Tue Oct 21 20:07:45 UTC 2025 I: starting to build berkeley-express/forky/amd64 on jenkins on '2025-10-21 20:07' Tue Oct 21 20:07:45 UTC 2025 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_16/75417/console.log Tue Oct 21 20:07:45 UTC 2025 I: Downloading source for forky/berkeley-express=1.5.3+dfsg-4 --2025-10-21 20:07:45-- http://deb.debian.org/debian/pool/main/b/berkeley-express/berkeley-express_1.5.3%2bdfsg-4.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2495 (2.4K) [text/prs.lines.tag] Saving to: ‘berkeley-express_1.5.3+dfsg-4.dsc’ 0K .. 100% 279M=0s 2025-10-21 20:07:45 (279 MB/s) - ‘berkeley-express_1.5.3+dfsg-4.dsc’ saved [2495/2495] Tue Oct 21 20:07:46 UTC 2025 I: berkeley-express_1.5.3+dfsg-4.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-4 Maintainer: Debian Med Packaging Team Uploaders: Michael R. Crusoe , Homepage: http://bio.math.berkeley.edu/eXpress/index.html Standards-Version: 4.7.2 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 6527fe752a733fb12fb0be837f45ac0d047d408f 10760 berkeley-express_1.5.3+dfsg-4.debian.tar.xz Checksums-Sha256: f26e2f6e4e04671a64619f014ab2195f42d53fbac8b8b84f46082c5cdc6d845b 365872 berkeley-express_1.5.3+dfsg.orig.tar.xz e77ca7cfacac3fbf96bd38f94397c2b94fa8c4cce23ce35b74f4827daef8bcb9 10760 berkeley-express_1.5.3+dfsg-4.debian.tar.xz Files: cdb0c73b54ec20a662c14e6bfee0e384 365872 berkeley-express_1.5.3+dfsg.orig.tar.xz f52654fdb8cd5aff48feea1193b12063 10760 berkeley-express_1.5.3+dfsg-4.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCgAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAmjwr3ARHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtECOQ//S5DlYaYBpu3fhRrVVGMWCQfdSoRuOOsr QNaBDAJAqXa9wVvDXAOtnsIxiCXNZIbAvQBaOHQ5NyJ8w1VkvVKIkoVBtNV4THfO lLp1CE4mu2tASyo2oKtBYA0Tl4Oel3zn3lg06VOZBMRcgPbSQiJosq9+l4Xo1+/G efARE65bIhUn1ZNLjxXMGzW/pHm8UbYjZRuASIfKT3W6DZbrwHUmHsRWe2+bT4Mj +RzwB00pmq5+mViN15bIOGWAkJ3Io/eT9gYtMzp1IWBwcIyeu2qXHyaYjcn2gkL0 7y9jrpzjxgMZCwGbaFraJ3Sazo6Mq1oD/BmmCzkcGhujLHy4A0CsCM6xpzeoinZ/ No+2VtMnCGratI0yud98elR9py671dqfNbDl6A+0DlJZu4tZjXT92BRqL9BJlB2G BhfCpm+FwERW8e3JCnYU0wgDJRrP9wW/SJi5klAg5B1WDW9tyQezAKiZ66TbRIUk WB98w5DE6EAjMdJ5+xjYULx7BVcnncMxQ5ZYrlrlGlpMn2m4ehaDiGuiB2K4xMYf 78GYZ1zqbKyLM8/ZpsMEy9Y40bMhVOZQh43LHvrK3xPRa0jrMdW9ddBEHS2smzWW JKymH6jNgIvYenlbMWBPPDVBbBDl9gPYRADq/MyL1wlkP37JI71JvgSM8u4Q3c/o akB/wKhlosM= =kxyu -----END PGP SIGNATURE----- Tue Oct 21 20:07:46 UTC 2025 I: Checking whether the package is not for us Tue Oct 21 20:07:46 UTC 2025 I: Starting 1st build on remote node ionos15-amd64.debian.net. Tue Oct 21 20:07:46 UTC 2025 I: Preparing to do remote build '1' on ionos15-amd64.debian.net. Tue Oct 21 20:09:39 UTC 2025 I: Deleting $TMPDIR on ionos15-amd64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Mon Nov 23 14:30:44 -12 2026 I: pbuilder-time-stamp: 1795487444 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/forky-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-4.dsc] I: copying [./berkeley-express_1.5.3+dfsg.orig.tar.xz] I: copying [./berkeley-express_1.5.3+dfsg-4.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./berkeley-express_1.5.3+dfsg-4.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-4.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/1502234/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='amd64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 ' DISTRIBUTION='forky' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='b54de6b3c8d74392a2ac75ad2d20e2b4' 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='1502234' 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.UukGIJIk/pbuilderrc_1UvT --distribution forky --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/forky-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.UukGIJIk/b1 --logfile b1/build.log berkeley-express_1.5.3+dfsg-4.dsc' SUDO_GID='111' SUDO_HOME='/var/lib/jenkins' SUDO_UID='106' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://213.165.73.152:3128' I: uname -a Linux ionos15-amd64 6.12.48+deb13-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.48-1 (2025-09-20) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 10 2025 /bin -> usr/bin I: user script /srv/workspace/pbuilder/1502234/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: amd64 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 ... 