Mock Version: 3.0 Mock Version: 3.0 Mock Version: 3.0 ENTER ['do_with_status'](['bash', '--login', '-c', '/usr/bin/rpmbuild -bs --target i686 --nodeps /builddir/build/SPECS/python-pysam.spec'], chrootPath='/var/lib/mock/f37-build-36322311-4670399/root'env={'TERM': 'vt100', 'SHELL': '/bin/bash', 'HOME': '/builddir', 'HOSTNAME': 'mock', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'PROMPT_COMMAND': 'printf "\\033]0;\\007"', 'PS1': ' \\s-\\v\\$ ', 'LANG': 'C.UTF-8'}shell=Falselogger=timeout=201600uid=1000gid=425user='mockbuild'nspawn_args=[]unshare_net=TrueprintOutput=False) Executing command: ['bash', '--login', '-c', '/usr/bin/rpmbuild -bs --target i686 --nodeps /builddir/build/SPECS/python-pysam.spec'] with env {'TERM': 'vt100', 'SHELL': '/bin/bash', 'HOME': '/builddir', 'HOSTNAME': 'mock', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'PROMPT_COMMAND': 'printf "\\033]0;\\007"', 'PS1': ' \\s-\\v\\$ ', 'LANG': 'C.UTF-8'} and shell False Building target platforms: i686 Building for target i686 setting SOURCE_DATE_EPOCH=1655856000 Wrote: /builddir/build/SRPMS/python-pysam-0.19.0-4.fc37.src.rpm Child return code was: 0 ENTER ['do_with_status'](['bash', '--login', '-c', '/usr/bin/rpmbuild -bb --target i686 --nodeps /builddir/build/SPECS/python-pysam.spec'], chrootPath='/var/lib/mock/f37-build-36322311-4670399/root'env={'TERM': 'vt100', 'SHELL': '/bin/bash', 'HOME': '/builddir', 'HOSTNAME': 'mock', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'PROMPT_COMMAND': 'printf "\\033]0;\\007"', 'PS1': ' \\s-\\v\\$ ', 'LANG': 'C.UTF-8'}shell=Falselogger=timeout=201600uid=1000gid=425user='mockbuild'nspawn_args=[]unshare_net=TrueprintOutput=False) Executing command: ['bash', '--login', '-c', '/usr/bin/rpmbuild -bb --target i686 --nodeps /builddir/build/SPECS/python-pysam.spec'] with env {'TERM': 'vt100', 'SHELL': '/bin/bash', 'HOME': '/builddir', 'HOSTNAME': 'mock', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'PROMPT_COMMAND': 'printf "\\033]0;\\007"', 'PS1': ' \\s-\\v\\$ ', 'LANG': 'C.UTF-8'} and shell False Building target platforms: i686 Building for target i686 setting SOURCE_DATE_EPOCH=1655856000 Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.i9OLcz + umask 022 + cd /builddir/build/BUILD + cd /builddir/build/BUILD + rm -rf pysam-0.19.0 + /usr/lib/rpm/rpmuncompress -x /builddir/build/SOURCES/pysam-0.19.0.tar.gz + STATUS=0 + '[' 0 -ne 0 ']' + cd pysam-0.19.0 + /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w . + /usr/lib/rpm/rpmuncompress /builddir/build/SOURCES/b2194969ba42cbec0ebc4960bf1a64c96b19acad.patch + /usr/bin/patch -p1 -s --fuzz=0 --no-backup-if-mismatch -f + rm -rf pysam.egg-info ++ grep -rl '/\* Generated by Cython' + rm pysam/libcalignedsegment.c pysam/libcalignmentfile.c pysam/libcbcf.c pysam/libcbcftools.c pysam/libcbgzf.c pysam/libcfaidx.c pysam/libchtslib.c pysam/libcsamfile.c pysam/libcsamtools.c pysam/libctabix.c pysam/libctabixproxies.c pysam/libcutils.c pysam/libcvcf.c + RPM_EC=0 ++ jobs -p + exit 0 Executing(%build): /bin/sh -e /var/tmp/rpm-tmp.7bmY8G + umask 022 + cd /builddir/build/BUILD + 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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection' + export CFLAGS + CXXFLAGS='-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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection' + export CXXFLAGS + FFLAGS='-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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib/gfortran/modules' + export FFLAGS + FCFLAGS='-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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib/gfortran/modules' + export FCFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -Wl,-dT,/builddir/build/BUILD/pysam-0.19.0/.package_note-python-pysam-0.19.0-4.fc37.i386.ld' + export LDFLAGS + LT_SYS_LIBRARY_PATH=/usr/lib: + export LT_SYS_LIBRARY_PATH + CC=gcc + export CC + CXX=g++ + export CXX + '[' -f /usr/lib/rpm/generate-rpm-note.sh ']' + /usr/lib/rpm/generate-rpm-note.sh python-pysam 0.19.0-4.fc37 i386 + cd pysam-0.19.0 + FORCE_CYTHON=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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -Wl,-dT,/builddir/build/BUILD/pysam-0.19.0/.package_note-python-pysam-0.19.0-4.fc37.i386.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: (env) CC=gcc # 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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -Wl,-dT,/builddir/build/BUILD/pysam-0.19.0/.package_note-python-pysam-0.19.0-4.fc37.i386.ld checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking for ranlib... ranlib checking for grep that handles long lines and -e... /usr/bin/grep checking for C compiler warning flags... -Wall checking 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... 64 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 -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 for srand48_deterministic... no checking whether fdatasync is declared... yes checking for fdatasync... yes checking for library containing log... -lm checking for zlib.h... yes checking for inflate in -lz... yes checking for library containing recv... none required checking for bzlib.h... yes checking for BZ2_bzBuffToBuffCompress in -lbz2... yes checking for lzma.h... yes checking for lzma_easy_buffer_encode in -llzma... yes checking whether htscodecs files are present... yes checking for libdeflate.h... no checking for libdeflate_deflate_compress in -ldeflate... no checking for curl/curl.h... no checking for curl_easy_pause in -lcurl... no checking for curl_easy_init in -lcurl... no configure: error: libcurl library not found Support for HTTPS and other SSL-based URLs requires routines from the libcurl library . Building HTSlib with libcurl enabled requires libcurl development files to be installed on the build machine; you may need to ensure a package such as libcurl4-{gnutls,nss,openssl}-dev (on Debian or Ubuntu Linux) or libcurl-devel (on RPM-based Linux distributions or Cygwin) is installed. Either configure with --disable-libcurl or resolve this error to build HTSlib. checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking for ranlib... ranlib checking for grep that handles long lines and -e... /usr/bin/grep checking for C compiler warning flags... -Wall checking 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... 64 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 -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 for srand48_deterministic... no checking whether fdatasync is declared... yes checking for fdatasync... yes checking for library containing log... -lm checking for zlib.h... yes checking for inflate in -lz... yes checking for library containing recv... none required checking for bzlib.h... yes checking for BZ2_bzBuffToBuffCompress in -lbz2... yes checking for lzma.h... yes checking for lzma_easy_buffer_encode in -llzma... yes checking whether htscodecs files are present... yes checking for libdeflate.h... no checking for libdeflate_deflate_compress in -ldeflate... no configure: WARNING: GCS support not enabled: requires libcurl support configure: WARNING: S3 support not enabled: requires libcurl support checking for library containing regcomp... none required 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: linking htscodecs_bundled.mk to htscodecs.mk # pysam: htslib configure options: --disable-libcurl # pysam: htslib_config LIBHTS_OBJS=kfunc.o kstring.o bcf_sr_sort.o bgzf.o errmod.o faidx.o header.o hfile.o hts.o hts_expr.o hts_os.o md5.o multipart.o probaln.o realn.o regidx.o region.o sam.o synced_bcf_reader.o vcf_sweep.o tbx.o textutils.o thread_pool.o vcf.o vcfutils.o cram/cram_codecs.o cram/cram_decode.o cram/cram_encode.o cram/cram_external.o cram/cram_index.o cram/cram_io.o cram/cram_stats.o cram/mFILE.o cram/open_trace_file.o cram/pooled_alloc.o cram/string_alloc.o htscodecs/htscodecs/arith_dynamic.o htscodecs/htscodecs/fqzcomp_qual.o htscodecs/htscodecs/htscodecs.o htscodecs/htscodecs/pack.o htscodecs/htscodecs/rANS_static4x16pr.o htscodecs/htscodecs/rANS_static.o htscodecs/htscodecs/rle.o htscodecs/htscodecs/tokenise_name3.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-i686-3.11 creating build/lib.linux-i686-3.11/pysam copying pysam/Pileup.py -> build/lib.linux-i686-3.11/pysam copying pysam/__init__.py -> build/lib.linux-i686-3.11/pysam copying pysam/bcftools.py -> build/lib.linux-i686-3.11/pysam copying pysam/samtools.py -> build/lib.linux-i686-3.11/pysam copying pysam/utils.py -> build/lib.linux-i686-3.11/pysam copying pysam/version.py -> build/lib.linux-i686-3.11/pysam copying pysam/config.py -> build/lib.linux-i686-3.11/pysam creating build/lib.linux-i686-3.11/pysam/include copying pysam/include/__init__.py -> build/lib.linux-i686-3.11/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/libcalignedsegment.pxd -> build/lib.linux-i686-3.11/pysam copying pysam/libcalignmentfile.pxd -> build/lib.linux-i686-3.11/pysam copying pysam/libcbcf.pxd -> build/lib.linux-i686-3.11/pysam copying pysam/libcbcftools.pxd -> build/lib.linux-i686-3.11/pysam copying pysam/libcfaidx.pxd -> build/lib.linux-i686-3.11/pysam copying pysam/libchtslib.pxd -> build/lib.linux-i686-3.11/pysam copying pysam/libcsamfile.pxd -> build/lib.linux-i686-3.11/pysam copying pysam/libcsamtools.pxd -> build/lib.linux-i686-3.11/pysam copying pysam/libctabix.pxd -> build/lib.linux-i686-3.11/pysam copying pysam/libctabixproxies.pxd -> build/lib.linux-i686-3.11/pysam copying pysam/libcutils.pxd -> build/lib.linux-i686-3.11/pysam copying pysam/libcvcf.pxd -> build/lib.linux-i686-3.11/pysam copying pysam/cbcftools_util.h -> build/lib.linux-i686-3.11/pysam copying pysam/csamtools_util.h -> build/lib.linux-i686-3.11/pysam copying pysam/htslib_util.h -> build/lib.linux-i686-3.11/pysam copying pysam/pysam_stream.h -> build/lib.linux-i686-3.11/pysam copying pysam/pysam_util.h -> build/lib.linux-i686-3.11/pysam copying pysam/version.h -> build/lib.linux-i686-3.11/pysam copying pysam/py.typed -> build/lib.linux-i686-3.11/pysam copying pysam/libcalignedsegment.pyi -> build/lib.linux-i686-3.11/pysam copying pysam/libcalignmentfile.pyi -> build/lib.linux-i686-3.11/pysam copying pysam/libcbcf.pyi -> build/lib.linux-i686-3.11/pysam copying pysam/libcbcftools.pyi -> build/lib.linux-i686-3.11/pysam copying pysam/libcbgzf.pyi -> build/lib.linux-i686-3.11/pysam copying pysam/libcfaidx.pyi -> build/lib.linux-i686-3.11/pysam copying pysam/libchtslib.pyi -> build/lib.linux-i686-3.11/pysam copying pysam/libcsamfile.pyi -> build/lib.linux-i686-3.11/pysam copying pysam/libcsamtools.pyi -> build/lib.linux-i686-3.11/pysam copying pysam/libctabix.pyi -> build/lib.linux-i686-3.11/pysam copying pysam/libctabixproxies.pyi -> build/lib.linux-i686-3.11/pysam copying pysam/libcutils.pyi -> build/lib.linux-i686-3.11/pysam copying pysam/libcvcf.pyi -> build/lib.linux-i686-3.11/pysam copying pysam/version.pyi -> build/lib.linux-i686-3.11/pysam creating build/lib.linux-i686-3.11/pysam/include/samtools copying samtools/bam.h -> build/lib.linux-i686-3.11/pysam/include/samtools copying samtools/bam_ampliconclip.h -> build/lib.linux-i686-3.11/pysam/include/samtools copying samtools/bam_lpileup.h -> build/lib.linux-i686-3.11/pysam/include/samtools copying samtools/bam_plbuf.h -> build/lib.linux-i686-3.11/pysam/include/samtools copying samtools/bedidx.h -> build/lib.linux-i686-3.11/pysam/include/samtools copying samtools/consensus_pileup.h -> build/lib.linux-i686-3.11/pysam/include/samtools copying samtools/sam_opts.h -> build/lib.linux-i686-3.11/pysam/include/samtools copying samtools/sample.h -> build/lib.linux-i686-3.11/pysam/include/samtools copying samtools/samtools.h -> build/lib.linux-i686-3.11/pysam/include/samtools copying samtools/samtools.pysam.h -> build/lib.linux-i686-3.11/pysam/include/samtools copying samtools/splaysort.h -> build/lib.linux-i686-3.11/pysam/include/samtools copying samtools/stats_isize.h -> build/lib.linux-i686-3.11/pysam/include/samtools copying samtools/tmp_file.h -> build/lib.linux-i686-3.11/pysam/include/samtools copying samtools/config.h -> build/lib.linux-i686-3.11/pysam/include/samtools creating build/lib.linux-i686-3.11/pysam/include/bcftools copying bcftools/HMM.h -> build/lib.linux-i686-3.11/pysam/include/bcftools copying bcftools/abuf.h -> build/lib.linux-i686-3.11/pysam/include/bcftools copying bcftools/bam2bcf.h -> build/lib.linux-i686-3.11/pysam/include/bcftools copying bcftools/bam_sample.h -> build/lib.linux-i686-3.11/pysam/include/bcftools copying bcftools/bcftools.h -> build/lib.linux-i686-3.11/pysam/include/bcftools copying bcftools/bcftools.pysam.h -> build/lib.linux-i686-3.11/pysam/include/bcftools copying bcftools/bin.h -> build/lib.linux-i686-3.11/pysam/include/bcftools copying bcftools/call.h -> build/lib.linux-i686-3.11/pysam/include/bcftools copying bcftools/cols.h -> build/lib.linux-i686-3.11/pysam/include/bcftools copying bcftools/convert.h -> build/lib.linux-i686-3.11/pysam/include/bcftools copying bcftools/dist.h -> build/lib.linux-i686-3.11/pysam/include/bcftools copying bcftools/extsort.h -> build/lib.linux-i686-3.11/pysam/include/bcftools copying bcftools/filter.h -> build/lib.linux-i686-3.11/pysam/include/bcftools copying bcftools/gvcf.h -> build/lib.linux-i686-3.11/pysam/include/bcftools copying bcftools/hclust.h -> build/lib.linux-i686-3.11/pysam/include/bcftools copying bcftools/hex.h -> build/lib.linux-i686-3.11/pysam/include/bcftools copying bcftools/khash_str2str.h -> build/lib.linux-i686-3.11/pysam/include/bcftools copying bcftools/kheap.h -> build/lib.linux-i686-3.11/pysam/include/bcftools copying bcftools/kmin.h -> build/lib.linux-i686-3.11/pysam/include/bcftools copying bcftools/mw.h -> build/lib.linux-i686-3.11/pysam/include/bcftools copying bcftools/ploidy.h -> build/lib.linux-i686-3.11/pysam/include/bcftools copying bcftools/prob1.h -> build/lib.linux-i686-3.11/pysam/include/bcftools copying bcftools/rbuf.h -> build/lib.linux-i686-3.11/pysam/include/bcftools copying bcftools/regidx.h -> build/lib.linux-i686-3.11/pysam/include/bcftools copying bcftools/smpl_ilist.h -> build/lib.linux-i686-3.11/pysam/include/bcftools copying bcftools/str_finder.h -> build/lib.linux-i686-3.11/pysam/include/bcftools copying bcftools/tsv2vcf.h -> build/lib.linux-i686-3.11/pysam/include/bcftools copying bcftools/utlist.h -> build/lib.linux-i686-3.11/pysam/include/bcftools copying bcftools/variantkey.h -> build/lib.linux-i686-3.11/pysam/include/bcftools copying bcftools/vcfbuf.h -> build/lib.linux-i686-3.11/pysam/include/bcftools copying bcftools/vcmp.h -> build/lib.linux-i686-3.11/pysam/include/bcftools copying bcftools/config.h -> build/lib.linux-i686-3.11/pysam/include/bcftools creating build/lib.linux-i686-3.11/pysam/include/htslib copying htslib/bcf_sr_sort.h -> build/lib.linux-i686-3.11/pysam/include/htslib copying htslib/header.h -> build/lib.linux-i686-3.11/pysam/include/htslib copying htslib/hfile_internal.h -> build/lib.linux-i686-3.11/pysam/include/htslib copying htslib/hts_internal.h -> build/lib.linux-i686-3.11/pysam/include/htslib copying htslib/sam_internal.h -> build/lib.linux-i686-3.11/pysam/include/htslib copying htslib/textutils_internal.h -> build/lib.linux-i686-3.11/pysam/include/htslib copying htslib/thread_pool_internal.h -> build/lib.linux-i686-3.11/pysam/include/htslib copying htslib/config.h -> build/lib.linux-i686-3.11/pysam/include/htslib creating build/lib.linux-i686-3.11/pysam/include/htslib/htslib copying htslib/htslib/bgzf.h -> build/lib.linux-i686-3.11/pysam/include/htslib/htslib copying htslib/htslib/cram.h -> build/lib.linux-i686-3.11/pysam/include/htslib/htslib copying htslib/htslib/faidx.h -> build/lib.linux-i686-3.11/pysam/include/htslib/htslib copying htslib/htslib/hfile.h -> build/lib.linux-i686-3.11/pysam/include/htslib/htslib copying htslib/htslib/hts.h -> build/lib.linux-i686-3.11/pysam/include/htslib/htslib copying htslib/htslib/hts_defs.h -> build/lib.linux-i686-3.11/pysam/include/htslib/htslib copying htslib/htslib/hts_endian.h -> build/lib.linux-i686-3.11/pysam/include/htslib/htslib copying htslib/htslib/hts_expr.h -> build/lib.linux-i686-3.11/pysam/include/htslib/htslib copying htslib/htslib/hts_log.h -> build/lib.linux-i686-3.11/pysam/include/htslib/htslib copying htslib/htslib/hts_os.h -> build/lib.linux-i686-3.11/pysam/include/htslib/htslib copying htslib/htslib/kbitset.h -> build/lib.linux-i686-3.11/pysam/include/htslib/htslib copying htslib/htslib/kfunc.h -> build/lib.linux-i686-3.11/pysam/include/htslib/htslib copying htslib/htslib/khash.h -> build/lib.linux-i686-3.11/pysam/include/htslib/htslib copying htslib/htslib/khash_str2int.h -> build/lib.linux-i686-3.11/pysam/include/htslib/htslib copying htslib/htslib/klist.h -> build/lib.linux-i686-3.11/pysam/include/htslib/htslib copying htslib/htslib/knetfile.h -> build/lib.linux-i686-3.11/pysam/include/htslib/htslib copying htslib/htslib/kroundup.h -> build/lib.linux-i686-3.11/pysam/include/htslib/htslib copying htslib/htslib/kseq.h -> build/lib.linux-i686-3.11/pysam/include/htslib/htslib copying htslib/htslib/ksort.h -> build/lib.linux-i686-3.11/pysam/include/htslib/htslib copying htslib/htslib/kstring.h -> build/lib.linux-i686-3.11/pysam/include/htslib/htslib copying htslib/htslib/regidx.h -> build/lib.linux-i686-3.11/pysam/include/htslib/htslib copying htslib/htslib/sam.h -> build/lib.linux-i686-3.11/pysam/include/htslib/htslib copying htslib/htslib/synced_bcf_reader.h -> build/lib.linux-i686-3.11/pysam/include/htslib/htslib copying htslib/htslib/tbx.h -> build/lib.linux-i686-3.11/pysam/include/htslib/htslib copying htslib/htslib/thread_pool.h -> build/lib.linux-i686-3.11/pysam/include/htslib/htslib copying htslib/htslib/vcf.h -> build/lib.linux-i686-3.11/pysam/include/htslib/htslib copying htslib/htslib/vcf_sweep.h -> build/lib.linux-i686-3.11/pysam/include/htslib/htslib copying htslib/htslib/vcfutils.h -> build/lib.linux-i686-3.11/pysam/include/htslib/htslib running build_ext cythoning pysam/libchtslib.pyx to pysam/libchtslib.c /usr/lib/python3.11/site-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /builddir/build/BUILD/pysam-0.19.0/pysam/libchtslib.pxd tree = Parsing.p_module(s, pxd, full_module_name) cythoning pysam/libcsamtools.pyx to pysam/libcsamtools.c /usr/lib/python3.11/site-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /builddir/build/BUILD/pysam-0.19.0/pysam/libcsamtools.pxd tree = Parsing.p_module(s, pxd, full_module_name) cythoning pysam/libcbcftools.pyx to pysam/libcbcftools.c /usr/lib/python3.11/site-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /builddir/build/BUILD/pysam-0.19.0/pysam/libcbcftools.pxd tree = Parsing.p_module(s, pxd, full_module_name) cythoning pysam/libcutils.pyx to pysam/libcutils.c /usr/lib/python3.11/site-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /builddir/build/BUILD/pysam-0.19.0/pysam/libcutils.pxd tree = Parsing.p_module(s, pxd, full_module_name) cythoning pysam/libcalignmentfile.pyx to pysam/libcalignmentfile.c /usr/lib/python3.11/site-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /builddir/build/BUILD/pysam-0.19.0/pysam/libcalignmentfile.pxd tree = Parsing.p_module(s, pxd, full_module_name) warning: pysam/libcalignmentfile.pyx:2573:49: Casting a GIL-requiring function into a nogil function circumvents GIL validation warning: pysam/libcalignmentfile.pyx:2578:49: Casting a GIL-requiring function into a nogil function circumvents GIL validation warning: pysam/libcalignmentfile.pyx:2583:49: Casting a GIL-requiring function into a nogil function circumvents GIL validation warning: pysam/libcalignmentfile.pyx:2622:49: Casting a GIL-requiring function into a nogil function circumvents GIL validation warning: pysam/libcalignmentfile.pyx:2627:49: Casting a GIL-requiring function into a nogil function circumvents GIL validation warning: pysam/libcalignmentfile.pyx:2632:49: Casting a GIL-requiring function into a nogil function circumvents GIL validation cythoning pysam/libcsamfile.pyx to pysam/libcsamfile.c /usr/lib/python3.11/site-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /builddir/build/BUILD/pysam-0.19.0/pysam/libcsamfile.pxd tree = Parsing.p_module(s, pxd, full_module_name) cythoning pysam/libcalignedsegment.pyx to pysam/libcalignedsegment.c /usr/lib/python3.11/site-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /builddir/build/BUILD/pysam-0.19.0/pysam/libcalignedsegment.pxd tree = Parsing.p_module(s, pxd, full_module_name) cythoning pysam/libctabix.pyx to pysam/libctabix.c /usr/lib/python3.11/site-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /builddir/build/BUILD/pysam-0.19.0/pysam/libctabix.pxd tree = Parsing.p_module(s, pxd, full_module_name) cythoning pysam/libcfaidx.pyx to pysam/libcfaidx.c /usr/lib/python3.11/site-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /builddir/build/BUILD/pysam-0.19.0/pysam/libcfaidx.pxd tree = Parsing.p_module(s, pxd, full_module_name) cythoning pysam/libcbcf.pyx to pysam/libcbcf.c /usr/lib/python3.11/site-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /builddir/build/BUILD/pysam-0.19.0/pysam/libcbcf.pxd tree = Parsing.p_module(s, pxd, full_module_name) cythoning pysam/libcbgzf.pyx to pysam/libcbgzf.c /usr/lib/python3.11/site-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /builddir/build/BUILD/pysam-0.19.0/pysam/libcbgzf.pyx tree = Parsing.p_module(s, pxd, full_module_name) cythoning pysam/libctabixproxies.pyx to pysam/libctabixproxies.c /usr/lib/python3.11/site-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /builddir/build/BUILD/pysam-0.19.0/pysam/libctabixproxies.pxd tree = Parsing.p_module(s, pxd, full_module_name) cythoning pysam/libcvcf.pyx to pysam/libcvcf.c /usr/lib/python3.11/site-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /builddir/build/BUILD/pysam-0.19.0/pysam/libcvcf.pxd tree = Parsing.p_module(s, pxd, full_module_name) warning: pysam/libcvcf.pyx:1083:27: Unreachable code creating htslib/config_vars.h for 'pysam.libchtslib' extension building 'pysam.libchtslib' extension creating build/temp.linux-i686-3.11 creating build/temp.linux-i686-3.11/htslib creating build/temp.linux-i686-3.11/htslib/cram creating build/temp.linux-i686-3.11/htslib/htscodecs creating build/temp.linux-i686-3.11/htslib/htscodecs/htscodecs creating build/temp.linux-i686-3.11/pysam gcc -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.19.0/htslib -I/builddir/build/BUILD/pysam-0.19.0/samtools -I/builddir/build/BUILD/pysam-0.19.