Sun Feb 16 20:37:12 UTC 2025 I: starting to build berkeley-express/unstable/i386 on jenkins on '2025-02-16 20:36' Sun Feb 16 20:37:12 UTC 2025 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/i386_3/54607/console.log Sun Feb 16 20:37:12 UTC 2025 I: Downloading source for unstable/berkeley-express=1.5.3+dfsg-3 --2025-02-16 20:37:12-- http://deb.debian.org/debian/pool/main/b/berkeley-express/berkeley-express_1.5.3%2bdfsg-3.dsc Connecting to 46.16.76.132:3128... 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% 245M=0s 2025-02-16 20:37:12 (245 MB/s) - ‘berkeley-express_1.5.3+dfsg-3.dsc’ saved [2493/2493] Sun Feb 16 20:37:12 UTC 2025 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----- Sun Feb 16 20:37:12 UTC 2025 I: Checking whether the package is not for us Sun Feb 16 20:37:12 UTC 2025 I: Starting 1st build on remote node ionos2-i386.debian.net. Sun Feb 16 20:37:12 UTC 2025 I: Preparing to do remote build '1' on ionos2-i386.debian.net. Sun Feb 16 20:38:27 UTC 2025 I: Deleting $TMPDIR on ionos2-i386.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Sun Feb 16 08:37:14 -12 2025 I: pbuilder-time-stamp: 1739738234 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-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: using eatmydata during job 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 dpkg-source: warning: cannot verify inline signature for ./berkeley-express_1.5.3+dfsg-3.dsc: unsupported subcommand 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/12033/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='i386' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=11 ' DISTRIBUTION='unstable' HOME='/root' HOST_ARCH='i386' IFS=' ' INVOCATION_ID='e561a594c35a4240a5fe09d1cdb6135e' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' LD_LIBRARY_PATH='/usr/lib/libeatmydata' LD_PRELOAD='libeatmydata.so' 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='12033' 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.hxg8dsgY/pbuilderrc_1Z9z --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.hxg8dsgY/b1 --logfile b1/build.log berkeley-express_1.5.3+dfsg-3.dsc' SUDO_GID='112' SUDO_UID='107' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://46.16.76.132:3128' I: uname -a Linux ionos2-i386 6.1.0-31-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.128-1 (2025-02-07) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin I: user script /srv/workspace/pbuilder/12033/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: i386 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 ... 19794 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} libarchive13t64{a} libbamtools-dev{a} libbamtools2.5.2{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} libgnutls30t64{a} libgoogle-perftools-dev{a} libgoogle-perftools4t64{a} libgssapi-krb5-2{a} libicu72{a} libidn2-0{a} libjsoncpp26{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} libldap2{a} libmagic-mgc{a} libmagic1t64{a} libnghttp2-14{a} libnghttp3-9{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} libtasn1-6{a} libtcmalloc-minimal4t64{a} libtool{a} libuchardet0{a} libunistring5{a} libuv1t64{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 krb5-locales libarchive-cpio-perl libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules linux-sysctl-defaults lynx psmisc publicsuffix wget 0 packages upgraded, 95 newly installed, 0 to remove and 0 not upgraded. Need to get 65.0 MB of archives. After unpacking 388 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main i386 libproc2-0 i386 2:4.0.4-7 [66.0 kB] Get: 