Running as unit: rb-build-arm64_16-38298.service ==================================================================================== Tue Nov 26 01:50:58 UTC 2024 - running /srv/jenkins/bin/reproducible_build.sh (for job reproducible_builder_arm64_16) on jenkins, called using "codethink02-arm64 codethink01-arm64" as arguments. Tue Nov 26 01:50:58 UTC 2024 - actually running "reproducible_build.sh" (md5sum 68e686e434c9ab7bc3ec047d8b309cbc) as "/tmp/jenkins-script-9MDkYmT7" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Tue Nov 26 01:50:58 UTC 2024 - checking /var/lib/jenkins/offline_nodes if codethink02-arm64.debian.net is marked as down. Tue Nov 26 01:50:58 UTC 2024 - checking via ssh if codethink02-arm64.debian.net is up. removed '/tmp/read-only-fs-test-C9EX2W' Tue Nov 26 01:50:59 UTC 2024 - checking /var/lib/jenkins/offline_nodes if codethink01-arm64.debian.net is marked as down. Tue Nov 26 01:50:59 UTC 2024 - checking via ssh if codethink01-arm64.debian.net is up. removed '/tmp/read-only-fs-test-Twn2Cr' ok, let's check if sibelia is building anywhere yet… ok, sibelia is not building anywhere… UPDATE 1 ============================================================================= Initialising reproducibly build of sibelia in experimental on arm64 on jenkins now. 1st build will be done on codethink02-arm64.debian.net. 2nd build will be done on codethink01-arm64.debian.net. ============================================================================= Tue Nov 26 01:51:07 UTC 2024 I: starting to build sibelia/experimental/arm64 on jenkins on '2024-11-26 01:50' Tue Nov 26 01:51:07 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/arm64_16/38298/console.log 1732585867 arm64 experimental sibelia Tue Nov 26 01:51:07 UTC 2024 I: Downloading source for experimental/sibelia=3.0.7+dfsg-4 --2024-11-26 01:51:07-- http://cdn-fastly.deb.debian.org/debian/pool/main/s/sibelia/sibelia_3.0.7%2bdfsg-4.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2156 (2.1K) [text/prs.lines.tag] Saving to: ‘sibelia_3.0.7+dfsg-4.dsc’ 0K .. 100% 163M=0s 2024-11-26 01:51:07 (163 MB/s) - ‘sibelia_3.0.7+dfsg-4.dsc’ saved [2156/2156] --2024-11-26 01:51:07-- http://cdn-fastly.deb.debian.org/debian/pool/main/s/sibelia/sibelia_3.0.7%2bdfsg-4.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2156 (2.1K) [text/prs.lines.tag] Saving to: ‘sibelia_3.0.7+dfsg-4.dsc’ 0K .. 100% 163M=0s 2024-11-26 01:51:07 (163 MB/s) - ‘sibelia_3.0.7+dfsg-4.dsc’ saved [2156/2156] Tue Nov 26 01:51:07 UTC 2024 I: sibelia_3.0.7+dfsg-4.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: sibelia Binary: sibelia, sibelia-examples Architecture: any all Version: 3.0.7+dfsg-4 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille Homepage: http://bioinf.spbau.ru/sibelia Standards-Version: 4.5.0 Vcs-Browser: https://salsa.debian.org/med-team/sibelia Vcs-Git: https://salsa.debian.org/med-team/sibelia.git Testsuite: autopkgtest Build-Depends: debhelper-compat (= 12), cmake, libdivsufsort-dev, libboost-dev, libseqan2-dev (= 2.5.0~rc3+dfsg-1), libtclap-dev, libhts-dev Package-List: sibelia deb science optional arch=any sibelia-examples deb science optional arch=all Checksums-Sha1: fab5441d7decc4e9dedbf1169549d85241c132cc 4833128 sibelia_3.0.7+dfsg.orig.tar.xz 6f4addde5d61cc1dd5960d3cdeeb2d77e87e6382 10944 sibelia_3.0.7+dfsg-4.debian.tar.xz Checksums-Sha256: d4dd618fe9f373be8ad90f9b1d670ac8e45a7386d67e28b0d055e1d77f9d7caa 4833128 sibelia_3.0.7+dfsg.orig.tar.xz d3ebaa37e8b651f2d4e514ac9bc0d35241b46028aa42204ce8121729eb5f3839 10944 sibelia_3.0.7+dfsg-4.debian.tar.xz Files: 38311be6d2eee4d5e4d4a8ccf2d9c85e 4833128 sibelia_3.0.7+dfsg.orig.tar.xz 911a7c03314a180e74dd61b09556317f 10944 sibelia_3.0.7+dfsg-4.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJGBAEBCgAwFiEEck1gkzcRPHEFUNdHPCZ2P2xn5uIFAmdEibQSHGNydXNvZUBk ZWJpYW4ub3JnAAoJEDwmdj9sZ+bi3RUQAIdehFdvi/It6vgG8ywQ1cOtVEZ9vkUS 1QsFw7ltBZUsm3yOQuBI6Mxx1a/ka35Iqsb7l1byyIIb6LiR63+N1MvoDxd+9IaS UZgf/Uxzhpo/wCHOMjLtxoMvfvU+eow6+OOnjmkUFGDXkcLVgvIimB6sezgVtsK4 QyKbcJuMDiXXDHcVg8epVptArU2jX58dRoxUJkoC4A3pEe7nmgnNcMEJ14PH00rF XNHx+y/nUZ+RqH/CuIaXJt1K56xWMlQEIvMbwv+ez3XZp1a0pfzJmQQh+vduRgPP Y/4ZS6bBOderVlwLIt9fXc9efA10hKIJOhvZp8OCgagNIQ59rXr5xQLNkQObK0/4 ZyXQGcwHxHPwDnbMUhYJFl5VqLueupmxM1MX/YJoCndkPObigw0x3fnST36UXUpX WZNFKCr4QXGnVl5fE8PX+xg/Zbm82g0CgGHtleDXR4P6+UD8Cdg3DakysidUjoSC Wn6hHBaWbO3IJpCIOU3ta1gC8ifZAbdNcbOFp98MErK0yeDetyfGwQ6+V+fH5GXv d5iYWispg22udGzcLuubFtyvW8TF2bLkRLncR83vgnsTNptKprcHHieyFgl9z5TB EGUyhyV2NIkUCgLrqBUgWmd1KtF5H3dKc7LTbx1FhEZrgzeQv93y/7GXp66qNZUo SbPDqx4gkgqh =w//5 -----END PGP SIGNATURE----- Tue Nov 26 01:51:07 UTC 2024 I: Checking whether the package is not for us Tue Nov 26 01:51:07 UTC 2024 I: Starting 1st build on remote node codethink02-arm64.debian.net. Tue Nov 26 01:51:07 UTC 2024 I: Preparing to do remote build '1' on codethink02-arm64.debian.net. Tue Nov 26 01:51:07 UTC 2024 - checking /var/lib/jenkins/offline_nodes if codethink02-arm64.debian.net is marked as down. Tue Nov 26 01:51:07 UTC 2024 - checking via ssh if codethink02-arm64.debian.net is up. removed '/tmp/read-only-fs-test-i1TdkR' ==================================================================================== Tue Nov 26 01:51:09 UTC 2024 - running /srv/jenkins/bin/reproducible_build.sh (for job /srv/jenkins/bin/reproducible_build.sh) on codethink02-arm64, called using "1 sibelia experimental /srv/reproducible-results/rbuild-debian/r-b-build.Jw2wMKXd 3.0.7+dfsg-4" as arguments. Tue Nov 26 01:51:09 UTC 2024 - actually running "reproducible_build.sh" (md5sum 68e686e434c9ab7bc3ec047d8b309cbc) as "/tmp/jenkins-script-K5MiMNG6" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Tue Nov 26 01:51:09 UTC 2024 I: Downloading source for experimental/sibelia=3.0.7+dfsg-4 Reading package lists... NOTICE: 'sibelia' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/sibelia.git Please use: git clone https://salsa.debian.org/med-team/sibelia.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 4846 kB of source archives. Get:1 http://deb.debian.org/debian experimental/main sibelia 3.0.7+dfsg-4 (dsc) [2156 B] Get:2 http://deb.debian.org/debian experimental/main sibelia 3.0.7+dfsg-4 (tar) [4833 kB] Get:3 http://deb.debian.org/debian experimental/main sibelia 3.0.7+dfsg-4 (diff) [10.9 kB] Fetched 4846 kB in 0s (18.6 MB/s) Download complete and in download only mode Reading package lists... NOTICE: 'sibelia' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/sibelia.git Please use: git clone https://salsa.debian.org/med-team/sibelia.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 4846 kB of source archives. Get:1 http://deb.debian.org/debian experimental/main sibelia 3.0.7+dfsg-4 (dsc) [2156 B] Get:2 http://deb.debian.org/debian experimental/main sibelia 3.0.7+dfsg-4 (tar) [4833 kB] Get:3 http://deb.debian.org/debian experimental/main sibelia 3.0.7+dfsg-4 (diff) [10.9 kB] Fetched 4846 kB in 0s (18.6 MB/s) Download complete and in download only mode ============================================================================= Building sibelia in experimental on arm64 on codethink02-arm64 now. Date: Tue Nov 26 01:51:10 GMT 2024 Date UTC: Tue Nov 26 01:51:10 UTC 2024 ============================================================================= W: /root/.pbuilderrc does not exist I: Logging to b1/build.log I: pbuilder: network access will be disabled during build I: Current time: Mon Nov 25 13:51:10 -12 2024 I: pbuilder-time-stamp: 1732585870 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/experimental-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 [sibelia_3.0.7+dfsg-4.dsc] I: copying [./sibelia_3.0.7+dfsg.orig.tar.xz] I: copying [./sibelia_3.0.7+dfsg-4.debian.tar.xz] I: Extracting source gpgv: Signature made Mon Nov 25 14:29:08 2024 gpgv: using RSA key 724D609337113C710550D7473C26763F6C67E6E2 gpgv: issuer "crusoe@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./sibelia_3.0.7+dfsg-4.dsc: no acceptable signature found dpkg-source: info: extracting sibelia in sibelia-3.0.7+dfsg dpkg-source: info: unpacking sibelia_3.0.7+dfsg.orig.tar.xz dpkg-source: info: unpacking sibelia_3.0.7+dfsg-4.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying use_debian_packaged_libdivsufsort.patch dpkg-source: info: applying use_debian_packaged_lagan.patch dpkg-source: info: applying snpeff_is_removed.patch dpkg-source: info: applying 2to3.patch dpkg-source: info: applying 0005-Upgrade-to-SeqAn-2.5.0.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/1763354/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='arm64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' DISTRIBUTION='experimental' HOME='/root' HOST_ARCH='arm64' IFS=' ' INVOCATION_ID='b3d452d9c6b640c7907b6cff8d400475' 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='1763354' 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.Jw2wMKXd/pbuilderrc_7ddl --distribution experimental --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/experimental-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.Jw2wMKXd/b1 --logfile b1/build.log sibelia_3.0.7+dfsg-4.dsc' SUDO_GID='109' SUDO_UID='104' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://192.168.101.4:3128' I: uname -a Linux codethink02-arm64 6.1.0-28-cloud-arm64 #1 SMP Debian 6.1.119-1 (2024-11-22) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 4 21:30 /bin -> usr/bin I: user script /srv/workspace/pbuilder/1763354/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: arm64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 12), cmake, libdivsufsort-dev, libboost-dev, libseqan2-dev (= 2.5.0~rc3+dfsg-1), libtclap-dev, libhts-dev dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 20083 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 (= 12); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on cmake; however: Package cmake is not installed. pbuilder-satisfydepends-dummy depends on libdivsufsort-dev; however: Package libdivsufsort-dev is not installed. pbuilder-satisfydepends-dummy depends on libboost-dev; however: Package libboost-dev is not installed. pbuilder-satisfydepends-dummy depends on libseqan2-dev (= 2.5.0~rc3+dfsg-1); however: Package libseqan2-dev is not installed. pbuilder-satisfydepends-dummy depends on libtclap-dev; however: Package libtclap-dev is not installed. pbuilder-satisfydepends-dummy depends on libhts-dev; however: Package libhts-dev is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} cmake{a} cmake-data{a} comerr-dev{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} krb5-multidev{a} libarchive-zip-perl{a} libarchive13t64{a} libboost-dev{a} libboost1.83-dev{a} libbrotli-dev{a} libbrotli1{a} libbz2-dev{a} libcom-err2{a} libcurl3t64-gnutls{a} libcurl4-gnutls-dev{a} libcurl4t64{a} libdebhelper-perl{a} libdeflate-dev{a} libdeflate0{a} libdivsufsort-dev{a} libdivsufsort3{a} libelf1t64{a} libevent-2.1-7t64{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libgmp-dev{a} libgmpxx4ldbl{a} libgnutls-dane0t64{a} libgnutls-openssl27t64{a} libgnutls28-dev{a} libgssapi-krb5-2{a} libgssrpc4t64{a} libhts-dev{a} libhts3t64{a} libhtscodecs2{a} libicu72{a} libidn2-dev{a} libjsoncpp26{a} libk5crypto3{a} libkadm5clnt-mit12{a} libkadm5srv-mit12{a} libkdb5-10t64{a} libkeyutils1{a} libkrb5-3{a} libkrb5-dev{a} libkrb5support0{a} libldap-2.5-0{a} libldap-dev{a} liblzma-dev{a} libmagic-mgc{a} libmagic1t64{a} libnghttp2-14{a} libnghttp2-dev{a} libnghttp3-9{a} libnghttp3-dev{a} libngtcp2-16{a} libngtcp2-crypto-gnutls-dev{a} libngtcp2-crypto-gnutls8{a} libngtcp2-dev{a} libp11-kit-dev{a} libpipeline1{a} libpkgconf3{a} libproc2-0{a} libpsl-dev{a} libpsl5t64{a} librhash1{a} librtmp-dev{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libssh2-1-dev{a} libssh2-1t64{a} libssl-dev{a} libtasn1-6-dev{a} libtclap-dev{a} libtool{a} libuchardet0{a} libunbound8{a} libuv1t64{a} libxml2{a} libzstd-dev{a} m4{a} man-db{a} nettle-dev{a} pkgconf{a} pkgconf-bin{a} po-debconf{a} procps{a} sensible-utils{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 