Fri Apr 21 12:31:09 UTC 2023 I: starting to build berkeley-express/bookworm/arm64 on jenkins on '2023-04-21 12:30' Fri Apr 21 12:31:09 UTC 2023 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/arm64_12/6857/console.log Fri Apr 21 12:31:09 UTC 2023 I: Downloading source for bookworm/berkeley-express=1.5.3+dfsg-3 --2023-04-21 12:31:10-- http://cdn-fastly.deb.debian.org/debian/pool/main/b/berkeley-express/berkeley-express_1.5.3%2bdfsg-3.dsc Connecting to 78.137.99.97:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2493 (2.4K) [text/prs.lines.tag] Saving to: ‘berkeley-express_1.5.3+dfsg-3.dsc’ 0K .. 100% 290M=0s 2023-04-21 12:31:10 (290 MB/s) - ‘berkeley-express_1.5.3+dfsg-3.dsc’ saved [2493/2493] Fri Apr 21 12:31:10 UTC 2023 I: berkeley-express_1.5.3+dfsg-3.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: berkeley-express Binary: berkeley-express, berkeley-express-doc Architecture: any all Version: 1.5.3+dfsg-3 Maintainer: Debian Med Packaging Team Uploaders: Michael R. Crusoe Homepage: http://bio.math.berkeley.edu/eXpress/index.html Standards-Version: 4.6.1 Vcs-Browser: https://salsa.debian.org/med-team/berkeley-express Vcs-Git: https://salsa.debian.org/med-team/berkeley-express.git Testsuite: autopkgtest Testsuite-Triggers: bowtie, gzip, samtools Build-Depends: debhelper-compat (= 13), libboost-thread-dev, libboost-system-dev, libboost-filesystem-dev, libboost-program-options-dev, libboost-date-time-dev, libbamtools-dev, libboost-tools-dev, libgoogle-perftools-dev [amd64 arm64 armel armhf i386 powerpc ppc64el], cmake, libprotobuf-dev, protobuf-compiler Package-List: berkeley-express deb science optional arch=any berkeley-express-doc deb doc optional arch=all Checksums-Sha1: a24eee0a32da390f2f75be7526bf6a9a971bd3a3 365872 berkeley-express_1.5.3+dfsg.orig.tar.xz a679511b3d10abf44d8f09520b343aeeb1366aa6 10708 berkeley-express_1.5.3+dfsg-3.debian.tar.xz Checksums-Sha256: f26e2f6e4e04671a64619f014ab2195f42d53fbac8b8b84f46082c5cdc6d845b 365872 berkeley-express_1.5.3+dfsg.orig.tar.xz b752f5df4349aa6d900f3ec04a12171d4d8dac95216b39088456699262468877 10708 berkeley-express_1.5.3+dfsg-3.debian.tar.xz Files: cdb0c73b54ec20a662c14e6bfee0e384 365872 berkeley-express_1.5.3+dfsg.orig.tar.xz 9082cd7721eff5483fd4549ad5a08d6d 10708 berkeley-express_1.5.3+dfsg-3.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCgAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAmNhcO4RHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtFsMw//a+uP2LcnIdBTlBbN9sFY7p5xuobosyYB mLdbCEqSedmNE0ggOBc887KcYljY1DgvSp0vmxfOyijvi4gwra2nZMjSAa9bWN+I 3WSPKHOm+9MKGlsn4HJwyAYgrHwSJ2JE1KNOVXQ0dDsRryqiBEFkq/OURCCWlN1l GWjZ1o8lGsY8M2aIAhDQEPH/QDRy6bO65ovkp2+eMe9+zQsOZ7c4EK6aZCi2XquN QkKTMoC1JnZZul0czC2ZdC6LR5DtCVYF8rjSSMC1LVyjnINMsWWKMyD/5QOuomBB pBFZz0BvDaRzoWa+PGxb0wKmgDthGlfX9ScTiBab3DcMao1MFbhfVTPQJTHDs6+q BojhN+CDryJYyzwEGj9U+39U5SrVZejuy/lhIVycOGIWkcGLViQ5Pj7+M7pxudem qkBOXtyDktBCOYKIPaircc2GepA9t//ziq5He/gcrfLBLvly3hK8jq9Z5Xe5L9+k Fzb9BPBicqINOHnW/dyP4++JPL7YHt6ihWjP3UW+EXKbaK2PJ86/gAbMmT6swam5 wAaL4ng3RmNP1/pwG+Lrd+zDBWlcehsz3/vqI+eCHX3S81hbW+Kq2qyIQrDKR/eX 3O1liU4PQpU1tpIVbUxmzZEbgD7EcWrFLLDY80GJBMsdAhtoQKYU/c3NRllyBa9n r8OyAl4B1iA= =9sdj -----END PGP SIGNATURE----- Fri Apr 21 12:31:10 UTC 2023 I: Checking whether the package is not for us Fri Apr 21 12:31:10 UTC 2023 I: Starting 1st build on remote node codethink11-arm64.debian.net. Fri Apr 21 12:31:10 UTC 2023 I: Preparing to do remote build '1' on codethink11-arm64.debian.net. Fri Apr 21 12:33:29 UTC 2023 I: Deleting $TMPDIR on codethink11-arm64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Thu May 23 06:54:12 -12 2024 I: pbuilder-time-stamp: 1716490452 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bookworm-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 [berkeley-express_1.5.3+dfsg-3.dsc] I: copying [./berkeley-express_1.5.3+dfsg.orig.tar.xz] I: copying [./berkeley-express_1.5.3+dfsg-3.debian.tar.xz] I: Extracting source gpgv: Signature made Tue Nov 1 07:18:06 2022 -12 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./berkeley-express_1.5.3+dfsg-3.dsc: no acceptable signature found dpkg-source: info: extracting berkeley-express in berkeley-express-1.5.3+dfsg dpkg-source: info: unpacking berkeley-express_1.5.3+dfsg.orig.tar.xz dpkg-source: info: unpacking berkeley-express_1.5.3+dfsg-3.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying spelling-fixes dpkg-source: info: applying fix-bamtools-path dpkg-source: info: applying drop-zlib dpkg-source: info: applying correct-debug-flags.patch dpkg-source: info: applying privacy-breach.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/5740/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 parallel=8' DISTRIBUTION='bookworm' 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='5740' 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.bZfWVmtN/pbuilderrc_ipd4 --distribution bookworm --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.bZfWVmtN/b1 --logfile b1/build.log berkeley-express_1.5.3+dfsg-3.