Thu Nov 7 23:26:07 UTC 2024 I: starting to build shapeit4/trixie/armhf on jenkins on '2024-11-07 23:25' Thu Nov 7 23:26:07 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/armhf_13/6475/console.log Thu Nov 7 23:26:07 UTC 2024 I: Downloading source for trixie/shapeit4=4.2.2+dfsg-1 --2024-11-07 23:26:08-- http://deb.debian.org/debian/pool/main/s/shapeit4/shapeit4_4.2.2%2bdfsg-1.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2134 (2.1K) [text/prs.lines.tag] Saving to: ‘shapeit4_4.2.2+dfsg-1.dsc’ 0K .. 100% 192M=0s 2024-11-07 23:26:08 (192 MB/s) - ‘shapeit4_4.2.2+dfsg-1.dsc’ saved [2134/2134] Thu Nov 7 23:26:08 UTC 2024 I: shapeit4_4.2.2+dfsg-1.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: shapeit4 Binary: shapeit4, shapeit4-example Architecture: any all Version: 4.2.2+dfsg-1 Maintainer: Debian Med Packaging Team Uploaders: Dylan Aïssi Homepage: https://odelaneau.github.io/shapeit4/ Standards-Version: 4.6.0 Vcs-Browser: https://salsa.debian.org/med-team/shapeit4 Vcs-Git: https://salsa.debian.org/med-team/shapeit4.git Testsuite: autopkgtest Build-Depends: debhelper-compat (= 13), libboost-iostreams-dev, libboost-program-options-dev, libbz2-dev, libhts-dev, libssl-dev Package-List: shapeit4 deb science optional arch=any shapeit4-example deb doc optional arch=all Checksums-Sha1: 74489c1b97358dbbfa9245812b131d8df69cc742 58962780 shapeit4_4.2.2+dfsg.orig.tar.xz e019b0ec958bd082337abbf437e5a1aea5d92a76 5200 shapeit4_4.2.2+dfsg-1.debian.tar.xz Checksums-Sha256: 0a8c5da94ab21a092a6acb77e795d91a40c5034a2ee80b9ffa679cd95114937c 58962780 shapeit4_4.2.2+dfsg.orig.tar.xz d42b9df3505c3874e9c18d676af83ef315e84afb57dc7036737a2f71af121bc0 5200 shapeit4_4.2.2+dfsg-1.debian.tar.xz Files: f3e35676c663d0ecba185a9b98cd95c5 58962780 shapeit4_4.2.2+dfsg.orig.tar.xz 0e07e040f73ac50205869fe79f473919 5200 shapeit4_4.2.2+dfsg-1.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQIzBAEBCgAdFiEEmjwHvQbeL0FugTpdYS7xYT4FD1QFAmFEidwACgkQYS7xYT4F D1Qb4RAAqTHiJ8+FbSoRqNnKtGk9hQXBr2hehl0lrN6zuc41Jk8wy8Q9mlOS3BSp Ki4oYYNjhTs8gLuttkdo4oRnF6DBeeqw8NTZ77osUkFYVZ7kJzokGvN+px/XKJDK uTAAllhoNIoUsA9iz0ACg4r6kAZJ5v/X5AoZ+Y+CQa5uUBzCFObtCIyj8Qyk7EIT dzWe4taxmUQaHmLSjtkGrk0bS6UiNoQzdqNpNZpRBrneKqyXYxA5Xy7rKfO5MeOE YO0Imv/Gtnvfz/3MXdtHWcwELvQZYmHrPymEqs7+ogElSKTMoOxyzOQ9t/2x6BRh dLZjS7vQmfAhfrMJRXChxUiD+m9cGif6lQSW8iVpnaUywMjgV4hwSysTmxpWiMZF 61wbV4yNu8SiemB36fN2vGbKmM6lvMrfTK5Hs9AP/VVxCPCVpreLfQ8arS624kaH vLr6LfMny44Hg3YtEf0bzJUZ9vc49Mb0DeQbIvEhJXP4xbQ0metnAkA18EH/3e+t VmQe19uJSV3R7UF+mfA7oLS5pDF+Ut21gRmcMwSuTqn4klWKD0PIJFj+aWHGKwPz qBHXc4WUJ2HcKj79h5e+OP6xLZoo4bWmzvf1nq+fTbJg+Oz6uE+KMjmy9r6ms13p jf9/Y1TxKqhrUC6PfV/xYoTtEIAJn+PHgcDmNvjm3+IHOojIATo= =RH/t -----END PGP SIGNATURE----- Thu Nov 7 23:26:08 UTC 2024 I: Checking whether the package is not for us Thu Nov 7 23:26:08 UTC 2024 I: Starting 1st build on remote node ff64a-armhf-rb.debian.net. Thu Nov 7 23:26:08 UTC 2024 I: Preparing to do remote build '1' on ff64a-armhf-rb.debian.net. Thu Nov 7 23:44:29 UTC 2024 I: Deleting $TMPDIR on ff64a-armhf-rb.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Thu Nov 7 11:26:20 -12 2024 I: pbuilder-time-stamp: 1731021980 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [shapeit4_4.2.2+dfsg-1.dsc] I: copying [./shapeit4_4.2.2+dfsg.orig.tar.xz] I: copying [./shapeit4_4.2.2+dfsg-1.debian.tar.xz] I: Extracting source gpgv: Signature made Fri Sep 17 12:28:12 2021 gpgv: using RSA key 9A3C07BD06DE2F416E813A5D612EF1613E050F54 gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./shapeit4_4.2.2+dfsg-1.dsc: no acceptable signature found dpkg-source: info: extracting shapeit4 in shapeit4-4.2.2+dfsg dpkg-source: info: unpacking shapeit4_4.2.2+dfsg.orig.tar.xz dpkg-source: info: unpacking shapeit4_4.2.2+dfsg-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying use_shared_libs.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/7756/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='armhf' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=5 ' DISTRIBUTION='trixie' HOME='/root' HOST_ARCH='armhf' IFS=' ' INVOCATION_ID='a3ba23970f41445bb9ce3f1616bc2fc4' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='7756' PS1='# ' PS2='> ' PS4='+ ' PWD='/' SHELL='/bin/bash' SHLVL='2' SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.hOZkEMzy/pbuilderrc_1jib --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.hOZkEMzy/b1 --logfile b1/build.log shapeit4_4.2.2+dfsg-1.dsc' SUDO_GID='114' SUDO_UID='109' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://10.0.0.15:3142/' I: uname -a Linux ff64a 6.1.0-26-arm64 #1 SMP Debian 6.1.112-1 (2024-09-30) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 4 21:30 /bin -> usr/bin I: user script /srv/workspace/pbuilder/7756/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: armhf Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), libboost-iostreams-dev, libboost-program-options-dev, libbz2-dev, libhts-dev, libssl-dev dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19690 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on libboost-iostreams-dev; however: Package libboost-iostreams-dev is not installed. pbuilder-satisfydepends-dummy depends on libboost-program-options-dev; however: Package libboost-program-options-dev is not installed. pbuilder-satisfydepends-dummy depends on libbz2-dev; however: Package libbz2-dev is not installed. pbuilder-satisfydepends-dummy depends on libhts-dev; however: Package libhts-dev is not installed. pbuilder-satisfydepends-dummy depends on libssl-dev; however: Package libssl-dev is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} icu-devtools{a} intltool-debian{a} libarchive-zip-perl{a} libboost-iostreams-dev{a} libboost-iostreams1.83-dev{a} libboost-program-options-dev{a} libboost-program-options1.83-dev{a} libboost-program-options1.83.0{a} libboost-regex1.83-dev{a} libboost-regex1.83.0{a} libboost1.83-dev{a} libbrotli-dev{a} libbrotli1{a} libbz2-dev{a} libcom-err2{a} libcurl3t64-gnutls{a} libcurl4-gnutls-dev{a} libdebhelper-perl{a} libdeflate-dev{a} libdeflate0{a} libelf1t64{a} libevent-2.1-7t64{a} libfile-stripnondeterminism-perl{a} libgmp-dev{a} libgmpxx4ldbl{a} libgnutls-dane0t64{a} libgnutls-openssl27t64{a} libgnutls28-dev{a} libgssapi-krb5-2{a} libhts-dev{a} libhts3t64{a} libhtscodecs2{a} libicu-dev{a} libicu72{a} libidn2-dev{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} libldap-2.5-0{a} liblzma-dev{a} libmagic-mgc{a} libmagic1t64{a} libnghttp2-14{a} libnghttp2-dev{a} libnghttp3-9{a} libnghttp3-dev{a} libngtcp2-16{a} libngtcp2-crypto-gnutls-dev{a} libngtcp2-crypto-gnutls8{a} libngtcp2-dev{a} libp11-kit-dev{a} libpipeline1{a} libpkgconf3{a} libpsl-dev{a} libpsl5t64{a} librtmp-dev{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libssh2-1-dev{a} libssh2-1t64{a} libssl-dev{a} libtasn1-6-dev{a} libtool{a} libuchardet0{a} libunbound8{a} libxml2{a} libzstd-dev{a} m4{a} man-db{a} nettle-dev{a} pkgconf{a} pkgconf-bin{a} po-debconf{a} sensible-utils{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: bzip2-doc ca-certificates curl