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.19.0/bcftools -I/builddir/build/BUILD/pysam-0.19.0/pysam -I/builddir/build/BUILD/pysam-0.19.0 -I/usr/include/python3.11 -c htslib/bcf_sr_sort.c -o build/temp.linux-i686-3.11/htslib/bcf_sr_sort.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.19.0/htslib -I/builddir/build/BUILD/pysam-0.19.0/samtools -I/builddir/build/BUILD/pysam-0.19.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.19.0/bcftools -I/builddir/build/BUILD/pysam-0.19.0/pysam -I/builddir/build/BUILD/pysam-0.19.0 -I/usr/include/python3.11 -c htslib/bgzf.c -o build/temp.linux-i686-3.11/htslib/bgzf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.19.0/htslib -I/builddir/build/BUILD/pysam-0.19.0/samtools -I/builddir/build/BUILD/pysam-0.19.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.19.0/bcftools -I/builddir/build/BUILD/pysam-0.19.0/pysam -I/builddir/build/BUILD/pysam-0.19.0 -I/usr/include/python3.11 -c htslib/cram/cram_codecs.c -o build/temp.linux-i686-3.11/htslib/cram/cram_codecs.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.19.0/htslib -I/builddir/build/BUILD/pysam-0.19.0/samtools -I/builddir/build/BUILD/pysam-0.19.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.19.0/bcftools -I/builddir/build/BUILD/pysam-0.19.0/pysam -I/builddir/build/BUILD/pysam-0.19.0 -I/usr/include/python3.11 -c htslib/cram/cram_decode.c -o build/temp.linux-i686-3.11/htslib/cram/cram_decode.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.19.0/htslib -I/builddir/build/BUILD/pysam-0.19.0/samtools -I/builddir/build/BUILD/pysam-0.19.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.19.0/bcftools -I/builddir/build/BUILD/pysam-0.19.0/pysam -I/builddir/build/BUILD/pysam-0.19.0 -I/usr/include/python3.11 -c htslib/cram/cram_encode.c -o build/temp.linux-i686-3.11/htslib/cram/cram_encode.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.19.0/htslib -I/builddir/build/BUILD/pysam-0.19.0/samtools -I/builddir/build/BUILD/pysam-0.19.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.19.0/bcftools -I/builddir/build/BUILD/pysam-0.19.0/pysam -I/builddir/build/BUILD/pysam-0.19.0 -I/usr/include/python3.11 -c htslib/cram/cram_external.c -o build/temp.linux-i686-3.11/htslib/cram/cram_external.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.19.0/htslib -I/builddir/build/BUILD/pysam-0.19.0/samtools -I/builddir/build/BUILD/pysam-0.19.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.19.0/bcftools -I/builddir/build/BUILD/pysam-0.19.0/pysam -I/builddir/build/BUILD/pysam-0.19.0 -I/usr/include/python3.11 -c htslib/cram/cram_index.c -o build/temp.linux-i686-3.11/htslib/cram/cram_index.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.19.0/htslib -I/builddir/build/BUILD/pysam-0.19.0/samtools -I/builddir/build/BUILD/pysam-0.19.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.19.0/bcftools -I/builddir/build/BUILD/pysam-0.19.0/pysam -I/builddir/build/BUILD/pysam-0.19.0 -I/usr/include/python3.11 -c htslib/cram/cram_io.c -o build/temp.linux-i686-3.11/htslib/cram/cram_io.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.19.0/htslib -I/builddir/build/BUILD/pysam-0.19.0/samtools -I/builddir/build/BUILD/pysam-0.19.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.19.0/bcftools -I/builddir/build/BUILD/pysam-0.19.0/pysam -I/builddir/build/BUILD/pysam-0.19.0 -I/usr/include/python3.11 -c htslib/cram/cram_stats.c -o build/temp.linux-i686-3.11/htslib/cram/cram_stats.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.19.0/htslib -I/builddir/build/BUILD/pysam-0.19.0/samtools -I/builddir/build/BUILD/pysam-0.19.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.19.0/bcftools -I/builddir/build/BUILD/pysam-0.19.0/pysam -I/builddir/build/BUILD/pysam-0.19.0 -I/usr/include/python3.11 -c htslib/cram/mFILE.c -o build/temp.linux-i686-3.11/htslib/cram/mFILE.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.19.0/htslib -I/builddir/build/BUILD/pysam-0.19.0/samtools -I/builddir/build/BUILD/pysam-0.19.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.19.0/bcftools -I/builddir/build/BUILD/pysam-0.19.0/pysam -I/builddir/build/BUILD/pysam-0.19.0 -I/usr/include/python3.11 -c htslib/cram/open_trace_file.c -o build/temp.linux-i686-3.11/htslib/cram/open_trace_file.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.19.0/htslib -I/builddir/build/BUILD/pysam-0.19.0/samtools -I/builddir/build/BUILD/pysam-0.19.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.19.0/bcftools -I/builddir/build/BUILD/pysam-0.19.0/pysam -I/builddir/build/BUILD/pysam-0.19.0 -I/usr/include/python3.11 -c htslib/cram/pooled_alloc.c -o build/temp.linux-i686-3.11/htslib/cram/pooled_alloc.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.19.0/htslib -I/builddir/build/BUILD/pysam-0.19.0/samtools -I/builddir/build/BUILD/pysam-0.19.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.19.0/bcftools -I/builddir/build/BUILD/pysam-0.19.0/pysam -I/builddir/build/BUILD/pysam-0.19.0 -I/usr/include/python3.11 -c htslib/cram/string_alloc.c -o build/temp.linux-i686-3.11/htslib/cram/string_alloc.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.19.0/htslib -I/builddir/build/BUILD/pysam-0.19.0/samtools -I/builddir/build/BUILD/pysam-0.19.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.19.0/bcftools -I/builddir/build/BUILD/pysam-0.19.0/pysam -I/builddir/build/BUILD/pysam-0.19.0 -I/usr/include/python3.11 -c htslib/errmod.c -o build/temp.linux-i686-3.11/htslib/errmod.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.19.0/htslib -I/builddir/build/BUILD/pysam-0.19.0/samtools -I/builddir/build/BUILD/pysam-0.19.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.19.0/bcftools -I/builddir/build/BUILD/pysam-0.19.0/pysam -I/builddir/build/BUILD/pysam-0.19.0 -I/usr/include/python3.11 -c htslib/faidx.c -o build/temp.linux-i686-3.11/htslib/faidx.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.19.0/htslib -I/builddir/build/BUILD/pysam-0.19.0/samtools -I/builddir/build/BUILD/pysam-0.19.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.19.0/bcftools -I/builddir/build/BUILD/pysam-0.19.0/pysam -I/builddir/build/BUILD/pysam-0.19.0 -I/usr/include/python3.11 -c htslib/header.c -o build/temp.linux-i686-3.11/htslib/header.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.19.0/htslib -I/builddir/build/BUILD/pysam-0.19.0/samtools -I/builddir/build/BUILD/pysam-0.19.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.19.0/bcftools -I/builddir/build/BUILD/pysam-0.19.0/pysam -I/builddir/build/BUILD/pysam-0.19.0 -I/usr/include/python3.11 -c htslib/hfile.c -o build/temp.linux-i686-3.11/htslib/hfile.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.19.0/htslib -I/builddir/build/BUILD/pysam-0.19.0/samtools -I/builddir/build/BUILD/pysam-0.19.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.19.0/bcftools -I/builddir/build/BUILD/pysam-0.19.0/pysam -I/builddir/build/BUILD/pysam-0.19.0 -I/usr/include/python3.11 -c htslib/hts.c -o build/temp.linux-i686-3.11/htslib/hts.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement htslib/hts.c: In function ‘hts_hopen’: htslib/hts.c:1355:31: warning: ‘%s’ directive output between 503 and 2147483645 bytes may cause result to exceed ‘INT_MAX’ [-Wformat-truncation=] 1355 | snprintf(fn2, fn2_len, "%s%s", prefix, fn); | ^~ In file included from /usr/include/stdio.h:894, from htslib/hts.c:30: In function ‘snprintf’, inlined from ‘hts_crypt4gh_redirect’ at htslib/hts.c:1355:5, inlined from ‘hts_hopen’ at htslib/hts.c:1414:21: /usr/include/bits/stdio2.h:71:10: note: ‘__snprintf_chk’ output between 513 and 2147483655 bytes into a destination of size 2147483655 71 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 72 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 73 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ gcc -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.19.0/htslib -I/builddir/build/BUILD/pysam-0.19.0/samtools -I/builddir/build/BUILD/pysam-0.19.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.19.0/bcftools -I/builddir/build/BUILD/pysam-0.19.0/pysam -I/builddir/build/BUILD/pysam-0.19.0 -I/usr/include/python3.11 -c htslib/hts_expr.c -o build/temp.linux-i686-3.11/htslib/hts_expr.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.19.0/htslib -I/builddir/build/BUILD/pysam-0.19.0/samtools -I/builddir/build/BUILD/pysam-0.19.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.19.0/bcftools -I/builddir/build/BUILD/pysam-0.19.0/pysam -I/builddir/build/BUILD/pysam-0.19.0 -I/usr/include/python3.11 -c htslib/hts_os.c -o build/temp.linux-i686-3.11/htslib/hts_os.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.19.0/htslib -I/builddir/build/BUILD/pysam-0.19.0/samtools -I/builddir/build/BUILD/pysam-0.19.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.19.0/bcftools -I/builddir/build/BUILD/pysam-0.19.0/pysam -I/builddir/build/BUILD/pysam-0.19.0 -I/usr/include/python3.11 -c htslib/htscodecs/htscodecs/arith_dynamic.c -o build/temp.linux-i686-3.11/htslib/htscodecs/htscodecs/arith_dynamic.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.19.0/htslib -I/builddir/build/BUILD/pysam-0.19.0/samtools -I/builddir/build/BUILD/pysam-0.19.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.19.0/bcftools -I/builddir/build/BUILD/pysam-0.19.0/pysam -I/builddir/build/BUILD/pysam-0.19.0 -I/usr/include/python3.11 -c htslib/htscodecs/htscodecs/fqzcomp_qual.c -o build/temp.linux-i686-3.11/htslib/htscodecs/htscodecs/fqzcomp_qual.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.19.0/htslib -I/builddir/build/BUILD/pysam-0.19.0/samtools -I/builddir/build/BUILD/pysam-0.19.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.19.0/bcftools -I/builddir/build/BUILD/pysam-0.19.0/pysam -I/builddir/build/BUILD/pysam-0.19.0 -I/usr/include/python3.11 -c htslib/htscodecs/htscodecs/htscodecs.c -o build/temp.linux-i686-3.11/htslib/htscodecs/htscodecs/htscodecs.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.19.0/htslib -I/builddir/build/BUILD/pysam-0.19.0/samtools -I/builddir/build/BUILD/pysam-0.19.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.19.0/bcftools -I/builddir/build/BUILD/pysam-0.19.0/pysam -I/builddir/build/BUILD/pysam-0.19.0 -I/usr/include/python3.11 -c htslib/htscodecs/htscodecs/pack.c -o build/temp.linux-i686-3.11/htslib/htscodecs/htscodecs/pack.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.19.0/htslib -I/builddir/build/BUILD/pysam-0.19.0/samtools -I/builddir/build/BUILD/pysam-0.19.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.19.0/bcftools -I/builddir/build/BUILD/pysam-0.19.0/pysam -I/builddir/build/BUILD/pysam-0.19.0 -I/usr/include/python3.11 -c htslib/htscodecs/htscodecs/rANS_static.c -o build/temp.linux-i686-3.11/htslib/htscodecs/htscodecs/rANS_static.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.19.0/htslib -I/builddir/build/BUILD/pysam-0.19.0/samtools -I/builddir/build/BUILD/pysam-0.19.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.19.0/bcftools -I/builddir/build/BUILD/pysam-0.19.0/pysam -I/builddir/build/BUILD/pysam-0.19.0 -I/usr/include/python3.11 -c htslib/htscodecs/htscodecs/rANS_static4x16pr.c -o build/temp.linux-i686-3.11/htslib/htscodecs/htscodecs/rANS_static4x16pr.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement In file included from htslib/htscodecs/htscodecs/rANS_static4x16pr.c:74: In function ‘RansEncFlush’, inlined from ‘rans_compress_O1_4x16.isra.0’ at htslib/htscodecs/htscodecs/rANS_static4x16pr.c:840:5: htslib/htscodecs/htscodecs/rANS_word.h:109:9: warning: ‘ptr’ may be used uninitialized [-Wmaybe-uninitialized] 109 | ptr -= 4; | ~~~~^~~~ htslib/htscodecs/htscodecs/rANS_static4x16pr.c: In function ‘rans_compress_O1_4x16.isra.0’: htslib/htscodecs/htscodecs/rANS_static4x16pr.c:793:14: note: ‘ptr’ was declared here 793 | uint8_t* ptr = out_end; | ^~~ gcc -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.19.0/htslib -I/builddir/build/BUILD/pysam-0.19.0/samtools -I/builddir/build/BUILD/pysam-0.19.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.19.0/bcftools -I/builddir/build/BUILD/pysam-0.19.0/pysam -I/builddir/build/BUILD/pysam-0.19.0 -I/usr/include/python3.11 -c htslib/htscodecs/htscodecs/rle.c -o build/temp.linux-i686-3.11/htslib/htscodecs/htscodecs/rle.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.19.0/htslib -I/builddir/build/BUILD/pysam-0.19.0/samtools -I/builddir/build/BUILD/pysam-0.19.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.19.0/bcftools -I/builddir/build/BUILD/pysam-0.19.0/pysam -I/builddir/build/BUILD/pysam-0.19.0 -I/usr/include/python3.11 -c htslib/htscodecs/htscodecs/tokenise_name3.c -o build/temp.linux-i686-3.11/htslib/htscodecs/htscodecs/tokenise_name3.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.19.0/htslib -I/builddir/build/BUILD/pysam-0.19.0/samtools -I/builddir/build/BUILD/pysam-0.19.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.19.0/bcftools -I/builddir/build/BUILD/pysam-0.19.0/pysam -I/builddir/build/BUILD/pysam-0.19.0 -I/usr/include/python3.11 -c htslib/kfunc.c -o build/temp.linux-i686-3.11/htslib/kfunc.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.19.0/htslib -I/builddir/build/BUILD/pysam-0.19.0/samtools -I/builddir/build/BUILD/pysam-0.19.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.19.0/bcftools -I/builddir/build/BUILD/pysam-0.19.0/pysam -I/builddir/build/BUILD/pysam-0.19.0 -I/usr/include/python3.11 -c htslib/kstring.c -o build/temp.linux-i686-3.11/htslib/kstring.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.19.0/htslib -I/builddir/build/BUILD/pysam-0.19.0/samtools -I/builddir/build/BUILD/pysam-0.19.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.19.0/bcftools -I/builddir/build/BUILD/pysam-0.19.0/pysam -I/builddir/build/BUILD/pysam-0.19.0 -I/usr/include/python3.11 -c htslib/md5.c -o build/temp.linux-i686-3.11/htslib/md5.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.19.0/htslib -I/builddir/build/BUILD/pysam-0.19.0/samtools -I/builddir/build/BUILD/pysam-0.19.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.19.0/bcftools -I/builddir/build/BUILD/pysam-0.19.0/pysam -I/builddir/build/BUILD/pysam-0.19.0 -I/usr/include/python3.11 -c htslib/multipart.c -o build/temp.linux-i686-3.11/htslib/multipart.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.19.0/htslib -I/builddir/build/BUILD/pysam-0.19.0/samtools -I/builddir/build/BUILD/pysam-0.19.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.19.0/bcftools -I/builddir/build/BUILD/pysam-0.19.0/pysam -I/builddir/build/BUILD/pysam-0.19.0 -I/usr/include/python3.11 -c htslib/probaln.c -o build/temp.linux-i686-3.11/htslib/probaln.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.19.0/htslib -I/builddir/build/BUILD/pysam-0.19.0/samtools -I/builddir/build/BUILD/pysam-0.19.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.19.0/bcftools -I/builddir/build/BUILD/pysam-0.19.0/pysam -I/builddir/build/BUILD/pysam-0.19.0 -I/usr/include/python3.11 -c htslib/realn.c -o build/temp.linux-i686-3.11/htslib/realn.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.19.0/htslib -I/builddir/build/BUILD/pysam-0.19.0/samtools -I/builddir/build/BUILD/pysam-0.19.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.19.0/bcftools -I/builddir/build/BUILD/pysam-0.19.0/pysam -I/builddir/build/BUILD/pysam-0.19.0 -I/usr/include/python3.11 -c htslib/regidx.c -o build/temp.linux-i686-3.11/htslib/regidx.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.19.0/htslib -I/builddir/build/BUILD/pysam-0.19.0/samtools -I/builddir/build/BUILD/pysam-0.19.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.19.0/bcftools -I/builddir/build/BUILD/pysam-0.19.0/pysam -I/builddir/build/BUILD/pysam-0.19.0 -I/usr/include/python3.11 -c htslib/region.c -o build/temp.linux-i686-3.11/htslib/region.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.19.0/htslib -I/builddir/build/BUILD/pysam-0.19.0/samtools -I/builddir/build/BUILD/pysam-0.19.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.19.0/bcftools -I/builddir/build/BUILD/pysam-0.19.0/pysam -I/builddir/build/BUILD/pysam-0.19.0 -I/usr/include/python3.11 -c htslib/sam.c -o build/temp.linux-i686-3.11/htslib/sam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.19.0/htslib -I/builddir/build/BUILD/pysam-0.19.0/samtools -I/builddir/build/BUILD/pysam-0.19.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.19.0/bcftools -I/builddir/build/BUILD/pysam-0.19.0/pysam -I/builddir/build/BUILD/pysam-0.19.0 -I/usr/include/python3.11 -c htslib/synced_bcf_reader.c -o build/temp.linux-i686-3.11/htslib/synced_bcf_reader.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.19.0/htslib -I/builddir/build/BUILD/pysam-0.19.0/samtools -I/builddir/build/BUILD/pysam-0.19.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.19.0/bcftools -I/builddir/build/BUILD/pysam-0.19.0/pysam -I/builddir/build/BUILD/pysam-0.19.0 -I/usr/include/python3.11 -c htslib/tbx.c -o build/temp.linux-i686-3.11/htslib/tbx.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.19.0/htslib -I/builddir/build/BUILD/pysam-0.19.0/samtools -I/builddir/build/BUILD/pysam-0.19.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.19.0/bcftools -I/builddir/build/BUILD/pysam-0.19.0/pysam -I/builddir/build/BUILD/pysam-0.19.0 -I/usr/include/python3.11 -c htslib/textutils.c -o build/temp.linux-i686-3.11/htslib/textutils.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.19.0/htslib -I/builddir/build/BUILD/pysam-0.19.0/samtools -I/builddir/build/BUILD/pysam-0.19.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.19.0/bcftools -I/builddir/build/BUILD/pysam-0.19.0/pysam -I/builddir/build/BUILD/pysam-0.19.0 -I/usr/include/python3.11 -c htslib/thread_pool.c -o build/temp.linux-i686-3.11/htslib/thread_pool.