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 codethink11-arm64 4.15.0-209-generic #220-Ubuntu SMP Tue Mar 21 19:52:44 UTC 2023 aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 May 21 04:47 /bin -> usr/bin I: user script /srv/workspace/pbuilder/5740/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-thread-dev, libboost-system-dev, libboost-filesystem-dev, libboost-program-options-dev, libboost-date-time-dev, libbamtools-dev, libboost-tools-dev, libgoogle-perftools-dev, cmake, libprotobuf-dev, protobuf-compiler dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19616 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-thread-dev; however: Package libboost-thread-dev is not installed. pbuilder-satisfydepends-dummy depends on libboost-system-dev; however: Package libboost-system-dev is not installed. pbuilder-satisfydepends-dummy depends on libboost-filesystem-dev; however: Package libboost-filesystem-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 libboost-date-time-dev; however: Package libboost-date-time-dev is not installed. pbuilder-satisfydepends-dummy depends on libbamtools-dev; however: Package libbamtools-dev is not installed. pbuilder-satisfydepends-dummy depends on libboost-tools-dev; however: Package libboost-tools-dev is not installed. pbuilder-satisfydepends-dummy depends on libgoogle-perftools-dev; however: Package libgoogle-perftools-dev is not installed. pbuilder-satisfydepends-dummy depends on cmake; however: Package cmake is not installed. pbuilder-satisfydepends-dummy depends on libprotobuf-dev; however: Package libprotobuf-dev is not installed. pbuilder-satisfydepends-dummy depends on protobuf-compiler; however: Package protobuf-compiler 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} cmake{a} cmake-data{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libarchive13{a} libbamtools-dev{a} libbamtools2.5.2{a} libboost-atomic1.74-dev{a} libboost-atomic1.74.0{a} libboost-chrono1.74-dev{a} libboost-chrono1.74.0{a} libboost-date-time-dev{a} libboost-date-time1.74-dev{a} libboost-date-time1.74.0{a} libboost-filesystem-dev{a} libboost-filesystem1.74-dev{a} libboost-filesystem1.74.0{a} libboost-program-options-dev{a} libboost-program-options1.74-dev{a} libboost-program-options1.74.0{a} libboost-serialization1.74-dev{a} libboost-serialization1.74.0{a} libboost-system-dev{a} libboost-system1.74-dev{a} libboost-system1.74.0{a} libboost-thread-dev{a} libboost-thread1.74-dev{a} libboost-thread1.74.0{a} libboost-tools-dev{a} libboost1.74-dev{a} libboost1.74-tools-dev{a} libbrotli1{a} libcurl4{a} libdebhelper-perl{a} libelf1{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libgoogle-perftools-dev{a} libgoogle-perftools4{a} libicu72{a} libjsoncpp25{a} libldap-2.5-0{a} libmagic-mgc{a} libmagic1{a} libnghttp2-14{a} libpipeline1{a} libproc2-0{a} libprotobuf-dev{a} libprotobuf-lite32{a} libprotobuf32{a} libprotoc32{a} libpsl5{a} librhash0{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libssh2-1{a} libsub-override-perl{a} libtcmalloc-minimal4{a} libtool{a} libuchardet0{a} libuv1{a} libxml2{a} m4{a} man-db{a} po-debconf{a} procps{a} protobuf-compiler{a} sensible-utils{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: ca-certificates curl libarchive-cpio-perl libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules lynx psmisc publicsuffix wget 0 packages upgraded, 83 newly installed, 0 to remove and 0 not upgraded. Need to get 50.0 MB of archives. After unpacking 335 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bookworm/main arm64 libproc2-0 arm64 2:4.0.2-3 [60.1 kB] Get: 2 http://deb.debian.org/debian bookworm/main arm64 procps arm64 2:4.0.2-3 [698 kB] Get: 3 http://deb.debian.org/debian bookworm/main arm64 sensible-utils all 0.0.17+nmu1 [19.0 kB] Get: 4 http://deb.debian.org/debian bookworm/main arm64 libmagic-mgc arm64 1:5.44-3 [305 kB] Get: 5 http://deb.debian.org/debian bookworm/main arm64 libmagic1 arm64 1:5.44-3 [98.5 kB] Get: 6 http://deb.debian.org/debian bookworm/main arm64 file arm64 1:5.44-3 [42.5 kB] Get: 7 http://deb.debian.org/debian bookworm/main arm64 gettext-base arm64 0.21-12 [159 kB] Get: 8 http://deb.debian.org/debian bookworm/main arm64 libuchardet0 arm64 0.0.7-1 [67.9 kB] Get: 9 http://deb.debian.org/debian bookworm/main arm64 groff-base arm64 1.22.4-10 [861 kB] Get: 10 http://deb.debian.org/debian bookworm/main arm64 bsdextrautils arm64 2.38.1-5+b1 [86.9 kB] Get: 11 http://deb.debian.org/debian bookworm/main arm64 libpipeline1 arm64 1.5.7-1 [36.4 kB] Get: 12 http://deb.debian.org/debian bookworm/main arm64 man-db arm64 2.11.2-2 [1369 kB] Get: 13 http://deb.debian.org/debian bookworm/main arm64 m4 arm64 1.4.19-3 [276 kB] Get: 14 http://deb.debian.org/debian bookworm/main arm64 autoconf all 2.71-3 [332 kB] Get: 15 http://deb.debian.org/debian bookworm/main arm64 autotools-dev all 20220109.1 [51.6 kB] Get: 16 http://deb.debian.org/debian bookworm/main arm64 automake all 1:1.16.5-1.3 [823 kB] Get: 17 http://deb.debian.org/debian bookworm/main arm64 autopoint all 0.21-12 [495 kB] Get: 18 http://deb.debian.org/debian