python3.9/site-packages/pysam/include/htslib/htslib copying build/lib.linux-x86_64-3.9/pysam/include/htslib/htslib/vcf_sweep.h -> /builddir/build/BUILDROOT/python-pysam-0.16.0.1-1.fc34.x86_64/usr/lib64/python3.9/site-packages/pysam/include/htslib/htslib copying build/lib.linux-x86_64-3.9/pysam/include/htslib/htslib/ksort.h -> /builddir/build/BUILDROOT/python-pysam-0.16.0.1-1.fc34.x86_64/usr/lib64/python3.9/site-packages/pysam/include/htslib/htslib copying build/lib.linux-x86_64-3.9/pysam/include/htslib/htslib/thread_pool.h -> /builddir/build/BUILDROOT/python-pysam-0.16.0.1-1.fc34.x86_64/usr/lib64/python3.9/site-packages/pysam/include/htslib/htslib copying build/lib.linux-x86_64-3.9/pysam/include/htslib/htslib/sam.h -> /builddir/build/BUILDROOT/python-pysam-0.16.0.1-1.fc34.x86_64/usr/lib64/python3.9/site-packages/pysam/include/htslib/htslib copying build/lib.linux-x86_64-3.9/pysam/include/htslib/htslib/khash.h -> /builddir/build/BUILDROOT/python-pysam-0.16.0.1-1.fc34.x86_64/usr/lib64/python3.9/site-packages/pysam/include/htslib/htslib copying build/lib.linux-x86_64-3.9/pysam/include/htslib/htslib/klist.h -> /builddir/build/BUILDROOT/python-pysam-0.16.0.1-1.fc34.x86_64/usr/lib64/python3.9/site-packages/pysam/include/htslib/htslib copying build/lib.linux-x86_64-3.9/pysam/include/htslib/htslib/knetfile.h -> /builddir/build/BUILDROOT/python-pysam-0.16.0.1-1.fc34.x86_64/usr/lib64/python3.9/site-packages/pysam/include/htslib/htslib copying build/lib.linux-x86_64-3.9/pysam/include/htslib/htslib/kstring.h -> /builddir/build/BUILDROOT/python-pysam-0.16.0.1-1.fc34.x86_64/usr/lib64/python3.9/site-packages/pysam/include/htslib/htslib copying build/lib.linux-x86_64-3.9/pysam/include/htslib/htslib/kseq.h -> /builddir/build/BUILDROOT/python-pysam-0.16.0.1-1.fc34.x86_64/usr/lib64/python3.9/site-packages/pysam/include/htslib/htslib copying build/lib.linux-x86_64-3.9/pysam/include/htslib/htslib/hts_defs.h -> /builddir/build/BUILDROOT/python-pysam-0.16.0.1-1.fc34.x86_64/usr/lib64/python3.9/site-packages/pysam/include/htslib/htslib copying build/lib.linux-x86_64-3.9/pysam/include/htslib/htslib/regidx.h -> /builddir/build/BUILDROOT/python-pysam-0.16.0.1-1.fc34.x86_64/usr/lib64/python3.9/site-packages/pysam/include/htslib/htslib copying build/lib.linux-x86_64-3.9/pysam/include/htslib/htslib/hts_log.h -> /builddir/build/BUILDROOT/python-pysam-0.16.0.1-1.fc34.x86_64/usr/lib64/python3.9/site-packages/pysam/include/htslib/htslib copying build/lib.linux-x86_64-3.9/pysam/include/htslib/htslib/tbx.h -> /builddir/build/BUILDROOT/python-pysam-0.16.0.1-1.fc34.x86_64/usr/lib64/python3.9/site-packages/pysam/include/htslib/htslib copying build/lib.linux-x86_64-3.9/pysam/include/htslib/htslib/kbitset.h -> /builddir/build/BUILDROOT/python-pysam-0.16.0.1-1.fc34.x86_64/usr/lib64/python3.9/site-packages/pysam/include/htslib/htslib copying build/lib.linux-x86_64-3.9/pysam/include/htslib/htslib/khash_str2int.h -> /builddir/build/BUILDROOT/python-pysam-0.16.0.1-1.fc34.x86_64/usr/lib64/python3.9/site-packages/pysam/include/htslib/htslib copying build/lib.linux-x86_64-3.9/pysam/include/htslib/htslib/hts_os.h -> /builddir/build/BUILDROOT/python-pysam-0.16.0.1-1.fc34.x86_64/usr/lib64/python3.9/site-packages/pysam/include/htslib/htslib copying build/lib.linux-x86_64-3.9/pysam/include/htslib/htslib/vcfutils.h -> /builddir/build/BUILDROOT/python-pysam-0.16.0.1-1.fc34.x86_64/usr/lib64/python3.9/site-packages/pysam/include/htslib/htslib