Input buildinfo: https://buildinfos.debian.net/buildinfo-pool/s/samtools-legacy/samtools-legacy_0.1.19+dfsg-5_amd64.buildinfo Use metasnap for getting required timestamps New buildinfo file: /tmp/samtools-legacy-0.1.19+dfsg-5bfk_0k01/samtools-legacy_0.1.19+dfsg-5_amd64.buildinfo Get source package info: samtools-legacy=0.1.19+dfsg-5 Source URL: http://snapshot.notset.fr/mr/package/samtools-legacy/0.1.19+dfsg-5/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=5.1-6 binutils=2.37.50.20220106-2 binutils-common=2.37.50.20220106-2 binutils-x86-64-linux-gnu=2.37.50.20220106-2 bsdextrautils=2.37.2-6 bsdutils=1:2.37.2-6 build-essential=12.9 bzip2=1.0.8-5 coreutils=8.32-4.1 cpp=4:11.2.0-2 cpp-11=11.2.0-14 dash=0.5.11+git20210903+057cd650a4ed-3 debconf=1.5.79 debhelper=13.6 debianutils=5.5-1 dh-autoreconf=20 dh-strip-nondeterminism=1.13.0-1 diffutils=1:3.7-5 dpkg=1.21.1 dpkg-dev=1.21.1 dwz=0.14-1 file=1:5.41-2 findutils=4.8.0-1 g++=4:11.2.0-2 g++-11=11.2.0-14 gcc=4:11.2.0-2 gcc-11=11.2.0-14 gcc-11-base=11.2.0-14 gettext=0.21-4 gettext-base=0.21-4 grep=3.7-1 groff-base=1.22.4-8 gzip=1.10-4 hostname=3.23 init-system-helpers=1.61 intltool-debian=0.35.0+20060710.5 libacl1=2.3.1-1 libarchive-zip-perl=1.68-1 libasan6=11.2.0-14 libatomic1=11.2.0-14 libattr1=1:2.5.1-1 libaudit-common=1:3.0.6-1 libaudit1=1:3.0.6-1+b1 libbinutils=2.37.50.20220106-2 libblkid1=2.37.2-6 libbz2-1.0=1.0.8-5 libc-bin=2.33-2 libc-dev-bin=2.33-2 libc6=2.33-2 libc6-dev=2.33-2 libcap-ng0=0.7.9-2.2+b1 libcap2=1:2.44-1 libcc1-0=11.2.0-14 libcom-err2=1.46.5-2 libcrypt-dev=1:4.4.27-1 libcrypt1=1:4.4.27-1 libctf-nobfd0=2.37.50.20220106-2 libctf0=2.37.50.20220106-2 libdb5.3=5.3.28+dfsg1-0.8 libdebconfclient0=0.261 libdebhelper-perl=13.6 libdpkg-perl=1.21.1 libelf1=0.186-1 libfile-stripnondeterminism-perl=1.13.0-1 libgcc-11-dev=11.2.0-14 libgcc-s1=11.2.0-14 libgcrypt20=1.9.4-5 libgdbm-compat4=1.22-1 libgdbm6=1.22-1 libgmp10=2:6.2.1+dfsg-3 libgomp1=11.2.0-14 libgpg-error0=1.43-2 libgssapi-krb5-2=1.18.3-7 libicu67=67.1-7 libisl23=0.24-2 libitm1=11.2.0-14 libk5crypto3=1.18.3-7 libkeyutils1=1.6.1-2 libkrb5-3=1.18.3-7 libkrb5support0=1.18.3-7 liblsan0=11.2.0-14 liblz4-1=1.9.3-2 liblzma5=5.2.5-2 libmagic-mgc=1:5.41-2 libmagic1=1:5.41-2 libmount1=2.37.2-6 libmpc3=1.2.1-1 libmpfr6=4.1.0-3 libncurses-dev=6.3-2 libncurses5-dev=6.3-2 libncurses6=6.3-2 libncursesw6=6.3-2 libnsl-dev=1.3.0-2 libnsl2=1.3.0-2 libpam-modules=1.4.0-11 libpam-modules-bin=1.4.0-11 libpam-runtime=1.4.0-11 libpam0g=1.4.0-11 libpcre2-8-0=10.39-3 libpcre3=2:8.39-13 libperl5.32=5.32.1-6 libpipeline1=1.5.5-1 libquadmath0=11.2.0-14 libseccomp2=2.5.3-2 libselinux1=3.3-1+b1 libsigsegv2=2.13-1 libsmartcols1=2.37.2-6 libssl1.1=1.1.1m-1 libstdc++-11-dev=11.2.0-14 libstdc++6=11.2.0-14 libsub-override-perl=0.09-2 libsystemd0=250.2-3 libtinfo6=6.3-2 libtirpc-common=1.3.2-2 libtirpc-dev=1.3.2-2 libtirpc3=1.3.2-2 libtool=2.4.6-15 libtsan0=11.2.0-14 libubsan1=11.2.0-14 libuchardet0=0.0.7-1 libudev1=250.2-3 libunistring2=0.9.10-6 libuuid1=2.37.2-6 libxml2=2.9.12+dfsg-5+b1 libzstd1=1.4.8+dfsg-3 linux-libc-dev=5.15.5-2 login=1:4.8.1-2 lsb-base=11.1.0 m4=1.4.18-5 make=4.3-4.1 man-db=2.9.4-4 mawk=1.3.4.20200120-2 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 rpcsvc-proto=1.4.2-4 sed=4.8-1 sensible-utils=0.0.17 sysvinit-utils=3.01-1 tar=1.34+dfsg-1 util-linux=2.37.2-6 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/20220121T030821Z/ bookworm main deb-src http://snapshot.notset.fr/archive/debian/20220121T030821Z/ bookworm main deb http://snapshot.notset.fr/archive/debian/20220402T210321Z/ unstable main deb http://snapshot.notset.fr/archive/debian/20220116T145127Z/ 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 samtools-legacy=0.1.19+dfsg-5 && mkdir -p /build/samtools-legacy-JbU72u && dpkg-source --no-check -x /*.dsc /build/samtools-legacy-JbU72u/samtools-legacy-0.1.19+dfsg && chown -R builduser:builduser /build/samtools-legacy-JbU72u" --customize-hook=chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/samtools-legacy-JbU72u/samtools-legacy-0.1.19+dfsg && env DEB_BUILD_OPTIONS="parallel=4" LC_ALL="C.UTF-8" LC_COLLATE="C.UTF-8" SOURCE_DATE_EPOCH="1642528154" DEB_BUILD_OPTIONS=nocheck dpkg-buildpackage -uc -a amd64 --build=any" --customize-hook=sync-out /build/samtools-legacy-JbU72u /tmp/samtools-legacy-0.1.19+dfsg-5bfk_0k01 bookworm /dev/null deb http://snapshot.notset.fr/archive/debian/20220116T145127Z 