krb5-locales libarchive-cpio-perl libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules libtasn1-doc lynx publicsuffix wget 0 packages upgraded, 90 newly installed, 0 to remove and 0 not upgraded. Need to get 56.9 MB of archives. After unpacking 330 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main armhf sensible-utils all 0.0.24 [24.8 kB] Get: 2 http://deb.debian.org/debian trixie/main armhf libmagic-mgc armhf 1:5.45-3+b1 [314 kB] Get: 3 http://deb.debian.org/debian trixie/main armhf libmagic1t64 armhf 1:5.45-3+b1 [98.5 kB] Get: 4 http://deb.debian.org/debian trixie/main armhf file armhf 1:5.45-3+b1 [42.3 kB] Get: 5 http://deb.debian.org/debian trixie/main armhf gettext-base armhf 0.22.5-2 [195 kB] Get: 6 http://deb.debian.org/debian trixie/main armhf libuchardet0 armhf 0.0.8-1+b2 [65.6 kB] Get: 7 http://deb.debian.org/debian trixie/main armhf groff-base armhf 1.23.0-5 [1091 kB] Get: 8 http://deb.debian.org/debian trixie/main armhf bsdextrautils armhf 2.40.2-9 [88.8 kB] Get: 9 http://deb.debian.org/debian trixie/main armhf libpipeline1 armhf 1.5.8-1 [35.0 kB] Get: 10 http://deb.debian.org/debian trixie/main armhf man-db armhf 2.13.0-1 [1382 kB] Get: 11 http://deb.debian.org/debian trixie/main armhf m4 armhf 1.4.19-4 [264 kB] Get: 12 http://deb.debian.org/debian trixie/main armhf autoconf all 2.72-3 [493 kB] Get: 13 http://deb.debian.org/debian trixie/main armhf autotools-dev all 20220109.1 [51.6 kB] Get: 14 http://deb.debian.org/debian trixie/main armhf automake all 1:1.16.5-1.3 [823 kB] Get: 15 http://deb.debian.org/debian trixie/main armhf autopoint all 0.22.5-2 [723 kB] Get: 16 http://deb.debian.org/debian trixie/main armhf libdebhelper-perl all 13.20 [89.7 kB] Get: 17 http://deb.debian.org/debian trixie/main armhf libtool all 2.4.7-8 [517 kB] Get: 18 http://deb.debian.org/debian trixie/main armhf dh-autoreconf all 20 [17.1 kB] Get: 19 http://deb.debian.org/debian trixie/main armhf libarchive-zip-perl all 1.68-1 [104 kB] Get: 20 http://deb.debian.org/debian trixie/main armhf libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 21 http://deb.debian.org/debian trixie/main armhf dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 22 http://deb.debian.org/debian trixie/main armhf libelf1t64 armhf 0.192-4 [184 kB] Get: 23 http://deb.debian.org/debian trixie/main armhf dwz armhf 0.15-1+b2 [106 kB] Get: 24 http://deb.debian.org/debian trixie/main armhf libicu72 armhf 72.1-5+b1 [9088 kB] Get: 25 http://deb.debian.org/debian trixie/main armhf libxml2 armhf 2.12.7+dfsg+really2.9.14-0.1 [604 kB] Get: 26 http://deb.debian.org/debian trixie/main armhf gettext armhf 0.22.5-2 [1485 kB] Get: 27 http://deb.debian.org/debian trixie/main armhf intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 28 http://deb.debian.org/debian trixie/main armhf po-debconf all 1.0.21+nmu1 [248 kB] Get: 29 http://deb.debian.org/debian trixie/main armhf debhelper all 13.20 [915 kB] Get: 30 http://deb.debian.org/debian trixie/main armhf icu-devtools armhf 72.1-5+b1 [187 kB] Get: 31 http://deb.debian.org/debian trixie/main armhf libboost1.83-dev armhf 1.83.0-3.2 [10.6 MB] Get: 32 http://deb.debian.org/debian trixie/main armhf libboost-regex1.83.0 armhf 1.83.0-3.2 [307 kB] Get: 33 http://deb.debian.org/debian trixie/main armhf libicu-dev armhf 72.1-5+b1 [10.1 MB] Get: 34 http://deb.debian.org/debian trixie/main armhf libboost-regex1.83-dev armhf 1.83.0-3.2 [335 kB] Get: 35 http://deb.debian.org/debian trixie/main armhf libboost-iostreams1.83-dev armhf 1.83.0-3.2 [260 kB] Get: 36 http://deb.debian.org/debian trixie/main armhf libboost-iostreams-dev armhf 1.83.0.2+b2 [3568 B] Get: 37 http://deb.debian.org/debian trixie/main armhf libboost-program-options1.83.0 armhf 1.83.0-3.2 [326 kB] Get: 38 http://deb.debian.org/debian trixie/main armhf libboost-program-options1.83-dev armhf 1.83.0-3.2 [369 kB] Get: 39 http://deb.debian.org/debian trixie/main armhf libboost-program-options-dev armhf 1.83.0.2+b2 [3604 B] Get: 40 http://deb.debian.org/debian trixie/main armhf libbrotli1 armhf 1.1.0-2+b5 [296 kB] Get: 41 http://deb.debian.org/debian trixie/main armhf libbrotli-dev armhf 1.1.0-2+b5 [294 kB] Get: 42 http://deb.debian.org/debian trixie/main armhf libbz2-dev armhf 1.0.8-6 [28.7 kB] Get: 43 http://deb.debian.org/debian trixie/main armhf libcom-err2 armhf 1.47.1-1+b1 [22.3 kB] Get: 44 http://deb.debian.org/debian trixie/main armhf libkrb5support0 armhf 1.21.3-3 [30.0 kB] Get: 45 http://deb.debian.org/debian trixie/main armhf libk5crypto3 armhf 1.21.3-3 [75.8 kB] Get: 46 http://deb.debian.org/debian trixie/main armhf libkeyutils1 armhf 1.6.3-4 [8096 B] Get: 47 http://deb.debian.org/debian trixie/main armhf libkrb5-3 armhf 1.21.3-3 [283 kB] Get: 48 http://deb.debian.org/debian trixie/main armhf libgssapi-krb5-2 armhf 1.21.3-3 [114 kB] Get: 49 http://deb.debian.org/debian trixie/main armhf libsasl2-modules-db armhf 2.1.28+dfsg1-8 [18.2 kB] Get: 50 http://deb.debian.org/debian trixie/main armhf libsasl2-2 armhf 2.1.28+dfsg1-8 [50.2 kB] Get: 51 http://deb.debian.org/debian trixie/main armhf libldap-2.5-0 armhf 2.5.18+dfsg-3+b1 [163 kB] Get: 52 http://deb.debian.org/debian trixie/main armhf libnghttp2-14 armhf 1.64.0-1 [62.9 kB] Get: 53 http://deb.debian.org/debian trixie/main armhf libnghttp3-9 armhf 1.4.0-1+b1 [55.0 kB] Get: 54 http://deb.debian.org/debian trixie/main armhf libngtcp2-16 armhf 1.6.0-1 [118 kB] Get: 55 http://deb.debian.org/debian trixie/main armhf libngtcp2-crypto-gnutls8 armhf 1.6.0-1 [17.1 kB] Get: 56 http://deb.debian.org/debian trixie/main armhf libpsl5t64 armhf 0.21.2-1.1+b1 [55.8 kB] Get: 57 http://deb.debian.org/debian trixie/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2+b5 [53.2 kB] Get: 58 http://deb.debian.org/debian trixie/main armhf libssh2-1t64 armhf 1.11.1-1 [227 kB] Get: 59 http://deb.debian.org/debian trixie/main armhf libcurl3t64-gnutls armhf 8.10.1-2 [308 kB] Get: 60 http://deb.debian.org/debian trixie/main armhf libevent-2.1-7t64 armhf 2.1.12-stable-10+b1 [164 kB] Get: 61 http://deb.debian.org/debian trixie/main armhf libunbound8 armhf 1.22.0-1 [539 kB] Get: 62 http://deb.debian.org/debian trixie/main armhf libgnutls-dane0t64 armhf 3.8.6-2+b1 [432 kB] Get: 63 http://deb.debian.org/debian trixie/main armhf libgnutls-openssl27t64 armhf 3.8.6-2+b1 [432 kB] Get: 64 http://deb.debian.org/debian trixie/main armhf libidn2-dev armhf 2.3.7-2+b1 [119 kB] Get: 65 http://deb.debian.org/debian trixie/main armhf libp11-kit-dev armhf 0.25.5-2+b1 [208 kB] Get: 66 http://deb.debian.org/debian trixie/main armhf libtasn1-6-dev armhf 4.19.0-3+b3 [93.2 kB] Get: 67 http://deb.debian.org/debian trixie/main armhf libgmpxx4ldbl armhf 2:6.3.0+dfsg-2+b2 [328 kB] Get: 68 http://deb.debian.org/debian trixie/main armhf libgmp-dev armhf 2:6.3.0+dfsg-2+b2 [593 kB] Get: 69 http://deb.debian.org/debian trixie/main armhf nettle-dev armhf 3.10-1+b1 [1313 kB] Get: 70 http://deb.debian.org/debian trixie/main armhf libgnutls28-dev armhf 3.8.6-2+b1 [1322 kB] Get: 71 http://deb.debian.org/debian trixie/main armhf libpkgconf3 armhf 