Input buildinfo: https://buildinfos.debian.net/buildinfo-pool/p/python-pysam/python-pysam_0.17.0+ds-2+b1_amd64.buildinfo Use metasnap for getting required timestamps New buildinfo file: /tmp/python-pysam-0.17.0+ds-2+b1cx_mu81o/python-pysam_0.17.0+ds-2+b1_amd64.buildinfo Get source package info: python-pysam=0.17.0+ds-2 Source URL: http://snapshot.notset.fr/mr/package/python-pysam/0.17.0+ds-2/srcfiles?fileinfo=1 env -i PATH=/usr/sbin:/usr/bin:/sbin:/bin TMPDIR=/tmp mmdebstrap --arch=amd64 --include=autoconf=2.71-2 automake=1:1.16.5-1.1 autopoint=0.21-4 autotools-dev=20180224.1+nmu1 base-files=12 base-passwd=3.5.52 bash=5.1-3.1 bcftools=1.13-1 binutils=2.37-9 binutils-common=2.37-9 binutils-x86-64-linux-gnu=2.37-9 bsdextrautils=2.37.2-4 bsdutils=1:2.37.2-4 build-essential=12.9 bzip2=1.0.8-4 coreutils=8.32-4.1 cpp=4:11.2.0-2 cpp-11=11.2.0-10 cython3=0.29.24-1+b1 dash=0.5.11+git20210903+057cd650a4ed-3 debconf=1.5.79 debhelper=13.5.2 debianutils=5.5-1 dh-autoreconf=20 dh-exec=0.23.4 dh-python=5.20211114 dh-strip-nondeterminism=1.12.0-2 diffutils=1:3.7-5 dpkg=1.20.9 dpkg-dev=1.20.9 dwz=0.14-1 file=1:5.41-2 findutils=4.8.0-1 g++=4:11.2.0-2 g++-11=11.2.0-10 gcc=4:11.2.0-2 gcc-11=11.2.0-10 gcc-11-base=11.2.0-10 gettext=0.21-4 gettext-base=0.21-4 grep=3.7-1 groff-base=1.22.4-7 gzip=1.10-4 hostname=3.23 init-system-helpers=1.60 intltool-debian=0.35.0+20060710.5 libacl1=2.3.1-1 libarchive-zip-perl=1.68-1 libasan6=11.2.0-10 libatomic1=11.2.0-10 libattr1=1:2.5.1-1 libaudit-common=1:3.0.6-1 libaudit1=1:3.0.6-1 libbinutils=2.37-9 libblkid1=2.37.2-4 libbrotli1=1.0.9-2+b3 libbsd0=0.11.3-1 libbz2-1.0=1.0.8-4 libc-bin=2.32-4 libc-dev-bin=2.32-4 libc6=2.32-4 libc6-dev=2.32-4 libcap-ng0=0.7.9-2.2+b1 libcap2=1:2.44-1 libcc1-0=11.2.0-10 libcom-err2=1.46.4-1 libcrypt-dev=1:4.4.26-1 libcrypt1=1:4.4.26-1 libctf-nobfd0=2.37-9 libctf0=2.37-9 libcurl3-gnutls=7.79.1-2 libcurl4-gnutls-dev=7.79.1-2 libdb5.3=5.3.28+dfsg1-0.8 libdebconfclient0=0.261 libdebhelper-perl=13.5.2 libdeflate-dev=1.8-1 libdeflate0=1.8-1 libdpkg-perl=1.20.9 libedit2=3.1-20210910-1 libelf1=0.186-1 libexpat1=2.4.1-3 libexpat1-dev=2.4.1-3 libffi8=3.4.2-3 libfile-stripnondeterminism-perl=1.12.0-2 libgcc-11-dev=11.2.0-10 libgcc-s1=11.2.0-10 libgcrypt20=1.9.4-3+b1 libgdbm-compat4=1.22-1 libgdbm6=1.22-1 libgmp10=2:6.2.1+dfsg-3 libgnutls30=3.7.2-2 libgomp1=11.2.0-10 libgpg-error0=1.42-3 libgssapi-krb5-2=1.18.3-7 libhogweed6=3.7.3-1 libhts-dev=1.13+ds-2 libhts3=1.13+ds-2 libhtscodecs2=1.1.1-3+b1 libicu67=67.1-7 libidn2-0=2.3.2-2 libisl23=0.24-2 libitm1=11.2.0-10 libjs-jquery=3.5.1+dfsg+~3.5.5-8 libjs-sphinxdoc=4.2.0-5 libjs-underscore=1.9.1~dfsg-4 libk5crypto3=1.18.3-7 libkeyutils1=1.6.1-2 libkrb5-3=1.18.3-7 libkrb5support0=1.18.3-7 libldap-2.4-2=2.4.59+dfsg-1 liblsan0=11.2.0-10 liblz4-1=1.9.3-2 liblzma-dev=5.2.5-2 liblzma5=5.2.5-2 libmagic-mgc=1:5.41-2 libmagic1=1:5.41-2 libmd0=1.0.4-1 libmount1=2.37.2-4 libmpc3=1.2.1-1 libmpdec3=2.5.1-2 libmpfr6=4.1.0-3 libncurses6=6.3-1 libncursesw6=6.3-1 libnettle8=3.7.3-1 libnghttp2-14=1.43.0-1 libnsl-dev=1.3.0-2 libnsl2=1.3.0-2 libp11-kit0=0.24.0-5 libpam-modules=1.4.0-10 libpam-modules-bin=1.4.0-10 libpam-runtime=1.4.0-10 libpam0g=1.4.0-10 libpcre2-8-0=10.39-3 libpcre3=2:8.39-13 libperl5.32=5.32.1-6 libpipeline1=1.5.4-1 libpsl5=0.21.0-1.2 libpython3-all-dev=3.9.8-1 libpython3-dev=3.9.8-1 libpython3-stdlib=3.9.8-1 libpython3.10=3.10.0-5 libpython3.10-dev=3.10.0-5 libpython3.10-minimal=3.10.0-5 libpython3.10-stdlib=3.10.0-5 libpython3.9=3.9.9-1 libpython3.9-dev=3.9.9-1 libpython3.9-minimal=3.9.9-1 libpython3.9-stdlib=3.9.9-1 libquadmath0=11.2.0-10 libreadline8=8.1-2 librtmp1=2.4+20151223.gitfa8646d.1-2+b2 libsasl2-2=2.1.27+dfsg2-2 libsasl2-modules-db=2.1.27+dfsg2-2 libseccomp2=2.5.2-2 libselinux1=3.3-1 libsigsegv2=2.13-1 libsmartcols1=2.37.2-4 libsqlite3-0=3.36.0-2 libssh2-1=1.10.0-2 libssl1.1=1.1.1l-1 libstdc++-11-dev=11.2.0-10 libstdc++6=11.2.0-10 libsub-override-perl=0.09-2 libsystemd0=249.6-2 libtasn1-6=4.18.0-4 libtinfo6=6.3-1 libtirpc-common=1.3.2-2 libtirpc-dev=1.3.2-2 libtirpc3=1.3.2-2 libtool=2.4.6-15 libtsan0=11.2.0-10 libubsan1=11.2.0-10 libuchardet0=0.0.7-1 libudev1=249.6-2 libunistring2=0.9.10-6 libuuid1=2.37.2-4 libxml2=2.9.12+dfsg-5+b1 libzstd1=1.4.8+dfsg-3 linux-libc-dev=5.14.16-1 login=1:4.8.1-2 lsb-base=11.1.0 m4=1.4.18-5 mailcap=3.70 make=4.3-4.1 man-db=2.9.4-2 mawk=1.3.4.20200120-2 media-types=4.0.0 mime-support=3.66 ncurses-base=6.3-1 ncurses-bin=6.3-1 patch=2.7.6-7 perl=5.32.1-6 perl-base=5.32.1-6 perl-modules-5.32=5.32.1-6 po-debconf=1.0.21+nmu1 python3=3.9.8-1 python3-all=3.9.8-1 python3-all-dev=3.9.8-1 python3-attr=20.3.0-1 python3-dev=3.9.8-1 python3-distutils=3.9.9-2 python3-importlib-metadata=4.6.4-1 python3-iniconfig=1.1.1-1 python3-lib2to3=3.9.9-2 python3-minimal=3.9.8-1 python3-more-itertools=8.10.0-2 python3-packaging=21.2-1 python3-pkg-resources=58.2.0-1 python3-pluggy=0.13.0-7.1 python3-py=1.10.0-1 python3-pyparsing=2.4.7-1 python3-pytest=6.2.5-1 python3-setuptools=58.2.0-1 python3-toml=0.10.2-1 python3-zipp=1.0.0-3 python3.10=3.10.0-5 python3.10-dev=3.10.0-5 python3.10-minimal=3.10.0-5 python3.9=3.9.9-1 python3.9-dev=3.9.9-1 python3.9-minimal=3.9.9-1 readline-common=8.1-2 rpcsvc-proto=1.4.2-4 samtools=1.13-4 sed=4.8-1 sensible-utils=0.0.17 sysvinit-utils=3.00-1 tabix=1.13+ds-2 tar=1.34+dfsg-1 tzdata=2021e-1 util-linux=2.37.2-4 xz-utils=5.2.5-2 zlib1g=1:1.2.11.dfsg-2 zlib1g-dev=1:1.2.11.dfsg-2 --variant=apt --aptopt=Acquire::Check-Valid-Until "false" --aptopt=Acquire::http::Dl-Limit "1000"; --aptopt=Acquire::https::Dl-Limit "1000"; --aptopt=Acquire::Retries "5"; --aptopt=APT::Get::allow-downgrades "true"; --keyring=/usr/share/keyrings/ --essential-hook=chroot "$1" sh -c "apt-get --yes install fakeroot util-linux" --essential-hook=copy-in /usr/share/keyrings/debian-archive-bullseye-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-security-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-stable.gpg /usr/share/keyrings/debian-archive-buster-automatic.gpg /usr/share/keyrings/debian-archive-buster-security-automatic.gpg /usr/share/keyrings/debian-archive-buster-stable.gpg /usr/share/keyrings/debian-archive-keyring.gpg /usr/share/keyrings/debian-archive-removed-keys.gpg /usr/share/keyrings/debian-archive-stretch-automatic.gpg /usr/share/keyrings/debian-archive-stretch-security-automatic.gpg /usr/share/keyrings/debian-archive-stretch-stable.gpg /usr/share/keyrings/debian-ports-archive-keyring-removed.gpg /usr/share/keyrings/debian-ports-archive-keyring.gpg /usr/share/keyrings/debian-keyring.gpg /etc/apt/trusted.gpg.d/ --essential-hook=chroot "$1" sh -c "rm /etc/apt/sources.list && echo 'deb http://snapshot.notset.fr/archive/debian/20211017T024714Z/ bookworm main deb-src http://snapshot.notset.fr/archive/debian/20211017T024714Z/ bookworm main deb http://snapshot.notset.fr/archive/debian/20211227T221822Z/ unstable main deb http://snapshot.notset.fr/archive/debian/20211118T084946Z/ unstable main' >> /etc/apt/sources.list && apt-get update" --customize-hook=chroot "$1" useradd --no-create-home -d /nonexistent -p "" builduser -s /bin/bash --customize-hook=chroot "$1" env sh -c "apt-get source --only-source -d python-pysam=0.17.0+ds-2 && mkdir -p /build/python-pysam-TG7D0j && dpkg-source --no-check -x /*.dsc /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds && cd /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds && { printf '%s' 'python-pysam (0.17.0+ds-2+b1) sid; urgency=low, binary-only=yes * Binary-only non-maintainer upload for amd64; no source changes. * Add Python 3.10 as supported version -- amd64 / i386 Build Daemon (x86-csail-01) Sun, 21 Nov 2021 07:58:04 +0000 '; cat debian/changelog; } > debian/changelog.debrebuild && mv debian/changelog.debrebuild debian/changelog && chown -R builduser:builduser /build/python-pysam-TG7D0j" --customize-hook=chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds && env DEB_BUILD_OPTIONS="parallel=4" LC_ALL="C.UTF-8" LC_COLLATE="C.UTF-8" SOURCE_DATE_EPOCH="1637481484" DEB_BUILD_OPTIONS=nocheck dpkg-buildpackage -uc -a amd64 --build=any" --customize-hook=sync-out /build/python-pysam-TG7D0j /tmp/python-pysam-0.17.0+ds-2+b1cx_mu81o bookworm /dev/null deb http://snapshot.notset.fr/archive/debian/20211118T084946Z unstable main I: automatically chosen mode: root I: chroot architecture amd64 is equal to the host's architecture I: automatically chosen format: null I: using /tmp/mmdebstrap.718MyYN9IH as tempdir I: running apt-get update... I: downloading packages with apt... I: extracting archives... I: installing essential packages... I: running --essential-hook in shell: sh -c 'chroot "$1" sh -c "apt-get --yes install fakeroot util-linux"' exec /tmp/mmdebstrap.718MyYN9IH Reading package lists... Building dependency tree... util-linux is already the newest version (2.37.2-4). The following NEW packages will be installed: fakeroot libfakeroot 0 upgraded, 2 newly installed, 0 to remove and 0 not upgraded. Need to get 134 kB of archives. After this operation, 397 kB of additional disk space will be used. Get:1 http://snapshot.notset.fr/archive/debian/20211118T084946Z unstable/main amd64 libfakeroot amd64 1.26-1 [47.3 kB] Get:2 http://snapshot.notset.fr/archive/debian/20211118T084946Z unstable/main amd64 fakeroot amd64 1.26-1 [87.1 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 134 kB in 0s (1031 kB/s) Selecting previously unselected package libfakeroot:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 4669 files and directories currently installed.) Preparing to unpack .../libfakeroot_1.26-1_amd64.deb ... Unpacking libfakeroot:amd64 (1.26-1) ... Selecting previously unselected package fakeroot. Preparing to unpack .../fakeroot_1.26-1_amd64.deb ... Unpacking fakeroot (1.26-1) ... Setting up libfakeroot:amd64 (1.26-1) ... Setting up fakeroot (1.26-1) ... update-alternatives: using /usr/bin/fakeroot-sysv to provide /usr/bin/fakeroot (fakeroot) in auto mode Processing triggers for libc-bin (2.32-4) ... I: running special hook: copy-in /usr/share/keyrings/debian-archive-bullseye-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-security-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-stable.gpg /usr/share/keyrings/debian-archive-buster-automatic.gpg /usr/share/keyrings/debian-archive-buster-security-automatic.gpg /usr/share/keyrings/debian-archive-buster-stable.gpg /usr/share/keyrings/debian-archive-keyring.gpg /usr/share/keyrings/debian-archive-removed-keys.gpg /usr/share/keyrings/debian-archive-stretch-automatic.gpg /usr/share/keyrings/debian-archive-stretch-security-automatic.gpg /usr/share/keyrings/debian-archive-stretch-stable.gpg /usr/share/keyrings/debian-ports-archive-keyring-removed.gpg /usr/share/keyrings/debian-ports-archive-keyring.gpg /usr/share/keyrings/debian-keyring.gpg /etc/apt/trusted.gpg.d/ I: running --essential-hook in shell: sh -c 'chroot "$1" sh -c "rm /etc/apt/sources.list && echo 'deb http://snapshot.notset.fr/archive/debian/20211017T024714Z/ bookworm main deb-src http://snapshot.notset.fr/archive/debian/20211017T024714Z/ bookworm main deb http://snapshot.notset.fr/archive/debian/20211227T221822Z/ unstable main deb http://snapshot.notset.fr/archive/debian/20211118T084946Z/ unstable main' >> /etc/apt/sources.list && apt-get update"' exec /tmp/mmdebstrap.718MyYN9IH Get:1 http://snapshot.notset.fr/archive/debian/20211017T024714Z bookworm InRelease [128 kB] Get:2 http://snapshot.notset.fr/archive/debian/20211227T221822Z unstable InRelease [165 kB] Hit:3 http://snapshot.notset.fr/archive/debian/20211118T084946Z unstable InRelease Ign:4 http://snapshot.notset.fr/archive/debian/20211017T024714Z bookworm/main Sources Ign:5 http://snapshot.notset.fr/archive/debian/20211017T024714Z bookworm/main amd64 Packages Ign:4 http://snapshot.notset.fr/archive/debian/20211017T024714Z bookworm/main Sources Ign:5 http://snapshot.notset.fr/archive/debian/20211017T024714Z bookworm/main amd64 Packages Ign:4 http://snapshot.notset.fr/archive/debian/20211017T024714Z bookworm/main Sources Ign:5 http://snapshot.notset.fr/archive/debian/20211017T024714Z bookworm/main amd64 Packages Get:4 http://snapshot.notset.fr/archive/debian/20211017T024714Z bookworm/main Sources [11.7 MB] Get:5 http://snapshot.notset.fr/archive/debian/20211017T024714Z bookworm/main amd64 Packages [11.2 MB] Ign:6 http://snapshot.notset.fr/archive/debian/20211227T221822Z unstable/main amd64 Packages Err:6 http://snapshot.notset.fr/archive/debian/20211227T221822Z unstable/main amd64 Packages 404 Not Found [IP: 10.13.0.253 80] Ign:6 http://snapshot.notset.fr/archive/debian/20211227T221822Z unstable/main amd64 Packages Get:6 http://snapshot.notset.fr/archive/debian/20211227T221822Z unstable/main amd64 Packages [12.0 MB] Fetched 35.2 MB in 29s (1209 kB/s) Reading package lists... I: installing remaining packages inside the chroot... I: running --customize-hook in shell: sh -c 'chroot "$1" useradd --no-create-home -d /nonexistent -p "" builduser -s /bin/bash' exec /tmp/mmdebstrap.718MyYN9IH I: running --customize-hook in shell: sh -c 'chroot "$1" env sh -c "apt-get source --only-source -d python-pysam=0.17.0+ds-2 && mkdir -p /build/python-pysam-TG7D0j && dpkg-source --no-check -x /*.dsc /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds && cd /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds && { printf '%s' 'python-pysam (0.17.0+ds-2+b1) sid; urgency=low, binary-only=yes * Binary-only non-maintainer upload for amd64; no source changes. * Add Python 3.10 as supported version -- amd64 / i386 Build Daemon (x86-csail-01) Sun, 21 Nov 2021 07:58:04 +0000 '; cat debian/changelog; } > debian/changelog.debrebuild && mv debian/changelog.debrebuild debian/changelog && chown -R builduser:builduser /build/python-pysam-TG7D0j"' exec /tmp/mmdebstrap.718MyYN9IH Reading package lists... NOTICE: 'python-pysam' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/python-pysam.git Please use: git clone https://salsa.debian.org/med-team/python-pysam.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 1807 kB of source archives. Get:1 http://snapshot.notset.fr/archive/debian/20211017T024714Z bookworm/main python-pysam 0.17.0+ds-2 (dsc) [2425 B] Get:2 http://snapshot.notset.fr/archive/debian/20211017T024714Z bookworm/main python-pysam 0.17.0+ds-2 (tar) [1430 kB] Get:3 http://snapshot.notset.fr/archive/debian/20211017T024714Z bookworm/main python-pysam 0.17.0+ds-2 (diff) [374 kB] Fetched 1807 kB in 1s (1211 kB/s) Download complete and in download only mode W: Download is performed unsandboxed as root as file 'python-pysam_0.17.0+ds-2.dsc' couldn't be accessed by user '_apt'. - pkgAcquire::Run (13: Permission denied) dpkg-source: info: extracting python-pysam in /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds dpkg-source: info: unpacking python-pysam_0.17.0+ds.orig.tar.xz dpkg-source: info: unpacking python-pysam_0.17.0+ds-2.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying skip_test_remote.patch dpkg-source: info: applying clean_less dpkg-source: info: applying skip-test-on-32-bit.patch I: running --customize-hook in shell: sh -c 'chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds && env DEB_BUILD_OPTIONS="parallel=4" LC_ALL="C.UTF-8" LC_COLLATE="C.UTF-8" SOURCE_DATE_EPOCH="1637481484" DEB_BUILD_OPTIONS=nocheck dpkg-buildpackage -uc -a amd64 --build=any"' exec /tmp/mmdebstrap.718MyYN9IH dpkg-buildpackage: info: source package python-pysam dpkg-buildpackage: info: source version 0.17.0+ds-2+b1 dpkg-buildpackage: info: source distribution sid dpkg-buildpackage: info: source changed by amd64 / i386 Build Daemon (x86-csail-01) dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean cd tests/pysam_data && /usr/bin/make clean make[1]: Entering directory '/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/tests/pysam_data' rm -fr *.bai *.csi *.fai *.gzi *.pileup* [a-z]*.cram *.crai \ all.stamp *~ calDepth *.dSYM pysam_*.sam \ ex2.sam ex2.sam.gz ex1.sam ex1.fa.gz \ with_md.sam.gz \ *.fq.gz make[1]: Leaving directory '/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/tests/pysam_data' cd tests/cbcf_data && /usr/bin/make clean make[1]: Entering directory '/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/tests/cbcf_data' rm -f all.stamp *.gz *.tbi *.csi *.bcf make[1]: Leaving directory '/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/tests/cbcf_data' find . -name "*.pyc" -delete find . -name "*.pyxbldc" -delete find . -name "tmp_*.bam" -delete find . -name "*.bai*" -delete find . -name "*.cram*" -delete find . -name "pysam_uncompressed.bam" -delete rm -rf tests/pysam_test_work \ tests/example_htslib.gtf.gz.tbi \ tests/log.txt \ tests/test.bam \ tests/_compile_test.c \ tests/pysam_ex2.sam \ tests/__pycache__ \ pysam/calignmentfile.c \ pysam/cbcf.c \ tests/GRCh38_full_analysis_set_plus_decoy_hla.fa.fai \ tests/pysam_data/ex1.fa.gz \ tests/pysam_data/ex1.fa.gz.gzi \ tests/pysam_data/ex1_csi.bam.csi rm -rf .pytest_cache/ dh clean --with python3 --buildsystem=pybuild debian/rules override_dh_auto_clean make[1]: Entering directory '/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds' dh_auto_clean I: pybuild base:237: python3.10 setup.py clean /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/setup.py:32: DeprecationWarning: The distutils package is deprecated and slated for removal in Python 3.12. Use setuptools or check PEP 632 for potential alternatives from distutils import log # pysam: cython is available - using cythonize if necessary # pysam: htslib mode is external # pysam: HTSLIB_CONFIGURE_OPTIONS=None running clean removing '/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build' (and everything under it) 'build/bdist.linux-x86_64' does not exist -- can't clean it 'build/scripts-3.10' does not exist -- can't clean it I: pybuild base:237: python3.9 setup.py clean # pysam: cython is available - using cythonize if necessary # pysam: htslib mode is external # pysam: HTSLIB_CONFIGURE_OPTIONS=None running clean removing '/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build' (and everything under it) 'build/bdist.linux-x86_64' does not exist -- can't clean it 'build/scripts-3.9' does not exist -- can't clean it rm -f \ pysam/config.py \ pysam/config.h \ pysam/lib*.c \ samtools/config.h \ bcftools/config.h rm -rf pysam.egg-info make[1]: Leaving directory '/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds' dh_autoreconf_clean -O--buildsystem=pybuild dh_clean -O--buildsystem=pybuild debian/rules binary-arch dh binary-arch --with python3 --buildsystem=pybuild dh_update_autotools_config -a -O--buildsystem=pybuild dh_autoreconf -a -O--buildsystem=pybuild dh_auto_configure -a -O--buildsystem=pybuild I: pybuild base:237: python3.10 setup.py config /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/setup.py:32: DeprecationWarning: The distutils package is deprecated and slated for removal in Python 3.12. Use setuptools or check PEP 632 for potential alternatives from distutils import log # pysam: cython is available - using cythonize if necessary # pysam: htslib mode is external # pysam: HTSLIB_CONFIGURE_OPTIONS=None running config I: pybuild base:237: python3.9 setup.py config # pysam: cython is available - using cythonize if necessary # pysam: htslib mode is external # pysam: HTSLIB_CONFIGURE_OPTIONS=None running config dh_auto_build -a -O--buildsystem=pybuild I: pybuild base:237: /usr/bin/python3.10 setup.py build /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/setup.py:32: DeprecationWarning: The distutils package is deprecated and slated for removal in Python 3.12. Use setuptools or check PEP 632 for potential alternatives from distutils import log # pysam: cython is available - using cythonize if necessary # pysam: htslib mode is external # pysam: HTSLIB_CONFIGURE_OPTIONS=None running build running build_py creating /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam copying pysam/Pileup.py -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam copying pysam/__init__.py -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam copying pysam/bcftools.py -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam copying pysam/samtools.py -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam copying pysam/utils.py -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam copying pysam/version.py -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam copying pysam/config.py -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam creating /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam/include copying pysam/include/__init__.py -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/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) copying pysam/libcalignedsegment.pxd -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam copying pysam/libcalignmentfile.pxd -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam copying pysam/libcbcf.pxd -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam copying pysam/libcbcftools.pxd -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam copying pysam/libcfaidx.pxd -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam copying pysam/libchtslib.pxd -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam copying pysam/libcsamfile.pxd -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam copying pysam/libcsamtools.pxd -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam copying pysam/libctabix.pxd -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam copying pysam/libctabixproxies.pxd -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam copying pysam/libcutils.pxd -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam copying pysam/libcvcf.pxd -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam copying pysam/cbcftools_util.h -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam copying pysam/csamtools_util.h -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam copying pysam/htslib_util.h -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam copying pysam/pysam_stream.h -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam copying pysam/pysam_util.h -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam copying pysam/version.h -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam creating /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam/include/samtools copying samtools/bam.h -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam/include/samtools copying samtools/bam2bcf.h -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam/include/samtools copying samtools/bam_ampliconclip.h -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam/include/samtools copying samtools/bam_endian.h -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam/include/samtools copying samtools/bam_lpileup.h -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam/include/samtools copying samtools/bam_plbuf.h -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam/include/samtools copying samtools/bedidx.h -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam/include/samtools copying samtools/sam.h -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam/include/samtools copying samtools/sam_opts.h -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam/include/samtools copying samtools/sample.h -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam/include/samtools copying samtools/samtools.h -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam/include/samtools copying samtools/samtools.pysam.h -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam/include/samtools copying samtools/stats_isize.h -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam/include/samtools copying samtools/tmp_file.h -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam/include/samtools copying samtools/config.h -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam/include/samtools creating /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam/include/bcftools copying bcftools/HMM.h -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam/include/bcftools copying bcftools/abuf.h -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam/include/bcftools copying bcftools/bam2bcf.h -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam/include/bcftools copying bcftools/bam_sample.h -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam/include/bcftools copying bcftools/bcftools.h -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam/include/bcftools copying bcftools/bcftools.pysam.h -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam/include/bcftools copying bcftools/bin.h -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam/include/bcftools copying bcftools/call.h -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam/include/bcftools copying bcftools/cols.h -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam/include/bcftools copying bcftools/convert.h -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam/include/bcftools copying bcftools/dist.h -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam/include/bcftools copying bcftools/extsort.h -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam/include/bcftools copying bcftools/filter.h -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam/include/bcftools copying bcftools/gvcf.h -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam/include/bcftools copying bcftools/hclust.h -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam/include/bcftools copying bcftools/hex.h -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam/include/bcftools copying bcftools/khash_str2str.h -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam/include/bcftools copying bcftools/kheap.h -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam/include/bcftools copying bcftools/kmin.h -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam/include/bcftools copying bcftools/mw.h -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam/include/bcftools copying bcftools/ploidy.h -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam/include/bcftools copying bcftools/prob1.h -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam/include/bcftools copying bcftools/rbuf.h -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam/include/bcftools copying bcftools/regidx.h -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam/include/bcftools copying bcftools/smpl_ilist.h -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam/include/bcftools copying bcftools/str_finder.h -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam/include/bcftools copying bcftools/tsv2vcf.h -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam/include/bcftools copying bcftools/utlist.h -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam/include/bcftools copying bcftools/variantkey.h -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam/include/bcftools copying bcftools/vcfbuf.h -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam/include/bcftools copying bcftools/vcmp.h -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam/include/bcftools copying bcftools/config.h -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam/include/bcftools running build_ext cythoning pysam/libchtslib.pyx to pysam/libchtslib.c /usr/lib/python3/dist-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: /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam/libchtslib.pxd tree = Parsing.p_module(s, pxd, full_module_name) cythoning pysam/libcsamtools.pyx to pysam/libcsamtools.c /usr/lib/python3/dist-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: /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam/libcsamtools.pxd tree = Parsing.p_module(s, pxd, full_module_name) cythoning pysam/libcbcftools.pyx to pysam/libcbcftools.c /usr/lib/python3/dist-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: /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam/libcbcftools.pxd tree = Parsing.p_module(s, pxd, full_module_name) cythoning pysam/libcutils.pyx to pysam/libcutils.c /usr/lib/python3/dist-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: /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam/libcutils.pxd tree = Parsing.p_module(s, pxd, full_module_name) cythoning pysam/libcalignmentfile.pyx to pysam/libcalignmentfile.c /usr/lib/python3/dist-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: /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam/libcalignmentfile.pxd tree = Parsing.p_module(s, pxd, full_module_name) warning: pysam/libcalignmentfile.pyx:2564:49: Casting a GIL-requiring function into a nogil function circumvents GIL validation warning: pysam/libcalignmentfile.pyx:2569:49: Casting a GIL-requiring function into a nogil function circumvents GIL validation warning: pysam/libcalignmentfile.pyx:2574:49: Casting a GIL-requiring function into a nogil function circumvents GIL validation warning: pysam/libcalignmentfile.pyx:2613:49: Casting a GIL-requiring function into a nogil function circumvents GIL validation warning: pysam/libcalignmentfile.pyx:2618:49: Casting a GIL-requiring function into a nogil function circumvents GIL validation warning: pysam/libcalignmentfile.pyx:2623:49: Casting a GIL-requiring function into a nogil function circumvents GIL validation cythoning pysam/libcsamfile.pyx to pysam/libcsamfile.c /usr/lib/python3/dist-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: /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam/libcsamfile.pxd tree = Parsing.p_module(s, pxd, full_module_name) cythoning pysam/libcalignedsegment.pyx to pysam/libcalignedsegment.c /usr/lib/python3/dist-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: /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam/libcalignedsegment.pxd tree = Parsing.p_module(s, pxd, full_module_name) cythoning pysam/libctabix.pyx to pysam/libctabix.c /usr/lib/python3/dist-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: /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam/libctabix.pxd tree = Parsing.p_module(s, pxd, full_module_name) cythoning pysam/libcfaidx.pyx to pysam/libcfaidx.c /usr/lib/python3/dist-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: /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam/libcfaidx.pxd tree = Parsing.p_module(s, pxd, full_module_name) cythoning pysam/libcbcf.pyx to pysam/libcbcf.c /usr/lib/python3/dist-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: /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam/libcbcf.pxd tree = Parsing.p_module(s, pxd, full_module_name) cythoning pysam/libcbgzf.pyx to pysam/libcbgzf.c /usr/lib/python3/dist-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: /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam/libcbgzf.pyx tree = Parsing.p_module(s, pxd, full_module_name) cythoning pysam/libctabixproxies.pyx to pysam/libctabixproxies.c /usr/lib/python3/dist-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: /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam/libctabixproxies.pxd tree = Parsing.p_module(s, pxd, full_module_name) cythoning pysam/libcvcf.pyx to pysam/libcvcf.c /usr/lib/python3/dist-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: /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam/libcvcf.pxd tree = Parsing.p_module(s, pxd, full_module_name) warning: pysam/libcvcf.pyx:1083:27: Unreachable code building 'pysam.libchtslib' extension creating build creating build/temp.linux-x86_64-3.10 creating build/temp.linux-x86_64-3.10/pysam x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools/lz4 -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/bcftools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds -I/usr/include/python3.10 -c pysam/htslib_util.c -o build/temp.linux-x86_64-3.10/pysam/htslib_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools/lz4 -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/bcftools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds -I/usr/include/python3.10 -c pysam/libchtslib.c -o build/temp.linux-x86_64-3.10/pysam/libchtslib.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-3.10/pysam/htslib_util.o build/temp.linux-x86_64-3.10/pysam/libchtslib.o -L/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -L/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam -lz -lhts -o /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam/libchtslib.cpython-310-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN creating samtools/samtools_config_vars.h for 'pysam.libcsamtools' extension building 'pysam.libcsamtools' extension creating build/temp.linux-x86_64-3.10/samtools creating build/temp.linux-x86_64-3.10/samtools/lz4 x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools/lz4 -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/bcftools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds -I/usr/include/python3.10 -c pysam/libcsamtools.c -o build/temp.linux-x86_64-3.10/pysam/libcsamtools.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools/lz4 -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/bcftools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds -I/usr/include/python3.10 -c samtools/amplicon_stats.c.pysam.c -o build/temp.linux-x86_64-3.10/samtools/amplicon_stats.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools/lz4 -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/bcftools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds -I/usr/include/python3.10 -c samtools/bam.c.pysam.c -o build/temp.linux-x86_64-3.10/samtools/bam.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools/lz4 -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/bcftools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds -I/usr/include/python3.10 -c samtools/bam2bcf.c.pysam.c -o build/temp.linux-x86_64-3.10/samtools/bam2bcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools/lz4 -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/bcftools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds -I/usr/include/python3.10 -c samtools/bam2bcf_indel.c.pysam.c -o build/temp.linux-x86_64-3.10/samtools/bam2bcf_indel.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools/lz4 -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/bcftools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds -I/usr/include/python3.10 -c samtools/bam2depth.c.pysam.c -o build/temp.linux-x86_64-3.10/samtools/bam2depth.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools/lz4 -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/bcftools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds -I/usr/include/python3.10 -c samtools/bam_addrprg.c.pysam.c -o build/temp.linux-x86_64-3.10/samtools/bam_addrprg.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools/lz4 -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/bcftools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds -I/usr/include/python3.10 -c samtools/bam_ampliconclip.c.pysam.c -o build/temp.linux-x86_64-3.10/samtools/bam_ampliconclip.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools/lz4 -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/bcftools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds -I/usr/include/python3.10 -c samtools/bam_aux.c.pysam.c -o build/temp.linux-x86_64-3.10/samtools/bam_aux.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools/lz4 -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/bcftools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds -I/usr/include/python3.10 -c samtools/bam_cat.c.pysam.c -o build/temp.linux-x86_64-3.10/samtools/bam_cat.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools/lz4 -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/bcftools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds -I/usr/include/python3.10 -c samtools/bam_color.c.pysam.c -o build/temp.linux-x86_64-3.10/samtools/bam_color.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools/lz4 -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/bcftools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds -I/usr/include/python3.10 -c samtools/bam_fastq.c.pysam.c -o build/temp.linux-x86_64-3.10/samtools/bam_fastq.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools/lz4 -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/bcftools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds -I/usr/include/python3.10 -c samtools/bam_flags.c.pysam.c -o build/temp.linux-x86_64-3.10/samtools/bam_flags.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools/lz4 -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/bcftools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds -I/usr/include/python3.10 -c samtools/bam_import.c.pysam.c -o build/temp.linux-x86_64-3.10/samtools/bam_import.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools/lz4 -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/bcftools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds -I/usr/include/python3.10 -c samtools/bam_index.c.pysam.c -o build/temp.linux-x86_64-3.10/samtools/bam_index.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools/lz4 -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/bcftools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds -I/usr/include/python3.10 -c samtools/bam_lpileup.c.pysam.c -o build/temp.linux-x86_64-3.10/samtools/bam_lpileup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools/lz4 -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/bcftools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds -I/usr/include/python3.10 -c samtools/bam_markdup.c.pysam.c -o build/temp.linux-x86_64-3.10/samtools/bam_markdup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools/lz4 -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/bcftools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds -I/usr/include/python3.10 -c samtools/bam_mate.c.pysam.c -o build/temp.linux-x86_64-3.10/samtools/bam_mate.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools/lz4 -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/bcftools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds -I/usr/include/python3.10 -c samtools/bam_md.c.pysam.c -o build/temp.linux-x86_64-3.10/samtools/bam_md.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools/lz4 -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/bcftools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds -I/usr/include/python3.10 -c samtools/bam_plbuf.c.pysam.c -o build/temp.linux-x86_64-3.10/samtools/bam_plbuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools/lz4 -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/bcftools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds -I/usr/include/python3.10 -c samtools/bam_plcmd.c.pysam.c -o build/temp.linux-x86_64-3.10/samtools/bam_plcmd.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools/lz4 -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/bcftools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds -I/usr/include/python3.10 -c samtools/bam_quickcheck.c.pysam.c -o build/temp.linux-x86_64-3.10/samtools/bam_quickcheck.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools/lz4 -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/bcftools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds -I/usr/include/python3.10 -c samtools/bam_reheader.c.pysam.c -o build/temp.linux-x86_64-3.10/samtools/bam_reheader.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools/lz4 -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/bcftools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds -I/usr/include/python3.10 -c samtools/bam_rmdup.c.pysam.c -o build/temp.linux-x86_64-3.10/samtools/bam_rmdup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools/lz4 -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/bcftools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds -I/usr/include/python3.10 -c samtools/bam_rmdupse.c.pysam.c -o build/temp.linux-x86_64-3.10/samtools/bam_rmdupse.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools/lz4 -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/bcftools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds -I/usr/include/python3.10 -c samtools/bam_sort.c.pysam.c -o build/temp.linux-x86_64-3.10/samtools/bam_sort.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools/lz4 -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/bcftools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds -I/usr/include/python3.10 -c samtools/bam_split.c.pysam.c -o build/temp.linux-x86_64-3.10/samtools/bam_split.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools/lz4 -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/bcftools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds -I/usr/include/python3.10 -c samtools/bam_stat.c.pysam.c -o build/temp.linux-x86_64-3.10/samtools/bam_stat.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools/lz4 -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/bcftools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds -I/usr/include/python3.10 -c samtools/bamshuf.c.pysam.c -o build/temp.linux-x86_64-3.10/samtools/bamshuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools/lz4 -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/bcftools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds -I/usr/include/python3.10 -c samtools/bamtk.c.pysam.c -o build/temp.linux-x86_64-3.10/samtools/bamtk.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools/lz4 -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/bcftools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds -I/usr/include/python3.10 -c samtools/bedcov.c.pysam.c -o build/temp.linux-x86_64-3.10/samtools/bedcov.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools/lz4 -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/bcftools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds -I/usr/include/python3.10 -c samtools/bedidx.c.pysam.c -o build/temp.linux-x86_64-3.10/samtools/bedidx.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools/lz4 -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/bcftools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds -I/usr/include/python3.10 -c samtools/coverage.c.pysam.c -o build/temp.linux-x86_64-3.10/samtools/coverage.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools/lz4 -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/bcftools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds -I/usr/include/python3.10 -c samtools/cut_target.c.pysam.c -o build/temp.linux-x86_64-3.10/samtools/cut_target.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools/lz4 -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/bcftools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds -I/usr/include/python3.10 -c samtools/dict.c.pysam.c -o build/temp.linux-x86_64-3.10/samtools/dict.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools/lz4 -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/bcftools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds -I/usr/include/python3.10 -c samtools/faidx.c.pysam.c -o build/temp.linux-x86_64-3.10/samtools/faidx.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools/lz4 -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/bcftools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds -I/usr/include/python3.10 -c samtools/lz4/lz4.c -o build/temp.linux-x86_64-3.10/samtools/lz4/lz4.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools/lz4 -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/bcftools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds -I/usr/include/python3.10 -c samtools/padding.c.pysam.c -o build/temp.linux-x86_64-3.10/samtools/padding.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools/lz4 -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/bcftools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds -I/usr/include/python3.10 -c samtools/phase.c.pysam.c -o build/temp.linux-x86_64-3.10/samtools/phase.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools/lz4 -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/bcftools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds -I/usr/include/python3.10 -c samtools/sam.c.pysam.c -o build/temp.linux-x86_64-3.10/samtools/sam.