copying build/lib.linux-x86_64-3.9/pysam/include/htslib/htslib/hts_endian.h -> /builddir/build/BUILDROOT/python-pysam-0.16.0.1-1.fc34.x86_64/usr/lib64/python3.9/site-packages/pysam/include/htslib/htslib copying build/lib.linux-x86_64-3.9/pysam/include/htslib/htslib/bgzf.h -> /builddir/build/BUILDROOT/python-pysam-0.16.0.1-1.fc34.x86_64/usr/lib64/python3.9/site-packages/pysam/include/htslib/htslib copying build/lib.linux-x86_64-3.9/pysam/include/htslib/htslib/cram.h -> /builddir/build/BUILDROOT/python-pysam-0.16.0.1-1.fc34.x86_64/usr/lib64/python3.9/site-packages/pysam/include/htslib/htslib copying build/lib.linux-x86_64-3.9/pysam/include/htslib/htslib/vcf.h -> /builddir/build/BUILDROOT/python-pysam-0.16.0.1-1.fc34.x86_64/usr/lib64/python3.9/site-packages/pysam/include/htslib/htslib copying build/lib.linux-x86_64-3.9/pysam/include/htslib/hts_internal.h -> /builddir/build/BUILDROOT/python-pysam-0.16.0.1-1.fc34.x86_64/usr/lib64/python3.9/site-packages/pysam/include/htslib copying build/lib.linux-x86_64-3.9/pysam/include/htslib/thread_pool_internal.h -> /builddir/build/BUILDROOT/python-pysam-0.16.0.1-1.fc34.x86_64/usr/lib64/python3.9/site-packages/pysam/include/htslib copying build/lib.linux-x86_64-3.9/pysam/include/htslib/hfile_internal.h -> /builddir/build/BUILDROOT/python-pysam-0.16.0.1-1.fc34.x86_64/usr/lib64/python3.9/site-packages/pysam/include/htslib copying build/lib.linux-x86_64-3.9/pysam/include/htslib/header.h -> /builddir/build/BUILDROOT/python-pysam-0.16.0.1-1.fc34.x86_64/usr/lib64/python3.9/site-packages/pysam/include/htslib copying build/lib.linux-x86_64-3.9/pysam/include/htslib/sam_internal.h -> /builddir/build/BUILDROOT/python-pysam-0.16.0.1-1.fc34.x86_64/usr/lib64/python3.9/site-packages/pysam/include/htslib copying build/lib.linux-x86_64-3.9/pysam/include/htslib/bcf_sr_sort.h -> /builddir/build/BUILDROOT/python-pysam-0.16.0.1-1.fc34.x86_64/usr/lib64/python3.9/site-packages/pysam/include/htslib copying build/lib.linux-x86_64-3.9/pysam/include/htslib/textutils_internal.h -> /builddir/build/BUILDROOT/python-pysam-0.16.0.1-1.fc34.x86_64/usr/lib64/python3.9/site-packages/pysam/include/htslib copying build/lib.linux-x86_64-3.9/pysam/include/htslib/config.h -> /builddir/build/BUILDROOT/python-pysam-0.16.0.1-1.fc34.x86_64/usr/lib64/python3.9/site-packages/pysam/include/htslib creating /builddir/build/BUILDROOT/python-pysam-0.16.0.1-1.fc34.x86_64/usr/lib64/python3.9/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-3.9/pysam/include/bcftools/bcftools.h -> /builddir/build/BUILDROOT/python-pysam-0.16.0.1-1.fc34.x86_64/usr/lib64/python3.9/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-3.9/pysam/include/bcftools/hclust.h -> /builddir/build/BUILDROOT/python-pysam-0.16.0.1-1.fc34.x86_64/usr/lib64/python3.9/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-3.9/pysam/include/bcftools/bcftools.pysam.h -> /builddir/build/BUILDROOT/python-pysam-0.16.0.1-1.fc34.x86_64/usr/lib64/python3.9/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-3.9/pysam/include/bcftools/convert.h -> /builddir/build/BUILDROOT/python-pysam-0.16.0.1-1.fc34.x86_64/usr/lib64/python3.9/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-3.9/pysam/include/bcftools/bam_sample.h -> /builddir/build/BUILDROOT/python-pysam-0.16.0.1-1.fc34.x86_64/usr/lib64/python3.9/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-3.9/pysam/include/bcftools/tsv2vcf.h -> /builddir/build/BUILDROOT/python-pysam-0.16.0.1-1.fc34.x86_64/usr/lib64/python3.9/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-3.9/pysam/include/bcftools/HMM.h -> /builddir/build/BUILDROOT/python-pysam-0.16.0.1-1.fc34.x86_64/usr/lib64/python3.9/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-3.9/pysam/include/bcftools/regidx.h -> /builddir/build/BUILDROOT/python-pysam-0.16.0.1-1.fc34.x86_64/usr/lib64/python3.9/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-3.9/pysam/include/bcftools/vcmp.h -> /builddir/build/BUILDROOT/python-pysam-0.16.0.1-1.fc34.x86_64/usr/lib64/python3.9/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-3.9/pysam/include/bcftools/call.h -> /builddir/build/BUILDROOT/python-pysam-0.16.0.1-1.fc34.x86_64/usr/lib64/python3.9/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-3.9/pysam/include/bcftools/mw.h -> /builddir/build/BUILDROOT/python-pysam-0.16.0.1-1.fc34.x86_64/usr/lib64/python3.9/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-3.9/pysam/include/bcftools/prob1.h -> /builddir/build/BUILDROOT/python-pysam-0.16.0.1-1.fc34.x86_64/usr/lib64/python3.9/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-3.9/pysam/include/bcftools/vcfbuf.h -> /builddir/build/BUILDROOT/python-pysam-0.16.0.1-1.fc34.x86_64/usr/lib64/python3.9/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-3.9/pysam/include/bcftools/filter.h -> /builddir/build/BUILDROOT/python-pysam-0.16.0.1-1.fc34.x86_64/usr/lib64/python3.9/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-3.9/pysam/include/bcftools/cols.h -> /builddir/build/BUILDROOT/python-pysam-0.16.0.1-1.fc34.x86_64/usr/lib64/python3.9/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-3.9/pysam/include/bcftools/smpl_ilist.h -> /builddir/build/BUILDROOT/python-pysam-0.16.0.1-1.fc34.x86_64/usr/lib64/python3.9/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-3.9/pysam/include/bcftools/hex.h -> /builddir/build/BUILDROOT/python-pysam-0.16.0.1-1.fc34.x86_64/usr/lib64/python3.9/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-3.9/pysam/include/bcftools/gvcf.h -> /builddir/build/BUILDROOT/python-pysam-0.16.0.1-1.fc34.x86_64/usr/lib64/python3.9/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-3.9/pysam/include/bcftools/kmin.h -> /builddir/build/BUILDROOT/python-pysam-0.16.0.1-1.fc34.x86_64/usr/lib64/python3.9/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-3.9/pysam/include/bcftools/kheap.h -> /builddir/build/BUILDROOT/python-pysam-0.16.0.1-1.fc34.x86_64/usr/lib64/python3.9/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-3.9/pysam/include/bcftools/bin.h -> /builddir/build/BUILDROOT/python-pysam-0.16.0.1-1.fc34.x86_64/usr/lib64/python3.9/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-3.9/pysam/include/bcftools/khash_str2str.h -> /builddir/build/BUILDROOT/python-pysam-0.16.0.1-1.fc34.x86_64/usr/lib64/python3.9/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-3.9/pysam/include/bcftools/rbuf.h -> /builddir/build/BUILDROOT/python-pysam-0.16.0.1-1.fc34.x86_64/usr/lib64/python3.9/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-3.9/pysam/include/bcftools/ploidy.h -> /builddir/build/BUILDROOT/python-pysam-0.16.0.1-1.fc34.x86_64/usr/lib64/python3.9/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-3.9/pysam/include/bcftools/bam2bcf.h -> /builddir/build/BUILDROOT/python-pysam-0.16.0.1-1.fc34.x86_64/usr/lib64/python3.9/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-3.9/pysam/include/bcftools/variantkey.h -> /builddir/build/BUILDROOT/python-pysam-0.16.0.1-1.fc34.x86_64/usr/lib64/python3.9/site-packages/pysam/include/bcftools copying build/lib.linux-x86_64-3.9/pysam/include/bcftools/config.h -> /builddir/build/BUILDROOT/python-pysam-0.16.0.1-1.fc34.x86_64/usr/lib64/python3.9/site-packages/pysam/include/bcftools creating /builddir/build/BUILDROOT/python-pysam-0.16.0.1-1.fc34.x86_64/usr/lib64/python3.9/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-3.9/pysam/include/samtools/bam.h -> /builddir/build/BUILDROOT/python-pysam-0.16.0.1-1.fc34.x86_64/usr/lib64/python3.9/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-3.9/pysam/include/samtools/bedidx.h -> /builddir/build/BUILDROOT/python-pysam-0.16.0.1-1.fc34.x86_64/usr/lib64/python3.9/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-3.9/pysam/include/samtools/sam.h -> /builddir/build/BUILDROOT/python-pysam-0.16.0.1-1.fc34.x86_64/usr/lib64/python3.9/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-3.9/pysam/include/samtools/samtools.h -> /builddir/build/BUILDROOT/python-pysam-0.16.0.1-1.fc34.x86_64/usr/lib64/python3.9/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-3.9/pysam/include/samtools/bam_endian.h -> /builddir/build/BUILDROOT/python-pysam-0.16.0.1-1.fc34.x86_64/usr/lib64/python3.9/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-3.9/pysam/include/samtools/sample.h -> /builddir/build/BUILDROOT/python-pysam-0.16.0.1-1.fc34.x86_64/usr/lib64/python3.9/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-3.9/pysam/include/samtools/samtools.pysam.h -> /builddir/build/BUILDROOT/python-pysam-0.16.0.1-1.fc34.x86_64/usr/lib64/python3.9/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-3.9/pysam/include/samtools/stats_isize.h -> /builddir/build/BUILDROOT/python-pysam-0.16.0.1-1.fc34.x86_64/usr/lib64/python3.9/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-3.9/pysam/include/samtools/sam_opts.h -> /builddir/build/BUILDROOT/python-pysam-0.16.0.1-1.fc34.x86_64/usr/lib64/python3.9/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-3.9/pysam/include/samtools/tmp_file.h -> /builddir/build/BUILDROOT/python-pysam-0.16.0.1-1.fc34.x86_64/usr/lib64/python3.9/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-3.9/pysam/include/samtools/bam_lpileup.h -> /builddir/build/BUILDROOT/python-pysam-0.16.0.1-1.fc34.x86_64/usr/lib64/python3.9/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-3.9/pysam/include/samtools/bam2bcf.h -> /builddir/build/BUILDROOT/python-pysam-0.16.0.1-1.fc34.x86_64/usr/lib64/python3.9/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-3.9/pysam/include/samtools/bam_plbuf.h -> /builddir/build/BUILDROOT/python-pysam-0.16.0.1-1.fc34.x86_64/usr/lib64/python3.9/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-3.9/pysam/include/samtools/config.h -> /builddir/build/BUILDROOT/python-pysam-0.16.0.1-1.fc34.x86_64/usr/lib64/python3.9/site-packages/pysam/include/samtools copying build/lib.linux-x86_64-3.9/pysam/include/__init__.py -> /builddir/build/BUILDROOT/python-pysam-0.16.0.1-1.fc34.x86_64/usr/lib64/python3.9/site-packages/pysam/include copying build/lib.linux-x86_64-3.9/pysam/samtools.py -> /builddir/build/BUILDROOT/python-pysam-0.16.0.1-1.fc34.x86_64/usr/lib64/python3.9/site-packages/pysam copying build/lib.linux-x86_64-3.9/pysam/utils.py -> /builddir/build/BUILDROOT/python-pysam-0.16.0.1-1.fc34.x86_64/usr/lib64/python3.9/site-packages/pysam copying