1.8.1-4 [31.8 kB] Get: 72 http://deb.debian.org/debian trixie/main armhf pkgconf-bin armhf 1.8.1-4 [29.2 kB] Get: 73 http://deb.debian.org/debian trixie/main armhf pkgconf armhf 1.8.1-4 [26.1 kB] Get: 74 http://deb.debian.org/debian trixie/main armhf libnghttp2-dev armhf 1.64.0-1 [103 kB] Get: 75 http://deb.debian.org/debian trixie/main armhf libnghttp3-dev armhf 1.4.0-1+b1 [79.8 kB] Get: 76 http://deb.debian.org/debian trixie/main armhf libngtcp2-crypto-gnutls-dev armhf 1.6.0-1 [22.1 kB] Get: 77 http://deb.debian.org/debian trixie/main armhf libngtcp2-dev armhf 1.6.0-1 [168 kB] Get: 78 http://deb.debian.org/debian trixie/main armhf libpsl-dev armhf 0.21.2-1.1+b1 [76.8 kB] Get: 79 http://deb.debian.org/debian trixie/main armhf zlib1g-dev armhf 1:1.3.dfsg+really1.3.1-1+b1 [905 kB] Get: 80 http://deb.debian.org/debian trixie/main armhf librtmp-dev armhf 2.4+20151223.gitfa8646d.1-2+b5 [63.6 kB] Get: 81 http://deb.debian.org/debian trixie/main armhf libssl-dev armhf 3.3.2-2 [2385 kB] Get: 82 http://deb.debian.org/debian trixie/main armhf libssh2-1-dev armhf 1.11.1-1 [378 kB] Get: 83 http://deb.debian.org/debian trixie/main armhf libzstd-dev armhf 1.5.6+dfsg-1+b1 [327 kB] Get: 84 http://deb.debian.org/debian trixie/main armhf libcurl4-gnutls-dev armhf 8.10.1-2 [431 kB] Get: 85 http://deb.debian.org/debian trixie/main armhf libdeflate0 armhf 1.22-1 [36.3 kB] Get: 86 http://deb.debian.org/debian trixie/main armhf libdeflate-dev armhf 1.22-1 [44.5 kB] Get: 87 http://deb.debian.org/debian trixie/main armhf libhtscodecs2 armhf 1.6.1-1 [63.1 kB] Get: 88 http://deb.debian.org/debian trixie/main armhf libhts3t64 armhf 1.20+ds-2 [401 kB] Get: 89 http://deb.debian.org/debian trixie/main armhf liblzma-dev armhf 5.6.3-1+b1 [304 kB] Get: 90 http://deb.debian.org/debian trixie/main armhf libhts-dev armhf 1.20+ds-2 [1625 kB] Fetched 56.9 MB in 4s (16.2 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package sensible-utils. (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 ... 19690 files and directories currently installed.) Preparing to unpack .../00-sensible-utils_0.0.24_all.deb ... Unpacking sensible-utils (0.0.24) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../01-libmagic-mgc_1%3a5.45-3+b1_armhf.deb ... Unpacking libmagic-mgc (1:5.45-3+b1) ... Selecting previously unselected package libmagic1t64:armhf. 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Unpacking dh-strip-nondeterminism (1.14.0-1) ... Selecting previously unselected package libelf1t64:armhf. Preparing to unpack .../21-libelf1t64_0.192-4_armhf.deb ... Unpacking libelf1t64:armhf (0.192-4) ... Selecting previously unselected package dwz. Preparing to unpack .../22-dwz_0.15-1+b2_armhf.deb ... Unpacking dwz (0.15-1+b2) ... Selecting previously unselected package libicu72:armhf. Preparing to unpack .../23-libicu72_72.1-5+b1_armhf.deb ... Unpacking libicu72:armhf (72.1-5+b1) ... Selecting previously unselected package libxml2:armhf. Preparing to unpack .../24-libxml2_2.12.7+dfsg+really2.9.14-0.1_armhf.deb ... Unpacking libxml2:armhf (2.12.7+dfsg+really2.9.14-0.1) ... Selecting previously unselected package gettext. Preparing to unpack .../25-gettext_0.22.5-2_armhf.deb ... Unpacking gettext (0.22.5-2) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../26-intltool-debian_0.35.0+20060710.6_all.deb ... Unpacking intltool-debian (0.35.0+20060710.6) ... Selecting previously unselected package po-debconf. Preparing to unpack .../27-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../28-debhelper_13.20_all.deb ... Unpacking debhelper (13.20) ... Selecting previously unselected package icu-devtools. Preparing to unpack .../29-icu-devtools_72.1-5+b1_armhf.deb ... Unpacking icu-devtools (72.1-5+b1) ... Selecting previously unselected package libboost1.83-dev:armhf. Preparing to unpack .../30-libboost1.83-dev_1.83.0-3.2_armhf.deb ... Unpacking libboost1.83-dev:armhf (1.83.0-3.2) ... Selecting previously unselected package libboost-regex1.83.0:armhf. Preparing to unpack .../31-libboost-regex1.83.0_1.83.0-3.2_armhf.deb ... Unpacking libboost-regex1.83.0:armhf (1.83.0-3.2) ... Selecting previously unselected package libicu-dev:armhf. Preparing to unpack .../32-libicu-dev_72.1-5+b1_armhf.deb ... 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Unpacking libcom-err2:armhf (1.47.1-1+b1) ... Selecting previously unselected package libkrb5support0:armhf. Preparing to unpack .../43-libkrb5support0_1.21.3-3_armhf.deb ... Unpacking libkrb5support0:armhf (1.21.3-3) ... Selecting previously unselected package libk5crypto3:armhf. Preparing to unpack .../44-libk5crypto3_1.21.3-3_armhf.deb ... Unpacking libk5crypto3:armhf (1.21.3-3) ... Selecting previously unselected package libkeyutils1:armhf. Preparing to unpack .../45-libkeyutils1_1.6.3-4_armhf.deb ... Unpacking libkeyutils1:armhf (1.6.3-4) ... Selecting previously unselected package libkrb5-3:armhf. Preparing to unpack .../46-libkrb5-3_1.21.3-3_armhf.deb ... Unpacking libkrb5-3:armhf (1.21.3-3) ... Selecting previously unselected package libgssapi-krb5-2:armhf. Preparing to unpack .../47-libgssapi-krb5-2_1.21.3-3_armhf.deb ... Unpacking libgssapi-krb5-2:armhf (1.21.3-3) ... Selecting previously unselected package libsasl2-modules-db:armhf. 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Selecting previously unselected package libngtcp2-crypto-gnutls8:armhf. Preparing to unpack .../54-libngtcp2-crypto-gnutls8_1.6.0-1_armhf.deb ... Unpacking libngtcp2-crypto-gnutls8:armhf (1.6.0-1) ... Selecting previously unselected package libpsl5t64:armhf. Preparing to unpack .../55-libpsl5t64_0.21.2-1.1+b1_armhf.deb ... Unpacking libpsl5t64:armhf (0.21.2-1.1+b1) ... Selecting previously unselected package librtmp1:armhf. Preparing to unpack .../56-librtmp1_2.4+20151223.gitfa8646d.1-2+b5_armhf.deb ... Unpacking librtmp1:armhf (2.4+20151223.gitfa8646d.1-2+b5) ... Selecting previously unselected package libssh2-1t64:armhf. Preparing to unpack .../57-libssh2-1t64_1.11.1-1_armhf.deb ... Unpacking libssh2-1t64:armhf (1.11.1-1) ... Selecting previously unselected package libcurl3t64-gnutls:armhf. Preparing to unpack .../58-libcurl3t64-gnutls_8.10.1-2_armhf.deb ... Unpacking libcurl3t64-gnutls:armhf (8.10.1-2) ... Selecting previously unselected package libevent-2.1-7t64:armhf. Preparing to unpack .../59-libevent-2.1-7t64_2.1.12-stable-10+b1_armhf.deb ... Unpacking libevent-2.1-7t64:armhf (2.1.12-stable-10+b1) ... Selecting previously unselected package libunbound8:armhf. Preparing to unpack .../60-libunbound8_1.22.0-1_armhf.deb ... Unpacking libunbound8:armhf (1.22.0-1) ... Selecting previously unselected package libgnutls-dane0t64:armhf. Preparing to unpack .../61-libgnutls-dane0t64_3.8.6-2+b1_armhf.deb ... Unpacking libgnutls-dane0t64:armhf (3.8.6-2+b1) ... Selecting previously unselected package libgnutls-openssl27t64:armhf. Preparing to unpack .../62-libgnutls-openssl27t64_3.8.6-2+b1_armhf.deb ... Unpacking libgnutls-openssl27t64:armhf (3.8.6-2+b1) ... Selecting previously unselected package libidn2-dev:armhf. Preparing to unpack .../63-libidn2-dev_2.3.7-2+b1_armhf.deb ... Unpacking libidn2-dev:armhf (2.3.7-2+b1) ... Selecting previously unselected package libp11-kit-dev:armhf. Preparing to unpack .../64-libp11-kit-dev_0.25.5-2+b1_armhf.deb ... 