19898 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} gcc-14-base{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libarchive13t64{a} libbamtools-dev{a} libbamtools2.5.3{a} libboost-atomic1.83-dev{a} libboost-atomic1.83.0{a} libboost-chrono1.83-dev{a} libboost-chrono1.83.0t64{a} libboost-date-time-dev{a} libboost-date-time1.83-dev{a} libboost-date-time1.83.0{a} libboost-filesystem-dev{a} libboost-filesystem1.83-dev{a} libboost-filesystem1.83.0{a} libboost-program-options-dev{a} libboost-program-options1.83-dev{a} libboost-program-options1.83.0{a} libboost-serialization1.83-dev{a} libboost-serialization1.83.0{a} libboost-system-dev{a} libboost-system1.83-dev{a} libboost-system1.83.0{a} libboost-thread-dev{a} libboost-thread1.83-dev{a} libboost-thread1.83.0{a} libboost-tools-dev{a} libboost1.83-dev{a} libboost1.83-tools-dev{a} libbrotli1{a} libcom-err2{a} libcurl4t64{a} libdebhelper-perl{a} libelf1t64{a} libexpat1{a} libffi8{a} libfile-stripnondeterminism-perl{a} libgcc-14-dev{a} libgnutls30t64{a} libgoogle-perftools-dev{a} libgoogle-perftools4t64{a} libgssapi-krb5-2{a} libidn2-0{a} libjsoncpp26{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} libldap2{a} liblzma-dev{a} libmagic-mgc{a} libmagic1t64{a} libnghttp2-14{a} libnghttp3-9{a} libngtcp2-16{a} libngtcp2-crypto-ossl0{a} libp11-kit0{a} libpipeline1{a} libproc2-0{a} libprotobuf-dev{a} libprotobuf-lite32t64{a} libprotobuf32t64{a} libprotoc32t64{a} libpsl5t64{a} librhash1{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libssh2-1t64{a} libstdc++-14-dev{a} libtasn1-6{a} libtcmalloc-minimal4t64{a} libtool{a} libuchardet0{a} libunistring5{a} libunwind-dev{a} libunwind8{a} libuv1t64{a} libxml2-16{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 krb5-locales libarchive-cpio-perl libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules linux-sysctl-defaults lynx psmisc publicsuffix wget 0 packages upgraded, 102 newly installed, 0 to remove and 0 not upgraded. Need to get 60.5 MB of archives. After unpacking 403 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian forky/main amd64 libexpat1 amd64 2.7.3-1 [112 kB] Get: 2 http://deb.debian.org/debian forky/main amd64 libproc2-0 amd64 2:4.0.4-9 [65.6 kB] Get: 3 http://deb.debian.org/debian forky/main amd64 procps amd64 2:4.0.4-9 [882 kB] Get: 4 http://deb.debian.org/debian forky/main amd64 sensible-utils all 0.0.26 [27.0 kB] Get: 5 http://deb.debian.org/debian forky/main amd64 libmagic-mgc amd64 1:5.46-5 [338 kB] Get: 6 http://deb.debian.org/debian forky/main amd64 libmagic1t64 amd64 1:5.46-5 [109 kB] Get: 7 http://deb.debian.org/debian forky/main amd64 file amd64 1:5.46-5 [43.6 kB] Get: 8 http://deb.debian.org/debian forky/main amd64 gettext-base amd64 0.23.1-2+b1 [244 kB] Get: 9 http://deb.debian.org/debian forky/main amd64 libuchardet0 amd64 0.0.8-2 [68.5 kB] Get: 10 http://deb.debian.org/debian forky/main amd64 groff-base amd64 1.23.0-9 [1187 kB] Get: 11 http://deb.debian.org/debian forky/main amd64 bsdextrautils amd64 2.41.2-1 [95.2 kB] Get: 12 http://deb.debian.org/debian forky/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get: 13 http://deb.debian.org/debian forky/main amd64 man-db amd64 2.13.1-1 [1469 kB] Get: 14 http://deb.debian.org/debian forky/main amd64 m4 amd64 1.4.20-2 [325 kB] Get: 15 http://deb.debian.org/debian forky/main amd64 autoconf all 2.72-3.1 [494 kB] Get: 16 http://deb.debian.org/debian forky/main amd64 autotools-dev all 20240727.1 [60.2 kB] Get: 17 http://deb.debian.org/debian forky/main amd64 