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools/lz4 -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/bcftools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds -I/usr/include/python3.10 -c samtools/sam_opts.c.pysam.c -o build/temp.linux-x86_64-3.10/samtools/sam_opts.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools/lz4 -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/bcftools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds -I/usr/include/python3.10 -c samtools/sam_utils.c.pysam.c -o build/temp.linux-x86_64-3.10/samtools/sam_utils.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools/lz4 -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/bcftools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds -I/usr/include/python3.10 -c samtools/sam_view.c.pysam.c -o build/temp.linux-x86_64-3.10/samtools/sam_view.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools/lz4 -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/bcftools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds -I/usr/include/python3.10 -c samtools/sample.c.pysam.c -o build/temp.linux-x86_64-3.10/samtools/sample.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools/lz4 -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/bcftools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds -I/usr/include/python3.10 -c samtools/samtools.pysam.c -o build/temp.linux-x86_64-3.10/samtools/samtools.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools/lz4 -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/bcftools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds -I/usr/include/python3.10 -c samtools/stats.c.pysam.c -o build/temp.linux-x86_64-3.10/samtools/stats.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools/lz4 -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/bcftools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds -I/usr/include/python3.10 -c samtools/stats_isize.c.pysam.c -o build/temp.linux-x86_64-3.10/samtools/stats_isize.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools/lz4 -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/bcftools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds -I/usr/include/python3.10 -c samtools/tmp_file.c.pysam.c -o build/temp.linux-x86_64-3.10/samtools/tmp_file.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-3.10/pysam/libcsamtools.o build/temp.linux-x86_64-3.10/samtools/amplicon_stats.c.pysam.o build/temp.linux-x86_64-3.10/samtools/bam.c.pysam.o build/temp.linux-x86_64-3.10/samtools/bam2bcf.c.pysam.o build/temp.linux-x86_64-3.10/samtools/bam2bcf_indel.c.pysam.o build/temp.linux-x86_64-3.10/samtools/bam2depth.c.pysam.o build/temp.linux-x86_64-3.10/samtools/bam_addrprg.c.pysam.o build/temp.linux-x86_64-3.10/samtools/bam_ampliconclip.c.pysam.o build/temp.linux-x86_64-3.10/samtools/bam_aux.c.pysam.o build/temp.linux-x86_64-3.10/samtools/bam_cat.c.pysam.o build/temp.linux-x86_64-3.10/samtools/bam_color.c.pysam.o build/temp.linux-x86_64-3.10/samtools/bam_fastq.c.pysam.o build/temp.linux-x86_64-3.10/samtools/bam_flags.c.pysam.o build/temp.linux-x86_64-3.10/samtools/bam_import.c.pysam.o build/temp.linux-x86_64-3.10/samtools/bam_index.c.pysam.o build/temp.linux-x86_64-3.10/samtools/bam_lpileup.c.pysam.o build/temp.linux-x86_64-3.10/samtools/bam_markdup.c.pysam.o build/temp.linux-x86_64-3.10/samtools/bam_mate.c.pysam.o build/temp.linux-x86_64-3.10/samtools/bam_md.c.pysam.o build/temp.linux-x86_64-3.10/samtools/bam_plbuf.c.pysam.o build/temp.linux-x86_64-3.10/samtools/bam_plcmd.c.pysam.o build/temp.linux-x86_64-3.10/samtools/bam_quickcheck.c.pysam.o build/temp.linux-x86_64-3.10/samtools/bam_reheader.c.pysam.o build/temp.linux-x86_64-3.10/samtools/bam_rmdup.c.pysam.o build/temp.linux-x86_64-3.10/samtools/bam_rmdupse.c.pysam.o build/temp.linux-x86_64-3.10/samtools/bam_sort.c.pysam.o build/temp.linux-x86_64-3.10/samtools/bam_split.c.pysam.o build/temp.linux-x86_64-3.10/samtools/bam_stat.c.pysam.o build/temp.linux-x86_64-3.10/samtools/bamshuf.c.pysam.o build/temp.linux-x86_64-3.10/samtools/bamtk.c.pysam.o build/temp.linux-x86_64-3.10/samtools/bedcov.c.pysam.o build/temp.linux-x86_64-3.10/samtools/bedidx.c.pysam.o build/temp.linux-x86_64-3.10/samtools/coverage.c.pysam.o build/temp.linux-x86_64-3.10/samtools/cut_target.c.pysam.o build/temp.linux-x86_64-3.10/samtools/dict.c.pysam.o build/temp.linux-x86_64-3.10/samtools/faidx.c.pysam.o build/temp.linux-x86_64-3.10/samtools/lz4/lz4.o build/temp.linux-x86_64-3.10/samtools/padding.c.pysam.o build/temp.linux-x86_64-3.10/samtools/phase.c.pysam.o build/temp.linux-x86_64-3.10/samtools/sam.c.pysam.o build/temp.linux-x86_64-3.10/samtools/sam_opts.c.pysam.o build/temp.linux-x86_64-3.10/samtools/sam_utils.c.pysam.o build/temp.linux-x86_64-3.10/samtools/sam_view.c.pysam.o build/temp.linux-x86_64-3.10/samtools/sample.c.pysam.o build/temp.linux-x86_64-3.10/samtools/samtools.pysam.o build/temp.linux-x86_64-3.10/samtools/stats.c.pysam.o build/temp.linux-x86_64-3.10/samtools/stats_isize.c.pysam.o build/temp.linux-x86_64-3.10/samtools/tmp_file.c.pysam.o -L/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -L/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam -L/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam -lz -lhts -lchtslib.cpython-310-x86_64-linux-gnu -o /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam/libcsamtools.cpython-310-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN building 'pysam.libcbcftools' extension creating build/temp.linux-x86_64-3.10/bcftools x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools/lz4 -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/bcftools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds -I/usr/include/python3.10 -c bcftools/HMM.c.pysam.c -o build/temp.linux-x86_64-3.10/bcftools/HMM.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools/lz4 -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/bcftools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds -I/usr/include/python3.10 -c bcftools/abuf.c.pysam.c -o build/temp.linux-x86_64-3.10/bcftools/abuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools/lz4 -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/bcftools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds -I/usr/include/python3.10 -c bcftools/bam2bcf.c.pysam.c -o build/temp.linux-x86_64-3.10/bcftools/bam2bcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools/lz4 -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/bcftools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds -I/usr/include/python3.10 -c bcftools/bam2bcf_indel.c.pysam.c -o build/temp.linux-x86_64-3.10/bcftools/bam2bcf_indel.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools/lz4 -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/bcftools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds -I/usr/include/python3.10 -c bcftools/bam_sample.c.pysam.c -o build/temp.linux-x86_64-3.10/bcftools/bam_sample.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools/lz4 -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/bcftools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds -I/usr/include/python3.10 -c bcftools/bcftools.pysam.c -o build/temp.linux-x86_64-3.10/bcftools/bcftools.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools/lz4 -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/bcftools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds -I/usr/include/python3.10 -c bcftools/bin.c.pysam.c -o build/temp.linux-x86_64-3.10/bcftools/bin.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools/lz4 -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/bcftools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds -I/usr/include/python3.10 -c bcftools/ccall.c.pysam.c -o build/temp.linux-x86_64-3.10/bcftools/ccall.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools/lz4 -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/bcftools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds -I/usr/include/python3.10 -c bcftools/cols.c.pysam.c -o build/temp.linux-x86_64-3.10/bcftools/cols.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools/lz4 -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/bcftools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds -I/usr/include/python3.10 -c bcftools/consensus.c.pysam.c -o build/temp.linux-x86_64-3.10/bcftools/consensus.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools/lz4 -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/bcftools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds -I/usr/include/python3.10 -c bcftools/convert.c.pysam.c -o build/temp.linux-x86_64-3.10/bcftools/convert.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools/lz4 -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/bcftools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds -I/usr/include/python3.10 -c bcftools/csq.c.pysam.c -o build/temp.linux-x86_64-3.10/bcftools/csq.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools/lz4 -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/bcftools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds -I/usr/include/python3.10 -c bcftools/dist.c.pysam.c -o build/temp.linux-x86_64-3.10/bcftools/dist.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools/lz4 -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/bcftools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds -I/usr/include/python3.10 -c bcftools/em.c.pysam.c -o build/temp.linux-x86_64-3.10/bcftools/em.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools/lz4 -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/bcftools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds -I/usr/include/python3.10 -c bcftools/extsort.c.pysam.c -o build/temp.linux-x86_64-3.10/bcftools/extsort.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools/lz4 -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/bcftools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds -I/usr/include/python3.10 -c bcftools/filter.c.pysam.c -o build/temp.linux-x86_64-3.10/bcftools/filter.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools/lz4 -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/bcftools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds -I/usr/include/python3.10 -c bcftools/gvcf.c.pysam.c -o build/temp.linux-x86_64-3.10/bcftools/gvcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools/lz4 -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/bcftools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds -I/usr/include/python3.10 -c bcftools/hclust.c.pysam.c -o build/temp.linux-x86_64-3.10/bcftools/hclust.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools/lz4 -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/bcftools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds -I/usr/include/python3.10 -c bcftools/kmin.c.pysam.c -o build/temp.linux-x86_64-3.10/bcftools/kmin.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools/lz4 -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/bcftools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds -I/usr/include/python3.10 -c bcftools/main.c.pysam.c -o build/temp.linux-x86_64-3.10/bcftools/main.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools/lz4 -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/bcftools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds -I/usr/include/python3.10 -c bcftools/mcall.c.pysam.c -o build/temp.linux-x86_64-3.10/bcftools/mcall.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools/lz4 -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/bcftools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds -I/usr/include/python3.10 -c bcftools/mpileup.c.pysam.c -o build/temp.linux-x86_64-3.10/bcftools/mpileup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools/lz4 -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/bcftools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds -I/usr/include/python3.10 -c bcftools/ploidy.c.pysam.c -o build/temp.linux-x86_64-3.10/bcftools/ploidy.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools/lz4 -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/bcftools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds -I/usr/include/python3.10 -c bcftools/prob1.c.pysam.c -o build/temp.linux-x86_64-3.10/bcftools/prob1.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools/lz4 -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/bcftools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds -I/usr/include/python3.10 -c bcftools/regidx.c.pysam.c -o build/temp.linux-x86_64-3.10/bcftools/regidx.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools/lz4 -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/bcftools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds -I/usr/include/python3.10 -c bcftools/reheader.c.pysam.c -o build/temp.linux-x86_64-3.10/bcftools/reheader.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools/lz4 -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/bcftools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds -I/usr/include/python3.10 -c bcftools/smpl_ilist.c.pysam.c -o build/temp.linux-x86_64-3.10/bcftools/smpl_ilist.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools/lz4 -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/bcftools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds -I/usr/include/python3.10 -c bcftools/str_finder.c.pysam.c -o build/temp.linux-x86_64-3.10/bcftools/str_finder.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools/lz4 -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/bcftools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds -I/usr/include/python3.10 -c bcftools/tabix.c.pysam.c -o build/temp.linux-x86_64-3.10/bcftools/tabix.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools/lz4 -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/bcftools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds -I/usr/include/python3.10 -c bcftools/tsv2vcf.c.pysam.c -o build/temp.linux-x86_64-3.10/bcftools/tsv2vcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools/lz4 -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/bcftools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds -I/usr/include/python3.10 -c bcftools/vcfannotate.c.pysam.c -o build/temp.linux-x86_64-3.10/bcftools/vcfannotate.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools/lz4 -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/bcftools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds -I/usr/include/python3.10 -c bcftools/vcfbuf.c.pysam.c -o build/temp.linux-x86_64-3.10/bcftools/vcfbuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools/lz4 -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/bcftools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds -I/usr/include/python3.10 -c bcftools/vcfcall.c.pysam.c -o build/temp.linux-x86_64-3.10/bcftools/vcfcall.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools/lz4 -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/bcftools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds -I/usr/include/python3.10 -c bcftools/vcfcnv.c.pysam.c -o build/temp.linux-x86_64-3.10/bcftools/vcfcnv.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools/lz4 -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/bcftools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds -I/usr/include/python3.10 -c bcftools/vcfconcat.c.pysam.c -o build/temp.linux-x86_64-3.10/bcftools/vcfconcat.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools/lz4 -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/bcftools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds -I/usr/include/python3.10 -c bcftools/vcfconvert.c.pysam.c -o build/temp.linux-x86_64-3.10/bcftools/vcfconvert.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools/lz4 -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/bcftools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds -I/usr/include/python3.10 -c bcftools/vcffilter.c.pysam.c -o build/temp.linux-x86_64-3.10/bcftools/vcffilter.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools/lz4 -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/bcftools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds -I/usr/include/python3.10 -c bcftools/vcfgtcheck.c.pysam.c -o build/temp.linux-x86_64-3.10/bcftools/vcfgtcheck.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools/lz4 -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/bcftools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds -I/usr/include/python3.10 -c bcftools/vcfindex.c.pysam.c -o build/temp.linux-x86_64-3.10/bcftools/vcfindex.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools/lz4 -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/bcftools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds -I/usr/include/python3.10 -c bcftools/vcfisec.c.pysam.c -o build/temp.linux-x86_64-3.10/bcftools/vcfisec.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools/lz4 -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/bcftools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds -I/usr/include/python3.10 -c bcftools/vcfmerge.c.pysam.c -o build/temp.linux-x86_64-3.10/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:733:34: warning: argument 1 range [18446744071562067968, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 733 | 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 /usr/include/htslib/kstring.h:30, from /usr/include/htslib/hts.h:37, from /usr/include/htslib/vcf.h:39, from bcftools/vcfmerge.c.pysam.c:35: /usr/include/stdlib.h:542:14: note: in a call to allocation function ‘calloc’ declared here 542 | extern void *calloc (size_t __nmemb, size_t __size) | ^~~~~~ x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools/lz4 -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/bcftools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds -I/usr/include/python3.10 -c bcftools/vcfnorm.c.pysam.c -o build/temp.linux-x86_64-3.10/bcftools/vcfnorm.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools/lz4 -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/bcftools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds -I/usr/include/python3.10 -c bcftools/vcfplugin.c.pysam.c -o build/temp.linux-x86_64-3.10/bcftools/vcfplugin.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools/lz4 -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/bcftools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds -I/usr/include/python3.10 -c bcftools/vcfquery.c.pysam.c -o build/temp.linux-x86_64-3.10/bcftools/vcfquery.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools/lz4 -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/bcftools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds -I/usr/include/python3.10 -c bcftools/vcfroh.c.pysam.c -o build/temp.linux-x86_64-3.10/bcftools/vcfroh.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools/lz4 -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/bcftools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds -I/usr/include/python3.10 -c bcftools/vcfsom.c.pysam.c -o build/temp.linux-x86_64-3.10/bcftools/vcfsom.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools/lz4 -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/bcftools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds -I/usr/include/python3.10 -c bcftools/vcfsort.c.pysam.c -o build/temp.linux-x86_64-3.10/bcftools/vcfsort.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools/lz4 -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/bcftools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds -I/usr/include/python3.10 -c bcftools/vcfstats.c.pysam.c -o build/temp.linux-x86_64-3.10/bcftools/vcfstats.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools/lz4 -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/bcftools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds -I/usr/include/python3.10 -c bcftools/vcfview.c.pysam.c -o build/temp.linux-x86_64-3.10/bcftools/vcfview.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools/lz4 -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/bcftools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds -I/usr/include/python3.10 -c bcftools/vcmp.c.pysam.c -o build/temp.linux-x86_64-3.10/bcftools/vcmp.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools/lz4 -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/bcftools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds -I/usr/include/python3.10 -c bcftools/version.c.pysam.c -o build/temp.linux-x86_64-3.10/bcftools/version.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools/lz4 -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/bcftools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds -I/usr/include/python3.10 -c pysam/libcbcftools.c -o build/temp.linux-x86_64-3.10/pysam/libcbcftools.