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.19.0/htslib -I/builddir/build/BUILD/pysam-0.19.0/samtools -I/builddir/build/BUILD/pysam-0.19.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.19.0/bcftools -I/builddir/build/BUILD/pysam-0.19.0/pysam -I/builddir/build/BUILD/pysam-0.19.0 -I/usr/include/python3.11 -c htslib/vcf.c -o build/temp.linux-i686-3.11/htslib/vcf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.19.0/htslib -I/builddir/build/BUILD/pysam-0.19.0/samtools -I/builddir/build/BUILD/pysam-0.19.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.19.0/bcftools -I/builddir/build/BUILD/pysam-0.19.0/pysam -I/builddir/build/BUILD/pysam-0.19.0 -I/usr/include/python3.11 -c htslib/vcf_sweep.c -o build/temp.linux-i686-3.11/htslib/vcf_sweep.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.19.0/htslib -I/builddir/build/BUILD/pysam-0.19.0/samtools -I/builddir/build/BUILD/pysam-0.19.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.19.0/bcftools -I/builddir/build/BUILD/pysam-0.19.0/pysam -I/builddir/build/BUILD/pysam-0.19.0 -I/usr/include/python3.11 -c htslib/vcfutils.c -o build/temp.linux-i686-3.11/htslib/vcfutils.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.19.0/htslib -I/builddir/build/BUILD/pysam-0.19.0/samtools -I/builddir/build/BUILD/pysam-0.19.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.19.0/bcftools -I/builddir/build/BUILD/pysam-0.19.0/pysam -I/builddir/build/BUILD/pysam-0.19.0 -I/usr/include/python3.11 -c pysam/htslib_util.c -o build/temp.linux-i686-3.11/pysam/htslib_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.19.0/htslib -I/builddir/build/BUILD/pysam-0.19.0/samtools -I/builddir/build/BUILD/pysam-0.19.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.19.0/bcftools -I/builddir/build/BUILD/pysam-0.19.0/pysam -I/builddir/build/BUILD/pysam-0.19.0 -I/usr/include/python3.11 -c pysam/libchtslib.c -o build/temp.linux-i686-3.11/pysam/libchtslib.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -shared -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -Wl,--build-id=sha1 -g -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -Wl,--build-id=sha1 -g -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -Wl,-dT,/builddir/build/BUILD/pysam-0.19.0/.package_note-python-pysam-0.19.0-4.fc37.i386.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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection build/temp.linux-i686-3.11/htslib/bcf_sr_sort.o build/temp.linux-i686-3.11/htslib/bgzf.o build/temp.linux-i686-3.11/htslib/cram/cram_codecs.o build/temp.linux-i686-3.11/htslib/cram/cram_decode.o build/temp.linux-i686-3.11/htslib/cram/cram_encode.o build/temp.linux-i686-3.11/htslib/cram/cram_external.o build/temp.linux-i686-3.11/htslib/cram/cram_index.o build/temp.linux-i686-3.11/htslib/cram/cram_io.o build/temp.linux-i686-3.11/htslib/cram/cram_stats.o build/temp.linux-i686-3.11/htslib/cram/mFILE.o build/temp.linux-i686-3.11/htslib/cram/open_trace_file.o build/temp.linux-i686-3.11/htslib/cram/pooled_alloc.o build/temp.linux-i686-3.11/htslib/cram/string_alloc.o build/temp.linux-i686-3.11/htslib/errmod.o build/temp.linux-i686-3.11/htslib/faidx.o build/temp.linux-i686-3.11/htslib/header.o build/temp.linux-i686-3.11/htslib/hfile.o build/temp.linux-i686-3.11/htslib/hts.o build/temp.linux-i686-3.11/htslib/hts_expr.o build/temp.linux-i686-3.11/htslib/hts_os.o build/temp.linux-i686-3.11/htslib/htscodecs/htscodecs/arith_dynamic.o build/temp.linux-i686-3.11/htslib/htscodecs/htscodecs/fqzcomp_qual.o build/temp.linux-i686-3.11/htslib/htscodecs/htscodecs/htscodecs.o build/temp.linux-i686-3.11/htslib/htscodecs/htscodecs/pack.o build/temp.linux-i686-3.11/htslib/htscodecs/htscodecs/rANS_static.o build/temp.linux-i686-3.11/htslib/htscodecs/htscodecs/rANS_static4x16pr.o build/temp.linux-i686-3.11/htslib/htscodecs/htscodecs/rle.o build/temp.linux-i686-3.11/htslib/htscodecs/htscodecs/tokenise_name3.o build/temp.linux-i686-3.11/htslib/kfunc.o build/temp.linux-i686-3.11/htslib/kstring.o build/temp.linux-i686-3.11/htslib/md5.o build/temp.linux-i686-3.11/htslib/multipart.o build/temp.linux-i686-3.11/htslib/probaln.o build/temp.linux-i686-3.11/htslib/realn.o build/temp.linux-i686-3.11/htslib/regidx.o build/temp.linux-i686-3.11/htslib/region.o build/temp.linux-i686-3.11/htslib/sam.o build/temp.linux-i686-3.11/htslib/synced_bcf_reader.o build/temp.linux-i686-3.11/htslib/tbx.o build/temp.linux-i686-3.11/htslib/textutils.o build/temp.linux-i686-3.11/htslib/thread_pool.o build/temp.linux-i686-3.11/htslib/vcf.o build/temp.linux-i686-3.11/htslib/vcf_sweep.o build/temp.linux-i686-3.11/htslib/vcfutils.o build/temp.linux-i686-3.11/pysam/htslib_util.o build/temp.linux-i686-3.11/pysam/libchtslib.o -L/builddir/build/BUILD/pysam-0.19.0/pysam -L/builddir/build/BUILD/pysam-0.19.0/pysam -L/builddir/build/BUILD/pysam-0.19.0 -L/builddir/build/BUILD/pysam-0.19.0/build/lib.linux-i686-3.11/pysam -Lbuild/lib.linux-i686-3.11/pysam -L/usr/lib -lz -llzma -lbz2 -lz -lm -o build/lib.linux-i686-3.11/pysam/libchtslib.cpython-311-i386-linux-gnu.so -Wl,-rpath,$ORIGIN creating samtools/samtools_config_vars.h for 'pysam.libcsamtools' extension building 'pysam.libcsamtools' extension creating build/temp.linux-i686-3.11/samtools creating build/temp.linux-i686-3.11/samtools/lz4 gcc -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.19.0/htslib -I/builddir/build/BUILD/pysam-0.19.0/samtools -I/builddir/build/BUILD/pysam-0.19.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.19.0/bcftools -I/builddir/build/BUILD/pysam-0.19.0/pysam -I/builddir/build/BUILD/pysam-0.19.0 -I/usr/include/python3.11 -c pysam/libcsamtools.c -o build/temp.linux-i686-3.11/pysam/libcsamtools.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.19.0/htslib -I/builddir/build/BUILD/pysam-0.19.0/samtools -I/builddir/build/BUILD/pysam-0.19.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.19.0/bcftools -I/builddir/build/BUILD/pysam-0.19.0/pysam -I/builddir/build/BUILD/pysam-0.19.0 -I/usr/include/python3.11 -c samtools/amplicon_stats.c.pysam.c -o build/temp.linux-i686-3.11/samtools/amplicon_stats.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.19.0/htslib -I/builddir/build/BUILD/pysam-0.19.0/samtools -I/builddir/build/BUILD/pysam-0.19.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.19.0/bcftools -I/builddir/build/BUILD/pysam-0.19.0/pysam -I/builddir/build/BUILD/pysam-0.19.0 -I/usr/include/python3.11 -c samtools/bam.c.pysam.c -o build/temp.linux-i686-3.11/samtools/bam.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.19.0/htslib -I/builddir/build/BUILD/pysam-0.19.0/samtools -I/builddir/build/BUILD/pysam-0.19.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.19.0/bcftools -I/builddir/build/BUILD/pysam-0.19.0/pysam -I/builddir/build/BUILD/pysam-0.19.0 -I/usr/include/python3.11 -c samtools/bam2depth.c.pysam.c -o build/temp.linux-i686-3.11/samtools/bam2depth.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.19.0/htslib -I/builddir/build/BUILD/pysam-0.19.0/samtools -I/builddir/build/BUILD/pysam-0.19.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.19.0/bcftools -I/builddir/build/BUILD/pysam-0.19.0/pysam -I/builddir/build/BUILD/pysam-0.19.0 -I/usr/include/python3.11 -c samtools/bam_addrprg.c.pysam.c -o build/temp.linux-i686-3.11/samtools/bam_addrprg.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.19.0/htslib -I/builddir/build/BUILD/pysam-0.19.0/samtools -I/builddir/build/BUILD/pysam-0.19.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.19.0/bcftools -I/builddir/build/BUILD/pysam-0.19.0/pysam -I/builddir/build/BUILD/pysam-0.19.0 -I/usr/include/python3.11 -c samtools/bam_ampliconclip.c.pysam.c -o build/temp.linux-i686-3.11/samtools/bam_ampliconclip.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.19.0/htslib -I/builddir/build/BUILD/pysam-0.19.0/samtools -I/builddir/build/BUILD/pysam-0.19.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.19.0/bcftools -I/builddir/build/BUILD/pysam-0.19.0/pysam -I/builddir/build/BUILD/pysam-0.19.0 -I/usr/include/python3.11 -c samtools/bam_aux.c.pysam.c -o build/temp.linux-i686-3.11/samtools/bam_aux.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.19.0/htslib -I/builddir/build/BUILD/pysam-0.19.0/samtools -I/builddir/build/BUILD/pysam-0.19.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.19.0/bcftools -I/builddir/build/BUILD/pysam-0.19.0/pysam -I/builddir/build/BUILD/pysam-0.19.0 -I/usr/include/python3.11 -c samtools/bam_cat.c.pysam.c -o build/temp.linux-i686-3.11/samtools/bam_cat.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.19.0/htslib -I/builddir/build/BUILD/pysam-0.19.0/samtools -I/builddir/build/BUILD/pysam-0.19.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.19.0/bcftools -I/builddir/build/BUILD/pysam-0.19.0/pysam -I/builddir/build/BUILD/pysam-0.19.0 -I/usr/include/python3.11 -c samtools/bam_color.c.pysam.c -o build/temp.linux-i686-3.11/samtools/bam_color.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.19.0/htslib -I/builddir/build/BUILD/pysam-0.19.0/samtools -I/builddir/build/BUILD/pysam-0.19.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.19.0/bcftools -I/builddir/build/BUILD/pysam-0.19.0/pysam -I/builddir/build/BUILD/pysam-0.19.0 -I/usr/include/python3.11 -c samtools/bam_consensus.c.pysam.c -o build/temp.linux-i686-3.11/samtools/bam_consensus.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.19.0/htslib -I/builddir/build/BUILD/pysam-0.19.0/samtools -I/builddir/build/BUILD/pysam-0.19.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.19.0/bcftools -I/builddir/build/BUILD/pysam-0.19.0/pysam -I/builddir/build/BUILD/pysam-0.19.0 -I/usr/include/python3.11 -c samtools/bam_fastq.c.pysam.c -o build/temp.linux-i686-3.11/samtools/bam_fastq.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.19.0/htslib -I/builddir/build/BUILD/pysam-0.19.0/samtools -I/builddir/build/BUILD/pysam-0.19.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.19.0/bcftools -I/builddir/build/BUILD/pysam-0.19.0/pysam -I/builddir/build/BUILD/pysam-0.19.0 -I/usr/include/python3.11 -c samtools/bam_flags.c.pysam.c -o build/temp.linux-i686-3.11/samtools/bam_flags.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.19.0/htslib -I/builddir/build/BUILD/pysam-0.19.0/samtools -I/builddir/build/BUILD/pysam-0.19.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.19.0/bcftools -I/builddir/build/BUILD/pysam-0.19.0/pysam -I/builddir/build/BUILD/pysam-0.19.0 -I/usr/include/python3.11 -c samtools/bam_import.c.pysam.c -o build/temp.linux-i686-3.11/samtools/bam_import.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.19.0/htslib -I/builddir/build/BUILD/pysam-0.19.0/samtools -I/builddir/build/BUILD/pysam-0.19.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.19.0/bcftools -I/builddir/build/BUILD/pysam-0.19.0/pysam -I/builddir/build/BUILD/pysam-0.19.0 -I/usr/include/python3.11 -c samtools/bam_index.c.pysam.c -o build/temp.linux-i686-3.11/samtools/bam_index.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.19.0/htslib -I/builddir/build/BUILD/pysam-0.19.0/samtools -I/builddir/build/BUILD/pysam-0.19.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.19.0/bcftools -I/builddir/build/BUILD/pysam-0.19.0/pysam -I/builddir/build/BUILD/pysam-0.19.0 -I/usr/include/python3.11 -c samtools/bam_lpileup.c.pysam.c -o build/temp.linux-i686-3.11/samtools/bam_lpileup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.19.0/htslib -I/builddir/build/BUILD/pysam-0.19.0/samtools -I/builddir/build/BUILD/pysam-0.19.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.19.0/bcftools -I/builddir/build/BUILD/pysam-0.19.0/pysam -I/builddir/build/BUILD/pysam-0.19.0 -I/usr/include/python3.11 -c samtools/bam_markdup.c.pysam.c -o build/temp.linux-i686-3.11/samtools/bam_markdup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.19.0/htslib -I/builddir/build/BUILD/pysam-0.19.0/samtools -I/builddir/build/BUILD/pysam-0.19.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.19.0/bcftools -I/builddir/build/BUILD/pysam-0.19.0/pysam -I/builddir/build/BUILD/pysam-0.19.0 -I/usr/include/python3.11 -c samtools/bam_mate.c.pysam.c -o build/temp.linux-i686-3.11/samtools/bam_mate.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.19.0/htslib -I/builddir/build/BUILD/pysam-0.19.0/samtools -I/builddir/build/BUILD/pysam-0.19.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.19.0/bcftools -I/builddir/build/BUILD/pysam-0.19.0/pysam -I/builddir/build/BUILD/pysam-0.19.0 -I/usr/include/python3.11 -c samtools/bam_md.c.pysam.c -o build/temp.linux-i686-3.11/samtools/bam_md.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.19.0/htslib -I/builddir/build/BUILD/pysam-0.19.0/samtools -I/builddir/build/BUILD/pysam-0.19.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.19.0/bcftools -I/builddir/build/BUILD/pysam-0.19.0/pysam -I/builddir/build/BUILD/pysam-0.19.0 -I/usr/include/python3.11 -c samtools/bam_plbuf.c.pysam.c -o build/temp.linux-i686-3.11/samtools/bam_plbuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.19.0/htslib -I/builddir/build/BUILD/pysam-0.19.0/samtools -I/builddir/build/BUILD/pysam-0.19.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.19.0/bcftools -I/builddir/build/BUILD/pysam-0.19.0/pysam -I/builddir/build/BUILD/pysam-0.19.0 -I/usr/include/python3.11 -c samtools/bam_plcmd.c.pysam.c -o build/temp.linux-i686-3.11/samtools/bam_plcmd.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.19.0/htslib -I/builddir/build/BUILD/pysam-0.19.0/samtools -I/builddir/build/BUILD/pysam-0.19.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.19.0/bcftools -I/builddir/build/BUILD/pysam-0.19.0/pysam -I/builddir/build/BUILD/pysam-0.19.0 -I/usr/include/python3.11 -c samtools/bam_quickcheck.c.pysam.c -o build/temp.linux-i686-3.11/samtools/bam_quickcheck.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.19.0/htslib -I/builddir/build/BUILD/pysam-0.19.0/samtools -I/builddir/build/BUILD/pysam-0.19.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.19.0/bcftools -I/builddir/build/BUILD/pysam-0.19.0/pysam -I/builddir/build/BUILD/pysam-0.19.0 -I/usr/include/python3.11 -c samtools/bam_reheader.c.pysam.c -o build/temp.linux-i686-3.11/samtools/bam_reheader.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.19.0/htslib -I/builddir/build/BUILD/pysam-0.19.0/samtools -I/builddir/build/BUILD/pysam-0.19.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.19.0/bcftools -I/builddir/build/BUILD/pysam-0.19.0/pysam -I/builddir/build/BUILD/pysam-0.19.0 -I/usr/include/python3.11 -c samtools/bam_rmdup.c.pysam.c -o build/temp.linux-i686-3.11/samtools/bam_rmdup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.19.0/htslib -I/builddir/build/BUILD/pysam-0.19.0/samtools -I/builddir/build/BUILD/pysam-0.19.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.19.0/bcftools -I/builddir/build/BUILD/pysam-0.19.0/pysam -I/builddir/build/BUILD/pysam-0.19.0 -I/usr/include/python3.11 -c samtools/bam_rmdupse.c.pysam.c -o build/temp.linux-i686-3.11/samtools/bam_rmdupse.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.19.0/htslib -I/builddir/build/BUILD/pysam-0.19.0/samtools -I/builddir/build/BUILD/pysam-0.19.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.19.0/bcftools -I/builddir/build/BUILD/pysam-0.19.0/pysam -I/builddir/build/BUILD/pysam-0.19.0 -I/usr/include/python3.11 -c samtools/bam_samples.c.pysam.c -o build/temp.linux-i686-3.11/samtools/bam_samples.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.19.0/htslib -I/builddir/build/BUILD/pysam-0.19.0/samtools -I/builddir/build/BUILD/pysam-0.19.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.19.0/bcftools -I/builddir/build/BUILD/pysam-0.19.0/pysam -I/builddir/build/BUILD/pysam-0.19.0 -I/usr/include/python3.11 -c samtools/bam_sort.c.pysam.c -o build/temp.linux-i686-3.11/samtools/bam_sort.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.19.0/htslib -I/builddir/build/BUILD/pysam-0.19.0/samtools -I/builddir/build/BUILD/pysam-0.19.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.19.0/bcftools -I/builddir/build/BUILD/pysam-0.19.0/pysam -I/builddir/build/BUILD/pysam-0.19.0 -I/usr/include/python3.11 -c samtools/bam_split.c.pysam.c -o build/temp.linux-i686-3.11/samtools/bam_split.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.19.0/htslib -I/builddir/build/BUILD/pysam-0.19.0/samtools -I/builddir/build/BUILD/pysam-0.19.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.19.0/bcftools -I/builddir/build/BUILD/pysam-0.19.0/pysam -I/builddir/build/BUILD/pysam-0.19.0 -I/usr/include/python3.11 -c samtools/bam_stat.c.pysam.c -o build/temp.linux-i686-3.11/samtools/bam_stat.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.19.0/htslib -I/builddir/build/BUILD/pysam-0.19.0/samtools -I/builddir/build/BUILD/pysam-0.19.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.19.0/bcftools -I/builddir/build/BUILD/pysam-0.19.0/pysam -I/builddir/build/BUILD/pysam-0.19.0 -I/usr/include/python3.11 -c samtools/bamshuf.c.pysam.c -o build/temp.linux-i686-3.11/samtools/bamshuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.19.0/htslib -I/builddir/build/BUILD/pysam-0.19.0/samtools -I/builddir/build/BUILD/pysam-0.19.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.19.0/bcftools -I/builddir/build/BUILD/pysam-0.19.0/pysam -I/builddir/build/BUILD/pysam-0.19.0 -I/usr/include/python3.11 -c samtools/bamtk.c.pysam.c -o build/temp.linux-i686-3.11/samtools/bamtk.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.19.0/htslib -I/builddir/build/BUILD/pysam-0.19.0/samtools -I/builddir/build/BUILD/pysam-0.19.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.19.0/bcftools -I/builddir/build/BUILD/pysam-0.19.0/pysam -I/builddir/build/BUILD/pysam-0.19.0 -I/usr/include/python3.11 -c samtools/bedcov.c.pysam.c -o build/temp.linux-i686-3.11/samtools/bedcov.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.19.0/htslib -I/builddir/build/BUILD/pysam-0.19.0/samtools -I/builddir/build/BUILD/pysam-0.19.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.19.0/bcftools -I/builddir/build/BUILD/pysam-0.19.0/pysam -I/builddir/build/BUILD/pysam-0.19.0 -I/usr/include/python3.11 -c samtools/bedidx.c.pysam.c -o build/temp.linux-i686-3.11/samtools/bedidx.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.19.0/htslib -I/builddir/build/BUILD/pysam-0.19.0/samtools -I/builddir/build/BUILD/pysam-0.19.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.19.0/bcftools -I/builddir/build/BUILD/pysam-0.19.0/pysam -I/builddir/build/BUILD/pysam-0.19.0 -I/usr/include/python3.11 -c samtools/consensus_pileup.c.pysam.c -o build/temp.linux-i686-3.11/samtools/consensus_pileup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.19.0/htslib -I/builddir/build/BUILD/pysam-0.19.0/samtools -I/builddir/build/BUILD/pysam-0.19.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.19.0/bcftools -I/builddir/build/BUILD/pysam-0.19.0/pysam -I/builddir/build/BUILD/pysam-0.19.0 -I/usr/include/python3.11 -c samtools/coverage.c.pysam.c -o build/temp.linux-i686-3.11/samtools/coverage.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.19.0/htslib -I/builddir/build/BUILD/pysam-0.19.0/samtools -I/builddir/build/BUILD/pysam-0.19.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.19.0/bcftools -I/builddir/build/BUILD/pysam-0.19.0/pysam -I/builddir/build/BUILD/pysam-0.19.0 -I/usr/include/python3.11 -c samtools/cut_target.c.pysam.c -o build/temp.linux-i686-3.11/samtools/cut_target.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.19.0/htslib -I/builddir/build/BUILD/pysam-0.19.0/samtools -I/builddir/build/BUILD/pysam-0.19.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.19.0/bcftools -I/builddir/build/BUILD/pysam-0.19.0/pysam -I/builddir/build/BUILD/pysam-0.19.0 -I/usr/include/python3.11 -c samtools/dict.c.pysam.c -o build/temp.linux-i686-3.11/samtools/dict.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.19.0/htslib -I/builddir/build/BUILD/pysam-0.19.0/samtools -I/builddir/build/BUILD/pysam-0.19.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.19.0/bcftools -I/builddir/build/BUILD/pysam-0.19.0/pysam -I/builddir/build/BUILD/pysam-0.19.0 -I/usr/include/python3.11 -c samtools/faidx.c.pysam.c -o build/temp.linux-i686-3.11/samtools/faidx.