Input buildinfo: https://buildinfos.debian.net/buildinfo-pool/s/samtools/samtools_1.13-4_all.buildinfo Use metasnap for getting required timestamps New buildinfo file: /tmp/samtools-1.13-4odivnhoy/samtools_1.13-4_all.buildinfo Get source package info: samtools=1.13-4 Source URL: http://snapshot.notset.fr/mr/package/samtools/1.13-4/srcfiles?fileinfo=1 env -i PATH=/usr/sbin:/usr/bin:/sbin:/bin TMPDIR=/tmp mmdebstrap --arch=amd64 --include=autoconf=2.71-2 autoconf-archive=20210219-2 automake=1:1.16.5-1 autopoint=0.21-4 autotools-dev=20180224.1+nmu1 base-files=12 base-passwd=3.5.52 bash=5.1-3+b2 bash-completion=1:2.11-4 binutils=2.37-7 binutils-common=2.37-7 binutils-x86-64-linux-gnu=2.37-7 bsdextrautils=2.37.2-4 bsdutils=1:2.37.2-4 build-essential=12.9 bzip2=1.0.8-4 coreutils=8.32-4+b1 cpp=4:11.2.0-2 cpp-11=11.2.0-10 dash=0.5.11+git20210120+802ebd4-2 debconf=1.5.78 debhelper=13.5.2 debianutils=5.5-1 dh-autoreconf=20 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=1:5.39-3 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=2.37-7 libblkid1=2.37.2-4 libbrotli1=1.0.9-2+b2 libbz2-1.0=1.0.8-4 libbz2-dev=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=1:4.4.25-2 libcrypt1=1:4.4.25-2 libctf-nobfd0=2.37-7 libctf0=2.37-7 libcurl3-gnutls=7.74.0-1.3+b1 libcurl4-gnutls-dev=7.74.0-1.3+b1 libdb5.3=5.3.28+dfsg1-0.8 libdebconfclient0=0.260 libdebhelper-perl=13.5.2 libdeflate-dev=1.8-1 libdeflate0=1.8-1 libdpkg-perl=1.20.9 libelf1=0.185-2 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 libglib2.0-0=2.70.0-3 libgmp10=2:6.2.1+dfsg-2 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 libio-pty-perl=1:1.15-2 libisl23=0.24-2 libitm1=11.2.0-10 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=1:5.39-3 libmagic1=1:5.39-3 libmount1=2.37.2-4 libmpc3=1.2.1-1 libmpfr6=4.1.0-3 libncurses-dev=6.2+20210905-1 libncurses5-dev=6.2+20210905-1 libncurses6=6.2+20210905-1 libncursesw6=6.2+20210905-1 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=10.36-2 libpcre3=2:8.39-13 libperl5.32=5.32.1-6 libpipeline1=1.5.3-1 libpsl5=0.21.0-1.2 libquadmath0=11.2.0-10 librtmp1=2.4+20151223.gitfa8646d.1-2+b2 libsasl2-2=2.1.27+dfsg-2.1 libsasl2-modules-db=2.1.27+dfsg-2.1 libseccomp2=2.5.2-2 libselinux1=3.1-3 libsigsegv2=2.13-1 libsmartcols1=2.37.2-4 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=249.5-1 libtasn1-6=4.17.0-2 libtinfo6=6.2+20210905-1 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=249.5-1 libunistring2=0.9.10-6 libuuid1=2.37.2-4 libxml2=2.9.12+dfsg-5 libzstd1=1.4.8+dfsg-3 linux-libc-dev=5.14.12-1 login=1:4.8.1-1 lsb-base=11.1.0 m4=1.4.18-5 make=4.3-4.1 man-db=2.9.4-2 mawk=1.3.4.20200120-2 ncurses-base=6.2+20210905-1 ncurses-bin=6.2+20210905-1 patch=2.7.6-7 perl=5.32.1-6 perl-base=5.32.1-6 perl-modules-5.32=5.32.1-6 pkg-config=0.29.2-1 po-debconf=1.0.21+nmu1 rpcsvc-proto=1.4.2-4 sed=4.8-1 sensible-utils=0.0.17 sysvinit-utils=3.00-1 tabix=1.13+ds-2 tar=1.34+dfsg-1 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/20211028T024824Z/ bookworm main deb-src http://snapshot.notset.fr/archive/debian/20211028T024824Z/ bookworm main deb http://snapshot.notset.fr/archive/debian/20211029T100155Z/ 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=1.13-4 && mkdir -p /build/samtools-UH0uh9 && dpkg-source --no-check -x /*.dsc /build/samtools-UH0uh9/samtools-1.13 && chown -R builduser:builduser /build/samtools-UH0uh9" --customize-hook=chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/samtools-UH0uh9/samtools-1.13 && env DEB_BUILD_OPTIONS="parallel=4" LC_ALL="C.UTF-8" LC_COLLATE="C.UTF-8" SOURCE_DATE_EPOCH="1635187983" DEB_BUILD_OPTIONS=nocheck dpkg-buildpackage -uc -a amd64 --build=all" --customize-hook=sync-out /build/samtools-UH0uh9 /tmp/samtools-1.13-4odivnhoy bookworm /dev/null deb http://snapshot.notset.fr/archive/debian/20211029T100155Z 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.38rphaW5EX 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.38rphaW5EX 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/20211029T100155Z unstable/main amd64 libfakeroot amd64 1.26-1 [47.3 kB] Get:2 http://snapshot.notset.fr/archive/debian/20211029T100155Z 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 (1038 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 ... 