2 http://deb.debian.org/debian unstable/main i386 procps i386 2:4.0.4-7 [876 kB] Get: 3 http://deb.debian.org/debian unstable/main i386 sensible-utils all 0.0.24 [24.8 kB] Get: 4 http://deb.debian.org/debian unstable/main i386 libmagic-mgc i386 1:5.45-3+b1 [314 kB] Get: 5 http://deb.debian.org/debian unstable/main i386 libmagic1t64 i386 1:5.45-3+b1 [115 kB] Get: 6 http://deb.debian.org/debian unstable/main i386 file i386 1:5.45-3+b1 [43.2 kB] Get: 7 http://deb.debian.org/debian unstable/main i386 gettext-base i386 0.23.1-1 [245 kB] Get: 8 http://deb.debian.org/debian unstable/main i386 libuchardet0 i386 0.0.8-1+b2 [69.2 kB] Get: 9 http://deb.debian.org/debian unstable/main i386 groff-base i386 1.23.0-7 [1199 kB] Get: 10 http://deb.debian.org/debian unstable/main i386 bsdextrautils i386 2.40.4-3 [96.2 kB] Get: 11 http://deb.debian.org/debian unstable/main i386 libpipeline1 i386 1.5.8-1 [41.2 kB] Get: 12 http://deb.debian.org/debian unstable/main i386 man-db i386 2.13.0-1 [1428 kB] Get: 13 http://deb.debian.org/debian unstable/main i386 m4 i386 1.4.19-5 [301 kB] Get: 14 http://deb.debian.org/debian unstable/main i386 autoconf all 2.72-3 [493 kB] Get: 15 http://deb.debian.org/debian unstable/main i386 autotools-dev all 20220109.1 [51.6 kB] Get: 16 http://deb.debian.org/debian unstable/main i386 automake all 1:1.17-3 [862 kB] Get: 17 http://deb.debian.org/debian unstable/main i386 autopoint all 0.23.1-1 [770 kB] Get: 18 http://deb.debian.org/debian unstable/main i386 cmake-data all 3.31.5-2 [2267 kB] Get: 19 http://deb.debian.org/debian unstable/main i386 libicu72 i386 72.1-6 [9582 kB] Get: 20 http://deb.debian.org/debian unstable/main i386 libxml2 i386 2.12.7+dfsg+really2.9.14-0.2+b1 [734 kB] Get: 21 http://deb.debian.org/debian unstable/main i386 libarchive13t64 i386 3.7.4-1.1 [390 kB] Get: 22 http://deb.debian.org/debian unstable/main i386 libbrotli1 i386 1.1.0-2+b6 [308 kB] Get: 23 http://deb.debian.org/debian unstable/main i386 libkrb5support0 i386 1.21.3-4 [35.0 kB] Get: 24 http://deb.debian.org/debian unstable/main i386 libcom-err2 i386 1.47.2-1 [24.3 kB] Get: 25 http://deb.debian.org/debian unstable/main i386 libk5crypto3 i386 1.21.3-4 [83.7 kB] Get: 26 http://deb.debian.org/debian unstable/main i386 libkeyutils1 i386 1.6.3-4 [9600 B] Get: 27 http://deb.debian.org/debian unstable/main i386 libkrb5-3 i386 1.21.3-4 [354 kB] Get: 28 http://deb.debian.org/debian unstable/main i386 libgssapi-krb5-2 i386 1.21.3-4 [149 kB] Get: 29 http://deb.debian.org/debian unstable/main i386 libunistring5 i386 1.3-1 [458 kB] Get: 30 http://deb.debian.org/debian unstable/main i386 libidn2-0 i386 2.3.7-2+b1 [130 kB] Get: 31 http://deb.debian.org/debian unstable/main i386 libsasl2-modules-db i386 2.1.28+dfsg1-8+b1 [20.9 kB] Get: 32 http://deb.debian.org/debian unstable/main i386 libsasl2-2 i386 2.1.28+dfsg1-8+b1 [61.3 kB] Get: 33 http://deb.debian.org/debian unstable/main i386 libldap2 i386 2.6.9+dfsg-1 [205 kB] Get: 34 http://deb.debian.org/debian unstable/main i386 libnghttp2-14 i386 1.64.0-1 [82.4 kB] Get: 35 http://deb.debian.org/debian unstable/main i386 libnghttp3-9 i386 1.6.0-2 [75.9 kB] Get: 36 http://deb.debian.org/debian unstable/main i386 libpsl5t64 i386 0.21.2-1.1+b1 [57.7 kB] Get: 37 http://deb.debian.org/debian unstable/main i386 libffi8 i386 3.4.7-1 [21.4 kB] Get: 38 http://deb.debian.org/debian unstable/main i386 libp11-kit0 i386 0.25.5-3 [423 kB] Get: 39 http://deb.debian.org/debian unstable/main i386 libtasn1-6 i386 4.20.0-2 [51.6 kB] Get: 40 http://deb.debian.org/debian unstable/main i386 libgnutls30t64 i386 