bookworm/main arm64 libicu72 arm64 72.1-3 [9204 kB] Get: 19 http://deb.debian.org/debian bookworm/main arm64 libxml2 arm64 2.9.14+dfsg-1.1+b3 [619 kB] Get: 20 http://deb.debian.org/debian bookworm/main arm64 libarchive13 arm64 3.6.2-1 [316 kB] Get: 21 http://deb.debian.org/debian bookworm/main arm64 libbrotli1 arm64 1.0.9-2+b6 [269 kB] Get: 22 http://deb.debian.org/debian bookworm/main arm64 libsasl2-modules-db arm64 2.1.28+dfsg-10 [20.8 kB] Get: 23 http://deb.debian.org/debian bookworm/main arm64 libsasl2-2 arm64 2.1.28+dfsg-10 [58.0 kB] Get: 24 http://deb.debian.org/debian bookworm/main arm64 libldap-2.5-0 arm64 2.5.13+dfsg-5 [171 kB] Get: 25 http://deb.debian.org/debian bookworm/main arm64 libnghttp2-14 arm64 1.52.0-1 [67.9 kB] Get: 26 http://deb.debian.org/debian bookworm/main arm64 libpsl5 arm64 0.21.2-1 [58.6 kB] Get: 27 http://deb.debian.org/debian bookworm/main arm64 librtmp1 arm64 2.4+20151223.gitfa8646d.1-2+b2 [59.4 kB] Get: 28 http://deb.debian.org/debian bookworm/main arm64 libssh2-1 arm64 1.10.0-3+b1 [172 kB] Get: 29 http://deb.debian.org/debian bookworm/main arm64 libcurl4 arm64 7.88.1-8 [361 kB] Get: 30 http://deb.debian.org/debian bookworm/main arm64 libexpat1 arm64 2.5.0-1 [84.8 kB] Get: 31 http://deb.debian.org/debian bookworm/main arm64 libjsoncpp25 arm64 1.9.5-4 [72.3 kB] Get: 32 http://deb.debian.org/debian bookworm/main arm64 librhash0 arm64 1.4.3-3 [131 kB] Get: 33 http://deb.debian.org/debian bookworm/main arm64 libuv1 arm64 1.44.2-1 [133 kB] Get: 34 http://deb.debian.org/debian bookworm/main arm64 cmake-data all 3.25.1-1 [2026 kB] Get: 35 http://deb.debian.org/debian bookworm/main arm64 cmake arm64 3.25.1-1 [6806 kB] Get: 36 http://deb.debian.org/debian bookworm/main arm64 libdebhelper-perl all 13.11.4 [81.2 kB] Get: 37 http://deb.debian.org/debian bookworm/main arm64 libtool all 2.4.7-5 [517 kB] Get: 38 http://deb.debian.org/debian bookworm/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 39 http://deb.debian.org/debian bookworm/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 40 http://deb.debian.org/debian bookworm/main arm64 libsub-override-perl all 0.09-4 [9304 B] Get: 41 http://deb.debian.org/debian bookworm/main arm64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 42 http://deb.debian.org/debian bookworm/main arm64 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 43 http://deb.debian.org/debian bookworm/main arm64 libelf1 arm64 0.188-2.1 [173 kB] Get: 44 http://deb.debian.org/debian bookworm/main arm64 dwz arm64 0.15-1 [101 kB] Get: 45 http://deb.debian.org/debian bookworm/main arm64 gettext arm64 0.21-12 [1248 kB] Get: 46 http://deb.debian.org/debian bookworm/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 47 http://deb.debian.org/debian bookworm/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 48 http://deb.debian.org/debian bookworm/main arm64 debhelper all 13.11.4 [942 kB] Get: 49 http://deb.debian.org/debian bookworm/main arm64 libbamtools2.5.2 arm64 2.5.2+dfsg-4 [134 kB] Get: 50 http://deb.debian.org/debian bookworm/main arm64 zlib1g-dev arm64 1:1.2.13.dfsg-1 [913 kB] Get: 51 http://deb.debian.org/debian bookworm/main arm64 libbamtools-dev arm64 2.5.2+dfsg-4 [204 kB] Get: 52 http://deb.debian.org/debian bookworm/main arm64 libboost1.74-dev arm64 1.74.0+ds1-20 [9510 kB] Get: 53 http://deb.debian.org/debian bookworm/main arm64 libboost-atomic1.74.0 arm64 1.74.0+ds1-20 [220 kB] Get: 54 http://deb.debian.org/debian bookworm/main arm64 libboost-atomic1.74-dev arm64 1.74.0+ds1-20 [221 kB] Get: 55 http://deb.debian.org/debian bookworm/main arm64 libboost-chrono1.74.0 arm64 1.74.0+ds1-20 [227 kB] Get: 56 http://deb.debian.org/debian bookworm/main arm64 libboost-chrono1.74-dev arm64 1.74.0+ds1-20 [235 kB] Get: 57 http://deb.debian.org/debian bookworm/main arm64 libboost-date-time1.74.0 arm64 1.74.0+ds1-20 [218 kB] Get: 58 http://deb.debian.org/debian bookworm/main arm64 libboost-serialization1.74.0 arm64 1.74.0+ds1-20 [308 kB] Get: 59 http://deb.debian.org/debian bookworm/main arm64 libboost-serialization1.74-dev arm64 1.74.0+ds1-20 [357 kB] Get: 60 http://deb.debian.org/debian bookworm/main arm64 libboost-date-time1.74-dev arm64 1.74.0+ds1-20 [226 kB] Get: 61 http://deb.debian.org/debian bookworm/main arm64 libboost-date-time-dev arm64 1.74.0.3 [4332 B] Get: 62 http://deb.debian.org/debian bookworm/main arm64 libboost-filesystem1.74.0 arm64 1.74.0+ds1-20 [254 kB] Get: 63 http://deb.debian.org/debian bookworm/main arm64 libboost-system1.74.0 arm64 1.74.0+ds1-20 [218 kB] Get: 64 http://deb.debian.org/debian bookworm/main arm64 libboost-system1.74-dev arm64 1.74.0+ds1-20 [219 kB] Get: 65 http://deb.debian.org/debian bookworm/main arm64 libboost-filesystem1.74-dev arm64 1.74.0+ds1-20 [277 kB] Get: 66 http://deb.debian.org/debian bookworm/main arm64 libboost-filesystem-dev arm64 1.74.0.3 [4368 B] Get: 67 http://deb.debian.org/debian bookworm/main arm64 libboost-program-options1.74.0 arm64 1.74.0+ds1-20 [317 kB] Get: 68 http://deb.debian.org/debian bookworm/main arm64 libboost-program-options1.74-dev