build/lib.linux-x86_64-3.9/pysam/config.py -> /builddir/build/BUILDROOT/python-pysam-0.16.0.1-1.fc34.x86_64/usr/lib64/python3.9/site-packages/pysam copying build/lib.linux-x86_64-3.9/pysam/version.py -> /builddir/build/BUILDROOT/python-pysam-0.16.0.1-1.fc34.x86_64/usr/lib64/python3.9/site-packages/pysam copying build/lib.linux-x86_64-3.9/pysam/__init__.py -> /builddir/build/BUILDROOT/python-pysam-0.16.0.1-1.fc34.x86_64/usr/lib64/python3.9/site-packages/pysam copying build/lib.linux-x86_64-3.9/pysam/Pileup.py -> /builddir/build/BUILDROOT/python-pysam-0.16.0.1-1.fc34.x86_64/usr/lib64/python3.9/site-packages/pysam copying build/lib.linux-x86_64-3.9/pysam/bcftools.py -> /builddir/build/BUILDROOT/python-pysam-0.16.0.1-1.fc34.x86_64/usr/lib64/python3.9/site-packages/pysam byte-compiling /builddir/build/BUILDROOT/python-pysam-0.16.0.1-1.fc34.x86_64/usr/lib64/python3.9/site-packages/pysam/include/__init__.py to __init__.cpython-39.pyc byte-compiling /builddir/build/BUILDROOT/python-pysam-0.16.0.1-1.fc34.x86_64/usr/lib64/python3.9/site-packages/pysam/bcftools.py to bcftools.cpython-39.pyc writing byte-compilation script '/tmp/tmpow7yjkga.py' /usr/bin/python3 /tmp/tmpow7yjkga.py removing /tmp/tmpow7yjkga.py running install_egg_info 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' package init file 'samtools/__init__.py' not found (or not a regular file) package init file 'bcftools/__init__.py' not found (or not a regular file) package init file 'htslib/__init__.py' not found (or not a regular file) package init file 'htslib/htslib/__init__.py' not found (or not a regular file) 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/' warning: no files found matching 'samtools/configure' warning: no files found matching 'samtools/config.mk.in' warning: no files found matching 'samtools/config.h.in' warning: no files found matching 'htslib/INSTALL' warning: no files found matching 'htslib/NEWS' writing manifest file 'pysam.egg-info/SOURCES.txt' Copying pysam.egg-info to /builddir/build/BUILDROOT/python-pysam-0.16.0.1-1.fc34.x86_64/usr/lib64/python3.9/site-packages/pysam-0.16.0.1-py3.9.egg-info running install_scripts + rm -rfv /builddir/build/BUILDROOT/python-pysam-0.16.0.1-1.fc34.x86_64/usr/bin/__pycache__ + /usr/lib/rpm/find-debuginfo.sh -j2 --strict-build-id -m -i --build-id-seed 0.16.0.1-1.fc34 --unique-debug-suffix -0.16.0.1-1.fc34.x86_64 --unique-debug-src-base python-pysam-0.16.0.1-1.fc34.x86_64 --run-dwz --dwz-low-mem-die-limit 10000000 --dwz-max-die-limit 110000000 -S debugsourcefiles.list /builddir/build/BUILD/pysam-0.16.0.1 explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/python-pysam-0.16.0.1-1.fc34.x86_64/usr/lib64/python3.9/site-packages/pysam/libcalignmentfile.cpython-39-x86_64-linux-gnu.so explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/python-pysam-0.16.0.1-1.fc34.x86_64/usr/lib64/python3.9/site-packages/pysam/libcalignedsegment.cpython-39-x86_64-linux-gnu.so extracting debug info from /builddir/build/BUILDROOT/python-pysam-0.16.0.1-1.fc34.x86_64/usr/lib64/python3.9/site-packages/pysam/libcalignedsegment.cpython-39-x86_64-linux-gnu.so extracting debug info from /builddir/build/BUILDROOT/python-pysam-0.16.0.1-1.fc34.x86_64/usr/lib64/python3.9/site-packages/pysam/libcalignmentfile.cpython-39-x86_64-linux-gnu.so explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/python-pysam-0.16.0.1-1.fc34.x86_64/usr/lib64/python3.9/site-packages/pysam/libcbcf.cpython-39-x86_64-linux-gnu.so