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Selecting previously unselected package libpkgconf3:armhf. Preparing to unpack .../70-libpkgconf3_1.8.1-4_armhf.deb ... Unpacking libpkgconf3:armhf (1.8.1-4) ... Selecting previously unselected package pkgconf-bin. Preparing to unpack .../71-pkgconf-bin_1.8.1-4_armhf.deb ... Unpacking pkgconf-bin (1.8.1-4) ... Selecting previously unselected package pkgconf:armhf. Preparing to unpack .../72-pkgconf_1.8.1-4_armhf.deb ... Unpacking pkgconf:armhf (1.8.1-4) ... Selecting previously unselected package libnghttp2-dev:armhf. Preparing to unpack .../73-libnghttp2-dev_1.64.0-1_armhf.deb ... Unpacking libnghttp2-dev:armhf (1.64.0-1) ... Selecting previously unselected package libnghttp3-dev:armhf. Preparing to unpack .../74-libnghttp3-dev_1.4.0-1+b1_armhf.deb ... Unpacking libnghttp3-dev:armhf (1.4.0-1+b1) ... Selecting previously unselected package libngtcp2-crypto-gnutls-dev:armhf. Preparing to unpack .../75-libngtcp2-crypto-gnutls-dev_1.6.0-1_armhf.deb ... 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Setting up libmagic-mgc (1:5.45-3+b1) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libboost-regex1.83.0:armhf (1.83.0-3.2) ... Setting up libdebhelper-perl (13.20) ... Setting up libbrotli1:armhf (1.1.0-2+b5) ... Setting up libmagic1t64:armhf (1:5.45-3+b1) ... Setting up libboost-program-options1.83-dev:armhf (1.83.0-3.2) ... Setting up libpsl5t64:armhf (0.21.2-1.1+b1) ... Setting up libnghttp2-14:armhf (1.64.0-1) ... Setting up libdeflate0:armhf (1.22-1) ... Setting up gettext-base (0.22.5-2) ... Setting up m4 (1.4.19-4) ... Setting up libevent-2.1-7t64:armhf (2.1.12-stable-10+b1) ... Setting up libcom-err2:armhf (1.47.1-1+b1) ... Setting up file (1:5.45-3+b1) ... Setting up libelf1t64:armhf (0.192-4) ... Setting up libpsl-dev:armhf (0.21.2-1.1+b1) ... Setting up libkrb5support0:armhf (1.21.3-3) ... Setting up libsasl2-modules-db:armhf (2.1.28+dfsg1-8) ... Setting up autotools-dev (20220109.1) ... Setting up libunbound8:armhf (1.22.0-1) ... 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Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/reproducible-path/shapeit4-4.2.2+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../shapeit4_4.2.2+dfsg-1_source.changes dpkg-buildpackage: info: source package shapeit4 dpkg-buildpackage: info: source version 4.2.2+dfsg-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Dylan Aïssi dpkg-source --before-build . dpkg-buildpackage: info: host architecture armhf debian/rules clean dh clean dh_auto_clean make -j5 clean make[1]: Entering directory '/build/reproducible-path/shapeit4-4.2.2+dfsg' rm -f obj/*.o bin/shapeit4.2 make[1]: Leaving directory '/build/reproducible-path/shapeit4-4.2.2+dfsg' dh_clean debian/rules binary dh binary dh_update_autotools_config dh_autoreconf dh_auto_configure dh_auto_build make -j5 "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/reproducible-path/shapeit4-4.2.2+dfsg' g++ -std=c++11 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/shapeit4-4.2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -c src/containers/genotype_set.cpp -o obj/genotype_set.o -Isrc -I/build/reproducible-path/shapeit4-4.2.2+dfsg/debian/.debhelper/generated/_source/home/Tools/htslib-1.11 -I/usr/include g++ -std=c++11 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/shapeit4-4.2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -c src/containers/haplotype_set.cpp -o obj/haplotype_set.o -Isrc -I/build/reproducible-path/shapeit4-4.2.2+dfsg/debian/.debhelper/generated/_source/home/Tools/htslib-1.11 -I/usr/include g++ -std=c++11 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/shapeit4-4.2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -c src/containers/bitmatrix.cpp -o obj/bitmatrix.o -Isrc -I/build/reproducible-path/shapeit4-4.2.2+dfsg/debian/.debhelper/generated/_source/home/Tools/htslib-1.11 -I/usr/include g++ -std=c++11 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/shapeit4-4.2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -c src/containers/variant_map.cpp -o obj/variant_map.o -Isrc -I/build/reproducible-path/shapeit4-4.2.2+dfsg/debian/.debhelper/generated/_source/home/Tools/htslib-1.11 -I/usr/include g++ -std=c++11 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/shapeit4-4.2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -c src/io/gmap_reader.cpp -o obj/gmap_reader.o -Isrc -I/build/reproducible-path/shapeit4-4.2.2+dfsg/debian/.debhelper/generated/_source/home/Tools/htslib-1.11 -I/usr/include In file included from src/containers/bitmatrix.cpp:22: src/containers/bitmatrix.h: In function 'unsigned int abracadabra(const unsigned int&, const unsigned int&)': src/containers/bitmatrix.h:28:116: warning: right shift count >= width of type [-Wshift-count-overflow] 28 | return static_cast((static_cast(i1) * static_cast(i2)) >> 32); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ In file included from src/containers/haplotype_set.h:27, from src/containers/haplotype_set.cpp:22: src/containers/bitmatrix.h: In function 'unsigned int abracadabra(const unsigned int&, const unsigned int&)': src/containers/bitmatrix.h:28:116: warning: right shift count >= width of type [-Wshift-count-overflow] 28 | return static_cast((static_cast(i1) * static_cast(i2)) >> 32); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ g++ -std=c++11 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/shapeit4-4.2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -c src/io/graph_writer.cpp -o obj/graph_writer.o -Isrc -I/build/reproducible-path/shapeit4-4.2.2+dfsg/debian/.debhelper/generated/_source/home/Tools/htslib-1.11 -I/usr/include g++ -std=c++11 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/shapeit4-4.2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -c src/io/genotype_reader2.cpp -o obj/genotype_reader2.o -Isrc -I/build/reproducible-path/shapeit4-4.2.2+dfsg/debian/.debhelper/generated/_source/home/Tools/htslib-1.11 -I/usr/include g++ -std=c++11 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/shapeit4-4.2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -c src/io/genotype_reader1.cpp -o obj/genotype_reader1.o -Isrc -I/build/reproducible-path/shapeit4-4.2.2+dfsg/debian/.debhelper/generated/_source/home/Tools/htslib-1.11 -I/usr/include g++ -std=c++11 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/shapeit4-4.2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -c src/io/haplotype_writer.cpp -o obj/haplotype_writer.o -Isrc -I/build/reproducible-path/shapeit4-4.2.2+dfsg/debian/.debhelper/generated/_source/home/Tools/htslib-1.11 -I/usr/include In file included from src/containers/haplotype_set.h:27, from src/io/genotype_reader.h:28, from src/io/genotype_reader2.cpp:22: src/containers/bitmatrix.h: In function 'unsigned int