Wed Jul 7 00:54:21 UTC 2021 I: starting to build shapeit4/bullseye/arm64 on jenkins on '2021-07-07 00:53' Wed Jul 7 00:54:21 UTC 2021 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/arm64_17/13605/console.log Wed Jul 7 00:54:21 UTC 2021 I: Downloading source for bullseye/shapeit4=4.2.0+dfsg-1 --2021-07-07 00:54:21-- http://cdn-fastly.deb.debian.org/debian/pool/main/s/shapeit4/shapeit4_4.2.0+dfsg-1.dsc Connecting to 78.137.99.97:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2147 (2.1K) Saving to: ‘shapeit4_4.2.0+dfsg-1.dsc’ 0K .. 100% 185M=0s 2021-07-07 00:54:21 (185 MB/s) - ‘shapeit4_4.2.0+dfsg-1.dsc’ saved [2147/2147] Wed Jul 7 00:54:21 UTC 2021 I: shapeit4_4.2.0+dfsg-1.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: shapeit4 Binary: shapeit4, shapeit4-example Architecture: any all Version: 4.2.0+dfsg-1 Maintainer: Debian Med Packaging Team Uploaders: Dylan Aïssi Homepage: https://odelaneau.github.io/shapeit4/ Standards-Version: 4.5.1 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 Package-List: shapeit4 deb science optional arch=any shapeit4-example deb doc optional arch=all Checksums-Sha1: ea108cb1d656ba5054bb4397b5a39c8d1d609238 58963660 shapeit4_4.2.0+dfsg.orig.tar.xz 3465efda50590f9dc0b9f5825949df21d07c9dd1 5188 shapeit4_4.2.0+dfsg-1.debian.tar.xz Checksums-Sha256: f9a9276b1bcc218a2e7cb79bc8e1ff34e97ec0d87892713fc83d50a002ae5d25 58963660 shapeit4_4.2.0+dfsg.orig.tar.xz f337cbdfa05ca06945d8825f165bba1d35225af2984c87d7e34f31292bb5ec3d 5188 shapeit4_4.2.0+dfsg-1.debian.tar.xz Files: efa9b0cf6f97568a5bb66466c06f78c7 58963660 shapeit4_4.2.0+dfsg.orig.tar.xz 360ca7fda9da2f870d645fb1ee6d835f 5188 shapeit4_4.2.0+dfsg-1.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJGBAEBCgAwFiEEmjwHvQbeL0FugTpdYS7xYT4FD1QFAmAby50SHGRhaXNzaUBk ZWJpYW4ub3JnAAoJEGEu8WE+BQ9U6rcP+wfeEdrJLKx3OfqGAcPLnx9ZxUz1ci1a aVzO+aVJ9xgeuUbn7TgjexYD9y6PwJhgpH61CkLyxVWe0FA30PMKq7+de6C0yCp5 uQ7pr2BQ+qKXKbifN9oo1QzI+2mwPEgjY/+wpP75LBurnsPZsWq9ap1YIX+75WxP 0SnYqfNXe7ZtQW0bR9YxJjrKSfjbwX+/UT6uqCxNVvO0HclDVBRSmC16QZrFASHd hG9pOdyWYm/zlVD+zbTxTxpD8eMG53XFsFXL05KTJ4PX2bjWJQcnSUr9xN7hZZ9g /ktvLUp6clUKfUtbELeSLvQNlEIPfdS41fYT4GUTaakH3rPiwsuA4I/0S7Zrxtsl e956H+np/PIS/0m97ytAmQDf+EOdOGlrER4chgg24bCfMTwodoOWs9RPCr9KiqHq 2uTRaDGvYPrQiPiiKoQcznFeWC3LLlTSjTqM2kZUYinNJnkC0H6ETCcv40lEhXAK iZInIb+ImSmezGeySlX/EuR2BWlTiz8ytNx2jfKPrymGOV4dOXwZmAPRO0/W++TI Y8UGeGmWm+9Uss/uFmP3QWtaz8+0DOtNAooC8useQ4M2uQ27Q14vt+LSXOcepuaE PkW0GQc1EeiChqXqiEOMuFl2BRGuo68edrrqyJLcJPnOOM2skL8QGI7vRA4palgD cr4kUyp6j4lf =tAU9 -----END PGP SIGNATURE----- Wed Jul 7 00:54:21 UTC 2021 I: Checking whether the package is not for us Wed Jul 7 00:54:21 UTC 2021 I: Starting 1st build on remote node codethink13-arm64.debian.net. Wed Jul 7 00:54:21 UTC 2021 I: Preparing to do remote build '1' on codethink13-arm64.debian.net. Wed Jul 7 00:58:35 UTC 2021 I: Deleting $TMPDIR on codethink13-arm64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Mon Aug 8 19:17:35 -12 2022 I: pbuilder-time-stamp: 1660029455 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bullseye-reproducible-base.tgz] I: copying local configuration 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_4.2.0+dfsg-1.dsc] I: copying [./shapeit4_4.2.0+dfsg.orig.tar.xz] I: copying [./shapeit4_4.2.0+dfsg-1.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/tmp/dpkg-verify-sig.hlQV5OfT/trustedkeys.kbx': General error gpgv: Signature made Wed Feb 3 22:25:33 2021 -12 gpgv: using RSA key 9A3C07BD06DE2F416E813A5D612EF1613E050F54 gpgv: issuer "daissi@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./shapeit4_4.2.0+dfsg-1.dsc dpkg-source: info: extracting shapeit4 in shapeit4-4.2.0+dfsg dpkg-source: info: unpacking shapeit4_4.2.0+dfsg.orig.tar.xz dpkg-source: info: unpacking shapeit4_4.2.0+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/23226/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='arm64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=8' DISTRIBUTION='' HOME='/var/lib/jenkins' HOST_ARCH='arm64' IFS=' ' 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='23226' 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/tmp.GEvFHoILJR/pbuilderrc_XPrw --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.GEvFHoILJR/b1 --logfile b1/build.log