Input buildinfo: https://buildinfos.debian.net/buildinfo-pool/b/bwa/bwa_0.7.17-7_amd64.buildinfo Use metasnap for getting required timestamps New buildinfo file: /tmp/bwa-0.7.17-7xffrlnk2/bwa_0.7.17-7_amd64.buildinfo Get source package info: bwa=0.7.17-7 Source URL: http://snapshot.notset.fr/mr/package/bwa/0.7.17-7/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=20220109.1 base-files=12.2 base-passwd=3.5.52 bash=5.1-6 binutils=2.38-2 binutils-common=2.38-2 binutils-x86-64-linux-gnu=2.38-2 bsdextrautils=2.37.3-1+b1 bsdutils=1:2.37.3-1+b1 build-essential=12.9 bzip2=1.0.8-5 coreutils=8.32-4.1 cpp=4:11.2.0-2 cpp-11=11.2.0-18 dash=0.5.11+git20210903+057cd650a4ed-3 debconf=1.5.79 debhelper=13.6 debianutils=5.7-0.1 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=4.9.0-2 g++=4:11.2.0-2 g++-11=11.2.0-18 gcc=4:11.2.0-2 gcc-11=11.2.0-18 gcc-11-base=11.2.0-18 gcc-12-base=12-20220302-1 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=1.62 intltool-debian=0.35.0+20060710.5 libacl1=2.3.1-1 libarchive-zip-perl=1.68-1 libasan6=11.2.0-18 libatomic1=12-20220302-1 libattr1=1:2.5.1-1 libaudit-common=1:3.0.7-1 libaudit1=1:3.0.7-1 libbinutils=2.38-2 libblkid1=2.37.3-1+b1 libbz2-1.0=1.0.8-5 libc-bin=2.33-7 libc-dev-bin=2.33-7 libc6=2.33-7 libc6-dev=2.33-7 libcap-ng0=0.7.9-2.2+b1 libcap2=1:2.44-1 libcc1-0=12-20220302-1 libcom-err2=1.46.5-2 libcrypt-dev=1:4.4.27-1.1 libcrypt1=1:4.4.27-1.1 libctf-nobfd0=2.38-2 libctf0=2.38-2 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=11.2.0-18 libgcc-s1=12-20220302-1 libgcrypt20=1.9.4-5 libgdbm-compat4=1.23-1 libgdbm6=1.23-1 libgmp10=2:6.2.1+dfsg-3 libgomp1=12-20220302-1 libgpg-error0=1.43-3 libgssapi-krb5-2=1.19.2-2 libicu67=67.1-7 libisl23=0.24-2 libitm1=12-20220302-1 libk5crypto3=1.19.2-2 libkeyutils1=1.6.1-2 libkrb5-3=1.19.2-2 libkrb5support0=1.19.2-2 liblsan0=12-20220302-1 liblz4-1=1.9.3-2 liblzma5=5.2.5-2 libmagic-mgc=1:5.41-2 libmagic1=1:5.41-2 libmount1=2.37.3-1+b1 libmpc3=1.2.1-1 libmpfr6=4.1.0-3 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 libperl5.34=5.34.0-3 libpipeline1=1.5.5-1 libquadmath0=12-20220302-1 libseccomp2=2.5.3-2 libselinux1=3.3-1+b1 libsigsegv2=2.14-1 libsimde-dev=0.7.2-6 libsmartcols1=2.37.3-1+b1 libssl1.1=1.1.1m-1 libstdc++-11-dev=11.2.0-18 libstdc++6=12-20220302-1 libsub-override-perl=0.09-2 libsystemd0=250.3-2 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=11.2.0-18 libubsan1=12-20220302-1 libuchardet0=0.0.7-1 libudev1=250.3-2 libunistring2=1.0-1 libuuid1=2.37.3-1+b1 libxml2=2.9.13+dfsg-1 libzstd1=1.4.8+dfsg-3 linux-libc-dev=5.16.11-1 login=1:4.11.1+dfsg1-1 lsb-base=11.1.0 m4=1.4.18-5 make=4.3-4.1 man-db=2.10.1-1 mawk=1.3.4.20200120-3+b1 ncurses-base=6.3-2 ncurses-bin=6.3-2 patch=2.7.6-7 perl=5.34.0-3 perl-base=5.34.0-3 perl-modules-5.34=5.34.0-3 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=2.37.3-1+b1 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/20220310T035035Z/ bookworm main deb-src http://snapshot.notset.fr/archive/debian/20220310T035035Z/ bookworm main deb http://snapshot.notset.fr/archive/debian/20220303T211415Z/ 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 bwa=0.7.17-7 && mkdir -p /build/bwa-0Zrahe && dpkg-source --no-check -x /*.dsc /build/bwa-0Zrahe/bwa-0.7.17 && chown -R builduser:builduser /build/bwa-0Zrahe" --customize-hook=chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/bwa-0Zrahe/bwa-0.7.17 && env DEB_BUILD_OPTIONS="parallel=4" LC_ALL="C.UTF-8" LC_COLLATE="C.UTF-8" SOURCE_DATE_EPOCH="1646599407" DEB_BUILD_OPTIONS=nocheck dpkg-buildpackage -uc -a amd64 --build=any" --customize-hook=sync-out /build/bwa-0Zrahe /tmp/bwa-0.7.17-7xffrlnk2 bookworm /dev/null deb http://snapshot.notset.fr/archive/debian/20220303T211415Z 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.ZWOY7NWrne 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.ZWOY7NWrne Reading package lists... Building dependency tree... util-linux is already the newest version (2.37.3-1+b1). The following NEW packages will be installed: fakeroot libfakeroot 0 upgraded, 2 newly installed, 0 to remove and 0 not upgraded. Need to get 136 kB of archives. After this operation, 406 kB of additional disk space will be used. Get:1 http://snapshot.notset.fr/archive/debian/20220303T211415Z unstable/main amd64 libfakeroot amd64 1.27-1 [48.5 kB] Get:2 http://snapshot.notset.fr/archive/debian/20220303T211415Z unstable/main amd64 fakeroot amd64 1.27-1 [87.2 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 136 kB in 0s (991 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 ... 4693 files and directories currently installed.) Preparing to unpack .../libfakeroot_1.27-1_amd64.deb ... Unpacking libfakeroot:amd64 (1.27-1) ... Selecting previously unselected package fakeroot. Preparing to unpack .../fakeroot_1.27-1_amd64.deb ... Unpacking fakeroot (1.27-1) ... Setting up libfakeroot:amd64 (1.27-1) ... Setting up fakeroot (1.27-1) ... update-alternatives: using /usr/bin/fakeroot-sysv to provide /usr/bin/fakeroot (fakeroot) in auto mode Processing triggers for libc-bin (2.33-7) ... 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/20220310T035035Z/ bookworm main deb-src http://snapshot.notset.fr/archive/debian/20220310T035035Z/ bookworm main deb http://snapshot.notset.fr/archive/debian/20220303T211415Z/ unstable main' >> /etc/apt/sources.list && apt-get update"' exec /tmp/mmdebstrap.ZWOY7NWrne Get:1 http://snapshot.notset.fr/archive/debian/20220310T035035Z bookworm InRelease [130 kB] Hit:2 http://snapshot.notset.fr/archive/debian/20220303T211415Z unstable InRelease Ign:3 http://snapshot.notset.fr/archive/debian/20220310T035035Z bookworm/main Sources Ign:4 http://snapshot.notset.fr/archive/debian/20220310T035035Z bookworm/main amd64 Packages Ign:3 http://snapshot.notset.fr/archive/debian/20220310T035035Z bookworm/main Sources Ign:4 http://snapshot.notset.fr/archive/debian/20220310T035035Z bookworm/main amd64 Packages Ign:3 http://snapshot.notset.fr/archive/debian/20220310T035035Z bookworm/main Sources Ign:4 http://snapshot.notset.fr/archive/debian/20220310T035035Z bookworm/main amd64 Packages Get:3 http://snapshot.notset.fr/archive/debian/20220310T035035Z bookworm/main Sources [11.9 MB] Get:4 http://snapshot.notset.fr/archive/debian/20220310T035035Z bookworm/main amd64 Packages [11.3 MB] Fetched 23.4 MB in 20s (1161 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.ZWOY7NWrne I: running --customize-hook in shell: sh -c 'chroot "$1" env sh -c "apt-get source --only-source -d bwa=0.7.17-7 && mkdir -p /build/bwa-0Zrahe && dpkg-source --no-check -x /*.dsc /build/bwa-0Zrahe/bwa-0.7.17 && chown -R builduser:builduser /build/bwa-0Zrahe"' exec /tmp/mmdebstrap.ZWOY7NWrne Reading package lists... NOTICE: 'bwa' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/bwa.git Please use: git clone https://salsa.debian.org/med-team/bwa.