automake all 1:1.17-4 [862 kB] Get: 18 http://deb.debian.org/debian forky/main amd64 autopoint all 0.23.1-2 [770 kB] Get: 19 http://deb.debian.org/debian forky/main amd64 cmake-data all 4.1.1+really3.31.6-2 [2268 kB] Get: 20 http://deb.debian.org/debian forky/main amd64 libxml2-16 amd64 2.14.6+dfsg-0.1 [651 kB] Get: 21 http://deb.debian.org/debian forky/main amd64 libarchive13t64 amd64 3.7.4-4+b1 [349 kB] Get: 22 http://deb.debian.org/debian forky/main amd64 libnghttp3-9 amd64 1.12.0-1 [68.4 kB] Get: 23 http://deb.debian.org/debian forky/main amd64 libngtcp2-16 amd64 1.16.0-1 [136 kB] Get: 24 http://deb.debian.org/debian forky/main amd64 libbrotli1 amd64 1.1.0-2+b7 [307 kB] Get: 25 http://deb.debian.org/debian forky/main amd64 libkrb5support0 amd64 1.21.3-5 [33.0 kB] Get: 26 http://deb.debian.org/debian forky/main amd64 libcom-err2 amd64 1.47.2-3+b3 [25.0 kB] Get: 27 http://deb.debian.org/debian forky/main amd64 libk5crypto3 amd64 1.21.3-5 [81.5 kB] Get: 28 http://deb.debian.org/debian forky/main amd64 libkeyutils1 amd64 1.6.3-6 [9456 B] Get: 29 http://deb.debian.org/debian forky/main amd64 libkrb5-3 amd64 1.21.3-5 [326 kB] Get: 30 http://deb.debian.org/debian forky/main amd64 libgssapi-krb5-2 amd64 1.21.3-5 [138 kB] Get: 31 http://deb.debian.org/debian forky/main amd64 libunistring5 amd64 1.3-2 [477 kB] Get: 32 http://deb.debian.org/debian forky/main amd64 libidn2-0 amd64 2.3.8-4 [110 kB] Get: 33 http://deb.debian.org/debian forky/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-10 [19.8 kB] Get: 34 http://deb.debian.org/debian forky/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-10 [57.8 kB] Get: 35 http://deb.debian.org/debian forky/main amd64 libldap2 amd64 2.6.10+dfsg-1 [194 kB] Get: 36 http://deb.debian.org/debian forky/main amd64 libnghttp2-14 amd64 1.64.0-1.1+b1 [76.2 kB] Get: 37 http://deb.debian.org/debian forky/main amd64 libngtcp2-crypto-ossl0 amd64 1.16.0-1 [27.5 kB] Get: 38 http://deb.debian.org/debian forky/main amd64 libpsl5t64 amd64 0.21.2-1.1+b1 [57.2 kB] Get: 39 http://deb.debian.org/debian forky/main amd64 libffi8 amd64 3.5.2-2 [25.5 kB] Get: 40 http://deb.debian.org/debian forky/main amd64 libp11-kit0 amd64 0.25.9-2 [443 kB] Get: 41 http://deb.debian.org/debian forky/main amd64 libtasn1-6 amd64 4.20.0-2 [49.9 kB] Get: 42 http://deb.debian.org/debian forky/main amd64 libgnutls30t64 amd64 3.8.10-2 [1484 kB] Get: 43 http://deb.debian.org/debian forky/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-3 [58.3 kB] Get: 44 http://deb.debian.org/debian forky/main amd64 libssh2-1t64 amd64 1.11.1-1 [245 kB] Get: 45 http://deb.debian.org/debian forky/main amd64 libcurl4t64 amd64 8.16.0-4 [408 kB] Get: 46 http://deb.debian.org/debian forky/main amd64 libjsoncpp26 amd64 1.9.6-4 [89.4 kB] Get: 47 http://deb.debian.org/debian forky/main amd64 librhash1 amd64 1.4.6-1 [137 kB] Get: 48 http://deb.debian.org/debian forky/main amd64 libuv1t64 amd64 1.51.0-2 [155 kB] Get: 49 http://deb.debian.org/debian forky/main amd64 cmake amd64 4.1.1+really3.31.6-2 [12.2 MB] Get: 50 http://deb.debian.org/debian forky/main amd64 libdebhelper-perl all 13.28 [92.4 kB] Get: 51 http://deb.debian.org/debian forky/main amd64 libtool all 2.5.4-5 [540 kB] Get: 52 http://deb.debian.org/debian forky/main amd64 dh-autoreconf all 21 [12.2 kB] Get: 53 http://deb.debian.org/debian forky/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 54 http://deb.debian.org/debian forky/main amd64 libfile-stripnondeterminism-perl all 1.15.0-1 [19.9 kB] Get: 55 http://deb.debian.org/debian forky/main amd64 dh-strip-nondeterminism all 1.15.0-1 [8812 B] Get: 56 http://deb.debian.org/debian forky/main amd64 libelf1t64 amd64 0.193-3 [192 kB] Get: 57 http://deb.debian.org/debian forky/main amd64 dwz amd64 0.16-2 [108 kB] Get: 58 http://deb.debian.org/debian forky/main amd64 gettext amd64 0.23.1-2+b1 [1680 kB] Get: 59 http://deb.debian.org/debian