3.8.9-2 [1462 kB] Get: 41 http://deb.debian.org/debian unstable/main i386 librtmp1 i386 2.4+20151223.gitfa8646d.1-2+b5 [62.4 kB] Get: 42 http://deb.debian.org/debian unstable/main i386 libssh2-1t64 i386 1.11.1-1 [256 kB] Get: 43 http://deb.debian.org/debian unstable/main i386 libcurl4t64 i386 8.12.1-2 [415 kB] Get: 44 http://deb.debian.org/debian unstable/main i386 libexpat1 i386 2.6.4-1 [107 kB] Get: 45 http://deb.debian.org/debian unstable/main i386 libjsoncpp26 i386 1.9.6-3 [90.0 kB] Get: 46 http://deb.debian.org/debian unstable/main i386 librhash1 i386 1.4.5-1 [144 kB] Get: 47 http://deb.debian.org/debian unstable/main i386 libuv1t64 i386 1.50.0-2 [163 kB] Get: 48 http://deb.debian.org/debian unstable/main i386 cmake i386 3.31.5-2 [13.1 MB] Get: 49 http://deb.debian.org/debian unstable/main i386 libdebhelper-perl all 13.24.1 [90.9 kB] Get: 50 http://deb.debian.org/debian unstable/main i386 libtool all 2.5.4-3 [539 kB] Get: 51 http://deb.debian.org/debian unstable/main i386 dh-autoreconf all 20 [17.1 kB] Get: 52 http://deb.debian.org/debian unstable/main i386 libarchive-zip-perl all 1.68-1 [104 kB] Get: 53 http://deb.debian.org/debian unstable/main i386 libfile-stripnondeterminism-perl all 1.14.1-2 [19.7 kB] Get: 54 http://deb.debian.org/debian unstable/main i386 dh-strip-nondeterminism all 1.14.1-2 [8620 B] Get: 55 http://deb.debian.org/debian unstable/main i386 libelf1t64 i386 0.192-4 [195 kB] Get: 56 http://deb.debian.org/debian unstable/main i386 dwz i386 0.15-1+b1 [116 kB] Get: 57 http://deb.debian.org/debian unstable/main i386 gettext i386 0.23.1-1 [1714 kB] Get: 58 http://deb.debian.org/debian unstable/main i386 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 59 http://deb.debian.org/debian unstable/main i386 po-debconf all 1.0.21+nmu1 [248 kB] Get: 60 http://deb.debian.org/debian unstable/main i386 debhelper all 13.24.1 [920 kB] Get: 61 http://deb.debian.org/debian unstable/main i386 libbamtools2.5.2 i386 2.5.2+dfsg-6+b1 [178 kB] Get: 62 http://deb.debian.org/debian unstable/main i386 zlib1g-dev i386 1:1.3.dfsg+really1.3.1-1+b1 [916 kB] Get: 63 http://deb.debian.org/debian unstable/main i386 libbamtools-dev i386 2.5.2+dfsg-6+b1 [242 kB] Get: 64 http://deb.debian.org/debian unstable/main i386 libboost1.83-dev i386 1.83.0-4.1 [10.6 MB] Get: 65 http://deb.debian.org/debian unstable/main i386 libboost-atomic1.83.0 i386 1.83.0-4.1 [234 kB] Get: 66 http://deb.debian.org/debian unstable/main i386 libboost-atomic1.83-dev i386 1.83.0-4.1 [235 kB] Get: 67 http://deb.debian.org/debian unstable/main i386 libboost-chrono1.83.0t64 i386 1.83.0-4.1 [241 kB] Get: 68 http://deb.debian.org/debian unstable/main i386 libboost-chrono1.83-dev i386 1.83.0-4.1 [247 kB] Get: 69 http://deb.debian.org/debian unstable/main i386 libboost-date-time1.83.0 i386 1.83.0-4.1 [230 kB] Get: 70 http://deb.debian.org/debian unstable/main i386 libboost-serialization1.83.0 i386 1.83.0-4.1 [343 kB] Get: 71 http://deb.debian.org/debian unstable/main i386 libboost-serialization1.83-dev i386 1.83.0-4.1 [386 kB] Get: 72 http://deb.debian.org/debian unstable/main i386 libboost-date-time1.83-dev i386 1.83.0-4.1 [239 kB] Get: 73 http://deb.debian.org/debian unstable/main i386 libboost-date-time-dev i386 1.83.0.2+b2 [3596 B] Get: 74 http://deb.debian.org/debian unstable/main i386 libboost-filesystem1.83.0 i386 1.83.0-4.1 [287 kB] Get: 75 http://deb.debian.org/debian unstable/main i386 libboost-system1.83.0 i386 1.83.0-4.1 [230 kB] Get: 76 http://deb.debian.org/debian unstable/main i386 libboost-system1.83-dev i386 1.83.0-4.1 [231 kB] Get: 77 