libtasn1-doc linux-sysctl-defaults lynx psmisc publicsuffix wget 0 packages upgraded, 103 newly installed, 0 to remove and 0 not upgraded. Need to get 64.8 MB of archives. After unpacking 370 MB will be used. The following packages have unmet dependencies: pbuilder-satisfydepends-dummy : Depends: libseqan2-dev (= 2.5.0~rc3+dfsg-1) but it is not going to be installed The following actions will resolve these dependencies: Install the following packages: 1) libseqan2-dev [2.5.0~rc3+dfsg-1 (experimental)] The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} cmake{a} cmake-data{a} comerr-dev{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} krb5-multidev{a} libarchive-zip-perl{a} libarchive13t64{a} libboost-dev{a} libboost1.83-dev{a} libbrotli-dev{a} libbrotli1{a} libbz2-dev{a} libcom-err2{a} libcurl3t64-gnutls{a} libcurl4-gnutls-dev{a} libcurl4t64{a} libdebhelper-perl{a} libdeflate-dev{a} libdeflate0{a} libdivsufsort-dev{a} libdivsufsort3{a} libelf1t64{a} libevent-2.1-7t64{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libgmp-dev{a} libgmpxx4ldbl{a} libgnutls-dane0t64{a} libgnutls-openssl27t64{a} libgnutls28-dev{a} libgssapi-krb5-2{a} libgssrpc4t64{a} libhts-dev{a} libhts3t64{a} libhtscodecs2{a} libicu72{a} libidn2-dev{a} libjsoncpp26{a} libk5crypto3{a} libkadm5clnt-mit12{a} libkadm5srv-mit12{a} libkdb5-10t64{a} libkeyutils1{a} libkrb5-3{a} libkrb5-dev{a} libkrb5support0{a} libldap-2.5-0{a} libldap-dev{a} liblzma-dev{a} libmagic-mgc{a} libmagic1t64{a} libnghttp2-14{a} libnghttp2-dev{a} libnghttp3-9{a} libnghttp3-dev{a} libngtcp2-16{a} libngtcp2-crypto-gnutls-dev{a} libngtcp2-crypto-gnutls8{a} libngtcp2-dev{a} libp11-kit-dev{a} libpipeline1{a} libpkgconf3{a} libproc2-0{a} libpsl-dev{a} libpsl5t64{a} librhash1{a} librtmp-dev{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libseqan2-dev{a} libssh2-1-dev{a} libssh2-1t64{a} libssl-dev{a} libtasn1-6-dev{a} libtclap-dev{a} libtool{a} libuchardet0{a} libunbound8{a} libuv1t64{a} libxml2{a} libzstd-dev{a} m4{a} man-db{a} nettle-dev{a} pkgconf{a} pkgconf-bin{a} po-debconf{a} procps{a} sensible-utils{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 libtasn1-doc linux-sysctl-defaults lynx psmisc publicsuffix wget 0 packages upgraded, 104 newly installed, 0 to remove and 0 not upgraded. Need to get 66.0 MB of archives. After unpacking 383 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main arm64 libproc2-0 arm64 2:4.0.4-6 [62.3 kB] Get: 2 http://deb.debian.org/debian unstable/main arm64 procps arm64 2:4.0.4-6 [872 kB] Get: 3 http://deb.debian.org/debian unstable/main arm64 sensible-utils all 0.0.24 [24.8 kB] Get: 4 http://deb.debian.org/debian unstable/main arm64 libmagic-mgc arm64 1:5.45-3+b1 [314 kB] Get: 5 http://deb.debian.org/debian unstable/main arm64 libmagic1t64 arm64 1:5.45-3+b1 [102 kB] Get: 6 http://deb.debian.org/debian unstable/main arm64 file arm64 1:5.45-3+b1 [43.4 kB] Get: 7 http://deb.debian.org/debian unstable/main arm64 gettext-base arm64 0.22.5-2 [198 kB] Get: 8 http://deb.debian.org/debian unstable/main arm64 libuchardet0 arm64 0.0.8-1+b2 [69.2 kB] Get: 9 http://deb.debian.org/debian unstable/main arm64 groff-base arm64 1.23.0-5 [1129 kB] Get: 10 http://deb.debian.org/debian unstable/main arm64 bsdextrautils arm64 2.40.2-11 [91.2 kB] Get: 11 http://deb.debian.org/debian unstable/main arm64 libpipeline1 arm64 1.5.8-1 [40.2 kB] Get: 12 http://deb.debian.org/debian unstable/main arm64 man-db arm64 2.13.0-1 [1404 kB] Get: 13 http://deb.debian.org/debian unstable/main arm64 m4 arm64 1.4.19-4 [277 kB] Get: 14 http://deb.debian.org/debian unstable/main arm64 autoconf all 2.72-3 [493 kB] Get: 15 http://deb.debian.org/debian unstable/main arm64 autotools-dev all 20220109.1 [51.6 kB] Get: 16 http://deb.debian.org/debian unstable/main arm64 automake all 1:1.16.5-1.3 [823 kB] Get: 17 http://deb.debian.org/debian unstable/main arm64 autopoint all 0.22.5-2 [723 kB] Get: 18 http://deb.debian.org/debian unstable/main arm64 cmake-data all 3.31.1-1 [2267 kB] Get: 19 http://deb.debian.org/debian unstable/main arm64 libicu72 arm64 72.1-5+b1 [9239 kB] Get: 20 http://deb.debian.org/debian unstable/main arm64 libxml2 arm64 2.12.7+dfsg+really2.9.14-0.2+b1 [630 kB] Get: 21 http://deb.debian.org/debian unstable/main arm64 libarchive13t64 arm64 3.7.4-1.1 [323 kB] Get: 22 http://deb.debian.org/debian unstable/main arm64 libbrotli1 arm64 1.1.0-2+b6 [297 kB] Get: 23 http://deb.debian.org/debian unstable/main arm64 libkrb5support0 arm64 1.21.3-3 [32.1 kB] Get: 24 http://deb.debian.org/debian unstable/main arm64 libcom-err2 arm64 1.47.1-1+b1 [23.1 kB] Get: 25 http://deb.debian.org/debian unstable/main arm64 libk5crypto3 arm64 1.21.3-3 [80.8 kB] Get: 26 http://deb.debian.org/debian unstable/main arm64 libkeyutils1 arm64 1.6.3-4 [9352 B] Get: 27 http://deb.debian.org/debian unstable/main arm64 libkrb5-3 arm64 1.21.3-3 [310 kB] Get: 28 http://deb.debian.org/debian unstable/main arm64 libgssapi-krb5-2 arm64 1.21.3-3 [126 kB] Get: 29 http://deb.debian.org/debian unstable/main arm64 libsasl2-modules-db arm64 2.1.28+dfsg1-8 [20.0 kB] Get: 30 http://deb.debian.org/debian unstable/main arm64 libsasl2-2 arm64 2.1.28+dfsg1-8 [55.4 kB] Get: 31 http://deb.debian.org/debian unstable/main arm64 libldap-2.5-0 arm64 2.5.18+dfsg-3+b1 [175 kB] Get: 32 http://deb.debian.org/debian unstable/main arm64 libnghttp2-14 arm64 1.64.0-1 [71.3 kB] Get: 33 http://deb.debian.org/debian unstable/main arm64 libpsl5t64 arm64 0.21.2-1.1+b1 [57.1 kB] Get: 34 http://deb.debian.org/debian unstable/main arm64 librtmp1 arm64 2.4+20151223.gitfa8646d.1-2+b5 [56.8 kB] Get: 35 http://deb.debian.org/debian unstable/main arm64 libssh2-1t64 arm64 1.11.1-1 [235 kB] Get: 36 http://deb.debian.org/debian unstable/main arm64 libcurl4t64 arm64 8.11.0-1 [322 kB] Get: 37 http://deb.debian.org/debian unstable/main arm64 libexpat1 arm64 2.6.4-1 [90.7 kB] Get: 38 http://deb.debian.org/debian unstable/main arm64 libjsoncpp26 arm64 1.9.6-3 [72.9 kB] Get: 39 http://deb.debian.org/debian unstable/main arm64 librhash1 arm64 1.4.5-1 [129 kB] Get: 40 http://deb.debian.org/debian unstable/main arm64 libuv1t64 arm64 1.48.0-7 [143 kB] Get: 41 http://deb.debian.org/debian unstable/main arm64 cmake arm64 3.31.1-1 [9873 kB] Get: 42 http://deb.debian.org/debian unstable/main arm64 comerr-dev arm64 2.1-1.47.1-1+b1 [55.1 kB] Get: 43 http://deb.debian.org/debian unstable/main arm64 libdebhelper-perl all 13.20 [89.7 kB] Get: 44 http://deb.debian.org/debian unstable/main arm64 libtool all 2.4.7-8 [517 kB] Get: 45 http://deb.debian.org/debian unstable/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 46 http://deb.debian.org/debian unstable/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 47 http://deb.debian.org/debian unstable/main arm64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 48 http://deb.debian.org/debian unstable/main arm64 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 49 http://deb.debian.org/debian unstable/main arm64 libelf1t64 arm64 0.192-4 [189 kB] Get: 50 http://deb.debian.org/debian unstable/main arm64 dwz arm64 0.15-1+b1 [102 kB] Get: 51 http://deb.debian.org/debian unstable/main arm64 gettext arm64 0.22.5-2 [1532 kB] Get: 52 http://deb.debian.org/debian unstable/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 53 http://deb.debian.org/debian unstable/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 54 http://deb.debian.org/debian unstable/main arm64 debhelper all 13.20 [915 kB] Get: 55 http://deb.debian.org/debian unstable/main arm64 libgssrpc4t64 arm64 1.21.3-3 [56.7 kB] Get: 56 http://deb.debian.org/debian unstable/main arm64 libkadm5clnt-mit12 arm64 1.21.3-3 [40.3 kB] Get: 57 http://deb.debian.org/debian unstable/main arm64 libkdb5-10t64 arm64 1.21.3-3 [40.8 kB] Get: 58 http://deb.debian.org/debian unstable/main arm64 libkadm5srv-mit12 arm64 1.21.3-3 [52.2 kB] Get: 59 http://deb.debian.org/debian unstable/main arm64 krb5-multidev arm64 1.21.3-3 [126 kB] Get: 60 http://deb.debian.org/debian unstable/main arm64 libboost1.83-dev arm64 1.83.0-3.2+b1 [10.6 MB] Get: 61 http://deb.debian.org/debian unstable/main arm64 libboost-dev arm64 1.83.0.2+b2 [3828 B] Get: 62 http://deb.debian.org/debian unstable/main arm64 libbrotli-dev arm64 1.1.0-2+b6 [308 kB] Get: 63 http://deb.debian.org/debian unstable/main arm64 libbz2-dev arm64 1.0.8-6 [31.9 kB] Get: 64 http://deb.debian.org/debian unstable/main arm64 libnghttp3-9 arm64 1.4.0-1+b1 [59.6 kB] Get: 65 http://deb.debian.org/debian unstable/main arm64 libngtcp2-16 arm64 1.6.0-1 [112 kB] Get: 66 http://deb.debian.org/debian unstable/main arm64 libngtcp2-crypto-gnutls8 arm64 1.6.0-1 [18.5 kB] Get: 67 http://deb.debian.org/debian unstable/main arm64 libcurl3t64-gnutls arm64 8.11.0-1 [331 kB] Get: 68 http://deb.debian.org/debian unstable/main arm64 libevent-2.1-7t64 arm64 2.1.12-stable-10+b1 [170 kB] Get: 69 http://deb.debian.org/debian unstable/main arm64 libunbound8 arm64 1.22.0-1 [553 kB] Get: 70 http://deb.debian.org/debian unstable/main arm64 libgnutls-dane0t64 arm64 3.8.8-2 [446 kB] Get: 71 http://deb.debian.org/debian unstable/main arm64 libgnutls-openssl27t64 arm64 3.8.8-2 [446 kB] Get: 72 http://deb.debian.org/debian unstable/main arm64 libidn2-dev arm64 2.3.7-2+b1 [122 kB] Get: 73 http://deb.debian.org/debian unstable/main arm64 libp11-kit-dev arm64 0.25.5-2+b1 [208 kB] Get: 74 http://deb.debian.org/debian unstable/main arm64 libtasn1-6-dev arm64 4.19.0-3+b3 [96.5 kB] Get: 75 http://deb.debian.org/debian unstable/main arm64 libgmpxx4ldbl arm64 2:6.3.0+dfsg-2+b2 [329 kB] Get: 76 http://deb.debian.org/debian unstable/main arm64 libgmp-dev arm64 2:6.3.0+dfsg-2+b2 [621 kB] Get: 77 http://deb.debian.org/debian unstable/main arm64 nettle-dev arm64 3.10-1+b1 [1324 kB] Get: 78 http://deb.debian.org/debian unstable/main arm64 libgnutls28-dev arm64 3.8.8-2 [1404 kB] Get: 79 http://deb.debian.org/debian unstable/main arm64 libkrb5-dev arm64 1.21.3-3 [15.8 kB] Get: 80 http://deb.debian.org/debian unstable/main arm64 libldap-dev arm64 2.5.18+dfsg-3+b1 [300 kB] Get: 81 http://deb.debian.org/debian unstable/main arm64 libpkgconf3 arm64 1.8.1-4 [35.3 kB] Get: 82 http://deb.debian.org/debian unstable/main arm64 pkgconf-bin arm64 1.8.1-4 [29.6 kB] Get: 83 http://deb.debian.org/debian unstable/main arm64 pkgconf arm64 1.8.1-4 [26.1 kB] Get: 84 http://deb.debian.org/debian unstable/main arm64 libnghttp2-dev arm64 1.64.0-1 [112 kB] Get: 85 http://deb.debian.org/debian unstable/main arm64 libnghttp3-dev arm64 1.4.0-1+b1 [85.2 kB] Get: 86 http://deb.debian.org/debian unstable/main arm64 libngtcp2-crypto-gnutls-dev arm64 1.6.0-1 [23.7 kB] Get: 87 