extracting debug info from /builddir/build/BUILDROOT/python-pysam-0.16.0.1-1.fc34.x86_64/usr/lib64/python3.9/site-packages/pysam/libcbcf.cpython-39-x86_64-linux-gnu.so explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/python-pysam-0.16.0.1-1.fc34.x86_64/usr/lib64/python3.9/site-packages/pysam/libcbcftools.cpython-39-x86_64-linux-gnu.so extracting debug info from /builddir/build/BUILDROOT/python-pysam-0.16.0.1-1.fc34.x86_64/usr/lib64/python3.9/site-packages/pysam/libcbcftools.cpython-39-x86_64-linux-gnu.so explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/python-pysam-0.16.0.1-1.fc34.x86_64/usr/lib64/python3.9/site-packages/pysam/libcbgzf.cpython-39-x86_64-linux-gnu.so explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/python-pysam-0.16.0.1-1.fc34.x86_64/usr/lib64/python3.9/site-packages/pysam/libcfaidx.cpython-39-x86_64-linux-gnu.so extracting debug info from /builddir/build/BUILDROOT/python-pysam-0.16.0.1-1.fc34.x86_64/usr/lib64/python3.9/site-packages/pysam/libcbgzf.cpython-39-x86_64-linux-gnu.so extracting debug info from /builddir/build/BUILDROOT/python-pysam-0.16.0.1-1.fc34.x86_64/usr/lib64/python3.9/site-packages/pysam/libcfaidx.cpython-39-x86_64-linux-gnu.so explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/python-pysam-0.16.0.1-1.fc34.x86_64/usr/lib64/python3.9/site-packages/pysam/libchtslib.cpython-39-x86_64-linux-gnu.so extracting debug info from /builddir/build/BUILDROOT/python-pysam-0.16.0.1-1.fc34.x86_64/usr/lib64/python3.9/site-packages/pysam/libchtslib.cpython-39-x86_64-linux-gnu.so explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/python-pysam-0.16.0.1-1.fc34.x86_64/usr/lib64/python3.9/site-packages/pysam/libcsamfile.cpython-39-x86_64-linux-gnu.so extracting debug info from /builddir/build/BUILDROOT/python-pysam-0.16.0.1-1.fc34.x86_64/usr/lib64/python3.9/site-packages/pysam/libcsamfile.cpython-39-x86_64-linux-gnu.so explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/python-pysam-0.16.0.1-1.fc34.x86_64/usr/lib64/python3.9/site-packages/pysam/libcsamtools.cpython-39-x86_64-linux-gnu.so extracting debug info from /builddir/build/BUILDROOT/python-pysam-0.16.0.1-1.fc34.x86_64/usr/lib64/python3.9/site-packages/pysam/libcsamtools.cpython-39-x86_64-linux-gnu.so explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/python-pysam-0.16.0.1-1.fc34.x86_64/usr/lib64/python3.9/site-packages/pysam/libctabix.cpython-39-x86_64-linux-gnu.so extracting debug info from /builddir/build/BUILDROOT/python-pysam-0.16.0.1-1.fc34.x86_64/usr/lib64/python3.9/site-packages/pysam/libctabix.cpython-39-x86_64-linux-gnu.so explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/python-pysam-0.16.0.1-1.fc34.x86_64/usr/lib64/python3.9/site-packages/pysam/libctabixproxies.cpython-39-x86_64-linux-gnu.so extracting debug info from /builddir/build/BUILDROOT/python-pysam-0.16.0.1-1.fc34.x86_64/usr/lib64/python3.9/site-packages/pysam/libctabixproxies.cpython-39-x86_64-linux-gnu.so explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/python-pysam-0.16.0.1-1.fc34.x86_64/usr/lib64/python3.9/site-packages/pysam/libcutils.cpython-39-x86_64-linux-gnu.so extracting debug info from /builddir/build/BUILDROOT/python-pysam-0.16.0.1-1.fc34.x86_64/usr/lib64/python3.9/site-packages/pysam/libcutils.cpython-39-x86_64-linux-gnu.so explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/python-pysam-0.16.0.1-1.fc34.x86_64/usr/lib64/python3.9/site-packages/pysam/libcvcf.cpython-39-x86_64-linux-gnu.so extracting debug info from /builddir/build/BUILDROOT/python-pysam-0.16.0.1-1.fc34.x86_64/usr/lib64/python3.9/site-packages/pysam/libcvcf.cpython-39-x86_64-linux-gnu.so original debug info size: 22068kB, size after compression: 20920kB /usr/lib/rpm/sepdebugcrcfix: Updated 13 CRC32s, 0 CRC32s did match. 