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.TNhlQOx_HQ 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.TNhlQOx_HQ Reading package lists... Building dependency tree... util-linux is already the newest version (2.37.2-6). The following NEW packages will be installed: fakeroot libfakeroot 0 upgraded, 2 newly installed, 0 to remove and 0 not upgraded. Need to get 135 kB of archives. After this operation, 406 kB of additional disk space will be used. Get:1 http://snapshot.notset.fr/archive/debian/20220116T145127Z unstable/main amd64 libfakeroot amd64 1.26-1.2 [48.0 kB] Get:2 http://snapshot.notset.fr/archive/debian/20220116T145127Z unstable/main amd64 fakeroot amd64 1.26-1.2 [87.1 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 135 kB in 0s (978 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 ... 4681 files and directories currently installed.) Preparing to unpack .../libfakeroot_1.26-1.2_amd64.deb ... Unpacking libfakeroot:amd64 (1.26-1.2) ... Selecting previously unselected package fakeroot. Preparing to unpack .../fakeroot_1.26-1.2_amd64.deb ... Unpacking fakeroot (1.26-1.2) ... Setting up libfakeroot:amd64 (1.26-1.2) ... Setting up fakeroot (1.26-1.2) ... update-alternatives: using /usr/bin/fakeroot-sysv to provide /usr/bin/fakeroot (fakeroot) in auto mode Processing triggers for libc-bin (2.33-2) ... 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/20220121T030821Z/ bookworm main deb-src http://snapshot.notset.fr/archive/debian/20220121T030821Z/ bookworm main deb http://snapshot.notset.fr/archive/debian/20220402T210321Z/ unstable main deb http://snapshot.notset.fr/archive/debian/20220116T145127Z/ unstable main' >> /etc/apt/sources.list && apt-get update"' exec /tmp/mmdebstrap.TNhlQOx_HQ Get:1 http://snapshot.notset.fr/archive/debian/20220121T030821Z bookworm InRelease [129 kB] Get:2 http://snapshot.notset.fr/archive/debian/20220402T210321Z unstable InRelease [165 kB] Hit:3 http://snapshot.notset.fr/archive/debian/20220116T145127Z unstable InRelease Ign:4 http://snapshot.notset.fr/archive/debian/20220121T030821Z bookworm/main Sources Ign:5 http://snapshot.notset.fr/archive/debian/20220121T030821Z bookworm/main amd64 Packages Ign:4 http://snapshot.notset.fr/archive/debian/20220121T030821Z bookworm/main Sources Ign:5 http://snapshot.notset.fr/archive/debian/20220121T030821Z bookworm/main amd64 Packages Ign:4 http://snapshot.notset.fr/archive/debian/20220121T030821Z bookworm/main Sources Ign:5 http://snapshot.notset.fr/archive/debian/20220121T030821Z bookworm/main amd64 Packages Get:4 http://snapshot.notset.fr/archive/debian/20220121T030821Z bookworm/main Sources [11.7 MB] Get:5 http://snapshot.notset.fr/archive/debian/20220121T030821Z bookworm/main amd64 Packages [11.2 MB] Ign:6 http://snapshot.notset.fr/archive/debian/20220402T210321Z unstable/main amd64 Packages Err:6 http://snapshot.notset.fr/archive/debian/20220402T210321Z unstable/main amd64 Packages 404 Not Found [IP: 10.13.0.253 80] Ign:6 http://snapshot.notset.fr/archive/debian/20220402T210321Z unstable/main amd64 Packages Get:6 http://snapshot.notset.fr/archive/debian/20220402T210321Z unstable/main amd64 Packages [12.4 MB] Fetched 35.6 MB in 29s (1224 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.TNhlQOx_HQ I: running --customize-hook in shell: sh -c 'chroot "$1" env sh -c "apt-get source --only-source -d samtools-legacy=0.1.19+dfsg-5 && mkdir -p /build/samtools-legacy-JbU72u && dpkg-source --no-check -x /*.dsc /build/samtools-legacy-JbU72u/samtools-legacy-0.1.19+dfsg && chown -R builduser:builduser /build/samtools-legacy-JbU72u"' exec /tmp/mmdebstrap.TNhlQOx_HQ Reading package lists... NOTICE: 'samtools-legacy' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/samtools-legacy.git Please use: git clone https://salsa.debian.org/med-team/samtools-legacy.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 382 kB of source archives. Get:1 http://snapshot.notset.fr/archive/debian/20220121T030821Z bookworm/main samtools-legacy 0.1.19+dfsg-5 (dsc) [2146 B] Get:2 http://snapshot.notset.fr/archive/debian/20220121T030821Z bookworm/main samtools-legacy 0.1.19+dfsg-5 (tar) [371 kB] Get:3 http://snapshot.notset.fr/archive/debian/20220121T030821Z bookworm/main samtools-legacy 0.1.19+dfsg-5 (diff) [8988 B] Fetched 382 kB in 0s (1010 kB/s) Download complete and in download only mode W: Download is performed unsandboxed as root as file 'samtools-legacy_0.1.19+dfsg-5.dsc' couldn't be accessed by user '_apt'. - pkgAcquire::Run (13: Permission denied) dpkg-source: info: extracting samtools-legacy in /build/samtools-legacy-JbU72u/samtools-legacy-0.1.19+dfsg dpkg-source: info: unpacking samtools-legacy_0.1.19+dfsg.orig.tar.xz dpkg-source: info: unpacking samtools-legacy_0.1.19+dfsg-5.