http://deb.debian.org/debian unstable/main i386 libboost-filesystem1.83-dev i386 1.83.0-4.1 [305 kB] Get: 78 http://deb.debian.org/debian unstable/main i386 libboost-filesystem-dev i386 1.83.0.2+b2 [3640 B] Get: 79 http://deb.debian.org/debian unstable/main i386 libboost-program-options1.83.0 i386 1.83.0-4.1 [361 kB] Get: 80 http://deb.debian.org/debian unstable/main i386 libboost-program-options1.83-dev i386 1.83.0-4.1 [390 kB] Get: 81 http://deb.debian.org/debian unstable/main i386 libboost-program-options-dev i386 1.83.0.2+b2 [3616 B] Get: 82 http://deb.debian.org/debian unstable/main i386 libboost-system-dev i386 1.83.0.2+b2 [3740 B] Get: 83 http://deb.debian.org/debian unstable/main i386 libboost-thread1.83.0 i386 1.83.0-4.1 [271 kB] Get: 84 http://deb.debian.org/debian unstable/main i386 libboost-thread1.83-dev i386 1.83.0-4.1 [279 kB] Get: 85 http://deb.debian.org/debian unstable/main i386 libboost-thread-dev i386 1.83.0.2+b2 [3632 B] Get: 86 http://deb.debian.org/debian unstable/main i386 libboost1.83-tools-dev i386 1.83.0-4.1 [1605 kB] Get: 87 http://deb.debian.org/debian unstable/main i386 libboost-tools-dev i386 1.83.0.2+b2 [3780 B] Get: 88 http://deb.debian.org/debian unstable/main i386 libtcmalloc-minimal4t64 i386 2.16-1 [91.4 kB] Get: 89 http://deb.debian.org/debian unstable/main i386 libgoogle-perftools4t64 i386 2.16-1 [196 kB] Get: 90 http://deb.debian.org/debian unstable/main i386 libgoogle-perftools-dev i386 2.16-1 [478 kB] Get: 91 http://deb.debian.org/debian unstable/main i386 libprotobuf32t64 i386 3.21.12-10+b4 [1067 kB] Get: 92 http://deb.debian.org/debian unstable/main i386 libprotobuf-lite32t64 i386 3.21.12-10+b4 [296 kB] Get: 93 http://deb.debian.org/debian unstable/main i386 libprotobuf-dev i386 3.21.12-10+b4 [1434 kB] Get: 94 http://deb.debian.org/debian unstable/main i386 libprotoc32t64 i386 3.21.12-10+b4 [986 kB] Get: 95 http://deb.debian.org/debian unstable/main i386 protobuf-compiler i386 3.21.12-10+b4 [84.9 kB] Fetched 65.0 MB in 1s (71.5 MB/s) Preconfiguring packages ... 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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-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 i386 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 dh_auto_configure cd obj-i686-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/i386-linux-gnu .. 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 14.2.0 -- The CXX compiler identification is GNU 14.2.0 -- 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/i386-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/i386-linux-gnu/libtcmalloc.so -- Found Protobuf: /usr/lib/i386-linux-gnu/libprotobuf.so (found version "3.21.12") -- Do not try to find libbamtools.a -- Configuring done (1.0s) -- 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 FETCHCONTENT_FULLY_DISCONNECTED -- Build files have been written to: /build/reproducible-path/berkeley-express-1.5.3+dfsg/obj-i686-linux-gnu dh_auto_build cd obj-i686-linux-gnu && make -j11 "INSTALL=install --strip-program=true" VERBOSE=1 make[1]: Entering directory '/build/reproducible-path/berkeley-express-1.5.3+dfsg/obj-i686-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-i686-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-i686-linux-gnu/CMakeFiles /build/reproducible-path/berkeley-express-1.5.3+dfsg/obj-i686-linux-gnu//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/build/reproducible-path/berkeley-express-1.5.3+dfsg/obj-i686-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-i686-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-i686-linux-gnu/src && /usr/bin/protoc --cpp_out :/build/reproducible-path/berkeley-express-1.5.3+dfsg/obj-i686-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-i686-linux-gnu/src && /usr/bin/protoc --cpp_out :/build/reproducible-path/berkeley-express-1.5.3+dfsg/obj-i686-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. (Defaulted to proto2 syntax.) cd /build/reproducible-path/berkeley-express-1.5.3+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/berkeley-express-1.5.3+dfsg /build/reproducible-path/berkeley-express-1.5.3+dfsg/src /build/reproducible-path/berkeley-express-1.5.3+dfsg/obj-i686-linux-gnu /build/reproducible-path/berkeley-express-1.5.3+dfsg/obj-i686-linux-gnu/src /build/reproducible-path/berkeley-express-1.5.3+dfsg/obj-i686-linux-gnu/src/CMakeFiles/express.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/berkeley-express-1.5.3+dfsg/obj-i686-linux-gnu' make -f src/CMakeFiles/express.dir/build.make src/CMakeFiles/express.dir/build make[3]: Entering directory '/build/reproducible-path/berkeley-express-1.5.3+dfsg/obj-i686-linux-gnu' [ 16%] Building CXX object src/CMakeFiles/express.dir/bundles.cpp.o [ 22%] Building CXX object src/CMakeFiles/express.dir/directiondetector.cpp.o [ 33%] Building CXX object 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/build/reproducible-path/berkeley-express-1.5.3+dfsg/src/fragments.cpp [ 66%] Building CXX object src/CMakeFiles/express.dir/mapparser.cpp.o cd /build/reproducible-path/berkeley-express-1.5.3+dfsg/obj-i686-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 -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/reproducible-path/berkeley-express-1.5.3+dfsg/src/lengthdistribution.cpp [ 66%] Building CXX object src/CMakeFiles/express.dir/robertsfilter.cpp.o cd /build/reproducible-path/berkeley-express-1.5.3+dfsg/obj-i686-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 -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/reproducible-path/berkeley-express-1.5.3+dfsg/src/markovmodel.cpp cd /build/reproducible-path/berkeley-express-1.5.3+dfsg/obj-i686-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 -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/reproducible-path/berkeley-express-1.5.3+dfsg/src/biascorrection.cpp cd /build/reproducible-path/berkeley-express-1.5.3+dfsg/obj-i686-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 -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/reproducible-path/berkeley-express-1.5.3+dfsg/src/main.cpp cd /build/reproducible-path/berkeley-express-1.5.3+dfsg/obj-i686-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 -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/reproducible-path/berkeley-express-1.5.3+dfsg/src/mapparser.cpp cd /build/reproducible-path/berkeley-express-1.5.3+dfsg/obj-i686-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 -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/reproducible-path/berkeley-express-1.5.3+dfsg/src/mismatchmodel.cpp cd /build/reproducible-path/berkeley-express-1.5.3+dfsg/obj-i686-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 -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/reproducible-path/berkeley-express-1.5.3+dfsg/src/robertsfilter.cpp [ 72%] Building CXX object src/CMakeFiles/express.dir/sequence.cpp.o : warning: "__FILE__" redefined [-Wbuiltin-macro-redefined] cd /build/reproducible-path/berkeley-express-1.5.3+dfsg/obj-i686-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 -Wformat -Werror=format-security -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 : 