abracadabra(const unsigned int&, const unsigned int&)': src/containers/bitmatrix.h:28:116: warning: right shift count >= width of type [-Wshift-count-overflow] 28 | return static_cast((static_cast(i1) * static_cast(i2)) >> 32); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ In file included from src/containers/haplotype_set.h:27, from src/io/genotype_reader.h:28, from src/io/genotype_reader1.cpp:22: src/containers/bitmatrix.h: In function 'unsigned int abracadabra(const unsigned int&, const unsigned int&)': src/containers/bitmatrix.h:28:116: warning: right shift count >= width of type [-Wshift-count-overflow] 28 | return static_cast((static_cast(i1) * static_cast(i2)) >> 32); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ g++ -std=c++11 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/shapeit4-4.2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -c src/phaser/phaser_finalise.cpp -o obj/phaser_finalise.o -Isrc -I/build/reproducible-path/shapeit4-4.2.2+dfsg/debian/.debhelper/generated/_source/home/Tools/htslib-1.11 -I/usr/include In file included from src/containers/haplotype_set.h:27, from src/io/haplotype_writer.h:28, from src/io/haplotype_writer.cpp:22: src/containers/bitmatrix.h: In function 'unsigned int abracadabra(const unsigned int&, const unsigned int&)': src/containers/bitmatrix.h:28:116: warning: right shift count >= width of type [-Wshift-count-overflow] 28 | return static_cast((static_cast(i1) * static_cast(i2)) >> 32); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ g++ -std=c++11 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/shapeit4-4.2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -c src/phaser/phaser_algorithm.cpp -o obj/phaser_algorithm.o -Isrc -I/build/reproducible-path/shapeit4-4.2.2+dfsg/debian/.debhelper/generated/_source/home/Tools/htslib-1.11 -I/usr/include In file included from src/containers/haplotype_set.h:27, from src/objects/compute_job.h:27, from src/models/haplotype_segment_single.h:26, from src/phaser/phaser_header.h:29, from src/phaser/phaser_finalise.cpp:22: src/containers/bitmatrix.h: In function 'unsigned int abracadabra(const unsigned int&, const unsigned int&)': src/containers/bitmatrix.h:28:116: warning: right shift count >= width of type [-Wshift-count-overflow] 28 | return static_cast((static_cast(i1) * static_cast(i2)) >> 32); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ g++ -std=c++11 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/shapeit4-4.2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -c src/phaser/phaser_parameters.cpp -o obj/phaser_parameters.o -Isrc -I/build/reproducible-path/shapeit4-4.2.2+dfsg/debian/.debhelper/generated/_source/home/Tools/htslib-1.11 -I/usr/include g++ -std=c++11 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/shapeit4-4.2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -c src/phaser/phaser_management.cpp -o obj/phaser_management.o -Isrc -I/build/reproducible-path/shapeit4-4.2.2+dfsg/debian/.debhelper/generated/_source/home/Tools/htslib-1.11 -I/usr/include g++ -std=c++11 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/shapeit4-4.2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -c src/phaser/phaser_initialise.cpp -o obj/phaser_initialise.o -Isrc -I/build/reproducible-path/shapeit4-4.2.2+dfsg/debian/.debhelper/generated/_source/home/Tools/htslib-1.11 -I/usr/include In file included from src/containers/haplotype_set.h:27, from src/objects/compute_job.h:27, from src/models/haplotype_segment_single.h:26, from src/phaser/phaser_header.h:29, from src/phaser/phaser_parameters.cpp:23: src/containers/bitmatrix.h: In function 'unsigned int abracadabra(const unsigned int&, const unsigned int&)': src/containers/bitmatrix.h:28:116: warning: right shift count >= width of type [-Wshift-count-overflow] 28 | return static_cast((static_cast(i1) * static_cast(i2)) >> 32); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ In file included from src/containers/haplotype_set.h:27, from src/objects/compute_job.h:27, from src/models/haplotype_segment_single.h:26, from src/phaser/phaser_header.h:29, from src/phaser/phaser_algorithm.cpp:22: src/containers/bitmatrix.h: In function 'unsigned int abracadabra(const unsigned int&, const unsigned int&)': src/containers/bitmatrix.h:28:116: warning: right shift count >= width of type [-Wshift-count-overflow] 28 | return static_cast((static_cast(i1) * static_cast(i2)) >> 32); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ In file included from src/containers/haplotype_set.h:27, from src/objects/compute_job.h:27, from src/models/haplotype_segment_single.h:26, from src/phaser/phaser_header.h:29, from src/phaser/phaser_management.cpp:22: src/containers/bitmatrix.h: In function 'unsigned int abracadabra(const unsigned int&, const unsigned int&)': src/containers/bitmatrix.h:28:116: warning: right shift count >= width of type [-Wshift-count-overflow] 28 | return static_cast((static_cast(i1) * static_cast(i2)) >> 32); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ In file included from src/containers/haplotype_set.h:27, from src/objects/compute_job.h:27, from src/models/haplotype_segment_single.h:26, from src/phaser/phaser_header.h:29, from src/phaser/phaser_initialise.cpp:22: src/containers/bitmatrix.h: In function 'unsigned int abracadabra(const unsigned int&, const unsigned int&)': src/containers/bitmatrix.h:28:116: warning: right shift count >= width of type [-Wshift-count-overflow] 28 | return static_cast((static_cast(i1) * static_cast(i2)) >> 32); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ g++ -std=c++11 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/shapeit4-4.2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -c src/objects/compute_job.cpp -o obj/compute_job.o -Isrc -I/build/reproducible-path/shapeit4-4.2.2+dfsg/debian/.debhelper/generated/_source/home/Tools/htslib-1.11 -I/usr/include g++ -std=c++11 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/shapeit4-4.2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -c src/objects/hmm_parameters.cpp -o obj/hmm_parameters.o -Isrc -I/build/reproducible-path/shapeit4-4.2.2+dfsg/debian/.debhelper/generated/_source/home/Tools/htslib-1.11 -I/usr/include g++ -std=c++11 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/shapeit4-4.2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -c src/objects/genotype/genotype_managment.cpp -o obj/genotype_managment.o -Isrc -I/build/reproducible-path/shapeit4-4.2.2+dfsg/debian/.debhelper/generated/_source/home/Tools/htslib-1.11 -I/usr/include g++ -std=c++11 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/shapeit4-4.2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -c src/objects/genotype/genotype_sweep.cpp -o obj/genotype_sweep.o -Isrc -I/build/reproducible-path/shapeit4-4.2.2+dfsg/debian/.debhelper/generated/_source/home/Tools/htslib-1.11 -I/usr/include In file included from src/containers/haplotype_set.h:27, from src/objects/compute_job.h:27, from src/objects/compute_job.cpp:22: src/containers/bitmatrix.h: In function 