Input buildinfo: https://buildinfos.debian.net/buildinfo-pool/p/phylonium/phylonium_1.3-1_amd64.buildinfo Use metasnap for getting required timestamps New buildinfo file: /tmp/phylonium-1.3-1u_wkoyc9/phylonium_1.3-1_amd64.buildinfo Get source package info: phylonium=1.3-1 Source URL: http://snapshot.notset.fr/mr/package/phylonium/1.3-1/srcfiles?fileinfo=1 env -i PATH=/usr/sbin:/usr/bin:/sbin:/bin TMPDIR=/tmp mmdebstrap --arch=amd64 --include=autoconf=2.69-11.1 automake=1:1.16.2-4 autopoint=0.19.8.1-10 autotools-dev=20180224.1 base-files=11 base-passwd=3.5.48 bash=5.1~rc2-1 binutils=2.35.1-2 binutils-common=2.35.1-2 binutils-x86-64-linux-gnu=2.35.1-2 bsdextrautils=2.36-3+b2 bsdutils=1:2.36-3+b2 build-essential=12.8 bzip2=1.0.8-4 coreutils=8.32-4+b1 cpp=4:10.2.0-1 cpp-10=10.2.0-16 dash=0.5.10.2-7 debconf=1.5.74 debhelper=13.2.1 debianutils=4.11.2 dh-autoreconf=19 dh-strip-nondeterminism=1.9.0-1 diffutils=1:3.7-3 dpkg=1.20.5 dpkg-dev=1.20.5 dwz=0.13-5 file=1:5.38-5 findutils=4.7.0+git20201010-2 g++=4:10.2.0-1 g++-10=10.2.0-16 gcc=4:10.2.0-1 gcc-10=10.2.0-16 gcc-10-base=10.2.0-16 gettext=0.19.8.1-10 gettext-base=0.19.8.1-10 grep=3.4-1 groff-base=1.22.4-5 gzip=1.10-2 hostname=3.23 init-system-helpers=1.58 intltool-debian=0.35.0+20060710.5 libacl1=2.2.53-8 libarchive-zip-perl=1.68-1 libasan6=10.2.0-16 libatomic1=10.2.0-16 libattr1=1:2.4.48-5 libaudit-common=1:2.8.5-3.1 libaudit1=1:2.8.5-3.1 libbinutils=2.35.1-2 libblkid1=2.36-3+b2 libbz2-1.0=1.0.8-4 libc-bin=2.31-4 libc-dev-bin=2.31-4 libc6=2.31-4 libc6-dev=2.31-4 libcap-ng0=0.7.9-2.2 libcc1-0=10.2.0-16 libcom-err2=1.45.6-1 libcroco3=0.6.13-1 libcrypt-dev=1:4.4.17-1 libcrypt1=1:4.4.17-1 libctf-nobfd0=2.35.1-2 libctf0=2.35.1-2 libdb5.3=5.3.28+dfsg1-0.6 libdebconfclient0=0.255 libdebhelper-perl=13.2.1 libdivsufsort-dev=2.0.1-4 libdivsufsort3=2.0.1-4 libdpkg-perl=1.20.5 libelf1=0.181-1 libffi7=3.3-4 libfile-stripnondeterminism-perl=1.9.0-1 libgcc-10-dev=10.2.0-16 libgcc-s1=10.2.0-16 libgcrypt20=1.8.7-2 libgdbm-compat4=1.18.1-5.1 libgdbm6=1.18.1-5.1 libglib2.0-0=2.66.2-1 libgmp10=2:6.2.0+dfsg-6 libgomp1=10.2.0-16 libgpg-error0=1.38-2 libgsl-dev=2.6+dfsg-2 libgsl25=2.6+dfsg-2 libgslcblas0=2.6+dfsg-2 libgssapi-krb5-2=1.17-10 libicu67=67.1-4 libisl22=0.22.1-1 libitm1=10.2.0-16 libk5crypto3=1.17-10 libkeyutils1=1.6.1-2 libkrb5-3=1.17-10 libkrb5support0=1.17-10 liblsan0=10.2.0-16 liblz4-1=1.9.2-2 liblzma5=5.2.4-1+b1 libmagic-mgc=1:5.38-5 libmagic1=1:5.38-5 libmount1=2.36-3+b2 libmpc3=1.2.0-1 libmpfr6=4.1.0-3 libnsl-dev=1.3.0-2 libnsl2=1.3.0-2 libnss-nis=3.1-4 libnss-nisplus=1.3-4 libpam-modules=1.3.1-5 libpam-modules-bin=1.3.1-5 libpam-runtime=1.3.1-5 libpam0g=1.3.1-5 libpcre2-8-0=10.34-7 libpcre3=2:8.39-13 libperl5.30=5.30.3-4 libpipeline1=1.5.3-1 libquadmath0=10.2.0-16 libseccomp2=2.4.4-1+b1 libselinux1=3.1-2+b1 libsigsegv2=2.12-2 libsmartcols1=2.36-3+b2 libssl1.1=1.1.1h-1 libstdc++-10-dev=10.2.0-16 libstdc++6=10.2.0-16 libsub-override-perl=0.09-2 libsystemd0=246.6-2 libtinfo6=6.2+20200918-1 libtirpc-common=1.2.6-3 libtirpc-dev=1.2.6-3 libtirpc3=1.2.6-3 libtool=2.4.6-14 libtsan0=10.2.0-16 libubsan1=10.2.0-16 libuchardet0=0.0.7-1 libudev1=246.6-2 libunistring2=0.9.10-4 libuuid1=2.36-3+b2 libxml2=2.9.10+dfsg-6.2 libzstd1=1.4.5+dfsg-4 linux-libc-dev=5.9.1-1 login=1:4.8.1-1 lsb-base=11.1.0 m4=1.4.18-4 make=4.3-4 man-db=2.9.3-2 mawk=1.3.4.20200120-2 ncurses-base=6.2+20200918-1 ncurses-bin=6.2+20200918-1 patch=2.7.6-6 perl=5.30.3-4 perl-base=5.30.3-4 perl-modules-5.30=5.30.3-4 po-debconf=1.0.21 sed=4.7-1 sensible-utils=0.0.12+nmu1 sysvinit-utils=2.96-5 tar=1.30+dfsg-7 util-linux=2.36-3+b2 xz-utils=5.2.4-1+b1 zlib1g=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/20210814T212851Z/ bookworm main deb-src http://snapshot.notset.fr/archive/debian/20210814T212851Z/ bookworm main deb http://snapshot.notset.fr/archive/debian/20201107T093238Z/ 