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 245 kB of source archives. Get:1 http://snapshot.notset.fr/archive/debian/20220310T035035Z bookworm/main bwa 0.7.17-7 (dsc) [2116 B] Get:2 http://snapshot.notset.fr/archive/debian/20220310T035035Z bookworm/main bwa 0.7.17-7 (tar) [233 kB] Get:3 http://snapshot.notset.fr/archive/debian/20220310T035035Z bookworm/main bwa 0.7.17-7 (diff) [10.7 kB] Fetched 245 kB in 0s (823 kB/s) Download complete and in download only mode W: Download is performed unsandboxed as root as file 'bwa_0.7.17-7.dsc' couldn't be accessed by user '_apt'. - pkgAcquire::Run (13: Permission denied) dpkg-source: info: extracting bwa in /build/bwa-0Zrahe/bwa-0.7.17 dpkg-source: info: unpacking bwa_0.7.17.orig.tar.gz dpkg-source: info: unpacking bwa_0.7.17-7.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying fix_heap_block_overrun dpkg-source: info: applying fix_build_on_freebsd.patch dpkg-source: info: applying CVE-2019-10269.patch dpkg-source: info: applying simde dpkg-source: info: applying spelling dpkg-source: info: applying gcc10.patch dpkg-source: info: applying hurd I: running --customize-hook in shell: sh -c 'chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/bwa-0Zrahe/bwa-0.7.17 && env DEB_BUILD_OPTIONS="parallel=4" LC_ALL="C.UTF-8" LC_COLLATE="C.UTF-8" SOURCE_DATE_EPOCH="1646599407" DEB_BUILD_OPTIONS=nocheck dpkg-buildpackage -uc -a amd64 --build=any"' exec /tmp/mmdebstrap.ZWOY7NWrne dpkg-buildpackage: info: source package bwa dpkg-buildpackage: info: source version 0.7.17-7 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Pierre Gruet 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/bwa-0Zrahe/bwa-0.7.17' rm -f gmon.out *.o a.out bwa *~ *.a make[1]: Leaving directory '/build/bwa-0Zrahe/bwa-0.7.17' 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/bwa-0Zrahe/bwa-0.7.17' dh_auto_build -- CFLAGS="-Wall -g -O2 -ffile-prefix-map=/build/bwa-0Zrahe/bwa-0.7.17=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now" DFLAGS="-DHAVE_PTHREAD" make -j10 "INSTALL=install --strip-program=true" "CFLAGS=-Wall -g -O2 -ffile-prefix-map=/build/bwa-0Zrahe/bwa-0.7.17=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now" DFLAGS=-DHAVE_PTHREAD make[2]: Entering directory '/build/bwa-0Zrahe/bwa-0.7.17' gcc -c -Wall -g -O2 -ffile-prefix-map=/build/bwa-0Zrahe/bwa-0.7.17=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DHAVE_PTHREAD utils.c -o utils.o gcc -c -Wall -g -O2 -ffile-prefix-map=/build/bwa-0Zrahe/bwa-0.7.17=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DHAVE_PTHREAD kthread.c -o kthread.o gcc -c -Wall -g -O2 -ffile-prefix-map=/build/bwa-0Zrahe/bwa-0.7.17=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DHAVE_PTHREAD kstring.c -o kstring.o gcc -c -Wall -g -O2 -ffile-prefix-map=/build/bwa-0Zrahe/bwa-0.7.17=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DHAVE_PTHREAD