'unsigned int abracadabra(const unsigned int&, const unsigned int&)': src/containers/bitmatrix.h:28:116: warning: right shift count >= width of type [-Wshift-count-overflow] 28 | return static_cast((static_cast(i1) * static_cast(i2)) >> 32); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ g++ -std=c++11 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/shapeit4-4.2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -c src/objects/genotype/genotype_prune.cpp -o obj/genotype_prune.o -Isrc -I/build/reproducible-path/shapeit4-4.2.2+dfsg/debian/.debhelper/generated/_source/home/Tools/htslib-1.11 -I/usr/include g++ -std=c++11 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/shapeit4-4.2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -c src/objects/genotype/genotype_build.cpp -o obj/genotype_build.o -Isrc -I/build/reproducible-path/shapeit4-4.2.2+dfsg/debian/.debhelper/generated/_source/home/Tools/htslib-1.11 -I/usr/include g++ -std=c++11 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/shapeit4-4.2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -c src/objects/genotype/genotype_mask.cpp -o obj/genotype_mask.o -Isrc -I/build/reproducible-path/shapeit4-4.2.2+dfsg/debian/.debhelper/generated/_source/home/Tools/htslib-1.11 -I/usr/include g++ -std=c++11 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/shapeit4-4.2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -c src/objects/variant.cpp -o obj/variant.o -Isrc -I/build/reproducible-path/shapeit4-4.2.2+dfsg/debian/.debhelper/generated/_source/home/Tools/htslib-1.11 -I/usr/include g++ -std=c++11 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/shapeit4-4.2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -c src/modules/builder.cpp -o obj/builder.o -Isrc -I/build/reproducible-path/shapeit4-4.2.2+dfsg/debian/.debhelper/generated/_source/home/Tools/htslib-1.11 -I/usr/include g++ -std=c++11 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/shapeit4-4.2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -c src/modules/pbwt_solver.cpp -o obj/pbwt_solver.o -Isrc -I/build/reproducible-path/shapeit4-4.2.2+dfsg/debian/.debhelper/generated/_source/home/Tools/htslib-1.11 -I/usr/include In file included from /usr/include/c++/14/queue:64, from src/utils/otools.h:28, from src/objects/genotype/genotype_header.h:25, from src/objects/genotype/genotype_prune.cpp:22: /usr/include/c++/14/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = TransStatistics; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/14/bits/stl_heap.h:224:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 224 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, | ^~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = Transition; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/14/bits/stl_heap.h:224:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 In file included from /usr/include/c++/14/algorithm:61, from src/utils/otools.h:35: /usr/include/c++/14/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/14/bits/stl_algo.h:1770:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1770 | __insertion_sort(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_algo.h:1770:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/14/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/14/bits/stl_algo.h:1770:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/14/bits/stl_algo.h:1770:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/14/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/14/bits/stl_algo.h:1876:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1876 | __introsort_loop(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_algo.h:1876:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/14/bits/stl_algo.h:1890:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1890 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/14/bits/stl_algo.h:1876:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1876 | __introsort_loop(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_algo.h:1876:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/14/bits/stl_algo.h:1890:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1890 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -std=c++11 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/shapeit4-4.2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -c src/main.cpp -o obj/main.o -Isrc -I/build/reproducible-path/shapeit4-4.2.2+dfsg/debian/.debhelper/generated/_source/home/Tools/htslib-1.11 -I/usr/include In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]' at /usr/include/c++/14/bits/stl_algo.h:4771:18, inlined from 'void genotype::mapMerges(std::vector&, double, std::vector&)' at src/objects/genotype/genotype_prune.cpp:82:9: /usr/include/c++/14/bits/stl_algo.h:1905:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1905 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1906 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1907 | __comp); | ~~~~~~~ In function 'void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', inlined from 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/14/bits/stl_algo.h:1908:31, inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]' at /usr/include/c++/14/bits/stl_algo.h:4771:18, inlined from 'void genotype::mapMerges(std::vector&, double, std::vector&)' at src/objects/genotype/genotype_prune.cpp:82:9: /usr/include/c++/14/bits/stl_algo.h:1817:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1817 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_algo.h:1822:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1822 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]' at /usr/include/c++/14/bits/stl_algo.h:4771:18, inlined from 'void genotype::mapMerges(std::vector&, double, std::vector&)' at src/objects/genotype/genotype_prune.cpp:122:6: /usr/include/c++/14/bits/stl_algo.h:1905:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1905 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1906 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1907 | __comp); | ~~~~~~~ In function 'void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', inlined from 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/14/bits/stl_algo.h:1908:31, inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]' at /usr/include/c++/14/bits/stl_algo.h:4771:18, inlined from 'void genotype::mapMerges(std::vector&, double, std::vector&)' at src/objects/genotype/genotype_prune.cpp:122:6: /usr/include/c++/14/bits/stl_algo.h:1817:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1817 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_algo.h:1822:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1822 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]' at /usr/include/c++/14/bits/stl_algo.h:4771:18, inlined from 'void genotype::performMerges(std::vector&, std::vector&)' at src/objects/genotype/genotype_prune.cpp:165:8: /usr/include/c++/14/bits/stl_algo.h:1905:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1905 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1906 