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 phylonium=1.3-1 && mkdir -p /build/phylonium-EhZZLy && dpkg-source --no-check -x /*.dsc /build/phylonium-EhZZLy/phylonium-1.3 && chown -R builduser:builduser /build/phylonium-EhZZLy" --customize-hook=chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/phylonium-EhZZLy/phylonium-1.3 && env DEB_BUILD_OPTIONS="parallel=4" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1604653057" dpkg-buildpackage -uc -a amd64 --build=any" --customize-hook=sync-out /build/phylonium-EhZZLy /tmp/phylonium-1.3-1u_wkoyc9 bullseye /dev/null deb http://snapshot.notset.fr/archive/debian/20201107T093238Z unstable main I: automatically chosen mode: root I: chroot architecture amd64 is equal to the host's architecture I: automatically chosen format: tar I: using /tmp/mmdebstrap.8u1G_WvIUK 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.8u1G_WvIUK Reading package lists... Building dependency tree... util-linux is already the newest version (2.36-3+b2). 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/20201107T093238Z unstable/main amd64 libfakeroot amd64 1.25.3-1 [47.0 kB] Get:2 http://snapshot.notset.fr/archive/debian/20201107T093238Z unstable/main amd64 fakeroot amd64 1.25.3-1 [87.0 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 134 kB in 0s (454 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 ... 4664 files and directories currently installed.) Preparing to unpack .../libfakeroot_1.25.3-1_amd64.deb ... Unpacking libfakeroot:amd64 (1.25.3-1) ... Selecting previously unselected package fakeroot. Preparing to unpack .../fakeroot_1.25.3-1_amd64.deb ... Unpacking fakeroot (1.25.3-1) ... Setting up libfakeroot:amd64 (1.25.3-1) ... Setting up fakeroot (1.25.3-1) ... update-alternatives: using /usr/bin/fakeroot-sysv to provide /usr/bin/fakeroot (fakeroot) in auto mode Processing triggers for libc-bin (2.31-4) ... 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/20210814T212851Z/ bookworm main deb-src http://snapshot.notset.fr/archive/debian/20210814T212851Z/ bookworm main deb http://snapshot.notset.fr/archive/debian/20201107T093238Z/ unstable main' >> /etc/apt/sources.list && apt-get update"' exec /tmp/mmdebstrap.8u1G_WvIUK Get:1 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm InRelease [81.6 kB] Hit:2 http://snapshot.notset.fr/archive/debian/20201107T093238Z unstable InRelease Ign:3 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main Sources Ign:4 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main amd64 Packages Ign:3 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main Sources Ign:4 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main amd64 Packages Ign:3 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main Sources Ign:4 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main amd64 Packages Get:3 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main Sources [11.4 MB] Get:4 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main amd64 Packages [11.1 MB] Fetched 22.6 MB in 20s (1131 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.8u1G_WvIUK I: running --customize-hook in shell: sh -c 'chroot "$1" env sh -c "apt-get source --only-source -d phylonium=1.3-1 && mkdir -p /build/phylonium-EhZZLy && dpkg-source --no-check -x /*.dsc /build/phylonium-EhZZLy/phylonium-1.3 && chown -R builduser:builduser /build/phylonium-EhZZLy"' exec /tmp/mmdebstrap.8u1G_WvIUK Reading package lists... NOTICE: 'phylonium' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/phylonium.git Please use: git clone https://salsa.debian.org/med-team/phylonium.