Thu Aug 8 08:10:58 UTC 2024 I: starting to build maffilter/trixie/armhf on jenkins on '2024-08-08 08:10' Thu Aug 8 08:10:58 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/armhf_34/10443/console.log Thu Aug 8 08:10:58 UTC 2024 I: Downloading source for trixie/maffilter=1.3.1+dfsg-6 --2024-08-08 08:10:59-- http://deb.debian.org/debian/pool/main/m/maffilter/maffilter_1.3.1%2bdfsg-6.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2238 (2.2K) [text/prs.lines.tag] Saving to: ‘maffilter_1.3.1+dfsg-6.dsc’ 0K .. 100% 268M=0s 2024-08-08 08:10:59 (268 MB/s) - ‘maffilter_1.3.1+dfsg-6.dsc’ saved [2238/2238] Thu Aug 8 08:10:59 UTC 2024 I: maffilter_1.3.1+dfsg-6.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: maffilter Binary: maffilter, maffilter-examples Architecture: any all Version: 1.3.1+dfsg-6 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille , Julien Dutheil , Pranav Ballaney Homepage: https://jydu.github.io/maffilter/ Standards-Version: 4.6.2 Vcs-Browser: https://salsa.debian.org/med-team/maffilter Vcs-Git: https://salsa.debian.org/med-team/maffilter.git Testsuite: autopkgtest Build-Depends: debhelper-compat (= 13), cmake, texinfo, libbpp-phyl-omics-dev, libboost-iostreams-dev, zlib1g-dev, libbz2-dev Package-List: maffilter deb science optional arch=any maffilter-examples deb science optional arch=all Checksums-Sha1: 52fb7acc20ef914ef4e44676b316cf3753c46c9b 78668340 maffilter_1.3.1+dfsg.orig.tar.xz 38d6a27b6cb4736f809d80ef7f0c00ea2fe31427 4940 maffilter_1.3.1+dfsg-6.debian.tar.xz Checksums-Sha256: 1767aae6061ca7d12682f7ded1e1b9f6ecad3d03fcfa02ff24b5351d51d8dc70 78668340 maffilter_1.3.1+dfsg.orig.tar.xz 99b7f757063096a6d5c51725e8da009e89a93db24fb2b8bec744df818abcfac6 4940 maffilter_1.3.1+dfsg-6.debian.tar.xz Files: 3548c76d884bacc4ce267d70f304435e 78668340 maffilter_1.3.1+dfsg.orig.tar.xz b33270bbd567a7c6555149285d1215a9 4940 maffilter_1.3.1+dfsg-6.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQIzBAEBCgAdFiEEck1gkzcRPHEFUNdHPCZ2P2xn5uIFAmYCrHwACgkQPCZ2P2xn 5uIpFhAArz+NErkZNwZCfY0Un+O+osPVGHYlzl9B+Ei7uLqrLQS9Gu2QYjcEH2R8 Ea0y17CIjIlTpDrd1VyaIVbmFE0H7RJSJu4MjNF6rkRFOfith+7gXvQqdLa5mAjC e8Yb2aB7hztTz4tz9nN2pfktzAfcGf9y0ryrSTYrrGx9455Sv/OVLL2PaagUzdyH dyGC/8eIGZrXRDgIoXegqoWJgzFgpfpnpf7MbOrb/15FmlbJ1vg2Kmyi9rviz8tF NdqGbkRIIMWxLJGWzIKEDq6gR2aFkjqemaqaeBObx/iONjwjTKHXP1UDhU8GXYNX C2Z0kVVzNg39Z8i13GqtCRLCfhz7pY79u8LOZfu7Ido5xkD9Qcmpb7pZJxTG4ikm PsZ0mN9o5rPmHHFGAh6PGRJ6NlzqZYq3CAPYHdIQbnZgx9SyyPKStBpMzV7HKpLp VbD0z//i8dX5xZLNV1GemeIqO7g0mjYBlYLtbna70PLz7IMz+djXYOCQE1ZLbnhD dIFjD1xL3keGDJIo/OuwnkPClp/2rhqBCpgZDhz4kXnhykEJU+ENb4DtgVSsZDyH 0whfX4BURxge53wYamh90oUtVV097O+JzPlL2EmOlK6Mr+I4dqyTRgwmTODDqtzp Hyq9dT7zOgbNp1c5kAmF/ct6eZAsoi6+0NpBFhvedJBzw+YxD3U= =UcyI -----END PGP SIGNATURE----- Thu Aug 8 08:10:59 UTC 2024 I: Checking whether the package is not for us Thu Aug 8 08:10:59 UTC 2024 I: Starting 1st build on remote node virt32z-armhf-rb.debian.net. Thu Aug 8 08:10:59 UTC 2024 I: Preparing to do remote build '1' on virt32z-armhf-rb.debian.net. Thu Aug 8 08:17:35 UTC 2024 I: Deleting $TMPDIR on virt32z-armhf-rb.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Wed Aug 7 20:11:20 -12 2024 I: pbuilder-time-stamp: 1723104680 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [maffilter_1.3.1+dfsg-6.dsc] I: copying [./maffilter_1.3.1+dfsg.orig.tar.xz] I: copying [./maffilter_1.3.1+dfsg-6.debian.tar.xz] I: Extracting source gpgv: Signature made Tue Mar 26 11:07:40 2024 gpgv: using RSA key 724D609337113C710550D7473C26763F6C67E6E2 gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./maffilter_1.3.1+dfsg-6.dsc: no acceptable signature found dpkg-source: info: extracting maffilter in maffilter-1.3.1+dfsg dpkg-source: info: unpacking maffilter_1.3.1+dfsg.orig.tar.xz dpkg-source: info: unpacking maffilter_1.3.1+dfsg-6.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying hardening I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/13617/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='armhf' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=3 ' DISTRIBUTION='trixie' HOME='/root' HOST_ARCH='armhf' IFS=' ' INVOCATION_ID='9341f629728640819dca3b7fbfd4fefa' 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='13617' 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.lxeLW6Pe/pbuilderrc_B7q5 --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.lxeLW6Pe/b1 --logfile b1/build.log maffilter_1.3.1+dfsg-6.dsc' SUDO_GID='110' SUDO_UID='103' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://10.0.0.15:3142/' I: uname -a Linux virt32z 6.1.0-23-armmp-lpae #1 SMP Debian 6.1.99-1 (2024-07-15) armv7l GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Jun 5 22:35 /bin -> usr/bin I: user script /srv/workspace/pbuilder/13617/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: armhf Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), cmake, texinfo, libbpp-phyl-omics-dev, libboost-iostreams-dev, zlib1g-dev, libbz2-dev dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19503 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 cmake; however: Package cmake is not installed. pbuilder-satisfydepends-dummy depends on texinfo; however: Package texinfo is not