39141 blocks + /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/redhat/brp-python-bytecompile '' 1 0 Bytecompiling .py files below /builddir/build/BUILDROOT/python-pysam-0.16.0.1-1.fc34.x86_64/usr/lib/debug/usr/lib64/python3.9 using /usr/bin/python3.9 Bytecompiling .py files below /builddir/build/BUILDROOT/python-pysam-0.16.0.1-1.fc34.x86_64/usr/lib64/python3.9 using /usr/bin/python3.9 + /usr/lib/rpm/brp-python-hardlink + /usr/lib/rpm/redhat/brp-mangle-shebangs Processing files: python3-pysam-0.16.0.1-1.fc34.x86_64 Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.vy7nBu + umask 022 + cd /builddir/build/BUILD + cd pysam-0.16.0.1 + DOCDIR=/builddir/build/BUILDROOT/python-pysam-0.16.0.1-1.fc34.x86_64/usr/share/doc/python3-pysam + export LC_ALL=C + LC_ALL=C + export DOCDIR + /usr/bin/mkdir -p /builddir/build/BUILDROOT/python-pysam-0.16.0.1-1.fc34.x86_64/usr/share/doc/python3-pysam + cp -pr README.rst /builddir/build/BUILDROOT/python-pysam-0.16.0.1-1.fc34.x86_64/usr/share/doc/python3-pysam + RPM_EC=0 ++ jobs -p + exit 0 Executing(%license): /bin/sh -e /var/tmp/rpm-tmp.w9CyKN + umask 022 + cd /builddir/build/BUILD + cd pysam-0.16.0.1 + LICENSEDIR=/builddir/build/BUILDROOT/python-pysam-0.16.0.1-1.fc34.x86_64/usr/share/licenses/python3-pysam + export LC_ALL=C + LC_ALL=C + export LICENSEDIR + /usr/bin/mkdir -p /builddir/build/BUILDROOT/python-pysam-0.16.0.1-1.fc34.x86_64/usr/share/licenses/python3-pysam + cp -pr COPYING /builddir/build/BUILDROOT/python-pysam-0.16.0.1-1.fc34.x86_64/usr/share/licenses/python3-pysam + RPM_EC=0 ++ jobs -p + exit 0 Provides: bundled(bcftools) = 1.9 bundled(htslib) = 1.9 bundled(samtools) = 1.9 libcalignedsegment.cpython-39-x86_64-linux-gnu.so()(64bit) libcalignmentfile.cpython-39-x86_64-linux-gnu.so()(64bit) libcbcf.cpython-39-x86_64-linux-gnu.so()(64bit) libcbcftools.cpython-39-x86_64-linux-gnu.so()(64bit) libcbgzf.cpython-39-x86_64-linux-gnu.so()(64bit) libcfaidx.cpython-39-x86_64-linux-gnu.so()(64bit) libchtslib.cpython-39-x86_64-linux-gnu.so()(64bit) libcsamfile.cpython-39-x86_64-linux-gnu.so()(64bit) libcsamtools.cpython-39-x86_64-linux-gnu.so()(64bit) libctabix.cpython-39-x86_64-linux-gnu.so()(64bit) libctabixproxies.cpython-39-x86_64-linux-gnu.so()(64bit) libcutils.cpython-39-x86_64-linux-gnu.so()(64bit) libcvcf.cpython-39-x86_64-linux-gnu.so()(64bit) python-pysam = 0.16.0.1-1.fc34 python3-pysam = 0.16.0.1-1.fc34 python3-pysam(x86-64) = 0.16.0.1-1.fc34 python3.9-pysam = 0.16.0.1-1.fc34 python3.9dist(pysam) = 0.16.0.1 python3dist(pysam) = 0.16.0.1 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: libbz2.so.1()(64bit) libc.so.6()(64bit) libc.so.6(GLIBC_2.14)(64bit) libc.so.6(GLIBC_2.15)(64bit) libc.so.6(GLIBC_2.2.5)(64bit) libc.so.6(GLIBC_2.3)(64bit) libc.so.6(GLIBC_2.3.2)(64bit) libc.so.6(GLIBC_2.3.4)(64bit) libc.so.6(GLIBC_2.33)(64bit) libc.so.6(GLIBC_2.4)(64bit) libc.so.6(GLIBC_2.7)(64bit) libcbcftools.cpython-39-x86_64-linux-gnu.so()(64bit) libchtslib.cpython-39-x86_64-linux-gnu.so()(64bit) libcsamtools.cpython-39-x86_64-linux-gnu.so()(64bit) liblzma.so.5()(64bit) liblzma.so.5(XZ_5.0)(64bit) libm.so.6()(64bit) libm.so.6(GLIBC_2.2.5)(64bit) libm.so.6(GLIBC_2.23)(64bit) libm.so.6(GLIBC_2.29)(64bit) libpthread.so.0()(64bit) libpthread.so.0(GLIBC_2.2.5)(64bit) libpthread.so.0(GLIBC_2.3.2)(64bit) libz.so.1()(64bit) python(abi) = 