forky/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 60 http://deb.debian.org/debian forky/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 61 http://deb.debian.org/debian forky/main amd64 debhelper all 13.28 [941 kB] Get: 62 http://deb.debian.org/debian forky/main amd64 gcc-14-base amd64 14.3.0-8 [52.1 kB] Get: 63 http://deb.debian.org/debian forky/main amd64 libbamtools2.5.3 amd64 2.5.3+dfsg-1 [161 kB] Get: 64 http://deb.debian.org/debian forky/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1+b1 [920 kB] Get: 65 http://deb.debian.org/debian forky/main amd64 libbamtools-dev amd64 2.5.3+dfsg-1 [221 kB] Get: 66 http://deb.debian.org/debian forky/main amd64 libgcc-14-dev amd64 14.3.0-8 [2670 kB] Get: 67 http://deb.debian.org/debian forky/main amd64 libstdc++-14-dev amd64 14.3.0-8 [2673 kB] Get: 68 http://deb.debian.org/debian forky/main amd64 libboost1.83-dev amd64 1.83.0-5 [10.6 MB] Get: 69 http://deb.debian.org/debian forky/main amd64 libboost-atomic1.83.0 amd64 1.83.0-5 [235 kB] Get: 70 http://deb.debian.org/debian forky/main amd64 libboost-atomic1.83-dev amd64 1.83.0-5 [236 kB] Get: 71 http://deb.debian.org/debian forky/main amd64 libboost-chrono1.83.0t64 amd64 1.83.0-5 [241 kB] Get: 72 http://deb.debian.org/debian forky/main amd64 libboost-chrono1.83-dev amd64 1.83.0-5 [247 kB] Get: 73 http://deb.debian.org/debian forky/main amd64 libboost-date-time1.83.0 amd64 1.83.0-5 [231 kB] Get: 74 http://deb.debian.org/debian forky/main amd64 libboost-serialization1.83.0 amd64 1.83.0-5 [343 kB] Get: 75 http://deb.debian.org/debian forky/main amd64 libboost-serialization1.83-dev amd64 1.83.0-5 [383 kB] Get: 76 http://deb.debian.org/debian forky/main amd64 libboost-date-time1.83-dev amd64 1.83.0-5 [239 kB] Get: 77 http://deb.debian.org/debian forky/main amd64 libboost-date-time-dev amd64 1.83.0.2+b2 [3596 B] Get: 78 http://deb.debian.org/debian forky/main amd64 libboost-filesystem1.83.0 amd64 1.83.0-5 [286 kB] Get: 79 http://deb.debian.org/debian forky/main amd64 libboost-system1.83.0 amd64 1.83.0-5 [231 kB] Get: 80 http://deb.debian.org/debian forky/main amd64 libboost-system1.83-dev amd64 1.83.0-5 [232 kB] Get: 81 http://deb.debian.org/debian forky/main amd64 libboost-filesystem1.83-dev amd64 1.83.0-5 [302 kB] Get: 82 http://deb.debian.org/debian forky/main amd64 libboost-filesystem-dev amd64 1.83.0.2+b2 [3628 B] Get: 83 http://deb.debian.org/debian forky/main amd64 libboost-program-options1.83.0 amd64 1.83.0-5 [355 kB] Get: 84 http://deb.debian.org/debian forky/main amd64 libboost-program-options1.83-dev amd64 1.83.0-5 [385 kB] Get: 85 http://deb.debian.org/debian forky/main amd64 libboost-program-options-dev amd64 1.83.0.2+b2 [3612 B] Get: 86 http://deb.debian.org/debian forky/main amd64 libboost-system-dev amd64 1.83.0.2+b2 [3736 B] Get: 87 http://deb.debian.org/debian forky/main amd64 libboost-thread1.83.0 amd64 1.83.0-5 [273 kB] Get: 88 http://deb.debian.org/debian forky/main amd64 libboost-thread1.83-dev amd64 1.83.0-5 [280 kB] Get: 89 http://deb.debian.org/debian forky/main amd64 libboost-thread-dev amd64 1.83.0.2+b2 [3624 B] Get: 90 http://deb.debian.org/debian forky/main amd64 libboost1.83-tools-dev amd64 1.83.0-5 [1591 kB] Get: 91 http://deb.debian.org/debian forky/main amd64 libboost-tools-dev amd64 1.83.0.2+b2 [3768 B] Get: 92 http://deb.debian.org/debian forky/main amd64 libtcmalloc-minimal4t64 amd64 2.16-1 [88.9 kB] Get: 93 http://deb.debian.org/debian forky/main amd64 libunwind8 amd64 1.8.1-0.1 [56.3 kB] Get: 94 http://deb.debian.org/debian forky/main amd64 libgoogle-perftools4t64 amd64 2.16-1 [194 kB] Get: 95 http://deb.debian.org/debian forky/main amd64 liblzma-dev amd64 5.8.1-2 [349 kB] Get: 96 http://deb.debian.org/debian forky/main amd64 libunwind-dev amd64 1.8.1-0.1 [500 kB] Get: 97 http://deb.debian.org/debian forky/main amd64 libgoogle-perftools-dev amd64 2.16-1 [468 kB] Get: 98 http://deb.debian.org/debian forky/main amd64 libprotobuf32t64 