http://deb.debian.org/debian unstable/main arm64 libngtcp2-dev arm64 1.6.0-1 [165 kB] Get: 88 http://deb.debian.org/debian unstable/main arm64 libpsl-dev arm64 0.21.2-1.1+b1 [77.9 kB] Get: 89 http://deb.debian.org/debian unstable/main arm64 zlib1g-dev arm64 1:1.3.dfsg+really1.3.1-1+b1 [917 kB] Get: 90 http://deb.debian.org/debian unstable/main arm64 librtmp-dev arm64 2.4+20151223.gitfa8646d.1-2+b5 [67.5 kB] Get: 91 http://deb.debian.org/debian unstable/main arm64 libssl-dev arm64 3.3.2-2 [3185 kB] Get: 92 http://deb.debian.org/debian unstable/main arm64 libssh2-1-dev arm64 1.11.1-1 [388 kB] Get: 93 http://deb.debian.org/debian unstable/main arm64 libzstd-dev arm64 1.5.6+dfsg-1+b1 [329 kB] Get: 94 http://deb.debian.org/debian unstable/main arm64 libcurl4-gnutls-dev arm64 8.11.0-1 [459 kB] Get: 95 http://deb.debian.org/debian unstable/main arm64 libdeflate0 arm64 1.22-1 [42.2 kB] Get: 96 http://deb.debian.org/debian unstable/main arm64 libdeflate-dev arm64 1.22-1 [51.2 kB] Get: 97 http://deb.debian.org/debian unstable/main arm64 libdivsufsort3 arm64 2.0.1-6+b1 [39.9 kB] Get: 98 http://deb.debian.org/debian unstable/main arm64 libdivsufsort-dev arm64 2.0.1-6+b1 [19.1 kB] Get: 99 http://deb.debian.org/debian unstable/main arm64 libhtscodecs2 arm64 1.6.1-1 [74.6 kB] Get: 100 http://deb.debian.org/debian unstable/main arm64 libhts3t64 arm64 1.20+ds-2 [420 kB] Get: 101 http://deb.debian.org/debian unstable/main arm64 liblzma-dev arm64 5.6.3-1+b1 [312 kB] Get: 102 http://deb.debian.org/debian unstable/main arm64 libhts-dev arm64 1.20+ds-2 [1626 kB] Get: 103 http://deb.debian.org/debian experimental/main arm64 libseqan2-dev all 2.5.0~rc3+dfsg-1 [1222 kB] Get: 104 http://deb.debian.org/debian unstable/main arm64 libtclap-dev arm64 1.2.5-1+b1 [3359 kB] Fetched 66.0 MB in 1s (109 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libproc2-0:arm64. (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 ... 20083 files and directories currently installed.) Preparing to unpack .../000-libproc2-0_2%3a4.0.4-6_arm64.deb ... Unpacking libproc2-0:arm64 (2:4.0.4-6) ... Selecting previously unselected package procps. Preparing to unpack .../001-procps_2%3a4.0.4-6_arm64.deb ... Unpacking procps (2:4.0.4-6) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../002-sensible-utils_0.0.24_all.deb ... Unpacking sensible-utils (0.0.24) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../003-libmagic-mgc_1%3a5.45-3+b1_arm64.deb ... Unpacking libmagic-mgc (1:5.45-3+b1) ... Selecting previously unselected package libmagic1t64:arm64. Preparing to unpack .../004-libmagic1t64_1%3a5.45-3+b1_arm64.deb ... Unpacking libmagic1t64:arm64 (1:5.45-3+b1) ... Selecting previously unselected package file. Preparing to unpack .../005-file_1%3a5.45-3+b1_arm64.deb ... Unpacking file (1:5.45-3+b1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../006-gettext-base_0.22.5-2_arm64.deb ... Unpacking gettext-base (0.22.5-2) ... Selecting previously unselected package libuchardet0:arm64. Preparing to unpack .../007-libuchardet0_0.0.8-1+b2_arm64.deb ... Unpacking libuchardet0:arm64 (0.0.8-1+b2) ... Selecting previously unselected package groff-base. Preparing to unpack .../008-groff-base_1.23.0-5_arm64.deb ... Unpacking groff-base (1.23.0-5) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../009-bsdextrautils_2.40.2-11_arm64.deb ... Unpacking bsdextrautils (2.40.2-11) ... Selecting previously unselected package libpipeline1:arm64. Preparing to unpack .../010-libpipeline1_1.5.8-1_arm64.deb ... Unpacking libpipeline1:arm64 (1.5.8-1) ... Selecting previously unselected package man-db. Preparing to unpack .../011-man-db_2.13.0-1_arm64.deb ... Unpacking man-db (2.13.0-1) ... Selecting previously unselected package m4. Preparing to unpack .../012-m4_1.4.19-4_arm64.deb ... Unpacking m4 (1.4.19-4) ... Selecting previously unselected package autoconf. Preparing to unpack .../013-autoconf_2.72-3_all.deb ... Unpacking autoconf (2.72-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../014-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../015-automake_1%3a1.16.5-1.3_all.deb ... Unpacking automake (1:1.16.5-1.3) ... Selecting previously unselected package autopoint. Preparing to unpack .../016-autopoint_0.22.5-2_all.deb ... Unpacking autopoint (0.22.5-2) ... Selecting previously unselected package cmake-data. Preparing to unpack .../017-cmake-data_3.31.1-1_all.deb ... Unpacking cmake-data (3.31.1-1) ... Selecting previously unselected package libicu72:arm64. Preparing to unpack .../018-libicu72_72.1-5+b1_arm64.deb ... Unpacking libicu72:arm64 (72.1-5+b1) ... Selecting previously unselected package libxml2:arm64. Preparing to unpack .../019-libxml2_2.12.7+dfsg+really2.9.14-0.2+b1_arm64.deb ... Unpacking libxml2:arm64 (2.12.7+dfsg+really2.9.14-0.2+b1) ... Selecting previously unselected package libarchive13t64:arm64. Preparing to unpack .../020-libarchive13t64_3.7.4-1.1_arm64.deb ... Unpacking libarchive13t64:arm64 (3.7.4-1.1) ... Selecting previously unselected package libbrotli1:arm64. Preparing to unpack .../021-libbrotli1_1.1.0-2+b6_arm64.deb ... Unpacking libbrotli1:arm64 (1.1.0-2+b6) ... Selecting previously unselected package libkrb5support0:arm64. Preparing to unpack .../022-libkrb5support0_1.21.3-3_arm64.deb ... Unpacking libkrb5support0:arm64 (1.21.3-3) ... Selecting previously unselected package libcom-err2:arm64. Preparing to unpack .../023-libcom-err2_1.47.1-1+b1_arm64.deb ... Unpacking libcom-err2:arm64 (1.47.1-1+b1) ... Selecting previously unselected package libk5crypto3:arm64. Preparing to unpack .../024-libk5crypto3_1.21.3-3_arm64.deb ... Unpacking libk5crypto3:arm64 (1.21.3-3) ... Selecting previously unselected package libkeyutils1:arm64. Preparing to unpack .../025-libkeyutils1_1.6.3-4_arm64.deb ... Unpacking libkeyutils1:arm64 (1.6.3-4) ... Selecting previously unselected package libkrb5-3:arm64. Preparing to unpack .../026-libkrb5-3_1.21.3-3_arm64.deb ... Unpacking libkrb5-3:arm64 (1.21.3-3) ... Selecting previously unselected package libgssapi-krb5-2:arm64. Preparing to unpack .../027-libgssapi-krb5-2_1.21.3-3_arm64.deb ... Unpacking libgssapi-krb5-2:arm64 (1.21.3-3) ... Selecting previously unselected package libsasl2-modules-db:arm64. Preparing to unpack .../028-libsasl2-modules-db_2.1.28+dfsg1-8_arm64.deb ... Unpacking libsasl2-modules-db:arm64 (2.1.28+dfsg1-8) ... Selecting previously unselected package libsasl2-2:arm64. Preparing to unpack .../029-libsasl2-2_2.1.28+dfsg1-8_arm64.deb ... Unpacking libsasl2-2:arm64 (2.1.28+dfsg1-8) ... Selecting previously unselected package libldap-2.5-0:arm64. Preparing to unpack .../030-libldap-2.5-0_2.5.18+dfsg-3+b1_arm64.deb ... Unpacking libldap-2.5-0:arm64 (2.5.18+dfsg-3+b1) ... Selecting previously unselected package libnghttp2-14:arm64. Preparing to unpack .../031-libnghttp2-14_1.64.0-1_arm64.deb ... Unpacking libnghttp2-14:arm64 (1.64.0-1) ... Selecting previously unselected package libpsl5t64:arm64. Preparing to unpack .../032-libpsl5t64_0.21.2-1.1+b1_arm64.deb ... Unpacking libpsl5t64:arm64 (0.21.2-1.1+b1) ... Selecting previously unselected package librtmp1:arm64. Preparing to unpack .../033-librtmp1_2.4+20151223.gitfa8646d.1-2+b5_arm64.deb ... Unpacking librtmp1:arm64 (2.4+20151223.gitfa8646d.1-2+b5) ... Selecting previously unselected package libssh2-1t64:arm64. Preparing to unpack .../034-libssh2-1t64_1.11.1-1_arm64.deb ... Unpacking libssh2-1t64:arm64 (1.11.1-1) ... Selecting previously unselected package libcurl4t64:arm64. Preparing to unpack .../035-libcurl4t64_8.11.0-1_arm64.deb ... Unpacking libcurl4t64:arm64 (8.11.0-1) ... Selecting previously unselected package libexpat1:arm64. Preparing to unpack .../036-libexpat1_2.6.4-1_arm64.deb ... Unpacking libexpat1:arm64 (2.6.4-1) ... Selecting previously unselected package libjsoncpp26:arm64. Preparing to unpack .../037-libjsoncpp26_1.9.6-3_arm64.deb ... Unpacking libjsoncpp26:arm64 (1.9.6-3) ... Selecting previously unselected package librhash1:arm64. Preparing to unpack .../038-librhash1_1.4.5-1_arm64.deb ... Unpacking librhash1:arm64 (1.4.5-1) ... Selecting previously unselected package libuv1t64:arm64. Preparing to unpack .../039-libuv1t64_1.48.0-7_arm64.deb ... Unpacking libuv1t64:arm64 (1.48.0-7) ... Selecting previously unselected package cmake. Preparing to unpack .../040-cmake_3.31.1-1_arm64.deb ... Unpacking cmake (3.31.1-1) ... Selecting previously unselected package comerr-dev:arm64. Preparing to unpack .../041-comerr-dev_2.1-1.47.1-1+b1_arm64.deb ... Unpacking comerr-dev:arm64 (2.1-1.47.1-1+b1) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../042-libdebhelper-perl_13.20_all.deb ... Unpacking libdebhelper-perl (13.20) ... Selecting previously unselected package libtool. Preparing to unpack .../043-libtool_2.4.7-8_all.deb ... Unpacking libtool (2.4.7-8) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../044-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../045-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../046-libfile-stripnondeterminism-perl_1.14.0-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.14.0-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../047-dh-strip-nondeterminism_1.14.0-1_all.deb ... Unpacking dh-strip-nondeterminism (1.14.0-1) ... Selecting previously unselected package libelf1t64:arm64. Preparing to unpack .../048-libelf1t64_0.192-4_arm64.deb ... Unpacking libelf1t64:arm64 (0.192-4) ... Selecting previously unselected package dwz. Preparing to unpack .../049-dwz_0.15-1+b1_arm64.deb ... Unpacking dwz (0.15-1+b1) ... Selecting previously unselected package gettext. Preparing to unpack .../050-gettext_0.22.5-2_arm64.deb ... Unpacking gettext (0.22.5-2) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../051-intltool-debian_0.35.0+20060710.6_all.deb ... Unpacking intltool-debian (0.35.0+20060710.6) ... Selecting previously unselected package po-debconf. Preparing to unpack .../052-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../053-debhelper_13.20_all.deb ... Unpacking debhelper (13.20) ... Selecting previously unselected package libgssrpc4t64:arm64. Preparing to unpack .../054-libgssrpc4t64_1.21.3-3_arm64.deb ... Unpacking libgssrpc4t64:arm64 (1.21.3-3) ... Selecting previously unselected package libkadm5clnt-mit12:arm64. Preparing to unpack .../055-libkadm5clnt-mit12_1.21.3-3_arm64.deb ... Unpacking libkadm5clnt-mit12:arm64 (1.21.3-3) ... Selecting previously unselected package libkdb5-10t64:arm64. Preparing to unpack .../056-libkdb5-10t64_1.21.3-3_arm64.deb ... Unpacking libkdb5-10t64:arm64 (1.21.3-3) ... Selecting previously unselected package libkadm5srv-mit12:arm64. Preparing to unpack .../057-libkadm5srv-mit12_1.21.3-3_arm64.deb ... Unpacking libkadm5srv-mit12:arm64 (1.21.3-3) ... Selecting previously unselected package krb5-multidev:arm64. Preparing to unpack .../058-krb5-multidev_1.21.3-3_arm64.deb ... Unpacking krb5-multidev:arm64 (1.21.3-3) ... Selecting previously unselected package libboost1.83-dev:arm64. Preparing to unpack .../059-libboost1.83-dev_1.83.0-3.2+b1_arm64.deb ... Unpacking libboost1.83-dev:arm64 (1.83.0-3.2+b1) ... Selecting previously unselected package libboost-dev:arm64. Preparing to unpack .../060-libboost-dev_1.83.0.2+b2_arm64.deb ... Unpacking libboost-dev:arm64 (1.83.0.2+b2) ... Selecting previously unselected package libbrotli-dev:arm64. 