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 44.5 MB of source archives. Get:1 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main phylonium 1.3-1 (dsc) [2304 B] Get:2 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main phylonium 1.3-1 (tar) [44.1 MB] Get:3 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main phylonium 1.3-1 (tar) [409 kB] Get:4 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main phylonium 1.3-1 (diff) [4804 B] Fetched 44.5 MB in 36s (1252 kB/s) Download complete and in download only mode W: Download is performed unsandboxed as root as file 'phylonium_1.3-1.dsc' couldn't be accessed by user '_apt'. - pkgAcquire::Run (13: Permission denied) dpkg-source: info: extracting phylonium in /build/phylonium-EhZZLy/phylonium-1.3 dpkg-source: info: unpacking phylonium_1.3.orig.tar.gz dpkg-source: info: unpacking phylonium_1.3.orig-debian-tests-data.tar.gz dpkg-source: info: unpacking phylonium_1.3-1.debian.tar.xz I: running --customize-hook in shell: sh -c 'chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/phylonium-EhZZLy/phylonium-1.3 && env DEB_BUILD_OPTIONS="parallel=4" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1604653057" dpkg-buildpackage -uc -a amd64 --build=any"' exec /tmp/mmdebstrap.8u1G_WvIUK dpkg-buildpackage: info: source package phylonium dpkg-buildpackage: info: source version 1.3-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Nilesh Patra dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean dh_clean debian/rules binary-arch dh binary-arch dh_update_autotools_config -a dh_autoreconf -a configure.ac:11: installing './ar-lib' configure.ac:6: installing './compile' configure.ac:3: installing './install-sh' configure.ac:3: installing './missing' parallel-tests: installing './test-driver' libs/Makefile.am: installing './depcomp' test/Makefile.am:7: warning: source file '$(top_srcdir)/src/esa.cxx' is in a subdirectory, test/Makefile.am:7: but option 'subdir-objects' is disabled automake: warning: possible forward-incompatibility. automake: At least a source file is in a subdirectory, but the 'subdir-objects' automake: automake option hasn't been enabled. For now, the corresponding output automake: object file(s) will be placed in the top-level directory. However, automake: this behaviour will change in future Automake versions: they will automake: unconditionally cause object files to be placed in the same subdirectory automake: of the corresponding sources. automake: You are advised to start using 'subdir-objects' option throughout your automake: project, to avoid future incompatibilities. test/Makefile.am:7: warning: source file '$(top_srcdir)/src/evo_model.cxx' is in a subdirectory, test/Makefile.am:7: but option 'subdir-objects' is disabled test/Makefile.am:7: warning: source file '$(top_srcdir)/src/process.cxx' is in a subdirectory, test/Makefile.am:7: but option 'subdir-objects' is disabled test/Makefile.am:7: warning: source file '$(top_srcdir)/src/sequence.cxx' is in a subdirectory, test/Makefile.am:7: but option 'subdir-objects' is disabled debian/rules override_dh_auto_configure make[1]: Entering directory '/build/phylonium-EhZZLy/phylonium-1.3' dh_auto_configure -- ./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 checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /bin/mkdir -p checking for gawk... no checking for mawk... mawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking whether gcc understands -c and -o together... yes checking whether make supports the include directive... yes (GNU style) checking dependency style of gcc... none checking for g++... g++ checking whether we are using the GNU C++ compiler... yes checking whether g++ accepts -g... yes checking dependency style of g++... none checking whether make sets $(MAKE)... (cached) yes checking how to run the C preprocessor... gcc -E checking for ranlib... ranlib checking for ar... ar checking the archiver (ar) interface... ar checking for g++ option to support OpenMP... -fopenmp checking whether g++ supports C++14 features with -std=gnu++14... yes