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.19.0/htslib -I/builddir/build/BUILD/pysam-0.19.0/samtools -I/builddir/build/BUILD/pysam-0.19.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.19.0/bcftools -I/builddir/build/BUILD/pysam-0.19.0/pysam -I/builddir/build/BUILD/pysam-0.19.0 -I/usr/include/python3.11 -c samtools/lz4/lz4.c -o build/temp.linux-i686-3.11/samtools/lz4/lz4.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.19.0/htslib -I/builddir/build/BUILD/pysam-0.19.0/samtools -I/builddir/build/BUILD/pysam-0.19.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.19.0/bcftools -I/builddir/build/BUILD/pysam-0.19.0/pysam -I/builddir/build/BUILD/pysam-0.19.0 -I/usr/include/python3.11 -c samtools/padding.c.pysam.c -o build/temp.linux-i686-3.11/samtools/padding.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.19.0/htslib -I/builddir/build/BUILD/pysam-0.19.0/samtools -I/builddir/build/BUILD/pysam-0.19.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.19.0/bcftools -I/builddir/build/BUILD/pysam-0.19.0/pysam -I/builddir/build/BUILD/pysam-0.19.0 -I/usr/include/python3.11 -c samtools/phase.c.pysam.c -o build/temp.linux-i686-3.11/samtools/phase.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.19.0/htslib -I/builddir/build/BUILD/pysam-0.19.0/samtools -I/builddir/build/BUILD/pysam-0.19.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.19.0/bcftools -I/builddir/build/BUILD/pysam-0.19.0/pysam -I/builddir/build/BUILD/pysam-0.19.0 -I/usr/include/python3.11 -c samtools/sam_opts.c.pysam.c -o build/temp.linux-i686-3.11/samtools/sam_opts.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.19.0/htslib -I/builddir/build/BUILD/pysam-0.19.0/samtools -I/builddir/build/BUILD/pysam-0.19.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.19.0/bcftools -I/builddir/build/BUILD/pysam-0.19.0/pysam -I/builddir/build/BUILD/pysam-0.19.0 -I/usr/include/python3.11 -c samtools/sam_utils.c.pysam.c -o build/temp.linux-i686-3.11/samtools/sam_utils.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.19.0/htslib -I/builddir/build/BUILD/pysam-0.19.0/samtools -I/builddir/build/BUILD/pysam-0.19.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.19.0/bcftools -I/builddir/build/BUILD/pysam-0.19.0/pysam -I/builddir/build/BUILD/pysam-0.19.0 -I/usr/include/python3.11 -c samtools/sam_view.c.pysam.c -o build/temp.linux-i686-3.11/samtools/sam_view.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.19.0/htslib -I/builddir/build/BUILD/pysam-0.19.0/samtools -I/builddir/build/BUILD/pysam-0.19.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.19.0/bcftools -I/builddir/build/BUILD/pysam-0.19.0/pysam -I/builddir/build/BUILD/pysam-0.19.0 -I/usr/include/python3.11 -c samtools/sample.c.pysam.c -o build/temp.linux-i686-3.11/samtools/sample.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.19.0/htslib -I/builddir/build/BUILD/pysam-0.19.0/samtools -I/builddir/build/BUILD/pysam-0.19.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.19.0/bcftools -I/builddir/build/BUILD/pysam-0.19.0/pysam -I/builddir/build/BUILD/pysam-0.19.0 -I/usr/include/python3.11 -c samtools/samtools.pysam.c -o build/temp.linux-i686-3.11/samtools/samtools.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.19.0/htslib -I/builddir/build/BUILD/pysam-0.19.0/samtools -I/builddir/build/BUILD/pysam-0.19.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.19.0/bcftools -I/builddir/build/BUILD/pysam-0.19.0/pysam -I/builddir/build/BUILD/pysam-0.19.0 -I/usr/include/python3.11 -c samtools/stats.c.pysam.c -o build/temp.linux-i686-3.11/samtools/stats.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.19.0/htslib -I/builddir/build/BUILD/pysam-0.19.0/samtools -I/builddir/build/BUILD/pysam-0.19.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.19.0/bcftools -I/builddir/build/BUILD/pysam-0.19.0/pysam -I/builddir/build/BUILD/pysam-0.19.0 -I/usr/include/python3.11 -c samtools/stats_isize.c.pysam.c -o build/temp.linux-i686-3.11/samtools/stats_isize.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.19.0/htslib -I/builddir/build/BUILD/pysam-0.19.0/samtools -I/builddir/build/BUILD/pysam-0.19.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.19.0/bcftools -I/builddir/build/BUILD/pysam-0.19.0/pysam -I/builddir/build/BUILD/pysam-0.19.0 -I/usr/include/python3.11 -c samtools/tmp_file.c.pysam.c -o build/temp.linux-i686-3.11/samtools/tmp_file.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -shared -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -Wl,--build-id=sha1 -g -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -Wl,--build-id=sha1 -g -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -Wl,-dT,/builddir/build/BUILD/pysam-0.19.0/.package_note-python-pysam-0.19.0-4.fc37.i386.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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection build/temp.linux-i686-3.11/pysam/libcsamtools.o build/temp.linux-i686-3.11/samtools/amplicon_stats.c.pysam.o build/temp.linux-i686-3.11/samtools/bam.c.pysam.o build/temp.linux-i686-3.11/samtools/bam2depth.c.pysam.o build/temp.linux-i686-3.11/samtools/bam_addrprg.c.pysam.o build/temp.linux-i686-3.11/samtools/bam_ampliconclip.c.pysam.o build/temp.linux-i686-3.11/samtools/bam_aux.c.pysam.o build/temp.linux-i686-3.11/samtools/bam_cat.c.pysam.o build/temp.linux-i686-3.11/samtools/bam_color.c.pysam.o build/temp.linux-i686-3.11/samtools/bam_consensus.c.pysam.o build/temp.linux-i686-3.11/samtools/bam_fastq.c.pysam.o build/temp.linux-i686-3.11/samtools/bam_flags.c.pysam.o build/temp.linux-i686-3.11/samtools/bam_import.c.pysam.o build/temp.linux-i686-3.11/samtools/bam_index.c.pysam.o build/temp.linux-i686-3.11/samtools/bam_lpileup.c.pysam.o build/temp.linux-i686-3.11/samtools/bam_markdup.c.pysam.o build/temp.linux-i686-3.11/samtools/bam_mate.c.pysam.o build/temp.linux-i686-3.11/samtools/bam_md.c.pysam.o build/temp.linux-i686-3.11/samtools/bam_plbuf.c.pysam.o build/temp.linux-i686-3.11/samtools/bam_plcmd.c.pysam.o build/temp.linux-i686-3.11/samtools/bam_quickcheck.c.pysam.o build/temp.linux-i686-3.11/samtools/bam_reheader.c.pysam.o build/temp.linux-i686-3.11/samtools/bam_rmdup.c.pysam.o build/temp.linux-i686-3.11/samtools/bam_rmdupse.c.pysam.o build/temp.linux-i686-3.11/samtools/bam_samples.c.pysam.o build/temp.linux-i686-3.11/samtools/bam_sort.c.pysam.o build/temp.linux-i686-3.11/samtools/bam_split.c.pysam.o build/temp.linux-i686-3.11/samtools/bam_stat.c.pysam.o build/temp.linux-i686-3.11/samtools/bamshuf.c.pysam.o build/temp.linux-i686-3.11/samtools/bamtk.c.pysam.o build/temp.linux-i686-3.11/samtools/bedcov.c.pysam.o build/temp.linux-i686-3.11/samtools/bedidx.c.pysam.o build/temp.linux-i686-3.11/samtools/consensus_pileup.c.pysam.o build/temp.linux-i686-3.11/samtools/coverage.c.pysam.o build/temp.linux-i686-3.11/samtools/cut_target.c.pysam.o build/temp.linux-i686-3.11/samtools/dict.c.pysam.o build/temp.linux-i686-3.11/samtools/faidx.c.pysam.o build/temp.linux-i686-3.11/samtools/lz4/lz4.o build/temp.linux-i686-3.11/samtools/padding.c.pysam.o build/temp.linux-i686-3.11/samtools/phase.c.pysam.o build/temp.linux-i686-3.11/samtools/sam_opts.c.pysam.o build/temp.linux-i686-3.11/samtools/sam_utils.c.pysam.o build/temp.linux-i686-3.11/samtools/sam_view.c.pysam.o build/temp.linux-i686-3.11/samtools/sample.c.pysam.o build/temp.linux-i686-3.11/samtools/samtools.pysam.o build/temp.linux-i686-3.11/samtools/stats.c.pysam.o build/temp.linux-i686-3.11/samtools/stats_isize.c.pysam.o build/temp.linux-i686-3.11/samtools/tmp_file.c.pysam.o -L/builddir/build/BUILD/pysam-0.19.0/pysam -L/builddir/build/BUILD/pysam-0.19.0/pysam -L/builddir/build/BUILD/pysam-0.19.0 -L/builddir/build/BUILD/pysam-0.19.0/build/lib.linux-i686-3.11/pysam -Lbuild/lib.linux-i686-3.11/pysam -Lbuild/lib.linux-i686-3.11/pysam -L/usr/lib -lz -llzma -lbz2 -lz -lm -lchtslib.cpython-311-i386-linux-gnu -o build/lib.linux-i686-3.11/pysam/libcsamtools.cpython-311-i386-linux-gnu.so -Wl,-rpath,$ORIGIN building 'pysam.libcbcftools' extension creating build/temp.linux-i686-3.11/bcftools gcc -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.19.0/htslib -I/builddir/build/BUILD/pysam-0.19.0/samtools -I/builddir/build/BUILD/pysam-0.19.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.19.0/bcftools -I/builddir/build/BUILD/pysam-0.19.0/pysam -I/builddir/build/BUILD/pysam-0.19.0 -I/usr/include/python3.11 -c bcftools/HMM.c.pysam.c -o build/temp.linux-i686-3.11/bcftools/HMM.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.19.0/htslib -I/builddir/build/BUILD/pysam-0.19.0/samtools -I/builddir/build/BUILD/pysam-0.19.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.19.0/bcftools -I/builddir/build/BUILD/pysam-0.19.0/pysam -I/builddir/build/BUILD/pysam-0.19.0 -I/usr/include/python3.11 -c bcftools/abuf.c.pysam.c -o build/temp.linux-i686-3.11/bcftools/abuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign 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-I/builddir/build/BUILD/pysam-0.19.0/bcftools -I/builddir/build/BUILD/pysam-0.19.0/pysam -I/builddir/build/BUILD/pysam-0.19.0 -I/usr/include/python3.11 -c bcftools/bam2bcf.c.pysam.c -o build/temp.linux-i686-3.11/bcftools/bam2bcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.19.0/htslib -I/builddir/build/BUILD/pysam-0.19.0/samtools -I/builddir/build/BUILD/pysam-0.19.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.19.0/bcftools -I/builddir/build/BUILD/pysam-0.19.0/pysam -I/builddir/build/BUILD/pysam-0.19.0 -I/usr/include/python3.11 -c bcftools/bam2bcf_indel.c.pysam.c -o build/temp.linux-i686-3.11/bcftools/bam2bcf_indel.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.19.0/htslib -I/builddir/build/BUILD/pysam-0.19.0/samtools -I/builddir/build/BUILD/pysam-0.19.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.19.0/bcftools -I/builddir/build/BUILD/pysam-0.19.0/pysam -I/builddir/build/BUILD/pysam-0.19.0 -I/usr/include/python3.11 -c bcftools/bam_sample.c.pysam.c -o build/temp.linux-i686-3.11/bcftools/bam_sample.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.19.0/htslib -I/builddir/build/BUILD/pysam-0.19.0/samtools -I/builddir/build/BUILD/pysam-0.19.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.19.0/bcftools -I/builddir/build/BUILD/pysam-0.19.0/pysam -I/builddir/build/BUILD/pysam-0.19.0 -I/usr/include/python3.11 -c bcftools/bcftools.pysam.c -o build/temp.linux-i686-3.11/bcftools/bcftools.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.19.0/htslib -I/builddir/build/BUILD/pysam-0.19.0/samtools -I/builddir/build/BUILD/pysam-0.19.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.19.0/bcftools -I/builddir/build/BUILD/pysam-0.19.0/pysam -I/builddir/build/BUILD/pysam-0.19.0 -I/usr/include/python3.11 -c bcftools/bin.c.pysam.c -o build/temp.linux-i686-3.11/bcftools/bin.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign 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-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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.19.0/htslib -I/builddir/build/BUILD/pysam-0.19.0/samtools -I/builddir/build/BUILD/pysam-0.19.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.19.0/bcftools -I/builddir/build/BUILD/pysam-0.19.0/pysam -I/builddir/build/BUILD/pysam-0.19.0 -I/usr/include/python3.11 -c bcftools/cols.c.pysam.c -o build/temp.linux-i686-3.11/bcftools/cols.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches 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-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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.19.0/htslib -I/builddir/build/BUILD/pysam-0.19.0/samtools -I/builddir/build/BUILD/pysam-0.19.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.19.0/bcftools -I/builddir/build/BUILD/pysam-0.19.0/pysam -I/builddir/build/BUILD/pysam-0.19.0 -I/usr/include/python3.11 -c bcftools/consensus.c.pysam.c -o build/temp.linux-i686-3.11/bcftools/consensus.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -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 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-specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.19.0/htslib -I/builddir/build/BUILD/pysam-0.19.0/samtools -I/builddir/build/BUILD/pysam-0.19.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.19.0/bcftools -I/builddir/build/BUILD/pysam-0.19.0/pysam -I/builddir/build/BUILD/pysam-0.19.0 -I/usr/include/python3.11 -c bcftools/convert.c.pysam.c -o build/temp.linux-i686-3.11/bcftools/convert.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse 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-specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.19.0/htslib -I/builddir/build/BUILD/pysam-0.19.0/samtools -I/builddir/build/BUILD/pysam-0.19.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.19.0/bcftools -I/builddir/build/BUILD/pysam-0.19.0/pysam -I/builddir/build/BUILD/pysam-0.19.0 -I/usr/include/python3.11 -c bcftools/csq.c.pysam.c -o build/temp.linux-i686-3.11/bcftools/csq.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection 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-mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.19.0/htslib -I/builddir/build/BUILD/pysam-0.19.0/samtools -I/builddir/build/BUILD/pysam-0.19.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.19.0/bcftools -I/builddir/build/BUILD/pysam-0.19.0/pysam -I/builddir/build/BUILD/pysam-0.19.0 -I/usr/include/python3.11 -c bcftools/dist.c.pysam.c -o build/temp.linux-i686-3.11/bcftools/dist.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.19.0/htslib -I/builddir/build/BUILD/pysam-0.19.0/samtools -I/builddir/build/BUILD/pysam-0.19.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.19.0/bcftools -I/builddir/build/BUILD/pysam-0.19.0/pysam -I/builddir/build/BUILD/pysam-0.19.0 -I/usr/include/python3.11 -c bcftools/em.c.pysam.c -o build/temp.linux-i686-3.11/bcftools/em.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.19.0/htslib -I/builddir/build/BUILD/pysam-0.19.0/samtools -I/builddir/build/BUILD/pysam-0.19.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.19.0/bcftools -I/builddir/build/BUILD/pysam-0.19.0/pysam -I/builddir/build/BUILD/pysam-0.19.0 -I/usr/include/python3.11 -c bcftools/extsort.c.pysam.c -o build/temp.linux-i686-3.11/bcftools/extsort.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign 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-I/builddir/build/BUILD/pysam-0.19.0/bcftools -I/builddir/build/BUILD/pysam-0.19.0/pysam -I/builddir/build/BUILD/pysam-0.19.0 -I/usr/include/python3.11 -c bcftools/filter.c.pysam.c -o build/temp.linux-i686-3.11/bcftools/filter.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.19.0/htslib -I/builddir/build/BUILD/pysam-0.19.0/samtools -I/builddir/build/BUILD/pysam-0.19.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.19.0/bcftools -I/builddir/build/BUILD/pysam-0.19.0/pysam -I/builddir/build/BUILD/pysam-0.19.0 -I/usr/include/python3.11 -c bcftools/gvcf.c.pysam.c -o build/temp.linux-i686-3.11/bcftools/gvcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.19.0/htslib -I/builddir/build/BUILD/pysam-0.19.0/samtools -I/builddir/build/BUILD/pysam-0.19.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.19.0/bcftools -I/builddir/build/BUILD/pysam-0.19.0/pysam -I/builddir/build/BUILD/pysam-0.19.0 -I/usr/include/python3.11 -c bcftools/hclust.c.pysam.c -o build/temp.linux-i686-3.11/bcftools/hclust.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS 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-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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.19.0/htslib -I/builddir/build/BUILD/pysam-0.19.0/samtools -I/builddir/build/BUILD/pysam-0.19.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.19.0/bcftools -I/builddir/build/BUILD/pysam-0.19.0/pysam -I/builddir/build/BUILD/pysam-0.19.0 -I/usr/include/python3.11 -c bcftools/main.c.pysam.c -o build/temp.linux-i686-3.11/bcftools/main.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -Wsign-compare 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-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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.19.0/htslib -I/builddir/build/BUILD/pysam-0.19.0/samtools -I/builddir/build/BUILD/pysam-0.19.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.19.0/bcftools -I/builddir/build/BUILD/pysam-0.19.0/pysam -I/builddir/build/BUILD/pysam-0.19.0 -I/usr/include/python3.11 -c bcftools/mcall.c.pysam.c -o build/temp.linux-i686-3.11/bcftools/mcall.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.19.0/htslib -I/builddir/build/BUILD/pysam-0.19.0/samtools -I/builddir/build/BUILD/pysam-0.19.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.19.0/bcftools -I/builddir/build/BUILD/pysam-0.19.0/pysam -I/builddir/build/BUILD/pysam-0.19.0 -I/usr/include/python3.11 -c bcftools/mpileup.c.pysam.c -o build/temp.linux-i686-3.11/bcftools/mpileup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -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 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-specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.19.0/htslib -I/builddir/build/BUILD/pysam-0.19.0/samtools -I/builddir/build/BUILD/pysam-0.19.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.19.0/bcftools -I/builddir/build/BUILD/pysam-0.19.0/pysam -I/builddir/build/BUILD/pysam-0.19.0 -I/usr/include/python3.11 -c bcftools/ploidy.c.pysam.c -o build/temp.linux-i686-3.11/bcftools/ploidy.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.19.0/htslib -I/builddir/build/BUILD/pysam-0.19.0/samtools -I/builddir/build/BUILD/pysam-0.19.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.19.0/bcftools -I/builddir/build/BUILD/pysam-0.19.0/pysam -I/builddir/build/BUILD/pysam-0.19.0 -I/usr/include/python3.11 -c bcftools/prob1.c.pysam.c -o build/temp.linux-i686-3.11/bcftools/prob1.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.19.0/htslib -I/builddir/build/BUILD/pysam-0.19.0/samtools -I/builddir/build/BUILD/pysam-0.19.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.19.0/bcftools -I/builddir/build/BUILD/pysam-0.19.0/pysam -I/builddir/build/BUILD/pysam-0.19.0 -I/usr/include/python3.11 -c bcftools/regidx.c.pysam.c -o build/temp.linux-i686-3.11/bcftools/regidx.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.19.0/htslib -I/builddir/build/BUILD/pysam-0.19.0/samtools -I/builddir/build/BUILD/pysam-0.19.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.19.0/bcftools -I/builddir/build/BUILD/pysam-0.19.0/pysam -I/builddir/build/BUILD/pysam-0.19.0 -I/usr/include/python3.11 -c bcftools/reheader.c.pysam.c -o build/temp.linux-i686-3.11/bcftools/reheader.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS 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-I/builddir/build/BUILD/pysam-0.19.0/samtools -I/builddir/build/BUILD/pysam-0.19.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.19.0/bcftools -I/builddir/build/BUILD/pysam-0.19.0/pysam -I/builddir/build/BUILD/pysam-0.19.0 -I/usr/include/python3.11 -c bcftools/smpl_ilist.c.pysam.c -o build/temp.linux-i686-3.11/bcftools/smpl_ilist.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic 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-I/builddir/build/BUILD/pysam-0.19.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.19.0/bcftools -I/builddir/build/BUILD/pysam-0.19.0/pysam -I/builddir/build/BUILD/pysam-0.19.0 -I/usr/include/python3.11 -c bcftools/str_finder.c.pysam.c -o build/temp.linux-i686-3.11/bcftools/str_finder.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign 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-I/builddir/build/BUILD/pysam-0.19.0/bcftools -I/builddir/build/BUILD/pysam-0.19.0/pysam -I/builddir/build/BUILD/pysam-0.19.0 -I/usr/include/python3.11 -c bcftools/tabix.c.pysam.c -o build/temp.linux-i686-3.11/bcftools/tabix.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.19.0/htslib -I/builddir/build/BUILD/pysam-0.19.0/samtools -I/builddir/build/BUILD/pysam-0.19.