installed. pbuilder-satisfydepends-dummy depends on libbpp-phyl-omics-dev; however: Package libbpp-phyl-omics-dev is not installed. pbuilder-satisfydepends-dummy depends on libboost-iostreams-dev; however: Package libboost-iostreams-dev is not installed. pbuilder-satisfydepends-dummy depends on zlib1g-dev; however: Package zlib1g-dev is not installed. pbuilder-satisfydepends-dummy depends on libbz2-dev; however: Package libbz2-dev is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} 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} icu-devtools{a} intltool-debian{a} libarchive-zip-perl{a} libarchive13t64{a} libboost-iostreams-dev{a} libboost-iostreams1.83-dev{a} libboost-regex1.83-dev{a} libboost-regex1.83.0{a} libboost1.83-dev{a} libbpp-core-dev{a} libbpp-core4t64{a} libbpp-phyl-dev{a} libbpp-phyl-omics-dev{a} libbpp-phyl-omics3t64{a} libbpp-phyl12t64{a} libbpp-seq-dev{a} libbpp-seq-omics-dev{a} libbpp-seq-omics3t64{a} libbpp-seq12t64{a} libbrotli1{a} libbz2-dev{a} libcom-err2{a} libcurl4t64{a} libdebhelper-perl{a} libelf1t64{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libgssapi-krb5-2{a} libicu-dev{a} libicu72{a} libjsoncpp25{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} libldap-2.5-0{a} libmagic-mgc{a} libmagic1t64{a} libnghttp2-14{a} libpipeline1{a} libproc2-0{a} libpsl5t64{a} librhash0{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libssh2-1t64{a} libtext-unidecode-perl{a} libtool{a} libuchardet0{a} libuv1t64{a} libxml-libxml-perl{a} libxml-namespacesupport-perl{a} libxml-sax-base-perl{a} libxml-sax-perl{a} libxml2{a} m4{a} man-db{a} po-debconf{a} procps{a} sensible-utils{a} tex-common{a} texinfo{a} texinfo-lib{a} ucf{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: bzip2-doc ca-certificates curl krb5-locales libarchive-cpio-perl libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules libwww-perl libxml-sax-expat-perl linux-sysctl-defaults lynx psmisc publicsuffix wget 0 packages upgraded, 81 newly installed, 0 to remove and 0 not upgraded. Need to get 63.0 MB of archives. After unpacking 399 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main armhf libproc2-0 armhf 2:4.0.4-5 [55.8 kB] Get: 2 http://deb.debian.org/debian trixie/main armhf procps armhf 2:4.0.4-5 [863 kB] Get: 3 http://deb.debian.org/debian trixie/main armhf sensible-utils all 0.0.24 [24.8 kB] Get: 4 http://deb.debian.org/debian trixie/main armhf libmagic-mgc armhf 1:5.45-3 [314 kB] Get: 5 http://deb.debian.org/debian trixie/main armhf libmagic1t64 armhf 1:5.45-3 [98.1 kB] Get: 6 http://deb.debian.org/debian trixie/main armhf file armhf 1:5.45-3 [42.0 kB] Get: 7 http://deb.debian.org/debian trixie/main armhf gettext-base armhf 0.22.5-2 [195 kB] Get: 8 http://deb.debian.org/debian trixie/main armhf libuchardet0 armhf 0.0.8-1+b1 [65.7 kB] Get: 9 http://deb.debian.org/debian trixie/main armhf groff-base armhf 1.23.0-5 [1091 kB] Get: 10 http://deb.debian.org/debian trixie/main armhf bsdextrautils armhf 2.40.2-1 [87.8 kB] Get: 11 http://deb.debian.org/debian trixie/main armhf libpipeline1 armhf 1.5.7-2 [33.3 kB] Get: 12 http://deb.debian.org/debian trixie/main armhf man-db armhf 2.12.1-2 [1376 kB] Get: 13 http://deb.debian.org/debian trixie/main armhf ucf all 3.0043+nmu1 [55.2 kB] Get: 14 http://deb.debian.org/debian trixie/main armhf m4 armhf 1.4.19-4 [264 kB] Get: 15 http://deb.debian.org/debian trixie/main armhf autoconf all 2.71-3 [332 kB] Get: 16 http://deb.debian.org/debian trixie/main armhf autotools-dev all 20220109.1 [51.6 kB] Get: 17 http://deb.debian.org/debian trixie/main armhf automake all 1:1.16.5-1.3 [823 kB] Get: 18 http://deb.debian.org/debian trixie/main armhf autopoint all 0.22.5-2 [723 kB] Get: 19 http://deb.debian.org/debian trixie/main armhf libicu72 armhf 72.1-5 [9075 kB] Get: 20 http://deb.debian.org/debian trixie/main armhf libxml2 armhf 2.9.14+dfsg-1.3+b3 [598 kB] Get: 21 http://deb.debian.org/debian trixie/main armhf libarchive13t64 armhf 3.7.2-2.1 [304 kB] Get: 22 http://deb.debian.org/debian trixie/main armhf libbrotli1 armhf 1.1.0-2+b4 [293 kB] Get: 23 http://deb.debian.org/debian trixie/main armhf libkrb5support0 armhf 1.21.3-3 [30.0 kB] Get: 24 http://deb.debian.org/debian trixie/main armhf libcom-err2 armhf 1.47.1-1 [22.1 kB] Get: 25 http://deb.debian.org/debian trixie/main armhf libk5crypto3 armhf 1.21.3-3 [75.8 kB] Get: 26 http://deb.debian.org/debian trixie/main armhf libkeyutils1 armhf 1.6.3-3 [7908 B] Get: 27 http://deb.debian.org/debian trixie/main armhf libkrb5-3 armhf 1.21.3-3 [283 kB] Get: 28 http://deb.debian.org/debian trixie/main armhf libgssapi-krb5-2 armhf 1.21.3-3 [114 kB] Get: 29 http://deb.debian.org/debian trixie/main armhf libsasl2-modules-db armhf 2.1.28+dfsg1-6 [18.0 kB] Get: 30 http://deb.debian.org/debian trixie/main armhf libsasl2-2 armhf 2.1.28+dfsg1-6 [50.1 kB] Get: 31 http://deb.debian.org/debian trixie/main armhf libldap-2.5-0 armhf 2.5.18+dfsg-2 [162 kB] Get: 32 http://deb.debian.org/debian trixie/main armhf libnghttp2-14 armhf 1.62.1-2 [63.7 kB] Get: 33 http://deb.debian.org/debian trixie/main armhf libpsl5t64 armhf 0.21.2-1.1 [55.6 kB] Get: 34 http://deb.debian.org/debian trixie/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2+b4 [53.2 kB] Get: 35 http://deb.debian.org/debian trixie/main armhf libssh2-1t64 armhf 1.11.0-7 [199 kB] Get: 36 http://deb.debian.org/debian trixie/main armhf libcurl4t64 armhf 8.8.0-4 [399 kB] Get: 37 http://deb.debian.org/debian trixie/main armhf libexpat1 armhf 2.6.2-1 [83.5 kB] Get: 38 http://deb.debian.org/debian trixie/main armhf libjsoncpp25 armhf 1.9.5-6+b2 [69.9 kB] Get: 39 http://deb.debian.org/debian trixie/main armhf librhash0 armhf 1.4.3-3+b1 [143 kB] Get: 40 http://deb.debian.org/debian trixie/main armhf libuv1t64 armhf 1.48.0-5 [134 kB] Get: 41 http://deb.debian.org/debian trixie/main armhf cmake-data all 3.29.6-1 [2168 kB] Get: 42 http://deb.debian.org/debian trixie/main armhf cmake armhf 3.29.6-1 [5216 kB] Get: 43 http://deb.debian.org/debian trixie/main armhf libdebhelper-perl all 13.16 [88.6 kB] Get: 44 http://deb.debian.org/debian trixie/main armhf libtool all 2.4.7-7 [517 kB] Get: 45 http://deb.debian.org/debian trixie/main armhf dh-autoreconf all 20 [17.1 kB] Get: 46 http://deb.debian.org/debian trixie/main armhf libarchive-zip-perl all 1.68-1 [104 kB] Get: 47 http://deb.debian.org/debian trixie/main armhf libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 48 http://deb.debian.org/debian trixie/main armhf dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 49 http://deb.debian.org/debian trixie/main armhf libelf1t64 armhf 0.191-2 [183 kB] Get: 50 http://deb.debian.org/debian trixie/main armhf dwz armhf 0.15-1+b2 [106 kB] Get: 51 http://deb.debian.org/debian trixie/main armhf gettext armhf 0.22.5-2 [1485 kB] Get: 52 http://deb.debian.org/debian trixie/main armhf intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 53 http://deb.debian.org/debian trixie/main armhf po-debconf all 1.0.21+nmu1 [248 kB] Get: 54 http://deb.debian.org/debian trixie/main armhf debhelper all 13.16 [891 kB] Get: 55 http://deb.debian.org/debian trixie/main armhf icu-devtools armhf 72.1-5 [185 kB] Get: 56 http://deb.debian.org/debian trixie/main armhf libboost1.83-dev armhf 1.83.0-3+b2 [10.6 MB] Get: 57 http://deb.debian.org/debian trixie/main armhf libboost-regex1.83.0 armhf 1.83.0-3+b2 [307 kB] Get: 58 http://deb.debian.org/debian trixie/main armhf libicu-dev armhf 72.1-5 [10.1 MB] Get: 59 http://deb.debian.org/debian trixie/main armhf libboost-regex1.83-dev armhf 1.83.0-3+b2 [335 kB] Get: 60 http://deb.debian.org/debian trixie/main armhf libboost-iostreams1.83-dev armhf 1.83.0-3+b2 [261 kB] Get: 61 http://deb.debian.org/debian trixie/main armhf libboost-iostreams-dev armhf 1.83.0.2+b2 [3568 B] Get: 62 http://deb.debian.org/debian trixie/main armhf libbpp-core4t64 armhf 2.4.1-13 [525 kB] Get: 63 http://deb.debian.org/debian trixie/main armhf libbpp-core-dev armhf 2.4.1-13 [958 kB] Get: 64 http://deb.debian.org/debian trixie/main armhf libbpp-seq12t64 armhf 2.4.1-12 [438 kB] Get: 65 http://deb.debian.org/debian trixie/main armhf libbpp-phyl12t64 armhf 2.4.1-11 [1465 kB] Get: 66 http://deb.debian.org/debian trixie/main armhf libbpp-seq-dev armhf 2.4.1-12 [742 kB] Get: 67 http://deb.debian.org/debian trixie/main armhf libbpp-phyl-dev armhf 2.4.1-11 [3133 kB] Get: 68 http://deb.debian.org/debian trixie/main armhf libbpp-seq-omics3t64 armhf 2.4.1-11 [195 kB] Get: 69 http://deb.debian.org/debian trixie/main armhf libbpp-phyl-omics3t64 armhf 2.4.1-7 [62.6 kB] Get: 70 http://deb.debian.org/debian trixie/main armhf libbpp-seq-omics-dev armhf 2.4.1-11 [385 kB] Get: 71 http://deb.debian.org/debian trixie/main armhf libbpp-phyl-omics-dev armhf 2.4.1-7 [148 kB] Get: 72 http://deb.debian.org/debian trixie/main armhf libbz2-dev armhf 1.0.8-5.1 [28.3 kB] Get: 73 http://deb.debian.org/debian trixie/main armhf libtext-unidecode-perl all 1.30-3 [101 kB] Get: 74 http://deb.debian.org/debian trixie/main armhf libxml-namespacesupport-perl all 1.12-2 [15.1 kB] Get: 75 http://deb.debian.org/debian trixie/main armhf libxml-sax-base-perl all 1.09-3 [20.6 kB] Get: 76 http://deb.debian.org/debian trixie/main armhf libxml-sax-perl all 1.02+dfsg-3 [59.4 kB] Get: 77 http://deb.debian.org/debian trixie/main armhf libxml-libxml-perl armhf 2.0207+dfsg+really+2.0134-1+b4 [297 kB] Get: 78 http://deb.debian.org/debian trixie/main armhf tex-common all 6.18 [32.5 kB] Get: 79 http://deb.debian.org/debian trixie/main armhf texinfo-lib armhf 7.1-3+b2 [205 kB] Get: 80 http://deb.debian.org/debian trixie/main armhf texinfo all 7.1-3 [1748 kB] Get: 81 http://deb.debian.org/debian trixie/main armhf zlib1g-dev armhf 1:1.3.dfsg+really1.3.1-1 [904 kB] Fetched 63.0 MB in 3s (19.5 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libproc2-0:armhf. (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 ... 19503 files and directories currently installed.) Preparing to unpack .../00-libproc2-0_2%3a4.0.4-5_armhf.deb ... Unpacking libproc2-0:armhf (2:4.0.4-5) ... Selecting previously unselected package procps. Preparing to unpack .../01-procps_2%3a4.0.4-5_armhf.deb ... Unpacking procps (2:4.0.4-5) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../02-sensible-utils_0.0.24_all.deb ... 