4665 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/20211028T024824Z/ bookworm main deb-src http://snapshot.notset.fr/archive/debian/20211028T024824Z/ bookworm main deb http://snapshot.notset.fr/archive/debian/20211029T100155Z/ unstable main' >> /etc/apt/sources.list && apt-get update"' exec /tmp/mmdebstrap.38rphaW5EX Get:1 http://snapshot.notset.fr/archive/debian/20211028T024824Z bookworm InRelease [128 kB] Hit:2 http://snapshot.notset.fr/archive/debian/20211029T100155Z unstable InRelease Ign:3 http://snapshot.notset.fr/archive/debian/20211028T024824Z bookworm/main Sources Ign:4 http://snapshot.notset.fr/archive/debian/20211028T024824Z bookworm/main amd64 Packages Ign:3 http://snapshot.notset.fr/archive/debian/20211028T024824Z bookworm/main Sources Ign:4 http://snapshot.notset.fr/archive/debian/20211028T024824Z bookworm/main amd64 Packages Ign:3 http://snapshot.notset.fr/archive/debian/20211028T024824Z bookworm/main Sources Ign:4 http://snapshot.notset.fr/archive/debian/20211028T024824Z bookworm/main amd64 Packages Get:3 http://snapshot.notset.fr/archive/debian/20211028T024824Z bookworm/main Sources [11.7 MB] Get:4 http://snapshot.notset.fr/archive/debian/20211028T024824Z bookworm/main amd64 Packages [11.2 MB] Fetched 23.0 MB in 20s (1175 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.38rphaW5EX I: running --customize-hook in shell: sh -c 'chroot "$1" env sh -c "apt-get source --only-source -d samtools=1.13-4 && mkdir -p /build/samtools-UH0uh9 && dpkg-source --no-check -x /*.dsc /build/samtools-UH0uh9/samtools-1.13 && chown -R builduser:builduser /build/samtools-UH0uh9"' exec /tmp/mmdebstrap.38rphaW5EX Reading package lists... NOTICE: 'samtools' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/samtools.git Please use: git clone https://salsa.debian.org/med-team/samtools.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 4574 kB of source archives. Get:1 http://snapshot.notset.fr/archive/debian/20211028T024824Z bookworm/main samtools 1.13-4 (dsc) [2294 B] Get:2 http://snapshot.notset.fr/archive/debian/20211028T024824Z bookworm/main samtools 1.13-4 (tar) [4550 kB] Get:3 http://snapshot.notset.fr/archive/debian/20211028T024824Z bookworm/main samtools 1.13-4 (diff) [21.6 kB] Fetched 4574 kB in 4s (1241 kB/s) Download complete and in download only mode W: Download is performed unsandboxed as root as file 'samtools_1.13-4.dsc' couldn't be accessed by user '_apt'. - pkgAcquire::Run (13: Permission denied) dpkg-source: info: extracting samtools in /build/samtools-UH0uh9/samtools-1.13 dpkg-source: info: unpacking samtools_1.13.orig.tar.gz dpkg-source: info: unpacking samtools_1.13-4.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying reproducible.patch dpkg-source: info: applying fix-ftbfs-mvprintw.patch dpkg-source: info: applying samtools-fasta-q-whatis.patch I: running --customize-hook in shell: sh -c 'chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/samtools-UH0uh9/samtools-1.13 && env DEB_BUILD_OPTIONS="parallel=4" LC_ALL="C.UTF-8" LC_COLLATE="C.UTF-8" SOURCE_DATE_EPOCH="1635187983" DEB_BUILD_OPTIONS=nocheck dpkg-buildpackage -uc -a amd64 --build=all"' exec /tmp/mmdebstrap.38rphaW5EX dpkg-buildpackage: info: source package samtools dpkg-buildpackage: info: source version 1.13-4 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Étienne Mollier dpkg-source --before-build . dpkg-source: info: using options from samtools-1.13/debian/source/options: --single-debian-patch --extend-diff-ignore=^(\.travis.*|README.md)$ debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/build/samtools-UH0uh9/samtools-1.13' rm -f config.mk touch config.mk dh_auto_clean -- install -d /build/samtools-UH0uh9/samtools-1.13/debian/.debhelper/generated/_source/home make -j10 distclean make[2]: Entering directory '/build/samtools-UH0uh9/samtools-1.13' rm -f test/*.new test/*.tmp test/*/*.new test/*/*.tmp test/*/*.tmp.* cd test/dat && rm -f test_input_*.bam.bai cd test/mpileup && rm -f FAIL-*.out* PASS-*.out* anomalous.[bc]*am indels.[bc]*am mpileup.*.[cs]*am mpileup.*.crai overlap50.[bc]*am expected/1.out xx#depth*.bam* rm -f *.o misc/*.o test/*.o test/*/*.o version.h ./lz4/lz4.o rm -f samtools libbam.a libst.a misc/ace2sam misc/maq2sam-long misc/maq2sam-short misc/md5fa misc/md5sum-lite misc/wgsim test/merge/test_bam_translate test/merge/test_rtrans_build test/merge/test_trans_tbl_init test/split/test_count_rg test/split/test_expand_format_string test/split/test_filter_header_rg test/split/test_parse_args test/vcf-miniview rm -f config.cache config.h config.log config.mk config.status rm -f TAGS rm -rf autom4te.cache make[2]: Leaving directory '/build/samtools-UH0uh9/samtools-1.13' make[1]: Leaving directory '/build/samtools-UH0uh9/samtools-1.13' dh_clean rm -f debian/debhelper-build-stamp rm -rf debian/.debhelper/ rm -f -- debian/samtools.substvars debian/samtools-test.substvars debian/files rm -fr -- debian/samtools/ debian/tmp/ debian/samtools-test/ find . \( \( \ \( -path .\*/.git -o -path .\*/.svn -o -path .\*/.bzr -o -path .\*/.hg -o -path .\*/CVS -o -path .\*/.pc -o -path .\*/_darcs \) -prune -o -type f -a \ \( -name '#*#' -o -name '.*~' -o -name '*~' -o -name DEADJOE \ -o -name '*.orig' -o -name '*.rej' -o -name '*.bak' \ -o -name '.*.orig' -o -name .