shapeit4_4.2.0+dfsg-1.dsc' SUDO_GID='117' SUDO_UID='110' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' USERNAME='root' _='/usr/bin/systemd-run' http_proxy='http://192.168.101.16:3128' I: uname -a Linux codethink13-arm64 4.15.0-147-generic #151-Ubuntu SMP Fri Jun 18 19:18:37 UTC 2021 aarch64 GNU/Linux I: ls -l /bin total 5252 -rwxr-xr-x 1 root root 1282512 Jun 21 2021 bash -rwxr-xr-x 3 root root 34808 Jul 20 2020 bunzip2 -rwxr-xr-x 3 root root 34808 Jul 20 2020 bzcat lrwxrwxrwx 1 root root 6 Jul 20 2020 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2225 Jul 20 2020 bzdiff lrwxrwxrwx 1 root root 6 Jul 20 2020 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4877 Sep 4 2019 bzexe lrwxrwxrwx 1 root root 6 Jul 20 2020 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3775 Jul 20 2020 bzgrep -rwxr-xr-x 3 root root 34808 Jul 20 2020 bzip2 -rwxr-xr-x 1 root root 14264 Jul 20 2020 bzip2recover lrwxrwxrwx 1 root root 6 Jul 20 2020 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Jul 20 2020 bzmore -rwxr-xr-x 1 root root 39832 Sep 22 2020 cat -rwxr-xr-x 1 root root 64512 Sep 22 2020 chgrp -rwxr-xr-x 1 root root 60368 Sep 22 2020 chmod -rwxr-xr-x 1 root root 64528 Sep 22 2020 chown -rwxr-xr-x 1 root root 138896 Sep 22 2020 cp -rwxr-xr-x 1 root root 129544 Dec 10 2020 dash -rwxr-xr-x 1 root root 101384 Sep 22 2020 date -rwxr-xr-x 1 root root 80984 Sep 22 2020 dd -rwxr-xr-x 1 root root 89824 Sep 22 2020 df -rwxr-xr-x 1 root root 143088 Sep 22 2020 dir -rwxr-xr-x 1 root root 76152 Feb 7 2021 dmesg lrwxrwxrwx 1 root root 8 Nov 6 2019 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Nov 6 2019 domainname -> hostname -rwxr-xr-x 1 root root 35632 Sep 22 2020 echo -rwxr-xr-x 1 root root 28 Nov 9 2020 egrep -rwxr-xr-x 1 root root 31512 Sep 22 2020 false -rwxr-xr-x 1 root root 28 Nov 9 2020 fgrep -rwxr-xr-x 1 root root 64856 Feb 7 2021 findmnt -rwsr-xr-x 1 root root 34824 Feb 26 2021 fusermount -rwxr-xr-x 1 root root 178400 Nov 9 2020 grep -rwxr-xr-x 2 root root 2346 Mar 2 2021 gunzip -rwxr-xr-x 1 root root 6376 Mar 2 2021 gzexe -rwxr-xr-x 1 root root 93744 Mar 2 2021 gzip -rwxr-xr-x 1 root root 18440 Nov 6 2019 hostname -rwxr-xr-x 1 root root 68720 Sep 22 2020 ln -rwxr-xr-x 1 root root 52720 Feb 7 2020 login -rwxr-xr-x 1 root root 143088 Sep 22 2020 ls -rwxr-xr-x 1 root root 161960 Feb 7 2021 lsblk -rwxr-xr-x 1 root root 85200 Sep 22 2020 mkdir -rwxr-xr-x 1 root root 68744 Sep 22 2020 mknod -rwxr-xr-x 1 root root 43976 Sep 22 2020 mktemp -rwxr-xr-x 1 root root 51368 Feb 7 2021 more -rwsr-xr-x 1 root root 51360 Feb 7 2021 mount -rwxr-xr-x 1 root root 14496 Feb 7 2021 mountpoint -rwxr-xr-x 1 root root 134808 Sep 22 2020 mv lrwxrwxrwx 1 root root 8 Nov 6 2019 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Apr 18 2021 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 35720 Sep 22 2020 pwd lrwxrwxrwx 1 root root 4 Jun 21 2021 rbash -> bash -rwxr-xr-x 1 root root 43872 Sep 22 2020 readlink -rwxr-xr-x 1 root root 68592 Sep 22 2020 rm -rwxr-xr-x 1 root root 43880 Sep 22 2020 rmdir -rwxr-xr-x 1 root root 19208 Sep 27 2020 run-parts -rwxr-xr-x 1 root root 114016 Dec 22 2018 sed lrwxrwxrwx 1 root root 4 Aug 7 03:48 sh -> dash -rwxr-xr-x 1 root root 35656 Sep 22 2020 sleep -rwxr-xr-x 1 root root 72640 Sep 22 2020 stty -rwsr-xr-x 1 root root 67776 Feb 7 2021 su -rwxr-xr-x 1 root root 35672 Sep 22 2020 sync -rwxr-xr-x 1 root root 535768 Feb 16 2021 tar -rwxr-xr-x 1 root root 10568 Sep 27 2020 tempfile -rwxr-xr-x 1 root root 89120 Sep 22 2020 touch -rwxr-xr-x 1 root root 31512 Sep 22 2020 true -rwxr-xr-x 1 root root 14264 Feb 26 2021 ulockmgr_server -rwsr-xr-x 1 root root 30880 Feb 7 2021 umount -rwxr-xr-x 1 root root 35640 Sep 22 2020 uname -rwxr-xr-x 2 root root 2346 Mar 2 2021 uncompress -rwxr-xr-x 1 root root 143088 Sep 22 2020 vdir -rwxr-xr-x 1 root root 59584 Feb 7 2021 wdctl lrwxrwxrwx 1 root root 8 Nov 6 2019 ypdomainname -> hostname -rwxr-xr-x 1 root root 1984 Mar 2 2021 zcat -rwxr-xr-x 1 root root 1678 Mar 2 2021 zcmp -rwxr-xr-x 1 root root 5880 Mar 2 2021 zdiff -rwxr-xr-x 1 root root 29 Mar 2 2021 zegrep -rwxr-xr-x 1 root root 29 Mar 2 2021 zfgrep -rwxr-xr-x 1 root root 2081 Mar 2 2021 zforce -rwxr-xr-x 1 root root 7585 Mar 2 2021 zgrep -rwxr-xr-x 1 root root 2206 Mar 2 2021 zless -rwxr-xr-x 1 root root 1842 Mar 2 2021 zmore -rwxr-xr-x 1 root root 4553 Mar 2 2021 znew I: user script /srv/workspace/pbuilder/23226/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: arm64 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 dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19646 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. 