arm64 1.74.0+ds1-20 [354 kB] Get: 69 http://deb.debian.org/debian bookworm/main arm64 libboost-program-options-dev arm64 1.74.0.3 [4340 B] Get: 70 http://deb.debian.org/debian bookworm/main arm64 libboost-system-dev arm64 1.74.0.3 [4468 B] Get: 71 http://deb.debian.org/debian bookworm/main arm64 libboost-thread1.74.0 arm64 1.74.0+ds1-20 [253 kB] Get: 72 http://deb.debian.org/debian bookworm/main arm64 libboost-thread1.74-dev arm64 1.74.0+ds1-20 [267 kB] Get: 73 http://deb.debian.org/debian bookworm/main arm64 libboost-thread-dev arm64 1.74.0.3 [4356 B] Get: 74 http://deb.debian.org/debian bookworm/main arm64 libboost1.74-tools-dev arm64 1.74.0+ds1-20 [1328 kB] Get: 75 http://deb.debian.org/debian bookworm/main arm64 libboost-tools-dev arm64 1.74.0.3 [4508 B] Get: 76 http://deb.debian.org/debian bookworm/main arm64 libtcmalloc-minimal4 arm64 2.10-1 [88.5 kB] Get: 77 http://deb.debian.org/debian bookworm/main arm64 libgoogle-perftools4 arm64 2.10-1 [187 kB] Get: 78 http://deb.debian.org/debian bookworm/main arm64 libgoogle-perftools-dev arm64 2.10-1 [457 kB] Get: 79 http://deb.debian.org/debian bookworm/main arm64 libprotobuf32 arm64 3.21.12-3 [821 kB] Get: 80 http://deb.debian.org/debian bookworm/main arm64 libprotobuf-lite32 arm64 3.21.12-3 [240 kB] Get: 81 http://deb.debian.org/debian bookworm/main arm64 libprotobuf-dev arm64 3.21.12-3 [1219 kB] Get: 82 http://deb.debian.org/debian bookworm/main arm64 libprotoc32 arm64 3.21.12-3 [718 kB] Get: 83 http://deb.debian.org/debian bookworm/main arm64 protobuf-compiler arm64 3.21.12-3 [83.9 kB] Fetched 50.0 MB in 3s (14.6 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libproc2-0:arm64. 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Setting up libldap-2.5-0:arm64 (2.5.13+dfsg-5) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up libprotobuf-dev:arm64 (3.21.12-3) ... Setting up dh-autoreconf (20) ... Setting up libbamtools-dev:arm64 (2.5.2+dfsg-4) ... Setting up libboost-serialization1.74-dev:arm64 (1.74.0+ds1-20) ... Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up dwz (0.15-1) ... Setting up groff-base (1.22.4-10) ... Setting up libcurl4:arm64 (7.88.1-8) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up man-db (2.11.2-2) ... Not building database; man-db/auto-update is not 'true'. Setting up libboost-date-time1.74-dev:arm64 (1.74.0+ds1-20) ... Setting up libboost-date-time-dev:arm64 (1.74.0.3) ... Setting up cmake (3.25.1-1) ... Setting up libboost-thread1.74-dev:arm64 (1.74.0+ds1-20) ... Setting up libboost-thread-dev:arm64 (1.74.0.3) ... Setting up debhelper (13.11.4) ... Processing triggers for libc-bin (2.36-9) ... Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/berkeley-express-1.5.3+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 > ../berkeley-express_1.5.3+dfsg-3_source.changes dpkg-buildpackage: info: source package berkeley-express dpkg-buildpackage: info: source version 1.5.3+dfsg-3 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 debian/rules clean dh clean debian/rules override_dh_clean make[1]: Entering directory '/build/berkeley-express-1.5.3+dfsg' dh_clean src/config.h make[1]: Leaving directory '/build/berkeley-express-1.5.3+dfsg' debian/rules binary dh binary dh_update_autotools_config dh_autoreconf dh_auto_configure cd obj-aarch64-linux-gnu && cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=None -DCMAKE_INSTALL_SYSCONFDIR=/etc -DCMAKE_INSTALL_LOCALSTATEDIR=/var -DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON -DCMAKE_FIND_USE_PACKAGE_REGISTRY=OFF -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON -DFETCHCONTENT_FULLY_DISCONNECTED=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run -DCMAKE_SKIP_INSTALL_ALL_DEPENDENCY=ON "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/aarch64-linux-gnu .. CMake Deprecation Warning at CMakeLists.txt:1 (cmake_minimum_required): Compatibility with CMake < 2.8.12 will be removed from a future version of CMake. Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions. -- The C compiler identification is GNU 12.2.0 -- The CXX compiler identification is GNU 12.2.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/cc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Found Boost: /usr/lib/aarch64-linux-gnu/cmake/Boost-1.74.0/BoostConfig.cmake (found suitable version "1.74.0", minimum required is "1.39") found components: thread system filesystem program_options date_time -- Found GPERFTOOLS_TCMALLOC: /usr/lib/aarch64-linux-gnu/libtcmalloc.so -- Found Protobuf: /usr/lib/aarch64-linux-gnu/libprotobuf.so (found version "3.21.12") -- Do not try to find libbamtools.a -- Configuring done -- Generating done CMake Warning: Manually-specified variables were not used by the project: CMAKE_EXPORT_NO_PACKAGE_REGISTRY CMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY CMAKE_INSTALL_LIBDIR CMAKE_INSTALL_LOCALSTATEDIR CMAKE_INSTALL_RUNSTATEDIR CMAKE_INSTALL_SYSCONFDIR FETCHCONTENT_FULLY_DISCONNECTED -- Build files have been written to: /build/berkeley-express-1.5.3+dfsg/obj-aarch64-linux-gnu dh_auto_build