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Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/reproducible-path/sibelia-3.0.7+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 > ../sibelia_3.0.7+dfsg-4_source.changes dpkg-buildpackage: info: source package sibelia dpkg-buildpackage: info: source version 3.0.7+dfsg-4 dpkg-buildpackage: info: source distribution experimental dpkg-buildpackage: info: source changed by Michael R. Crusoe dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 debian/rules clean dh clean --sourcedirectory=src dh_auto_clean -O--sourcedirectory=src dh_autoreconf_clean -O--sourcedirectory=src dh_clean -O--sourcedirectory=src debian/rules binary dh binary --sourcedirectory=src dh_update_autotools_config -O--sourcedirectory=src dh_autoreconf -O--sourcedirectory=src dh_auto_configure -O--sourcedirectory=src cd obj-aarch64-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 "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/aarch64-linux-gnu ../src 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 CXX compiler identification is GNU 14.2.0 -- 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 -- Configuring done (0.6s) -- 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_FIND_USE_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/sibelia-3.0.7+dfsg/obj-aarch64-linux-gnu dh_auto_build -O--sourcedirectory=src cd obj-aarch64-linux-gnu && make -j12 "INSTALL=install --strip-program=true" VERBOSE=1 make[1]: Entering directory '/build/reproducible-path/sibelia-3.0.7+dfsg/obj-aarch64-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/sibelia-3.0.7+dfsg/src -B/build/reproducible-path/sibelia-3.0.7+dfsg/obj-aarch64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/sibelia-3.0.7+dfsg/obj-aarch64-linux-gnu/CMakeFiles /build/reproducible-path/sibelia-3.0.7+dfsg/obj-aarch64-linux-gnu//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/build/reproducible-path/sibelia-3.0.7+dfsg/obj-aarch64-linux-gnu' make -f CMakeFiles/Sibelia.dir/build.make CMakeFiles/Sibelia.dir/depend make[3]: Entering directory '/build/reproducible-path/sibelia-3.0.7+dfsg/obj-aarch64-linux-gnu' cd /build/reproducible-path/sibelia-3.0.7+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sibelia-3.0.7+dfsg/src /build/reproducible-path/sibelia-3.0.7+dfsg/src /build/reproducible-path/sibelia-3.0.7+dfsg/obj-aarch64-linux-gnu /build/reproducible-path/sibelia-3.0.7+dfsg/obj-aarch64-linux-gnu /build/reproducible-path/sibelia-3.0.7+dfsg/obj-aarch64-linux-gnu/CMakeFiles/Sibelia.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/sibelia-3.0.7+dfsg/obj-aarch64-linux-gnu' make -f CMakeFiles/Sibelia.dir/build.make CMakeFiles/Sibelia.dir/build make[3]: Entering directory '/build/reproducible-path/sibelia-3.0.7+dfsg/obj-aarch64-linux-gnu' [ 5%] Building CXX object CMakeFiles/Sibelia.dir/util.cpp.o /usr/bin/c++ -I/build/reproducible-path/sibelia-3.0.7+dfsg/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/sibelia-3.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -MD -MT CMakeFiles/Sibelia.dir/util.cpp.o -MF CMakeFiles/Sibelia.dir/util.cpp.o.d -o CMakeFiles/Sibelia.dir/util.cpp.o -c 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CMakeFiles/Sibelia.dir/outputgenerator.cpp.o -MF CMakeFiles/Sibelia.dir/outputgenerator.cpp.o.d -o CMakeFiles/Sibelia.dir/outputgenerator.cpp.o -c /build/reproducible-path/sibelia-3.0.7+dfsg/src/outputgenerator.cpp /usr/bin/c++ -I/build/reproducible-path/sibelia-3.0.7+dfsg/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/sibelia-3.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -MD -MT CMakeFiles/Sibelia.dir/blockinstance.cpp.o -MF CMakeFiles/Sibelia.dir/blockinstance.cpp.o.d -o CMakeFiles/Sibelia.dir/blockinstance.cpp.o -c /build/reproducible-path/sibelia-3.0.7+dfsg/src/blockinstance.cpp /usr/bin/c++ -I/build/reproducible-path/sibelia-3.0.7+dfsg/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/sibelia-3.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -MD -MT CMakeFiles/Sibelia.dir/dnasequence.cpp.o -MF CMakeFiles/Sibelia.dir/dnasequence.cpp.o.d -o CMakeFiles/Sibelia.dir/dnasequence.cpp.o -c /build/reproducible-path/sibelia-3.0.7+dfsg/src/dnasequence.cpp [ 45%] Building CXX object CMakeFiles/Sibelia.dir/sibelia.cpp.o [ 50%] Building CXX object CMakeFiles/Sibelia.dir/fasta.cpp.o [ 55%] Building CXX object CMakeFiles/Sibelia.dir/edge.cpp.o /usr/bin/c++ -I/build/reproducible-path/sibelia-3.0.7+dfsg/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/sibelia-3.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -MD -MT CMakeFiles/Sibelia.dir/fasta.cpp.o -MF CMakeFiles/Sibelia.dir/fasta.cpp.o.d -o CMakeFiles/Sibelia.dir/fasta.cpp.o -c /build/reproducible-path/sibelia-3.0.7+dfsg/src/fasta.cpp /usr/bin/c++ -I/build/reproducible-path/sibelia-3.0.7+dfsg/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/sibelia-3.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -MD -MT CMakeFiles/Sibelia.dir/sibelia.cpp.o -MF CMakeFiles/Sibelia.dir/sibelia.cpp.o.d -o CMakeFiles/Sibelia.dir/sibelia.cpp.o -c /build/reproducible-path/sibelia-3.0.7+dfsg/src/sibelia.cpp /usr/bin/c++ -I/build/reproducible-path/sibelia-3.0.7+dfsg/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/sibelia-3.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -MD -MT CMakeFiles/Sibelia.dir/edge.cpp.o -MF CMakeFiles/Sibelia.dir/edge.cpp.o.d -o CMakeFiles/Sibelia.dir/edge.cpp.o -c /build/reproducible-path/sibelia-3.0.7+dfsg/src/edge.cpp [ 60%] Building CXX object CMakeFiles/Sibelia.dir/bifurcationstorage.cpp.o /usr/bin/c++ -I/build/reproducible-path/sibelia-3.0.7+dfsg/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/sibelia-3.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -MD -MT CMakeFiles/Sibelia.dir/bifurcationstorage.cpp.o -MF CMakeFiles/Sibelia.dir/bifurcationstorage.cpp.o.d -o CMakeFiles/Sibelia.dir/bifurcationstorage.cpp.o -c /build/reproducible-path/sibelia-3.0.7+dfsg/src/bifurcationstorage.cpp In file included from /usr/include/boost/bind/detail/requires_cxx11.hpp:9, from /usr/include/boost/bind/bind.hpp:24, from /usr/include/boost/bind.hpp:29, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:31, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/blockinstance.h:10, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/blockfinder.h:10, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/blockfinder.cpp:7: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/bind/detail/requires_cxx11.hpp:9, from /usr/include/boost/bind/bind.hpp:24, from /usr/include/boost/bind.hpp:29, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:31, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/blockinstance.h:10, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/blockinstance.cpp:7: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/bind/detail/requires_cxx11.hpp:9, from /usr/include/boost/bind/bind.hpp:24, from /usr/include/boost/bind.hpp:29, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:31, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/fasta.h:10, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/dnasequence.h:10, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/dnasequence.cpp:7: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/bind/detail/requires_cxx11.hpp:9, from /usr/include/boost/bind/bind.hpp:24, from /usr/include/boost/bind.hpp:29, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:31, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/blockinstance.h:10, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/blockfinder.h:10, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/bulgeremoval.cpp:7: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/bind/detail/requires_cxx11.hpp:9, from /usr/include/boost/bind/bind.hpp:24, from /usr/include/boost/bind.hpp:29, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:31, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/blockinstance.h:10, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/blockfinder.h:10, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/edge.cpp:7: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/bind/detail/requires_cxx11.hpp:9, from /usr/include/boost/bind/bind.hpp:24, from /usr/include/boost/bind.hpp:29, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:31, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/blockinstance.h:10, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/blockfinder.h:10, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/util.h:10, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/outputgenerator.h:10, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/outputgenerator.cpp:9: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/bind/detail/requires_cxx11.hpp:9, from /usr/include/boost/bind/bind.hpp:24, from /usr/include/boost/bind.hpp:29, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:31, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/fasta.h:10, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/dnasequence.h:10, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/hashing.h:10, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/indexedsequence.h:10, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/indexedsequence.cpp:7: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/bind/detail/requires_cxx11.hpp:9, from /usr/include/boost/bind/bind.hpp:24, from /usr/include/boost/bind.hpp:29, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:31, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/blockinstance.h:10, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/blockfinder.h:10, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/util.h:10, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/util.cpp:7: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/bind/detail/requires_cxx11.hpp:9, from /usr/include/boost/bind/bind.hpp:24, from /usr/include/boost/bind.hpp:29, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:31, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/fasta.h:10, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/dnasequence.h:10, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/bifurcationstorage.h:11, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/bifurcationstorage.cpp:7: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/bind/detail/requires_cxx11.hpp:9, from /usr/include/boost/bind/bind.hpp:24, from /usr/include/boost/bind.hpp:29, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:31, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/fasta.h:10, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/fasta.cpp:7: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:104:51: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 104 | struct FancyIterator: public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/14/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/14/string:47, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:12: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/sibelia-3.0.7+dfsg/src/dnasequence.h:12, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/blockinstance.h:11: /build/reproducible-path/sibelia-3.0.7+dfsg/src/unrolledlist.h:36:45: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 36 | class iterator: public std::iterator | ^~~~~~~~ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:104:51: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 104 | struct FancyIterator: public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/14/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/14/string:47, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:12: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/sibelia-3.0.7+dfsg/src/dnasequence.h:51:51: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 51 | class StrandIterator: public std::iterator | ^~~~~~~~ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:104:51: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 104 | struct FancyIterator: public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/14/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/14/string:47, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:12: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/sibelia-3.0.7+dfsg/src/dnasequence.h:12, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/blockinstance.h:11: /build/reproducible-path/sibelia-3.0.7+dfsg/src/unrolledlist.h:36:45: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 36 | class iterator: public std::iterator | ^~~~~~~~ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/sibelia-3.0.7+dfsg/src/dnasequence.h:12: /build/reproducible-path/sibelia-3.0.7+dfsg/src/unrolledlist.h:36:45: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 36 | class iterator: public std::iterator | ^~~~~~~~ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/sibelia-3.0.7+dfsg/src/dnasequence.h:51:51: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 51 | class StrandIterator: public std::iterator | ^~~~~~~~ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:104:51: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 104 | struct FancyIterator: public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/14/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/14/string:47, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:12: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/sibelia-3.0.7+dfsg/src/dnasequence.h:51:51: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 51 | class StrandIterator: public std::iterator | ^~~~~~~~ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/sibelia-3.0.7+dfsg/src/dnasequence.h:12: /build/reproducible-path/sibelia-3.0.7+dfsg/src/unrolledlist.h:36:45: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 36 | class iterator: public std::iterator | ^~~~~~~~ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:104:51: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 104 | struct FancyIterator: public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/14/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/14/string:47, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:12: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/sibelia-3.0.7+dfsg/src/dnasequence.h:51:51: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 51 | class StrandIterator: public std::iterator | ^~~~~~~~ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/sibelia-3.0.7+dfsg/src/dnasequence.h:12, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/blockinstance.h:11: /build/reproducible-path/sibelia-3.0.7+dfsg/src/unrolledlist.h:36:45: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 36 | class iterator: public std::iterator | ^~~~~~~~ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/sibelia-3.0.7+dfsg/src/dnasequence.h:51:51: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 51 | class StrandIterator: public std::iterator | ^~~~~~~~ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:104:51: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 104 | struct FancyIterator: public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/14/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/14/string:47, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:12: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/sibelia-3.0.7+dfsg/src/dnasequence.h:12, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/blockinstance.h:11: /build/reproducible-path/sibelia-3.0.7+dfsg/src/unrolledlist.h:36:45: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 36 | class iterator: public std::iterator | ^~~~~~~~ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:104:51: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 104 | struct FancyIterator: public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/14/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/14/string:47, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:12: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/sibelia-3.0.7+dfsg/src/blockfinder.h:11: /build/reproducible-path/sibelia-3.0.7+dfsg/src/indexedsequence.h:37:22: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 37 | std::auto_ptr sequence_; | ^~~~~~~~ In file included from /usr/include/c++/14/memory:78, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:20: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ /build/reproducible-path/sibelia-3.0.7+dfsg/src/indexedsequence.h:38:22: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 38 | std::auto_ptr bifStorage_; | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ /build/reproducible-path/sibelia-3.0.7+dfsg/src/dnasequence.h:51:51: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 51 | class StrandIterator: public std::iterator | ^~~~~~~~ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/sibelia-3.0.7+dfsg/src/dnasequence.h:12, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/blockinstance.h:11: /build/reproducible-path/sibelia-3.0.7+dfsg/src/unrolledlist.h:36:45: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 36 | class iterator: public std::iterator | ^~~~~~~~ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/sibelia-3.0.7+dfsg/src/dnasequence.h:51:51: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 51 | class StrandIterator: public std::iterator | ^~~~~~~~ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:104:51: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 104 | struct FancyIterator: public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/14/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/14/string:47, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:12: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/sibelia-3.0.7+dfsg/src/dnasequence.h:12, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/blockinstance.h:11: /build/reproducible-path/sibelia-3.0.7+dfsg/src/unrolledlist.h:36:45: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 36 | class iterator: public std::iterator | ^~~~~~~~ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/sibelia-3.0.7+dfsg/src/indexedsequence.h:37:22: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 37 | std::auto_ptr sequence_; | ^~~~~~~~ In file included from /usr/include/c++/14/memory:78, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:20: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ /build/reproducible-path/sibelia-3.0.7+dfsg/src/indexedsequence.h:38:22: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 38 | std::auto_ptr bifStorage_; | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ /build/reproducible-path/sibelia-3.0.7+dfsg/src/dnasequence.h:51:51: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 51 | class StrandIterator: public std::iterator | ^~~~~~~~ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:104:51: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 104 | struct FancyIterator: public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/14/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/14/string:47, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:12: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/sibelia-3.0.7+dfsg/src/dnasequence.h:12: /build/reproducible-path/sibelia-3.0.7+dfsg/src/unrolledlist.h:36:45: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 36 | class iterator: public std::iterator | ^~~~~~~~ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/sibelia-3.0.7+dfsg/src/dnasequence.h:51:51: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 51 | class StrandIterator: public std::iterator | ^~~~~~~~ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/sibelia-3.0.7+dfsg/src/blockfinder.h:11: /build/reproducible-path/sibelia-3.0.7+dfsg/src/indexedsequence.h:37:22: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 37 | std::auto_ptr sequence_; | ^~~~~~~~ In file included from /usr/include/c++/14/memory:78, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:20: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ /build/reproducible-path/sibelia-3.0.7+dfsg/src/indexedsequence.h:38:22: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 38 | std::auto_ptr bifStorage_; | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from /build/reproducible-path/sibelia-3.0.7+dfsg/src/blockfinder.h:11: /build/reproducible-path/sibelia-3.0.7+dfsg/src/indexedsequence.h:37:22: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 37 | std::auto_ptr sequence_; | ^~~~~~~~ In file included from /usr/include/c++/14/memory:78, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:20: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ /build/reproducible-path/sibelia-3.0.7+dfsg/src/indexedsequence.h:38:22: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 38 | std::auto_ptr bifStorage_; | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from /build/reproducible-path/sibelia-3.0.7+dfsg/src/blockfinder.h:11: /build/reproducible-path/sibelia-3.0.7+dfsg/src/indexedsequence.h:37:22: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 37 | std::auto_ptr sequence_; | ^~~~~~~~ In file included from /usr/include/c++/14/memory:78, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:20: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ /build/reproducible-path/sibelia-3.0.7+dfsg/src/indexedsequence.h:38:22: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 38 | std::auto_ptr bifStorage_; | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from /build/reproducible-path/sibelia-3.0.7+dfsg/src/blockfinder.h:11: /build/reproducible-path/sibelia-3.0.7+dfsg/src/indexedsequence.h:37:22: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 37 | std::auto_ptr sequence_; | ^~~~~~~~ In file included from /usr/include/c++/14/memory:78, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:20: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ /build/reproducible-path/sibelia-3.0.7+dfsg/src/indexedsequence.h:38:22: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 38 | std::auto_ptr bifStorage_; | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:104:51: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 104 | struct FancyIterator: public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/14/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/14/string:47, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:12: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 65%] Building CXX object CMakeFiles/Sibelia.dir/serialization.cpp.o /usr/bin/c++ -I/build/reproducible-path/sibelia-3.0.7+dfsg/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/sibelia-3.