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-iostreams1.74-dev{a} libboost-program-options-dev{a} libboost-program-options1.74-dev{a} libboost-program-options1.74.0{a} libboost-regex1.74-dev{a} libboost-regex1.74.0{a} libboost1.74-dev{a} libbrotli1{a} libbz2-dev{a} libcurl3-gnutls{a} libcurl4-gnutls-dev{a} libdebhelper-perl{a} libdeflate-dev{a} libdeflate0{a} libelf1{a} libfile-stripnondeterminism-perl{a} libhts-dev{a} libhts3{a} libicu-dev{a} libicu67{a} libldap-2.4-2{a} liblzma-dev{a} libmagic-mgc{a} libmagic1{a} libnghttp2-14{a} libpipeline1{a} libpsl5{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsigsegv2{a} libssh2-1{a} libsub-override-perl{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{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 libarchive-cpio-perl libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules lynx publicsuffix wget 0 packages upgraded, 58 newly installed, 0 to remove and 0 not upgraded. Need to get 45.6 MB of archives. After unpacking 283 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bullseye/main arm64 bsdextrautils arm64 2.36.1-7 [141 kB] Get: 2 http://deb.debian.org/debian bullseye/main arm64 libuchardet0 arm64 0.0.7-1 [67.9 kB] Get: 3 http://deb.debian.org/debian bullseye/main arm64 groff-base arm64 1.22.4-6 [883 kB] Get: 4 http://deb.debian.org/debian bullseye/main arm64 libpipeline1 arm64 1.5.3-1 [33.0 kB] Get: 5 http://deb.debian.org/debian bullseye/main arm64 man-db arm64 2.9.4-2 [1336 kB] Get: 6 http://deb.debian.org/debian bullseye/main arm64 sensible-utils all 0.0.14 [14.8 kB] Get: 7 http://deb.debian.org/debian bullseye/main arm64 libmagic-mgc arm64 1:5.39-3 [273 kB] Get: 8 http://deb.debian.org/debian bullseye/main arm64 libmagic1 arm64 1:5.39-3 [121 kB] Get: 9 http://deb.debian.org/debian bullseye/main arm64 file arm64 1:5.39-3 [69.1 kB] Get: 10 http://deb.debian.org/debian bullseye/main arm64 gettext-base arm64 0.21-4 [173 kB] Get: 11 http://deb.debian.org/debian bullseye/main arm64 libsigsegv2 arm64 2.13-1 [34.7 kB] Get: 12 http://deb.debian.org/debian bullseye/main arm64 m4 arm64 1.4.18-5 [199 kB] Get: 13 http://deb.debian.org/debian bullseye/main arm64 autoconf all 2.69-14 [313 kB] Get: 14 http://deb.debian.org/debian bullseye/main arm64 autotools-dev all 20180224.1+nmu1 [77.1 kB] Get: 15 http://deb.debian.org/debian bullseye/main arm64 automake all 1:1.16.3-2 [814 kB] Get: 16 http://deb.debian.org/debian bullseye/main arm64 autopoint all 0.21-4 [510 kB] Get: 17 http://deb.debian.org/debian bullseye/main arm64 libdebhelper-perl all 13.3.4 [189 kB] Get: 18 http://deb.debian.org/debian bullseye/main arm64 libtool all 2.4.6-15 [513 kB] Get: 19 http://deb.debian.org/debian bullseye/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 20 http://deb.debian.org/debian bullseye/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 21 http://deb.debian.org/debian bullseye/main arm64 libsub-override-perl all 0.09-2 [10.2 kB] Get: 22 http://deb.debian.org/debian bullseye/main arm64 libfile-stripnondeterminism-perl all 1.11.0-1 [25.6 kB] Get: 23 http://deb.debian.org/debian bullseye/main arm64 dh-strip-nondeterminism all 1.11.0-1 [15.3 kB] Get: 24 http://deb.debian.org/debian bullseye/main arm64 libelf1 arm64 0.183-1 [164 kB] Get: 25 http://deb.debian.org/debian bullseye/main arm64 dwz arm64 0.13+20210201-1 [155 kB] Get: 26 http://deb.debian.org/debian bullseye/main arm64 libicu67 arm64 67.1-7 [8467 kB] Get: 27 http://deb.debian.org/debian bullseye/main arm64 libxml2 arm64 2.9.10+dfsg-6.7 [629 kB] Get: 28 http://deb.debian.org/debian bullseye/main arm64 gettext arm64 0.21-4 [1261 kB] Get: 29 http://deb.debian.org/debian bullseye/main arm64 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 30 http://deb.debian.org/debian bullseye/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 31 http://deb.debian.org/debian bullseye/main arm64 debhelper all 13.3.4 [1049 kB] Get: 32 http://deb.debian.org/debian bullseye/main arm64 icu-devtools arm64 67.1-7 [189 kB] Get: 33 http://deb.debian.org/debian bullseye/main arm64 libboost1.74-dev arm64 1.74.0-9 [9534 kB] Get: 34 http://deb.debian.org/debian