cd obj-aarch64-linux-gnu && make -j8 "INSTALL=install --strip-program=true" VERBOSE=1 make[1]: Entering directory '/build/berkeley-express-1.5.3+dfsg/obj-aarch64-linux-gnu' /usr/bin/cmake -S/build/berkeley-express-1.5.3+dfsg -B/build/berkeley-express-1.5.3+dfsg/obj-aarch64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/berkeley-express-1.5.3+dfsg/obj-aarch64-linux-gnu/CMakeFiles /build/berkeley-express-1.5.3+dfsg/obj-aarch64-linux-gnu//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/build/berkeley-express-1.5.3+dfsg/obj-aarch64-linux-gnu' make -f src/CMakeFiles/express.dir/build.make src/CMakeFiles/express.dir/depend make[3]: Entering directory '/build/berkeley-express-1.5.3+dfsg/obj-aarch64-linux-gnu' [ 11%] Running cpp protocol buffer compiler on /build/berkeley-express-1.5.3+dfsg/src/targets.proto [ 11%] Running cpp protocol buffer compiler on /build/berkeley-express-1.5.3+dfsg/src/alignments.proto cd /build/berkeley-express-1.5.3+dfsg/obj-aarch64-linux-gnu/src && /usr/bin/protoc --cpp_out /build/berkeley-express-1.5.3+dfsg/obj-aarch64-linux-gnu/src -I /build/berkeley-express-1.5.3+dfsg/src /build/berkeley-express-1.5.3+dfsg/src/targets.proto cd /build/berkeley-express-1.5.3+dfsg/obj-aarch64-linux-gnu/src && /usr/bin/protoc --cpp_out /build/berkeley-express-1.5.3+dfsg/obj-aarch64-linux-gnu/src -I /build/berkeley-express-1.5.3+dfsg/src /build/berkeley-express-1.5.3+dfsg/src/alignments.proto [libprotobuf WARNING google/protobuf/compiler/parser.cc:646] No syntax specified for the proto file: alignments.proto. Please use 'syntax = "proto2";' or 'syntax = "proto3";' to specify a syntax version. (Defaulted to proto2 syntax.) [libprotobuf WARNING google/protobuf/compiler/parser.cc:646] No syntax specified for the proto file: targets.proto. Please use 'syntax = "proto2";' or 'syntax = "proto3";' to specify a syntax version. (Defaulted to proto2 syntax.) cd /build/berkeley-express-1.5.3+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/berkeley-express-1.5.3+dfsg /build/berkeley-express-1.5.3+dfsg/src /build/berkeley-express-1.5.3+dfsg/obj-aarch64-linux-gnu /build/berkeley-express-1.5.3+dfsg/obj-aarch64-linux-gnu/src /build/berkeley-express-1.5.3+dfsg/obj-aarch64-linux-gnu/src/CMakeFiles/express.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/berkeley-express-1.5.3+dfsg/obj-aarch64-linux-gnu' make -f src/CMakeFiles/express.dir/build.make src/CMakeFiles/express.dir/build make[3]: Entering directory '/build/berkeley-express-1.5.3+dfsg/obj-aarch64-linux-gnu' [ 16%] Building CXX object src/CMakeFiles/express.dir/fragments.cpp.o [ 22%] Building CXX object src/CMakeFiles/express.dir/biascorrection.cpp.o [ 33%] Building CXX object src/CMakeFiles/express.dir/directiondetector.cpp.o [ 33%] Building CXX object src/CMakeFiles/express.dir/lengthdistribution.cpp.o [ 38%] Building CXX object src/CMakeFiles/express.dir/bundles.cpp.o cd /build/berkeley-express-1.5.3+dfsg/obj-aarch64-linux-gnu/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_ATOMIC_DYN_LINK -DBOOST_DATE_TIME_DYN_LINK -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DBOOST_THREAD_DYN_LINK -I/usr/include/bamtools -g -O2 -ffile-prefix-map=/build/berkeley-express-1.5.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D__FILE__=\"\" -std=gnu++11 -MD -MT src/CMakeFiles/express.dir/biascorrection.cpp.o -MF CMakeFiles/express.dir/biascorrection.cpp.o.d -o CMakeFiles/express.dir/biascorrection.cpp.o -c /build/berkeley-express-1.5.3+dfsg/src/biascorrection.cpp cd /build/berkeley-express-1.5.3+dfsg/obj-aarch64-linux-gnu/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_ATOMIC_DYN_LINK -DBOOST_DATE_TIME_DYN_LINK -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DBOOST_THREAD_DYN_LINK -I/usr/include/bamtools -g -O2 -ffile-prefix-map=/build/berkeley-express-1.5.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D__FILE__=\"\" -std=gnu++11 -MD -MT src/CMakeFiles/express.dir/directiondetector.cpp.o -MF CMakeFiles/express.dir/directiondetector.cpp.o.d -o CMakeFiles/express.dir/directiondetector.cpp.o -c /build/berkeley-express-1.5.3+dfsg/src/directiondetector.cpp cd /build/berkeley-express-1.5.3+dfsg/obj-aarch64-linux-gnu/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_ATOMIC_DYN_LINK -DBOOST_DATE_TIME_DYN_LINK -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DBOOST_THREAD_DYN_LINK -I/usr/include/bamtools -g -O2 -ffile-prefix-map=/build/berkeley-express-1.5.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D__FILE__=\"\" -std=gnu++11 -MD -MT src/CMakeFiles/express.dir/bundles.cpp.o -MF CMakeFiles/express.dir/bundles.cpp.o.d -o CMakeFiles/express.dir/bundles.cpp.o -c /build/berkeley-express-1.5.3+dfsg/src/bundles.cpp cd /build/berkeley-express-1.5.3+dfsg/obj-aarch64-linux-gnu/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_ATOMIC_DYN_LINK -DBOOST_DATE_TIME_DYN_LINK -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DBOOST_THREAD_DYN_LINK -I/usr/include/bamtools -g -O2 -ffile-prefix-map=/build/berkeley-express-1.5.