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-3.10/bcftools/HMM.c.pysam.o build/temp.linux-x86_64-3.10/bcftools/abuf.c.pysam.o build/temp.linux-x86_64-3.10/bcftools/bam2bcf.c.pysam.o build/temp.linux-x86_64-3.10/bcftools/bam2bcf_indel.c.pysam.o build/temp.linux-x86_64-3.10/bcftools/bam_sample.c.pysam.o build/temp.linux-x86_64-3.10/bcftools/bcftools.pysam.o build/temp.linux-x86_64-3.10/bcftools/bin.c.pysam.o build/temp.linux-x86_64-3.10/bcftools/ccall.c.pysam.o build/temp.linux-x86_64-3.10/bcftools/cols.c.pysam.o build/temp.linux-x86_64-3.10/bcftools/consensus.c.pysam.o build/temp.linux-x86_64-3.10/bcftools/convert.c.pysam.o build/temp.linux-x86_64-3.10/bcftools/csq.c.pysam.o build/temp.linux-x86_64-3.10/bcftools/dist.c.pysam.o build/temp.linux-x86_64-3.10/bcftools/em.c.pysam.o build/temp.linux-x86_64-3.10/bcftools/extsort.c.pysam.o build/temp.linux-x86_64-3.10/bcftools/filter.c.pysam.o build/temp.linux-x86_64-3.10/bcftools/gvcf.c.pysam.o build/temp.linux-x86_64-3.10/bcftools/hclust.c.pysam.o build/temp.linux-x86_64-3.10/bcftools/kmin.c.pysam.o build/temp.linux-x86_64-3.10/bcftools/main.c.pysam.o build/temp.linux-x86_64-3.10/bcftools/mcall.c.pysam.o build/temp.linux-x86_64-3.10/bcftools/mpileup.c.pysam.o build/temp.linux-x86_64-3.10/bcftools/ploidy.c.pysam.o build/temp.linux-x86_64-3.10/bcftools/prob1.c.pysam.o build/temp.linux-x86_64-3.10/bcftools/regidx.c.pysam.o build/temp.linux-x86_64-3.10/bcftools/reheader.c.pysam.o build/temp.linux-x86_64-3.10/bcftools/smpl_ilist.c.pysam.o build/temp.linux-x86_64-3.10/bcftools/str_finder.c.pysam.o build/temp.linux-x86_64-3.10/bcftools/tabix.c.pysam.o build/temp.linux-x86_64-3.10/bcftools/tsv2vcf.c.pysam.o build/temp.linux-x86_64-3.10/bcftools/vcfannotate.c.pysam.o build/temp.linux-x86_64-3.10/bcftools/vcfbuf.c.pysam.o build/temp.linux-x86_64-3.10/bcftools/vcfcall.c.pysam.o build/temp.linux-x86_64-3.10/bcftools/vcfcnv.c.pysam.o build/temp.linux-x86_64-3.10/bcftools/vcfconcat.c.pysam.o build/temp.linux-x86_64-3.10/bcftools/vcfconvert.c.pysam.o build/temp.linux-x86_64-3.10/bcftools/vcffilter.c.pysam.o build/temp.linux-x86_64-3.10/bcftools/vcfgtcheck.c.pysam.o build/temp.linux-x86_64-3.10/bcftools/vcfindex.c.pysam.o build/temp.linux-x86_64-3.10/bcftools/vcfisec.c.pysam.o build/temp.linux-x86_64-3.10/bcftools/vcfmerge.c.pysam.o build/temp.linux-x86_64-3.10/bcftools/vcfnorm.c.pysam.o build/temp.linux-x86_64-3.10/bcftools/vcfplugin.c.pysam.o build/temp.linux-x86_64-3.10/bcftools/vcfquery.c.pysam.o build/temp.linux-x86_64-3.10/bcftools/vcfroh.c.pysam.o build/temp.linux-x86_64-3.10/bcftools/vcfsom.c.pysam.o build/temp.linux-x86_64-3.10/bcftools/vcfsort.c.pysam.o build/temp.linux-x86_64-3.10/bcftools/vcfstats.c.pysam.o build/temp.linux-x86_64-3.10/bcftools/vcfview.c.pysam.o build/temp.linux-x86_64-3.10/bcftools/vcmp.c.pysam.o build/temp.linux-x86_64-3.10/bcftools/version.c.pysam.o build/temp.linux-x86_64-3.10/pysam/libcbcftools.o -L/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -L/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam -L/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam -L/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam -lz -lhts -lchtslib.cpython-310-x86_64-linux-gnu -o /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam/libcbcftools.cpython-310-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN building 'pysam.libcutils' extension x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools/lz4 -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/bcftools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds -I/usr/include/python3.10 -c pysam/libcutils.c -o build/temp.linux-x86_64-3.10/pysam/libcutils.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement pysam/libcutils.c: In function ‘__pyx_pw_5pysam_9libcutils_15_pysam_dispatch’: pysam/libcutils.c:534:40: warning: ‘__pyx_v_retval’ may be used uninitialized in this function [-Wmaybe-uninitialized] 534 | #define PyInt_FromLong PyLong_FromLong | ^~~~~~~~~~~~~~~ pysam/libcutils.c:6778:7: note: ‘__pyx_v_retval’ was declared here 6778 | int __pyx_v_retval; | ^~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools/lz4 -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/bcftools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds -I/usr/include/python3.10 -c pysam/pysam_util.c -o build/temp.linux-x86_64-3.10/pysam/pysam_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-3.10/pysam/libcutils.o build/temp.linux-x86_64-3.10/pysam/pysam_util.o -L/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -L/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam -L/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam -L/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam -L/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam -lz -lhts -lchtslib.cpython-310-x86_64-linux-gnu -lcsamtools.cpython-310-x86_64-linux-gnu -lcbcftools.cpython-310-x86_64-linux-gnu -o /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam/libcutils.cpython-310-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN building 'pysam.libcalignmentfile' extension x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools/lz4 -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/bcftools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds -I/usr/include/python3.10 -c pysam/libcalignmentfile.c -o build/temp.linux-x86_64-3.10/pysam/libcalignmentfile.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-3.10/pysam/libcalignmentfile.o -L/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -L/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam -L/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam -L/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam -L/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam -L/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam -lz -lhts -lchtslib.cpython-310-x86_64-linux-gnu -lcutils.cpython-310-x86_64-linux-gnu -o /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam/libcalignmentfile.cpython-310-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN building 'pysam.libcsamfile' extension x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools/lz4 -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/bcftools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds -I/usr/include/python3.10 -c pysam/libcsamfile.c -o build/temp.linux-x86_64-3.10/pysam/libcsamfile.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-3.10/pysam/libcsamfile.o -L/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -L/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam -L/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam -L/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam -L/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam -L/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam -L/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam -lz -lhts -lchtslib.cpython-310-x86_64-linux-gnu -lcutils.cpython-310-x86_64-linux-gnu -o /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam/libcsamfile.cpython-310-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN building 'pysam.libcalignedsegment' extension x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools/lz4 -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/bcftools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds -I/usr/include/python3.10 -c pysam/libcalignedsegment.c -o build/temp.linux-x86_64-3.10/pysam/libcalignedsegment.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-3.10/pysam/libcalignedsegment.o -L/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -L/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam -L/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam -L/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam -L/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam -L/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam -L/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam -L/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam -lz -lhts -lchtslib.cpython-310-x86_64-linux-gnu -lcutils.cpython-310-x86_64-linux-gnu -o /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam/libcalignedsegment.cpython-310-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN building 'pysam.libctabix' extension x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools/lz4 -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/bcftools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds -I/usr/include/python3.10 -c pysam/libctabix.c -o build/temp.linux-x86_64-3.10/pysam/libctabix.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-3.10/pysam/libctabix.o -L/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -L/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam -L/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam -L/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam -L/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam -L/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam -L/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam -L/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam -L/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam -lz -lhts -lchtslib.cpython-310-x86_64-linux-gnu -lcutils.cpython-310-x86_64-linux-gnu -o /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam/libctabix.cpython-310-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN building 'pysam.libcfaidx' extension x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools/lz4 -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/bcftools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds -I/usr/include/python3.10 -c pysam/libcfaidx.c -o build/temp.linux-x86_64-3.10/pysam/libcfaidx.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-3.10/pysam/libcfaidx.o -L/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -L/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam -L/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam -L/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam -L/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam -L/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam -L/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam -L/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam -L/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam -L/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam -lz -lhts -lchtslib.cpython-310-x86_64-linux-gnu -lcutils.cpython-310-x86_64-linux-gnu -o /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam/libcfaidx.cpython-310-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN building 'pysam.libcbcf' extension x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools/lz4 -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/bcftools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds -I/usr/include/python3.10 -c pysam/libcbcf.c -o build/temp.linux-x86_64-3.10/pysam/libcbcf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-3.10/pysam/libcbcf.o -L/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -L/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam -L/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam -L/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam -L/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam -L/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam -L/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam -L/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam -L/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam -L/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam -L/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam -lz -lhts -lchtslib.cpython-310-x86_64-linux-gnu -lcutils.cpython-310-x86_64-linux-gnu -o /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam/libcbcf.cpython-310-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN building 'pysam.libcbgzf' extension x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools/lz4 -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/bcftools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds -I/usr/include/python3.10 -c pysam/libcbgzf.c -o build/temp.linux-x86_64-3.10/pysam/libcbgzf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-3.10/pysam/libcbgzf.o -L/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -L/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam -L/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam -L/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam -L/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam -L/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam -L/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam -L/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam -L/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam -L/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam -L/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam -L/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam -lz -lhts -lchtslib.cpython-310-x86_64-linux-gnu -lcutils.cpython-310-x86_64-linux-gnu -o /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam/libcbgzf.cpython-310-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN building 'pysam.libctabixproxies' extension x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools/lz4 -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/bcftools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds -I/usr/include/python3.10 -c pysam/libctabixproxies.c -o build/temp.linux-x86_64-3.10/pysam/libctabixproxies.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-3.10/pysam/libctabixproxies.o -L/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -L/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam -L/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam -L/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam -L/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam -L/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam -L/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam -L/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam -L/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam -L/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam -L/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam -L/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam -L/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam -lz -lhts -lchtslib.cpython-310-x86_64-linux-gnu -lcutils.cpython-310-x86_64-linux-gnu -o /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam/libctabixproxies.cpython-310-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN building 'pysam.libcvcf' extension x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools/lz4 -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/bcftools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds -I/usr/include/python3.10 -c pysam/libcvcf.c -o build/temp.linux-x86_64-3.10/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’: pysam/libcvcf.c:25076:16: warning: ‘__pyx_v_qual’ may be used uninitialized in this function [-Wmaybe-uninitialized] 25076 | __pyx_t_12 = PyFloat_FromDouble(__pyx_v_qual); if (unlikely(!__pyx_t_12)) __PYX_ERR(0, 873, __pyx_L1_error) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-3.10/pysam/libcvcf.o -L/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -L/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam -L/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam -L/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam -L/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam -L/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam -L/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam -L/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam -L/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam -L/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam -L/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam -L/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam -L/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam -L/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam -lz -lhts -lchtslib.cpython-310-x86_64-linux-gnu -lcutils.cpython-310-x86_64-linux-gnu -o /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam/libcvcf.cpython-310-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN I: pybuild base:237: /usr/bin/python3 setup.py build # pysam: cython is available - using cythonize if necessary # pysam: htslib mode is external # pysam: HTSLIB_CONFIGURE_OPTIONS=None running build running build_py creating /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam copying pysam/Pileup.py -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam copying pysam/__init__.py -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam copying pysam/bcftools.py -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam copying pysam/samtools.py -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam copying pysam/utils.py -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam copying pysam/version.py -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam copying pysam/config.py -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam creating /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include copying pysam/include/__init__.py -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/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) copying pysam/libcalignedsegment.pxd -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam copying pysam/libcalignmentfile.pxd -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam copying pysam/libcbcf.pxd -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam copying pysam/libcbcftools.pxd -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam copying pysam/libcfaidx.pxd -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam copying pysam/libchtslib.pxd -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam copying pysam/libcsamfile.pxd -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam copying pysam/libcsamtools.pxd -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam copying pysam/libctabix.pxd -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam copying pysam/libctabixproxies.pxd -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam copying pysam/libcutils.pxd -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam copying pysam/libcvcf.pxd -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam copying pysam/cbcftools_util.h -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam copying pysam/csamtools_util.h -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam copying pysam/htslib_util.h -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam copying pysam/pysam_stream.h -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam copying pysam/pysam_util.h -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam copying pysam/version.h -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam creating /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/samtools copying samtools/bam.h -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/samtools copying samtools/bam2bcf.h -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/samtools copying samtools/bam_ampliconclip.h -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/samtools copying samtools/bam_endian.h -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/samtools copying samtools/bam_lpileup.h -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/samtools copying samtools/bam_plbuf.h -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/samtools copying samtools/bedidx.h -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/samtools copying samtools/sam.h -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/samtools copying samtools/sam_opts.h -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/samtools copying samtools/sample.h -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/samtools copying samtools/samtools.h -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/samtools copying samtools/samtools.pysam.h -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/samtools copying samtools/stats_isize.h -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/samtools copying samtools/tmp_file.h -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/samtools copying samtools/config.h -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/samtools copying samtools/samtools_config_vars.h -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/samtools creating /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools copying bcftools/HMM.h -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools copying bcftools/abuf.h -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools copying bcftools/bam2bcf.h -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools copying bcftools/bam_sample.h -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools copying bcftools/bcftools.h -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools copying bcftools/bcftools.pysam.h -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools copying bcftools/bin.h -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools copying bcftools/call.h -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools copying bcftools/cols.h -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools copying bcftools/convert.h -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools copying bcftools/dist.h -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools copying bcftools/extsort.h -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools copying bcftools/filter.h -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools copying bcftools/gvcf.h -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools copying bcftools/hclust.h -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools copying bcftools/hex.h -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools copying bcftools/khash_str2str.h -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools copying bcftools/kheap.h -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools copying bcftools/kmin.h -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools copying bcftools/mw.h -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools copying bcftools/ploidy.h -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools copying bcftools/prob1.h -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools copying bcftools/rbuf.h -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools copying bcftools/regidx.h -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools copying bcftools/smpl_ilist.h -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools copying bcftools/str_finder.h -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools copying bcftools/tsv2vcf.h -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools copying bcftools/utlist.h -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools copying bcftools/variantkey.h -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools copying bcftools/vcfbuf.h -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools copying bcftools/vcmp.h -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools copying bcftools/config.h -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools running build_ext skipping 'pysam/libchtslib.c' Cython extension (up-to-date) skipping 'pysam/libcsamtools.c' Cython extension (up-to-date) skipping 'pysam/libcbcftools.c' Cython extension (up-to-date) skipping 'pysam/libcutils.c' Cython extension (up-to-date) skipping 'pysam/libcalignmentfile.c' Cython extension (up-to-date) skipping 'pysam/libcsamfile.c' Cython extension (up-to-date) skipping 'pysam/libcalignedsegment.c' Cython extension (up-to-date) skipping 'pysam/libctabix.c' Cython extension (up-to-date) skipping 'pysam/libcfaidx.c' Cython extension (up-to-date) skipping 'pysam/libcbcf.c' Cython extension (up-to-date) skipping 'pysam/libcbgzf.c' Cython extension (up-to-date) skipping 'pysam/libctabixproxies.c' Cython extension (up-to-date) skipping 'pysam/libcvcf.c' Cython extension (up-to-date) building 'pysam.libchtslib' extension creating build/temp.linux-x86_64-3.9 creating build/temp.linux-x86_64-3.9/pysam x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools/lz4 -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/bcftools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds -I/usr/include/python3.9 -c pysam/htslib_util.c -o build/temp.linux-x86_64-3.9/pysam/htslib_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools/lz4 -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/bcftools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds -I/usr/include/python3.9 -c pysam/libchtslib.c -o build/temp.linux-x86_64-3.9/pysam/libchtslib.