bullseye/main arm64 libboost-regex1.74.0 arm64 1.74.0-9 [473 kB] Get: 35 http://deb.debian.org/debian bullseye/main arm64 libicu-dev arm64 67.1-7 [9468 kB] Get: 36 http://deb.debian.org/debian bullseye/main arm64 libboost-regex1.74-dev arm64 1.74.0-9 [549 kB] Get: 37 http://deb.debian.org/debian bullseye/main arm64 libboost-iostreams1.74-dev arm64 1.74.0-9 [272 kB] Get: 38 http://deb.debian.org/debian bullseye/main arm64 libboost-iostreams-dev arm64 1.74.0.3 [4316 B] Get: 39 http://deb.debian.org/debian bullseye/main arm64 libboost-program-options1.74.0 arm64 1.74.0-9 [344 kB] Get: 40 http://deb.debian.org/debian bullseye/main arm64 libboost-program-options1.74-dev arm64 1.74.0-9 [382 kB] Get: 41 http://deb.debian.org/debian bullseye/main arm64 libboost-program-options-dev arm64 1.74.0.3 [4340 B] Get: 42 http://deb.debian.org/debian bullseye/main arm64 libbrotli1 arm64 1.0.9-2+b2 [267 kB] Get: 43 http://deb.debian.org/debian bullseye/main arm64 libbz2-dev arm64 1.0.8-4 [31.5 kB] Get: 44 http://deb.debian.org/debian bullseye/main arm64 libsasl2-modules-db arm64 2.1.27+dfsg-2.1 [69.3 kB] Get: 45 http://deb.debian.org/debian bullseye/main arm64 libsasl2-2 arm64 2.1.27+dfsg-2.1 [105 kB] Get: 46 http://deb.debian.org/debian bullseye/main arm64 libldap-2.4-2 arm64 2.4.57+dfsg-3 [222 kB] Get: 47 http://deb.debian.org/debian bullseye/main arm64 libnghttp2-14 arm64 1.43.0-1 [73.8 kB] Get: 48 http://deb.debian.org/debian bullseye/main arm64 libpsl5 arm64 0.21.0-1.2 [57.1 kB] Get: 49 http://deb.debian.org/debian bullseye/main arm64 librtmp1 arm64 2.4+20151223.gitfa8646d.1-2+b2 [59.4 kB] Get: 50 http://deb.debian.org/debian bullseye/main arm64 libssh2-1 arm64 1.9.0-2 [150 kB] Get: 51 http://deb.debian.org/debian bullseye/main arm64 libcurl3-gnutls arm64 7.74.0-1.3 [317 kB] Get: 52 http://deb.debian.org/debian bullseye/main arm64 libcurl4-gnutls-dev arm64 7.74.0-1.3 [419 kB] Get: 53 http://deb.debian.org/debian bullseye/main arm64 libdeflate0 arm64 1.7-1 [47.7 kB] Get: 54 http://deb.debian.org/debian bullseye/main arm64 libdeflate-dev arm64 1.7-1 [44.5 kB] Get: 55 http://deb.debian.org/debian bullseye/main arm64 libhts3 arm64 1.11-4 [346 kB] Get: 56 http://deb.debian.org/debian bullseye/main arm64 liblzma-dev arm64 5.2.5-2 [227 kB] Get: 57 http://deb.debian.org/debian bullseye/main arm64 zlib1g-dev arm64 1:1.2.11.dfsg-2 [189 kB] Get: 58 http://deb.debian.org/debian bullseye/main arm64 libhts-dev arm64 1.11-4 [3856 kB] Fetched 45.6 MB in 1s (51.0 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package bsdextrautils. (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 ... 19646 files and directories currently installed.) Preparing to unpack .../00-bsdextrautils_2.36.1-7_arm64.deb ... Unpacking bsdextrautils (2.36.1-7) ... Selecting previously unselected package libuchardet0:arm64. Preparing to unpack .../01-libuchardet0_0.0.7-1_arm64.deb ... Unpacking libuchardet0:arm64 (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../02-groff-base_1.22.4-6_arm64.deb ... 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Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/shapeit4-4.2.0+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_4.2.0+dfsg-1_source.changes dpkg-buildpackage: info: source package shapeit4 dpkg-buildpackage: info: source version 4.2.0+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 arm64 debian/rules clean dh clean dh_auto_clean make -j8 clean make[1]: Entering directory '/build/shapeit4-4.2.0+dfsg' rm -f obj/*.o bin/shapeit4.2 make[1]: Leaving directory '/build/shapeit4-4.2.0+dfsg' dh_clean debian/rules binary dh binary dh_update_autotools_config dh_autoreconf dh_auto_configure dh_auto_build make -j8 "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/shapeit4-4.2.0+dfsg' g++ -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/shapeit4-4.2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -c src/phaser/phaser_parameters.cpp -o obj/phaser_parameters.o -Isrc -I/build/shapeit4-4.2.0+dfsg/debian/.debhelper/generated/_source/home/Tools/htslib-1.9 -I/usr/include g++ -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/shapeit4-4.2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -c src/phaser/phaser_management.cpp -o obj/phaser_management.o -Isrc -I/build/shapeit4-4.2.0+dfsg/debian/.debhelper/generated/_source/home/Tools/htslib-1.9 -I/usr/include g++ -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/shapeit4-4.2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -c src/phaser/phaser_initialise.cpp -o obj/phaser_initialise.o -Isrc -I/build/shapeit4-4.2.0+dfsg/debian/.debhelper/generated/_source/home/Tools/htslib-1.9 -I/usr/include g++ -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/shapeit4-4.2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -c src/phaser/phaser_finalise.cpp -o obj/phaser_finalise.o -Isrc -I/build/shapeit4-4.2.0+dfsg/debian/.debhelper/generated/_source/home/Tools/htslib-1.9 -I/usr/include g++ -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/shapeit4-4.2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -c src/phaser/phaser_algorithm.cpp -o obj/phaser_algorithm.o -Isrc -I/build/shapeit4-4.2.0+dfsg/debian/.debhelper/generated/_source/home/Tools/htslib-1.9 -I/usr/include g++ -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/shapeit4-4.2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -c src/objects/variant.cpp -o obj/variant.o -Isrc -I/build/shapeit4-4.2.0+dfsg/debian/.debhelper/generated/_source/home/Tools/htslib-1.9 -I/usr/include g++ -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/shapeit4-4.2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -c src/objects/hmm_parameters.cpp -o obj/hmm_parameters.o -Isrc -I/build/shapeit4-4.2.0+dfsg/debian/.debhelper/generated/_source/home/Tools/htslib-1.9 -I/usr/include g++ -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/shapeit4-4.2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -c src/objects/genotype/genotype_sweep.cpp -o obj/genotype_sweep.o -Isrc -I/build/shapeit4-4.2.0+dfsg/debian/.debhelper/generated/_source/home/Tools/htslib-1.9 -I/usr/include In file included 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/haplotype_set.h: In member function 'bool IBD2track::merge(const IBD2track&)': src/containers/haplotype_set.h:53:2: warning: no return statement in function returning non-void [-Wreturn-type] 53 | } | ^ In file included 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/haplotype_set.h: In member function 'bool IBD2track::merge(const IBD2track&)': src/containers/haplotype_set.h:53:2: warning: no return statement in function returning non-void [-Wreturn-type] 53 | } | ^ In file included 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/haplotype_set.h: In member function 'bool IBD2track::merge(const IBD2track&)': src/containers/haplotype_set.h:53:2: warning: no return statement in function returning non-void [-Wreturn-type] 53 | } | ^ In file included 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/haplotype_set.h: In member function 'bool IBD2track::merge(const IBD2track&)': src/containers/haplotype_set.h:53:2: warning: no return statement in function returning non-void [-Wreturn-type] 53 | } | ^ In file included 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/haplotype_set.h: In member function 'bool IBD2track::merge(const IBD2track&)': src/containers/haplotype_set.h:53:2: warning: no return statement in function returning non-void [-Wreturn-type] 53 | } | ^ g++ -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/shapeit4-4.2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -c src/objects/genotype/genotype_prune.cpp -o obj/genotype_prune.o -Isrc -I/build/shapeit4-4.2.0+dfsg/debian/.debhelper/generated/_source/home/Tools/htslib-1.9 -I/usr/include g++ -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/shapeit4-4.2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -c src/objects/genotype/genotype_mask.cpp -o obj/genotype_mask.o -Isrc -I/build/shapeit4-4.2.0+dfsg/debian/.debhelper/generated/_source/home/Tools/htslib-1.9 -I/usr/include g++ -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/shapeit4-4.2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -c src/objects/genotype/genotype_managment.cpp -o obj/genotype_managment.o -Isrc -I/build/shapeit4-4.2.0+dfsg/debian/.debhelper/generated/_source/home/Tools/htslib-1.9 -I/usr/include g++ -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/shapeit4-4.2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -c src/objects/genotype/genotype_build.cpp -o obj/genotype_build.o -Isrc -I/build/shapeit4-4.2.0+dfsg/debian/.debhelper/generated/_source/home/Tools/htslib-1.9 -I/usr/include