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)" | ^~~~~~~ [ 77%] Building CXX object src/CMakeFiles/express.dir/targets.cpp.o cd /build/reproducible-path/berkeley-express-1.5.3+dfsg/obj-i686-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 -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/reproducible-path/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/reproducible-path/berkeley-express-1.5.3+dfsg/obj-i686-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 -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/reproducible-path/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/reproducible-path/berkeley-express-1.5.3+dfsg/obj-i686-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 -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/reproducible-path/berkeley-express-1.5.3+dfsg/obj-i686-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/reproducible-path/berkeley-express-1.5.3+dfsg/obj-i686-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 -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/reproducible-path/berkeley-express-1.5.3+dfsg/obj-i686-linux-gnu/src/targets.pb.cc : warning: "__FILE__" redefined [-Wbuiltin-macro-redefined] [100%] Linking CXX executable express cd /build/reproducible-path/berkeley-express-1.5.3+dfsg/obj-i686-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/reproducible-path/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 -Wl,--dependency-file=CMakeFiles/express.dir/link.d 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/i386-linux-gnu/libboost_thread.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_system.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_program_options.so.1.83.0 /usr/lib/i386-linux-gnu/libboost_date_time.so.1.83.0 -lbamtools -lprotobuf -lpthread -lrt /usr/lib/i386-linux-gnu/libboost_atomic.so.1.83.0 make[3]: Leaving directory '/build/reproducible-path/berkeley-express-1.5.3+dfsg/obj-i686-linux-gnu' [100%] Built target express make[2]: Leaving directory '/build/reproducible-path/berkeley-express-1.5.3+dfsg/obj-i686-linux-gnu' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/berkeley-express-1.5.3+dfsg/obj-i686-linux-gnu/CMakeFiles 0 make[1]: Leaving directory '/build/reproducible-path/berkeley-express-1.5.3+dfsg/obj-i686-linux-gnu' dh_auto_test create-stamp debian/debhelper-build-stamp dh_prep dh_installdirs dh_auto_install cd obj-i686-linux-gnu && make -j11 install DESTDIR=/build/reproducible-path/berkeley-express-1.5.3\+dfsg/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/reproducible-path/berkeley-express-1.5.3+dfsg/obj-i686-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-i686-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 preinstall make[2]: Entering directory '/build/reproducible-path/berkeley-express-1.5.3+dfsg/obj-i686-linux-gnu' make[2]: Nothing to be done for 'preinstall'. make[2]: Leaving directory '/build/reproducible-path/berkeley-express-1.5.3+dfsg/obj-i686-linux-gnu' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "None" -- Installing: /build/reproducible-path/berkeley-express-1.5.3+dfsg/debian/tmp/usr/bin/express make[1]: Leaving directory '/build/reproducible-path/berkeley-express-1.5.3+dfsg/obj-i686-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/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-3_i386.deb'. dpkg-deb: building package 'berkeley-express-doc' in '../berkeley-express-doc_1.5.3+dfsg-3_all.deb'. dpkg-deb: building package 'berkeley-express-dbgsym' in '../berkeley-express-dbgsym_1.5.3+dfsg-3_i386.deb'. dpkg-genbuildinfo --build=binary -O../berkeley-express_1.5.3+dfsg-3_i386.buildinfo dpkg-genchanges --build=binary -O../berkeley-express_1.5.3+dfsg-3_i386.