*.rej -o -name '.SUMS' \ -o -name TAGS -o \( -path '*/.deps/*' -a -name '*.P' \) \ \) -exec rm -f {} + \) -o \ \( -type d -a -name autom4te.cache -prune -exec rm -rf {} + \) \) debian/rules binary-indep dh binary-indep dh_update_autotools_config -i dh_autoreconf -i find ! -ipath "./debian/*" -a ! \( -path '*/.git/*' -o -path '*/.hg/*' -o -path '*/.bzr/*' -o -path '*/.svn/*' -o -path '*/CVS/*' \) -a -type f -exec md5sum {} + -o -type l -printf "symlink %p " > debian/autoreconf.before grep -q ^XDT_ configure.ac autoreconf -f -i configure.ac:64: warning: _AC_CONFIG_SUBDIRS: you should use literals ./lib/autoconf/status.m4:1096: AC_CONFIG_SUBDIRS is expanded from... m4/ax_with_htslib.m4:55: AX_WITH_HTSLIB is expanded from... configure.ac:64: the top level find ! -ipath "./debian/*" -a ! \( -path '*/.git/*' -o -path '*/.hg/*' -o -path '*/.bzr/*' -o -path '*/.svn/*' -o -path '*/CVS/*' \) -a -type f -exec md5sum {} + -o -type l -printf "symlink %p " > debian/autoreconf.after debian/rules override_dh_auto_configure make[1]: Entering directory '/build/samtools-UH0uh9/samtools-1.13' touch config.mk aclocal --force -I debian/ -I /usr/share/aclocal autoconf configure.ac:64: warning: _AC_CONFIG_SUBDIRS: you should use literals ./lib/autoconf/status.m4:1096: AC_CONFIG_SUBDIRS is expanded from... m4/ax_with_htslib.m4:55: AX_WITH_HTSLIB is expanded from... configure.ac:64: the top level dh_auto_configure -- --with-htslib=system install -d /build/samtools-UH0uh9/samtools-1.13/debian/.debhelper/generated/_source/home ./configure --build=x86_64-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/x86_64-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking --with-htslib=system checking for gawk... no checking for mawk... mawk checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether the compiler supports GNU C... yes checking whether gcc accepts -g... yes checking for gcc option to enable C11 features... none needed checking for grep that handles long lines and -e... /bin/grep checking for C compiler warning flags... -Wall checking for special C compiler options needed for large files... no checking for _FILE_OFFSET_BITS value needed for large files... no checking for htslib/sam.h... yes checking for hts_version in -lhts... yes checking for Curses library... yes checking for working curses.h... yes checking for X/Open Enhanced Curses conformance... no checking for Curses color functions... yes checking for obsolete Curses functions... yes checking for library containing cbreak... none required checking for zlib.h... yes checking for inflate in -lz... yes checking for library containing regcomp... none required configure: creating ./config.status config.status: creating config.mk config.status: creating config.h make[1]: Leaving directory '/build/samtools-UH0uh9/samtools-1.13' rm -f debian/samtools-test.debhelper.log debian/rules override_dh_auto_build make[1]: Entering directory '/build/samtools-UH0uh9/samtools-1.13' dh_auto_build -- \ CFLAGS="$(dpkg-buildflags --get CFLAGS)" \ CPPFLAGS="\$(DFLAGS) \$(INCLUDES) $(dpkg-buildflags --get CPPFLAGS)" \ LDFLAGS="$(dpkg-buildflags --get LDFLAGS)" make -j10 "CFLAGS=-g -O2 -ffile-prefix-map=/build/samtools-UH0uh9/samtools-1.13=. -fstack-protector-strong -Wformat -Werror=format-security" "CPPFLAGS=\$(DFLAGS) \$(INCLUDES) -Wdate-time -D_FORTIFY_SOURCE=2" "LDFLAGS=-Wl,-z,relro -Wl,-z,now" make[2]: Entering directory '/build/samtools-UH0uh9/samtools-1.13' gcc -g -O2 -ffile-prefix-map=/build/samtools-UH0uh9/samtools-1.13=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_index.o bam_index.c gcc -g -O2 -ffile-prefix-map=/build/samtools-UH0uh9/samtools-1.13=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_plcmd.o bam_plcmd.c gcc -g -O2 -ffile-prefix-map=/build/samtools-UH0uh9/samtools-1.13=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sam_view.o sam_view.c gcc -g -O2 -ffile-prefix-map=/build/samtools-UH0uh9/samtools-1.13=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_fastq.o bam_fastq.c gcc -g -O2 -ffile-prefix-map=/build/samtools-UH0uh9/samtools-1.13=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_cat.o bam_cat.c gcc -g -O2 -ffile-prefix-map=/build/samtools-UH0uh9/samtools-1.13=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_md.o bam_md.c gcc -g -O2 -ffile-prefix-map=/build/samtools-UH0uh9/samtools-1.13=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_reheader.o bam_reheader.c gcc -g -O2 -ffile-prefix-map=/build/samtools-UH0uh9/samtools-1.13=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_sort.o bam_sort.c gcc -g -O2 -ffile-prefix-map=/build/samtools-UH0uh9/samtools-1.13=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_rmdup.o bam_rmdup.c cc1: warning: command-line option ‘-frelease’ is valid