ksw.c -o ksw.o gcc -c -Wall -g -O2 -ffile-prefix-map=/build/bwa-0Zrahe/bwa-0.7.17=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DHAVE_PTHREAD bwt.c -o bwt.o gcc -c -Wall -g -O2 -ffile-prefix-map=/build/bwa-0Zrahe/bwa-0.7.17=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DHAVE_PTHREAD bntseq.c -o bntseq.o gcc -c -Wall -g -O2 -ffile-prefix-map=/build/bwa-0Zrahe/bwa-0.7.17=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DHAVE_PTHREAD bwa.c -o bwa.o gcc -c -Wall -g -O2 -ffile-prefix-map=/build/bwa-0Zrahe/bwa-0.7.17=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DHAVE_PTHREAD bwamem.c -o bwamem.o gcc -c -Wall -g -O2 -ffile-prefix-map=/build/bwa-0Zrahe/bwa-0.7.17=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DHAVE_PTHREAD bwamem_pair.c -o bwamem_pair.o gcc -c -Wall -g -O2 -ffile-prefix-map=/build/bwa-0Zrahe/bwa-0.7.17=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DHAVE_PTHREAD bwamem_extra.c -o bwamem_extra.o gcc -c -Wall -g -O2 -ffile-prefix-map=/build/bwa-0Zrahe/bwa-0.7.17=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DHAVE_PTHREAD malloc_wrap.c -o malloc_wrap.o gcc -c -Wall -g -O2 -ffile-prefix-map=/build/bwa-0Zrahe/bwa-0.7.17=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DHAVE_PTHREAD QSufSort.c -o QSufSort.o gcc -c -Wall -g -O2 -ffile-prefix-map=/build/bwa-0Zrahe/bwa-0.7.17=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DHAVE_PTHREAD bwt_gen.c -o bwt_gen.o bwt_gen.c: In function ‘BWTIncBuildRelativeRank’: bwt_gen.c:879:17: warning: variable ‘oldInverseSa0RelativeRank’ set but not used [-Wunused-but-set-variable] 879 | bgint_t oldInverseSa0RelativeRank = 0; | ^~~~~~~~~~~~~~~~~~~~~~~~~ bwt_gen.c: In function ‘BWTIncMergeBwt’: bwt_gen.c:953:22: warning: variable ‘bitsInWordMinusBitPerChar’ set but not used [-Wunused-but-set-variable] 953 | unsigned int bitsInWordMinusBitPerChar; | ^~~~~~~~~~~~~~~~~~~~~~~~~ gcc -c -Wall -g -O2 -ffile-prefix-map=/build/bwa-0Zrahe/bwa-0.7.17=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DHAVE_PTHREAD rope.c -o rope.o rope.c: In function ‘rope_restore_node’: rope.c:282:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 282 | fread(&is_bottom, 1, 1, fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ rope.c:283:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 283 | fread(&n, 2, 1, fp); | ^~~~~~~~~~~~~~~~~~~ rope.c:291:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 291 | fread(p[i].c, 8, 6, fp); | ^~~~~~~~~~~~~~~~~~~~~~~ rope.c:292:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 292 | fread(q, 2, 1, fp); | ^~~~~~~~~~~~~~~~~~ rope.c:293:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 293 | fread(q + 1, 1, *q, fp); | ^~~~~~~~~~~~~~~~~~~~~~~ rope.c: In function ‘rope_restore’: rope.c:312:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 312 | fread(&r->max_nodes, 4, 1, fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ rope.c:313:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 313 | fread(&r->block_len, 4, 1, fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -c -Wall -g -O2 -ffile-prefix-map=/build/bwa-0Zrahe/bwa-0.7.17=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DHAVE_PTHREAD