amd64 3.21.12-14 [988 kB] Get: 99 http://deb.debian.org/debian forky/main amd64 libprotobuf-lite32t64 amd64 3.21.12-14 [281 kB] Get: 100 http://deb.debian.org/debian forky/main amd64 libprotobuf-dev amd64 3.21.12-14 [1338 kB] Get: 101 http://deb.debian.org/debian forky/main amd64 libprotoc32t64 amd64 3.21.12-14 [938 kB] Get: 102 http://deb.debian.org/debian forky/main amd64 protobuf-compiler amd64 3.21.12-14 [85.0 kB] Fetched 60.5 MB in 14s (4450 kB/s) Preconfiguring packages ... Selecting previously unselected package libexpat1:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19898 files and directories currently installed.) Preparing to unpack .../000-libexpat1_2.7.3-1_amd64.deb ... Unpacking libexpat1:amd64 (2.7.3-1) ... Selecting previously unselected package libproc2-0:amd64. Preparing to unpack .../001-libproc2-0_2%3a4.0.4-9_amd64.deb ... Unpacking libproc2-0:amd64 (2:4.0.4-9) ... Selecting previously unselected package procps. 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Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/reproducible-path/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-4_source.changes dpkg-buildpackage: info: source package berkeley-express dpkg-buildpackage: info: source version 1.5.3+dfsg-4 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean debian/rules override_dh_clean make[1]: Entering directory '/build/reproducible-path/berkeley-express-1.5.3+dfsg' dh_clean src/config.h make[1]: Leaving directory '/build/reproducible-path/berkeley-express-1.5.3+dfsg' debian/rules binary dh binary dh_update_autotools_config dh_autoreconf debian/rules override_dh_auto_configure make[1]: Entering directory '/build/reproducible-path/berkeley-express-1.5.3+dfsg' dh_auto_configure -- -DCMAKE_POLICY_VERSION_MINIMUM=3.5 cd obj-x86_64-linux-gnu && DEB_PYTHON_INSTALL_LAYOUT=deb PKG_CONFIG=/usr/bin/pkg-config 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/x86_64-linux-gnu -DCMAKE_POLICY_VERSION_MINIMUM=3.5 .. CMake Deprecation Warning at CMakeLists.txt:1 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- The C compiler identification is GNU 15.2.0 -- The CXX compiler identification is GNU 15.2.0 -- 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 CMake Warning (dev) at CMakeLists.txt:20 (find_package): Policy CMP0167 is not set: The FindBoost module is removed. Run "cmake --help-policy CMP0167" for policy details. Use the cmake_policy command to set the policy and suppress this warning. This warning is for project developers. Use -Wno-dev to suppress it. -- Found Boost: /usr/lib/x86_64-linux-gnu/cmake/Boost-1.83.0/BoostConfig.cmake (found suitable version "1.83.0", minimum required is "1.39") found components: thread system filesystem program_options date_time -- Found GPERFTOOLS_TCMALLOC: /usr/lib/x86_64-linux-gnu/libtcmalloc.so -- Found Protobuf: /usr/lib/x86_64-linux-gnu/libprotobuf.so (found version "3.21.12") -- Do not try to find libbamtools.a -- Configuring done (0.7s) -- Generating done (0.0s) 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 CMAKE_POLICY_VERSION_MINIMUM FETCHCONTENT_FULLY_DISCONNECTED -- Build files have been written to: /build/reproducible-path/berkeley-express-1.5.3+dfsg/obj-x86_64-linux-gnu make[1]: Leaving directory '/build/reproducible-path/berkeley-express-1.5.3+dfsg' dh_auto_build cd obj-x86_64-linux-gnu && make -j42 INSTALL="install --strip-program=true" VERBOSE=1 make[1]: Entering directory '/build/reproducible-path/berkeley-express-1.5.3+dfsg/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/berkeley-express-1.5.3+dfsg -B/build/reproducible-path/berkeley-express-1.5.3+dfsg/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/berkeley-express-1.5.3+dfsg/obj-x86_64-linux-gnu/CMakeFiles /build/reproducible-path/berkeley-express-1.5.3+dfsg/obj-x86_64-linux-gnu//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/build/reproducible-path/berkeley-express-1.5.3+dfsg/obj-x86_64-linux-gnu' make -f src/CMakeFiles/express.dir/build.make src/CMakeFiles/express.dir/depend make[3]: Entering directory '/build/reproducible-path/berkeley-express-1.5.3+dfsg/obj-x86_64-linux-gnu' [ 11%] Running cpp protocol buffer compiler on /build/reproducible-path/berkeley-express-1.5.3+dfsg/src/alignments.proto [ 11%] Running cpp protocol buffer compiler on /build/reproducible-path/berkeley-express-1.5.3+dfsg/src/targets.proto cd /build/reproducible-path/berkeley-express-1.5.3+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/protoc --cpp_out :/build/reproducible-path/berkeley-express-1.5.3+dfsg/obj-x86_64-linux-gnu/src -I /build/reproducible-path/berkeley-express-1.5.3+dfsg/src /build/reproducible-path/berkeley-express-1.5.3+dfsg/src/targets.proto cd /build/reproducible-path/berkeley-express-1.5.3+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/protoc --cpp_out :/build/reproducible-path/berkeley-express-1.5.3+dfsg/obj-x86_64-linux-gnu/src -I /build/reproducible-path/berkeley-express-1.5.3+dfsg/src /build/reproducible-path/berkeley-express-1.5.3+dfsg/src/alignments.proto [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.) [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. 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-DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -I/usr/include/bamtools -g -O2 -ffile-prefix-map=/build/reproducible-path/berkeley-express-1.5.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/berkeley-express-1.5.3+dfsg/src/biascorrection.cpp [ 77%] Building CXX object src/CMakeFiles/express.dir/targets.cpp.o [ 83%] Building CXX object src/CMakeFiles/express.dir/threadsafety.cpp.o cd /build/reproducible-path/berkeley-express-1.5.3+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_DATE_TIME_DYN_LINK -DBOOST_DATE_TIME_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -I/usr/include/bamtools -g -O2 -ffile-prefix-map=/build/reproducible-path/berkeley-express-1.5.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/berkeley-express-1.5.3+dfsg/src/bundles.cpp cd /build/reproducible-path/berkeley-express-1.5.3+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_DATE_TIME_DYN_LINK -DBOOST_DATE_TIME_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -I/usr/include/bamtools -g -O2 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CMakeFiles/express.dir/markovmodel.cpp.o.d -o CMakeFiles/express.dir/markovmodel.cpp.o -c /build/reproducible-path/berkeley-express-1.5.3+dfsg/src/markovmodel.cpp cd /build/reproducible-path/berkeley-express-1.5.3+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_DATE_TIME_DYN_LINK -DBOOST_DATE_TIME_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -I/usr/include/bamtools -g -O2 -ffile-prefix-map=/build/reproducible-path/berkeley-express-1.5.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/berkeley-express-1.5.3+dfsg/src/mismatchmodel.cpp cd /build/reproducible-path/berkeley-express-1.5.3+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_DATE_TIME_DYN_LINK -DBOOST_DATE_TIME_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -I/usr/include/bamtools -g -O2 -ffile-prefix-map=/build/reproducible-path/berkeley-express-1.5.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/berkeley-express-1.5.3+dfsg/src/robertsfilter.cpp cd /build/reproducible-path/berkeley-express-1.5.3+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_DATE_TIME_DYN_LINK -DBOOST_DATE_TIME_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -I/usr/include/bamtools -g -O2 -ffile-prefix-map=/build/reproducible-path/berkeley-express-1.5.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -D__FILE__=\"\" -std=gnu++11 -MD -MT src/CMakeFiles/express.dir/sequence.cpp.o -MF CMakeFiles/express.dir/sequence.cpp.o.d -o CMakeFiles/express.dir/sequence.cpp.o -c /build/reproducible-path/berkeley-express-1.5.3+dfsg/src/sequence.cpp cd /build/reproducible-path/berkeley-express-1.5.3+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_DATE_TIME_DYN_LINK -DBOOST_DATE_TIME_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -I/usr/include/bamtools -g -O2 -ffile-prefix-map=/build/reproducible-path/berkeley-express-1.5.