g++ -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/shapeit4-4.2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -c src/objects/compute_job.cpp -o obj/compute_job.o -Isrc -I/build/shapeit4-4.2.0+dfsg/debian/.debhelper/generated/_source/home/Tools/htslib-1.9 -I/usr/include g++ -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/shapeit4-4.2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -c src/modules/pbwt_solver.cpp -o obj/pbwt_solver.o -Isrc -I/build/shapeit4-4.2.0+dfsg/debian/.debhelper/generated/_source/home/Tools/htslib-1.9 -I/usr/include g++ -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/shapeit4-4.2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -c src/modules/builder.cpp -o obj/builder.o -Isrc -I/build/shapeit4-4.2.0+dfsg/debian/.debhelper/generated/_source/home/Tools/htslib-1.9 -I/usr/include In file included from src/objects/compute_job.h:27, from src/objects/compute_job.cpp:22: src/containers/haplotype_set.h: In member function 'bool IBD2track::merge(const IBD2track&)': src/containers/haplotype_set.h:53:2: warning: no return statement in function returning non-void [-Wreturn-type] 53 | } | ^ In file included from src/modules/pbwt_solver.h:26, from src/modules/pbwt_solver.cpp:22: src/containers/haplotype_set.h: In member function 'bool IBD2track::merge(const IBD2track&)': src/containers/haplotype_set.h:53:2: warning: no return statement in function returning non-void [-Wreturn-type] 53 | } | ^ src/modules/pbwt_solver.cpp: In member function 'void pbwt_solver::sweep(genotype_set&)': src/modules/pbwt_solver.cpp:93:57: 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:94:45: 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:103:49: 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:103:68: 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:104:53: 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:105:71: 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:134:26: 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:136:26: 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; | ^~~~ g++ -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/shapeit4-4.2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -c src/models/haplotype_segment_single.cpp -o obj/haplotype_segment_single.o -Isrc -I/build/shapeit4-4.2.0+dfsg/debian/.debhelper/generated/_source/home/Tools/htslib-1.9 -I/usr/include g++ -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/shapeit4-4.2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -c src/models/haplotype_segment_double.cpp -o obj/haplotype_segment_double.o -Isrc -I/build/shapeit4-4.2.0+dfsg/debian/.debhelper/generated/_source/home/Tools/htslib-1.9 -I/usr/include g++ -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/shapeit4-4.2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -c src/main.cpp -o obj/main.o -Isrc -I/build/shapeit4-4.2.0+dfsg/debian/.debhelper/generated/_source/home/Tools/htslib-1.9 -I/usr/include g++ -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/shapeit4-4.2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -c src/io/haplotype_writer.cpp -o obj/haplotype_writer.o -Isrc -I/build/shapeit4-4.2.0+dfsg/debian/.debhelper/generated/_source/home/Tools/htslib-1.9 -I/usr/include g++ -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/shapeit4-4.2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -c src/io/graph_writer.cpp -o obj/graph_writer.o -Isrc -I/build/shapeit4-4.2.0+dfsg/debian/.debhelper/generated/_source/home/Tools/htslib-1.9 -I/usr/include In file included 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/haplotype_set.h: In member function 'bool IBD2track::merge(const IBD2track&)': src/containers/haplotype_set.h:53:2: warning: no return statement in function returning non-void [-Wreturn-type] 53 | } | ^ g++ -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/shapeit4-4.2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -c src/io/gmap_reader.cpp -o obj/gmap_reader.o -Isrc -I/build/shapeit4-4.2.0+dfsg/debian/.debhelper/generated/_source/home/Tools/htslib-1.9 -I/usr/include g++ -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/shapeit4-4.2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -c src/io/genotype_reader2.cpp -o obj/genotype_reader2.o -Isrc -I/build/shapeit4-4.2.0+dfsg/debian/.debhelper/generated/_source/home/Tools/htslib-1.9 -I/usr/include g++ -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/shapeit4-4.2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -c src/io/genotype_reader1.cpp -o obj/genotype_reader1.o -Isrc -I/build/shapeit4-4.2.0+dfsg/debian/.debhelper/generated/_source/home/Tools/htslib-1.9 -I/usr/include In file included 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/haplotype_set.h: In member function 'bool IBD2track::merge(const IBD2track&)': src/containers/haplotype_set.h:53:2: warning: no return statement in function returning non-void [-Wreturn-type] 53 | } | ^ In file included 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/haplotype_set.h: In member function 'bool IBD2track::merge(const IBD2track&)': src/containers/haplotype_set.h:53:2: warning: no return statement in function returning non-void [-Wreturn-type] 53 | } | ^ In file included from src/io/haplotype_writer.h:28, from src/io/haplotype_writer.cpp:22: src/containers/haplotype_set.h: In member function 'bool IBD2track::merge(const IBD2track&)': src/containers/haplotype_set.h:53:2: warning: no return statement in function returning non-void [-Wreturn-type] 53 | } | ^ src/io/haplotype_writer.cpp: In member function 'void haplotype_writer::writeHaplotypes(std::string)': src/io/haplotype_writer.cpp:59:15: warning: ignoring return value of 'int bcf_hdr_write(htsFile*, bcf_hdr_t*)' declared with attribute 'warn_unused_result' [-Wunused-result] 59 | bcf_hdr_write(fp, hdr); | ~~~~~~~~~~~~~^~~~~~~~~ g++ -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/shapeit4-4.2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -c src/containers/variant_map.cpp -o obj/variant_map.o -Isrc -I/build/shapeit4-4.2.0+dfsg/debian/.debhelper/generated/_source/home/Tools/htslib-1.9 -I/usr/include In file included from src/io/genotype_reader.h:28, from src/io/genotype_reader2.cpp:22: src/containers/haplotype_set.h: In member function 'bool IBD2track::merge(const IBD2track&)': src/containers/haplotype_set.h:53:2: warning: no return statement in function returning non-void [-Wreturn-type] 53 | } | ^ In file included from src/io/genotype_reader.h:28, from src/io/genotype_reader1.cpp:22: src/containers/haplotype_set.h: In member function 'bool IBD2track::merge(const IBD2track&)': src/containers/haplotype_set.h:53:2: warning: no return statement in function returning non-void [-Wreturn-type] 53 | } | ^ g++ -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/shapeit4-4.2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -c src/containers/haplotype_set.cpp -o obj/haplotype_set.o -Isrc -I/build/shapeit4-4.2.0+dfsg/debian/.debhelper/generated/_source/home/Tools/htslib-1.9 -I/usr/include g++ -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/shapeit4-4.2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -c src/containers/genotype_set.cpp -o obj/genotype_set.o -Isrc -I/build/shapeit4-4.2.0+dfsg/debian/.debhelper/generated/_source/home/Tools/htslib-1.9 -I/usr/include g++ -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/shapeit4-4.2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -c src/containers/bitmatrix.cpp -o obj/bitmatrix.o -Isrc -I/build/shapeit4-4.2.0+dfsg/debian/.debhelper/generated/_source/home/Tools/htslib-1.9 -I/usr/include In file included from src/containers/haplotype_set.cpp:22: src/containers/haplotype_set.h: In member function 'bool IBD2track::merge(const IBD2track&)': src/containers/haplotype_set.h:53:2: warning: no return statement in function returning non-void [-Wreturn-type] 53 | } | ^ g++ -std=c++11 -Wl,-z,relro -Wl,-z,now -O3 obj/phaser_parameters.o obj/phaser_management.o obj/phaser_initialise.o obj/phaser_finalise.o obj/phaser_algorithm.o obj/variant.o obj/hmm_parameters.o obj/genotype_sweep.o obj/genotype_prune.o obj/genotype_mask.o obj/genotype_managment.o obj/genotype_build.o obj/compute_job.o obj/pbwt_solver.o obj/builder.o obj/haplotype_segment_single.o obj/haplotype_segment_double.o obj/main.o obj/haplotype_writer.o obj/graph_writer.o obj/gmap_reader.o obj/genotype_reader2.o obj/genotype_reader1.o obj/variant_map.o obj/haplotype_set.o obj/genotype_set.o obj/bitmatrix.o -lhts -lboost_iostreams -lboost_program_options -o bin/shapeit4.2 -lz -lbz2 -lm -lpthread -llzma make[1]: Leaving directory '/build/shapeit4-4.2.0+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 dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'shapeit4-dbgsym' in '../shapeit4-dbgsym_4.2.0+dfsg-1_arm64.deb'. dpkg-deb: building package 'shapeit4' in '../shapeit4_4.2.0+dfsg-1_arm64.deb'. dpkg-deb: building package 'shapeit4-example' in '../shapeit4-example_4.2.0+dfsg-1_all.