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-3.9/pysam/htslib_util.o build/temp.linux-x86_64-3.9/pysam/libchtslib.o -L/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -L/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam -lz -lhts -o /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/libchtslib.cpython-39-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN creating samtools/samtools_config_vars.h for 'pysam.libcsamtools' extension building 'pysam.libcsamtools' extension creating build/temp.linux-x86_64-3.9/samtools creating build/temp.linux-x86_64-3.9/samtools/lz4 x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools/lz4 -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/bcftools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds -I/usr/include/python3.9 -c pysam/libcsamtools.c -o build/temp.linux-x86_64-3.9/pysam/libcsamtools.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools/lz4 -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/bcftools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds -I/usr/include/python3.9 -c samtools/amplicon_stats.c.pysam.c -o build/temp.linux-x86_64-3.9/samtools/amplicon_stats.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools/lz4 -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/bcftools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds -I/usr/include/python3.9 -c samtools/bam.c.pysam.c -o build/temp.linux-x86_64-3.9/samtools/bam.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools/lz4 -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/bcftools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds -I/usr/include/python3.9 -c samtools/bam2bcf.c.pysam.c -o build/temp.linux-x86_64-3.9/samtools/bam2bcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools/lz4 -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/bcftools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds -I/usr/include/python3.9 -c samtools/bam2bcf_indel.c.pysam.c -o build/temp.linux-x86_64-3.9/samtools/bam2bcf_indel.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools/lz4 -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/bcftools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds -I/usr/include/python3.9 -c samtools/bam2depth.c.pysam.c -o build/temp.linux-x86_64-3.9/samtools/bam2depth.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools/lz4 -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/bcftools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds -I/usr/include/python3.9 -c samtools/bam_addrprg.c.pysam.c -o build/temp.linux-x86_64-3.9/samtools/bam_addrprg.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools/lz4 -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/bcftools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds -I/usr/include/python3.9 -c samtools/bam_ampliconclip.c.pysam.c -o build/temp.linux-x86_64-3.9/samtools/bam_ampliconclip.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools/lz4 -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/bcftools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds -I/usr/include/python3.9 -c samtools/bam_aux.c.pysam.c -o build/temp.linux-x86_64-3.9/samtools/bam_aux.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools/lz4 -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/bcftools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds -I/usr/include/python3.9 -c samtools/bam_cat.c.pysam.c -o build/temp.linux-x86_64-3.9/samtools/bam_cat.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools/lz4 -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/bcftools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds -I/usr/include/python3.9 -c samtools/bam_color.c.pysam.c -o build/temp.linux-x86_64-3.9/samtools/bam_color.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools/lz4 -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/bcftools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds -I/usr/include/python3.9 -c samtools/bam_fastq.c.pysam.c -o build/temp.linux-x86_64-3.9/samtools/bam_fastq.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools/lz4 -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/bcftools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds -I/usr/include/python3.9 -c samtools/bam_flags.c.pysam.c -o build/temp.linux-x86_64-3.9/samtools/bam_flags.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools/lz4 -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/bcftools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds -I/usr/include/python3.9 -c samtools/bam_import.c.pysam.c -o build/temp.linux-x86_64-3.9/samtools/bam_import.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools/lz4 -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/bcftools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds -I/usr/include/python3.9 -c samtools/bam_index.c.pysam.c -o build/temp.linux-x86_64-3.9/samtools/bam_index.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools/lz4 -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/bcftools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds -I/usr/include/python3.9 -c samtools/bam_lpileup.c.pysam.c -o build/temp.linux-x86_64-3.9/samtools/bam_lpileup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools/lz4 -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/bcftools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds -I/usr/include/python3.9 -c samtools/bam_markdup.c.pysam.c -o build/temp.linux-x86_64-3.9/samtools/bam_markdup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools/lz4 -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/bcftools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds -I/usr/include/python3.9 -c samtools/bam_mate.c.pysam.c -o build/temp.linux-x86_64-3.9/samtools/bam_mate.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools/lz4 -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/bcftools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds -I/usr/include/python3.9 -c samtools/bam_md.c.pysam.c -o build/temp.linux-x86_64-3.9/samtools/bam_md.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools/lz4 -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/bcftools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds -I/usr/include/python3.9 -c samtools/bam_plbuf.c.pysam.c -o build/temp.linux-x86_64-3.9/samtools/bam_plbuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools/lz4 -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/bcftools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds -I/usr/include/python3.9 -c samtools/bam_plcmd.c.pysam.c -o build/temp.linux-x86_64-3.9/samtools/bam_plcmd.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools/lz4 -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/bcftools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds -I/usr/include/python3.9 -c samtools/bam_quickcheck.c.pysam.c -o build/temp.linux-x86_64-3.9/samtools/bam_quickcheck.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools/lz4 -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/bcftools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds -I/usr/include/python3.9 -c samtools/bam_reheader.c.pysam.c -o build/temp.linux-x86_64-3.9/samtools/bam_reheader.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools/lz4 -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/bcftools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds -I/usr/include/python3.9 -c samtools/bam_rmdup.c.pysam.c -o build/temp.linux-x86_64-3.9/samtools/bam_rmdup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools/lz4 -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/bcftools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds -I/usr/include/python3.9 -c samtools/bam_rmdupse.c.pysam.c -o build/temp.linux-x86_64-3.9/samtools/bam_rmdupse.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools/lz4 -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/bcftools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds -I/usr/include/python3.9 -c samtools/bam_sort.c.pysam.c -o build/temp.linux-x86_64-3.9/samtools/bam_sort.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools/lz4 -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/bcftools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds -I/usr/include/python3.9 -c samtools/bam_split.c.pysam.c -o build/temp.linux-x86_64-3.9/samtools/bam_split.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools/lz4 -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/bcftools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds -I/usr/include/python3.9 -c samtools/bam_stat.c.pysam.c -o build/temp.linux-x86_64-3.9/samtools/bam_stat.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools/lz4 -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/bcftools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds -I/usr/include/python3.9 -c samtools/bamshuf.c.pysam.c -o build/temp.linux-x86_64-3.9/samtools/bamshuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools/lz4 -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/bcftools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds -I/usr/include/python3.9 -c samtools/bamtk.c.pysam.c -o build/temp.linux-x86_64-3.9/samtools/bamtk.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools/lz4 -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/bcftools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds -I/usr/include/python3.9 -c samtools/bedcov.c.pysam.c -o build/temp.linux-x86_64-3.9/samtools/bedcov.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools/lz4 -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/bcftools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds -I/usr/include/python3.9 -c samtools/bedidx.c.pysam.c -o build/temp.linux-x86_64-3.9/samtools/bedidx.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools/lz4 -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/bcftools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds -I/usr/include/python3.9 -c samtools/coverage.c.pysam.c -o build/temp.linux-x86_64-3.9/samtools/coverage.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools/lz4 -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/bcftools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds -I/usr/include/python3.9 -c samtools/cut_target.c.pysam.c -o build/temp.linux-x86_64-3.9/samtools/cut_target.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools/lz4 -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/bcftools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds -I/usr/include/python3.9 -c samtools/dict.c.pysam.c -o build/temp.linux-x86_64-3.9/samtools/dict.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools/lz4 -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/bcftools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds -I/usr/include/python3.9 -c samtools/faidx.c.pysam.c -o build/temp.linux-x86_64-3.9/samtools/faidx.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools/lz4 -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/bcftools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds -I/usr/include/python3.9 -c samtools/lz4/lz4.c -o build/temp.linux-x86_64-3.9/samtools/lz4/lz4.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools/lz4 -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/bcftools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds -I/usr/include/python3.9 -c samtools/padding.c.pysam.c -o build/temp.linux-x86_64-3.9/samtools/padding.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools/lz4 -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/bcftools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds -I/usr/include/python3.9 -c samtools/phase.c.pysam.c -o build/temp.linux-x86_64-3.9/samtools/phase.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools/lz4 -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/bcftools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds -I/usr/include/python3.9 -c samtools/sam.c.pysam.c -o build/temp.linux-x86_64-3.9/samtools/sam.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools/lz4 -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/bcftools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds -I/usr/include/python3.9 -c samtools/sam_opts.c.pysam.c -o build/temp.linux-x86_64-3.9/samtools/sam_opts.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools/lz4 -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/bcftools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds -I/usr/include/python3.9 -c samtools/sam_utils.c.pysam.c -o build/temp.linux-x86_64-3.9/samtools/sam_utils.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools/lz4 -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/bcftools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds -I/usr/include/python3.9 -c samtools/sam_view.c.pysam.c -o build/temp.linux-x86_64-3.9/samtools/sam_view.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools/lz4 -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/bcftools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds -I/usr/include/python3.9 -c samtools/sample.c.pysam.c -o build/temp.linux-x86_64-3.9/samtools/sample.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools/lz4 -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/bcftools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds -I/usr/include/python3.9 -c samtools/samtools.pysam.c -o build/temp.linux-x86_64-3.9/samtools/samtools.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools/lz4 -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/bcftools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds -I/usr/include/python3.9 -c samtools/stats.c.pysam.c -o build/temp.linux-x86_64-3.9/samtools/stats.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools/lz4 -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/bcftools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds -I/usr/include/python3.9 -c samtools/stats_isize.c.pysam.c -o build/temp.linux-x86_64-3.9/samtools/stats_isize.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools/lz4 -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/bcftools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds -I/usr/include/python3.9 -c samtools/tmp_file.c.pysam.c -o build/temp.linux-x86_64-3.9/samtools/tmp_file.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-3.9/pysam/libcsamtools.o build/temp.linux-x86_64-3.9/samtools/amplicon_stats.c.pysam.o build/temp.linux-x86_64-3.9/samtools/bam.c.pysam.o build/temp.linux-x86_64-3.9/samtools/bam2bcf.c.pysam.o build/temp.linux-x86_64-3.9/samtools/bam2bcf_indel.c.pysam.o build/temp.linux-x86_64-3.9/samtools/bam2depth.c.pysam.o build/temp.linux-x86_64-3.9/samtools/bam_addrprg.c.pysam.o build/temp.linux-x86_64-3.9/samtools/bam_ampliconclip.c.pysam.o build/temp.linux-x86_64-3.9/samtools/bam_aux.c.pysam.o build/temp.linux-x86_64-3.9/samtools/bam_cat.c.pysam.o build/temp.linux-x86_64-3.9/samtools/bam_color.c.pysam.o build/temp.linux-x86_64-3.9/samtools/bam_fastq.c.pysam.o build/temp.linux-x86_64-3.9/samtools/bam_flags.c.pysam.o build/temp.linux-x86_64-3.9/samtools/bam_import.c.pysam.o build/temp.linux-x86_64-3.9/samtools/bam_index.c.pysam.o build/temp.linux-x86_64-3.9/samtools/bam_lpileup.c.pysam.o build/temp.linux-x86_64-3.9/samtools/bam_markdup.c.pysam.o build/temp.linux-x86_64-3.9/samtools/bam_mate.c.pysam.o build/temp.linux-x86_64-3.9/samtools/bam_md.c.pysam.o build/temp.linux-x86_64-3.9/samtools/bam_plbuf.c.pysam.o build/temp.linux-x86_64-3.9/samtools/bam_plcmd.c.pysam.o build/temp.linux-x86_64-3.9/samtools/bam_quickcheck.c.pysam.o build/temp.linux-x86_64-3.9/samtools/bam_reheader.c.pysam.o build/temp.linux-x86_64-3.9/samtools/bam_rmdup.c.pysam.o build/temp.linux-x86_64-3.9/samtools/bam_rmdupse.c.pysam.o build/temp.linux-x86_64-3.9/samtools/bam_sort.c.pysam.o build/temp.linux-x86_64-3.9/samtools/bam_split.c.pysam.o build/temp.linux-x86_64-3.9/samtools/bam_stat.c.pysam.o build/temp.linux-x86_64-3.9/samtools/bamshuf.c.pysam.o build/temp.linux-x86_64-3.9/samtools/bamtk.c.pysam.o build/temp.linux-x86_64-3.9/samtools/bedcov.c.pysam.o build/temp.linux-x86_64-3.9/samtools/bedidx.c.pysam.o build/temp.linux-x86_64-3.9/samtools/coverage.c.pysam.o build/temp.linux-x86_64-3.9/samtools/cut_target.c.pysam.o build/temp.linux-x86_64-3.9/samtools/dict.c.pysam.o build/temp.linux-x86_64-3.9/samtools/faidx.c.pysam.o build/temp.linux-x86_64-3.9/samtools/lz4/lz4.o build/temp.linux-x86_64-3.9/samtools/padding.c.pysam.o build/temp.linux-x86_64-3.9/samtools/phase.c.pysam.o build/temp.linux-x86_64-3.9/samtools/sam.c.pysam.o build/temp.linux-x86_64-3.9/samtools/sam_opts.c.pysam.o build/temp.linux-x86_64-3.9/samtools/sam_utils.c.pysam.o build/temp.linux-x86_64-3.9/samtools/sam_view.c.pysam.o build/temp.linux-x86_64-3.9/samtools/sample.c.pysam.o build/temp.linux-x86_64-3.9/samtools/samtools.pysam.o build/temp.linux-x86_64-3.9/samtools/stats.c.pysam.o build/temp.linux-x86_64-3.9/samtools/stats_isize.c.pysam.o build/temp.linux-x86_64-3.9/samtools/tmp_file.c.pysam.o -L/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -L/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam -lz -lhts -lchtslib.cpython-39-x86_64-linux-gnu -o /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/libcsamtools.cpython-39-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN building 'pysam.libcbcftools' extension creating build/temp.linux-x86_64-3.9/bcftools x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools/lz4 -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/bcftools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds -I/usr/include/python3.9 -c bcftools/HMM.c.pysam.c -o build/temp.linux-x86_64-3.9/bcftools/HMM.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools/lz4 -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/bcftools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds -I/usr/include/python3.9 -c bcftools/abuf.c.pysam.c -o build/temp.linux-x86_64-3.9/bcftools/abuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools/lz4 -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/bcftools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds -I/usr/include/python3.9 -c bcftools/bam2bcf.c.pysam.c -o build/temp.linux-x86_64-3.9/bcftools/bam2bcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools/lz4 -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/bcftools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds -I/usr/include/python3.9 -c bcftools/bam2bcf_indel.c.pysam.c -o build/temp.linux-x86_64-3.9/bcftools/bam2bcf_indel.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools/lz4 -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/bcftools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds -I/usr/include/python3.9 -c bcftools/bam_sample.c.pysam.c -o build/temp.linux-x86_64-3.9/bcftools/bam_sample.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools/lz4 -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/bcftools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds -I/usr/include/python3.9 -c bcftools/bcftools.pysam.c -o build/temp.linux-x86_64-3.9/bcftools/bcftools.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools/lz4 -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/bcftools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds -I/usr/include/python3.9 -c bcftools/bin.c.pysam.c -o build/temp.linux-x86_64-3.9/bcftools/bin.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools/lz4 -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/bcftools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds -I/usr/include/python3.9 -c bcftools/ccall.c.pysam.c -o build/temp.linux-x86_64-3.9/bcftools/ccall.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools/lz4 -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/bcftools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds -I/usr/include/python3.9 -c bcftools/cols.c.pysam.c -o build/temp.linux-x86_64-3.9/bcftools/cols.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools/lz4 -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/bcftools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds -I/usr/include/python3.9 -c bcftools/consensus.c.pysam.c -o build/temp.linux-x86_64-3.9/bcftools/consensus.