checking for gcc option to support OpenMP... -fopenmp checking for __attribute__((ifunc))... yes checking for cos in -lm... yes checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking divsufsort.h usability... yes checking divsufsort.h presence... yes checking for divsufsort.h... yes checking for divsufsort in -ldivsufsort... yes checking limits.h usability... yes checking limits.h presence... yes checking for limits.h... yes checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking for unistd.h... (cached) yes checking for stdint.h... (cached) yes checking for inttypes.h... (cached) yes checking err.h usability... yes checking err.h presence... yes checking for err.h... yes checking errno.h usability... yes checking errno.h presence... yes checking for errno.h... yes checking fcntl.h usability... yes checking fcntl.h presence... yes checking for fcntl.h... yes checking for inline... inline checking for size_t... yes checking for ssize_t... yes checking for int32_t... yes checking for uint8_t... yes checking for stdbool.h that conforms to C99... yes checking for _Bool... yes checking for floor... yes checking for pow... yes checking for sqrt... yes checking for strdup... yes checking for strerror... yes checking for strtoul... yes checking for strtod... yes checking for reallocarray... yes checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating libs/Makefile config.status: creating Makefile config.status: creating man/phylonium.1 config.status: creating src/Makefile config.status: creating test/Makefile config.status: creating config.h config.status: executing depfiles commands make[1]: Leaving directory '/build/phylonium-EhZZLy/phylonium-1.3' dh_auto_build -a make -j4 make[1]: Entering directory '/build/phylonium-EhZZLy/phylonium-1.3' make all-recursive make[2]: Entering directory '/build/phylonium-EhZZLy/phylonium-1.3' Making all in libs make[3]: Entering directory '/build/phylonium-EhZZLy/phylonium-1.3/libs' rm -f libcompat.a gcc -DHAVE_CONFIG_H -I. -I.. -I../opt -Wdate-time -D_FORTIFY_SOURCE=2 -fms-extensions -g -O2 -fdebug-prefix-map=/build/phylonium-EhZZLy/phylonium-1.3=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libpfasta_a-pfasta.o `test -f 'pfasta.c' || echo './'`pfasta.c gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -fms-extensions -g -O2 -fdebug-prefix-map=/build/phylonium-EhZZLy/phylonium-1.3=. -fstack-protector-strong -Wformat -Werror=format-security -c -o revseqcmp.o revseqcmp.c gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -fms-extensions -mpopcnt -mssse3 -g -O2 -fdebug-prefix-map=/build/phylonium-EhZZLy/phylonium-1.3=. -fstack-protector-strong -Wformat -Werror=format-security -c -o librevseqcmp_ssse3_a-revseqcmp_ssse3.o `test -f 'revseqcmp_ssse3.c' || echo './'`revseqcmp_ssse3.c ar cru libcompat.a ar: `u' modifier ignored since `D' is the default (see `U') ranlib libcompat.a gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -fms-extensions -mpopcnt -mavx2 -g -O2 -fdebug-prefix-map=/build/phylonium-EhZZLy/phylonium-1.3=. -fstack-protector-strong -Wformat -Werror=format-security -c -o librevseqcmp_avx2_a-revseqcmp_avx2.o `test -f 'revseqcmp_avx2.c' || echo './'`revseqcmp_avx2.c gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -fms-extensions -g -O2 -fdebug-prefix-map=/build/phylonium-EhZZLy/phylonium-1.3=. -fstack-protector-strong -Wformat -Werror=format-security -c -o seqcmp.o seqcmp.c gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -fms-extensions -mpopcnt -msse2 -g -O2 -fdebug-prefix-map=/build/phylonium-EhZZLy/phylonium-1.3=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libseqcmp_sse2_a-seqcmp_sse2.o `test -f 'seqcmp_sse2.c' || echo './'`seqcmp_sse2.c gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -fms-extensions -mpopcnt -mavx2 -g -O2 -fdebug-prefix-map=/build/phylonium-EhZZLy/phylonium-1.3=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libseqcmp_avx2_a-seqcmp_avx2.o `test -f 'seqcmp_avx2.c' || echo './'`seqcmp_avx2.c gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -fms-extensions -mpopcnt -mavx512bw -mavx512vl -g -O2 -fdebug-prefix-map=/build/phylonium-EhZZLy/phylonium-1.3=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libseqcmp_avx512_a-seqcmp_avx512.o `test -f 'seqcmp_avx512.c' || echo './'`seqcmp_avx512.c rm -f librevseqcmp_ssse3.a ar cru librevseqcmp_ssse3.a librevseqcmp_ssse3_a-revseqcmp_ssse3.o ar: `u' modifier ignored since `D' is the default (see `U') ranlib librevseqcmp_ssse3.a rm -f librevseqcmp_avx2.a rm -f libseqcmp_sse2.a ar cru librevseqcmp_avx2.a librevseqcmp_avx2_a-revseqcmp_avx2.o ar cru libseqcmp_sse2.a libseqcmp_sse2_a-seqcmp_sse2.o ar: `u' modifier ignored since `D' is the default (see `U') ar: `u' modifier ignored since `D' is the default (see `U') ranlib librevseqcmp_avx2.a ranlib libseqcmp_sse2.a rm -f libpfasta.a rm -f librevseqcmp.a ar cru libpfasta.a libpfasta_a-pfasta.o ar cru librevseqcmp.a revseqcmp.o librevseqcmp_ssse3.a librevseqcmp_avx2.a ar: `u' modifier ignored since `D' is the default (see `U') ranlib libpfasta.a ar: `u' modifier ignored since `D' is the default (see `U') ranlib librevseqcmp.a rm -f libseqcmp_avx512.a ar cru libseqcmp_avx512.a libseqcmp_avx512_a-seqcmp_avx512.o ar: `u' modifier ignored since `D' is the default (see `U') ranlib libseqcmp_avx512.a rm -f libseqcmp_avx2.a ar cru libseqcmp_avx2.a libseqcmp_avx2_a-seqcmp_avx2.o ar: `u' modifier ignored since `D' is the default (see `U') ranlib libseqcmp_avx2.a rm -f libseqcmp.a ar cru libseqcmp.a seqcmp.o libseqcmp_sse2.a libseqcmp_avx2.a libseqcmp_avx512.a ar: `u' modifier ignored since `D' is the default (see `U') ranlib libseqcmp.a make[3]: Leaving directory '/build/phylonium-EhZZLy/phylonium-1.3/libs' Making all in src make[3]: Entering directory '/build/phylonium-EhZZLy/phylonium-1.3/src' g++ -std=gnu++14 -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++14 -Wall -Wextra -I../libs -Wdate-time -D_FORTIFY_SOURCE=2 -fms-extensions -fopenmp -O2 -ggdb -g -O2 -fdebug-prefix-map=/build/phylonium-EhZZLy/phylonium-1.3=. -fstack-protector-strong -Wformat -Werror=format-security -c -o phylonium-phylonium.o `test -f 'phylonium.cxx' || echo './'`phylonium.cxx g++ -std=gnu++14 -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++14 -Wall -Wextra -I../libs -Wdate-time -D_FORTIFY_SOURCE=2 -fms-extensions -fopenmp -O2 -ggdb -g -O2 -fdebug-prefix-map=/build/phylonium-EhZZLy/phylonium-1.3=. -fstack-protector-strong -Wformat -Werror=format-security -c -o phylonium-io.o `test -f 'io.cxx' || echo './'`io.cxx g++ -std=gnu++14 -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++14 -Wall -Wextra -I../libs -Wdate-time -D_FORTIFY_SOURCE=2 -fms-extensions -fopenmp -O2 -ggdb -g -O2 -fdebug-prefix-map=/build/phylonium-EhZZLy/phylonium-1.3=. -fstack-protector-strong -Wformat -Werror=format-security -c -o phylonium-sequence.o `test -f 'sequence.cxx' || echo './'`sequence.cxx g++ -std=gnu++14 -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++14 -Wall -Wextra -I../libs -Wdate-time -D_FORTIFY_SOURCE=2 -fms-extensions -fopenmp -O2 -ggdb -g -O2 -fdebug-prefix-map=/build/phylonium-EhZZLy/phylonium-1.3=. -fstack-protector-strong -Wformat -Werror=format-security -c -o phylonium-esa.o `test -f 'esa.cxx' || echo './'`esa.cxx esa.cxx: In constructor ‘esa::esa(const sequence&)’: esa.cxx:63:55: warning: narrowing conversion of ‘(((& seq)->sequence::size() * 2) + 1)’ from ‘long unsigned int’ to ‘int’ [-Wnarrowing] 63 | esa::esa(const sequence &seq) : m_size{seq.size() * 2 + 1} | ~~~~~~~~~~~~~~~^~~ g++ -std=gnu++14 -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++14 -Wall -Wextra -I../libs -Wdate-time -D_FORTIFY_SOURCE=2 -fms-extensions -fopenmp -O2 -ggdb -g -O2 -fdebug-prefix-map=/build/phylonium-EhZZLy/phylonium-1.3=. -fstack-protector-strong -Wformat -Werror=format-security -c -o phylonium-process.o `test -f 'process.cxx' || echo './'`process.cxx g++ -std=gnu++14 -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++14 -Wall -Wextra -I../libs -Wdate-time -D_FORTIFY_SOURCE=2 -fms-extensions -fopenmp -O2 -ggdb -g -O2 -fdebug-prefix-map=/build/phylonium-EhZZLy/phylonium-1.3=. -fstack-protector-strong -Wformat -Werror=format-security -c -o phylonium-evo_model.o `test -f 'evo_model.cxx' || echo './'`evo_model.cxx g++ -std=gnu++14 -fopenmp -O2 -ggdb -g -O2 -fdebug-prefix-map=/build/phylonium-EhZZLy/phylonium-1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o phylonium phylonium-phylonium.o phylonium-io.o phylonium-sequence.o phylonium-esa.o phylonium-process.o phylonium-evo_model.o ../libs/libcompat.a ../libs/libpfasta.a ../libs/librevseqcmp.a ../libs/libseqcmp.a ../libs/librevseqcmp_avx2.a ../libs/librevseqcmp_ssse3.a ../libs/libseqcmp_avx2.a ../libs/libseqcmp_sse2.a ../libs/libseqcmp_avx512.a -ldivsufsort -lm make[3]: Leaving directory '/build/phylonium-EhZZLy/phylonium-1.3/src' Making all in test make[3]: Entering directory '/build/phylonium-EhZZLy/phylonium-1.3/test' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/build/phylonium-EhZZLy/phylonium-1.3/test' Making all in . make[3]: Entering directory '/build/phylonium-EhZZLy/phylonium-1.3' make[3]: Leaving directory '/build/phylonium-EhZZLy/phylonium-1.3' make[2]: Leaving directory '/build/phylonium-EhZZLy/phylonium-1.3' make[1]: Leaving directory '/build/phylonium-EhZZLy/phylonium-1.3' dh_auto_test -a make -j4 check VERBOSE=1 make[1]: Entering directory '/build/phylonium-EhZZLy/phylonium-1.3' Making check in libs make[2]: Entering directory '/build/phylonium-EhZZLy/phylonium-1.3/libs' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/phylonium-EhZZLy/phylonium-1.3/libs' Making check in src make[2]: Entering directory '/build/phylonium-EhZZLy/phylonium-1.3/src' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/phylonium-EhZZLy/phylonium-1.3/src' Making check in test make[2]: Entering directory '/build/phylonium-EhZZLy/phylonium-1.3/test' make simf unittests make[3]: Entering directory '/build/phylonium-EhZZLy/phylonium-1.3/test' g++ -std=gnu++14 -DHAVE_CONFIG_H -I. -I.. -std=c++14 -Wall -Wextra -Wdate-time -D_FORTIFY_SOURCE=2 -fms-extensions -ggdb -g -O2 -fdebug-prefix-map=/build/phylonium-EhZZLy/phylonium-1.3=. -fstack-protector-strong -Wformat -Werror=format-security -c -o simf-simf.o `test -f 'simf.cxx' || echo './'`simf.cxx g++ -std=gnu++14 -DHAVE_CONFIG_H -I. -I.. -I../src -I../libs -std=c++14 -Wall -Wextra -Wdate-time -D_FORTIFY_SOURCE=2 -fms-extensions -ggdb -g -O2 -fdebug-prefix-map=/build/phylonium-EhZZLy/phylonium-1.3=. -fstack-protector-strong -Wformat -Werror=format-security -c -o unittests-esa.o `test -f '../src/esa.cxx' || echo './'`../src/esa.cxx g++ -std=gnu++14 -DHAVE_CONFIG_H -I. -I.. -I../src -I../libs -std=c++14 -Wall -Wextra -Wdate-time -D_FORTIFY_SOURCE=2 -fms-extensions -ggdb -g -O2 -fdebug-prefix-map=/build/phylonium-EhZZLy/phylonium-1.3=. -fstack-protector-strong -Wformat -Werror=format-security -c -o unittests-evo_model.o `test -f '../src/evo_model.cxx' || echo './'`../src/evo_model.cxx g++ -std=gnu++14 -DHAVE_CONFIG_H -I. -I.. -I../src -I../libs -std=c++14 -Wall -Wextra -Wdate-time -D_FORTIFY_SOURCE=2 -fms-extensions -ggdb -g -O2 -fdebug-prefix-map=/build/phylonium-EhZZLy/phylonium-1.3=. -fstack-protector-strong -Wformat -Werror=format-security -c -o unittests-process.o `test -f '../src/process.cxx' || echo './'`../src/process.cxx ../src/process.cxx:420: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas] 420 | #pragma omp parallel for num_threads(THREADS) | ../src/process.cxx:432: warning: ignoring ‘#pragma omp critical’ [-Wunknown-pragmas] 432 | #pragma omp critical | ../src/process.cxx:435: warning: ignoring ‘#pragma omp atomic’ [-Wunknown-pragmas] 435 | #pragma omp atomic | ../src/process.cxx:441: warning: ignoring ‘#pragma omp critical’ [-Wunknown-pragmas] 441 | #pragma omp critical | ../src/process.cxx:511: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas] 511 | #pragma omp parallel for num_threads(THREADS) | ../src/process.cxx:518: warning: ignoring ‘#pragma omp atomic’ [-Wunknown-pragmas] 518 | #pragma omp atomic | ../src/process.cxx:526: warning: ignoring ‘#pragma omp atomic’ [-Wunknown-pragmas] 526 | #pragma omp atomic read | ../src/process.cxx:532: warning: ignoring ‘#pragma omp critical’ [-Wunknown-pragmas] 532 | #pragma omp critical | ../src/esa.cxx: In constructor ‘esa::esa(const sequence&)’: ../src/esa.cxx:63:55: warning: narrowing conversion of ‘(((& seq)->sequence::size() * 2) + 1)’ from ‘long unsigned int’ to ‘int’ [-Wnarrowing] 63 | esa::esa(const sequence &seq) : m_size{seq.size() * 2 + 1} | ~~~~~~~~~~~~~~~^~~ g++ -std=gnu++14 -DHAVE_CONFIG_H -I. -I.. -I../src -I../libs -std=c++14 -Wall -Wextra -Wdate-time -D_FORTIFY_SOURCE=2 -fms-extensions -ggdb -g -O2 -fdebug-prefix-map=/build/phylonium-EhZZLy/phylonium-1.3=. -fstack-protector-strong -Wformat -Werror=format-security -c -o unittests-sequence.o `test -f '../src/sequence.cxx' || echo './'`../src/sequence.cxx g++ -std=gnu++14 -DHAVE_CONFIG_H -I. -I.. -I../src -I../libs -std=c++14 -Wall -Wextra -Wdate-time -D_FORTIFY_SOURCE=2 -fms-extensions -ggdb -g -O2 -fdebug-prefix-map=/build/phylonium-EhZZLy/phylonium-1.3=. -fstack-protector-strong -Wformat -Werror=format-security -c -o unittests-Tmain.o `test -f 'Tmain.cxx' || echo './'`Tmain.cxx g++ -std=gnu++14 -DHAVE_CONFIG_H -I. -I.. -I../src -I../libs -std=c++14 -Wall -Wextra -Wdate-time -D_FORTIFY_SOURCE=2 -fms-extensions -ggdb -g -O2 -fdebug-prefix-map=/build/phylonium-EhZZLy/phylonium-1.3=. -fstack-protector-strong -Wformat -Werror=format-security -c -o unittests-Tprocess.o `test -f 'Tprocess.cxx' || echo './'`Tprocess.cxx g++ -std=gnu++14 -DHAVE_CONFIG_H -I. -I.. -I../src -I../libs -std=c++14 -Wall -Wextra -Wdate-time -D_FORTIFY_SOURCE=2 -fms-extensions -ggdb -g -O2 -fdebug-prefix-map=/build/phylonium-EhZZLy/phylonium-1.3=. -fstack-protector-strong -Wformat -Werror=format-security -c -o unittests-Tsequence.o `test -f 'Tsequence.cxx' || echo './'`Tsequence.cxx g++ -std=gnu++14 -ggdb -g -O2 -fdebug-prefix-map=/build/phylonium-EhZZLy/phylonium-1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o simf simf-simf.o -ldivsufsort -lm g++ -std=gnu++14 -ggdb -g -O2 -fdebug-prefix-map=/build/phylonium-EhZZLy/phylonium-1.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o unittests unittests-esa.o unittests-evo_model.o unittests-process.o unittests-sequence.o unittests-Tmain.o unittests-Tprocess.o unittests-Tsequence.o ../libs/libcompat.a ../libs/libpfasta.a ../libs/librevseqcmp.a ../libs/libseqcmp.a ../libs/librevseqcmp_avx2.a ../libs/librevseqcmp_ssse3.a ../libs/libseqcmp_avx2.a ../libs/libseqcmp_sse2.a ../libs/libseqcmp_avx512.a -ldivsufsort -lm make[3]: Leaving directory '/build/phylonium-EhZZLy/phylonium-1.3/test' make[2]: Leaving directory '/build/phylonium-EhZZLy/phylonium-1.3/test' Making check in . make[2]: Entering directory '/build/phylonium-EhZZLy/phylonium-1.3' make check-TESTS make[3]: Entering directory '/build/phylonium-EhZZLy/phylonium-1.3' make[4]: Entering directory '/build/phylonium-EhZZLy/phylonium-1.3' PASS: test/unittests PASS: test/simple.sh ============================================================================ Testsuite summary for phylonium 1.3 ============================================================================ # TOTAL: 2 # PASS: 2 # SKIP: 0 # XFAIL: 0 # FAIL: 0 # XPASS: 0 # ERROR: 0 ============================================================================ make[4]: Leaving directory '/build/phylonium-EhZZLy/phylonium-1.3' make[3]: Leaving directory '/build/phylonium-EhZZLy/phylonium-1.3' make[2]: Leaving directory '/build/phylonium-EhZZLy/phylonium-1.3' make[1]: Leaving directory '/build/phylonium-EhZZLy/phylonium-1.3' create-stamp debian/debhelper-build-stamp dh_testroot -a dh_prep -a dh_auto_install -a make -j4 install DESTDIR=/build/phylonium-EhZZLy/phylonium-1.3/debian/phylonium AM_UPDATE_INFO_DIR=no make[1]: Entering directory '/build/phylonium-EhZZLy/phylonium-1.3' Making install in libs make[2]: Entering directory '/build/phylonium-EhZZLy/phylonium-1.3/libs' make[3]: Entering directory '/build/phylonium-EhZZLy/phylonium-1.3/libs' make[3]: Nothing to be done for 'install-exec-am'. make[3]: Nothing to be done for 'install-data-am'. make[3]: Leaving directory '/build/phylonium-EhZZLy/phylonium-1.3/libs' make[2]: Leaving directory '/build/phylonium-EhZZLy/phylonium-1.3/libs' Making install in src make[2]: Entering directory '/build/phylonium-EhZZLy/phylonium-1.3/src' make[3]: Entering directory '/build/phylonium-EhZZLy/phylonium-1.3/src' make[3]: Nothing to be done for 'install-data-am'. /bin/mkdir -p '/build/phylonium-EhZZLy/phylonium-1.3/debian/phylonium/usr/bin' /usr/bin/install -c phylonium '/build/phylonium-EhZZLy/phylonium-1.3/debian/phylonium/usr/bin' make[3]: Leaving directory '/build/phylonium-EhZZLy/phylonium-1.3/src' make[2]: Leaving directory '/build/phylonium-EhZZLy/phylonium-1.3/src' Making install in test make[2]: Entering directory '/build/phylonium-EhZZLy/phylonium-1.3/test' make[3]: Entering directory '/build/phylonium-EhZZLy/phylonium-1.3/test' make[3]: Nothing to be done for 'install-exec-am'. make[3]: Nothing to be done for 'install-data-am'. make[3]: Leaving directory '/build/phylonium-EhZZLy/phylonium-1.3/test' make[2]: Leaving directory '/build/phylonium-EhZZLy/phylonium-1.3/test' Making install in . make[2]: Entering directory '/build/phylonium-EhZZLy/phylonium-1.3' make[3]: Entering directory '/build/phylonium-EhZZLy/phylonium-1.3' make[3]: Nothing to be done for 'install-exec-am'. /bin/mkdir -p '/build/phylonium-EhZZLy/phylonium-1.3/debian/phylonium/usr/share/doc/phylonium' /bin/mkdir -p '/build/phylonium-EhZZLy/phylonium-1.3/debian/phylonium/usr/share/man/man1' /usr/bin/install -c -m 644 documentation/manual.pdf '/build/phylonium-EhZZLy/phylonium-1.3/debian/phylonium/usr/share/doc/phylonium' /usr/bin/install -c -m 644 man/phylonium.1 '/build/phylonium-EhZZLy/phylonium-1.3/debian/phylonium/usr/share/man/man1' make[3]: Leaving directory '/build/phylonium-EhZZLy/phylonium-1.3' make[2]: Leaving directory '/build/phylonium-EhZZLy/phylonium-1.3' make[1]: Leaving directory '/build/phylonium-EhZZLy/phylonium-1.3' dh_installdocs -a dh_installdocs: warning: Could not parse doc-base for doc-base Document id; skipping dh_installchangelogs -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 -a dh_strip -a -a dh_makeshlibs -a -a dh_shlibdeps -a -a dh_installdeb -a dh_gencontrol -a dh_md5sums -a dh_builddeb -a dpkg-deb: building package 'phylonium' in '../phylonium_1.3-1_amd64.deb'. dpkg-deb: building package 'phylonium-dbgsym' in '../phylonium-dbgsym_1.3-1_amd64.deb'. dpkg-genbuildinfo --build=any dpkg-genchanges --build=any >../phylonium_1.3-1_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/phylonium-EhZZLy /tmp/phylonium-1.3-1u_wkoyc9 I: cleaning package lists and apt cache... I: creating tarball... I: done I: removing tempdir /tmp/mmdebstrap.8u1G_WvIUK... I: success in 778.1462 seconds md5: phylonium-dbgsym_1.3-1_amd64.deb: OK md5: phylonium_1.3-1_amd64.deb: OK sha1: phylonium-dbgsym_1.3-1_amd64.deb: OK sha1: phylonium_1.3-1_amd64.deb: OK sha256: phylonium-dbgsym_1.3-1_amd64.deb: OK sha256: phylonium_1.3-1_amd64.deb: OK Checksums: OK