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.19.0/bcftools -I/builddir/build/BUILD/pysam-0.19.0/pysam -I/builddir/build/BUILD/pysam-0.19.0 -I/usr/include/python3.11 -c bcftools/tsv2vcf.c.pysam.c -o build/temp.linux-i686-3.11/bcftools/tsv2vcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.19.0/htslib -I/builddir/build/BUILD/pysam-0.19.0/samtools -I/builddir/build/BUILD/pysam-0.19.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.19.0/bcftools -I/builddir/build/BUILD/pysam-0.19.0/pysam -I/builddir/build/BUILD/pysam-0.19.0 -I/usr/include/python3.11 -c bcftools/vcfannotate.c.pysam.c -o build/temp.linux-i686-3.11/bcftools/vcfannotate.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.19.0/htslib -I/builddir/build/BUILD/pysam-0.19.0/samtools -I/builddir/build/BUILD/pysam-0.19.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.19.0/bcftools -I/builddir/build/BUILD/pysam-0.19.0/pysam -I/builddir/build/BUILD/pysam-0.19.0 -I/usr/include/python3.11 -c bcftools/vcfbuf.c.pysam.c -o build/temp.linux-i686-3.11/bcftools/vcfbuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.19.0/htslib -I/builddir/build/BUILD/pysam-0.19.0/samtools -I/builddir/build/BUILD/pysam-0.19.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.19.0/bcftools -I/builddir/build/BUILD/pysam-0.19.0/pysam -I/builddir/build/BUILD/pysam-0.19.0 -I/usr/include/python3.11 -c bcftools/vcfcall.c.pysam.c -o build/temp.linux-i686-3.11/bcftools/vcfcall.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.19.0/htslib -I/builddir/build/BUILD/pysam-0.19.0/samtools -I/builddir/build/BUILD/pysam-0.19.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.19.0/bcftools -I/builddir/build/BUILD/pysam-0.19.0/pysam -I/builddir/build/BUILD/pysam-0.19.0 -I/usr/include/python3.11 -c bcftools/vcfcnv.c.pysam.c -o build/temp.linux-i686-3.11/bcftools/vcfcnv.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc 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-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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.19.0/htslib -I/builddir/build/BUILD/pysam-0.19.0/samtools -I/builddir/build/BUILD/pysam-0.19.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.19.0/bcftools -I/builddir/build/BUILD/pysam-0.19.0/pysam -I/builddir/build/BUILD/pysam-0.19.0 -I/usr/include/python3.11 -c bcftools/vcfconcat.c.pysam.c -o build/temp.linux-i686-3.11/bcftools/vcfconcat.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.19.0/htslib -I/builddir/build/BUILD/pysam-0.19.0/samtools -I/builddir/build/BUILD/pysam-0.19.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.19.0/bcftools -I/builddir/build/BUILD/pysam-0.19.0/pysam -I/builddir/build/BUILD/pysam-0.19.0 -I/usr/include/python3.11 -c bcftools/vcfconvert.c.pysam.c -o build/temp.linux-i686-3.11/bcftools/vcfconvert.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.19.0/htslib -I/builddir/build/BUILD/pysam-0.19.0/samtools -I/builddir/build/BUILD/pysam-0.19.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.19.0/bcftools -I/builddir/build/BUILD/pysam-0.19.0/pysam -I/builddir/build/BUILD/pysam-0.19.0 -I/usr/include/python3.11 -c bcftools/vcffilter.c.pysam.c -o build/temp.linux-i686-3.11/bcftools/vcffilter.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.19.0/htslib -I/builddir/build/BUILD/pysam-0.19.0/samtools -I/builddir/build/BUILD/pysam-0.19.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.19.0/bcftools -I/builddir/build/BUILD/pysam-0.19.0/pysam -I/builddir/build/BUILD/pysam-0.19.0 -I/usr/include/python3.11 -c bcftools/vcfgtcheck.c.pysam.c -o build/temp.linux-i686-3.11/bcftools/vcfgtcheck.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.19.0/htslib -I/builddir/build/BUILD/pysam-0.19.0/samtools -I/builddir/build/BUILD/pysam-0.19.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.19.0/bcftools -I/builddir/build/BUILD/pysam-0.19.0/pysam -I/builddir/build/BUILD/pysam-0.19.0 -I/usr/include/python3.11 -c bcftools/vcfhead.c.pysam.c -o build/temp.linux-i686-3.11/bcftools/vcfhead.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.19.0/htslib -I/builddir/build/BUILD/pysam-0.19.0/samtools -I/builddir/build/BUILD/pysam-0.19.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.19.0/bcftools -I/builddir/build/BUILD/pysam-0.19.0/pysam -I/builddir/build/BUILD/pysam-0.19.0 -I/usr/include/python3.11 -c bcftools/vcfindex.c.pysam.c -o build/temp.linux-i686-3.11/bcftools/vcfindex.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.19.0/htslib -I/builddir/build/BUILD/pysam-0.19.0/samtools -I/builddir/build/BUILD/pysam-0.19.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.19.0/bcftools -I/builddir/build/BUILD/pysam-0.19.0/pysam -I/builddir/build/BUILD/pysam-0.19.0 -I/usr/include/python3.11 -c bcftools/vcfisec.c.pysam.c -o build/temp.linux-i686-3.11/bcftools/vcfisec.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.19.0/htslib -I/builddir/build/BUILD/pysam-0.19.0/samtools -I/builddir/build/BUILD/pysam-0.19.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.19.0/bcftools -I/builddir/build/BUILD/pysam-0.19.0/pysam -I/builddir/build/BUILD/pysam-0.19.0 -I/usr/include/python3.11 -c bcftools/vcfmerge.c.pysam.c -o build/temp.linux-i686-3.11/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:749:34: warning: argument 1 range [2147483648, 4294967295] exceeds maximum object size 2147483647 [-Walloc-size-larger-than=] 749 | ma->gvcf = (gvcf_aux_t*) calloc(ma->n,sizeof(gvcf_aux_t)); // -Walloc-size-larger-than gives a harmless warning caused by signed integer ma->n | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/pysam-0.19.0/htslib/htslib/kstring.h:30, from /builddir/build/BUILD/pysam-0.19.0/htslib/htslib/hts.h:37, from /builddir/build/BUILD/pysam-0.19.0/htslib/htslib/vcf.h:39, from bcftools/vcfmerge.c.pysam.c:35: /usr/include/stdlib.h:543:14: note: in a call to allocation function ‘calloc’ declared here 543 | extern void *calloc (size_t __nmemb, size_t __size) | ^~~~~~ gcc -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.19.0/htslib -I/builddir/build/BUILD/pysam-0.19.0/samtools -I/builddir/build/BUILD/pysam-0.19.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.19.0/bcftools -I/builddir/build/BUILD/pysam-0.19.0/pysam -I/builddir/build/BUILD/pysam-0.19.0 -I/usr/include/python3.11 -c bcftools/vcfnorm.c.pysam.c -o build/temp.linux-i686-3.11/bcftools/vcfnorm.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.19.0/htslib -I/builddir/build/BUILD/pysam-0.19.0/samtools -I/builddir/build/BUILD/pysam-0.19.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.19.0/bcftools -I/builddir/build/BUILD/pysam-0.19.0/pysam -I/builddir/build/BUILD/pysam-0.19.0 -I/usr/include/python3.11 -c bcftools/vcfplugin.c.pysam.c -o build/temp.linux-i686-3.11/bcftools/vcfplugin.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.19.0/htslib -I/builddir/build/BUILD/pysam-0.19.0/samtools -I/builddir/build/BUILD/pysam-0.19.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.19.0/bcftools -I/builddir/build/BUILD/pysam-0.19.0/pysam -I/builddir/build/BUILD/pysam-0.19.0 -I/usr/include/python3.11 -c bcftools/vcfquery.c.pysam.c -o build/temp.linux-i686-3.11/bcftools/vcfquery.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.19.0/htslib -I/builddir/build/BUILD/pysam-0.19.0/samtools -I/builddir/build/BUILD/pysam-0.19.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.19.0/bcftools -I/builddir/build/BUILD/pysam-0.19.0/pysam -I/builddir/build/BUILD/pysam-0.19.0 -I/usr/include/python3.11 -c bcftools/vcfroh.c.pysam.c -o build/temp.linux-i686-3.11/bcftools/vcfroh.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -Wsign-compare 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-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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.19.0/htslib -I/builddir/build/BUILD/pysam-0.19.0/samtools -I/builddir/build/BUILD/pysam-0.19.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.19.0/bcftools -I/builddir/build/BUILD/pysam-0.19.0/pysam -I/builddir/build/BUILD/pysam-0.19.0 -I/usr/include/python3.11 -c bcftools/vcfsom.c.pysam.c -o build/temp.linux-i686-3.11/bcftools/vcfsom.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.19.0/htslib -I/builddir/build/BUILD/pysam-0.19.0/samtools -I/builddir/build/BUILD/pysam-0.19.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.19.0/bcftools -I/builddir/build/BUILD/pysam-0.19.0/pysam -I/builddir/build/BUILD/pysam-0.19.0 -I/usr/include/python3.11 -c bcftools/vcfsort.c.pysam.c -o build/temp.linux-i686-3.11/bcftools/vcfsort.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.19.0/htslib -I/builddir/build/BUILD/pysam-0.19.0/samtools -I/builddir/build/BUILD/pysam-0.19.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.19.0/bcftools -I/builddir/build/BUILD/pysam-0.19.0/pysam -I/builddir/build/BUILD/pysam-0.19.0 -I/usr/include/python3.11 -c bcftools/vcfstats.c.pysam.c -o build/temp.linux-i686-3.11/bcftools/vcfstats.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.19.0/htslib -I/builddir/build/BUILD/pysam-0.19.0/samtools -I/builddir/build/BUILD/pysam-0.19.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.19.0/bcftools -I/builddir/build/BUILD/pysam-0.19.0/pysam -I/builddir/build/BUILD/pysam-0.19.0 -I/usr/include/python3.11 -c bcftools/vcfview.c.pysam.c -o build/temp.linux-i686-3.11/bcftools/vcfview.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.19.0/htslib -I/builddir/build/BUILD/pysam-0.19.0/samtools -I/builddir/build/BUILD/pysam-0.19.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.19.0/bcftools -I/builddir/build/BUILD/pysam-0.19.0/pysam -I/builddir/build/BUILD/pysam-0.19.0 -I/usr/include/python3.11 -c bcftools/vcmp.c.pysam.c -o build/temp.linux-i686-3.11/bcftools/vcmp.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall 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-I/builddir/build/BUILD/pysam-0.19.0/htslib -I/builddir/build/BUILD/pysam-0.19.0/samtools -I/builddir/build/BUILD/pysam-0.19.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.19.0/bcftools -I/builddir/build/BUILD/pysam-0.19.0/pysam -I/builddir/build/BUILD/pysam-0.19.0 -I/usr/include/python3.11 -c bcftools/version.c.pysam.c -o build/temp.linux-i686-3.11/bcftools/version.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.19.0/htslib -I/builddir/build/BUILD/pysam-0.19.0/samtools -I/builddir/build/BUILD/pysam-0.19.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.19.0/bcftools -I/builddir/build/BUILD/pysam-0.19.0/pysam -I/builddir/build/BUILD/pysam-0.19.0 -I/usr/include/python3.11 -c pysam/libcbcftools.c -o build/temp.linux-i686-3.11/pysam/libcbcftools.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -shared -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -Wl,--build-id=sha1 -g -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -Wl,--build-id=sha1 -g -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -Wl,-dT,/builddir/build/BUILD/pysam-0.19.0/.package_note-python-pysam-0.19.0-4.fc37.i386.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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection build/temp.linux-i686-3.11/bcftools/HMM.c.pysam.o build/temp.linux-i686-3.11/bcftools/abuf.c.pysam.o build/temp.linux-i686-3.11/bcftools/bam2bcf.c.pysam.o build/temp.linux-i686-3.11/bcftools/bam2bcf_indel.c.pysam.o build/temp.linux-i686-3.11/bcftools/bam_sample.c.pysam.o build/temp.linux-i686-3.11/bcftools/bcftools.pysam.o build/temp.linux-i686-3.11/bcftools/bin.c.pysam.o build/temp.linux-i686-3.11/bcftools/ccall.c.pysam.o build/temp.linux-i686-3.11/bcftools/cols.c.pysam.o build/temp.linux-i686-3.11/bcftools/consensus.c.pysam.o build/temp.linux-i686-3.11/bcftools/convert.c.pysam.o build/temp.linux-i686-3.11/bcftools/csq.c.pysam.o build/temp.linux-i686-3.11/bcftools/dist.c.pysam.o build/temp.linux-i686-3.11/bcftools/em.c.pysam.o build/temp.linux-i686-3.11/bcftools/extsort.c.pysam.o build/temp.linux-i686-3.11/bcftools/filter.c.pysam.o build/temp.linux-i686-3.11/bcftools/gvcf.c.pysam.o build/temp.linux-i686-3.11/bcftools/hclust.c.pysam.o build/temp.linux-i686-3.11/bcftools/kmin.c.pysam.o build/temp.linux-i686-3.11/bcftools/main.c.pysam.o build/temp.linux-i686-3.11/bcftools/mcall.c.pysam.o build/temp.linux-i686-3.11/bcftools/mpileup.c.pysam.o build/temp.linux-i686-3.11/bcftools/ploidy.c.pysam.o build/temp.linux-i686-3.11/bcftools/prob1.c.pysam.o build/temp.linux-i686-3.11/bcftools/regidx.c.pysam.o build/temp.linux-i686-3.11/bcftools/reheader.c.pysam.o build/temp.linux-i686-3.11/bcftools/smpl_ilist.c.pysam.o build/temp.linux-i686-3.11/bcftools/str_finder.c.pysam.o build/temp.linux-i686-3.11/bcftools/tabix.c.pysam.o build/temp.linux-i686-3.11/bcftools/tsv2vcf.c.pysam.o build/temp.linux-i686-3.11/bcftools/vcfannotate.c.pysam.o build/temp.linux-i686-3.11/bcftools/vcfbuf.c.pysam.o build/temp.linux-i686-3.11/bcftools/vcfcall.c.pysam.o build/temp.linux-i686-3.11/bcftools/vcfcnv.c.pysam.o build/temp.linux-i686-3.11/bcftools/vcfconcat.c.pysam.o build/temp.linux-i686-3.11/bcftools/vcfconvert.c.pysam.o build/temp.linux-i686-3.11/bcftools/vcffilter.c.pysam.o build/temp.linux-i686-3.11/bcftools/vcfgtcheck.c.pysam.o build/temp.linux-i686-3.11/bcftools/vcfhead.c.pysam.o build/temp.linux-i686-3.11/bcftools/vcfindex.c.pysam.o build/temp.linux-i686-3.11/bcftools/vcfisec.c.pysam.o build/temp.linux-i686-3.11/bcftools/vcfmerge.c.pysam.o build/temp.linux-i686-3.11/bcftools/vcfnorm.c.pysam.o build/temp.linux-i686-3.11/bcftools/vcfplugin.c.pysam.o build/temp.linux-i686-3.11/bcftools/vcfquery.c.pysam.o build/temp.linux-i686-3.11/bcftools/vcfroh.c.pysam.o build/temp.linux-i686-3.11/bcftools/vcfsom.c.pysam.o build/temp.linux-i686-3.11/bcftools/vcfsort.c.pysam.o build/temp.linux-i686-3.11/bcftools/vcfstats.c.pysam.o build/temp.linux-i686-3.11/bcftools/vcfview.c.pysam.o build/temp.linux-i686-3.11/bcftools/vcmp.c.pysam.o build/temp.linux-i686-3.11/bcftools/version.c.pysam.o build/temp.linux-i686-3.11/pysam/libcbcftools.o -L/builddir/build/BUILD/pysam-0.19.0/pysam -L/builddir/build/BUILD/pysam-0.19.0/pysam -L/builddir/build/BUILD/pysam-0.19.0 -L/builddir/build/BUILD/pysam-0.19.0/build/lib.linux-i686-3.11/pysam -Lbuild/lib.linux-i686-3.11/pysam -Lbuild/lib.linux-i686-3.11/pysam -Lbuild/lib.linux-i686-3.11/pysam -L/usr/lib -lz -llzma -lbz2 -lz -lm -lchtslib.cpython-311-i386-linux-gnu -o build/lib.linux-i686-3.11/pysam/libcbcftools.cpython-311-i386-linux-gnu.so -Wl,-rpath,$ORIGIN bcftools/vcfmerge.c.pysam.c: In function ‘maux_init’: bcftools/vcfmerge.c.pysam.c:749:34: warning: argument 1 range [2147483648, 4294967295] exceeds maximum object size 2147483647 [-Walloc-size-larger-than=] 749 | ma->gvcf = (gvcf_aux_t*) calloc(ma->n,sizeof(gvcf_aux_t)); // -Walloc-size-larger-than gives a harmless warning caused by signed integer ma->n | ^ /usr/include/stdlib.h:543:14: note: in a call to allocation function ‘calloc’ declared here 543 | extern void *calloc (size_t __nmemb, size_t __size) | ^ building 'pysam.libcutils' extension gcc -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.19.0/htslib -I/builddir/build/BUILD/pysam-0.19.0/samtools -I/builddir/build/BUILD/pysam-0.19.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.19.0/bcftools -I/builddir/build/BUILD/pysam-0.19.0/pysam -I/builddir/build/BUILD/pysam-0.19.0 -I/usr/include/python3.11 -c pysam/libcutils.c -o build/temp.linux-i686-3.11/pysam/libcutils.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.19.0/htslib -I/builddir/build/BUILD/pysam-0.19.0/samtools -I/builddir/build/BUILD/pysam-0.19.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.19.0/bcftools -I/builddir/build/BUILD/pysam-0.19.0/pysam -I/builddir/build/BUILD/pysam-0.19.0 -I/usr/include/python3.11 -c pysam/pysam_util.c -o build/temp.linux-i686-3.11/pysam/pysam_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -shared -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -Wl,--build-id=sha1 -g -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -Wl,--build-id=sha1 -g -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -Wl,-dT,/builddir/build/BUILD/pysam-0.19.0/.package_note-python-pysam-0.19.0-4.fc37.i386.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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection build/temp.linux-i686-3.11/pysam/libcutils.o build/temp.linux-i686-3.11/pysam/pysam_util.o -L/builddir/build/BUILD/pysam-0.19.0/pysam -L/builddir/build/BUILD/pysam-0.19.0/pysam -L/builddir/build/BUILD/pysam-0.19.0 -L/builddir/build/BUILD/pysam-0.19.0/build/lib.linux-i686-3.11/pysam -Lbuild/lib.linux-i686-3.11/pysam -Lbuild/lib.linux-i686-3.11/pysam -Lbuild/lib.linux-i686-3.11/pysam -Lbuild/lib.linux-i686-3.11/pysam -L/usr/lib -lz -llzma -lbz2 -lz -lm -lchtslib.cpython-311-i386-linux-gnu -lcsamtools.cpython-311-i386-linux-gnu -lcbcftools.cpython-311-i386-linux-gnu -o build/lib.linux-i686-3.11/pysam/libcutils.cpython-311-i386-linux-gnu.so -Wl,-rpath,$ORIGIN building 'pysam.libcalignmentfile' extension gcc -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.19.0/htslib -I/builddir/build/BUILD/pysam-0.19.0/samtools -I/builddir/build/BUILD/pysam-0.19.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.19.0/bcftools -I/builddir/build/BUILD/pysam-0.19.0/pysam -I/builddir/build/BUILD/pysam-0.19.0 -I/usr/include/python3.11 -c pysam/libcalignmentfile.c -o build/temp.linux-i686-3.11/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_20IteratorRowSelection_cnext’: pysam/libcalignmentfile.c:28463:16: warning: ignoring return value of ‘bgzf_seek’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 28463 | (void)(bgzf_seek(hts_get_bgzfp(__pyx_v_self->__pyx_base.htsfile), __pyx_v_pos, 0)); | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pysam/libcalignmentfile.c: In function ‘__pyx_pf_5pysam_17libcalignmentfile_13AlignmentFile_6_open’: pysam/libcalignmentfile.c:14180:20: warning: ignoring return value of ‘sam_hdr_write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 14180 | (void)(sam_hdr_write(__pyx_v_self->__pyx_base.htsfile, __pyx_v_hdr)); | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -shared -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -Wl,--build-id=sha1 -g -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -Wl,--build-id=sha1 -g -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -Wl,-dT,/builddir/build/BUILD/pysam-0.19.0/.package_note-python-pysam-0.19.0-4.fc37.i386.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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection build/temp.linux-i686-3.11/pysam/libcalignmentfile.o -L/builddir/build/BUILD/pysam-0.19.0/pysam -L/builddir/build/BUILD/pysam-0.19.0/pysam -L/builddir/build/BUILD/pysam-0.19.0 -L/builddir/build/BUILD/pysam-0.19.0/build/lib.linux-i686-3.11/pysam -Lbuild/lib.linux-i686-3.11/pysam -Lbuild/lib.linux-i686-3.11/pysam -Lbuild/lib.linux-i686-3.11/pysam -Lbuild/lib.linux-i686-3.11/pysam -Lbuild/lib.linux-i686-3.11/pysam -L/usr/lib -lz -llzma -lbz2 -lz -lm -lchtslib.cpython-311-i386-linux-gnu -lcutils.cpython-311-i386-linux-gnu -o build/lib.linux-i686-3.11/pysam/libcalignmentfile.cpython-311-i386-linux-gnu.so -Wl,-rpath,$ORIGIN building 'pysam.libcsamfile' extension gcc -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.19.0/htslib -I/builddir/build/BUILD/pysam-0.19.0/samtools -I/builddir/build/BUILD/pysam-0.19.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.19.0/bcftools -I/builddir/build/BUILD/pysam-0.19.0/pysam -I/builddir/build/BUILD/pysam-0.19.0 -I/usr/include/python3.11 -c pysam/libcsamfile.c -o build/temp.linux-i686-3.11/pysam/libcsamfile.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -shared -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -Wl,--build-id=sha1 -g -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -Wl,--build-id=sha1 -g -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -Wl,-dT,/builddir/build/BUILD/pysam-0.19.0/.package_note-python-pysam-0.19.0-4.fc37.i386.