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/berkeley-express-1.5.3+dfsg/src/targets.cpp cd /build/reproducible-path/berkeley-express-1.5.3+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_DATE_TIME_DYN_LINK -DBOOST_DATE_TIME_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB 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-I/usr/include/bamtools -g -O2 -ffile-prefix-map=/build/reproducible-path/berkeley-express-1.5.3+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/berkeley-express-1.5.3+dfsg/obj-x86_64-linux-gnu/src/targets.pb.cc : 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] : 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] In file included from /usr/include/boost/math/special_functions/detail/round_fwd.hpp:11, from /usr/include/boost/math/special_functions/math_fwd.hpp:29, from /usr/include/boost/math/special_functions/beta.hpp:13, from /usr/include/boost/math/distributions/binomial.hpp:83, from /build/reproducible-path/berkeley-express-1.5.3+dfsg/src/lengthdistribution.cpp:15: /usr/include/boost/math/tools/config.hpp:23:6: warning: #warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)" [-Wcpp] 23 | # warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)" | ^~~~~~~ In file included from /usr/include/boost/math/special_functions/detail/round_fwd.hpp:11, from /usr/include/boost/math/special_functions/math_fwd.hpp:29, from /usr/include/boost/math/special_functions/beta.hpp:13, from /usr/include/boost/math/distributions/binomial.hpp:83, from /build/reproducible-path/berkeley-express-1.5.3+dfsg/src/sequence.cpp:11: /usr/include/boost/math/tools/config.hpp:23:6: warning: #warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)" [-Wcpp] 23 | # warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)" | ^~~~~~~ [100%] Linking CXX executable express cd /build/reproducible-path/berkeley-express-1.5.3+dfsg/obj-x86_64-linux-gnu/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/express.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 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/usr/lib/x86_64-linux-gnu/libboost_system.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_program_options.so.1.83.0 /usr/lib/x86_64-linux-gnu/libboost_date_time.so.1.83.0 -lbamtools -lprotobuf -lpthread -lrt /usr/lib/x86_64-linux-gnu/libboost_atomic.so.1.83.0 make[3]: Leaving directory '/build/reproducible-path/berkeley-express-1.5.3+dfsg/obj-x86_64-linux-gnu' [100%] Built target express make[2]: Leaving directory '/build/reproducible-path/berkeley-express-1.5.3+dfsg/obj-x86_64-linux-gnu' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/berkeley-express-1.5.3+dfsg/obj-x86_64-linux-gnu/CMakeFiles 0 make[1]: Leaving directory '/build/reproducible-path/berkeley-express-1.5.3+dfsg/obj-x86_64-linux-gnu' dh_auto_test create-stamp debian/debhelper-build-stamp dh_prep dh_installdirs dh_auto_install cd obj-x86_64-linux-gnu && make -j42 install DESTDIR=/build/reproducible-path/berkeley-express-1.5.3\+dfsg/debian/tmp 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dh_installexamples dh_installman dh_perl dh_link dh_strip_nondeterminism debian/rules override_dh_compress make[1]: Entering directory '/build/reproducible-path/berkeley-express-1.5.3+dfsg' dh_compress --exclude=express-doc.pdf make[1]: Leaving directory '/build/reproducible-path/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' in '../berkeley-express_1.5.3+dfsg-4_amd64.deb'. dpkg-deb: building package 'berkeley-express-dbgsym' in '../berkeley-express-dbgsym_1.5.3+dfsg-4_amd64.deb'. dpkg-deb: building package 'berkeley-express-doc' in '../berkeley-express-doc_1.5.3+dfsg-4_all.deb'. dpkg-genbuildinfo --build=binary -O../berkeley-express_1.5.3+dfsg-4_amd64.buildinfo dpkg-genchanges --build=binary -O../berkeley-express_1.5.3+dfsg-4_amd64.