for D but not for C gcc -g -O2 -ffile-prefix-map=/build/samtools-UH0uh9/samtools-1.13=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_rmdupse.o bam_rmdupse.c cc1: warning: command-line option ‘-frelease’ is valid for D but not for C cc1: warning: command-line option ‘-frelease’ is valid for D but not for C cc1: warning: command-line option ‘-frelease’ is valid for D but not for C cc1: warning: command-line option ‘-frelease’ is valid for D but not for C cc1: warning: command-line option ‘-frelease’ is valid for D but not for C cc1: warning: command-line option ‘-frelease’ is valid for D but not for C cc1: warning: command-line option ‘-frelease’ is valid for D but not for C cc1: warning: command-line option ‘-frelease’ is valid for D but not for C cc1: warning: command-line option ‘-frelease’ is valid for D but not for C gcc -g -O2 -ffile-prefix-map=/build/samtools-UH0uh9/samtools-1.13=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_mate.o bam_mate.c cc1: warning: command-line option ‘-frelease’ is valid for D but not for C gcc -g -O2 -ffile-prefix-map=/build/samtools-UH0uh9/samtools-1.13=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_stat.o bam_stat.c cc1: warning: command-line option ‘-frelease’ is valid for D but not for C gcc -g -O2 -ffile-prefix-map=/build/samtools-UH0uh9/samtools-1.13=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_color.o bam_color.c cc1: warning: command-line option ‘-frelease’ is valid for D but not for C echo '#define SAMTOOLS_VERSION "1.13"' > version.h echo '#define SAMTOOLS_CC "gcc"' >> version.h gcc -g -O2 -ffile-prefix-map=/build/samtools-UH0uh9/samtools-1.13=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam2bcf.o bam2bcf.c echo '#define SAMTOOLS_CPPFLAGS "-frelease -Wdate-time -D_FORTIFY_SOURCE=2"' >> version.h echo '#define SAMTOOLS_CFLAGS "-g -O2 -ffile-prefix-map=/build/samtools-UH0uh9/samtools-1.13=. -fstack-protector-strong -Wformat -Werror=format-security"' >> version.h cc1: warning: command-line option ‘-frelease’ is valid for D but not for C echo '#define SAMTOOLS_LDFLAGS "-Wl,-z,relro -Wl,-z,now"' >> version.h echo '#define SAMTOOLS_HTSDIR ""' >> version.h echo '#define SAMTOOLS_LIBS ""' >> version.h gcc -g -O2 -ffile-prefix-map=/build/samtools-UH0uh9/samtools-1.13=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam2bcf_indel.o bam2bcf_indel.c echo '#define SAMTOOLS_CURSES_LIB "-lcurses"' >> version.h gcc -g -O2 -ffile-prefix-map=/build/samtools-UH0uh9/samtools-1.13=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sample.o sample.c sed -i -e 's@/build/samtools-UH0uh9/samtools-1.13@«BUILDPATH»@g' version.h cc1: warning: command-line option ‘-frelease’ is valid for D but not for C gcc -g -O2 -ffile-prefix-map=/build/samtools-UH0uh9/samtools-1.13=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cut_target.o cut_target.c cc1: warning: command-line option ‘-frelease’ is valid for D but not for C cc1: warning: command-line option ‘-frelease’ is valid for D but not for C gcc -g -O2 -ffile-prefix-map=/build/samtools-UH0uh9/samtools-1.13=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o phase.o phase.c gcc -g -O2 -ffile-prefix-map=/build/samtools-UH0uh9/samtools-1.13=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam2depth.o bam2depth.c cc1: warning: command-line option ‘-frelease’ is valid for D but not for C cc1: warning: command-line option ‘-frelease’ is valid for D but not for C gcc -g -O2 -ffile-prefix-map=/build/samtools-UH0uh9/samtools-1.13=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o coverage.o coverage.c gcc -g -O2 -ffile-prefix-map=/build/samtools-UH0uh9/samtools-1.13=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o padding.o padding.c cc1: warning: command-line option ‘-frelease’ is valid for D but not for C cc1: warning: command-line option ‘-frelease’ is valid for D but not for C gcc -g -O2 -ffile-prefix-map=/build/samtools-UH0uh9/samtools-1.13=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bedcov.o bedcov.c cc1: warning: command-line option ‘-frelease’ is valid for D but not for C gcc -g -O2 -ffile-prefix-map=/build/samtools-UH0uh9/samtools-1.13=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bamshuf.o bamshuf.c cc1: warning: command-line option ‘-frelease’ is valid for D but not for C gcc -g -O2 -ffile-prefix-map=/build/samtools-UH0uh9/samtools-1.13=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o faidx.o faidx.c cc1: warning: command-line option ‘-frelease’ is valid for D but not for C gcc -g -O2 -ffile-prefix-map=/build/samtools-UH0uh9/samtools-1.13=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o dict.o dict.c gcc -g -O2 -ffile-prefix-map=/build/samtools-UH0uh9/samtools-1.13=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o