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/12033 and its subdirectories I: Current time: Sun Feb 16 08:38:26 -12 2025 I: pbuilder-time-stamp: 1739738306 Sun Feb 16 20:38:27 UTC 2025 I: 1st build successful. Starting 2nd build on remote node ionos16-i386.debian.net. Sun Feb 16 20:38:27 UTC 2025 I: Preparing to do remote build '2' on ionos16-i386.debian.net. Sun Feb 16 20:39:19 UTC 2025 I: Deleting $TMPDIR on ionos16-i386.debian.net. Sun Feb 16 20:39:20 UTC 2025 I: berkeley-express_1.5.3+dfsg-3_i386.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: i386 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: 165d7efeed5507c656b0f3ccddf958b41ff5eb31 4405220 berkeley-express-dbgsym_1.5.3+dfsg-3_i386.deb e73bb85fcf8d8dac8b0692c5891de66383f1a504 706136 berkeley-express-doc_1.5.3+dfsg-3_all.deb aea903748f5f1e4a57a65d4075e65b30ebc1a726 7669 berkeley-express_1.5.3+dfsg-3_i386.buildinfo d9dd350dff46c8197faff6af842b25c9dd7559cf 239160 berkeley-express_1.5.3+dfsg-3_i386.deb Checksums-Sha256: 2753d61e52047b889719e47d3c6b24e5b8bc9243703986e9edd76df91f77261e 4405220 berkeley-express-dbgsym_1.5.3+dfsg-3_i386.deb ac2db6596c8c6c2f7dd2b52531cc0709af4146ae9e685673b205e302ff015343 706136 berkeley-express-doc_1.5.3+dfsg-3_all.deb 7fc22a47bdca6eb90d1924e040cb72f61fbd56511b2c006b1a1ea98646f093f7 7669 berkeley-express_1.5.3+dfsg-3_i386.buildinfo 1c63f73b9e3a20c192a5bb0e932870a65a004915bbab9b3be890c992406de3fa 239160 berkeley-express_1.5.3+dfsg-3_i386.deb Files: 4061e4dc1796309fd35652bf5deb1533 4405220 debug optional berkeley-express-dbgsym_1.5.3+dfsg-3_i386.deb 974185f49f0af606f086b9405d617d6e 706136 doc optional berkeley-express-doc_1.5.3+dfsg-3_all.deb a6f8eee5a07e059dc422d16ece720edb 7669 science optional berkeley-express_1.5.3+dfsg-3_i386.buildinfo ee1caca8a949880f83fad7ea93b2ff0c 239160 science optional berkeley-express_1.5.3+dfsg-3_i386.deb Sun Feb 16 20:39:22 UTC 2025 I: diffoscope 288 will be used to compare the two builds: Running as unit: rb-diffoscope-i386_3-54607.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.hxg8dsgY/berkeley-express_1.5.3+dfsg-3.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.hxg8dsgY/berkeley-express_1.5.3+dfsg-3.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.hxg8dsgY/berkeley-express_1.5.3+dfsg-3.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.hxg8dsgY/b1/berkeley-express_1.5.3+dfsg-3_i386.changes /srv/reproducible-results/rbuild-debian/r-b-build.hxg8dsgY/b2/berkeley-express_1.5.3+dfsg-3_i386.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 Service runtime: 232ms CPU time consumed: 232ms Sun Feb 16 20:55:12 UTC 2025 I: diffoscope 288 found no differences in the changes files, and a .buildinfo file also exists. Sun Feb 16 20:55:12 UTC 2025 I: berkeley-express from unstable built successfully and reproducibly on i386. Sun Feb 16 20:55:16 UTC 2025 I: Submitting .buildinfo files to external archives: Sun Feb 16 20:55:16 UTC 2025 I: Submitting 12K b1/berkeley-express_1.5.3+dfsg-3_i386.buildinfo.asc Sun Feb 16 20:55:24 UTC 2025 I: Submitting 12K b2/berkeley-express_1.5.3+dfsg-3_i386.buildinfo.asc Sun Feb 16 20:55:41 UTC 2025 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Sun Feb 16 20:55:41 UTC 2025 I: Done submitting .buildinfo files. Sun Feb 16 20:55:41 UTC 2025 I: Removing signed berkeley-express_1.5.3+dfsg-3_i386.buildinfo.asc files: removed './b1/berkeley-express_1.5.3+dfsg-3_i386.buildinfo.asc' removed './b2/berkeley-express_1.5.3+dfsg-3_i386.buildinfo.asc'