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D__FILE__=\"\" -std=gnu++11 -MD -MT src/CMakeFiles/express.dir/fragments.cpp.o -MF CMakeFiles/express.dir/fragments.cpp.o.d -o CMakeFiles/express.dir/fragments.cpp.o -c /build/berkeley-express-1.5.3+dfsg/src/fragments.cpp cd /build/berkeley-express-1.5.3+dfsg/obj-aarch64-linux-gnu/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_ATOMIC_DYN_LINK -DBOOST_DATE_TIME_DYN_LINK -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DBOOST_THREAD_DYN_LINK -I/usr/include/bamtools -g -O2 -ffile-prefix-map=/build/berkeley-express-1.5.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D__FILE__=\"\" -std=gnu++11 -MD -MT src/CMakeFiles/express.dir/lengthdistribution.cpp.o -MF CMakeFiles/express.dir/lengthdistribution.cpp.o.d -o CMakeFiles/express.dir/lengthdistribution.cpp.o -c /build/berkeley-express-1.5.3+dfsg/src/lengthdistribution.cpp [ 44%] Building CXX object src/CMakeFiles/express.dir/markovmodel.cpp.o [ 50%] Building CXX object src/CMakeFiles/express.dir/mapparser.cpp.o [ 55%] Building CXX object src/CMakeFiles/express.dir/main.cpp.o cd /build/berkeley-express-1.5.3+dfsg/obj-aarch64-linux-gnu/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_ATOMIC_DYN_LINK -DBOOST_DATE_TIME_DYN_LINK -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DBOOST_THREAD_DYN_LINK -I/usr/include/bamtools -g -O2 -ffile-prefix-map=/build/berkeley-express-1.5.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D__FILE__=\"\" -std=gnu++11 -MD -MT src/CMakeFiles/express.dir/mapparser.cpp.o -MF CMakeFiles/express.dir/mapparser.cpp.o.d -o CMakeFiles/express.dir/mapparser.cpp.o -c /build/berkeley-express-1.5.3+dfsg/src/mapparser.cpp cd /build/berkeley-express-1.5.3+dfsg/obj-aarch64-linux-gnu/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_ATOMIC_DYN_LINK -DBOOST_DATE_TIME_DYN_LINK -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DBOOST_THREAD_DYN_LINK -I/usr/include/bamtools -g -O2 -ffile-prefix-map=/build/berkeley-express-1.5.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D__FILE__=\"\" -std=gnu++11 -MD -MT src/CMakeFiles/express.dir/main.cpp.o -MF CMakeFiles/express.dir/main.cpp.o.d -o CMakeFiles/express.dir/main.cpp.o -c /build/berkeley-express-1.5.3+dfsg/src/main.cpp cd /build/berkeley-express-1.5.3+dfsg/obj-aarch64-linux-gnu/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_ATOMIC_DYN_LINK -DBOOST_DATE_TIME_DYN_LINK -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DBOOST_THREAD_DYN_LINK -I/usr/include/bamtools -g -O2 -ffile-prefix-map=/build/berkeley-express-1.5.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D__FILE__=\"\" -std=gnu++11 -MD -MT src/CMakeFiles/express.dir/markovmodel.cpp.o -MF CMakeFiles/express.dir/markovmodel.cpp.o.d -o CMakeFiles/express.dir/markovmodel.cpp.o -c /build/berkeley-express-1.5.3+dfsg/src/markovmodel.cpp : warning: "__FILE__" redefined [-Wbuiltin-macro-redefined] : warning: "__FILE__" redefined [-Wbuiltin-macro-redefined] : warning: "__FILE__" redefined [-Wbuiltin-macro-redefined] : warning: "__FILE__" redefined [-Wbuiltin-macro-redefined] : warning: "__FILE__" redefined [-Wbuiltin-macro-redefined] : warning: "__FILE__" redefined [-Wbuiltin-macro-redefined] : warning: "__FILE__" redefined [-Wbuiltin-macro-redefined] : warning: "__FILE__" redefined [-Wbuiltin-macro-redefined] [ 61%] Building CXX object src/CMakeFiles/express.dir/mismatchmodel.cpp.o cd /build/berkeley-express-1.5.3+dfsg/obj-aarch64-linux-gnu/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_ATOMIC_DYN_LINK -DBOOST_DATE_TIME_DYN_LINK -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DBOOST_THREAD_DYN_LINK -I/usr/include/bamtools -g -O2 -ffile-prefix-map=/build/berkeley-express-1.5.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D__FILE__=\"\" -std=gnu++11 -MD -MT src/CMakeFiles/express.dir/mismatchmodel.cpp.o -MF CMakeFiles/express.dir/mismatchmodel.cpp.o.d -o CMakeFiles/express.dir/mismatchmodel.cpp.o -c /build/berkeley-express-1.5.3+dfsg/src/mismatchmodel.cpp : warning: "__FILE__" redefined [-Wbuiltin-macro-redefined] [ 66%] Building CXX object src/CMakeFiles/express.dir/robertsfilter.cpp.o cd /build/berkeley-express-1.5.3+dfsg/obj-aarch64-linux-gnu/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_ATOMIC_DYN_LINK -DBOOST_DATE_TIME_DYN_LINK -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DBOOST_THREAD_DYN_LINK -I/usr/include/bamtools -g -O2 -ffile-prefix-map=/build/berkeley-express-1.5.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D__FILE__=\"\" -std=gnu++11 -MD -MT src/CMakeFiles/express.dir/robertsfilter.cpp.o -MF CMakeFiles/express.dir/robertsfilter.cpp.o.d -o CMakeFiles/express.dir/robertsfilter.cpp.o -c /build/berkeley-express-1.5.3+dfsg/src/robertsfilter.cpp : warning: "__FILE__" redefined [-Wbuiltin-macro-redefined] [ 72%] Building CXX object src/CMakeFiles/express.dir/sequence.cpp.o cd /build/berkeley-express-1.5.3+dfsg/obj-aarch64-linux-gnu/src && /usr/bin/c++ 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-ffile-prefix-map=/build/berkeley-express-1.5.