stats.o stats.c cc1: warning: command-line option ‘-frelease’ is valid for D but not for C cc1: warning: command-line option ‘-frelease’ is valid for D but not for C gcc -g -O2 -ffile-prefix-map=/build/samtools-UH0uh9/samtools-1.13=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o stats_isize.o stats_isize.c gcc -g -O2 -ffile-prefix-map=/build/samtools-UH0uh9/samtools-1.13=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_flags.o bam_flags.c cc1: warning: command-line option ‘-frelease’ is valid for D but not for C cc1: warning: command-line option ‘-frelease’ is valid for D but not for C gcc -g -O2 -ffile-prefix-map=/build/samtools-UH0uh9/samtools-1.13=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_split.o bam_split.c gcc -g -O2 -ffile-prefix-map=/build/samtools-UH0uh9/samtools-1.13=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_tview.o bam_tview.c cc1: warning: command-line option ‘-frelease’ is valid for D but not for C cc1: warning: command-line option ‘-frelease’ is valid for D but not for C gcc -g -O2 -ffile-prefix-map=/build/samtools-UH0uh9/samtools-1.13=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_tview_curses.o bam_tview_curses.c gcc -g -O2 -ffile-prefix-map=/build/samtools-UH0uh9/samtools-1.13=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_tview_html.o bam_tview_html.c gcc -g -O2 -ffile-prefix-map=/build/samtools-UH0uh9/samtools-1.13=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_lpileup.o bam_lpileup.c cc1: warning: command-line option ‘-frelease’ is valid for D but not for C cc1: warning: command-line option ‘-frelease’ is valid for D but not for C cc1: warning: command-line option ‘-frelease’ is valid for D but not for C gcc -g -O2 -ffile-prefix-map=/build/samtools-UH0uh9/samtools-1.13=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_quickcheck.o bam_quickcheck.c gcc -g -O2 -ffile-prefix-map=/build/samtools-UH0uh9/samtools-1.13=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_addrprg.o bam_addrprg.c cc1: warning: command-line option ‘-frelease’ is valid for D but not for C cc1: warning: command-line option ‘-frelease’ is valid for D but not for C gcc -g -O2 -ffile-prefix-map=/build/samtools-UH0uh9/samtools-1.13=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_markdup.o bam_markdup.c cc1: warning: command-line option ‘-frelease’ is valid for D but not for C gcc -g -O2 -ffile-prefix-map=/build/samtools-UH0uh9/samtools-1.13=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tmp_file.o tmp_file.c cc1: warning: command-line option ‘-frelease’ is valid for D but not for C gcc -g -O2 -ffile-prefix-map=/build/samtools-UH0uh9/samtools-1.13=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_ampliconclip.o bam_ampliconclip.c cc1: warning: command-line option ‘-frelease’ is valid for D but not for C gcc -g -O2 -ffile-prefix-map=/build/samtools-UH0uh9/samtools-1.13=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o amplicon_stats.o amplicon_stats.c cc1: warning: command-line option ‘-frelease’ is valid for D but not for C gcc -g -O2 -ffile-prefix-map=/build/samtools-UH0uh9/samtools-1.13=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_import.o bam_import.c cc1: warning: command-line option ‘-frelease’ is valid for D but not for C gcc -g -O2 -ffile-prefix-map=/build/samtools-UH0uh9/samtools-1.13=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o lz4/lz4.o lz4/lz4.c gcc -g -O2 -ffile-prefix-map=/build/samtools-UH0uh9/samtools-1.13=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_aux.o bam_aux.c cc1: warning: command-line option ‘-frelease’ is valid for D but not for C cc1: warning: command-line option ‘-frelease’ is valid for D but not for C gcc -g -O2 -ffile-prefix-map=/build/samtools-UH0uh9/samtools-1.13=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam.o bam.c cc1: warning: command-line option ‘-frelease’ is valid for D but not for C gcc -g -O2 -ffile-prefix-map=/build/samtools-UH0uh9/samtools-1.13=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sam.o sam.c gcc -g -O2 -ffile-prefix-map=/build/samtools-UH0uh9/samtools-1.13=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_plbuf.o bam_plbuf.c cc1: warning: command-line option ‘-frelease’ is valid for D but not for C cc1: warning: command-line option ‘-frelease’ is valid for D but not for C gcc -g -O2 -ffile-prefix-map=/build/samtools-UH0uh9/samtools-1.13=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sam_opts.o sam_opts.c cc1: warning: command-line option ‘-frelease’ is valid for D but not for C gcc -g -O2 -ffile-prefix-map=/build/samtools-UH0uh9/samtools-1.13=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sam_utils.o sam_utils.c cc1: warning: command-line option ‘-frelease’ is valid for D but not for C