rle.c -o rle.o gcc -c -Wall -g -O2 -ffile-prefix-map=/build/bwa-0Zrahe/bwa-0.7.17=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DHAVE_PTHREAD is.c -o is.o gcc -c -Wall -g -O2 -ffile-prefix-map=/build/bwa-0Zrahe/bwa-0.7.17=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DHAVE_PTHREAD bwtindex.c -o bwtindex.o gcc -c -Wall -g -O2 -ffile-prefix-map=/build/bwa-0Zrahe/bwa-0.7.17=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DHAVE_PTHREAD bwashm.c -o bwashm.o gcc -c -Wall -g -O2 -ffile-prefix-map=/build/bwa-0Zrahe/bwa-0.7.17=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DHAVE_PTHREAD bwase.c -o bwase.o gcc -c -Wall -g -O2 -ffile-prefix-map=/build/bwa-0Zrahe/bwa-0.7.17=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DHAVE_PTHREAD bwaseqio.c -o bwaseqio.o gcc -c -Wall -g -O2 -ffile-prefix-map=/build/bwa-0Zrahe/bwa-0.7.17=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DHAVE_PTHREAD bwtgap.c -o bwtgap.o gcc -c -Wall -g -O2 -ffile-prefix-map=/build/bwa-0Zrahe/bwa-0.7.17=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DHAVE_PTHREAD bwtaln.c -o bwtaln.o bwashm.c: In function ‘bwa_shm_stage’: bwashm.c:33:9: warning: ignoring return value of ‘ftruncate’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 33 | ftruncate(shmid, BWA_CTL_SIZE); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ bwashm.c:70:9: warning: ignoring return value of ‘ftruncate’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 70 | ftruncate(shmid, idx->l_mem); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -c -Wall -g -O2 -ffile-prefix-map=/build/bwa-0Zrahe/bwa-0.7.17=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DHAVE_PTHREAD bamlite.c -o bamlite.o gcc -c -Wall -g -O2 -ffile-prefix-map=/build/bwa-0Zrahe/bwa-0.7.17=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DHAVE_PTHREAD bwape.c -o bwape.o gcc -c -Wall -g -O2 -ffile-prefix-map=/build/bwa-0Zrahe/bwa-0.7.17=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DHAVE_PTHREAD kopen.c -o kopen.o gcc -c -Wall -g -O2 -ffile-prefix-map=/build/bwa-0Zrahe/bwa-0.7.17=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DHAVE_PTHREAD pemerge.c -o pemerge.o gcc -c -Wall -g -O2 -ffile-prefix-map=/build/bwa-0Zrahe/bwa-0.7.17=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DHAVE_PTHREAD maxk.c -o maxk.o gcc -c -Wall -g -O2 -ffile-prefix-map=/build/bwa-0Zrahe/bwa-0.7.17=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DHAVE_PTHREAD bwtsw2_core.c -o bwtsw2_core.o gcc -c -Wall -g -O2 -ffile-prefix-map=/build/bwa-0Zrahe/bwa-0.7.17=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DHAVE_PTHREAD bwtsw2_main.c -o bwtsw2_main.o gcc -c -Wall -g -O2 -ffile-prefix-map=/build/bwa-0Zrahe/bwa-0.7.17=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DHAVE_PTHREAD bwtsw2_aux.c -o bwtsw2_aux.o gcc -c -Wall -g -O2 -ffile-prefix-map=/build/bwa-0Zrahe/bwa-0.7.17=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DHAVE_PTHREAD bwt_lite.c -o bwt_lite.o gcc -c -Wall -g -O2 -ffile-prefix-map=/build/bwa-0Zrahe/bwa-0.7.17=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DHAVE_PTHREAD bwtsw2_chain.c -o bwtsw2_chain.o gcc -c -Wall -g -O2 -ffile-prefix-map=/build/bwa-0Zrahe/bwa-0.7.17=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DHAVE_PTHREAD