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying fix_example_makefile.patch dpkg-source: info: applying fix_segfault_with_small_ref.patch dpkg-source: info: applying fix_coverage_cap.patch dpkg-source: info: applying hardening.patch dpkg-source: info: applying gcc-11.patch I: running --customize-hook in shell: sh -c 'chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/samtools-legacy-JbU72u/samtools-legacy-0.1.19+dfsg && env DEB_BUILD_OPTIONS="parallel=4" LC_ALL="C.UTF-8" LC_COLLATE="C.UTF-8" SOURCE_DATE_EPOCH="1642528154" DEB_BUILD_OPTIONS=nocheck dpkg-buildpackage -uc -a amd64 --build=any"' exec /tmp/mmdebstrap.TNhlQOx_HQ dpkg-buildpackage: info: source package samtools-legacy dpkg-buildpackage: info: source version 0.1.19+dfsg-5 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean dh_auto_clean make -j10 clean make[1]: Entering directory '/build/samtools-legacy-JbU72u/samtools-legacy-0.1.19+dfsg' make[2]: Entering directory '/build/samtools-legacy-JbU72u/samtools-legacy-0.1.19+dfsg' rm -fr gmon.out *.o a.out *.exe *.dSYM razip bgzip samtools *~ *.a *.so.* *.so *.dylib make[2]: Leaving directory '/build/samtools-legacy-JbU72u/samtools-legacy-0.1.19+dfsg' make[2]: Entering directory '/build/samtools-legacy-JbU72u/samtools-legacy-0.1.19+dfsg/bcftools' rm -fr gmon.out *.o a.out *.dSYM bcftools *~ *.a bcf.aux bcf.log bcf.pdf *.class libbcf.*.dylib libbcf.so* make[2]: Leaving directory '/build/samtools-legacy-JbU72u/samtools-legacy-0.1.19+dfsg/bcftools' make[2]: Entering directory '/build/samtools-legacy-JbU72u/samtools-legacy-0.1.19+dfsg/misc' rm -fr gmon.out *.o a.out *.exe *.dSYM md5sum-lite md5fa maq2sam-short maq2sam-long ace2sam wgsim bamcheck *~ *.a make[2]: Leaving directory '/build/samtools-legacy-JbU72u/samtools-legacy-0.1.19+dfsg/misc' make[1]: Leaving directory '/build/samtools-legacy-JbU72u/samtools-legacy-0.1.19+dfsg' dh_clean debian/rules binary-arch dh binary-arch dh_update_autotools_config -a dh_autoreconf -a dh_auto_configure -a debian/rules override_dh_auto_build make[1]: Entering directory '/build/samtools-legacy-JbU72u/samtools-legacy-0.1.19+dfsg' dh_auto_build -- all all-recur razip lib CFLAGS="-g -O2 -ffile-prefix-map=/build/samtools-legacy-JbU72u/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2" make -j10 "INSTALL=install --strip-program=true" all all-recur razip lib "CFLAGS=-g -O2 -ffile-prefix-map=/build/samtools-legacy-JbU72u/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2" make[2]: Entering directory '/build/samtools-legacy-JbU72u/samtools-legacy-0.1.19+dfsg' gcc -c -g -O2 -ffile-prefix-map=/build/samtools-legacy-JbU72u/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview.c -o bam_tview.o gcc -c -g -O2 -ffile-prefix-map=/build/samtools-legacy-JbU72u/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_plcmd.c -o bam_plcmd.o gcc -c -g -O2 -ffile-prefix-map=/build/samtools-legacy-JbU72u/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_view.c -o sam_view.o make[3]: Entering directory '/build/samtools-legacy-JbU72u/samtools-legacy-0.1.19+dfsg' gcc -c -g -O2 -ffile-prefix-map=/build/samtools-legacy-JbU72u/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -DBGZF_CACHE -I. bgzf.c -o bgzf.o gcc -c -g -O2 -ffile-prefix-map=/build/samtools-legacy-JbU72u/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_rmdup.c -o bam_rmdup.o gcc -c -g -O2 -ffile-prefix-map=/build/samtools-legacy-JbU72u/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_rmdupse.c -o bam_rmdupse.o gcc -c -g -O2 -ffile-prefix-map=/build/samtools-legacy-JbU72u/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_mate.c -o bam_mate.o gcc -c -g -O2 -ffile-prefix-map=/build/samtools-legacy-JbU72u/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_stat.c -o bam_stat.o gcc -c -g -O2 -ffile-prefix-map=/build/samtools-legacy-JbU72u/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_color.c -o bam_color.o gcc -c -g -O2 -ffile-prefix-map=/build/samtools-legacy-JbU72u/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kstring.c -o kstring.o