gcc -g -O2 -ffile-prefix-map=/build/samtools-UH0uh9/samtools-1.13=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bedidx.o bedidx.c cc1: warning: command-line option ‘-frelease’ is valid for D but not for C gcc -g -O2 -ffile-prefix-map=/build/samtools-UH0uh9/samtools-1.13=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o misc/ace2sam.o misc/ace2sam.c cc1: warning: command-line option ‘-frelease’ is valid for D but not for C gcc -g -O2 -ffile-prefix-map=/build/samtools-UH0uh9/samtools-1.13=. -fstack-protector-strong -Wformat -Werror=format-security -DMAQ_LONGREADS -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o misc/maq2sam-long.o misc/maq2sam.c cc1: warning: command-line option ‘-frelease’ is valid for D but not for C gcc -g -O2 -ffile-prefix-map=/build/samtools-UH0uh9/samtools-1.13=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o misc/maq2sam-short.o misc/maq2sam.c cc1: warning: command-line option ‘-frelease’ is valid for D but not for C gcc -g -O2 -ffile-prefix-map=/build/samtools-UH0uh9/samtools-1.13=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o misc/md5fa.o misc/md5fa.c cc1: warning: command-line option ‘-frelease’ is valid for D but not for C gcc -g -O2 -ffile-prefix-map=/build/samtools-UH0uh9/samtools-1.13=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o misc/md5sum-lite.o misc/md5sum-lite.c cc1: warning: command-line option ‘-frelease’ is valid for D but not for C gcc -g -O2 -ffile-prefix-map=/build/samtools-UH0uh9/samtools-1.13=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o misc/wgsim.o misc/wgsim.c gcc -g -O2 -ffile-prefix-map=/build/samtools-UH0uh9/samtools-1.13=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test.o test/test.c cc1: warning: command-line option ‘-frelease’ is valid for D but not for C cc1: warning: command-line option ‘-frelease’ is valid for D but not for C gcc -g -O2 -ffile-prefix-map=/build/samtools-UH0uh9/samtools-1.13=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/split/test_count_rg.o test/split/test_count_rg.c cc1: warning: command-line option ‘-frelease’ is valid for D but not for C gcc -g -O2 -ffile-prefix-map=/build/samtools-UH0uh9/samtools-1.13=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/split/test_expand_format_string.o test/split/test_expand_format_string.c gcc -g -O2 -ffile-prefix-map=/build/samtools-UH0uh9/samtools-1.13=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/split/test_filter_header_rg.o test/split/test_filter_header_rg.c cc1: warning: command-line option ‘-frelease’ is valid for D but not for C cc1: warning: command-line option ‘-frelease’ is valid for D but not for C gcc -g -O2 -ffile-prefix-map=/build/samtools-UH0uh9/samtools-1.13=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/split/test_parse_args.o test/split/test_parse_args.c gcc -g -O2 -ffile-prefix-map=/build/samtools-UH0uh9/samtools-1.13=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/vcf-miniview.o test/vcf-miniview.c cc1: warning: command-line option ‘-frelease’ is valid for D but not for C gcc -g -O2 -ffile-prefix-map=/build/samtools-UH0uh9/samtools-1.13=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bamtk.o bamtk.c cc1: warning: command-line option ‘-frelease’ is valid for D but not for C cc1: warning: command-line option ‘-frelease’ is valid for D but not for C ar -csru libbam.a bam_aux.o bam.o sam.o bam_plbuf.o ar: `u' modifier ignored since `D' is the default (see `U') ar -rcs libst.a sam_opts.o sam_utils.o bedidx.o gcc -Wl,-z,relro -Wl,-z,now -o misc/maq2sam-long misc/maq2sam-long.o -lz gcc -Wl,-z,relro -Wl,-z,now -o misc/maq2sam-short misc/maq2sam-short.o -lz gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o misc/md5fa misc/md5fa.o -lhts -lz gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o misc/md5sum-lite misc/md5sum-lite.o -lhts -lz gcc -g -O2 -ffile-prefix-map=/build/samtools-UH0uh9/samtools-1.13=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/merge/test_bam_translate.o test/merge/test_bam_translate.c cc1: warning: command-line option ‘-frelease’ is valid for D but not for C gcc -g -O2 -ffile-prefix-map=/build/samtools-UH0uh9/samtools-1.13=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/merge/test_rtrans_build.o test/merge/test_rtrans_build.c gcc -g -O2 -ffile-prefix-map=/build/samtools-UH0uh9/samtools-1.13=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I./lz4 -frelease -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/merge/test_trans_tbl_init.o test/merge/test_trans_tbl_init.c cc1: warning: command-line option ‘-frelease’ is valid for D but not for C gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o test/split/test_filter_header_rg test/split/test_filter_header_rg.o test/test.o libst.a -lhts -lz -lpthread cc1: warning: command-line option ‘-frelease’ is valid for D but not for C gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o test/vcf-miniview test/vcf-miniview.o -lhts -lz -lpthread gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o test/split/test_expand_format_string test/split/test_expand_format_string.o test/test.o libst.a -lhts -lz -lpthread gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o test/split/test_count_rg test/split/test_count_rg.o test/test.o libst.a -lhts -lz -lpthread gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o test/split/test_parse_args test/split/test_parse_args.o test/test.o libst.a -lhts -lz -lpthread gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o misc/ace2sam misc/ace2sam.o -lhts -lz gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o misc/wgsim misc/wgsim.o -lm -lhts -lz gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o samtools bam_index.o bam_plcmd.o sam_view.o bam_fastq.o bam_cat.o bam_md.o bam_reheader.o bam_sort.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o bam2bcf.o bam2bcf_indel.o sample.o cut_target.o phase.o bam2depth.o coverage.o padding.o bedcov.o bamshuf.o faidx.o dict.o stats.o stats_isize.o bam_flags.o bam_split.o bam_tview.o bam_tview_curses.o bam_tview_html.o bam_lpileup.o bam_quickcheck.o bam_addrprg.o bam_markdup.o tmp_file.o bam_ampliconclip.o amplicon_stats.o bam_import.o ./lz4/lz4.o libbam.a libst.a -lhts -lcurses -lm -lz -lpthread gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o test/merge/test_bam_translate test/merge/test_bam_translate.o test/test.o libst.a -lhts -lz -lpthread gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o test/merge/test_trans_tbl_init test/merge/test_trans_tbl_init.o test/test.o libst.a -lhts -lz -lpthread gcc -L./lz4 -Wl,-z,relro -Wl,-z,now -o test/merge/test_rtrans_build test/merge/test_rtrans_build.o test/test.o libst.a -lhts -lz -lpthread make[2]: Leaving directory '/build/samtools-UH0uh9/samtools-1.13' make[1]: Leaving directory '/build/samtools-UH0uh9/samtools-1.13' create-stamp debian/debhelper-build-stamp dh_prep -i rm -f -- debian/samtools-test.substvars rm -fr -- debian/.debhelper/generated/samtools-test/ debian/samtools-test/ debian/tmp/ rm -f debian/samtools-test.debhelper.log debian/rules override_dh_auto_install make[1]: Entering directory '/build/samtools-UH0uh9/samtools-1.13' dh_auto_install -- \ prefix=/usr install -d /build/samtools-UH0uh9/samtools-1.13/debian/tmp make -j10 install DESTDIR=/build/samtools-UH0uh9/samtools-1.13/debian/tmp AM_UPDATE_INFO_DIR=no prefix=/usr make[2]: Entering directory '/build/samtools-UH0uh9/samtools-1.13' mkdir -p -m 755 /build/samtools-UH0uh9/samtools-1.13/debian/tmp/usr/bin /build/samtools-UH0uh9/samtools-1.13/debian/tmp/usr/bin /build/samtools-UH0uh9/samtools-1.13/debian/tmp/usr/share/man/man1 install -p samtools /build/samtools-UH0uh9/samtools-1.13/debian/tmp/usr/bin install -p misc/ace2sam misc/maq2sam-long misc/maq2sam-short misc/md5fa misc/md5sum-lite misc/wgsim /build/samtools-UH0uh9/samtools-1.13/debian/tmp/usr/bin install -p misc/blast2sam.pl misc/bowtie2sam.pl misc/export2sam.pl misc/fasta-sanitize.pl misc/interpolate_sam.pl misc/novo2sam.pl misc/plot-ampliconstats misc/plot-bamstats misc/psl2sam.pl misc/sam2vcf.pl misc/samtools.pl misc/seq_cache_populate.pl misc/soap2sam.pl misc/wgsim_eval.pl misc/zoom2sam.pl /build/samtools-UH0uh9/samtools-1.13/debian/tmp/usr/bin install -p -m 644 doc/samtools*.1 misc/wgsim.1 /build/samtools-UH0uh9/samtools-1.13/debian/tmp/usr/share/man/man1 make[2]: Leaving directory '/build/samtools-UH0uh9/samtools-1.13' make clean make[2]: Entering directory '/build/samtools-UH0uh9/samtools-1.13' rm -f test/*.new test/*.tmp test/*/*.new test/*/*.tmp test/*/*.tmp.* cd test/dat && rm -f test_input_*.bam.bai cd test/mpileup && rm -f FAIL-*.out* PASS-*.out* anomalous.[bc]*am indels.[bc]*am mpileup.*.[cs]*am mpileup.*.crai overlap50.[bc]*am expected/1.out xx#depth*.bam* rm -f *.o misc/*.o test/*.o test/*/*.o version.h ./lz4/lz4.o rm -f samtools libbam.a libst.a misc/ace2sam misc/maq2sam-long misc/maq2sam-short misc/md5fa misc/md5sum-lite misc/wgsim test/merge/test_bam_translate test/merge/test_rtrans_build test/merge/test_trans_tbl_init test/split/test_count_rg test/split/test_expand_format_string test/split/test_filter_header_rg test/split/test_parse_args test/vcf-miniview make[2]: Leaving directory '/build/samtools-UH0uh9/samtools-1.13' make[1]: Leaving directory '/build/samtools-UH0uh9/samtools-1.13' rm -f debian/samtools-test.debhelper.log debian/rules override_dh_install make[1]: Entering directory '/build/samtools-UH0uh9/samtools-1.13' dh_install install -d debian/.debhelper/generated/samtools install -d debian/samtools-test/usr/share/samtools cp --reflink=auto -a ./test debian/samtools-test/usr/share/samtools/ install -d debian/.debhelper/generated/samtools-test # Fix Perl interpreter PATH for pscript in `grep -Rl '#!