fastmap.c -o fastmap.o gcc -c -Wall -g -O2 -ffile-prefix-map=/build/bwa-0Zrahe/bwa-0.7.17=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DHAVE_PTHREAD bwtsw2_pair.c -o bwtsw2_pair.o gcc -c -Wall -g -O2 -ffile-prefix-map=/build/bwa-0Zrahe/bwa-0.7.17=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DHAVE_PTHREAD main.c -o main.o ar -csru libbwa.a utils.o kthread.o kstring.o ksw.o bwt.o bntseq.o bwa.o bwamem.o bwamem_pair.o bwamem_extra.o malloc_wrap.o QSufSort.o bwt_gen.o rope.o rle.o is.o bwtindex.o ar: `u' modifier ignored since `D' is the default (see `U') gcc -Wall -g -O2 -ffile-prefix-map=/build/bwa-0Zrahe/bwa-0.7.17=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DHAVE_PTHREAD bwashm.o bwase.o bwaseqio.o bwtgap.o bwtaln.o bamlite.o bwape.o kopen.o pemerge.o maxk.o bwtsw2_core.o bwtsw2_main.o bwtsw2_aux.o bwt_lite.o bwtsw2_chain.o fastmap.o bwtsw2_pair.o main.o -o bwa -L. -lbwa -lm -lz -lpthread -lrt make[2]: Leaving directory '/build/bwa-0Zrahe/bwa-0.7.17' make[1]: Leaving directory '/build/bwa-0Zrahe/bwa-0.7.17' dh: command-omitted: The call to "dh_auto_test -a" was omitted due to "DEB_BUILD_OPTIONS=nocheck" create-stamp debian/debhelper-build-stamp dh_prep -a dh_auto_install -a debian/rules override_dh_install make[1]: Entering directory '/build/bwa-0Zrahe/bwa-0.7.17' dh_install for pl in `grep -Rl '#!/usr/bin/env[[:space:]]\+perl' debian/*/usr/*` ; do \ sed -i '1s?^#!/usr/bin/env[[:space:]]\+perl?#!/usr/bin/perl?' ${pl} ; \ done make[1]: Leaving directory '/build/bwa-0Zrahe/bwa-0.7.17' dh_installdocs -a debian/rules override_dh_installchangelogs make[1]: Entering directory '/build/bwa-0Zrahe/bwa-0.7.17' dh_installchangelogs NEWS.md make[1]: Leaving directory '/build/bwa-0Zrahe/bwa-0.7.17' dh_installexamples -a dh_installman -a 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 debian/rules override_dh_gencontrol make[1]: Entering directory '/build/bwa-0Zrahe/bwa-0.7.17' dh_gencontrol -- -Vsimde:Built-Using="simde (= 0.7.2-6), " dpkg-gencontrol: warning: package bwa: substitution variable ${perl:Depends} unused, but is defined dpkg-gencontrol: warning: package bwa: substitution variable ${perl:Depends} unused, but is defined make[1]: Leaving directory '/build/bwa-0Zrahe/bwa-0.7.17' dh_md5sums -a dh_builddeb -a dpkg-deb: building package 'bwa-dbgsym' in '../bwa-dbgsym_0.7.17-7_amd64.deb'. dpkg-deb: building package 'bwa' in '../bwa_0.7.17-7_amd64.deb'. dpkg-deb: building package 'libbwa-dev' in '../libbwa-dev_0.7.17-7_amd64.deb'. dpkg-genbuildinfo --build=any -O../bwa_0.7.17-7_amd64.buildinfo dpkg-genchanges --build=any -O../bwa_0.7.17-7_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/bwa-0Zrahe /tmp/bwa-0.7.17-7xffrlnk2 I: cleaning package lists and apt cache... I: removing tempdir /tmp/mmdebstrap.ZWOY7NWrne... I: success in 323.1469 seconds md5: bwa-dbgsym_0.7.17-7_amd64.deb: OK md5: bwa_0.7.17-7_amd64.deb: OK md5: libbwa-dev_0.7.17-7_amd64.deb: OK sha1: bwa-dbgsym_0.7.17-7_amd64.deb: OK sha1: bwa_0.7.17-7_amd64.deb: OK sha1: libbwa-dev_0.7.17-7_amd64.deb: OK sha256: bwa-dbgsym_0.7.17-7_amd64.deb: OK sha256: bwa_0.7.17-7_amd64.deb: OK sha256: libbwa-dev_0.7.17-7_amd64.deb: OK Checksums: OK