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools/lz4 -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/bcftools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds -I/usr/include/python3.9 -c bcftools/convert.c.pysam.c -o build/temp.linux-x86_64-3.9/bcftools/convert.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools/lz4 -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/bcftools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds -I/usr/include/python3.9 -c bcftools/csq.c.pysam.c -o build/temp.linux-x86_64-3.9/bcftools/csq.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools/lz4 -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/bcftools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds -I/usr/include/python3.9 -c bcftools/dist.c.pysam.c -o build/temp.linux-x86_64-3.9/bcftools/dist.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools/lz4 -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/bcftools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds -I/usr/include/python3.9 -c bcftools/em.c.pysam.c -o build/temp.linux-x86_64-3.9/bcftools/em.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools/lz4 -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/bcftools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds -I/usr/include/python3.9 -c bcftools/extsort.c.pysam.c -o build/temp.linux-x86_64-3.9/bcftools/extsort.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools/lz4 -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/bcftools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds -I/usr/include/python3.9 -c bcftools/filter.c.pysam.c -o build/temp.linux-x86_64-3.9/bcftools/filter.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools/lz4 -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/bcftools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds -I/usr/include/python3.9 -c bcftools/gvcf.c.pysam.c -o build/temp.linux-x86_64-3.9/bcftools/gvcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools/lz4 -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/bcftools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds -I/usr/include/python3.9 -c bcftools/hclust.c.pysam.c -o build/temp.linux-x86_64-3.9/bcftools/hclust.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools/lz4 -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/bcftools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds -I/usr/include/python3.9 -c bcftools/kmin.c.pysam.c -o build/temp.linux-x86_64-3.9/bcftools/kmin.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools/lz4 -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/bcftools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds -I/usr/include/python3.9 -c bcftools/main.c.pysam.c -o build/temp.linux-x86_64-3.9/bcftools/main.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools/lz4 -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/bcftools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds -I/usr/include/python3.9 -c bcftools/mcall.c.pysam.c -o build/temp.linux-x86_64-3.9/bcftools/mcall.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools/lz4 -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/bcftools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds -I/usr/include/python3.9 -c bcftools/mpileup.c.pysam.c -o build/temp.linux-x86_64-3.9/bcftools/mpileup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools/lz4 -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/bcftools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds -I/usr/include/python3.9 -c bcftools/ploidy.c.pysam.c -o build/temp.linux-x86_64-3.9/bcftools/ploidy.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools/lz4 -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/bcftools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds -I/usr/include/python3.9 -c bcftools/prob1.c.pysam.c -o build/temp.linux-x86_64-3.9/bcftools/prob1.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools/lz4 -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/bcftools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds -I/usr/include/python3.9 -c bcftools/regidx.c.pysam.c -o build/temp.linux-x86_64-3.9/bcftools/regidx.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools/lz4 -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/bcftools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds -I/usr/include/python3.9 -c bcftools/reheader.c.pysam.c -o build/temp.linux-x86_64-3.9/bcftools/reheader.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools/lz4 -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/bcftools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds -I/usr/include/python3.9 -c bcftools/smpl_ilist.c.pysam.c -o build/temp.linux-x86_64-3.9/bcftools/smpl_ilist.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools/lz4 -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/bcftools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds -I/usr/include/python3.9 -c bcftools/str_finder.c.pysam.c -o build/temp.linux-x86_64-3.9/bcftools/str_finder.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools/lz4 -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/bcftools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds -I/usr/include/python3.9 -c bcftools/tabix.c.pysam.c -o build/temp.linux-x86_64-3.9/bcftools/tabix.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools/lz4 -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/bcftools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds -I/usr/include/python3.9 -c bcftools/tsv2vcf.c.pysam.c -o build/temp.linux-x86_64-3.9/bcftools/tsv2vcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools/lz4 -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/bcftools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds -I/usr/include/python3.9 -c bcftools/vcfannotate.c.pysam.c -o build/temp.linux-x86_64-3.9/bcftools/vcfannotate.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools/lz4 -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/bcftools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds -I/usr/include/python3.9 -c bcftools/vcfbuf.c.pysam.c -o build/temp.linux-x86_64-3.9/bcftools/vcfbuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools/lz4 -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/bcftools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds -I/usr/include/python3.9 -c bcftools/vcfcall.c.pysam.c -o build/temp.linux-x86_64-3.9/bcftools/vcfcall.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools/lz4 -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/bcftools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds -I/usr/include/python3.9 -c bcftools/vcfcnv.c.pysam.c -o build/temp.linux-x86_64-3.9/bcftools/vcfcnv.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools/lz4 -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/bcftools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds -I/usr/include/python3.9 -c bcftools/vcfconcat.c.pysam.c -o build/temp.linux-x86_64-3.9/bcftools/vcfconcat.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools/lz4 -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/bcftools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds -I/usr/include/python3.9 -c bcftools/vcfconvert.c.pysam.c -o build/temp.linux-x86_64-3.9/bcftools/vcfconvert.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools/lz4 -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/bcftools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds -I/usr/include/python3.9 -c bcftools/vcffilter.c.pysam.c -o build/temp.linux-x86_64-3.9/bcftools/vcffilter.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools/lz4 -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/bcftools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds -I/usr/include/python3.9 -c bcftools/vcfgtcheck.c.pysam.c -o build/temp.linux-x86_64-3.9/bcftools/vcfgtcheck.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools/lz4 -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/bcftools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds -I/usr/include/python3.9 -c bcftools/vcfindex.c.pysam.c -o build/temp.linux-x86_64-3.9/bcftools/vcfindex.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools/lz4 -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/bcftools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds -I/usr/include/python3.9 -c bcftools/vcfisec.c.pysam.c -o build/temp.linux-x86_64-3.9/bcftools/vcfisec.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools/lz4 -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/bcftools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds -I/usr/include/python3.9 -c bcftools/vcfmerge.c.pysam.c -o build/temp.linux-x86_64-3.9/bcftools/vcfmerge.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement bcftools/vcfmerge.c.pysam.c: In function ‘maux_init’: bcftools/vcfmerge.c.pysam.c:733:34: warning: argument 1 range [18446744071562067968, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 733 | 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 /usr/include/htslib/kstring.h:30, from /usr/include/htslib/hts.h:37, from /usr/include/htslib/vcf.h:39, from bcftools/vcfmerge.c.pysam.c:35: /usr/include/stdlib.h:542:14: note: in a call to allocation function ‘calloc’ declared here 542 | extern void *calloc (size_t __nmemb, size_t __size) | ^~~~~~ x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools/lz4 -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/bcftools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds -I/usr/include/python3.9 -c bcftools/vcfnorm.c.pysam.c -o build/temp.linux-x86_64-3.9/bcftools/vcfnorm.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools/lz4 -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/bcftools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds -I/usr/include/python3.9 -c bcftools/vcfplugin.c.pysam.c -o build/temp.linux-x86_64-3.9/bcftools/vcfplugin.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools/lz4 -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/bcftools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds -I/usr/include/python3.9 -c bcftools/vcfquery.c.pysam.c -o build/temp.linux-x86_64-3.9/bcftools/vcfquery.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools/lz4 -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/bcftools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds -I/usr/include/python3.9 -c bcftools/vcfroh.c.pysam.c -o build/temp.linux-x86_64-3.9/bcftools/vcfroh.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools/lz4 -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/bcftools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds -I/usr/include/python3.9 -c bcftools/vcfsom.c.pysam.c -o build/temp.linux-x86_64-3.9/bcftools/vcfsom.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools/lz4 -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/bcftools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds -I/usr/include/python3.9 -c bcftools/vcfsort.c.pysam.c -o build/temp.linux-x86_64-3.9/bcftools/vcfsort.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools/lz4 -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/bcftools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds -I/usr/include/python3.9 -c bcftools/vcfstats.c.pysam.c -o build/temp.linux-x86_64-3.9/bcftools/vcfstats.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools/lz4 -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/bcftools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds -I/usr/include/python3.9 -c bcftools/vcfview.c.pysam.c -o build/temp.linux-x86_64-3.9/bcftools/vcfview.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools/lz4 -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/bcftools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds -I/usr/include/python3.9 -c bcftools/vcmp.c.pysam.c -o build/temp.linux-x86_64-3.9/bcftools/vcmp.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools/lz4 -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/bcftools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds -I/usr/include/python3.9 -c bcftools/version.c.pysam.c -o build/temp.linux-x86_64-3.9/bcftools/version.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools/lz4 -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/bcftools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds -I/usr/include/python3.9 -c pysam/libcbcftools.c -o build/temp.linux-x86_64-3.9/pysam/libcbcftools.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-3.9/bcftools/HMM.c.pysam.o build/temp.linux-x86_64-3.9/bcftools/abuf.c.pysam.o build/temp.linux-x86_64-3.9/bcftools/bam2bcf.c.pysam.o build/temp.linux-x86_64-3.9/bcftools/bam2bcf_indel.c.pysam.o build/temp.linux-x86_64-3.9/bcftools/bam_sample.c.pysam.o build/temp.linux-x86_64-3.9/bcftools/bcftools.pysam.o build/temp.linux-x86_64-3.9/bcftools/bin.c.pysam.o build/temp.linux-x86_64-3.9/bcftools/ccall.c.pysam.o build/temp.linux-x86_64-3.9/bcftools/cols.c.pysam.o build/temp.linux-x86_64-3.9/bcftools/consensus.c.pysam.o build/temp.linux-x86_64-3.9/bcftools/convert.c.pysam.o build/temp.linux-x86_64-3.9/bcftools/csq.c.pysam.o build/temp.linux-x86_64-3.9/bcftools/dist.c.pysam.o build/temp.linux-x86_64-3.9/bcftools/em.c.pysam.o build/temp.linux-x86_64-3.9/bcftools/extsort.c.pysam.o build/temp.linux-x86_64-3.9/bcftools/filter.c.pysam.o build/temp.linux-x86_64-3.9/bcftools/gvcf.c.pysam.o build/temp.linux-x86_64-3.9/bcftools/hclust.c.pysam.o build/temp.linux-x86_64-3.9/bcftools/kmin.c.pysam.o build/temp.linux-x86_64-3.9/bcftools/main.c.pysam.o build/temp.linux-x86_64-3.9/bcftools/mcall.c.pysam.o build/temp.linux-x86_64-3.9/bcftools/mpileup.c.pysam.o build/temp.linux-x86_64-3.9/bcftools/ploidy.c.pysam.o build/temp.linux-x86_64-3.9/bcftools/prob1.c.pysam.o build/temp.linux-x86_64-3.9/bcftools/regidx.c.pysam.o build/temp.linux-x86_64-3.9/bcftools/reheader.c.pysam.o build/temp.linux-x86_64-3.9/bcftools/smpl_ilist.c.pysam.o build/temp.linux-x86_64-3.9/bcftools/str_finder.c.pysam.o build/temp.linux-x86_64-3.9/bcftools/tabix.c.pysam.o build/temp.linux-x86_64-3.9/bcftools/tsv2vcf.c.pysam.o build/temp.linux-x86_64-3.9/bcftools/vcfannotate.c.pysam.o build/temp.linux-x86_64-3.9/bcftools/vcfbuf.c.pysam.o build/temp.linux-x86_64-3.9/bcftools/vcfcall.c.pysam.o build/temp.linux-x86_64-3.9/bcftools/vcfcnv.c.pysam.o build/temp.linux-x86_64-3.9/bcftools/vcfconcat.c.pysam.o build/temp.linux-x86_64-3.9/bcftools/vcfconvert.c.pysam.o build/temp.linux-x86_64-3.9/bcftools/vcffilter.c.pysam.o build/temp.linux-x86_64-3.9/bcftools/vcfgtcheck.c.pysam.o build/temp.linux-x86_64-3.9/bcftools/vcfindex.c.pysam.o build/temp.linux-x86_64-3.9/bcftools/vcfisec.c.pysam.o build/temp.linux-x86_64-3.9/bcftools/vcfmerge.c.pysam.o build/temp.linux-x86_64-3.9/bcftools/vcfnorm.c.pysam.o build/temp.linux-x86_64-3.9/bcftools/vcfplugin.c.pysam.o build/temp.linux-x86_64-3.9/bcftools/vcfquery.c.pysam.o build/temp.linux-x86_64-3.9/bcftools/vcfroh.c.pysam.o build/temp.linux-x86_64-3.9/bcftools/vcfsom.c.pysam.o build/temp.linux-x86_64-3.9/bcftools/vcfsort.c.pysam.o build/temp.linux-x86_64-3.9/bcftools/vcfstats.c.pysam.o build/temp.linux-x86_64-3.9/bcftools/vcfview.c.pysam.o build/temp.linux-x86_64-3.9/bcftools/vcmp.c.pysam.o build/temp.linux-x86_64-3.9/bcftools/version.c.pysam.o build/temp.linux-x86_64-3.9/pysam/libcbcftools.o -L/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -L/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam -lz -lhts -lchtslib.cpython-39-x86_64-linux-gnu -o /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/libcbcftools.cpython-39-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN building 'pysam.libcutils' extension x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools/lz4 -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/bcftools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds -I/usr/include/python3.9 -c pysam/libcutils.c -o build/temp.linux-x86_64-3.9/pysam/libcutils.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement pysam/libcutils.c: In function ‘__pyx_pw_5pysam_9libcutils_15_pysam_dispatch’: pysam/libcutils.c:534:40: warning: ‘__pyx_v_retval’ may be used uninitialized in this function [-Wmaybe-uninitialized] 534 | #define PyInt_FromLong PyLong_FromLong | ^~~~~~~~~~~~~~~ pysam/libcutils.c:6778:7: note: ‘__pyx_v_retval’ was declared here 6778 | int __pyx_v_retval; | ^~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools/lz4 -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/bcftools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds -I/usr/include/python3.9 -c pysam/pysam_util.c -o build/temp.linux-x86_64-3.9/pysam/pysam_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-3.9/pysam/libcutils.o build/temp.linux-x86_64-3.9/pysam/pysam_util.o -L/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -L/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam -lz -lhts -lchtslib.cpython-39-x86_64-linux-gnu -lcsamtools.cpython-39-x86_64-linux-gnu -lcbcftools.cpython-39-x86_64-linux-gnu -o /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/libcutils.cpython-39-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN building 'pysam.libcalignmentfile' extension x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools/lz4 -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/bcftools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds -I/usr/include/python3.9 -c pysam/libcalignmentfile.c -o build/temp.linux-x86_64-3.9/pysam/libcalignmentfile.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-3.9/pysam/libcalignmentfile.o -L/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -L/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam -lz -lhts -lchtslib.cpython-39-x86_64-linux-gnu -lcutils.cpython-39-x86_64-linux-gnu -o /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/libcalignmentfile.cpython-39-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN building 'pysam.libcsamfile' extension x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools/lz4 -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/bcftools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds -I/usr/include/python3.9 -c pysam/libcsamfile.c -o build/temp.linux-x86_64-3.9/pysam/libcsamfile.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-3.9/pysam/libcsamfile.o -L/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -L/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam -lz -lhts -lchtslib.cpython-39-x86_64-linux-gnu -lcutils.cpython-39-x86_64-linux-gnu -o /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/libcsamfile.cpython-39-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN building 'pysam.libcalignedsegment' extension x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools/lz4 -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/bcftools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds -I/usr/include/python3.9 -c pysam/libcalignedsegment.c -o build/temp.linux-x86_64-3.9/pysam/libcalignedsegment.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-3.9/pysam/libcalignedsegment.o -L/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -L/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam -lz -lhts -lchtslib.cpython-39-x86_64-linux-gnu -lcutils.cpython-39-x86_64-linux-gnu -o /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/libcalignedsegment.cpython-39-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN building 'pysam.libctabix' extension x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools/lz4 -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/bcftools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds -I/usr/include/python3.9 -c pysam/libctabix.c -o build/temp.linux-x86_64-3.9/pysam/libctabix.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-3.9/pysam/libctabix.o -L/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -L/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam -lz -lhts -lchtslib.cpython-39-x86_64-linux-gnu -lcutils.cpython-39-x86_64-linux-gnu -o /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/libctabix.cpython-39-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN building 'pysam.libcfaidx' extension x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools/lz4 -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/bcftools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds -I/usr/include/python3.9 -c pysam/libcfaidx.c -o build/temp.linux-x86_64-3.9/pysam/libcfaidx.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-3.9/pysam/libcfaidx.o -L/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -L/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam -lz -lhts -lchtslib.cpython-39-x86_64-linux-gnu -lcutils.cpython-39-x86_64-linux-gnu -o /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/libcfaidx.cpython-39-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN building 'pysam.libcbcf' extension x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools/lz4 -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/bcftools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds -I/usr/include/python3.9 -c pysam/libcbcf.c -o build/temp.linux-x86_64-3.9/pysam/libcbcf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-3.9/pysam/libcbcf.o -L/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -L/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam -lz -lhts -lchtslib.cpython-39-x86_64-linux-gnu -lcutils.cpython-39-x86_64-linux-gnu -o /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/libcbcf.cpython-39-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN building 'pysam.libcbgzf' extension x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools/lz4 -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/bcftools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds -I/usr/include/python3.9 -c pysam/libcbgzf.c -o build/temp.linux-x86_64-3.9/pysam/libcbgzf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-3.9/pysam/libcbgzf.o -L/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -L/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam -lz -lhts -lchtslib.cpython-39-x86_64-linux-gnu -lcutils.cpython-39-x86_64-linux-gnu -o /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/libcbgzf.cpython-39-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN building 'pysam.libctabixproxies' extension x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools/lz4 -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/bcftools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds -I/usr/include/python3.9 -c pysam/libctabixproxies.c -o build/temp.linux-x86_64-3.9/pysam/libctabixproxies.