3.9 rtld(GNU_HASH) Obsoletes: python-pysam < 0.16.0.1-1.fc34 Processing files: python3-pysam-devel-0.16.0.1-1.fc34.x86_64 Provides: python-pysam-devel = 0.16.0.1-1.fc34 python3-pysam-devel = 0.16.0.1-1.fc34 python3-pysam-devel(x86-64) = 0.16.0.1-1.fc34 python3.9-pysam-devel = 0.16.0.1-1.fc34 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: python(abi) = 3.9 Processing files: python-pysam-doc-0.16.0.1-1.fc34.noarch Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.RdbyGg + umask 022 + cd /builddir/build/BUILD + cd pysam-0.16.0.1 + DOCDIR=/builddir/build/BUILDROOT/python-pysam-0.16.0.1-1.fc34.x86_64/usr/share/doc/python-pysam-doc + export LC_ALL=C + LC_ALL=C + export DOCDIR + /usr/bin/mkdir -p /builddir/build/BUILDROOT/python-pysam-0.16.0.1-1.fc34.x86_64/usr/share/doc/python-pysam-doc + cp -pr html /builddir/build/BUILDROOT/python-pysam-0.16.0.1-1.fc34.x86_64/usr/share/doc/python-pysam-doc + RPM_EC=0 ++ jobs -p + exit 0 Provides: python-pysam-doc = 0.16.0.1-1.fc34 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Processing files: python-pysam-debugsource-0.16.0.1-1.fc34.x86_64 Provides: python-pysam-debugsource = 0.16.0.1-1.fc34 python-pysam-debugsource(x86-64) = 0.16.0.1-1.fc34 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Processing files: python3-pysam-debuginfo-0.16.0.1-1.fc34.x86_64 Provides: debuginfo(build-id) = 0b3054278829bcb1129075eeac78788270c2c572 debuginfo(build-id) = 11d70185e93e2da619461b72a181e024f764bd41 debuginfo(build-id) = 131e9df93d2a96ada5a07a6b46507de9b224afce debuginfo(build-id) = 1af590e3dcfa489d7b0e3c6b5599dc8b5f9d183a debuginfo(build-id) = 2d49bc4e56d2cedcae44345a2974178720bdeb29 debuginfo(build-id) = 3d29187a6499e47407681f9ab559eeade41536f2 debuginfo(build-id) = 3f516c114e18e8171345a4f493b98c196c984a73 debuginfo(build-id) = 50a23f0c8c938b6b265f872528fdaeae7ea6d7eb debuginfo(build-id) = 77a271f73538b3093b1719ff231c8c5599fb7122 debuginfo(build-id) = 96b275cc8e999723c7193c0b4ccf9df3d397f5cd debuginfo(build-id) = af36d760143b330528d6557a04d960a72f603b77 debuginfo(build-id) = d27036e3ff7dc41a287d50d330fc5b206911ded7 debuginfo(build-id) = df48be0d7653403c29e36a2539d3bdd5dba8b798 python-pysam-debuginfo = 0.16.0.1-1.fc34 python3-pysam-debuginfo = 0.16.0.1-1.fc34 python3-pysam-debuginfo(x86-64) = 0.16.0.1-1.fc34 python3.9-pysam-debuginfo = 0.16.0.1-1.fc34 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Recommends: python-pysam-debugsource(x86-64) = 0.16.0.1-1.fc34 Checking for unpackaged file(s): /usr/lib/rpm/check-files /builddir/build/BUILDROOT/python-pysam-0.16.0.1-1.fc34.x86_64 Wrote: /builddir/build/RPMS/python3-pysam-debuginfo-0.16.0.1-1.fc34.x86_64.rpm Wrote: /builddir/build/RPMS/python3-pysam-0.16.0.1-1.fc34.x86_64.rpm Wrote: /builddir/build/RPMS/python-pysam-doc-0.16.0.1-1.fc34.noarch.rpm Wrote: /builddir/build/RPMS/python-pysam-debugsource-0.16.0.1-1.fc34.x86_64.rpm Wrote: /builddir/build/RPMS/python3-pysam-devel-0.16.0.1-1.fc34.x86_64.rpm Executing(%clean): /bin/sh -e /var/tmp/rpm-tmp.kWdcJa + umask 022 + cd /builddir/build/BUILD + cd pysam-0.16.0.1 + /usr/bin/rm -rf /builddir/build/BUILDROOT/python-pysam-0.16.0.1-1.fc34.x86_64 + RPM_EC=0 ++ jobs -p + exit 0 Child return code was: 0