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1907 | __comp); | ~~~~~~~ In function 'void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', inlined from 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/14/bits/stl_algo.h:1908:31, inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]' at /usr/include/c++/14/bits/stl_algo.h:4771:18, inlined from 'void genotype::performMerges(std::vector&, std::vector&)' at src/objects/genotype/genotype_prune.cpp:165:8: /usr/include/c++/14/bits/stl_algo.h:1817:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1817 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_algo.h:1822:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1822 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ g++ -std=c++11 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/shapeit4-4.2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -c src/models/haplotype_segment_double.cpp -o obj/haplotype_segment_double.o -Isrc -I/build/reproducible-path/shapeit4-4.2.2+dfsg/debian/.debhelper/generated/_source/home/Tools/htslib-1.11 -I/usr/include g++ -std=c++11 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/shapeit4-4.2.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -c src/models/haplotype_segment_single.cpp -o obj/haplotype_segment_single.o -Isrc -I/build/reproducible-path/shapeit4-4.2.2+dfsg/debian/.debhelper/generated/_source/home/Tools/htslib-1.11 -I/usr/include In file included from src/containers/haplotype_set.h:27, from src/modules/pbwt_solver.h:26, from src/modules/pbwt_solver.cpp:22: src/containers/bitmatrix.h: In function 'unsigned int abracadabra(const unsigned int&, const unsigned int&)': src/containers/bitmatrix.h:28:116: warning: right shift count >= width of type [-Wshift-count-overflow] 28 | return static_cast((static_cast(i1) * static_cast(i2)) >> 32); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ src/modules/pbwt_solver.cpp: In member function 'void pbwt_solver::sweep(genotype_set&)': src/modules/pbwt_solver.cpp:93:106: warning: overflow in conversion from 'double' to '__gnu_cxx::__alloc_traits, char>::value_type' {aka 'char'} changes value from '-1.0e+0' to '0' [-Woverflow] 93 | if (s > thresh) { Guess[h+0] = 1.0; Guess[h+1] = -1.0; Amb[i] = false; } | ^~~~ src/modules/pbwt_solver.cpp:94:94: warning: overflow in conversion from 'double' to '__gnu_cxx::__alloc_traits, char>::value_type' {aka 'char'} changes value from '-1.0e+0' to '0' [-Woverflow] 94 | else if (s < -thresh) { Guess[h+0] = -1.0; Guess[h+1] = 1.0; Amb[i] = false; } | ^~~~ src/modules/pbwt_solver.cpp:103:98: warning: overflow in conversion from 'double' to '__gnu_cxx::__alloc_traits, char>::value_type' {aka 'char'} changes value from '-1.0e+0' to '0' [-Woverflow] 103 | if (s0 == -2 && s1 == -2) { Guess[h+0] = -1.0; Guess[h+1] = -1.0; Amb[i] = false; } | ^~~~ src/modules/pbwt_solver.cpp:103:117: warning: overflow in conversion from 'double' to '__gnu_cxx::__alloc_traits, char>::value_type' {aka 'char'} changes value from '-1.0e+0' to '0' [-Woverflow] 103 | if (s0 == -2 && s1 == -2) { Guess[h+0] = -1.0; Guess[h+1] = -1.0; Amb[i] = false; } | ^~~~ src/modules/pbwt_solver.cpp:104:102: warning: overflow in conversion from 'double' to '__gnu_cxx::__alloc_traits, char>::value_type' {aka 'char'} changes value from '-1.0e+0' to '0' [-Woverflow] 104 | else if (s0 == -2 && s1 == 2) { Guess[h+0] = -1.0; Guess[h+1] = 1.0; Amb[i] = false; } | ^~~~ src/modules/pbwt_solver.cpp:105:120: warning: overflow in conversion from 'double' to '__gnu_cxx::__alloc_traits, char>::value_type' {aka 'char'} changes value from '-1.0e+0' to '0' [-Woverflow] 105 | else if (s0 == 2 && s1 == -2) { Guess[h+0] = 1.0; Guess[h+1] = -1.0; Amb[i] = false; } | ^~~~ src/modules/pbwt_solver.cpp:134:75: warning: overflow in conversion from 'double' to '__gnu_cxx::__alloc_traits, char>::value_type' {aka 'char'} changes value from '-1.0e+0' to '0' [-Woverflow] 134 | else Guess[h+0] = -1.0; | ^~~~ src/modules/pbwt_solver.cpp:136:75: warning: overflow in conversion from 'double' to '__gnu_cxx::__alloc_traits, char>::value_type' {aka 'char'} changes value from '-1.0e+0' to '0' [-Woverflow] 136 | else Guess[h+1] = -1.0; | ^~~~ In file included from src/containers/haplotype_set.h:27, from src/objects/compute_job.h:27, from src/models/haplotype_segment_single.h:26, from src/phaser/phaser_header.h:29, from src/main.cpp:23: src/containers/bitmatrix.h: In function 'unsigned int abracadabra(const unsigned int&, const unsigned int&)': src/containers/bitmatrix.h:28:116: warning: right shift count >= width of type [-Wshift-count-overflow] 28 | return static_cast((static_cast(i1) * static_cast(i2)) >> 32); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ In file included from src/containers/haplotype_set.h:27, from src/objects/compute_job.h:27, from src/models/haplotype_segment_double.h:26, from src/models/haplotype_segment_double.cpp:22: src/containers/bitmatrix.h: In function 'unsigned int abracadabra(const unsigned int&, const unsigned int&)': src/containers/bitmatrix.h:28:116: warning: right shift count >= width of type [-Wshift-count-overflow] 28 | return static_cast((static_cast(i1) * static_cast(i2)) >> 32); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ In file included from src/containers/haplotype_set.h:27, from src/objects/compute_job.h:27, from src/models/haplotype_segment_single.h:26, from src/models/haplotype_segment_single.cpp:22: src/containers/bitmatrix.h: In function 'unsigned int abracadabra(const unsigned int&, const unsigned int&)': src/containers/bitmatrix.h:28:116: warning: right shift count >= width of type [-Wshift-count-overflow] 28 | return static_cast((static_cast(i1) * static_cast(i2)) >> 32); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ g++ -std=c++11 -Wl,-z,relro -Wl,-z,now -O3 obj/genotype_set.o obj/haplotype_set.o obj/bitmatrix.o obj/variant_map.o obj/gmap_reader.o obj/graph_writer.o obj/genotype_reader2.o obj/genotype_reader1.o obj/haplotype_writer.o obj/phaser_finalise.o obj/phaser_algorithm.o obj/phaser_parameters.o obj/phaser_management.o obj/phaser_initialise.o obj/compute_job.o obj/hmm_parameters.o obj/genotype_managment.o obj/genotype_sweep.o obj/genotype_prune.o obj/genotype_build.o obj/genotype_mask.o obj/variant.o obj/builder.o obj/pbwt_solver.o obj/main.o obj/haplotype_segment_double.o obj/haplotype_segment_single.o -lhts -lboost_iostreams -lboost_program_options -o bin/shapeit4.2 -lz -lbz2 -lm -lpthread -llzma -lcurl -lssl -lcrypto make[1]: Leaving directory '/build/reproducible-path/shapeit4-4.2.2+dfsg' dh_auto_test create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install dh_install dh_installdocs dh_installchangelogs dh_installman dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 from: /lib/ld-linux-armhf.so.3 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 to: /lib/ld-linux-armhf.so.3.usr-is-merged dpkg-shlibdeps: warning: debian/shapeit4/usr/bin/shapeit4.2 contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'shapeit4' in '../shapeit4_4.2.2+dfsg-1_armhf.deb'. dpkg-deb: building package 'shapeit4-dbgsym' in '../shapeit4-dbgsym_4.2.2+dfsg-1_armhf.deb'. dpkg-deb: building package 'shapeit4-example' in '../shapeit4-example_4.2.2+dfsg-1_all.deb'. dpkg-genbuildinfo --build=binary -O../shapeit4_4.2.2+dfsg-1_armhf.buildinfo dpkg-genchanges --build=binary -O../shapeit4_4.2.2+dfsg-1_armhf.