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D__FILE__=\"\" -std=gnu++11 -MD -MT src/CMakeFiles/express.dir/targets.cpp.o -MF CMakeFiles/express.dir/targets.cpp.o.d -o CMakeFiles/express.dir/targets.cpp.o -c /build/berkeley-express-1.5.3+dfsg/src/targets.cpp : warning: "__FILE__" redefined [-Wbuiltin-macro-redefined] [ 83%] Building CXX object src/CMakeFiles/express.dir/threadsafety.cpp.o cd /build/berkeley-express-1.5.3+dfsg/obj-aarch64-linux-gnu/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_ATOMIC_DYN_LINK -DBOOST_DATE_TIME_DYN_LINK -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DBOOST_THREAD_DYN_LINK -I/usr/include/bamtools -g -O2 -ffile-prefix-map=/build/berkeley-express-1.5.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D__FILE__=\"\" -std=gnu++11 -MD -MT src/CMakeFiles/express.dir/threadsafety.cpp.o -MF CMakeFiles/express.dir/threadsafety.cpp.o.d -o CMakeFiles/express.dir/threadsafety.cpp.o -c /build/berkeley-express-1.5.3+dfsg/src/threadsafety.cpp : warning: "__FILE__" redefined [-Wbuiltin-macro-redefined] [ 88%] Building CXX object src/CMakeFiles/express.dir/alignments.pb.cc.o cd /build/berkeley-express-1.5.3+dfsg/obj-aarch64-linux-gnu/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_ATOMIC_DYN_LINK -DBOOST_DATE_TIME_DYN_LINK -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DBOOST_THREAD_DYN_LINK -I/usr/include/bamtools -g -O2 -ffile-prefix-map=/build/berkeley-express-1.5.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D__FILE__=\"\" -std=gnu++11 -MD -MT src/CMakeFiles/express.dir/alignments.pb.cc.o -MF CMakeFiles/express.dir/alignments.pb.cc.o.d -o CMakeFiles/express.dir/alignments.pb.cc.o -c /build/berkeley-express-1.5.3+dfsg/obj-aarch64-linux-gnu/src/alignments.pb.cc : warning: "__FILE__" redefined [-Wbuiltin-macro-redefined] [ 94%] Building CXX object src/CMakeFiles/express.dir/targets.pb.cc.o cd /build/berkeley-express-1.5.3+dfsg/obj-aarch64-linux-gnu/src && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_ATOMIC_DYN_LINK -DBOOST_DATE_TIME_DYN_LINK -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DBOOST_THREAD_DYN_LINK -I/usr/include/bamtools -g -O2 -ffile-prefix-map=/build/berkeley-express-1.5.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D__FILE__=\"\" -std=gnu++11 -MD -MT src/CMakeFiles/express.dir/targets.pb.cc.o -MF CMakeFiles/express.dir/targets.pb.cc.o.d -o CMakeFiles/express.dir/targets.pb.cc.o -c /build/berkeley-express-1.5.3+dfsg/obj-aarch64-linux-gnu/src/targets.pb.cc : warning: "__FILE__" redefined [-Wbuiltin-macro-redefined] [100%] Linking CXX executable express cd /build/berkeley-express-1.5.3+dfsg/obj-aarch64-linux-gnu/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/express.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/berkeley-express-1.5.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -D__FILE__=\"\" -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/express.dir/biascorrection.cpp.o CMakeFiles/express.dir/bundles.cpp.o CMakeFiles/express.dir/directiondetector.cpp.o CMakeFiles/express.dir/fragments.cpp.o CMakeFiles/express.dir/lengthdistribution.cpp.o CMakeFiles/express.dir/main.cpp.o CMakeFiles/express.dir/mapparser.cpp.o CMakeFiles/express.dir/markovmodel.cpp.o CMakeFiles/express.dir/mismatchmodel.cpp.o CMakeFiles/express.dir/robertsfilter.cpp.o CMakeFiles/express.dir/sequence.cpp.o CMakeFiles/express.dir/targets.cpp.o CMakeFiles/express.dir/threadsafety.cpp.o CMakeFiles/express.dir/alignments.pb.cc.o CMakeFiles/express.dir/targets.pb.cc.o -o express /usr/lib/aarch64-linux-gnu/libboost_thread.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_system.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_program_options.so.1.74.0 /usr/lib/aarch64-linux-gnu/libboost_date_time.so.1.74.0 -lbamtools -lprotobuf -lpthread -lrt /usr/lib/aarch64-linux-gnu/libboost_atomic.so.1.74.0 make[3]: Leaving directory '/build/berkeley-express-1.5.3+dfsg/obj-aarch64-linux-gnu' [100%] Built target express make[2]: Leaving directory '/build/berkeley-express-1.5.3+dfsg/obj-aarch64-linux-gnu' /usr/bin/cmake -E cmake_progress_start /build/berkeley-express-1.5.3+dfsg/obj-aarch64-linux-gnu/CMakeFiles 0 make[1]: Leaving directory '/build/berkeley-express-1.5.3+dfsg/obj-aarch64-linux-gnu' dh_auto_test create-stamp debian/debhelper-build-stamp dh_prep dh_installdirs dh_auto_install cd obj-aarch64-linux-gnu && make -j8 install DESTDIR=/build/berkeley-express-1.5.3\+dfsg/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/berkeley-express-1.5.3+dfsg/obj-aarch64-linux-gnu' /usr/bin/cmake -S/build/berkeley-express-1.5.3+dfsg -B/build/berkeley-express-1.5.3+dfsg/obj-aarch64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 preinstall make[2]: Entering directory '/build/berkeley-express-1.5.3+dfsg/obj-aarch64-linux-gnu' make[2]: Nothing to be done for 'preinstall'. make[2]: Leaving directory '/build/berkeley-express-1.5.3+dfsg/obj-aarch64-linux-gnu' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "None" -- Installing: /build/berkeley-express-1.5.3+dfsg/debian/tmp/usr/bin/express make[1]: Leaving directory '/build/berkeley-express-1.5.3+dfsg/obj-aarch64-linux-gnu' dh_install dh_installdocs dh_installchangelogs dh_installexamples dh_installman dh_perl dh_link dh_strip_nondeterminism debian/rules override_dh_compress make[1]: Entering directory '/build/berkeley-express-1.5.3+dfsg' dh_compress --exclude=express-doc.pdf make[1]: Leaving directory '/build/berkeley-express-1.5.3+dfsg' 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 'berkeley-express-dbgsym' in '../berkeley-express-dbgsym_1.5.3+dfsg-3_arm64.deb'. dpkg-deb: building package 'berkeley-express' in '../berkeley-express_1.5.3+dfsg-3_arm64.deb'. dpkg-deb: building package 'berkeley-express-doc' in '../berkeley-express-doc_1.5.3+dfsg-3_all.deb'. dpkg-genbuildinfo --build=binary -O../berkeley-express_1.5.3+dfsg-3_arm64.buildinfo dpkg-genchanges --build=binary -O../berkeley-express_1.5.3+dfsg-3_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: not including original 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/5740 and its subdirectories I: Current time: Thu May 23 06:56:28 -12 2024 I: pbuilder-time-stamp: 1716490588 Fri Apr 21 12:33:30 UTC 2023 I: 1st build successful. Starting 2nd build on remote node codethink16-arm64.debian.net. Fri Apr 21 12:33:30 UTC 2023 I: Preparing to do remote build '2' on codethink16-arm64.debian.net. Fri Apr 21 12:38:23 UTC 2023 I: Deleting $TMPDIR on codethink16-arm64.debian.net. Fri Apr 21 12:38:24 UTC 2023 I: berkeley-express_1.5.3+dfsg-3_arm64.changes: Format: 1.8 Date: Tue, 01 Nov 2022 20:13:24 +0100 Source: berkeley-express Binary: berkeley-express berkeley-express-dbgsym berkeley-express-doc Architecture: arm64 all Version: 1.5.3+dfsg-3 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: berkeley-express - Streaming quantification for high-throughput sequencing berkeley-express-doc - Documentation for RNA-Seq tool eXpress Changes: berkeley-express (1.5.3+dfsg-3) unstable; urgency=medium . * Team upload. * Fix watch file * Standards-Version: 4.6.1 (routine-update) * Lintian-overrides for false positives Checksums-Sha1: 011b1aba1fc77942a91ea1d1be3deef36147a45e 4672300 berkeley-express-dbgsym_1.5.3+dfsg-3_arm64.deb e73bb85fcf8d8dac8b0692c5891de66383f1a504 706136 berkeley-express-doc_1.5.3+dfsg-3_all.deb bed280b610ffdc6e33cee1f45f465ba12276238e 7685 berkeley-express_1.5.3+dfsg-3_arm64.buildinfo 03cd68e76d7e5941b4f67a30792e2a3b2078a9c9 209548 berkeley-express_1.5.3+dfsg-3_arm64.deb Checksums-Sha256: d604fed5cc611f930e6ad536f47f399f98ea2db744963d2f2013fbf4579fc8ef 4672300 berkeley-express-dbgsym_1.5.3+dfsg-3_arm64.deb ac2db6596c8c6c2f7dd2b52531cc0709af4146ae9e685673b205e302ff015343 706136 berkeley-express-doc_1.5.3+dfsg-3_all.deb 5bb0907d0145204604860da48b167d093e7fa7ab4fce59814c8a17330fa8313e 7685 berkeley-express_1.5.3+dfsg-3_arm64.buildinfo a334fa9bbb01e8be11ece8b7b689e8841f8ed7a1e539e2fbf166d8077c153674 209548 berkeley-express_1.5.3+dfsg-3_arm64.deb Files: 0525c8d2e8eb48f65649a3f3bcede4c8 4672300 debug optional berkeley-express-dbgsym_1.5.3+dfsg-3_arm64.deb 974185f49f0af606f086b9405d617d6e 706136 doc optional berkeley-express-doc_1.5.3+dfsg-3_all.deb 82e263949bfc439f38bfc9f72c25e664 7685 science optional berkeley-express_1.5.3+dfsg-3_arm64.buildinfo 32769d23a5cc585c5b9e4102395295c9 209548 science optional berkeley-express_1.5.3+dfsg-3_arm64.deb Fri Apr 21 12:38:25 UTC 2023 I: diffoscope 240 will be used to compare the two builds: # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.bZfWVmtN/berkeley-express_1.5.3+dfsg-3.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.bZfWVmtN/berkeley-express_1.5.3+dfsg-3.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.bZfWVmtN/berkeley-express_1.5.3+dfsg-3.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.bZfWVmtN/b1/berkeley-express_1.5.3+dfsg-3_arm64.changes /srv/reproducible-results/rbuild-debian/r-b-build.bZfWVmtN/b2/berkeley-express_1.5.3+dfsg-3_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: 0.455s) 0.455s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.092s) 0.092s 12 calls diffoscope.comparators.binary.FilesystemFile 0.000s 10 calls abc.DotChangesFile ## specialize (total time: 0.001s) 0.001s 1 call specialize Fri Apr 21 12:38:29 UTC 2023 I: diffoscope 240 found no differences in the changes files, and a .buildinfo file also exists. Fri Apr 21 12:38:29 UTC 2023 I: berkeley-express from bookworm built successfully and reproducibly on arm64. Fri Apr 21 12:38:31 UTC 2023 I: Submitting .buildinfo files to external archives: Fri Apr 21 12:38:31 UTC 2023 I: Submitting 12K b1/berkeley-express_1.5.3+dfsg-3_arm64.buildinfo.asc Fri Apr 21 12:38:33 UTC 2023 I: Submitting 12K b2/berkeley-express_1.5.3+dfsg-3_arm64.buildinfo.asc Fri Apr 21 12:38:35 UTC 2023 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Fri Apr 21 12:38:35 UTC 2023 I: Done submitting .buildinfo files. Fri Apr 21 12:38:35 UTC 2023 I: Removing signed berkeley-express_1.5.3+dfsg-3_arm64.buildinfo.asc files: removed './b1/berkeley-express_1.5.3+dfsg-3_arm64.buildinfo.asc' removed './b2/berkeley-express_1.5.3+dfsg-3_arm64.buildinfo.asc'