gcc -c -g -O2 -ffile-prefix-map=/build/samtools-legacy-JbU72u/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bamtk.c -o bamtk.o gcc -c -g -O2 -ffile-prefix-map=/build/samtools-legacy-JbU72u/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kaln.c -o kaln.o gcc -c -g -O2 -ffile-prefix-map=/build/samtools-legacy-JbU72u/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2bcf.c -o bam2bcf.o gcc -c -g -O2 -ffile-prefix-map=/build/samtools-legacy-JbU72u/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_aux.c -o bam_aux.o gcc -c -g -O2 -ffile-prefix-map=/build/samtools-legacy-JbU72u/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2bcf_indel.c -o bam2bcf_indel.o gcc -c -g -O2 -ffile-prefix-map=/build/samtools-legacy-JbU72u/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. errmod.c -o errmod.o gcc -c -g -O2 -ffile-prefix-map=/build/samtools-legacy-JbU72u/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sample.c -o sample.o gcc -c -g -O2 -ffile-prefix-map=/build/samtools-legacy-JbU72u/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. cut_target.c -o cut_target.o gcc -c -g -O2 -ffile-prefix-map=/build/samtools-legacy-JbU72u/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. phase.c -o phase.o gcc -c -g -O2 -ffile-prefix-map=/build/samtools-legacy-JbU72u/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam.c -o bam.o gcc -c -g -O2 -ffile-prefix-map=/build/samtools-legacy-JbU72u/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_import.c -o bam_import.o gcc -c -g -O2 -ffile-prefix-map=/build/samtools-legacy-JbU72u/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam.c -o sam.o gcc -c -g -O2 -ffile-prefix-map=/build/samtools-legacy-JbU72u/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_index.c -o bam_index.o gcc -c -g -O2 -ffile-prefix-map=/build/samtools-legacy-JbU72u/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2depth.c -o bam2depth.o gcc -c -g -O2 -ffile-prefix-map=/build/samtools-legacy-JbU72u/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. padding.c -o padding.o bam_index.c: In function ‘bam_index_core’: bam_index.c:178:42: warning: overflow in conversion from ‘uint32_t’ {aka ‘unsigned int’} to ‘int32_t’ {aka ‘int’} changes value from ‘last_bin = 4294967295’ to ‘-1’ [-Woverflow] 178 | save_bin = save_tid = last_tid = last_bin = 0xffffffffu; | ^~~~~~~~ bam_index.c: In function ‘bam_index_load_core’: bam_index.c:335:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 335 | fread(magic, 1, 4, fp); | ^~~~~~~~~~~~~~~~~~~~~~ bam_index.c:342:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 342 | fread(&idx->n, 4, 1, fp); | ^~~~~~~~~~~~~~~~~~~~~~~~ bam_index.c:355:17: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 355 | fread(&size, 4, 1, fp); | ^~~~~~~~~~~~~~~~~~~~~~ bam_index.c:358:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 358 | fread(&key, 4, 1, fp); | ^~~~~~~~~~~~~~~~~~~~~ bam_index.c:362:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 362 | fread(&p->n, 4, 1, fp); | ^~~~~~~~~~~~~~~~~~~~~~ bam_index.c:366:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 366 | fread(p->list, 16, p->n, fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ bam_index.c:376:17: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 376 | fread(&index2->n, 4, 1, fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ bam_index.c:380:17: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 380 | fread(index2->offset, index2->n, 8, fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -c -g -O2 -ffile-prefix-map=/build/samtools-legacy-JbU72u/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bedcov.c -o bedcov.o gcc -c -g -O2 -ffile-prefix-map=/build/samtools-legacy-JbU72u/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_pileup.c -o bam_pileup.o gcc -c -g -O2 -ffile-prefix-map=/build/samtools-legacy-JbU72u/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_lpileup.c -o bam_lpileup.o gcc -c -g -O2 -ffile-prefix-map=/build/samtools-legacy-JbU72u/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_md.c -o bam_md.o gcc -c -g -O2 -ffile-prefix-map=/build/samtools-legacy-JbU72u/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razf.c -o razf.o bam_md.c: In function ‘bam_prob_realn_core’: bam_md.c:214:35: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] 214 | *(bq - 3) = 'Z'; | ~~~~~~~~~~^~~~~ bam_md.c:198:19: note: at offset -2 into