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Setting up libbrotli1:armhf (1.1.0-2+b4) ... Setting up libuv1t64:armhf (1.48.0-5) ... Setting up libmagic1t64:armhf (1:5.45-3) ... Setting up libpsl5t64:armhf (0.21.2-1.1) ... Setting up libnghttp2-14:armhf (1.62.1-2) ... Setting up libxml-namespacesupport-perl (1.12-2) ... Setting up gettext-base (0.22.5-2) ... Setting up m4 (1.4.19-4) ... Setting up libcom-err2:armhf (1.47.1-1) ... Setting up file (1:5.45-3) ... Setting up texinfo-lib (7.1-3+b2) ... Setting up libelf1t64:armhf (0.191-2) ... Setting up libkrb5support0:armhf (1.21.3-3) ... Setting up libsasl2-modules-db:armhf (2.1.28+dfsg1-6) ... Setting up libbpp-core-dev:armhf (2.4.1-13) ... Setting up libxml-sax-base-perl (1.09-3) ... Setting up autotools-dev (20220109.1) ... Setting up librtmp1:armhf (2.4+20151223.gitfa8646d.1-2+b4) ... Setting up libproc2-0:armhf (2:4.0.4-5) ... Setting up autopoint (0.22.5-2) ... Setting up libjsoncpp25:armhf (1.9.5-6+b2) ... Setting up icu-devtools (72.1-5) ... Setting up libk5crypto3:armhf (1.21.3-3) ... Setting up libsasl2-2:armhf (2.1.28+dfsg1-6) ... Setting up autoconf (2.71-3) ... Setting up zlib1g-dev:armhf (1:1.3.dfsg+really1.3.1-1) ... Setting up dwz (0.15-1+b2) ... Setting up sensible-utils (0.0.24) ... Setting up librhash0:armhf (1.4.3-3+b1) ... Setting up libuchardet0:armhf (0.0.8-1+b1) ... Setting up procps (2:4.0.4-5) ... Setting up cmake-data (3.29.6-1) ... Setting up libkrb5-3:armhf (1.21.3-3) ... Setting up libssh2-1t64:armhf (1.11.0-7) ... Setting up libtext-unidecode-perl (1.30-3) ... Setting up libicu-dev:armhf (72.1-5) ... Setting up libxml2:armhf (2.9.14+dfsg-1.3+b3) ... Setting up libbz2-dev:armhf (1.0.8-5.1) ... Setting up libbpp-seq12t64:armhf (2.4.1-12) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.14.0-1) ... Setting up libbpp-seq-dev:armhf (2.4.1-12) ... Setting up gettext (0.22.5-2) ... Setting up libtool (2.4.7-7) ... Setting up libbpp-phyl12t64:armhf (2.4.1-11) ... Setting up libldap-2.5-0:armhf (2.5.18+dfsg-2) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up libbpp-phyl-dev:armhf (2.4.1-11) ... Setting up libgssapi-krb5-2:armhf (1.21.3-3) ... Setting up libboost-regex1.83-dev:armhf (1.83.0-3+b2) ... Setting up ucf (3.0043+nmu1) ... Setting up dh-strip-nondeterminism (1.14.0-1) ... Setting up groff-base (1.23.0-5) ... Setting up libbpp-seq-omics3t64:armhf (2.4.1-11) ... Setting up libarchive13t64:armhf (3.7.2-2.1) ... Setting up libbpp-phyl-omics3t64:armhf (2.4.1-7) ... Setting up libcurl4t64:armhf (8.8.0-4) ... Setting up libboost-iostreams1.83-dev:armhf (1.83.0-3+b2) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libboost-iostreams-dev:armhf (1.83.0.2+b2) ... Setting up man-db (2.12.1-2) ... Not building database; man-db/auto-update is not 'true'. Setting up libxml-sax-perl (1.02+dfsg-3) ... update-perl-sax-parsers: Registering Perl SAX parser XML::SAX::PurePerl with priority 10... update-perl-sax-parsers: Updating overall Perl SAX parser modules info file... Creating config file /etc/perl/XML/SAX/ParserDetails.ini with new version Setting up tex-common (6.18) ... update-language: texlive-base not installed and configured, doing nothing! Setting up libxml-libxml-perl (2.0207+dfsg+really+2.0134-1+b4) ... update-perl-sax-parsers: Registering Perl SAX parser XML::LibXML::SAX::Parser with priority 50... update-perl-sax-parsers: Registering Perl SAX parser XML::LibXML::SAX with priority 50... update-perl-sax-parsers: Updating overall Perl SAX parser modules info file... Replacing config file /etc/perl/XML/SAX/ParserDetails.ini with new version Setting up libbpp-seq-omics-dev:armhf (2.4.1-11) ... Setting up cmake (3.29.6-1) ... Setting up libbpp-phyl-omics-dev:armhf (2.4.1-7) ... Setting up debhelper (13.16) ... Setting up texinfo (7.1-3) ... Processing triggers for libc-bin (2.39-6) ... Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/reproducible-path/maffilter-1.3.1+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 > ../maffilter_1.3.1+dfsg-6_source.changes dpkg-buildpackage: info: source package maffilter dpkg-buildpackage: info: source version 1.3.1+dfsg-6 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Michael R. Crusoe dpkg-source --before-build . dpkg-buildpackage: info: host architecture armhf debian/rules clean dh clean dh_clean debian/rules binary dh binary dh_update_autotools_config dh_autoreconf dh_auto_configure cd obj-arm-linux-gnueabihf && DEB_PYTHON_INSTALL_LAYOUT=deb 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/arm-linux-gnueabihf .. CMake Deprecation Warning at CMakeLists.txt:6 (CMAKE_MINIMUM_REQUIRED): Compatibility with CMake < 3.5 will be removed from a future version of CMake. Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions. -- The CXX compiler identification is GNU 13.3.0 -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Found /usr/bin/gzip compression program, using file extension .gz -- bpp-core 4.1.0 found: -- static lib: /usr/lib/arm-linux-gnueabihf/libbpp-core.a -- shared lib: /usr/lib/arm-linux-gnueabihf/libbpp-core.so.4.1.0 -- includes: /usr/include -- bpp-seq 12.0.0 found: -- static lib: /usr/lib/arm-linux-gnueabihf/libbpp-seq.a -- shared lib: /usr/lib/arm-linux-gnueabihf/libbpp-seq.so.12.0.0 -- includes: /usr/include -- bpp-seq-omics 3.0.0 found: -- static lib: /usr/lib/arm-linux-gnueabihf/libbpp-seq-omics.a -- shared lib: /usr/lib/arm-linux-gnueabihf/libbpp-seq-omics.so.3.0.0 -- includes: /usr/include -- bpp-phyl 12.0.0 found: -- static lib: /usr/lib/arm-linux-gnueabihf/libbpp-phyl.a -- shared lib: /usr/lib/arm-linux-gnueabihf/libbpp-phyl.so.12.0.0 -- includes: /usr/include -- bpp-phyl-omics 3.0.0 found: -- static lib: /usr/lib/arm-linux-gnueabihf/libbpp-phyl-omics.a -- shared lib: /usr/lib/arm-linux-gnueabihf/libbpp-phyl-omics.so.3.0.0 -- includes: /usr/include -- Found Boost: /usr/lib/arm-linux-gnueabihf/cmake/Boost-1.83.0/BoostConfig.cmake (found suitable version "1.83.0", minimum required is "1.34.0") found components: iostreams -- Boost libraries found here: includes: /usr/include dynamic libraries: Boost::iostreams -- Library z found here: includes: /usr/include dynamic libraries: /usr/lib/arm-linux-gnueabihf/libz.so -- Library bz2 found here: includes: /usr/include dynamic libraries: /usr/lib/arm-linux-gnueabihf/libbz2.so -- Found /usr/bin/makeinfo: 'info' and 'html' target enabled (builds info/html doc) -- Found texi2dvi: 'pdf' target enabled (builds pdf doc) -- Configuring done (0.8s) -- 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 FETCHCONTENT_FULLY_DISCONNECTED -- Build files have been written to: /build/reproducible-path/maffilter-1.3.1+dfsg/obj-arm-linux-gnueabihf dh_auto_build cd obj-arm-linux-gnueabihf && make -j3 "INSTALL=install --strip-program=true" VERBOSE=1 make[1]: Entering directory '/build/reproducible-path/maffilter-1.3.1+dfsg/obj-arm-linux-gnueabihf' /usr/bin/cmake -S/build/reproducible-path/maffilter-1.3.1+dfsg -B/build/reproducible-path/maffilter-1.3.1+dfsg/obj-arm-linux-gnueabihf --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/maffilter-1.3.1+dfsg/obj-arm-linux-gnueabihf/CMakeFiles /build/reproducible-path/maffilter-1.3.1+dfsg/obj-arm-linux-gnueabihf//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/build/reproducible-path/maffilter-1.3.1+dfsg/obj-arm-linux-gnueabihf' make -f MafFilter/CMakeFiles/maffilter.dir/build.make MafFilter/CMakeFiles/maffilter.dir/depend make -f doc/CMakeFiles/info.dir/build.make doc/CMakeFiles/info.dir/depend make -f man/CMakeFiles/man.dir/build.make man/CMakeFiles/man.dir/depend make[3]: Entering directory '/build/reproducible-path/maffilter-1.3.1+dfsg/obj-arm-linux-gnueabihf' cd /build/reproducible-path/maffilter-1.3.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/maffilter-1.3.1+dfsg /build/reproducible-path/maffilter-1.3.1+dfsg/doc /build/reproducible-path/maffilter-1.3.1+dfsg/obj-arm-linux-gnueabihf /build/reproducible-path/maffilter-1.3.1+dfsg/obj-arm-linux-gnueabihf/doc /build/reproducible-path/maffilter-1.3.1+dfsg/obj-arm-linux-gnueabihf/doc/CMakeFiles/info.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/maffilter-1.3.1+dfsg/obj-arm-linux-gnueabihf' cd /build/reproducible-path/maffilter-1.3.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/maffilter-1.3.1+dfsg /build/reproducible-path/maffilter-1.3.1+dfsg/MafFilter /build/reproducible-path/maffilter-1.3.1+dfsg/obj-arm-linux-gnueabihf /build/reproducible-path/maffilter-1.3.1+dfsg/obj-arm-linux-gnueabihf/MafFilter /build/reproducible-path/maffilter-1.3.1+dfsg/obj-arm-linux-gnueabihf/MafFilter/CMakeFiles/maffilter.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/maffilter-1.3.1+dfsg/obj-arm-linux-gnueabihf' cd /build/reproducible-path/maffilter-1.3.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/maffilter-1.3.1+dfsg /build/reproducible-path/maffilter-1.3.1+dfsg/man /build/reproducible-path/maffilter-1.3.1+dfsg/obj-arm-linux-gnueabihf /build/reproducible-path/maffilter-1.3.1+dfsg/obj-arm-linux-gnueabihf/man /build/reproducible-path/maffilter-1.3.1+dfsg/obj-arm-linux-gnueabihf/man/CMakeFiles/man.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/maffilter-1.3.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Leaving directory '/build/reproducible-path/maffilter-1.3.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Leaving directory '/build/reproducible-path/maffilter-1.3.1+dfsg/obj-arm-linux-gnueabihf' make -f man/CMakeFiles/man.dir/build.make man/CMakeFiles/man.dir/build make -f MafFilter/CMakeFiles/maffilter.dir/build.make MafFilter/CMakeFiles/maffilter.dir/build make -f doc/CMakeFiles/info.dir/build.make doc/CMakeFiles/info.dir/build make[3]: Entering directory '/build/reproducible-path/maffilter-1.3.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Entering directory '/build/reproducible-path/maffilter-1.3.1+dfsg/obj-arm-linux-gnueabihf' make[3]: Entering directory '/build/reproducible-path/maffilter-1.3.1+dfsg/obj-arm-linux-gnueabihf' [ 12%] Compressing manpage maffilter.1 [ 25%] Building CXX object MafFilter/CMakeFiles/maffilter.dir/MafFilter.cpp.o [ 37%] Generating info page cd /build/reproducible-path/maffilter-1.3.1+dfsg/obj-arm-linux-gnueabihf/man && /usr/bin/gzip -c -n -9 /build/reproducible-path/maffilter-1.3.1+dfsg/man/maffilter.1 > /build/reproducible-path/maffilter-1.3.1+dfsg/obj-arm-linux-gnueabihf/man/maffilter.1.gz cd /build/reproducible-path/maffilter-1.3.1+dfsg/obj-arm-linux-gnueabihf/MafFilter && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/maffilter-1.3.