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement x86_64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-3.9/pysam/libctabixproxies.o -L/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -L/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam -lz -lhts -lchtslib.cpython-39-x86_64-linux-gnu -lcutils.cpython-39-x86_64-linux-gnu -o /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/libctabixproxies.cpython-39-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN building 'pysam.libcvcf' extension x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/samtools/lz4 -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/bcftools -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -I/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds -I/usr/include/python3.9 -c pysam/libcvcf.c -o build/temp.linux-x86_64-3.9/pysam/libcvcf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement pysam/libcvcf.c: In function ‘__pyx_pf_5pysam_7libcvcf_3VCF_32parse_data.constprop’: pysam/libcvcf.c:25076:16: warning: ‘__pyx_v_qual’ may be used uninitialized in this function [-Wmaybe-uninitialized] 25076 | __pyx_t_12 = PyFloat_FromDouble(__pyx_v_qual); if (unlikely(!__pyx_t_12)) __PYX_ERR(0, 873, __pyx_L1_error) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -ffile-prefix-map=/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-3.9/pysam/libcvcf.o -L/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/pysam -L/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam -L/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam -lz -lhts -lchtslib.cpython-39-x86_64-linux-gnu -lcutils.cpython-39-x86_64-linux-gnu -o /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/libcvcf.cpython-39-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN create-stamp debian/debhelper-build-stamp dh_testroot -a -O--buildsystem=pybuild dh_prep -a -O--buildsystem=pybuild dh_auto_install -a -O--buildsystem=pybuild I: pybuild base:237: /usr/bin/python3.10 setup.py install --root /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/debian/python3-pysam /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/setup.py:32: DeprecationWarning: The distutils package is deprecated and slated for removal in Python 3.12. Use setuptools or check PEP 632 for potential alternatives from distutils import log # pysam: cython is available - using cythonize if necessary # pysam: htslib mode is external # pysam: HTSLIB_CONFIGURE_OPTIONS=None running install running build running build_py copying pysam/config.py -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam 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) copying samtools/samtools_config_vars.h -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam/include/samtools running build_ext skipping 'pysam/libchtslib.c' Cython extension (up-to-date) skipping 'pysam/libcsamtools.c' Cython extension (up-to-date) skipping 'pysam/libcbcftools.c' Cython extension (up-to-date) skipping 'pysam/libcutils.c' Cython extension (up-to-date) skipping 'pysam/libcalignmentfile.c' Cython extension (up-to-date) skipping 'pysam/libcsamfile.c' Cython extension (up-to-date) skipping 'pysam/libcalignedsegment.c' Cython extension (up-to-date) skipping 'pysam/libctabix.c' Cython extension (up-to-date) skipping 'pysam/libcfaidx.c' Cython extension (up-to-date) skipping 'pysam/libcbcf.c' Cython extension (up-to-date) skipping 'pysam/libcbgzf.c' Cython extension (up-to-date) skipping 'pysam/libctabixproxies.c' Cython extension (up-to-date) skipping 'pysam/libcvcf.c' Cython extension (up-to-date) creating samtools/samtools_config_vars.h for 'pysam.libcsamtools' extension running install_lib creating /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/debian/python3-pysam creating /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/debian/python3-pysam/usr creating /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib creating /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.10 creating /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.10/dist-packages creating /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.10/dist-packages/pysam copying /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam/Pileup.py -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.10/dist-packages/pysam copying /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam/__init__.py -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.10/dist-packages/pysam copying /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam/bcftools.py -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.10/dist-packages/pysam copying /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam/samtools.py -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.10/dist-packages/pysam copying /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam/utils.py -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.10/dist-packages/pysam copying /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam/version.py -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.10/dist-packages/pysam creating /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.10/dist-packages/pysam/include copying /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam/include/__init__.py -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.10/dist-packages/pysam/include creating /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.10/dist-packages/pysam/include/samtools copying /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam/include/samtools/bam.h -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.10/dist-packages/pysam/include/samtools copying /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam/include/samtools/bam2bcf.h -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.10/dist-packages/pysam/include/samtools copying /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam/include/samtools/bam_ampliconclip.h -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.10/dist-packages/pysam/include/samtools copying /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam/include/samtools/bam_endian.h -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.10/dist-packages/pysam/include/samtools copying /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam/include/samtools/bam_lpileup.h -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.10/dist-packages/pysam/include/samtools copying /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam/include/samtools/bam_plbuf.h -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.10/dist-packages/pysam/include/samtools copying /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam/include/samtools/bedidx.h -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.10/dist-packages/pysam/include/samtools copying /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam/include/samtools/sam.h -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.10/dist-packages/pysam/include/samtools copying /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam/include/samtools/sam_opts.h -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.10/dist-packages/pysam/include/samtools copying /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam/include/samtools/sample.h -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.10/dist-packages/pysam/include/samtools copying /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam/include/samtools/samtools.h -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.10/dist-packages/pysam/include/samtools copying /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam/include/samtools/samtools.pysam.h -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.10/dist-packages/pysam/include/samtools copying /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam/include/samtools/stats_isize.h -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.10/dist-packages/pysam/include/samtools copying /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam/include/samtools/tmp_file.h -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.10/dist-packages/pysam/include/samtools copying /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam/include/samtools/config.h -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.10/dist-packages/pysam/include/samtools copying /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam/include/samtools/samtools_config_vars.h -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.10/dist-packages/pysam/include/samtools creating /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.10/dist-packages/pysam/include/bcftools copying /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam/include/bcftools/HMM.h -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.10/dist-packages/pysam/include/bcftools copying /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam/include/bcftools/abuf.h -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.10/dist-packages/pysam/include/bcftools copying /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam/include/bcftools/bam2bcf.h -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.10/dist-packages/pysam/include/bcftools copying /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam/include/bcftools/bam_sample.h -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.10/dist-packages/pysam/include/bcftools copying /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam/include/bcftools/bcftools.h -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.10/dist-packages/pysam/include/bcftools copying /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam/include/bcftools/bcftools.pysam.h -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.10/dist-packages/pysam/include/bcftools copying /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam/include/bcftools/bin.h -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.10/dist-packages/pysam/include/bcftools copying /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam/include/bcftools/call.h -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.10/dist-packages/pysam/include/bcftools copying /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam/include/bcftools/cols.h -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.10/dist-packages/pysam/include/bcftools copying /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam/include/bcftools/convert.h -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.10/dist-packages/pysam/include/bcftools copying /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam/include/bcftools/dist.h -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.10/dist-packages/pysam/include/bcftools copying /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam/include/bcftools/extsort.h -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.10/dist-packages/pysam/include/bcftools copying /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam/include/bcftools/filter.h -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.10/dist-packages/pysam/include/bcftools copying /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam/include/bcftools/gvcf.h -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.10/dist-packages/pysam/include/bcftools copying /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam/include/bcftools/hclust.h -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.10/dist-packages/pysam/include/bcftools copying /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam/include/bcftools/hex.h -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.10/dist-packages/pysam/include/bcftools copying /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam/include/bcftools/khash_str2str.h -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.10/dist-packages/pysam/include/bcftools copying /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam/include/bcftools/kheap.h -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.10/dist-packages/pysam/include/bcftools copying /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam/include/bcftools/kmin.h -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.10/dist-packages/pysam/include/bcftools copying /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam/include/bcftools/mw.h -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.10/dist-packages/pysam/include/bcftools copying /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam/include/bcftools/ploidy.h -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.10/dist-packages/pysam/include/bcftools copying /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam/include/bcftools/prob1.h -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.10/dist-packages/pysam/include/bcftools copying /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam/include/bcftools/rbuf.h -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.10/dist-packages/pysam/include/bcftools copying /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam/include/bcftools/regidx.h -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.10/dist-packages/pysam/include/bcftools copying /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam/include/bcftools/smpl_ilist.h -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.10/dist-packages/pysam/include/bcftools copying /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam/include/bcftools/str_finder.h -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.10/dist-packages/pysam/include/bcftools copying /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam/include/bcftools/tsv2vcf.h -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.10/dist-packages/pysam/include/bcftools copying /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam/include/bcftools/utlist.h -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.10/dist-packages/pysam/include/bcftools copying /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam/include/bcftools/variantkey.h -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.10/dist-packages/pysam/include/bcftools copying /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam/include/bcftools/vcfbuf.h -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.10/dist-packages/pysam/include/bcftools copying /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam/include/bcftools/vcmp.h -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.10/dist-packages/pysam/include/bcftools copying /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam/include/bcftools/config.h -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.10/dist-packages/pysam/include/bcftools copying /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam/libcalignedsegment.pxd -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.10/dist-packages/pysam copying /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam/libcalignmentfile.pxd -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.10/dist-packages/pysam copying /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam/libcbcf.pxd -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.10/dist-packages/pysam copying /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam/libcbcftools.pxd -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.10/dist-packages/pysam copying /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam/libcfaidx.pxd -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.10/dist-packages/pysam copying /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam/libchtslib.pxd -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.10/dist-packages/pysam copying /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam/libcsamfile.pxd -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.10/dist-packages/pysam copying /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam/libcsamtools.pxd -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.10/dist-packages/pysam copying /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam/libctabix.pxd -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.10/dist-packages/pysam copying /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam/libctabixproxies.pxd -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.10/dist-packages/pysam copying /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam/libcutils.pxd -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.10/dist-packages/pysam copying /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam/libcvcf.pxd -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.10/dist-packages/pysam copying /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam/cbcftools_util.h -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.10/dist-packages/pysam copying /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam/csamtools_util.h -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.10/dist-packages/pysam copying /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam/htslib_util.h -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.10/dist-packages/pysam copying /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam/pysam_stream.h -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.10/dist-packages/pysam copying /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam/pysam_util.h -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.10/dist-packages/pysam copying /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam/version.h -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.10/dist-packages/pysam copying /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam/libchtslib.cpython-310-x86_64-linux-gnu.so -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.10/dist-packages/pysam copying /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam/libcsamtools.cpython-310-x86_64-linux-gnu.so -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.10/dist-packages/pysam copying /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam/libcbcftools.cpython-310-x86_64-linux-gnu.so -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.10/dist-packages/pysam copying /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam/libcutils.cpython-310-x86_64-linux-gnu.so -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.10/dist-packages/pysam copying /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam/libcalignmentfile.cpython-310-x86_64-linux-gnu.so -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.10/dist-packages/pysam copying /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam/libcsamfile.cpython-310-x86_64-linux-gnu.so -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.10/dist-packages/pysam copying /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam/libcalignedsegment.cpython-310-x86_64-linux-gnu.so -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.10/dist-packages/pysam copying /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam/libctabix.cpython-310-x86_64-linux-gnu.so -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.10/dist-packages/pysam copying /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam/libcfaidx.cpython-310-x86_64-linux-gnu.so -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.10/dist-packages/pysam copying /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam/libcbcf.cpython-310-x86_64-linux-gnu.so -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.10/dist-packages/pysam copying /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam/libcbgzf.cpython-310-x86_64-linux-gnu.so -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.10/dist-packages/pysam copying /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam/libctabixproxies.cpython-310-x86_64-linux-gnu.so -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.10/dist-packages/pysam copying /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam/libcvcf.cpython-310-x86_64-linux-gnu.so -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.10/dist-packages/pysam copying /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.10_pysam/build/pysam/config.py -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.10/dist-packages/pysam byte-compiling /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.10/dist-packages/pysam/Pileup.py to Pileup.cpython-310.pyc byte-compiling /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.10/dist-packages/pysam/__init__.py to __init__.cpython-310.pyc byte-compiling /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.10/dist-packages/pysam/bcftools.py to bcftools.cpython-310.pyc byte-compiling /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.10/dist-packages/pysam/samtools.py to samtools.cpython-310.pyc byte-compiling /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.10/dist-packages/pysam/utils.py to utils.cpython-310.pyc byte-compiling /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.10/dist-packages/pysam/version.py to version.cpython-310.pyc byte-compiling /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.10/dist-packages/pysam/include/__init__.py to __init__.cpython-310.pyc byte-compiling /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.10/dist-packages/pysam/config.py to config.cpython-310.pyc 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' reading manifest file 'pysam.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no files found matching 'KNOWN_BUGS' warning: no files found matching 'THANKS' no previously-included directories found matching 'tests/' warning: no files found matching 'htslib/LICENSE' warning: no files found matching 'htslib/README' warning: no files found matching '*.