destination object of size [0, 9223372036854775807] allocated by ‘bam_aux_get’ 198 | if ((bq = bam_aux_get(b, "BQ")) != 0) ++bq; | ^~~~~~~~~~~~~~~~~~~~ razf.c: In function ‘razf_flush’: razf.c:221:17: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 221 | write(rz->x.fpw, rz->outbuf, RZ_BUFFER_SIZE - rz->stream->avail_out); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ razf.c:234:25: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 234 | write(rz->x.fpw, rz->outbuf, RZ_BUFFER_SIZE - rz->stream->avail_out); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ razf.c: In function ‘_razf_write’: razf.c:201:17: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 201 | write(rz->x.fpw, rz->outbuf, RZ_BUFFER_SIZE - rz->stream->avail_out); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ razf.c: In function ‘razf_close’: razf.c:804:25: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 804 | write(rz->x.fpw, &rz->in, sizeof(int64_t)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ razf.c:805:25: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 805 | write(rz->x.fpw, &rz->out, sizeof(int64_t)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ razf.c:808:25: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 808 | write(rz->x.fpw, &v64, sizeof(int64_t)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ razf.c:810:25: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 810 | write(rz->x.fpw, &v64, sizeof(int64_t)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ razf.c: In function ‘razf_end_flush’: razf.c:258:25: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 258 | write(rz->x.fpw, rz->outbuf, RZ_BUFFER_SIZE - rz->stream->avail_out); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ razf.c: In function ‘save_zindex’: razf.c:96:19: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 96 | if(is_be) write(fd, &rz->index->size, sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ razf.c:99:17: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 99 | write(fd, &v32, sizeof(uint32_t)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ razf.c:106:9: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 106 | write(fd, rz->index->bin_offsets, sizeof(int64_t) * v32); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ razf.c:107:9: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 107 | write(fd, rz->index->cell_offsets, sizeof(int32_t) * rz->index->size); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -c -g -O2 -ffile-prefix-map=/build/samtools-legacy-JbU72u/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bamshuf.c -o bamshuf.o gcc -c -g -O2 -ffile-prefix-map=/build/samtools-legacy-JbU72u/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. faidx.c -o faidx.o gcc -c -g -O2 -ffile-prefix-map=/build/samtools-legacy-JbU72u/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bedidx.c -o bedidx.o gcc -c -g -O2 -ffile-prefix-map=/build/samtools-legacy-JbU72u/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. knetfile.c -o knetfile.o gcc -c -g -O2 -ffile-prefix-map=/build/samtools-legacy-JbU72u/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_sort.c -o bam_sort.o gcc -c -g -O2 -ffile-prefix-map=/build/samtools-legacy-JbU72u/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_header.c -o sam_header.o In file included from knetfile.c:46: knetfile.c: In function ‘kftp_send_cmd’: knetfile.h:9:32: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 9 | #define netwrite(fd, ptr, len) write(fd, ptr, len) | ^~~~~~~~~~~~~~~~~~~ knetfile.c:236:9: note: in expansion of macro ‘netwrite’ 236 | netwrite(ftp->ctrl_fd, cmd, strlen(cmd)); | ^~~~~~~~ knetfile.c: In function ‘khttp_connect_file’: knetfile.h:9:32: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 9 | #define netwrite(fd, ptr, len) write(fd, ptr, len) | ^~~~~~~~~~~~~~~~~~~ knetfile.c:415:9: note: in expansion of macro ‘netwrite’ 415 | netwrite(fp->fd, buf, l); | ^~~~~~~~ gcc -c -g -O2 -ffile-prefix-map=/build/samtools-legacy-JbU72u/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview_curses.c -o bam_tview_curses.o gcc -c -g -O2 -ffile-prefix-map=/build/samtools-legacy-JbU72u/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_reheader.c -o bam_reheader.o gcc -c -g -O2 -ffile-prefix-map=/build/samtools-legacy-JbU72u/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview_html.c -o bam_tview_html.o make[3]: Entering directory '/build/samtools-legacy-JbU72u/samtools-legacy-0.1.19+dfsg' gcc -c -g -O2 -ffile-prefix-map=/build/samtools-legacy-JbU72u/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kprobaln.c -o kprobaln.o make[4]: Entering directory '/build/samtools-legacy-JbU72u/samtools-legacy-0.1.19+dfsg' gcc -c -g -O2 -ffile-prefix-map=/build/samtools-legacy-JbU72u/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_index.c -o bam_index.o gcc -c -g -O2 -ffile-prefix-map=/build/samtools-legacy-JbU72u/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_cat.c -o bam_cat.o gcc -c -g -O2 -ffile-prefix-map=/build/samtools-legacy-JbU72u/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. phase.c -o phase.o bam_index.c: In function ‘bam_index_core’: bam_index.c:178:42: warning: overflow in conversion from ‘uint32_t’ {aka ‘unsigned int’} to ‘int32_t’ {aka ‘int’} changes value from ‘last_bin = 4294967295’ to ‘-1’ [-Woverflow] 178 | save_bin = save_tid = last_tid = last_bin = 0xffffffffu; | ^~~~~~~~ bam_index.c: In function ‘bam_index_load_core’: bam_index.c:335:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 335 | fread(magic, 1, 4, fp); | ^~~~~~~~~~~~~~~~~~~~~~ bam_index.c:342:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 342 | fread(&idx->n, 4, 1, fp); | ^~~~~~~~~~~~~~~~~~~~~~~~ bam_index.c:355:17: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 355 | fread(&size, 4, 1, fp); | ^~~~~~~~~~~~~~~~~~~~~~ bam_index.c:358:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 358 | fread(&key, 4, 1, fp); | ^~~~~~~~~~~~~~~~~~~~~ bam_index.c:362:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 362 | fread(&p->n, 4, 1, fp); | ^~~~~~~~~~~~~~~~~~~~~~ bam_index.c:366:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 366 | fread(p->list, 16, p->n, fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ bam_index.c:376:17: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 376 | fread(&index2->n, 4, 1, fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ bam_index.c:380:17: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 380 | fread(index2->offset, index2->n, 8, fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -c -g -O2 -ffile-prefix-map=/build/samtools-legacy-JbU72u/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview_html.c -o bam_tview_html.o gcc -c -g -O2 -ffile-prefix-map=/build/samtools-legacy-JbU72u/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razip.c -o razip.o gcc -c -g -O2 -ffile-prefix-map=/build/samtools-legacy-JbU72u/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_sort.c -o bam_sort.o razip.c: In function ‘main’: razip.c:131:33: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 131 | write(f_dst, buffer, c); | ^~~~~~~~~~~~~~~~~~~~~~~ razip.c: In function ‘write_open’: razip.c:32:25: warning: ignoring return value of ‘scanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 32 | scanf("%c", &c); | ^~~~~~~~~~~~~~~ gcc -c -g -O2 -ffile-prefix-map=/build/samtools-legacy-JbU72u/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_header.c -o sam_header.o gcc -c -g -O2 -ffile-prefix-map=/build/samtools-legacy-JbU72u/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kprobaln.c -o kprobaln.o gcc -c -g -O2 -ffile-prefix-map=/build/samtools-legacy-JbU72u/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bedidx.c -o bedidx.o gcc -g -O2 -ffile-prefix-map=/build/samtools-legacy-JbU72u/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -o razip razip.o razf.o knetfile.o -lz gcc -c -g -O2 -ffile-prefix-map=/build/samtools-legacy-JbU72u/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_sort.c -o bam_sort.o gcc -c -g -O2 -ffile-prefix-map=/build/samtools-legacy-JbU72u/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kprobaln.c -o kprobaln.o ar -csru libbam.a bgzf.o kstring.o bam_aux.o bam.o bam_import.o sam.o bam_index.o bam_pileup.o bam_lpileup.o bam_md.o razf.o faidx.o bedidx.o knetfile.o bam_sort.o sam_header.o bam_reheader.o kprobaln.o bam_cat.o ar: `u' modifier ignored since `D' is the default (see `U') ar -csru libbam.a bgzf.o kstring.o bam_aux.o bam.o bam_import.o sam.o bam_index.o bam_pileup.o bam_lpileup.o bam_md.o razf.o faidx.o bedidx.o knetfile.o bam_sort.o sam_header.o bam_reheader.o kprobaln.o bam_cat.o ar: `u' modifier ignored since `D' is the default (see `U') make[4]: Leaving directory '/build/samtools-legacy-JbU72u/samtools-legacy-0.1.19+dfsg' make[4]: Entering directory '/build/samtools-legacy-JbU72u/samtools-legacy-0.1.19+dfsg/bcftools' gcc -c -g -O2 -ffile-prefix-map=/build/samtools-legacy-JbU72u/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf.c -o bcf.o gcc -c -g -O2 -ffile-prefix-map=/build/samtools-legacy-JbU72u/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. vcf.c -o vcf.o gcc -c -g -O2 -ffile-prefix-map=/build/samtools-legacy-JbU72u/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcfutils.c -o bcfutils.o gcc -c -g -O2 -ffile-prefix-map=/build/samtools-legacy-JbU72u/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. prob1.c -o prob1.o gcc -c -g -O2 -ffile-prefix-map=/build/samtools-legacy-JbU72u/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. em.c -o em.o gcc -c -g -O2 -ffile-prefix-map=/build/samtools-legacy-JbU72u/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. kfunc.c -o kfunc.o gcc -c -g -O2 -ffile-prefix-map=/build/samtools-legacy-JbU72u/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. kmin.c -o kmin.o gcc -c -g -O2 -ffile-prefix-map=/build/samtools-legacy-JbU72u/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. index.c -o index.o gcc -c -g -O2 -ffile-prefix-map=/build/samtools-legacy-JbU72u/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. fet.c -o fet.o gcc -c -g -O2 -ffile-prefix-map=/build/samtools-legacy-JbU72u/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. mut.c -o mut.o gcc -c -g -O2 -ffile-prefix-map=/build/samtools-legacy-JbU72u/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf2qcall.c -o bcf2qcall.o ar -csru libbam.a bgzf.o kstring.o bam_aux.o bam.o bam_import.o sam.o bam_index.o bam_pileup.o bam_lpileup.o bam_md.o razf.o faidx.o bedidx.o knetfile.o bam_sort.o sam_header.o bam_reheader.o kprobaln.o bam_cat.o ar: `u' modifier ignored since `D' is the default (see `U') make[3]: Leaving directory '/build/samtools-legacy-JbU72u/samtools-legacy-0.1.19+dfsg' make[3]: Entering directory '/build/samtools-legacy-JbU72u/samtools-legacy-0.1.19+dfsg/bcftools' gcc -c -g -O2 -ffile-prefix-map=/build/samtools-legacy-JbU72u/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf.c -o bcf.o gcc -c -g -O2 -ffile-prefix-map=/build/samtools-legacy-JbU72u/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. vcf.c -o vcf.o gcc -c -g -O2 -ffile-prefix-map=/build/samtools-legacy-JbU72u/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcfutils.c -o bcfutils.o gcc -c -g -O2 -ffile-prefix-map=/build/samtools-legacy-JbU72u/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. prob1.c -o prob1.o gcc -c -g -O2 -ffile-prefix-map=/build/samtools-legacy-JbU72u/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. em.c -o em.o gcc -c -g -O2 -ffile-prefix-map=/build/samtools-legacy-JbU72u/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf2qcall.c -o bcf2qcall.o ar -csru libbcf.a bcf.o vcf.o bcfutils.o prob1.o em.o kfunc.o kmin.o index.o fet.o mut.o bcf2qcall.o ar: `u' modifier ignored since `D' is the default (see `U') make[4]: Leaving directory '/build/samtools-legacy-JbU72u/samtools-legacy-0.1.19+dfsg/bcftools' make[4]: Entering directory '/build/samtools-legacy-JbU72u/samtools-legacy-0.1.19+dfsg/misc' make[4]: Nothing to be done for 'lib'. make[4]: Leaving directory '/build/samtools-legacy-JbU72u/samtools-legacy-0.1.19+dfsg/misc' gcc -g -O2 -ffile-prefix-map=/build/samtools-legacy-JbU72u/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -o samtools bam_tview.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o padding.o bedcov.o bamshuf.o bam_tview_curses.o bam_tview_html.o -Wl,-z,relro libbam.a -Lbcftools -lbcf -lcurses -lm -lz -lpthread make[3]: Leaving directory '/build/samtools-legacy-JbU72u/samtools-legacy-0.1.19+dfsg' make[3]: Entering directory '/build/samtools-legacy-JbU72u/samtools-legacy-0.1.19+dfsg/bcftools' gcc -c -g -O2 -ffile-prefix-map=/build/samtools-legacy-JbU72u/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. call1.c -o call1.o gcc -c -g -O2 -ffile-prefix-map=/build/samtools-legacy-JbU72u/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. main.c -o main.o ar -csru libbcf.a bcf.o vcf.o bcfutils.o prob1.o em.o kfunc.o kmin.o index.o fet.o mut.o bcf2qcall.o ar: `u' modifier ignored since `D' is the default (see `U') make[3]: Leaving directory '/build/samtools-legacy-JbU72u/samtools-legacy-0.1.19+dfsg/bcftools' make[3]: Entering directory '/build/samtools-legacy-JbU72u/samtools-legacy-0.1.19+dfsg/misc' make[3]: Nothing to be done for 'lib'. make[3]: Leaving directory '/build/samtools-legacy-JbU72u/samtools-legacy-0.1.19+dfsg/misc' gcc -g -O2 -ffile-prefix-map=/build/samtools-legacy-JbU72u/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -o samtools bam_tview.