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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection build/temp.linux-i686-3.11/pysam/libcsamfile.o -L/builddir/build/BUILD/pysam-0.19.0/pysam -L/builddir/build/BUILD/pysam-0.19.0/pysam -L/builddir/build/BUILD/pysam-0.19.0 -L/builddir/build/BUILD/pysam-0.19.0/build/lib.linux-i686-3.11/pysam -Lbuild/lib.linux-i686-3.11/pysam -Lbuild/lib.linux-i686-3.11/pysam -Lbuild/lib.linux-i686-3.11/pysam -Lbuild/lib.linux-i686-3.11/pysam -Lbuild/lib.linux-i686-3.11/pysam -Lbuild/lib.linux-i686-3.11/pysam -L/usr/lib -lz -llzma -lbz2 -lz -lm -lchtslib.cpython-311-i386-linux-gnu -lcutils.cpython-311-i386-linux-gnu -o build/lib.linux-i686-3.11/pysam/libcsamfile.cpython-311-i386-linux-gnu.so -Wl,-rpath,$ORIGIN building 'pysam.libcalignedsegment' extension gcc -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.19.0/htslib -I/builddir/build/BUILD/pysam-0.19.0/samtools -I/builddir/build/BUILD/pysam-0.19.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.19.0/bcftools -I/builddir/build/BUILD/pysam-0.19.0/pysam -I/builddir/build/BUILD/pysam-0.19.0 -I/usr/include/python3.11 -c pysam/libcalignedsegment.c -o build/temp.linux-i686-3.11/pysam/libcalignedsegment.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement pysam/libcalignedsegment.c: In function ‘__pyx_pf_5pysam_18libcalignedsegment_14AlignedSegment_18fromstring’: pysam/libcalignedsegment.c:14608:10: warning: ignoring return value of ‘sam_parse1’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 14608 | (void)(sam_parse1((&__pyx_v_line), __pyx_v_dest->header->ptr, __pyx_v_dest->_delegate)); | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -shared -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -Wl,--build-id=sha1 -g -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -Wl,--build-id=sha1 -g -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -Wl,-dT,/builddir/build/BUILD/pysam-0.19.0/.package_note-python-pysam-0.19.0-4.fc37.i386.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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection build/temp.linux-i686-3.11/pysam/libcalignedsegment.o -L/builddir/build/BUILD/pysam-0.19.0/pysam -L/builddir/build/BUILD/pysam-0.19.0/pysam -L/builddir/build/BUILD/pysam-0.19.0 -L/builddir/build/BUILD/pysam-0.19.0/build/lib.linux-i686-3.11/pysam -Lbuild/lib.linux-i686-3.11/pysam -Lbuild/lib.linux-i686-3.11/pysam -Lbuild/lib.linux-i686-3.11/pysam -Lbuild/lib.linux-i686-3.11/pysam -Lbuild/lib.linux-i686-3.11/pysam -Lbuild/lib.linux-i686-3.11/pysam -Lbuild/lib.linux-i686-3.11/pysam -L/usr/lib -lz -llzma -lbz2 -lz -lm -lchtslib.cpython-311-i386-linux-gnu -lcutils.cpython-311-i386-linux-gnu -o build/lib.linux-i686-3.11/pysam/libcalignedsegment.cpython-311-i386-linux-gnu.so -Wl,-rpath,$ORIGIN building 'pysam.libctabix' extension gcc -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.19.0/htslib -I/builddir/build/BUILD/pysam-0.19.0/samtools -I/builddir/build/BUILD/pysam-0.19.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.19.0/bcftools -I/builddir/build/BUILD/pysam-0.19.0/pysam -I/builddir/build/BUILD/pysam-0.19.0 -I/usr/include/python3.11 -c pysam/libctabix.c -o build/temp.linux-i686-3.11/pysam/libctabix.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -shared -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -Wl,--build-id=sha1 -g -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -Wl,--build-id=sha1 -g -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -Wl,-dT,/builddir/build/BUILD/pysam-0.19.0/.package_note-python-pysam-0.19.0-4.fc37.i386.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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection build/temp.linux-i686-3.11/pysam/libctabix.o -L/builddir/build/BUILD/pysam-0.19.0/pysam -L/builddir/build/BUILD/pysam-0.19.0/pysam -L/builddir/build/BUILD/pysam-0.19.0 -L/builddir/build/BUILD/pysam-0.19.0/build/lib.linux-i686-3.11/pysam -Lbuild/lib.linux-i686-3.11/pysam -Lbuild/lib.linux-i686-3.11/pysam -Lbuild/lib.linux-i686-3.11/pysam -Lbuild/lib.linux-i686-3.11/pysam -Lbuild/lib.linux-i686-3.11/pysam -Lbuild/lib.linux-i686-3.11/pysam -Lbuild/lib.linux-i686-3.11/pysam -Lbuild/lib.linux-i686-3.11/pysam -L/usr/lib -lz -llzma -lbz2 -lz -lm -lchtslib.cpython-311-i386-linux-gnu -lcutils.cpython-311-i386-linux-gnu -o build/lib.linux-i686-3.11/pysam/libctabix.cpython-311-i386-linux-gnu.so -Wl,-rpath,$ORIGIN building 'pysam.libcfaidx' extension gcc -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.19.0/htslib -I/builddir/build/BUILD/pysam-0.19.0/samtools -I/builddir/build/BUILD/pysam-0.19.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.19.0/bcftools -I/builddir/build/BUILD/pysam-0.19.0/pysam -I/builddir/build/BUILD/pysam-0.19.0 -I/usr/include/python3.11 -c pysam/libcfaidx.c -o build/temp.linux-i686-3.11/pysam/libcfaidx.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -shared -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -Wl,--build-id=sha1 -g -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -Wl,--build-id=sha1 -g -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -Wl,-dT,/builddir/build/BUILD/pysam-0.19.0/.package_note-python-pysam-0.19.0-4.fc37.i386.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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection build/temp.linux-i686-3.11/pysam/libcfaidx.o -L/builddir/build/BUILD/pysam-0.19.0/pysam -L/builddir/build/BUILD/pysam-0.19.0/pysam -L/builddir/build/BUILD/pysam-0.19.0 -L/builddir/build/BUILD/pysam-0.19.0/build/lib.linux-i686-3.11/pysam -Lbuild/lib.linux-i686-3.11/pysam -Lbuild/lib.linux-i686-3.11/pysam -Lbuild/lib.linux-i686-3.11/pysam -Lbuild/lib.linux-i686-3.11/pysam -Lbuild/lib.linux-i686-3.11/pysam -Lbuild/lib.linux-i686-3.11/pysam -Lbuild/lib.linux-i686-3.11/pysam -Lbuild/lib.linux-i686-3.11/pysam -Lbuild/lib.linux-i686-3.11/pysam -L/usr/lib -lz -llzma -lbz2 -lz -lm -lchtslib.cpython-311-i386-linux-gnu -lcutils.cpython-311-i386-linux-gnu -o build/lib.linux-i686-3.11/pysam/libcfaidx.cpython-311-i386-linux-gnu.so -Wl,-rpath,$ORIGIN building 'pysam.libcbcf' extension gcc -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.19.0/htslib -I/builddir/build/BUILD/pysam-0.19.0/samtools -I/builddir/build/BUILD/pysam-0.19.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.19.0/bcftools -I/builddir/build/BUILD/pysam-0.19.0/pysam -I/builddir/build/BUILD/pysam-0.19.0 -I/usr/include/python3.11 -c pysam/libcbcf.c -o build/temp.linux-i686-3.11/pysam/libcbcf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement pysam/libcbcf.c: In function ‘__pyx_pf_5pysam_7libcbcf_11VariantFile_6close’: pysam/libcbcf.c:66885:18: warning: ignoring return value of ‘bcf_hdr_write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 66885 | (void)(bcf_hdr_write(__pyx_v_self->__pyx_base.htsfile, __pyx_v_self->header->ptr)); | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pysam/libcbcf.c: In function ‘__pyx_pf_5pysam_7libcbcf_11VariantFile_4__dealloc__’: pysam/libcbcf.c:66610:18: warning: ignoring return value of ‘bcf_hdr_write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 66610 | (void)(bcf_hdr_write(__pyx_v_self->__pyx_base.htsfile, __pyx_v_self->header->ptr)); | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pysam/libcbcf.c: In function ‘__pyx_f_5pysam_7libcbcf_11VariantFile_write’: pysam/libcbcf.c:71728:18: warning: ignoring return value of ‘bcf_hdr_write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 71728 | (void)(bcf_hdr_write(__pyx_v_self->__pyx_base.htsfile, __pyx_v_self->header->ptr)); | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pysam/libcbcf.c: In function ‘__pyx_pf_5pysam_7libcbcf_13VariantHeader_22add_sample’: pysam/libcbcf.c:35694:12: warning: ignoring return value of ‘bcf_hdr_sync’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 35694 | (void)(bcf_hdr_sync(__pyx_v_self->ptr)); | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pysam/libcbcf.c: In function ‘__pyx_pf_5pysam_7libcbcf_13VariantHeader_20add_meta’: pysam/libcbcf.c:35394:11: warning: ignoring return value of ‘bcf_hrec_add_key’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 35394 | bcf_hrec_add_key(__pyx_v_hrec, __pyx_t_17, ((int)__pyx_t_18)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pysam/libcbcf.c:35420:11: warning: ignoring return value of ‘bcf_hrec_set_val’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 35420 | bcf_hrec_set_val(__pyx_v_hrec, (__pyx_v_hrec->nkeys - 1), __pyx_t_19, ((int)__pyx_t_18), __pyx_v_quoted); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pysam/libcbcf.c:35533:12: warning: ignoring return value of ‘bcf_hdr_sync’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 35533 | (void)(bcf_hdr_sync(__pyx_v_self->ptr)); | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pysam/libcbcf.c: In function ‘__pyx_pf_5pysam_7libcbcf_13VariantHeader_18add_line’: pysam/libcbcf.c:34959:12: warning: ignoring return value of ‘bcf_hdr_sync’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 34959 | (void)(bcf_hdr_sync(__pyx_v_self->ptr)); | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pysam/libcbcf.c: In function ‘__pyx_pf_5pysam_7libcbcf_13VariantHeader_16add_record’: pysam/libcbcf.c:34824:12: warning: ignoring return value of ‘bcf_hdr_sync’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 34824 | (void)(bcf_hdr_sync(__pyx_v_self->ptr)); | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -shared -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -Wl,--build-id=sha1 -g -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -Wl,--build-id=sha1 -g -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -Wl,-dT,/builddir/build/BUILD/pysam-0.19.0/.package_note-python-pysam-0.19.0-4.fc37.i386.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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection build/temp.linux-i686-3.11/pysam/libcbcf.o -L/builddir/build/BUILD/pysam-0.19.0/pysam -L/builddir/build/BUILD/pysam-0.19.0/pysam -L/builddir/build/BUILD/pysam-0.19.0 -L/builddir/build/BUILD/pysam-0.19.0/build/lib.linux-i686-3.11/pysam -Lbuild/lib.linux-i686-3.11/pysam -Lbuild/lib.linux-i686-3.11/pysam -Lbuild/lib.linux-i686-3.11/pysam -Lbuild/lib.linux-i686-3.11/pysam -Lbuild/lib.linux-i686-3.11/pysam -Lbuild/lib.linux-i686-3.11/pysam -Lbuild/lib.linux-i686-3.11/pysam -Lbuild/lib.linux-i686-3.11/pysam -Lbuild/lib.linux-i686-3.11/pysam -Lbuild/lib.linux-i686-3.11/pysam -L/usr/lib -lz -llzma -lbz2 -lz -lm -lchtslib.cpython-311-i386-linux-gnu -lcutils.cpython-311-i386-linux-gnu -o build/lib.linux-i686-3.11/pysam/libcbcf.cpython-311-i386-linux-gnu.so -Wl,-rpath,$ORIGIN building 'pysam.libcbgzf' extension gcc -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.19.0/htslib -I/builddir/build/BUILD/pysam-0.19.0/samtools -I/builddir/build/BUILD/pysam-0.19.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.19.0/bcftools -I/builddir/build/BUILD/pysam-0.19.0/pysam -I/builddir/build/BUILD/pysam-0.19.0 -I/usr/include/python3.11 -c pysam/libcbgzf.c -o build/temp.linux-i686-3.11/pysam/libcbgzf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -shared -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -Wl,--build-id=sha1 -g -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -Wl,--build-id=sha1 -g -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -Wl,-dT,/builddir/build/BUILD/pysam-0.19.0/.package_note-python-pysam-0.19.0-4.fc37.i386.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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection build/temp.linux-i686-3.11/pysam/libcbgzf.o -L/builddir/build/BUILD/pysam-0.19.0/pysam -L/builddir/build/BUILD/pysam-0.19.0/pysam -L/builddir/build/BUILD/pysam-0.19.0 -L/builddir/build/BUILD/pysam-0.19.0/build/lib.linux-i686-3.11/pysam -Lbuild/lib.linux-i686-3.11/pysam -Lbuild/lib.linux-i686-3.11/pysam -Lbuild/lib.linux-i686-3.11/pysam -Lbuild/lib.linux-i686-3.11/pysam -Lbuild/lib.linux-i686-3.11/pysam -Lbuild/lib.linux-i686-3.11/pysam -Lbuild/lib.linux-i686-3.11/pysam -Lbuild/lib.linux-i686-3.11/pysam -Lbuild/lib.linux-i686-3.11/pysam -Lbuild/lib.linux-i686-3.11/pysam -Lbuild/lib.linux-i686-3.11/pysam -L/usr/lib -lz -llzma -lbz2 -lz -lm -lchtslib.cpython-311-i386-linux-gnu -lcutils.cpython-311-i386-linux-gnu -o build/lib.linux-i686-3.11/pysam/libcbgzf.cpython-311-i386-linux-gnu.so -Wl,-rpath,$ORIGIN building 'pysam.libctabixproxies' extension gcc -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.19.0/htslib -I/builddir/build/BUILD/pysam-0.19.0/samtools -I/builddir/build/BUILD/pysam-0.19.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.19.0/bcftools -I/builddir/build/BUILD/pysam-0.19.0/pysam -I/builddir/build/BUILD/pysam-0.19.0 -I/usr/include/python3.11 -c pysam/libctabixproxies.c -o build/temp.linux-i686-3.11/pysam/libctabixproxies.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement gcc -shared -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -Wl,--build-id=sha1 -g -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -Wl,--build-id=sha1 -g -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -Wl,-dT,/builddir/build/BUILD/pysam-0.19.0/.package_note-python-pysam-0.19.0-4.fc37.i386.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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection build/temp.linux-i686-3.11/pysam/libctabixproxies.o -L/builddir/build/BUILD/pysam-0.19.0/pysam -L/builddir/build/BUILD/pysam-0.19.0/pysam -L/builddir/build/BUILD/pysam-0.19.0 -L/builddir/build/BUILD/pysam-0.19.0/build/lib.linux-i686-3.11/pysam -Lbuild/lib.linux-i686-3.11/pysam -Lbuild/lib.linux-i686-3.11/pysam -Lbuild/lib.linux-i686-3.11/pysam -Lbuild/lib.linux-i686-3.11/pysam -Lbuild/lib.linux-i686-3.11/pysam -Lbuild/lib.linux-i686-3.11/pysam -Lbuild/lib.linux-i686-3.11/pysam -Lbuild/lib.linux-i686-3.11/pysam -Lbuild/lib.linux-i686-3.11/pysam -Lbuild/lib.linux-i686-3.11/pysam -Lbuild/lib.linux-i686-3.11/pysam -Lbuild/lib.linux-i686-3.11/pysam -L/usr/lib -lz -llzma -lbz2 -lz -lm -lchtslib.cpython-311-i386-linux-gnu -lcutils.cpython-311-i386-linux-gnu -o build/lib.linux-i686-3.11/pysam/libctabixproxies.cpython-311-i386-linux-gnu.so -Wl,-rpath,$ORIGIN building 'pysam.libcvcf' extension gcc -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.19.0/htslib -I/builddir/build/BUILD/pysam-0.19.0/samtools -I/builddir/build/BUILD/pysam-0.19.0/samtools/lz4 -I/builddir/build/BUILD/pysam-0.19.0/bcftools -I/builddir/build/BUILD/pysam-0.19.0/pysam -I/builddir/build/BUILD/pysam-0.19.0 -I/usr/include/python3.11 -c pysam/libcvcf.c -o build/temp.linux-i686-3.11/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:25181:16: warning: ‘__pyx_v_qual’ may be used uninitialized [-Wmaybe-uninitialized] 25181 | __pyx_t_12 = PyFloat_FromDouble(__pyx_v_qual); if (unlikely(!__pyx_t_12)) __PYX_ERR(0, 873, __pyx_L1_error) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pysam/libcvcf.c:19901:10: note: ‘__pyx_v_qual’ was declared here 19901 | double __pyx_v_qual; | ^~~~~~~~~~~~ gcc -shared -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -Wl,--build-id=sha1 -g -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -Wl,--build-id=sha1 -g -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -Wl,-dT,/builddir/build/BUILD/pysam-0.19.0/.package_note-python-pysam-0.19.0-4.fc37.i386.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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection build/temp.linux-i686-3.11/pysam/libcvcf.o -L/builddir/build/BUILD/pysam-0.19.0/pysam -L/builddir/build/BUILD/pysam-0.19.0/pysam -L/builddir/build/BUILD/pysam-0.19.0 -L/builddir/build/BUILD/pysam-0.19.0/build/lib.linux-i686-3.11/pysam -Lbuild/lib.linux-i686-3.11/pysam -Lbuild/lib.linux-i686-3.11/pysam -Lbuild/lib.linux-i686-3.11/pysam -Lbuild/lib.linux-i686-3.11/pysam -Lbuild/lib.linux-i686-3.11/pysam -Lbuild/lib.linux-i686-3.11/pysam -Lbuild/lib.linux-i686-3.11/pysam -Lbuild/lib.linux-i686-3.11/pysam -Lbuild/lib.linux-i686-3.11/pysam -Lbuild/lib.linux-i686-3.11/pysam -Lbuild/lib.linux-i686-3.11/pysam -Lbuild/lib.linux-i686-3.11/pysam -Lbuild/lib.linux-i686-3.11/pysam -L/usr/lib -lz -llzma -lbz2 -lz -lm -lchtslib.cpython-311-i386-linux-gnu -lcutils.cpython-311-i386-linux-gnu -o build/lib.linux-i686-3.11/pysam/libcvcf.cpython-311-i386-linux-gnu.so -Wl,-rpath,$ORIGIN ++ echo /builddir/build/BUILD/pysam-0.19.0/build/lib.linux-i686-3.11 + PYTHONPATH=/builddir/build/BUILD/pysam-0.19.0/build/lib.linux-i686-3.11 + sphinx-build-3 doc html Running Sphinx v4.5.0 making output directory... done [autosummary] generating autosummary for: api.rst, benchmarking.rst, developer.rst, faq.rst, glossary.rst, index.rst, installation.rst, release.rst, usage.rst loading intersphinx inventory from https://docs.python.org/3.11/objects.inv... WARNING: failed to reach any of the inventories with the following issues: intersphinx inventory 'https://docs.python.org/3.11/objects.inv' not fetchable due to : HTTPSConnectionPool(host='docs.python.org', port=443): Max retries exceeded with url: /3.11/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 looking for now-outdated files... none found pickling environment... done checking consistency... 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 generating indices... 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, 1 warning. The HTML pages are in html. + rm -rf html/.doctrees html/.buildinfo + RPM_EC=0 ++ jobs -p + exit 0 Executing(%install): /bin/sh -e /var/tmp/rpm-tmp.YfbAav + umask 022 + cd /builddir/build/BUILD + '[' /builddir/build/BUILDROOT/python-pysam-0.19.0-4.fc37.i386 '!=' / ']' + rm -rf /builddir/build/BUILDROOT/python-pysam-0.19.0-4.fc37.i386 ++ dirname /builddir/build/BUILDROOT/python-pysam-0.19.0-4.fc37.i386 + mkdir -p /builddir/build/BUILDROOT + mkdir /builddir/build/BUILDROOT/python-pysam-0.19.0-4.fc37.i386 + 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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection' + export CFLAGS + CXXFLAGS='-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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection' + export CXXFLAGS + FFLAGS='-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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib/gfortran/modules' + export FFLAGS + FCFLAGS='-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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -I/usr/lib/gfortran/modules' + export FCFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -Wl,-dT,/builddir/build/BUILD/pysam-0.19.0/.package_note-python-pysam-0.19.0-4.fc37.i386.ld' + export LDFLAGS + LT_SYS_LIBRARY_PATH=/usr/lib: + export LT_SYS_LIBRARY_PATH + CC=gcc + export CC + CXX=g++ + export CXX + cd pysam-0.19.0 + 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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -Wl,-dT,/builddir/build/BUILD/pysam-0.19.0/.package_note-python-pysam-0.19.0-4.fc37.i386.ld' + /usr/bin/python3 setup.py install -O1 --skip-build --root /builddir/build/BUILDROOT/python-pysam-0.19.0-4.fc37.i386 --prefix /usr # pysam: cython is available - using cythonize if necessary # pysam: htslib mode is shared # pysam: HTSLIB_CONFIGURE_OPTIONS=None # pysam: (env) CC=gcc # pysam: (env) CFLAGS=-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-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 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -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 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -Wl,-dT,/builddir/build/BUILD/pysam-0.19.0/.package_note-python-pysam-0.19.0-4.fc37.i386.ld checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking for ranlib... ranlib checking for grep that handles long lines and -e... /usr/bin/grep checking for C compiler warning flags... -Wall checking 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... 