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../shapeit4_4.2.0+dfsg-1_arm64.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/23226 and its subdirectories I: Current time: Mon Aug 8 19:21:24 -12 2022 I: pbuilder-time-stamp: 1660029684 Wed Jul 7 00:58:36 UTC 2021 I: 1st build successful. Starting 2nd build on remote node codethink10-arm64.debian.net. Wed Jul 7 00:58:36 UTC 2021 I: Preparing to do remote build '2' on codethink10-arm64.debian.net. Wed Jul 7 01:03:18 UTC 2021 I: Deleting $TMPDIR on codethink10-arm64.debian.net. Wed Jul 7 01:03:19 UTC 2021 I: shapeit4_4.2.0+dfsg-1_arm64.changes: Format: 1.8 Date: Thu, 04 Feb 2021 11:20:55 +0100 Source: shapeit4 Binary: shapeit4 shapeit4-dbgsym shapeit4-example Architecture: arm64 all Version: 4.2.0+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 (4.2.0+dfsg-1) unstable; urgency=medium . * New upstream version * Standards-Version: 4.5.1 (routine-update) * debhelper-compat 13 (routine-update) * Add salsa-ci file (routine-update) * Rules-Requires-Root: no (routine-update) * Set upstream metadata fields: Bug-Database, Bug-Submit, Repository, Repository-Browse. Checksums-Sha1: 29daaa4ea44b19f6f61896bf4e12f49a87b9b850 3648628 shapeit4-dbgsym_4.2.0+dfsg-1_arm64.deb a12c37c4b8dd1a193ce97f7e98ef0ce143fdf70b 52265088 shapeit4-example_4.2.0+dfsg-1_all.deb 61b221ae9ace1d44a7dee212d9c43e2c4ee428e6 6281 shapeit4_4.2.0+dfsg-1_arm64.buildinfo f3a79f9a46f6a454a39746ba25ff40fb9e04c16d 170872 shapeit4_4.2.0+dfsg-1_arm64.deb Checksums-Sha256: 8b2e0baabff7e6fd3051ac50e82dbc348638cfeafc3ce8f82a7cbf0f35360b36 3648628 shapeit4-dbgsym_4.2.0+dfsg-1_arm64.deb e302de797af1a07ee9b48ada6175a5e88fd01662f17b3bd20e306abc319527ae 52265088 shapeit4-example_4.2.0+dfsg-1_all.deb 943a42d4da70e4d005e9c1a0237c51a5f65715537027e9b680ee33864089baab 6281 shapeit4_4.2.0+dfsg-1_arm64.buildinfo d71446f0afb0dbf38fe55f3f76c4366049102dde6952685eebfb60259547ed99 170872 shapeit4_4.2.0+dfsg-1_arm64.deb Files: 56882c1d84b704d9f887e1ac8164d0a1 3648628 debug optional shapeit4-dbgsym_4.2.0+dfsg-1_arm64.deb 639bcd4e04e50a697f0238c7e9f62a2d 52265088 doc optional shapeit4-example_4.2.0+dfsg-1_all.deb 816ac1bc449e73409898ed1fdf09896a 6281 science optional shapeit4_4.2.0+dfsg-1_arm64.buildinfo a6487fd48937ba7f40c0c6aea7599376 170872 science optional shapeit4_4.2.0+dfsg-1_arm64.deb Wed Jul 7 01:03:21 UTC 2021 I: diffoscope 177 will be used to compare the two builds: # Profiling output for: /usr/bin/diffoscope --html /srv/reproducible-results/rbuild-debian/tmp.GEvFHoILJR/shapeit4_4.2.0+dfsg-1.diffoscope.html --text /srv/reproducible-results/rbuild-debian/tmp.GEvFHoILJR/shapeit4_4.2.0+dfsg-1.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/tmp.GEvFHoILJR/shapeit4_4.2.0+dfsg-1.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/tmp.GEvFHoILJR/b1/shapeit4_4.2.0+dfsg-1_arm64.changes /srv/reproducible-results/rbuild-debian/tmp.GEvFHoILJR/b2/shapeit4_4.2.0+dfsg-1_arm64.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call abc.DotChangesFile ## main (total time: 4.833s) 4.833s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 4.558s) 4.557s 10 calls diffoscope.comparators.binary.FilesystemFile 0.000s 8 calls abc.DotChangesFile Wed Jul 7 01:03:31 UTC 2021 I: diffoscope 177 found no differences in the changes files, and a .buildinfo file also exists. Wed Jul 7 01:03:31 UTC 2021 I: shapeit4 from bullseye built successfully and reproducibly on arm64. Wed Jul 7 01:03:32 UTC 2021 I: Submitting .buildinfo files to external archives: Wed Jul 7 01:03:32 UTC 2021 I: Submitting 8.0K b1/shapeit4_4.2.0+dfsg-1_arm64.buildinfo.asc Wed Jul 7 01:03:33 UTC 2021 I: Submitting 8.0K b2/shapeit4_4.2.0+dfsg-1_arm64.buildinfo.asc Wed Jul 7 01:03:34 UTC 2021 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Wed Jul 7 01:03:34 UTC 2021 I: Done submitting .buildinfo files. Wed Jul 7 01:03:34 UTC 2021 I: Removing signed shapeit4_4.2.0+dfsg-1_arm64.buildinfo.asc files: removed './b1/shapeit4_4.2.0+dfsg-1_arm64.buildinfo.asc' removed './b2/shapeit4_4.2.0+dfsg-1_arm64.buildinfo.asc'