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o padding.o bedcov.o bamshuf.o bam_tview_curses.o bam_tview_html.o -Wl,-z,relro libbam.a -Lbcftools -lbcf -lcurses -lm -lz -lpthread gcc -g -O2 -ffile-prefix-map=/build/samtools-legacy-JbU72u/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -o bcftools call1.o main.o ../kstring.o ../bgzf.o ../knetfile.o ../bedidx.o -L. -lbcf -lm -lz -lpthread make[3]: Leaving directory '/build/samtools-legacy-JbU72u/samtools-legacy-0.1.19+dfsg/bcftools' make[3]: Entering directory '/build/samtools-legacy-JbU72u/samtools-legacy-0.1.19+dfsg/misc' gcc -c -g -O2 -ffile-prefix-map=/build/samtools-legacy-JbU72u/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -DMD5SUM_MAIN -o md5sum-lite.o md5.c gcc -c -g -O2 -ffile-prefix-map=/build/samtools-legacy-JbU72u/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. md5.c -o md5.o gcc -g -O2 -ffile-prefix-map=/build/samtools-legacy-JbU72u/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -c -I.. -o md5fa.o md5fa.c gcc -g -O2 -ffile-prefix-map=/build/samtools-legacy-JbU72u/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -o maq2sam-short maq2sam.c -lz gcc -g -O2 -ffile-prefix-map=/build/samtools-legacy-JbU72u/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -DMAQ_LONGREADS -o maq2sam-long maq2sam.c -lz gcc -g -O2 -ffile-prefix-map=/build/samtools-legacy-JbU72u/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -c -I.. -o ace2sam.o ace2sam.c gcc -g -O2 -ffile-prefix-map=/build/samtools-legacy-JbU72u/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -c -I.. -o wgsim.o wgsim.c gcc -g -O2 -ffile-prefix-map=/build/samtools-legacy-JbU72u/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -c -I.. -o bamcheck.o bamcheck.c gcc -g -O2 -ffile-prefix-map=/build/samtools-legacy-JbU72u/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -o md5fa md5.o md5fa.o -lz gcc -g -O2 -ffile-prefix-map=/build/samtools-legacy-JbU72u/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -o md5sum-lite md5sum-lite.o gcc -g -O2 -ffile-prefix-map=/build/samtools-legacy-JbU72u/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -o wgsim wgsim.o -lm -lz gcc -g -O2 -ffile-prefix-map=/build/samtools-legacy-JbU72u/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -o ace2sam ace2sam.o -lz gcc -g -O2 -ffile-prefix-map=/build/samtools-legacy-JbU72u/samtools-legacy-0.1.19+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -o bamcheck bamcheck.o -L.. -lm -lbam -lpthread -lz make[3]: Leaving directory '/build/samtools-legacy-JbU72u/samtools-legacy-0.1.19+dfsg/misc' make[2]: Leaving directory '/build/samtools-legacy-JbU72u/samtools-legacy-0.1.19+dfsg' make[1]: Leaving directory '/build/samtools-legacy-JbU72u/samtools-legacy-0.1.19+dfsg' create-stamp debian/debhelper-build-stamp dh_prep -a dh_auto_install --destdir=debian/libbam-dev/ -a dh_install -a dh_installdocs -a debian/rules override_dh_installchangelogs make[1]: Entering directory '/build/samtools-legacy-JbU72u/samtools-legacy-0.1.19+dfsg' dh_installchangelogs NEWS make[1]: Leaving directory '/build/samtools-legacy-JbU72u/samtools-legacy-0.1.19+dfsg' dh_perl -a dh_link -a dh_strip_nondeterminism -a dh_compress -a dh_fixperms -a dh_missing -a dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dh_installdeb -a dh_gencontrol -a dpkg-gencontrol: warning: Depends field of package libbam-dev: substitution variable ${shlibs:Depends} used, but is not defined dh_md5sums -a dh_builddeb -a dpkg-deb: building package 'libbam-dev' in '../libbam-dev_0.1.19+dfsg-5_amd64.deb'. dpkg-genbuildinfo --build=any -O../samtools-legacy_0.1.19+dfsg-5_amd64.buildinfo dpkg-genchanges --build=any -O../samtools-legacy_0.1.19+dfsg-5_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/samtools-legacy-JbU72u /tmp/samtools-legacy-0.1.19+dfsg-5bfk_0k01 I: cleaning package lists and apt cache... I: removing tempdir /tmp/mmdebstrap.TNhlQOx_HQ... I: success in 295.6341 seconds md5: libbam-dev_0.1.19+dfsg-5_amd64.deb: OK sha1: libbam-dev_0.1.19+dfsg-5_amd64.deb: OK sha256: libbam-dev_0.1.19+dfsg-5_amd64.deb: OK Checksums: OK