64 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 -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 for srand48_deterministic... no checking whether fdatasync is declared... yes checking for fdatasync... yes checking for library containing log... -lm checking for zlib.h... yes checking for inflate in -lz... yes checking for library containing recv... none required checking for bzlib.h... yes checking for BZ2_bzBuffToBuffCompress in -lbz2... yes checking for lzma.h... yes checking for lzma_easy_buffer_encode in -llzma... yes checking whether htscodecs files are present... yes checking for libdeflate.h... no checking for libdeflate_deflate_compress in -ldeflate... no checking for curl/curl.h... no checking for curl_easy_pause in -lcurl... no checking for curl_easy_init in -lcurl... no configure: error: libcurl library not found Support for HTTPS and other SSL-based URLs requires routines from the libcurl library . Building HTSlib with libcurl enabled requires libcurl development files to be installed on the build machine; you may need to ensure a package such as libcurl4-{gnutls,nss,openssl}-dev (on Debian or Ubuntu Linux) or libcurl-devel (on RPM-based Linux distributions or Cygwin) is installed. Either configure with --disable-libcurl or resolve this error to build HTSlib. checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking for ranlib... ranlib checking for grep that handles long lines and -e... /usr/bin/grep checking for C compiler warning flags... -Wall checking 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... 64 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 -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 for srand48_deterministic... no checking whether fdatasync is declared... yes checking for fdatasync... yes checking for library containing log... -lm checking for zlib.h... yes checking for inflate in -lz... yes checking for library containing recv... none required checking for bzlib.h... yes checking for BZ2_bzBuffToBuffCompress in -lbz2... yes checking for lzma.h... yes checking for lzma_easy_buffer_encode in -llzma... yes checking whether htscodecs files are present... yes checking for libdeflate.h... no checking for libdeflate_deflate_compress in -ldeflate... no checking for library containing regcomp... configure: WARNING: GCS support not enabled: requires libcurl support configure: WARNING: S3 support not enabled: requires libcurl support none required 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 config.status: linking htscodecs_bundled.mk to htscodecs.mk # pysam: htslib configure options: --disable-libcurl # pysam: htslib_config LIBHTS_OBJS=kfunc.o kstring.o bcf_sr_sort.o bgzf.o errmod.o faidx.o header.o hfile.o hts.o hts_expr.o hts_os.o md5.o multipart.o probaln.o realn.o regidx.o region.o sam.o synced_bcf_reader.o vcf_sweep.o tbx.o textutils.o thread_pool.o vcf.o vcfutils.o cram/cram_codecs.o cram/cram_decode.o cram/cram_encode.o cram/cram_external.o cram/cram_index.o cram/cram_io.o cram/cram_stats.o cram/mFILE.o cram/open_trace_file.o cram/pooled_alloc.o cram/string_alloc.o htscodecs/htscodecs/arith_dynamic.o htscodecs/htscodecs/fqzcomp_qual.o htscodecs/htscodecs/htscodecs.o htscodecs/htscodecs/pack.o htscodecs/htscodecs/rANS_static4x16pr.o htscodecs/htscodecs/rANS_static.o htscodecs/htscodecs/rle.o htscodecs/htscodecs/tokenise_name3.o # pysam: htslib_config LIBS=-llzma -lbz2 -lz -lm # pysam: htslib_config PLATFORM=default # pysam: config_option: ENABLE_GCS=0 # pysam: config_option: ENABLE_PLUGINS=0 # pysam: config_option: ENABLE_S3=0 # pysam: config_option: HAVE_COMMONCRYPTO=0 # pysam: config_option: HAVE_HMAC=0 # pysam: config_option: HAVE_LIBBZ2=1 # pysam: config_option: HAVE_LIBCURL=0 # pysam: config_option: HAVE_LIBDEFLATE=0 # pysam: config_option: HAVE_LIBLZMA=1 # pysam: config_option: HAVE_MMAP=1 running install /usr/lib/python3.11/site-packages/setuptools/command/install.py:34: SetuptoolsDeprecationWarning: setup.py install is deprecated. Use build and pip and other standards-based tools. warnings.warn( running install_lib creating /builddir/build/BUILDROOT/python-pysam-0.19.0-4.fc37.i386/usr creating /builddir/build/BUILDROOT/python-pysam-0.19.0-4.fc37.i386/usr/lib creating /builddir/build/BUILDROOT/python-pysam-0.19.0-4.fc37.i386/usr/lib/python3.11 creating /builddir/build/BUILDROOT/python-pysam-0.19.0-4.fc37.i386/usr/lib/python3.11/site-packages creating /builddir/build/BUILDROOT/python-pysam-0.19.0-4.fc37.i386/usr/lib/python3.11/site-packages/pysam copying build/lib.linux-i686-3.11/pysam/Pileup.py -> /builddir/build/BUILDROOT/python-pysam-0.19.0-4.fc37.i386/usr/lib/python3.11/site-packages/pysam copying build/lib.linux-i686-3.11/pysam/__init__.py -> /builddir/build/BUILDROOT/python-pysam-0.19.0-4.fc37.i386/usr/lib/python3.11/site-packages/pysam copying build/lib.linux-i686-3.11/pysam/bcftools.py -> /builddir/build/BUILDROOT/python-pysam-0.19.0-4.fc37.i386/usr/lib/python3.11/site-packages/pysam copying build/lib.linux-i686-3.11/pysam/samtools.py -> /builddir/build/BUILDROOT/python-pysam-0.19.0-4.fc37.i386/usr/lib/python3.11/site-packages/pysam copying build/lib.linux-i686-3.11/pysam/utils.py -> /builddir/build/BUILDROOT/python-pysam-0.19.0-4.fc37.i386/usr/lib/python3.11/site-packages/pysam copying build/lib.linux-i686-3.11/pysam/version.py -> /builddir/build/BUILDROOT/python-pysam-0.19.0-4.fc37.i386/usr/lib/python3.11/site-packages/pysam copying build/lib.linux-i686-3.11/pysam/config.py -> /builddir/build/BUILDROOT/python-pysam-0.19.0-4.fc37.i386/usr/lib/python3.11/site-packages/pysam creating /builddir/build/BUILDROOT/python-pysam-0.19.0-4.fc37.i386/usr/lib/python3.11/site-packages/pysam/include copying build/lib.linux-i686-3.11/pysam/include/__init__.py -> /builddir/build/BUILDROOT/python-pysam-0.19.0-4.fc37.i386/usr/lib/python3.11/site-packages/pysam/include creating /builddir/build/BUILDROOT/python-pysam-0.19.0-4.fc37.i386/usr/lib/python3.11/site-packages/pysam/include/samtools copying build/lib.linux-i686-3.11/pysam/include/samtools/bam.h -> /builddir/build/BUILDROOT/python-pysam-0.19.0-4.fc37.i386/usr/lib/python3.11/site-packages/pysam/include/samtools copying build/lib.linux-i686-3.11/pysam/include/samtools/bam_ampliconclip.h -> /builddir/build/BUILDROOT/python-pysam-0.19.0-4.fc37.i386/usr/lib/python3.11/site-packages/pysam/include/samtools copying build/lib.linux-i686-3.11/pysam/include/samtools/bam_lpileup.h -> /builddir/build/BUILDROOT/python-pysam-0.19.0-4.fc37.i386/usr/lib/python3.11/site-packages/pysam/include/samtools copying build/lib.linux-i686-3.11/pysam/include/samtools/bam_plbuf.h -> /builddir/build/BUILDROOT/python-pysam-0.19.0-4.fc37.i386/usr/lib/python3.11/site-packages/pysam/include/samtools copying build/lib.linux-i686-3.11/pysam/include/samtools/bedidx.h -> /builddir/build/BUILDROOT/python-pysam-0.19.0-4.fc37.i386/usr/lib/python3.11/site-packages/pysam/include/samtools copying build/lib.linux-i686-3.11/pysam/include/samtools/consensus_pileup.h -> /builddir/build/BUILDROOT/python-pysam-0.19.0-4.fc37.i386/usr/lib/python3.11/site-packages/pysam/include/samtools copying build/lib.linux-i686-3.11/pysam/include/samtools/sam_opts.h -> /builddir/build/BUILDROOT/python-pysam-0.19.0-4.fc37.i386/usr/lib/python3.11/site-packages/pysam/include/samtools copying build/lib.linux-i686-3.11/pysam/include/samtools/sample.h -> /builddir/build/BUILDROOT/python-pysam-0.19.0-4.fc37.i386/usr/lib/python3.11/site-packages/pysam/include/samtools copying build/lib.linux-i686-3.11/pysam/include/samtools/samtools.h -> /builddir/build/BUILDROOT/python-pysam-0.19.0-4.fc37.i386/usr/lib/python3.11/site-packages/pysam/include/samtools copying build/lib.linux-i686-3.11/pysam/include/samtools/samtools.pysam.h -> /builddir/build/BUILDROOT/python-pysam-0.19.0-4.fc37.i386/usr/lib/python3.11/site-packages/pysam/include/samtools copying build/lib.linux-i686-3.11/pysam/include/samtools/splaysort.h -> /builddir/build/BUILDROOT/python-pysam-0.19.0-4.fc37.i386/usr/lib/python3.11/site-packages/pysam/include/samtools copying build/lib.linux-i686-3.11/pysam/include/samtools/stats_isize.h -> /builddir/build/BUILDROOT/python-pysam-0.19.0-4.fc37.i386/usr/lib/python3.11/site-packages/pysam/include/samtools copying build/lib.linux-i686-3.11/pysam/include/samtools/tmp_file.h -> /builddir/build/BUILDROOT/python-pysam-0.19.0-4.fc37.i386/usr/lib/python3.11/site-packages/pysam/include/samtools copying build/lib.linux-i686-3.11/pysam/include/samtools/config.h -> /builddir/build/BUILDROOT/python-pysam-0.19.0-4.fc37.i386/usr/lib/python3.11/site-packages/pysam/include/samtools creating /builddir/build/BUILDROOT/python-pysam-0.19.0-4.fc37.i386/usr/lib/python3.11/site-packages/pysam/include/bcftools copying build/lib.linux-i686-3.11/pysam/include/bcftools/HMM.h -> /builddir/build/BUILDROOT/python-pysam-0.19.0-4.fc37.i386/usr/lib/python3.11/site-packages/pysam/include/bcftools copying build/lib.linux-i686-3.11/pysam/include/bcftools/abuf.h -> /builddir/build/BUILDROOT/python-pysam-0.19.0-4.fc37.i386/usr/lib/python3.11/site-packages/pysam/include/bcftools copying build/lib.linux-i686-3.11/pysam/include/bcftools/bam2bcf.h -> /builddir/build/BUILDROOT/python-pysam-0.19.0-4.fc37.i386/usr/lib/python3.11/site-packages/pysam/include/bcftools copying build/lib.linux-i686-3.11/pysam/include/bcftools/bam_sample.h -> /builddir/build/BUILDROOT/python-pysam-0.19.0-4.fc37.i386/usr/lib/python3.11/site-packages/pysam/include/bcftools copying build/lib.linux-i686-3.11/pysam/include/bcftools/bcftools.h -> /builddir/build/BUILDROOT/python-pysam-0.19.0-4.fc37.i386/usr/lib/python3.11/site-packages/pysam/include/bcftools copying build/lib.linux-i686-3.11/pysam/include/bcftools/bcftools.pysam.h -> /builddir/build/BUILDROOT/python-pysam-0.19.0-4.fc37.i386/usr/lib/python3.11/site-packages/pysam/include/bcftools copying build/lib.linux-i686-3.11/pysam/include/bcftools/bin.h -> /builddir/build/BUILDROOT/python-pysam-0.19.0-4.fc37.i386/usr/lib/python3.11/site-packages/pysam/include/bcftools copying build/lib.linux-i686-3.11/pysam/include/bcftools/call.h -> /builddir/build/BUILDROOT/python-pysam-0.19.0-4.fc37.i386/usr/lib/python3.11/site-packages/pysam/include/bcftools copying build/lib.linux-i686-3.11/pysam/include/bcftools/cols.h -> /builddir/build/BUILDROOT/python-pysam-0.19.0-4.fc37.i386/usr/lib/python3.11/site-packages/pysam/include/bcftools copying build/lib.linux-i686-3.11/pysam/include/bcftools/convert.h -> /builddir/build/BUILDROOT/python-pysam-0.19.0-4.fc37.i386/usr/lib/python3.11/site-packages/pysam/include/bcftools copying build/lib.linux-i686-3.11/pysam/include/bcftools/dist.h -> /builddir/build/BUILDROOT/python-pysam-0.19.0-4.fc37.i386/usr/lib/python3.11/site-packages/pysam/include/bcftools copying build/lib.linux-i686-3.11/pysam/include/bcftools/extsort.h -> /builddir/build/BUILDROOT/python-pysam-0.19.0-4.fc37.i386/usr/lib/python3.11/site-packages/pysam/include/bcftools copying build/lib.linux-i686-3.11/pysam/include/bcftools/filter.h -> /builddir/build/BUILDROOT/python-pysam-0.19.0-4.fc37.i386/usr/lib/python3.11/site-packages/pysam/include/bcftools copying build/lib.linux-i686-3.11/pysam/include/bcftools/gvcf.h -> /builddir/build/BUILDROOT/python-pysam-0.19.0-4.fc37.i386/usr/lib/python3.11/site-packages/pysam/include/bcftools copying build/lib.linux-i686-3.11/pysam/include/bcftools/hclust.h -> /builddir/build/BUILDROOT/python-pysam-0.19.0-4.fc37.i386/usr/lib/python3.11/site-packages/pysam/include/bcftools copying build/lib.linux-i686-3.11/pysam/include/bcftools/hex.h -> /builddir/build/BUILDROOT/python-pysam-0.19.0-4.fc37.i386/usr/lib/python3.11/site-packages/pysam/include/bcftools copying build/lib.linux-i686-3.11/pysam/include/bcftools/khash_str2str.h -> /builddir/build/BUILDROOT/python-pysam-0.19.0-4.fc37.i386/usr/lib/python3.11/site-packages/pysam/include/bcftools copying build/lib.linux-i686-3.11/pysam/include/bcftools/kheap.h -> /builddir/build/BUILDROOT/python-pysam-0.19.0-4.fc37.i386/usr/lib/python3.11/site-packages/pysam/include/bcftools copying build/lib.linux-i686-3.11/pysam/include/bcftools/kmin.h -> /builddir/build/BUILDROOT/python-pysam-0.19.0-4.fc37.i386/usr/lib/python3.11/site-packages/pysam/include/bcftools copying build/lib.linux-i686-3.11/pysam/include/bcftools/mw.h -> /builddir/build/BUILDROOT/python-pysam-0.19.0-4.fc37.i386/usr/lib/python3.11/site-packages/pysam/include/bcftools copying build/lib.linux-i686-3.11/pysam/include/bcftools/ploidy.h -> /builddir/build/BUILDROOT/python-pysam-0.19.0-4.fc37.i386/usr/lib/python3.11/site-packages/pysam/include/bcftools copying build/lib.linux-i686-3.11/pysam/include/bcftools/prob1.h -> /builddir/build/BUILDROOT/python-pysam-0.19.0-4.fc37.i386/usr/lib/python3.11/site-packages/pysam/include/bcftools copying build/lib.linux-i686-3.11/pysam/include/bcftools/rbuf.h -> /builddir/build/BUILDROOT/python-pysam-0.19.0-4.fc37.i386/usr/lib/python3.11/site-packages/pysam/include/bcftools copying build/lib.linux-i686-3.11/pysam/include/bcftools/regidx.h -> /builddir/build/BUILDROOT/python-pysam-0.19.0-4.fc37.i386/usr/lib/python3.11/site-packages/pysam/include/bcftools copying build/lib.linux-i686-3.11/pysam/include/bcftools/smpl_ilist.h -> /builddir/build/BUILDROOT/python-pysam-0.19.0-4.fc37.i386/usr/lib/python3.11/site-packages/pysam/include/bcftools copying build/lib.linux-i686-3.11/pysam/include/bcftools/str_finder.h -> /builddir/build/BUILDROOT/python-pysam-0.19.0-4.fc37.i386/usr/lib/python3.11/site-packages/pysam/include/bcftools copying build/lib.linux-i686-3.11/pysam/include/bcftools/tsv2vcf.h -> /builddir/build/BUILDROOT/python-pysam-0.19.0-4.fc37.i386/usr/lib/python3.11/site-packages/pysam/include/bcftools copying build/lib.linux-i686-3.11/pysam/include/bcftools/utlist.h -> /builddir/build/BUILDROOT/python-pysam-0.19.0-4.fc37.i386/usr/lib/python3.11/site-packages/pysam/include/bcftools copying build/lib.linux-i686-3.11/pysam/include/bcftools/variantkey.h -> /builddir/build/BUILDROOT/python-pysam-0.19.0-4.fc37.i386/usr/lib/python3.11/site-packages/pysam/include/bcftools copying build/lib.linux-i686-3.11/pysam/include/bcftools/vcfbuf.h -> /builddir/build/BUILDROOT/python-pysam-0.19.0-4.fc37.i386/usr/lib/python3.11/site-packages/pysam/include/bcftools copying build/lib.linux-i686-3.11/pysam/include/bcftools/vcmp.h -> /builddir/build/BUILDROOT/python-pysam-0.19.0-4.fc37.i386/usr/lib/python3.11/site-packages/pysam/include/bcftools copying build/lib.linux-i686-3.11/pysam/include/bcftools/config.h -> /builddir/build/BUILDROOT/python-pysam-0.19.0-4.fc37.i386/usr/lib/python3.11/site-packages/pysam/include/bcftools creating /builddir/build/BUILDROOT/python-pysam-0.19.0-4.fc37.i386/usr/lib/python3.11/site-packages/pysam/include/htslib copying build/lib.linux-i686-3.11/pysam/include/htslib/bcf_sr_sort.h -> /builddir/build/BUILDROOT/python-pysam-0.19.0-4.fc37.i386/usr/lib/python3.11/site-packages/pysam/include/htslib copying build/lib.linux-i686-3.11/pysam/include/htslib/header.h -> /builddir/build/BUILDROOT/python-pysam-0.19.0-4.fc37.i386/usr/lib/python3.11/site-packages/pysam/include/htslib copying build/lib.linux-i686-3.11/pysam/include/htslib/hfile_internal.h -> /builddir/build/BUILDROOT/python-pysam-0.19.0-4.fc37.i386/usr/lib/python3.11/site-packages/pysam/include/htslib copying build/lib.linux-i686-3.11/pysam/include/htslib/hts_internal.h -> /builddir/build/BUILDROOT/python-pysam-0.19.0-4.fc37.i386/usr/lib/python3.11/site-packages/pysam/include/htslib copying build/lib.linux-i686-3.11/pysam/include/htslib/sam_internal.h -> /builddir/build/BUILDROOT/python-pysam-0.19.0-4.fc37.i386/usr/lib/python3.11/site-packages/pysam/include/htslib copying build/lib.linux-i686-3.11/pysam/include/htslib/textutils_internal.h -> /builddir/build/BUILDROOT/python-pysam-0.19.0-4.fc37.i386/usr/lib/python3.11/site-packages/pysam/include/htslib copying build/lib.linux-i686-3.11/pysam/include/htslib/thread_pool_internal.h -> /builddir/build/BUILDROOT/python-pysam-0.19.0-4.fc37.i386/usr/lib/python3.11/site-packages/pysam/include/htslib copying build/lib.linux-i686-3.11/pysam/include/htslib/config.h -> /builddir/build/BUILDROOT/python-pysam-0.19.0-4.fc37.i386/usr/lib/python3.11/site-packages/pysam/include/htslib creating /builddir/build/BUILDROOT/python-pysam-0.19.0-4.fc37.i386/usr/lib/python3.11/site-packages/pysam/include/htslib/htslib copying build/lib.linux-i686-3.11/pysam/include/htslib/htslib/bgzf.h -> /builddir/build/BUILDROOT/python-pysam-0.19.0-4.fc37.i386/usr/lib/python3.11/site-packages/pysam/include/htslib/htslib copying build/lib.linux-i686-3.11/pysam/include/htslib/htslib/cram.h -> /builddir/build/BUILDROOT/python-pysam-0.19.0-4.fc37.i386/usr/lib/python3.11/site-packages/pysam/include/htslib/htslib copying build/lib.linux-i686-3.11/pysam/include/htslib/htslib/faidx.h -> /builddir/build/BUILDROOT/python-pysam-0.19.0-4.fc37.i386/usr/lib/python3.11/site-packages/pysam/include/htslib/htslib copying build/lib.linux-i686-3.11/pysam/include/htslib/htslib/hfile.h -> /builddir/build/BUILDROOT/python-pysam-0.19.0-4.fc37.i386/usr/lib/python3.11/site-packages/pysam/include/htslib/htslib copying build/lib.linux-i686-3.11/pysam/include/htslib/htslib/hts.h -> /builddir/build/BUILDROOT/python-pysam-0.19.0-4.fc37.i386/usr/lib/python3.11/site-packages/pysam/include/htslib/htslib copying build/lib.linux-i686-3.11/pysam/include/htslib/htslib/hts_defs.h -> /builddir/build/BUILDROOT/python-pysam-0.19.0-4.fc37.i386/usr/lib/python3.11/site-packages/pysam/include/htslib/htslib copying build/lib.linux-i686-3.11/pysam/include/htslib/htslib/hts_endian.h -> /builddir/build/BUILDROOT/python-pysam-0.19.0-4.fc37.i386/usr/lib/python3.11/site-packages/pysam/include/htslib/htslib copying build/lib.linux-i686-3.11/pysam/include/htslib/htslib/hts_expr.h -> /builddir/build/BUILDROOT/python-pysam-0.19.0-4.fc37.i386/usr/lib/python3.11/site-packages/pysam/include/htslib/htslib copying build/lib.linux-i686-3.11/pysam/include/htslib/htslib/hts_log.h -> /builddir/build/BUILDROOT/python-pysam-0.19.0-4.fc37.i386/usr/lib/python3.11/site-packages/pysam/include/htslib/htslib copying build/lib.linux-i686-3.11/pysam/include/htslib/htslib/hts_os.h -> /builddir/build/BUILDROOT/python-pysam-0.19.0-4.fc37.i386/usr/lib/python3.11/site-packages/pysam/include/htslib/htslib copying build/lib.linux-i686-3.11/pysam/include/htslib/htslib/kbitset.h -> /builddir/build/BUILDROOT/python-pysam-0.19.0-4.fc37.i386/usr/lib/python3.11/site-packages/pysam/include/htslib/htslib copying build/lib.linux-i686-3.11/pysam/include/htslib/htslib/kfunc.h -> /builddir/build/BUILDROOT/python-pysam-0.19.0-4.fc37.i386/usr/lib/python3.11/site-packages/pysam/include/htslib/htslib copying build/lib.linux-i686-3.11/pysam/include/htslib/htslib/khash.h -> /builddir/build/BUILDROOT/python-pysam-0.19.0-4.fc37.i386/usr/lib/python3.11/site-packages/pysam/include/htslib/htslib copying build/lib.linux-i686-3.11/pysam/include/htslib/htslib/khash_str2int.h -> /builddir/build/BUILDROOT/python-pysam-0.19.0-4.fc37.i386/usr/lib/python3.11/site-packages/pysam/include/htslib/htslib copying build/lib.linux-i686-3.11/pysam/include/htslib/htslib/klist.h -> /builddir/build/BUILDROOT/python-pysam-0.19.0-4.fc37.i386/usr/lib/python3.11/site-packages/pysam/include/htslib/htslib copying build/lib.linux-i686-3.11/pysam/include/htslib/htslib/knetfile.h -> /builddir/build/BUILDROOT/python-pysam-0.19.0-4.fc37.i386/usr/lib/python3.11/site-packages/pysam/include/htslib/htslib copying build/lib.linux-i686-3.11/pysam/include/htslib/htslib/kroundup.h -> /builddir/build/BUILDROOT/python-pysam-0.19.0-4.fc37.i386/usr/lib/python3.11/site-packages/pysam/include/htslib/htslib copying build/lib.linux-i686-3.11/pysam/include/htslib/htslib/kseq.h -> /builddir/build/BUILDROOT/python-pysam-0.19.0-4.fc37.i386/usr/lib/python3.11/site-packages/pysam/include/htslib/htslib copying build/lib.linux-i686-3.11/pysam/include/htslib/htslib/ksort.h -> /builddir/build/BUILDROOT/python-pysam-0.19.0-4.fc37.i386/usr/lib/python3.11/site-packages/pysam/include/htslib/htslib copying build/lib.linux-i686-3.11/pysam/include/htslib/htslib/kstring.h -> /builddir/build/BUILDROOT/python-pysam-0.19.0-4.fc37.i386/usr/lib/python3.11/site-packages/pysam/include/htslib/htslib copying build/lib.linux-i686-3.11/pysam/include/htslib/htslib/regidx.h -> /builddir/build/BUILDROOT/python-pysam-0.19.0-4.fc37.i386/usr/lib/python3.11/site-packages/pysam/include/htslib/htslib copying build/lib.linux-i686-3.11/pysam/include/htslib/htslib/sam.h -> /builddir/build/BUILDROOT/python-pysam-0.19.0-4.fc37.i386/usr/lib/python3.11/site-packages/pysam/include/htslib/htslib copying build/lib.linux-i686-3.11/pysam/include/htslib/htslib/synced_bcf_reader.h -> /builddir/build/BUILDROOT/python-pysam-0.19.0-4.fc37.i386/usr/lib/python3.11/site-packages/pysam/include/htslib/htslib copying build/lib.linux-i686-3.11/pysam/include/htslib/htslib/tbx.h -> /builddir/build/BUILDROOT/python-pysam-0.19.0-4.fc37.i386/usr/lib/python3.11/site-packages/pysam/include/htslib/htslib copying build/lib.linux-i686-3.11/pysam/include/htslib/htslib/thread_pool.h -> /builddir/build/BUILDROOT/python-pysam-0.19.0-4.fc37.i386/usr/lib/python3.11/site-packages/pysam/include/htslib/htslib copying build/lib.linux-i686-3.11/pysam/include/htslib/htslib/vcf.h -> /builddir/build/BUILDROOT/python-pysam-0.19.0-4.fc37.i386/usr/lib/python3.11/site-packages/pysam/include/htslib/htslib copying build/lib.linux-i686-3.11/pysam/include/htslib/htslib/vcf_sweep.h -> /builddir/build/BUILDROOT/python-pysam-0.19.0-4.fc37.i386/usr/lib/python3.11/site-packages/pysam/include/htslib/htslib copying build/lib.linux-i686-3.11/pysam/include/htslib/htslib/vcfutils.h -> /builddir/build/BUILDROOT/python-pysam-0.19.0-4.fc37.i386/usr/lib/python3.11/site-packages/pysam/include/htslib/htslib copying build/lib.linux-i686-3.11/pysam/libcalignedsegment.pxd -> /builddir/build/BUILDROOT/python-pysam-0.19.0-4.fc37.i386/usr/lib/python3.11/site-packages/pysam copying build/lib.linux-i686-3.11/pysam/libcalignmentfile.pxd -> /builddir/build/BUILDROOT/python-pysam-0.19.0-4.fc37.i386/usr/lib/python3.11/site-packages/pysam copying build/lib.linux-i686-3.11/pysam/libcbcf.pxd -> /builddir/build/BUILDROOT/python-pysam-0.19.0-4.fc37.i386/usr/lib/python3.11/site-packages/pysam copying build/lib.linux-i686-3.11/pysam/libcbcftools.pxd -> /builddir/build/BUILDROOT/python-pysam-0.19.0-4.fc37.i386/usr/lib/python3.11/site-packages/pysam copying build/lib.linux-i686-3.11/pysam/libcfaidx.pxd -> /builddir/build/BUILDROOT/python-pysam-0.19.0-4.fc37.i386/usr/lib/python3.11/site-packages/pysam copying build/lib.linux-i686-3.11/pysam/libchtslib.pxd -> /builddir/build/BUILDROOT/python-pysam-0.19.0-4.fc37.i386/usr/lib/python3.11/site-packages/pysam copying build/lib.linux-i686-3.11/pysam/libcsamfile.pxd -> /builddir/build/BUILDROOT/python-pysam-0.19.0-4.fc37.i386/usr/lib/python3.11/site-packages/pysam copying build/lib.linux-i686-3.11/pysam/libcsamtools.pxd -> /builddir/build/BUILDROOT/python-pysam-0.19.0-4.fc37.i386/usr/lib/python3.11/site-packages/pysam copying build/lib.linux-i686-3.11/pysam/libctabix.pxd -> /builddir/build/BUILDROOT/python-pysam-0.19.0-4.fc37.i386/usr/lib/python3.11/site-packages/pysam copying build/lib.linux-i686-3.11/pysam/libctabixproxies.pxd -> /builddir/build/BUILDROOT/python-pysam-0.19.0-4.fc37.i386/usr/lib/python3.11/site-packages/pysam copying build/lib.linux-i686-3.11/pysam/libcutils.pxd -> /builddir/build/BUILDROOT/python-pysam-0.19.0-4.fc37.i386/usr/lib/python3.11/site-packages/pysam copying build/lib.linux-i686-3.11/pysam/libcvcf.pxd -> /builddir/build/BUILDROOT/python-pysam-0.19.0-4.fc37.i386/usr/lib/python3.11/site-packages/pysam copying build/lib.linux-i686-3.11/pysam/cbcftools_util.h -> /builddir/build/BUILDROOT/python-pysam-0.19.0-4.fc37.i386/usr/lib/python3.11/site-packages/pysam copying build/lib.linux-i686-3.11/pysam/csamtools_util.h -> /builddir/build/BUILDROOT/python-pysam-0.19.0-4.fc37.i386/usr/lib/python3.11/site-packages/pysam copying build/lib.linux-i686-3.11/pysam/htslib_util.h -> /builddir/build/BUILDROOT/python-pysam-0.19.0-4.fc37.i386/usr/lib/python3.11/site-packages/pysam copying build/lib.linux-i686-3.11/pysam/pysam_stream.h -> /builddir/build/BUILDROOT/python-pysam-0.19.0-4.fc37.i386/usr/lib/python3.11/site-packages/pysam copying build/lib.linux-i686-3.11/pysam/pysam_util.h -> /builddir/build/BUILDROOT/python-pysam-0.19.0-4.fc37.i386/usr/lib/python3.11/site-packages/pysam copying build/lib.linux-i686-3.11/pysam/version.h -> /builddir/build/BUILDROOT/python-pysam-0.19.0-4.fc37.i386/usr/lib/python3.11/site-packages/pysam copying build/lib.linux-i686-3.11/pysam/py.typed -> /builddir/build/BUILDROOT/python-pysam-0.19.0-4.fc37.i386/usr/lib/python3.11/site-packages/pysam copying build/lib.linux-i686-3.11/pysam/libcalignedsegment.pyi -> /builddir/build/BUILDROOT/python-pysam-0.19.0-4.fc37.i386/usr/lib/python3.11/site-packages/pysam copying build/lib.linux-i686-3.11/pysam/libcalignmentfile.pyi -> /builddir/build/BUILDROOT/python-pysam-0.19.0-4.fc37.i386/usr/lib/python3.11/site-packages/pysam copying build/lib.linux-i686-3.11/pysam/libcbcf.pyi -> /builddir/build/BUILDROOT/python-pysam-0.19.0-4.fc37.i386/usr/lib/python3.11/site-packages/pysam copying build/lib.linux-i686-3.11/pysam/libcbcftools.pyi -> /builddir/build/BUILDROOT/python-pysam-0.19.0-4.fc37.i386/usr/lib/python3.11/site-packages/pysam copying build/lib.linux-i686-3.11/pysam/libcbgzf.pyi -> /builddir/build/BUILDROOT/python-pysam-0.19.0-4.fc37.i386/usr/lib/python3.11/site-packages/pysam copying build/lib.linux-i686-3.11/pysam/libcfaidx.pyi -> /builddir/build/BUILDROOT/python-pysam-0.19.0-4.fc37.i386/usr/lib/python3.11/site-packages/pysam copying build/lib.linux-i686-3.11/pysam/libchtslib.pyi -> /builddir/build/BUILDROOT/python-pysam-0.19.0-4.fc37.i386/usr/lib/python3.11/site-packages/pysam copying build/lib.linux-i686-3.11/pysam/libcsamfile.pyi -> /builddir/build/BUILDROOT/python-pysam-0.19.0-4.fc37.i386/usr/lib/python3.11/site-packages/pysam copying build/lib.linux-i686-3.11/pysam/libcsamtools.pyi -> /builddir/build/BUILDROOT/python-pysam-0.19.0-4.fc37.i386/usr/lib/python3.11/site-packages/pysam copying build/lib.linux-i686-3.11/pysam/libctabix.pyi -> /builddir/build/BUILDROOT/python-pysam-0.19.0-4.fc37.i386/usr/lib/python3.11/site-packages/pysam copying build/lib.linux-i686-3.11/pysam/libctabixproxies.pyi -> /builddir/build/BUILDROOT/python-pysam-0.19.0-4.fc37.i386/usr/lib/python3.11/site-packages/pysam copying build/lib.linux-i686-3.11/pysam/libcutils.pyi -> /builddir/build/BUILDROOT/python-pysam-0.19.0-4.fc37.i386/usr/lib/python3.11/site-packages/pysam copying build/lib.linux-i686-3.11/pysam/libcvcf.pyi -> /builddir/build/BUILDROOT/python-pysam-0.19.0-4.fc37.i386/usr/lib/python3.11/site-packages/pysam copying build/lib.linux-i686-3.11/pysam/version.pyi -> /builddir/build/BUILDROOT/python-pysam-0.19.0-4.fc37.i386/usr/lib/python3.11/site-packages/pysam copying build/lib.linux-i686-3.11/pysam/libchtslib.cpython-311-i386-linux-gnu.so -> /builddir/build/BUILDROOT/python-pysam-0.19.0-4.fc37.i386/usr/lib/python3.11/site-packages/pysam copying build/lib.linux-i686-3.11/pysam/libcsamtools.cpython-311-i386-linux-gnu.so -> /builddir/build/BUILDROOT/python-pysam-0.19.0-4.fc37.i386/usr/lib/python3.11/site-packages/pysam copying build/lib.linux-i686-3.11/pysam/libcbcftools.cpython-311-i386-linux-gnu.so -> /builddir/build/BUILDROOT/python-pysam-0.19.0-4.fc37.i386/usr/lib/python3.11/site-packages/pysam copying build/lib.linux-i686-3.11/pysam/libcutils.cpython-311-i386-linux-gnu.so -> /builddir/build/BUILDROOT/python-pysam-0.19.0-4.fc37.i386/usr/lib/python3.11/site-packages/pysam copying build/lib.linux-i686-3.11/pysam/libcalignmentfile.cpython-311-i386-linux-gnu.so -> /builddir/build/BUILDROOT/python-pysam-0.19.0-4.fc37.i386/usr/lib/python3.11/site-packages/pysam copying build/lib.linux-i686-3.11/pysam/libcsamfile.cpython-311-i386-linux-gnu.so -> /builddir/build/BUILDROOT/python-pysam-0.19.0-4.fc37.i386/usr/lib/python3.11/site-packages/pysam copying build/lib.linux-i686-3.11/pysam/libcalignedsegment.cpython-311-i386-linux-gnu.so -> /builddir/build/BUILDROOT/python-pysam-0.19.0-4.fc37.i386/usr/lib/python3.11/site-packages/pysam copying build/lib.linux-i686-3.11/pysam/libctabix.cpython-311-i386-linux-gnu.so -> /builddir/build/BUILDROOT/python-pysam-0.19.0-4.fc37.i386/usr/lib/python3.11/site-packages/pysam copying build/lib.linux-i686-3.11/pysam/libcfaidx.cpython-311-i386-linux-gnu.so -> /builddir/build/BUILDROOT/python-pysam-0.19.0-4.fc37.i386/usr/lib/python3.11/site-packages/pysam copying build/lib.linux-i686-3.11/pysam/libcbcf.cpython-311-i386-linux-gnu.so -> /builddir/build/BUILDROOT/python-pysam-0.19.0-4.fc37.i386/usr/lib/python3.11/site-packages/pysam copying build/lib.linux-i686-3.11/pysam/libcbgzf.cpython-311-i386-linux-gnu.so -> /builddir/build/BUILDROOT/python-pysam-0.19.0-4.fc37.i386/usr/lib/python3.11/site-packages/pysam copying build/lib.linux-i686-3.11/pysam/libctabixproxies.cpython-311-i386-linux-gnu.so -> /builddir/build/BUILDROOT/python-pysam-0.19.0-4.fc37.i386/usr/lib/python3.11/site-packages/pysam copying build/lib.linux-i686-3.11/pysam/libcvcf.cpython-311-i386-linux-gnu.so -> /builddir/build/BUILDROOT/python-pysam-0.19.0-4.fc37.i386/usr/lib/python3.11/site-packages/pysam creating /builddir/build/BUILDROOT/python-pysam-0.19.0-4.fc37.i386/usr/lib/python3.11/site-packages/pysam/__pycache__ copying build/lib.linux-i686-3.11/pysam/__pycache__/__init__.cpython-311.pyc -> /builddir/build/BUILDROOT/python-pysam-0.19.0-4.fc37.i386/usr/lib/python3.11/site-packages/pysam/__pycache__ copying build/lib.linux-i686-3.11/pysam/__pycache__/utils.cpython-311.pyc -> /builddir/build/BUILDROOT/python-pysam-0.19.0-4.fc37.i386/usr/lib/python3.11/site-packages/pysam/__pycache__ copying build/lib.linux-i686-3.11/pysam/__pycache__/Pileup.cpython-311.pyc -> /builddir/build/BUILDROOT/python-pysam-0.19.0-4.fc37.i386/usr/lib/python3.11/site-packages/pysam/__pycache__ copying build/lib.linux-i686-3.11/pysam/__pycache__/samtools.cpython-311.pyc -> /builddir/build/BUILDROOT/python-pysam-0.19.0-4.fc37.i386/usr/lib/python3.11/site-packages/pysam/__pycache__ copying build/lib.linux-i686-3.11/pysam/__pycache__/config.cpython-311.pyc -> /builddir/build/BUILDROOT/python-pysam-0.19.0-4.fc37.i386/usr/lib/python3.11/site-packages/pysam/__pycache__ copying build/lib.linux-i686-3.11/pysam/__pycache__/version.cpython-311.pyc -> /builddir/build/BUILDROOT/python-pysam-0.19.0-4.fc37.i386/usr/lib/python3.11/site-packages/pysam/__pycache__ byte-compiling /builddir/build/BUILDROOT/python-pysam-0.19.0-4.fc37.i386/usr/lib/python3.11/site-packages/pysam/bcftools.py to bcftools.cpython-311.pyc byte-compiling /builddir/build/BUILDROOT/python-pysam-0.19.0-4.fc37.i386/usr/lib/python3.11/site-packages/pysam/include/__init__.py to __init__.cpython-311.pyc writing byte-compilation script '/tmp/tmpd2l9em7d.py' /usr/bin/python3 /tmp/tmpd2l9em7d.py removing /tmp/tmpd2l9em7d.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/' adding license file 'COPYING' adding license file 'AUTHORS' writing manifest file 'pysam.egg-info/SOURCES.txt' Copying pysam.egg-info to /builddir/build/BUILDROOT/python-pysam-0.19.0-4.fc37.i386/usr/lib/python3.11/site-packages/pysam-0.19.0-py3.11.egg-info running install_scripts + rm -rfv /builddir/build/BUILDROOT/python-pysam-0.19.0-4.fc37.i386/usr/bin/__pycache__ + /usr/bin/find-debuginfo -j6 --strict-build-id -m -i --build-id-seed 0.19.0-4.fc37 --unique-debug-suffix -0.19.0-4.fc37.i386 --unique-debug-src-base python-pysam-0.19.0-4.fc37.i386 --run-dwz --dwz-low-mem-die-limit 10000000 --dwz-max-die-limit 50000000 -S debugsourcefiles.list /builddir/build/BUILD/pysam-0.19.0 extracting debug info from /builddir/build/BUILDROOT/python-pysam-0.19.0-4.fc37.i386/usr/lib/python3.11/site-packages/pysam/libcalignedsegment.cpython-311-i386-linux-gnu.so extracting debug info from /builddir/build/BUILDROOT/python-pysam-0.19.0-4.fc37.i386/usr/lib/python3.11/site-packages/pysam/libcbcf.cpython-311-i386-linux-gnu.so extracting debug info from /builddir/build/BUILDROOT/python-pysam-0.19.0-4.fc37.i386/usr/lib/python3.11/site-packages/pysam/libcbcftools.cpython-311-i386-linux-gnu.so extracting debug info from /builddir/build/BUILDROOT/python-pysam-0.19.0-4.fc37.i386/usr/lib/python3.11/site-packages/pysam/libcalignmentfile.cpython-311-i386-linux-gnu.so extracting debug info from /builddir/build/BUILDROOT/python-pysam-0.19.0-4.fc37.i386/usr/lib/python3.11/site-packages/pysam/libcfaidx.cpython-311-i386-linux-gnu.so extracting debug info from /builddir/build/BUILDROOT/python-pysam-0.19.0-4.fc37.i386/usr/lib/python3.11/site-packages/pysam/libcbgzf.cpython-311-i386-linux-gnu.so extracting debug info from /builddir/build/BUILDROOT/python-pysam-0.19.0-4.fc37.i386/usr/lib/python3.11/site-packages/pysam/libchtslib.cpython-311-i386-linux-gnu.so extracting debug info from /builddir/build/BUILDROOT/python-pysam-0.19.0-4.fc37.i386/usr/lib/python3.11/site-packages/pysam/libcsamfile.cpython-311-i386-linux-gnu.so extracting debug info from /builddir/build/BUILDROOT/python-pysam-0.19.0-4.fc37.i386/usr/lib/python3.11/site-packages/pysam/libcsamtools.cpython-311-i386-linux-gnu.so extracting debug info from /builddir/build/BUILDROOT/python-pysam-0.19.0-4.fc37.i386/usr/lib/python3.11/site-packages/pysam/libctabix.cpython-311-i386-linux-gnu.so extracting debug info from /builddir/build/BUILDROOT/python-pysam-0.19.0-4.fc37.i386/usr/lib/python3.11/site-packages/pysam/libctabixproxies.cpython-311-i386-linux-gnu.so extracting debug info from /builddir/build/BUILDROOT/python-pysam-0.19.0-4.fc37.i386/usr/lib/python3.11/site-packages/pysam/libcutils.cpython-311-i386-linux-gnu.so extracting debug info from /builddir/build/BUILDROOT/python-pysam-0.19.0-4.fc37.i386/usr/lib/python3.11/site-packages/pysam/libcvcf.cpython-311-i386-linux-gnu.so original debug info size: 21460kB, size after compression: 20236kB /usr/bin/sepdebugcrcfix: Updated 13 CRC32s, 0 CRC32s did match. 41767 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/check-rpaths + /usr/lib/rpm/redhat/brp-mangle-shebangs + /usr/lib/rpm/brp-remove-la-files + /usr/lib/rpm/redhat/brp-python-bytecompile '' 1 0 Bytecompiling .py files below /builddir/build/BUILDROOT/python-pysam-0.19.0-4.fc37.i386/usr/lib/python3.11 using python3.11 Bytecompiling .py files below /builddir/build/BUILDROOT/python-pysam-0.19.0-4.fc37.i386/usr/lib/debug/usr/lib/python3.11 using python3.11 + /usr/lib/rpm/redhat/brp-python-hardlink Processing files: python3-pysam-0.19.0-4.fc37.i686 Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.wszDU3 + umask 022 + cd /builddir/build/BUILD + cd pysam-0.19.0 + DOCDIR=/builddir/build/BUILDROOT/python-pysam-0.19.0-4.fc37.i386/usr/share/doc/python3-pysam + export LC_ALL=C + LC_ALL=C + export DOCDIR + /usr/bin/mkdir -p /builddir/build/BUILDROOT/python-pysam-0.19.0-4.fc37.i386/usr/share/doc/python3-pysam + cp -pr README.rst /builddir/build/BUILDROOT/python-pysam-0.19.0-4.fc37.i386/usr/share/doc/python3-pysam + RPM_EC=0 ++ jobs -p + exit 0 Executing(%license): /bin/sh -e /var/tmp/rpm-tmp.JEzyes + umask 022 + cd /builddir/build/BUILD + cd pysam-0.19.0 + LICENSEDIR=/builddir/build/BUILDROOT/python-pysam-0.19.0-4.fc37.i386/usr/share/licenses/python3-pysam + export LC_ALL=C + LC_ALL=C + export LICENSEDIR + /usr/bin/mkdir -p /builddir/build/BUILDROOT/python-pysam-0.19.0-4.fc37.i386/usr/share/licenses/python3-pysam + cp -pr COPYING /builddir/build/BUILDROOT/python-pysam-0.19.0-4.fc37.i386/usr/share/licenses/python3-pysam + RPM_EC=0 ++ jobs -p + exit 0 Provides: bundled(bcftools) = 1.15 bundled(htslib) = 1.15 bundled(samtools) = 1.15 libcalignedsegment.cpython-311-i386-linux-gnu.so libcalignmentfile.cpython-311-i386-linux-gnu.so libcbcf.cpython-311-i386-linux-gnu.so libcbcftools.cpython-311-i386-linux-gnu.so libcbgzf.cpython-311-i386-linux-gnu.so libcfaidx.cpython-311-i386-linux-gnu.so libchtslib.cpython-311-i386-linux-gnu.so libcsamfile.cpython-311-i386-linux-gnu.so libcsamtools.cpython-311-i386-linux-gnu.so libctabix.cpython-311-i386-linux-gnu.so libctabixproxies.cpython-311-i386-linux-gnu.so libcutils.cpython-311-i386-linux-gnu.so libcvcf.cpython-311-i386-linux-gnu.so python-pysam = 0.19.0-4.fc37 python3-pysam = 0.19.0-4.fc37 python3-pysam(x86-32) = 0.19.0-4.fc37 python3.11-pysam = 0.19.0-4.fc37 python3.11dist(pysam) = 0.19 python3dist(pysam) = 0.19 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 libc.so.6 libc.so.6(GLIBC_2.0) libc.so.6(GLIBC_2.1) libc.so.6(GLIBC_2.1.3) libc.so.6(GLIBC_2.11) libc.so.6(GLIBC_2.2) libc.so.6(GLIBC_2.3) libc.so.6(GLIBC_2.3.2) libc.so.6(GLIBC_2.3.4) libc.so.6(GLIBC_2.33) libc.so.6(GLIBC_2.34) libc.so.6(GLIBC_2.4) libc.so.6(GLIBC_2.7) libcbcftools.cpython-311-i386-linux-gnu.so libchtslib.cpython-311-i386-linux-gnu.so libcsamtools.cpython-311-i386-linux-gnu.so liblzma.so.5 liblzma.so.5(XZ_5.0) libm.so.6 libm.so.6(GLIBC_2.0) libm.so.6(GLIBC_2.1) libm.so.6(GLIBC_2.23) libm.so.6(GLIBC_2.29) libz.so.1 libz.so.1(ZLIB_1.2.3.3) python(abi) = 3.11 rtld(GNU_HASH) Obsoletes: python-pysam < 0.19.0-4.fc37 Processing files: python3-pysam-devel-0.19.0-4.fc37.i686 Provides: python-pysam-devel = 0.19.0-4.fc37 python3-pysam-devel = 0.19.0-4.fc37 python3-pysam-devel(x86-32) = 0.19.0-4.fc37 python3.11-pysam-devel = 0.19.0-4.fc37 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) = 3.11 Processing files: python-pysam-doc-0.19.0-4.fc37.noarch Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.wv87lp + umask 022 + cd /builddir/build/BUILD + cd pysam-0.19.0 + DOCDIR=/builddir/build/BUILDROOT/python-pysam-0.19.0-4.fc37.i386/usr/share/doc/python-pysam-doc + export LC_ALL=C + LC_ALL=C + export DOCDIR + /usr/bin/mkdir -p /builddir/build/BUILDROOT/python-pysam-0.19.0-4.fc37.i386/usr/share/doc/python-pysam-doc + cp -pr html /builddir/build/BUILDROOT/python-pysam-0.19.0-4.fc37.i386/usr/share/doc/python-pysam-doc + RPM_EC=0 ++ jobs -p + exit 0 Provides: python-pysam-doc = 0.19.0-4.fc37 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Processing files: python-pysam-debugsource-0.19.0-4.fc37.i686 Provides: python-pysam-debugsource = 0.19.0-4.fc37 python-pysam-debugsource(x86-32) = 0.19.0-4.fc37 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Processing files: python3-pysam-debuginfo-0.19.0-4.fc37.i686 Provides: debuginfo(build-id) = 1cc83225882177dabbeedca925537f3ca7bd14d0 debuginfo(build-id) = 3a5f064444b1758c8b9e9fd5666ba13e58fadb9e debuginfo(build-id) = 4ec6ab200487b3f901eaa2dfdcd3fe21e4110fab debuginfo(build-id) = 715bbc685c136732e51bad274ff1079259e9e0f9 debuginfo(build-id) = 7b3c9eba0476cbe7fd5c528ce4a1657fc5b1f933 debuginfo(build-id) = 88c531d72cb37a28614112fa94f3871dd74aa68e debuginfo(build-id) = 9c20dd7d3169739e84280cb1493ab0be8a79458f debuginfo(build-id) = a7c5caed5269fc71cdead75a9af8c83e0b52e1a5 debuginfo(build-id) = bb9f207f3a18c3acefb12acce6f610923619a41d debuginfo(build-id) = dbc716f3caf82e721747c4e1a81d9a0762a945dd debuginfo(build-id) = e274659abff49e1982a9d9b6e55cdeace339cd0e debuginfo(build-id) = e3ad0df4e0518456e1295b6002218d86302a52b1 debuginfo(build-id) = f78070a24634a0adb02a96f8cacff6a6360ac1b1 libcalignedsegment.cpython-311-i386-linux-gnu.so-0.19.0-4.fc37.i386.debug libcalignmentfile.cpython-311-i386-linux-gnu.so-0.19.0-4.fc37.i386.debug libcbcf.cpython-311-i386-linux-gnu.so-0.19.0-4.fc37.i386.debug libcbcftools.cpython-311-i386-linux-gnu.so-0.19.0-4.fc37.i386.debug libcbgzf.cpython-311-i386-linux-gnu.so-0.19.0-4.fc37.i386.debug libcfaidx.cpython-311-i386-linux-gnu.so-0.19.0-4.fc37.i386.debug libchtslib.cpython-311-i386-linux-gnu.so-0.19.0-4.fc37.i386.debug libcsamfile.cpython-311-i386-linux-gnu.so-0.19.0-4.fc37.i386.debug libcsamtools.cpython-311-i386-linux-gnu.so-0.19.0-4.fc37.i386.debug libctabix.cpython-311-i386-linux-gnu.so-0.19.0-4.fc37.i386.debug libctabixproxies.cpython-311-i386-linux-gnu.so-0.19.0-4.fc37.i386.debug libcutils.cpython-311-i386-linux-gnu.so-0.19.0-4.fc37.i386.debug libcvcf.cpython-311-i386-linux-gnu.so-0.19.0-4.fc37.i386.debug python-pysam-debuginfo = 0.19.0-4.fc37 python3-pysam-debuginfo = 0.19.0-4.fc37 python3-pysam-debuginfo(x86-32) = 0.19.0-4.fc37 python3.11-pysam-debuginfo = 0.19.0-4.fc37 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Recommends: python-pysam-debugsource(x86-32) = 0.19.0-4.fc37 Checking for unpackaged file(s): /usr/lib/rpm/check-files /builddir/build/BUILDROOT/python-pysam-0.19.0-4.fc37.i386 Wrote: /builddir/build/RPMS/python-pysam-doc-0.19.0-4.fc37.noarch.rpm Wrote: /builddir/build/RPMS/python3-pysam-devel-0.19.0-4.fc37.i686.rpm Wrote: /builddir/build/RPMS/python3-pysam-0.19.0-4.fc37.i686.rpm Wrote: /builddir/build/RPMS/python3-pysam-debuginfo-0.19.0-4.fc37.i686.rpm Wrote: /builddir/build/RPMS/python-pysam-debugsource-0.19.0-4.fc37.i686.rpm Executing(%clean): /bin/sh -e /var/tmp/rpm-tmp.Ni5cl3 + umask 022 + cd /builddir/build/BUILD + cd pysam-0.19.0 + /usr/bin/rm -rf /builddir/build/BUILDROOT/python-pysam-0.19.0-4.fc37.i386 + RPM_EC=0 ++ jobs -p + exit 0 Child return code was: 0