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -MD -MT MafFilter/CMakeFiles/maffilter.dir/MafFilter.cpp.o -MF CMakeFiles/maffilter.dir/MafFilter.cpp.o.d -o CMakeFiles/maffilter.dir/MafFilter.cpp.o -c /build/reproducible-path/maffilter-1.3.1+dfsg/MafFilter/MafFilter.cpp cd /build/reproducible-path/maffilter-1.3.1+dfsg/obj-arm-linux-gnueabihf/doc && /usr/bin/makeinfo --no-split -o /build/reproducible-path/maffilter-1.3.1+dfsg/obj-arm-linux-gnueabihf/doc/maffilter.info /build/reproducible-path/maffilter-1.3.1+dfsg/doc/maffilter.texi make[3]: Leaving directory '/build/reproducible-path/maffilter-1.3.1+dfsg/obj-arm-linux-gnueabihf' [ 37%] Built target man [ 50%] Building CXX object MafFilter/CMakeFiles/maffilter.dir/OutputAsFeaturesMafIterator.cpp.o cd /build/reproducible-path/maffilter-1.3.1+dfsg/obj-arm-linux-gnueabihf/MafFilter && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/maffilter-1.3.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -MD -MT MafFilter/CMakeFiles/maffilter.dir/OutputAsFeaturesMafIterator.cpp.o -MF CMakeFiles/maffilter.dir/OutputAsFeaturesMafIterator.cpp.o.d -o CMakeFiles/maffilter.dir/OutputAsFeaturesMafIterator.cpp.o -c /build/reproducible-path/maffilter-1.3.1+dfsg/MafFilter/OutputAsFeaturesMafIterator.cpp [ 62%] Compressing info page cd /build/reproducible-path/maffilter-1.3.1+dfsg/obj-arm-linux-gnueabihf/doc && /usr/bin/gzip -c -n -9 /build/reproducible-path/maffilter-1.3.1+dfsg/obj-arm-linux-gnueabihf/doc/maffilter.info > /build/reproducible-path/maffilter-1.3.1+dfsg/obj-arm-linux-gnueabihf/doc/maffilter.info.gz make[3]: Leaving directory '/build/reproducible-path/maffilter-1.3.1+dfsg/obj-arm-linux-gnueabihf' [ 62%] Built target info [ 75%] Building CXX object MafFilter/CMakeFiles/maffilter.dir/SystemCallMafIterator.cpp.o cd /build/reproducible-path/maffilter-1.3.1+dfsg/obj-arm-linux-gnueabihf/MafFilter && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/maffilter-1.3.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -MD -MT MafFilter/CMakeFiles/maffilter.dir/SystemCallMafIterator.cpp.o -MF CMakeFiles/maffilter.dir/SystemCallMafIterator.cpp.o.d -o CMakeFiles/maffilter.dir/SystemCallMafIterator.cpp.o -c /build/reproducible-path/maffilter-1.3.1+dfsg/MafFilter/SystemCallMafIterator.cpp [ 87%] Building CXX object MafFilter/CMakeFiles/maffilter.dir/TreeBuildingSystemCallMafIterator.cpp.o cd /build/reproducible-path/maffilter-1.3.1+dfsg/obj-arm-linux-gnueabihf/MafFilter && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_IOSTREAMS_NO_LIB -g -O2 -ffile-prefix-map=/build/reproducible-path/maffilter-1.3.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -MD -MT MafFilter/CMakeFiles/maffilter.dir/TreeBuildingSystemCallMafIterator.cpp.o -MF CMakeFiles/maffilter.dir/TreeBuildingSystemCallMafIterator.cpp.o.d -o CMakeFiles/maffilter.dir/TreeBuildingSystemCallMafIterator.cpp.o -c /build/reproducible-path/maffilter-1.3.1+dfsg/MafFilter/TreeBuildingSystemCallMafIterator.cpp In file included from /usr/include/c++/13/vector:72, from /usr/include/Bpp/Text/TextTools.h:49, from /usr/include/Bpp/Numeric/Range.h:43, from /usr/include/Bpp/Seq/Feature/SequenceFeature.h:51, from /usr/include/Bpp/Seq/Io/Maf/MafSequence.h:43, from /usr/include/Bpp/Seq/Io/Maf/MafBlock.h:43, from /usr/include/Bpp/Seq/Io/Maf/MafIterator.h:43, from /build/reproducible-path/maffilter-1.3.1+dfsg/MafFilter/TreeBuildingSystemCallMafIterator.h:43, from /build/reproducible-path/maffilter-1.3.1+dfsg/MafFilter/TreeBuildingSystemCallMafIterator.cpp:40: /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/vector:66: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'std::vector > bpp::TreeTemplate::getBranchLengths() [with N = bpp::Node]' at /usr/include/Bpp/Phyl/TreeTemplate.h:351:69: /usr/include/c++/13/bits/stl_vector.h:1292:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 1292 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algo.h:61, from /usr/include/c++/13/algorithm:61, from /usr/include/Bpp/Seq/Feature/SequenceFeature.h:47, from /usr/include/Bpp/Seq/Io/Maf/MafSequence.h:43, from /usr/include/Bpp/Seq/Io/Maf/MafBlock.h:43, from /usr/include/Bpp/Seq/Io/Maf/MafIterator.h:43, from /build/reproducible-path/maffilter-1.3.1+dfsg/MafFilter/OutputAsFeaturesMafIterator.h:43, from /build/reproducible-path/maffilter-1.3.1+dfsg/MafFilter/MafFilter.cpp:47: /usr/include/c++/13/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator > >; _Distance = int; _Tp = double; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/13/bits/stl_heap.h:224:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 224 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, | ^~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator > >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/13/bits/stl_algo.h:1812:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 1812 | __insertion_sort(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_algo.h:1812:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 /usr/include/c++/13/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator > >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/13/bits/stl_algo.h:1918:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 1918 | __introsort_loop(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_algo.h:1918:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 /usr/include/c++/13/bits/stl_algo.h:1932:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 1932 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator > >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator > >]' at /usr/include/c++/13/bits/stl_algo.h:4861:18, inlined from 'bpp::SiteFrequencySpectrumMafStatistics::Categorizer::Categorizer(const std::vector >&)' at /usr/include/Bpp/Seq/Io/Maf/MafStatistics.h:490:20, inlined from 'bpp::SiteFrequencySpectrumMafStatistics::SiteFrequencySpectrumMafStatistics(const bpp::Alphabet*, const std::vector >&, const std::vector >&, std::string)' at /usr/include/Bpp/Seq/Io/Maf/MafStatistics.h:519:7: /usr/include/c++/13/bits/stl_algo.h:1947:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 1947 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1948 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1949 | __comp); | ~~~~~~~ In function 'void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator > >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', inlined from 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator > >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/13/bits/stl_algo.h:1950:31, inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator > >]' at /usr/include/c++/13/bits/stl_algo.h:4861:18, inlined from 'bpp::SiteFrequencySpectrumMafStatistics::Categorizer::Categorizer(const std::vector >&)' at /usr/include/Bpp/Seq/Io/Maf/MafStatistics.h:490:20, inlined from 'bpp::SiteFrequencySpectrumMafStatistics::SiteFrequencySpectrumMafStatistics(const bpp::Alphabet*, const std::vector >&, const std::vector >&, std::string)' at /usr/include/Bpp/Seq/Io/Maf/MafStatistics.h:519:7: /usr/include/c++/13/bits/stl_algo.h:1859:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 1859 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_algo.h:1864:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 1864 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/vector:72, from /usr/include/Bpp/Text/TextTools.h:49, from /usr/include/Bpp/Numeric/Range.h:43, from /usr/include/Bpp/Seq/Feature/SequenceFeature.h:51: /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/vector:66: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'std::vector > bpp::TreeTemplate::getBranchLengths() [with N = bpp::Node]' at /usr/include/Bpp/Phyl/TreeTemplate.h:351:69: /usr/include/c++/13/bits/stl_vector.h:1292:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 1292 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ [100%] Linking CXX executable maffilter cd /build/reproducible-path/maffilter-1.3.1+dfsg/obj-arm-linux-gnueabihf/MafFilter && /usr/bin/cmake -E cmake_link_script CMakeFiles/maffilter.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/maffilter-1.3.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/maffilter.dir/MafFilter.cpp.o CMakeFiles/maffilter.dir/OutputAsFeaturesMafIterator.cpp.o CMakeFiles/maffilter.dir/SystemCallMafIterator.cpp.o CMakeFiles/maffilter.dir/TreeBuildingSystemCallMafIterator.cpp.o -o maffilter /usr/lib/arm-linux-gnueabihf/libbpp-phyl-omics.so.3.0.0 /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so.1.83.0 -lz -lbz2 /usr/lib/arm-linux-gnueabihf/libbpp-seq-omics.so.3.0.0 /usr/lib/arm-linux-gnueabihf/libbpp-phyl.so.12.0.0 /usr/lib/arm-linux-gnueabihf/libbpp-seq.so.12.0.0 /usr/lib/arm-linux-gnueabihf/libbpp-core.so.4.1.0 make[3]: Leaving directory '/build/reproducible-path/maffilter-1.3.1+dfsg/obj-arm-linux-gnueabihf' [100%] Built target maffilter make[2]: Leaving directory '/build/reproducible-path/maffilter-1.3.1+dfsg/obj-arm-linux-gnueabihf' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/maffilter-1.3.1+dfsg/obj-arm-linux-gnueabihf/CMakeFiles 0 make[1]: Leaving directory '/build/reproducible-path/maffilter-1.3.1+dfsg/obj-arm-linux-gnueabihf' dh_auto_test create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install cd obj-arm-linux-gnueabihf && make -j3 install DESTDIR=/build/reproducible-path/maffilter-1.3.1\+dfsg/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/reproducible-path/maffilter-1.3.1+dfsg/obj-arm-linux-gnueabihf' /usr/bin/cmake -S/build/reproducible-path/maffilter-1.3.1+dfsg -B/build/reproducible-path/maffilter-1.3.1+dfsg/obj-arm-linux-gnueabihf --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 preinstall make[2]: Entering directory '/build/reproducible-path/maffilter-1.3.1+dfsg/obj-arm-linux-gnueabihf' make[2]: Nothing to be done for 'preinstall'. make[2]: Leaving directory '/build/reproducible-path/maffilter-1.3.1+dfsg/obj-arm-linux-gnueabihf' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "None" -- Installing: /build/reproducible-path/maffilter-1.3.1+dfsg/debian/tmp/usr/bin/maffilter -- Installing: /build/reproducible-path/maffilter-1.3.1+dfsg/debian/tmp/usr/share/info/maffilter.info.gz -- Installing: /build/reproducible-path/maffilter-1.3.1+dfsg/debian/tmp/usr/share/man/man1/maffilter.1.gz make[1]: Leaving directory '/build/reproducible-path/maffilter-1.3.1+dfsg/obj-arm-linux-gnueabihf' dh_install dh_installdocs dh_installchangelogs dh_installman dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms debian/rules execute_after_dh_fixperms make[1]: Entering directory '/build/reproducible-path/maffilter-1.3.1+dfsg' find debian/*/usr/share -name "*.bpp" -executable -exec chmod -x \{\} \; make[1]: Leaving directory '/build/reproducible-path/maffilter-1.3.1+dfsg' dh_missing dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 from: /lib/ld-linux-armhf.so.3 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 to: /lib/ld-linux-armhf.so.3.usr-is-merged dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'maffilter-dbgsym' in '../maffilter-dbgsym_1.3.1+dfsg-6_armhf.deb'. dpkg-deb: building package 'maffilter' in '../maffilter_1.3.1+dfsg-6_armhf.deb'. dpkg-deb: building package 'maffilter-examples' in '../maffilter-examples_1.3.1+dfsg-6_all.deb'. dpkg-genbuildinfo --build=binary -O../maffilter_1.3.1+dfsg-6_armhf.buildinfo dpkg-genchanges --build=binary -O../maffilter_1.3.1+dfsg-6_armhf.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: 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/13617 and its subdirectories I: Current time: Wed Aug 7 20:15:16 -12 2024 I: pbuilder-time-stamp: 1723104916 Thu Aug 8 08:17:37 UTC 2024 I: 1st build successful. Starting 2nd build on remote node virt64a-armhf-rb.debian.net. Thu Aug 8 08:17:37 UTC 2024 I: Preparing to do remote build '2' on virt64a-armhf-rb.debian.net. Thu Aug 8 08:26:39 UTC 2024 I: Deleting $TMPDIR on virt64a-armhf-rb.debian.net. Thu Aug 8 08:26:41 UTC 2024 I: maffilter_1.3.1+dfsg-6_armhf.changes: Format: 1.8 Date: Tue, 26 Mar 2024 09:59:19 +0100 Source: maffilter Binary: maffilter maffilter-dbgsym maffilter-examples Architecture: armhf all Version: 1.3.1+dfsg-6 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Michael R. Crusoe Description: maffilter - process genome alignment in the Multiple Alignment Format maffilter-examples - process genome alignment in the Multiple Alignment Format (exampl Changes: maffilter (1.3.1+dfsg-6) unstable; urgency=medium . * Team upload. * Added patch to combine upstream's c++ flags with out own. * d/rules: simplified Checksums-Sha1: 7b904d9ee58e0eba82cd2368506307ea052aee84 2906792 maffilter-dbgsym_1.3.1+dfsg-6_armhf.deb 67b2e7e58203dcbd9c0a13d70955ce58a1b03644 79214828 maffilter-examples_1.3.1+dfsg-6_all.deb 143c3f3a3de4bdc47f972bfd8a7c5c11beb1f338 7077 maffilter_1.3.1+dfsg-6_armhf.buildinfo f3b9c3f89f8d887b3a78564f73c82468b138e4b5 234392 maffilter_1.3.1+dfsg-6_armhf.deb Checksums-Sha256: 21b52599adf413f64fdb4650fa62778518f21462e05a93fc60e900a26138532f 2906792 maffilter-dbgsym_1.3.1+dfsg-6_armhf.deb 06db35a5ab659358ee4e28773d80d3632896e16d3a382ad210fee976d392a2fa 79214828 maffilter-examples_1.3.1+dfsg-6_all.deb d85ef9cfc2263b3a6423f57430bfa827783b3bd312bbd79f921fb87e922ed810 7077 maffilter_1.3.1+dfsg-6_armhf.buildinfo 5c3fda62770c8f884b8f8677a577915059626c96b36e6acda74170a7bf8658a1 234392 maffilter_1.3.1+dfsg-6_armhf.deb Files: e7997524666903f51f406f51ebbc4986 2906792 debug optional maffilter-dbgsym_1.3.1+dfsg-6_armhf.deb 1ecf76f5a27fabf87fa64bd808cd5c93 79214828 science optional maffilter-examples_1.3.1+dfsg-6_all.deb d49cfd4f76e1c7b351125949c3f69f2e 7077 science optional maffilter_1.3.1+dfsg-6_armhf.buildinfo 6d12490c4bb7fcbfca6ec01fd8c51e43 234392 science optional maffilter_1.3.1+dfsg-6_armhf.deb Thu Aug 8 08:26:45 UTC 2024 I: diffoscope 273 will be used to compare the two builds: Running as unit: rb-diffoscope-armhf_34-10443.service Warning: program compiled against libxml 212 using older 209 # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.lxeLW6Pe/maffilter_1.3.1+dfsg-6.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.lxeLW6Pe/maffilter_1.3.1+dfsg-6.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.lxeLW6Pe/maffilter_1.3.1+dfsg-6.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.lxeLW6Pe/b1/maffilter_1.3.1+dfsg-6_armhf.changes /srv/reproducible-results/rbuild-debian/r-b-build.lxeLW6Pe/b2/maffilter_1.3.1+dfsg-6_armhf.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call abc.DotChangesFile ## main (total time: 2.932s) 2.932s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 2.223s) 2.223s 12 calls diffoscope.comparators.binary.FilesystemFile ## specialize (total time: 0.000s) 0.000s 1 call specialize Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 3.357s CPU time consumed: 3.176s Thu Aug 8 08:26:49 UTC 2024 I: diffoscope 273 found no differences in the changes files, and a .buildinfo file also exists. Thu Aug 8 08:26:49 UTC 2024 I: maffilter from trixie built successfully and reproducibly on armhf. Thu Aug 8 08:26:51 UTC 2024 I: Submitting .buildinfo files to external archives: Thu Aug 8 08:26:51 UTC 2024 I: Submitting 8.0K b1/maffilter_1.3.1+dfsg-6_armhf.buildinfo.asc Thu Aug 8 08:26:52 UTC 2024 I: Submitting 8.0K b2/maffilter_1.3.1+dfsg-6_armhf.buildinfo.asc Thu Aug 8 08:26:52 UTC 2024 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Thu Aug 8 08:26:52 UTC 2024 I: Done submitting .buildinfo files. Thu Aug 8 08:26:52 UTC 2024 I: Removing signed maffilter_1.3.1+dfsg-6_armhf.buildinfo.asc files: removed './b1/maffilter_1.3.1+dfsg-6_armhf.buildinfo.asc' removed './b2/maffilter_1.3.1+dfsg-6_armhf.buildinfo.asc'