/usr/bin/env \+perl' debian/*` ; do \ sed -i '1s?#!/usr/bin/env \+perl?#!/usr/bin/perl?' ${pscript} ; \ done # Disable the executable bit on a dataset. if [ -d debian/samtools-test ] \ ; then chmod 0644 debian/samtools-test/usr/share/samtools/test/ampliconclip/ac_test.bed \ ; fi make[1]: Leaving directory '/build/samtools-UH0uh9/samtools-1.13' dh_installdocs -i install -d debian/samtools-test/usr/share/doc/samtools-test install -p -m0644 debian/copyright debian/samtools-test/usr/share/doc/samtools-test/copyright rm -f debian/samtools-test.debhelper.log debian/rules override_dh_installchangelogs make[1]: Entering directory '/build/samtools-UH0uh9/samtools-1.13' dh_installchangelogs NEWS install -p -m0644 debian/changelog debian/samtools-test/usr/share/doc/samtools-test/changelog.Debian install -p -m0644 debian/NEWS debian/samtools-test/usr/share/doc/samtools-test/NEWS.Debian install -p -m0644 NEWS debian/samtools-test/usr/share/doc/samtools-test/changelog make[1]: Leaving directory '/build/samtools-UH0uh9/samtools-1.13' dh_installexamples -i rm -f debian/samtools-test.debhelper.log debian/rules execute_before_dh_installman make[1]: Entering directory '/build/samtools-UH0uh9/samtools-1.13' # Fix whatis entries for subcommands; "samtools subcommand \- desc." # will confuse the lexer, but "samtools-subcommand \- desc." will work. sed -i '/^\.SH NAME/{n;s/^\([^ ]\+\) \([^ ]\+\) \\- /\1-\2 \\- /}' \ debian/*/usr/share/man/man*/*.* # .EX expects a indentation width. sed -i 's/^.EX$/.EX 8/' debian/*/usr/share/man/man*/*.* make[1]: Leaving directory '/build/samtools-UH0uh9/samtools-1.13' dh_perl -i (grep -a -s -v perl:Depends debian/samtools-test.substvars; echo perl:Depends=perl:any) > debian/samtools-test.substvars.new mv debian/samtools-test.substvars.new debian/samtools-test.substvars dh_link -i dh_strip_nondeterminism -i Using 1635187983 as canonical time Normalizing debian/samtools-test/usr/share/samtools/test/mpileup/expected/1.out.f3-6.gz using File::StripNondeterminism::handlers::gzip dh_compress -i cd debian/samtools-test chmod a-x usr/share/doc/samtools-test/NEWS.Debian usr/share/doc/samtools-test/changelog usr/share/doc/samtools-test/changelog.Debian gzip -9nf usr/share/doc/samtools-test/NEWS.Debian usr/share/doc/samtools-test/changelog usr/share/doc/samtools-test/changelog.Debian cd '/build/samtools-UH0uh9/samtools-1.13' dh_fixperms -i find debian/samtools-test ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s find debian/samtools-test/usr/share/doc -type f -a -true -a ! -regex 'debian/samtools-test/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 find debian/samtools-test/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 find debian/samtools-test -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 dh_missing -i dh_installdeb -i install -d debian/samtools-test/DEBIAN dh_gencontrol -i echo misc:Depends= >> debian/samtools-test.substvars echo misc:Pre-Depends= >> debian/samtools-test.substvars dpkg-gencontrol -psamtools-test -ldebian/changelog -Tdebian/samtools-test.substvars -Pdebian/samtools-test dpkg-gencontrol: warning: package samtools-test: substitution variable ${perl:Depends} unused, but is defined chmod 0644 -- debian/samtools-test/DEBIAN/control dh_md5sums -i cd debian/samtools-test >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/samtools-test/DEBIAN/md5sums dh_builddeb -i dpkg-deb --root-owner-group --build debian/samtools-test .. dpkg-deb: building package 'samtools-test' in '../samtools-test_1.13-4_all.deb'. dpkg-genbuildinfo --build=all dpkg-genchanges --build=all >../samtools_1.13-4_all.changes dpkg-genchanges: info: binary-only arch-indep upload (source code and arch-specific packages not included) dpkg-source --after-build . dpkg-source: info: using options from samtools-1.13/debian/source/options: --single-debian-patch --extend-diff-ignore=^(\.travis.*|README.md)$ dpkg-buildpackage: info: binary-only upload (no source included) I: running special hook: sync-out /build/samtools-UH0uh9 /tmp/samtools-1.13-4odivnhoy I: cleaning package lists and apt cache... I: removing tempdir /tmp/mmdebstrap.38rphaW5EX... I: success in 420.5481 seconds md5: Value of 'md5' differs for samtools-test_1.13-4_all.deb md5: Size differs for samtools-test_1.13-4_all.deb sha1: Value of 'sha1' differs for samtools-test_1.13-4_all.deb sha1: Size differs for samtools-test_1.13-4_all.deb sha256: Value of 'sha256' differs for samtools-test_1.13-4_all.deb sha256: Size differs for samtools-test_1.13-4_all.deb Checksums: FAIL Cannot generate diffoscope for samtools-test_1.13-4_all.deb: RetryError[]