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: including full source code in upload I: copying local configuration I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/7756 and its subdirectories I: Current time: Thu Nov 7 11:40:42 -12 2024 I: pbuilder-time-stamp: 1731022842 Thu Nov 7 23:44:32 UTC 2024 I: 1st build successful. Starting 2nd build on remote node virt32b-armhf-rb.debian.net. Thu Nov 7 23:44:32 UTC 2024 I: Preparing to do remote build '2' on virt32b-armhf-rb.debian.net. Thu Nov 7 23:59:58 UTC 2024 I: Deleting $TMPDIR on virt32b-armhf-rb.debian.net. Fri Nov 8 00:00:01 UTC 2024 I: shapeit4_4.2.2+dfsg-1_armhf.changes: Format: 1.8 Date: Fri, 17 Sep 2021 14:24:24 +0200 Source: shapeit4 Binary: shapeit4 shapeit4-dbgsym shapeit4-example Architecture: armhf all Version: 4.2.2+dfsg-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Dylan Aïssi Description: shapeit4 - fast and accurate method for estimation of haplotypes (phasing) shapeit4-example - fast and accurate method for estimation of haplotypes (phasing) - Changes: shapeit4 (4.2.2+dfsg-1) unstable; urgency=medium . * New upstream version * Standards-Version: 4.6.0 (routine-update) Checksums-Sha1: c7f7e78f209a4a03e87f893b43cf1e046cdccdfb 4027528 shapeit4-dbgsym_4.2.2+dfsg-1_armhf.deb a0588f1806e27c38f76a91eeb42755d10af8e573 52265128 shapeit4-example_4.2.2+dfsg-1_all.deb 103ebcb33a0a004682fbbb029f9c6f42b346648f 7402 shapeit4_4.2.2+dfsg-1_armhf.buildinfo f2ea6125a82ebc50b68d0fc21b43f61145ad7474 182560 shapeit4_4.2.2+dfsg-1_armhf.deb Checksums-Sha256: da65697e95618dc082fd804308f365812dd8f4b8d45a1e47fc1ee66187e0f021 4027528 shapeit4-dbgsym_4.2.2+dfsg-1_armhf.deb e162c54fc9f9620323c2c1d4f4bf49943e8a7dee7541bc98f4512e8c7d97bff2 52265128 shapeit4-example_4.2.2+dfsg-1_all.deb 3796a025f352c70d8da5373e54088cbe84151d181611d0fa426b6a8a92e184b4 7402 shapeit4_4.2.2+dfsg-1_armhf.buildinfo 7ee97caffff2fdbe080af7a7183d2da2fe56f0546355a45b9c47e75c0aab289c 182560 shapeit4_4.2.2+dfsg-1_armhf.deb Files: 041604197f942b9623209a88cbe484e4 4027528 debug optional shapeit4-dbgsym_4.2.2+dfsg-1_armhf.deb 6d47a24ae760e549febabe0ddd725e99 52265128 doc optional shapeit4-example_4.2.2+dfsg-1_all.deb f671e62878f2d5eeb96096a1e0a51c24 7402 science optional shapeit4_4.2.2+dfsg-1_armhf.buildinfo 706eed61279a926daf9379a81f1b404e 182560 science optional shapeit4_4.2.2+dfsg-1_armhf.deb Fri Nov 8 00:00:02 UTC 2024 I: diffoscope 282 will be used to compare the two builds: Running as unit: rb-diffoscope-armhf_13-6475.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.hOZkEMzy/shapeit4_4.2.2+dfsg-1.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.hOZkEMzy/shapeit4_4.2.2+dfsg-1.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.hOZkEMzy/shapeit4_4.2.2+dfsg-1.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.hOZkEMzy/b1/shapeit4_4.2.2+dfsg-1_armhf.changes /srv/reproducible-results/rbuild-debian/r-b-build.hOZkEMzy/b2/shapeit4_4.2.2+dfsg-1_armhf.changes ## close_archive (total time: 0.000s) 0.000s 20 calls diffoscope.comparators.xz.XzContainer 0.000s 10 calls diffoscope.comparators.deb.DebContainer 0.000s 14 calls diffoscope.comparators.tar.TarContainer 0.000s 6 calls diffoscope.comparators.deb.DebTarContainer ## command (total time: 323.759s) 164.059s 1020 calls readelf 146.199s 112 calls diff 11.523s 132 calls objdump 1.122s 2 calls objcopy 0.496s 20 calls xz 0.190s 22 calls strings 0.084s 1 call cmp 0.084s 1 call cmp (external) 0.002s 20 calls cmp (internal) ## compare_files (cumulative) (total time: 926.461s) 180.321s 1 call abc.DotChangesFile 180.170s 2 calls abc.DebFile 180.087s 4 calls abc.XzFile 179.762s 2 calls abc.DebDataTarFile 179.290s 2 calls abc.ElfFile 25.145s 8 calls diffoscope.comparators.elf.ElfCodeSection 0.793s 2 calls diffoscope.comparators.elf.ElfStringSection 0.793s 37 calls diffoscope.comparators.elf.ElfSection 0.066s 2 calls abc.TarFile 0.014s 1 call abc.TextFile 0.011s 1 call diffoscope.comparators.elf.MonkeyPatchedElfSection 0.010s 2 calls abc.Md5sumsFile ## container_extract (total time: 0.878s) 0.497s 20 calls diffoscope.comparators.xz.XzContainer 0.323s 24 calls diffoscope.comparators.deb.DebContainer 0.046s 12 calls diffoscope.comparators.deb.DebTarContainer 0.012s 18 calls diffoscope.comparators.tar.TarContainer ## diff (total time: 5.299s) 5.299s 1085 calls linediff ## has_same_content_as (total time: 0.088s) 0.085s 3 calls abc.DebFile 0.001s 4 calls abc.TextFile 0.001s 4 calls abc.Md5sumsFile 0.000s 3 calls diffoscope.comparators.utils.libarchive.LibarchiveSymlink 0.000s 4 calls abc.XzFile 0.000s 2 calls abc.DebDataTarFile 0.000s 37 calls diffoscope.comparators.elf.ElfSection 0.000s 2 calls abc.TarFile 0.000s 2 calls abc.ElfFile 0.000s 1 call abc.DotChangesFile 0.000s 8 calls diffoscope.comparators.elf.ElfCodeSection 0.000s 2 calls diffoscope.comparators.elf.ElfStringSection 0.000s 1 call diffoscope.comparators.elf.MonkeyPatchedElfSection ## main (total time: 209.714s) 209.714s 2 calls outputs 0.001s 1 call cleanup ## open_archive (total time: 0.000s) 0.000s 20 calls diffoscope.comparators.xz.XzContainer 0.000s 14 calls diffoscope.comparators.tar.TarContainer 0.000s 10 calls diffoscope.comparators.deb.DebContainer 0.000s 6 calls diffoscope.comparators.deb.DebTarContainer ## output (total time: 28.209s) 16.920s 1 call html 6.976s 1 call text 4.313s 1 call json ## recognizes (total time: 1.625s) 0.711s 12 calls diffoscope.comparators.binary.FilesystemFile 0.505s 1808 calls diffoscope.comparators.utils.libarchive.LibarchiveMember 0.295s 900 calls diffoscope.comparators.utils.archive.ArchiveMember 0.114s 324 calls diffoscope.comparators.debian.DebControlMember ## specialize (total time: 0.146s) 0.146s 73 calls specialize Finished with result: success Main processes terminated with: code=exited/status=1 Service runtime: 3min 30.146s CPU time consumed: 4min 20.452s Fri Nov 8 00:03:35 UTC 2024 W: Diffoscope claims the build is reproducible, but there is a diffoscope file. Please investigate. Fri Nov 8 00:03:35 UTC 2024 E: shapeit4 failed to build reproducibly in trixie on armhf. Fri Nov 8 00:06:08 UTC 2024 I: Submitting .buildinfo files to external archives: Fri Nov 8 00:06:08 UTC 2024 I: Submitting 12K b1/shapeit4_4.2.2+dfsg-1_armhf.buildinfo.asc Fri Nov 8 00:06:09 UTC 2024 I: Submitting 12K b2/shapeit4_4.2.2+dfsg-1_armhf.buildinfo.asc Fri Nov 8 00:06:10 UTC 2024 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Fri Nov 8 00:06:10 UTC 2024 I: Done submitting .buildinfo files. Fri Nov 8 00:06:10 UTC 2024 I: Removing signed shapeit4_4.2.2+dfsg-1_armhf.buildinfo.asc files: removed './b1/shapeit4_4.2.2+dfsg-1_armhf.buildinfo.asc' removed './b2/shapeit4_4.2.2+dfsg-1_armhf.buildinfo.asc'