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/1502234 and its subdirectories I: Current time: Mon Nov 23 14:32:36 -12 2026 I: pbuilder-time-stamp: 1795487556 Tue Oct 21 20:09:39 UTC 2025 I: 1st build successful. Starting 2nd build on remote node ionos11-amd64.debian.net. Tue Oct 21 20:09:39 UTC 2025 I: Preparing to do remote build '2' on ionos11-amd64.debian.net. Tue Oct 21 20:14:37 UTC 2025 I: Deleting $TMPDIR on ionos11-amd64.debian.net. Tue Oct 21 20:14:38 UTC 2025 I: berkeley-express_1.5.3+dfsg-4_amd64.changes: Format: 1.8 Date: Thu, 16 Oct 2025 10:31:34 +0200 Source: berkeley-express Binary: berkeley-express berkeley-express-dbgsym berkeley-express-doc Architecture: amd64 all Version: 1.5.3+dfsg-4 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 Closes: 1112724 Changes: berkeley-express (1.5.3+dfsg-4) unstable; urgency=medium . * Team upload. * d/watch: version=5 * Fix build with CMake 4 Closes: #1112724 * Standards-Version: 4.7.2 (routine-update) * debputy lint --auto-fix (routine-update) Checksums-Sha1: 8c6415fbf3cd55e035250be08b7838fcb9ceed95 4598912 berkeley-express-dbgsym_1.5.3+dfsg-4_amd64.deb d05692d1c895c685d659a25ea568d618b0987d61 705852 berkeley-express-doc_1.5.3+dfsg-4_all.deb ef3235761a338c08b445580c00948f157a9062d9 7890 berkeley-express_1.5.3+dfsg-4_amd64.buildinfo 356f10165c95f3391350723256d3252f7962b42c 235980 berkeley-express_1.5.3+dfsg-4_amd64.deb Checksums-Sha256: dfb9451e2304dc6bbfc7a5d492799682182827d72c4ecabc2f35c6161c913e1e 4598912 berkeley-express-dbgsym_1.5.3+dfsg-4_amd64.deb 75ad14b0533150809d13f53b18c8ffe0a3022a1252cdc47fdc447893c9a63f03 705852 berkeley-express-doc_1.5.3+dfsg-4_all.deb 0aed50d0257e2f6369a3fb1f338195b2efe4523dd3217b7883fd0d1dad1b9101 7890 berkeley-express_1.5.3+dfsg-4_amd64.buildinfo 22b51a88f34d0086064326f71acb81bbaa00230f27aca3600dfce3a23bb523e0 235980 berkeley-express_1.5.3+dfsg-4_amd64.deb Files: 9cd5231554004fcbd0e2b9a08c50e52d 4598912 debug optional berkeley-express-dbgsym_1.5.3+dfsg-4_amd64.deb 26f678c49a4981371c127cb5546e37cf 705852 doc optional berkeley-express-doc_1.5.3+dfsg-4_all.deb 7b600da319a3f84a86551c073284d48e 7890 science optional berkeley-express_1.5.3+dfsg-4_amd64.buildinfo aaff251da197dc08e2918df7a8539476 235980 science optional berkeley-express_1.5.3+dfsg-4_amd64.deb Tue Oct 21 20:14:38 UTC 2025 I: diffoscope 306 will be used to compare the two builds: Running as unit: rb-diffoscope-amd64_16-75417.service; invocation ID: 69ece206d7584ebc86881c20ad6c1932 # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.UukGIJIk/berkeley-express_1.5.3+dfsg-4.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.UukGIJIk/berkeley-express_1.5.3+dfsg-4.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.UukGIJIk/berkeley-express_1.5.3+dfsg-4.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.UukGIJIk/b1/berkeley-express_1.5.3+dfsg-4_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.UukGIJIk/b2/berkeley-express_1.5.3+dfsg-4_amd64.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call diffoscope.comparators.binary.FilesystemFile ## main (total time: 0.003s) 0.003s 2 calls outputs 0.000s 1 call cleanup Finished with result: success Main processes terminated with: code=exited, status=0/SUCCESS Service runtime: 174ms CPU time consumed: 175ms Memory peak: 17.8M (swap: 0B) Tue Oct 21 20:14:39 UTC 2025 I: diffoscope 306 found no differences in the changes files, and a .buildinfo file also exists. Tue Oct 21 20:14:39 UTC 2025 I: berkeley-express from forky built successfully and reproducibly on amd64. Tue Oct 21 20:14:40 UTC 2025 I: Removing signed berkeley-express_1.5.3+dfsg-4_amd64.buildinfo.asc files: removed './b1/berkeley-express_1.5.3+dfsg-4_amd64.buildinfo.asc' removed './b2/berkeley-express_1.5.3+dfsg-4_amd64.buildinfo.asc'