[ch]' under directory 'htslib' warning: no previously-included files found matching 'htslib/*config*.h' warning: no files found matching 'htslib/configure.ac' warning: no files found matching 'htslib/m4/*.m4' warning: no files found matching 'htslib/*.in' warning: no files found matching 'htslib/configure' warning: no files found matching 'htslib/version.sh' warning: no files found matching 'htslib/Makefile' warning: no files found matching 'htslib/*.mk' warning: no previously-included files found matching 'htslib/config.mk' warning: no previously-included files found matching 'htslib/htscodecs.mk' adding license file 'COPYING' adding license file 'AUTHORS' writing manifest file 'pysam.egg-info/SOURCES.txt' Copying pysam.egg-info to /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.10/dist-packages/pysam-0.17.0.egg-info Skipping SOURCES.txt running install_scripts I: pybuild base:237: /usr/bin/python3 setup.py install --root /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/debian/python3-pysam # pysam: cython is available - using cythonize if necessary # pysam: htslib mode is external # pysam: HTSLIB_CONFIGURE_OPTIONS=None running install running build running build_py copying pysam/config.py -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam 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) copying samtools/samtools_config_vars.h -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/samtools running build_ext skipping 'pysam/libchtslib.c' Cython extension (up-to-date) skipping 'pysam/libcsamtools.c' Cython extension (up-to-date) skipping 'pysam/libcbcftools.c' Cython extension (up-to-date) skipping 'pysam/libcutils.c' Cython extension (up-to-date) skipping 'pysam/libcalignmentfile.c' Cython extension (up-to-date) skipping 'pysam/libcsamfile.c' Cython extension (up-to-date) skipping 'pysam/libcalignedsegment.c' Cython extension (up-to-date) skipping 'pysam/libctabix.c' Cython extension (up-to-date) skipping 'pysam/libcfaidx.c' Cython extension (up-to-date) skipping 'pysam/libcbcf.c' Cython extension (up-to-date) skipping 'pysam/libcbgzf.c' Cython extension (up-to-date) skipping 'pysam/libctabixproxies.c' Cython extension (up-to-date) skipping 'pysam/libcvcf.c' Cython extension (up-to-date) creating samtools/samtools_config_vars.h for 'pysam.libcsamtools' extension running install_lib creating /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.9 creating /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages creating /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam copying /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/Pileup.py -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam copying /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/__init__.py -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam copying /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/bcftools.py -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam copying /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/samtools.py -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam copying /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/utils.py -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam copying /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/version.py -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam creating /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/include copying /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/__init__.py -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/include creating /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/include/samtools copying /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/samtools/bam.h -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/include/samtools copying /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/samtools/bam2bcf.h -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/include/samtools copying /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/samtools/bam_ampliconclip.h -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/include/samtools copying /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/samtools/bam_endian.h -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/include/samtools copying /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/samtools/bam_lpileup.h -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/include/samtools copying /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/samtools/bam_plbuf.h -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/include/samtools copying /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/samtools/bedidx.h -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/include/samtools copying /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/samtools/sam.h -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/include/samtools copying /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/samtools/sam_opts.h -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/include/samtools copying /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/samtools/sample.h -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/include/samtools copying /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/samtools/samtools.h -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/include/samtools copying /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/samtools/samtools.pysam.h -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/include/samtools copying /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/samtools/stats_isize.h -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/include/samtools copying /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/samtools/tmp_file.h -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/include/samtools copying /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/samtools/config.h -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/include/samtools copying /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/samtools/samtools_config_vars.h -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/include/samtools creating /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/include/bcftools copying /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools/HMM.h -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/include/bcftools copying /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools/abuf.h -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/include/bcftools copying /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools/bam2bcf.h -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/include/bcftools copying /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools/bam_sample.h -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/include/bcftools copying /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools/bcftools.h -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/include/bcftools copying /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools/bcftools.pysam.h -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/include/bcftools copying /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools/bin.h -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/include/bcftools copying /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools/call.h -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/include/bcftools copying /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools/cols.h -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/include/bcftools copying /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools/convert.h -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/include/bcftools copying /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools/dist.h -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/include/bcftools copying /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools/extsort.h -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/include/bcftools copying /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools/filter.h -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/include/bcftools copying /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools/gvcf.h -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/include/bcftools copying /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools/hclust.h -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/include/bcftools copying /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools/hex.h -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/include/bcftools copying /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools/khash_str2str.h -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/include/bcftools copying /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools/kheap.h -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/include/bcftools copying /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools/kmin.h -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/include/bcftools copying /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools/mw.h -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/include/bcftools copying /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools/ploidy.h -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/include/bcftools copying /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools/prob1.h -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/include/bcftools copying /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools/rbuf.h -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/include/bcftools copying /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools/regidx.h -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/include/bcftools copying /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools/smpl_ilist.h -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/include/bcftools copying /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools/str_finder.h -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/include/bcftools copying /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools/tsv2vcf.h -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/include/bcftools copying /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools/utlist.h -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/include/bcftools copying /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools/variantkey.h -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/include/bcftools copying /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools/vcfbuf.h -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/include/bcftools copying /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools/vcmp.h -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/include/bcftools copying /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/include/bcftools/config.h -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/include/bcftools copying /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/libcalignedsegment.pxd -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam copying /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/libcalignmentfile.pxd -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam copying /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/libcbcf.pxd -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam copying /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/libcbcftools.pxd -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam copying /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/libcfaidx.pxd -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam copying /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/libchtslib.pxd -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam copying /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/libcsamfile.pxd -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam copying /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/libcsamtools.pxd -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam copying /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/libctabix.pxd -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam copying /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/libctabixproxies.pxd -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam copying /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/libcutils.pxd -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam copying /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/libcvcf.pxd -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam copying /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/cbcftools_util.h -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam copying /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/csamtools_util.h -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam copying /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/htslib_util.h -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam copying /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/pysam_stream.h -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam copying /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/pysam_util.h -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam copying /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/version.h -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam copying /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/libchtslib.cpython-39-x86_64-linux-gnu.so -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam copying /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/libcsamtools.cpython-39-x86_64-linux-gnu.so -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam copying /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/libcbcftools.cpython-39-x86_64-linux-gnu.so -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam copying /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/libcutils.cpython-39-x86_64-linux-gnu.so -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam copying /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/libcalignmentfile.cpython-39-x86_64-linux-gnu.so -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam copying /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/libcsamfile.cpython-39-x86_64-linux-gnu.so -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam copying /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/libcalignedsegment.cpython-39-x86_64-linux-gnu.so -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam copying /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/libctabix.cpython-39-x86_64-linux-gnu.so -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam copying /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/libcfaidx.cpython-39-x86_64-linux-gnu.so -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam copying /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/libcbcf.cpython-39-x86_64-linux-gnu.so -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam copying /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/libcbgzf.cpython-39-x86_64-linux-gnu.so -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam copying /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/libctabixproxies.cpython-39-x86_64-linux-gnu.so -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam copying /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/libcvcf.cpython-39-x86_64-linux-gnu.so -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam copying /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/.pybuild/cpython3_3.9_pysam/build/pysam/config.py -> /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam byte-compiling /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/Pileup.py to Pileup.cpython-39.pyc byte-compiling /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/__init__.py to __init__.cpython-39.pyc byte-compiling /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/bcftools.py to bcftools.cpython-39.pyc byte-compiling /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/samtools.py to samtools.cpython-39.pyc byte-compiling /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/utils.py to utils.cpython-39.pyc byte-compiling /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/version.py to version.cpython-39.pyc byte-compiling /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/include/__init__.py to __init__.cpython-39.pyc byte-compiling /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam/config.py to config.cpython-39.pyc running install_egg_info running egg_info writing pysam.egg-info/PKG-INFO writing dependency_links to pysam.egg-info/dependency_links.txt writing top-level names to pysam.egg-info/top_level.txt reading manifest file 'pysam.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no files found matching 'KNOWN_BUGS' warning: no files found matching 'THANKS' no previously-included directories found matching 'tests/' warning: no files found matching 'htslib/LICENSE' warning: no files found matching 'htslib/README' warning: no files found matching '*.[ch]' under directory 'htslib' warning: no previously-included files found matching 'htslib/*config*.h' warning: no files found matching 'htslib/configure.ac' warning: no files found matching 'htslib/m4/*.m4' warning: no files found matching 'htslib/*.in' warning: no files found matching 'htslib/configure' warning: no files found matching 'htslib/version.sh' warning: no files found matching 'htslib/Makefile' warning: no files found matching 'htslib/*.mk' warning: no previously-included files found matching 'htslib/config.mk' warning: no previously-included files found matching 'htslib/htscodecs.mk' adding license file 'COPYING' adding license file 'AUTHORS' writing manifest file 'pysam.egg-info/SOURCES.txt' Copying pysam.egg-info to /build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/debian/python3-pysam/usr/lib/python3.9/dist-packages/pysam-0.17.0.egg-info Skipping SOURCES.txt running install_scripts debian/rules override_dh_install make[1]: Entering directory '/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds' cd tests/pysam_data && /usr/bin/make clean make[2]: Entering directory '/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/tests/pysam_data' rm -fr *.bai *.csi *.fai *.gzi *.pileup* [a-z]*.cram *.crai \ all.stamp *~ calDepth *.dSYM pysam_*.sam \ ex2.sam ex2.sam.gz ex1.sam ex1.fa.gz \ with_md.sam.gz \ *.fq.gz make[2]: Leaving directory '/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/tests/pysam_data' cd tests/cbcf_data && /usr/bin/make clean make[2]: Entering directory '/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/tests/cbcf_data' rm -f all.stamp *.gz *.tbi *.csi *.bcf make[2]: Leaving directory '/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds/tests/cbcf_data' find . -name "*.pyc" -delete find . -name "*.pyxbldc" -delete find . -name "tmp_*.bam" -delete find . -name "*.bai*" -delete find . -name "*.cram*" -delete find . -name "pysam_uncompressed.bam" -delete rm -rf tests/pysam_test_work \ tests/example_htslib.gtf.gz.tbi \ tests/log.txt \ tests/test.bam \ tests/_compile_test.c \ tests/pysam_ex2.sam \ tests/__pycache__ \ pysam/calignmentfile.c \ pysam/cbcf.c \ tests/GRCh38_full_analysis_set_plus_decoy_hla.fa.fai \ tests/pysam_data/ex1.fa.gz \ tests/pysam_data/ex1.fa.gz.gzi \ tests/pysam_data/ex1_csi.bam.csi rm -rf .pytest_cache/ dh_install -Xtest.gtf.gz find debian -name log.txt -delete make[1]: Leaving directory '/build/python-pysam-TG7D0j/python-pysam-0.17.0+ds' dh_installdocs -a -O--buildsystem=pybuild dh_installchangelogs -a -O--buildsystem=pybuild dh_python3 -a -O--buildsystem=pybuild W: dh_python3 fs:113: Paths differ: debian/python3-pysam/usr/lib/python3.10/dist-packages/pysam/include/samtools/samtools_config_vars.h and debian/python3-pysam/usr/lib/python3/dist-packages/pysam/include/samtools/samtools_config_vars.h dh_installsystemduser -a -O--buildsystem=pybuild dh_lintian -a -O--buildsystem=pybuild dh_perl -a -O--buildsystem=pybuild dh_link -a -O--buildsystem=pybuild dh_strip_nondeterminism -a -O--buildsystem=pybuild dh_compress -a -O--buildsystem=pybuild dh_fixperms -a -O--buildsystem=pybuild dh_missing -a -O--buildsystem=pybuild dh_dwz -a -O--buildsystem=pybuild dh_strip -a -O--buildsystem=pybuild dh_makeshlibs -a -O--buildsystem=pybuild dh_shlibdeps -a -O--buildsystem=pybuild dh_installdeb -a -O--buildsystem=pybuild dh_gencontrol -a -O--buildsystem=pybuild dpkg-gencontrol: warning: package python3-pysam: substitution variable ${python3:Provides} unused, but is defined dpkg-gencontrol: warning: package python3-pysam: substitution variable ${python3:Versions} unused, but is defined dpkg-gencontrol: warning: package python3-pysam: substitution variable ${python3:Provides} unused, but is defined dpkg-gencontrol: warning: package python3-pysam: substitution variable ${python3:Versions} unused, but is defined dh_md5sums -a -O--buildsystem=pybuild dh_builddeb -a -O--buildsystem=pybuild dpkg-deb: building package 'python3-pysam-dbgsym' in '../python3-pysam-dbgsym_0.17.0+ds-2+b1_amd64.deb'. dpkg-deb: building package 'python3-pysam' in '../python3-pysam_0.17.0+ds-2+b1_amd64.deb'. dpkg-genbuildinfo --build=any dpkg-genchanges --build=any >../python-pysam_0.17.0+ds-2+b1_amd64.changes dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) I: running special hook: sync-out /build/python-pysam-TG7D0j /tmp/python-pysam-0.17.0+ds-2+b1cx_mu81o I: cleaning package lists and apt cache... I: removing tempdir /tmp/mmdebstrap.718MyYN9IH... I: success in 942.5683 seconds md5: python3-pysam-dbgsym_0.17.0+ds-2+b1_amd64.deb: OK md5: python3-pysam_0.17.0+ds-2+b1_amd64.deb: OK sha1: python3-pysam-dbgsym_0.17.0+ds-2+b1_amd64.deb: OK sha1: python3-pysam_0.17.0+ds-2+b1_amd64.deb: OK sha256: python3-pysam-dbgsym_0.17.0+ds-2+b1_amd64.deb: OK sha256: python3-pysam_0.17.0+ds-2+b1_amd64.deb: OK Checksums: OK