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -MD -MT CMakeFiles/Sibelia.dir/serialization.cpp.o -MF CMakeFiles/Sibelia.dir/serialization.cpp.o.d -o CMakeFiles/Sibelia.dir/serialization.cpp.o -c /build/reproducible-path/sibelia-3.0.7+dfsg/src/serialization.cpp [ 70%] Building CXX object CMakeFiles/Sibelia.dir/synteny.cpp.o /usr/bin/c++ -I/build/reproducible-path/sibelia-3.0.7+dfsg/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/sibelia-3.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -MD -MT CMakeFiles/Sibelia.dir/synteny.cpp.o -MF CMakeFiles/Sibelia.dir/synteny.cpp.o.d -o CMakeFiles/Sibelia.dir/synteny.cpp.o -c /build/reproducible-path/sibelia-3.0.7+dfsg/src/synteny.cpp [ 75%] Building CXX object CMakeFiles/Sibelia.dir/test/unrolledlisttest.cpp.o /usr/bin/c++ -I/build/reproducible-path/sibelia-3.0.7+dfsg/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/sibelia-3.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -MD -MT CMakeFiles/Sibelia.dir/test/unrolledlisttest.cpp.o -MF CMakeFiles/Sibelia.dir/test/unrolledlisttest.cpp.o.d -o CMakeFiles/Sibelia.dir/test/unrolledlisttest.cpp.o -c /build/reproducible-path/sibelia-3.0.7+dfsg/src/test/unrolledlisttest.cpp [ 80%] Building CXX object CMakeFiles/Sibelia.dir/platform.cpp.o /usr/bin/c++ -I/build/reproducible-path/sibelia-3.0.7+dfsg/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/sibelia-3.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -MD -MT CMakeFiles/Sibelia.dir/platform.cpp.o -MF CMakeFiles/Sibelia.dir/platform.cpp.o.d -o CMakeFiles/Sibelia.dir/platform.cpp.o -c /build/reproducible-path/sibelia-3.0.7+dfsg/src/platform.cpp [ 85%] Building CXX object CMakeFiles/Sibelia.dir/stranditerator.cpp.o /usr/bin/c++ -I/build/reproducible-path/sibelia-3.0.7+dfsg/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/sibelia-3.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -MD -MT CMakeFiles/Sibelia.dir/stranditerator.cpp.o -MF CMakeFiles/Sibelia.dir/stranditerator.cpp.o.d -o CMakeFiles/Sibelia.dir/stranditerator.cpp.o -c /build/reproducible-path/sibelia-3.0.7+dfsg/src/stranditerator.cpp [ 90%] Building CXX object CMakeFiles/Sibelia.dir/vertexenumeration.cpp.o /usr/bin/c++ -I/build/reproducible-path/sibelia-3.0.7+dfsg/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/sibelia-3.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -MD -MT CMakeFiles/Sibelia.dir/vertexenumeration.cpp.o -MF CMakeFiles/Sibelia.dir/vertexenumeration.cpp.o.d -o CMakeFiles/Sibelia.dir/vertexenumeration.cpp.o -c /build/reproducible-path/sibelia-3.0.7+dfsg/src/vertexenumeration.cpp In file included from /usr/include/boost/bind/detail/requires_cxx11.hpp:9, from /usr/include/boost/bind/bind.hpp:24, from /usr/include/boost/bind.hpp:29, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:31, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/blockinstance.h:10, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/blockfinder.h:10, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/serialization.cpp:7: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/bind/detail/requires_cxx11.hpp:9, from /usr/include/boost/bind/bind.hpp:24, from /usr/include/boost/bind.hpp:29, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/test/../common.h:31, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/test/unrolledlisttest.h:10, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/test/unrolledlisttest.cpp:7: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/bind/detail/requires_cxx11.hpp:9, from /usr/include/boost/bind/bind.hpp:24, from /usr/include/boost/bind.hpp:29, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:31, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/blockinstance.h:10, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/blockfinder.h:10, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/synteny.cpp:9: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/sibelia-3.0.7+dfsg/src/test/../common.h:104:51: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 104 | struct FancyIterator: public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/14/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/14/string:47, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/test/../common.h:12: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/sibelia-3.0.7+dfsg/src/test/unrolledlisttest.h:11: /build/reproducible-path/sibelia-3.0.7+dfsg/src/test/../unrolledlist.h:36:45: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 36 | class iterator: public std::iterator | ^~~~~~~~ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:104:51: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 104 | struct FancyIterator: public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/14/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/14/string:47, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:12: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/sibelia-3.0.7+dfsg/src/dnasequence.h:12, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/blockinstance.h:11: /build/reproducible-path/sibelia-3.0.7+dfsg/src/unrolledlist.h:36:45: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 36 | class iterator: public std::iterator | ^~~~~~~~ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/sibelia-3.0.7+dfsg/src/dnasequence.h:51:51: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 51 | class StrandIterator: public std::iterator | ^~~~~~~~ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 95%] Building CXX object CMakeFiles/Sibelia.dir/resource.cpp.o /usr/bin/c++ -I/build/reproducible-path/sibelia-3.0.7+dfsg/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/sibelia-3.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -MD -MT CMakeFiles/Sibelia.dir/resource.cpp.o -MF CMakeFiles/Sibelia.dir/resource.cpp.o.d -o CMakeFiles/Sibelia.dir/resource.cpp.o -c /build/reproducible-path/sibelia-3.0.7+dfsg/src/resource.cpp /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:104:51: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 104 | struct FancyIterator: public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/14/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/14/string:47, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:12: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/sibelia-3.0.7+dfsg/src/dnasequence.h:12, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/blockinstance.h:11: /build/reproducible-path/sibelia-3.0.7+dfsg/src/unrolledlist.h:36:45: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 36 | class iterator: public std::iterator | ^~~~~~~~ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/sibelia-3.0.7+dfsg/src/dnasequence.h:51:51: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 51 | class StrandIterator: public std::iterator | ^~~~~~~~ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/sibelia-3.0.7+dfsg/src/blockfinder.h:11: /build/reproducible-path/sibelia-3.0.7+dfsg/src/indexedsequence.h:37:22: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 37 | std::auto_ptr sequence_; | ^~~~~~~~ In file included from /usr/include/c++/14/memory:78, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:20: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ /build/reproducible-path/sibelia-3.0.7+dfsg/src/indexedsequence.h:38:22: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 38 | std::auto_ptr bifStorage_; | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from /build/reproducible-path/sibelia-3.0.7+dfsg/src/blockfinder.h:11: /build/reproducible-path/sibelia-3.0.7+dfsg/src/indexedsequence.h:37:22: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 37 | std::auto_ptr sequence_; | ^~~~~~~~ In file included from /usr/include/c++/14/memory:78, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:20: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ /build/reproducible-path/sibelia-3.0.7+dfsg/src/indexedsequence.h:38:22: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 38 | std::auto_ptr bifStorage_; | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from /usr/include/boost/bind/detail/requires_cxx11.hpp:9, from /usr/include/boost/bind/bind.hpp:24, from /usr/include/boost/bind.hpp:29, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:31, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/fasta.h:10, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/postprocessor.h:13, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/postprocessor.cpp:9: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/bind/detail/requires_cxx11.hpp:9, from /usr/include/boost/bind/bind.hpp:24, from /usr/include/boost/bind.hpp:29, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:31, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/platform.h:10, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/platform.cpp:7: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/bind/detail/requires_cxx11.hpp:9, from /usr/include/boost/bind/bind.hpp:24, from /usr/include/boost/bind.hpp:29, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:31, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/fasta.h:10, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/dnasequence.h:10, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/stranditerator.cpp:7: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:104:51: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 104 | struct FancyIterator: public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/14/bits/stl_algobase.h:65, from /usr/include/c++/14/algorithm:60, from /usr/include/seqan/align.h:53, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/postprocessor.h:10: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/sibelia-3.0.7+dfsg/src/dnasequence.h:12, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/blockinstance.h:11, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/postprocessor.h:14: /build/reproducible-path/sibelia-3.0.7+dfsg/src/unrolledlist.h:36:45: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 36 | class iterator: public std::iterator | ^~~~~~~~ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/sibelia-3.0.7+dfsg/src/dnasequence.h:51:51: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 51 | class StrandIterator: public std::iterator | ^~~~~~~~ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /usr/include/boost/bind/detail/requires_cxx11.hpp:9, from /usr/include/boost/bind/bind.hpp:24, from /usr/include/boost/bind.hpp:29, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:31, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/fasta.h:10, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/dnasequence.h:10, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/hashing.h:10, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/indexedsequence.h:10, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/vertexenumeration.cpp:7: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:104:51: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 104 | struct FancyIterator: public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/14/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/14/string:47, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:12: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /usr/include/boost/bind/detail/requires_cxx11.hpp:9, from /usr/include/boost/bind/bind.hpp:24, from /usr/include/boost/bind.hpp:29, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:31, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/fasta.h:10, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/postprocessor.h:13, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/sibelia.cpp:8: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:104:51: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 104 | struct FancyIterator: public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/14/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/14/string:47, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:12: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/sibelia-3.0.7+dfsg/src/dnasequence.h:12: /build/reproducible-path/sibelia-3.0.7+dfsg/src/unrolledlist.h:36:45: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 36 | class iterator: public std::iterator | ^~~~~~~~ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/sibelia-3.0.7+dfsg/src/dnasequence.h:51:51: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 51 | class StrandIterator: public std::iterator | ^~~~~~~~ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:104:51: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 104 | struct FancyIterator: public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/14/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/14/string:47, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:12: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/sibelia-3.0.7+dfsg/src/dnasequence.h:12: /build/reproducible-path/sibelia-3.0.7+dfsg/src/unrolledlist.h:36:45: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 36 | class iterator: public std::iterator | ^~~~~~~~ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/sibelia-3.0.7+dfsg/src/dnasequence.h:51:51: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 51 | class StrandIterator: public std::iterator | ^~~~~~~~ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/sibelia-3.0.7+dfsg/src/indexedsequence.h:37:22: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 37 | std::auto_ptr sequence_; | ^~~~~~~~ In file included from /usr/include/c++/14/memory:78, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:20: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ /build/reproducible-path/sibelia-3.0.7+dfsg/src/indexedsequence.h:38:22: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 38 | std::auto_ptr bifStorage_; | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from /usr/include/boost/bind/detail/requires_cxx11.hpp:9, from /usr/include/boost/bind/bind.hpp:24, from /usr/include/boost/bind.hpp:29, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:31, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/resource.h:6, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/resource.cpp:6: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:104:51: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 104 | struct FancyIterator: public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/14/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/14/string:47, from /usr/include/tclap/SwitchArg.h:29, from /usr/include/tclap/CmdLine.h:27, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/sibelia.cpp:7: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/sibelia-3.0.7+dfsg/src/dnasequence.h:12, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/blockinstance.h:11, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/postprocessor.h:14: /build/reproducible-path/sibelia-3.0.7+dfsg/src/unrolledlist.h:36:45: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 36 | class iterator: public std::iterator | ^~~~~~~~ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/sibelia-3.0.7+dfsg/src/dnasequence.h:51:51: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 51 | class StrandIterator: public std::iterator | ^~~~~~~~ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/sibelia-3.0.7+dfsg/src/blockfinder.h:11, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/util.h:10, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/sibelia.cpp:9: /build/reproducible-path/sibelia-3.0.7+dfsg/src/indexedsequence.h:37:22: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 37 | std::auto_ptr sequence_; | ^~~~~~~~ In file included from /usr/include/c++/14/memory:78, from /usr/include/seqan/basic/test_system.h:53, from /usr/include/seqan/basic.h:65, from /usr/include/seqan/align.h:55, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/postprocessor.h:10: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ /build/reproducible-path/sibelia-3.0.7+dfsg/src/indexedsequence.h:38:22: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 38 | std::auto_ptr bifStorage_; | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ /build/reproducible-path/sibelia-3.0.7+dfsg/src/sibelia.cpp: In function ‘int main(int, char**)’: /build/reproducible-path/sibelia-3.0.7+dfsg/src/sibelia.cpp:239:22: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 239 | std::auto_ptr finder(inRAM.isSet() ? new SyntenyFinder::BlockFinder(chrList) : new SyntenyFinder::BlockFinder(chrList, tempDir)); | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:104:51: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 104 | struct FancyIterator: public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/14/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/14/string:47, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:12: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [100%] Linking CXX executable Sibelia /usr/bin/cmake -E cmake_link_script CMakeFiles/Sibelia.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/sibelia-3.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file,CMakeFiles/Sibelia.dir/link.d CMakeFiles/Sibelia.dir/sibelia.cpp.o CMakeFiles/Sibelia.dir/postprocessor.cpp.o CMakeFiles/Sibelia.dir/indexedsequence.cpp.o CMakeFiles/Sibelia.dir/util.cpp.o CMakeFiles/Sibelia.dir/outputgenerator.cpp.o CMakeFiles/Sibelia.dir/blockfinder.cpp.o CMakeFiles/Sibelia.dir/blockinstance.cpp.o CMakeFiles/Sibelia.dir/bifurcationstorage.cpp.o CMakeFiles/Sibelia.dir/bulgeremoval.cpp.o CMakeFiles/Sibelia.dir/dnasequence.cpp.o CMakeFiles/Sibelia.dir/edge.cpp.o CMakeFiles/Sibelia.dir/fasta.cpp.o CMakeFiles/Sibelia.dir/serialization.cpp.o CMakeFiles/Sibelia.dir/synteny.cpp.o CMakeFiles/Sibelia.dir/test/unrolledlisttest.cpp.o CMakeFiles/Sibelia.dir/platform.cpp.o CMakeFiles/Sibelia.dir/stranditerator.cpp.o CMakeFiles/Sibelia.dir/vertexenumeration.cpp.o CMakeFiles/Sibelia.dir/resource.cpp.o -o Sibelia -ldivsufsort make[3]: Leaving directory '/build/reproducible-path/sibelia-3.0.7+dfsg/obj-aarch64-linux-gnu' [100%] Built target Sibelia make[2]: Leaving directory '/build/reproducible-path/sibelia-3.0.7+dfsg/obj-aarch64-linux-gnu' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/sibelia-3.0.7+dfsg/obj-aarch64-linux-gnu/CMakeFiles 0 make[1]: Leaving directory '/build/reproducible-path/sibelia-3.0.7+dfsg/obj-aarch64-linux-gnu' debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/sibelia-3.0.7+dfsg' dh_auto_test --no-parallel make[1]: Leaving directory '/build/reproducible-path/sibelia-3.0.7+dfsg' create-stamp debian/debhelper-build-stamp dh_testroot -O--sourcedirectory=src dh_prep -O--sourcedirectory=src dh_auto_install -O--sourcedirectory=src cd obj-aarch64-linux-gnu && make -j12 install DESTDIR=/build/reproducible-path/sibelia-3.0.7\+dfsg/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/reproducible-path/sibelia-3.0.7+dfsg/obj-aarch64-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/sibelia-3.0.7+dfsg/src -B/build/reproducible-path/sibelia-3.0.7+dfsg/obj-aarch64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/sibelia-3.0.7+dfsg/obj-aarch64-linux-gnu/CMakeFiles /build/reproducible-path/sibelia-3.0.7+dfsg/obj-aarch64-linux-gnu//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/build/reproducible-path/sibelia-3.0.7+dfsg/obj-aarch64-linux-gnu' make -f CMakeFiles/Sibelia.dir/build.make CMakeFiles/Sibelia.dir/depend make[3]: Entering directory '/build/reproducible-path/sibelia-3.0.7+dfsg/obj-aarch64-linux-gnu' cd /build/reproducible-path/sibelia-3.0.7+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sibelia-3.0.7+dfsg/src /build/reproducible-path/sibelia-3.0.7+dfsg/src /build/reproducible-path/sibelia-3.0.7+dfsg/obj-aarch64-linux-gnu /build/reproducible-path/sibelia-3.0.7+dfsg/obj-aarch64-linux-gnu /build/reproducible-path/sibelia-3.0.7+dfsg/obj-aarch64-linux-gnu/CMakeFiles/Sibelia.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/sibelia-3.0.7+dfsg/obj-aarch64-linux-gnu' make -f CMakeFiles/Sibelia.dir/build.make CMakeFiles/Sibelia.dir/build make[3]: Entering directory '/build/reproducible-path/sibelia-3.0.7+dfsg/obj-aarch64-linux-gnu' make[3]: Nothing to be done for 'CMakeFiles/Sibelia.dir/build'. make[3]: Leaving directory '/build/reproducible-path/sibelia-3.0.7+dfsg/obj-aarch64-linux-gnu' [100%] Built target Sibelia make[2]: Leaving directory '/build/reproducible-path/sibelia-3.0.7+dfsg/obj-aarch64-linux-gnu' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/sibelia-3.0.7+dfsg/obj-aarch64-linux-gnu/CMakeFiles 0 make -f CMakeFiles/Makefile2 preinstall make[2]: Entering directory '/build/reproducible-path/sibelia-3.0.7+dfsg/obj-aarch64-linux-gnu' make[2]: Nothing to be done for 'preinstall'. make[2]: Leaving directory '/build/reproducible-path/sibelia-3.0.7+dfsg/obj-aarch64-linux-gnu' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "Release" -- Installing: /build/reproducible-path/sibelia-3.0.7+dfsg/debian/tmp/usr/bin/Sibelia -- Installing: /build/reproducible-path/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/NEWS.md -- Installing: /build/reproducible-path/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/ANNOTATION.md -- Installing: /build/reproducible-path/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/README.md -- Installing: /build/reproducible-path/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/USAGE.md -- Installing: /build/reproducible-path/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/INSTALL.md -- Installing: /build/reproducible-path/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/SIBELIA.md -- Installing: /build/reproducible-path/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/C-SIBELIA.md -- Installing: /build/reproducible-path/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/LICENSE.txt -- Installing: /build/reproducible-path/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples -- Installing: /build/reproducible-path/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/C-Sibelia -- Installing: /build/reproducible-path/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/C-Sibelia/Staphylococcus_aureus -- Installing: /build/reproducible-path/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/C-Sibelia/Staphylococcus_aureus/RN4220.fasta -- Installing: /build/reproducible-path/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/C-Sibelia/Staphylococcus_aureus/README.txt -- Installing: /build/reproducible-path/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/C-Sibelia/Staphylococcus_aureus/NCTC8325.fasta -- Installing: /build/reproducible-path/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/C-Sibelia/Staphylococcus_aureus/variant.vcf -- Installing: /build/reproducible-path/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/Sibelia -- Installing: /build/reproducible-path/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/Sibelia/Helicobacter_pylori -- Installing: /build/reproducible-path/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/Sibelia/Helicobacter_pylori/genomes_permutations.txt -- Installing: /build/reproducible-path/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/Sibelia/Helicobacter_pylori/circos -- Installing: /build/reproducible-path/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/Sibelia/Helicobacter_pylori/circos/circos.image.conf -- Installing: /build/reproducible-path/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/Sibelia/Helicobacter_pylori/circos/circos.highlight2.txt -- Installing: /build/reproducible-path/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/Sibelia/Helicobacter_pylori/circos/circos.sequences.txt -- Installing: /build/reproducible-path/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/Sibelia/Helicobacter_pylori/circos/circos.highlight4.txt -- Installing: /build/reproducible-path/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/Sibelia/Helicobacter_pylori/circos/circos.highlight1.txt -- Installing: /build/reproducible-path/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/Sibelia/Helicobacter_pylori/circos/circos.highlight.txt -- Installing: /build/reproducible-path/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/Sibelia/Helicobacter_pylori/circos/circos.png -- Installing: /build/reproducible-path/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/Sibelia/Helicobacter_pylori/circos/circos.highlight3.txt -- Installing: /build/reproducible-path/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/Sibelia/Helicobacter_pylori/circos/circos.segdup.txt -- Installing: /build/reproducible-path/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/Sibelia/Helicobacter_pylori/circos/circos.svg -- Installing: /build/reproducible-path/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/Sibelia/Helicobacter_pylori/circos/circos.conf -- Installing: /build/reproducible-path/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/Sibelia/Helicobacter_pylori/coverage_report.txt -- Installing: /build/reproducible-path/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/Sibelia/Helicobacter_pylori/Helicobacter_pylori.fasta -- Installing: /build/reproducible-path/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/Sibelia/Helicobacter_pylori/blocks_coords.txt -- Installing: /build/reproducible-path/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/Sibelia/Helicobacter_pylori/README.txt -- Installing: /build/reproducible-path/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/Sibelia/Helicobacter_pylori/d3_blocks_diagram.html -- Installing: /build/reproducible-path/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/Sibelia/Staphylococcus_aureus -- Installing: /build/reproducible-path/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/Sibelia/Staphylococcus_aureus/genomes_permutations.txt -- Installing: /build/reproducible-path/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/Sibelia/Staphylococcus_aureus/circos -- Installing: /build/reproducible-path/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/Sibelia/Staphylococcus_aureus/circos/circos.image.conf -- Installing: /build/reproducible-path/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/Sibelia/Staphylococcus_aureus/circos/circos.sequences.txt -- Installing: /build/reproducible-path/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/Sibelia/Staphylococcus_aureus/circos/circos.highlight.txt -- Installing: /build/reproducible-path/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/Sibelia/Staphylococcus_aureus/circos/circos.png -- Installing: /build/reproducible-path/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/Sibelia/Staphylococcus_aureus/circos/circos.segdup.txt -- Installing: /build/reproducible-path/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/Sibelia/Staphylococcus_aureus/circos/circos.svg -- Installing: /build/reproducible-path/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/Sibelia/Staphylococcus_aureus/circos/circos.conf -- Installing: /build/reproducible-path/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/Sibelia/Staphylococcus_aureus/coverage_report.txt -- Installing: /build/reproducible-path/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/Sibelia/Staphylococcus_aureus/blocks_coords.txt -- Installing: /build/reproducible-path/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/Sibelia/Staphylococcus_aureus/README.txt -- Installing: /build/reproducible-path/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/Sibelia/Staphylococcus_aureus/Staphylococcus.fasta -- Installing: /build/reproducible-path/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/Sibelia/Staphylococcus_aureus/d3_blocks_diagram.html -- Installing: /build/reproducible-path/sibelia-3.0.7+dfsg/debian/tmp/usr/bin/C-Sibelia.py -- Installing: /build/reproducible-path/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/utils -- Installing: /build/reproducible-path/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/utils/hidemappedcontigs.py -- Installing: /build/reproducible-path/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/utils/sortsequences.py -- Installing: /build/reproducible-path/sibelia-3.0.7+dfsg/debian/tmp/usr/lib/Sibelia make[1]: Leaving directory '/build/reproducible-path/sibelia-3.0.7+dfsg/obj-aarch64-linux-gnu' debian/rules override_dh_install make[1]: Entering directory '/build/reproducible-path/sibelia-3.0.7+dfsg' dh_install find debian -name LICENSE.txt -delete find debian -name INSTALL.md -delete make[1]: Leaving directory '/build/reproducible-path/sibelia-3.0.7+dfsg' dh_installdocs -O--sourcedirectory=src dh_installchangelogs -O--sourcedirectory=src debian/rules override_dh_installman-arch make[1]: Entering directory '/build/reproducible-path/sibelia-3.0.7+dfsg' dh_installman -a mv debian/sibelia/usr/share/man/py/man1/C-Sibelia.1 debian/sibelia/usr/share/man/man1/C-Sibelia.py.1 rm -rf debian/sibelia/usr/share/man/py make[1]: Leaving directory '/build/reproducible-path/sibelia-3.0.7+dfsg' dh_installman -O--sourcedirectory=src -Nsibelia dh_installinit -O--sourcedirectory=src dh_installsystemduser -O--sourcedirectory=src dh_lintian -O--sourcedirectory=src dh_perl -O--sourcedirectory=src dh_link -O--sourcedirectory=src dh_strip_nondeterminism -O--sourcedirectory=src dh_compress -O--sourcedirectory=src dh_fixperms -O--sourcedirectory=src dh_missing -O--sourcedirectory=src dh_dwz -O--sourcedirectory=src dh_strip -O--sourcedirectory=src dh_makeshlibs -O--sourcedirectory=src dh_shlibdeps -O--sourcedirectory=src dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 from: /lib/ld-linux-aarch64.so.1 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 to: /lib/ld-linux-aarch64.so.1.usr-is-merged dh_installdeb -O--sourcedirectory=src dh_gencontrol -O--sourcedirectory=src dh_md5sums -O--sourcedirectory=src dh_builddeb -O--sourcedirectory=src dpkg-deb: building package 'sibelia-dbgsym' in '../sibelia-dbgsym_3.0.7+dfsg-4_arm64.deb'. dpkg-deb: building package 'sibelia' in '../sibelia_3.0.7+dfsg-4_arm64.deb'. dpkg-deb: building package 'sibelia-examples' in '../sibelia-examples_3.0.7+dfsg-4_all.deb'. dpkg-genbuildinfo --build=binary -O../sibelia_3.0.7+dfsg-4_arm64.buildinfo dpkg-genchanges --build=binary -O../sibelia_3.0.7+dfsg-4_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/1763354 and its subdirectories I: Current time: Mon Nov 25 13:53:26 -12 2024 I: pbuilder-time-stamp: 1732586006 Tue Nov 26 01:53:26 UTC 2024 I: Signing ./b1/sibelia_3.0.7+dfsg-4_arm64.buildinfo as sibelia_3.0.7+dfsg-4_arm64.buildinfo.asc Tue Nov 26 01:53:26 UTC 2024 I: Signed ./b1/sibelia_3.0.7+dfsg-4_arm64.buildinfo as ./b1/sibelia_3.0.7+dfsg-4_arm64.buildinfo.asc Tue Nov 26 01:53:26 UTC 2024 - build #1 for sibelia/experimental/arm64 on codethink02-arm64 done. Starting cleanup. All cleanup done. Tue Nov 26 01:53:26 UTC 2024 - reproducible_build.sh stopped running as /tmp/jenkins-script-K5MiMNG6, removing. /srv/reproducible-results/rbuild-debian/r-b-build.Jw2wMKXd: total 16 drwxr-xr-x 2 jenkins jenkins 4096 Nov 26 01:53 b1 drwxr-xr-x 2 jenkins jenkins 4096 Nov 26 01:51 b2 -rw------- 1 jenkins jenkins 3312 Nov 26 01:51 rbuildlog.dtL9asS -rw-r--r-- 1 jenkins jenkins 2156 Nov 25 14:32 sibelia_3.0.7+dfsg-4.dsc /srv/reproducible-results/rbuild-debian/r-b-build.Jw2wMKXd/b1: total 11644 -rw-r--r-- 1 jenkins jenkins 140092 Nov 26 01:53 build.log -rw-r--r-- 1 jenkins jenkins 3696536 Nov 26 01:53 sibelia-dbgsym_3.0.7+dfsg-4_arm64.deb -rw-r--r-- 1 jenkins jenkins 7704828 Nov 26 01:53 sibelia-examples_3.0.7+dfsg-4_all.deb -rw-r--r-- 1 jenkins jenkins 10944 Nov 26 01:53 sibelia_3.0.7+dfsg-4.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 2156 Nov 26 01:53 sibelia_3.0.7+dfsg-4.dsc -rw-r--r-- 1 jenkins jenkins 7882 Nov 26 01:53 sibelia_3.0.7+dfsg-4_arm64.buildinfo -rw-r--r-- 1 jenkins jenkins 8764 Nov 26 01:53 sibelia_3.0.7+dfsg-4_arm64.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 1867 Nov 26 01:53 sibelia_3.0.7+dfsg-4_arm64.changes -rw-r--r-- 1 jenkins jenkins 299476 Nov 26 01:53 sibelia_3.0.7+dfsg-4_arm64.deb -rw-r--r-- 1 jenkins jenkins 1368 Nov 26 01:53 sibelia_3.0.7+dfsg-4_source.changes /srv/reproducible-results/rbuild-debian/r-b-build.Jw2wMKXd/b2: total 0 Tue Nov 26 01:53:28 UTC 2024 I: Deleting $TMPDIR on codethink02-arm64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Mon Nov 25 13:51:10 -12 2024 I: pbuilder-time-stamp: 1732585870 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/experimental-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 [sibelia_3.0.7+dfsg-4.dsc] I: copying [./sibelia_3.0.7+dfsg.orig.tar.xz] I: copying [./sibelia_3.0.7+dfsg-4.debian.tar.xz] I: Extracting source gpgv: Signature made Mon Nov 25 14:29:08 2024 gpgv: using RSA key 724D609337113C710550D7473C26763F6C67E6E2 gpgv: issuer "crusoe@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./sibelia_3.0.7+dfsg-4.dsc: no acceptable signature found dpkg-source: info: extracting sibelia in sibelia-3.0.7+dfsg dpkg-source: info: unpacking sibelia_3.0.7+dfsg.orig.tar.xz dpkg-source: info: unpacking sibelia_3.0.7+dfsg-4.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying use_debian_packaged_libdivsufsort.patch dpkg-source: info: applying use_debian_packaged_lagan.patch dpkg-source: info: applying snpeff_is_removed.patch dpkg-source: info: applying 2to3.patch dpkg-source: info: applying 0005-Upgrade-to-SeqAn-2.5.0.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/1763354/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='arm64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' DISTRIBUTION='experimental' HOME='/root' HOST_ARCH='arm64' IFS=' ' INVOCATION_ID='b3d452d9c6b640c7907b6cff8d400475' 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='1763354' 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.Jw2wMKXd/pbuilderrc_7ddl --distribution experimental --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/experimental-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.Jw2wMKXd/b1 --logfile b1/build.log sibelia_3.0.7+dfsg-4.dsc' SUDO_GID='109' SUDO_UID='104' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://192.168.101.4:3128' I: uname -a Linux codethink02-arm64 6.1.0-28-cloud-arm64 #1 SMP Debian 6.1.119-1 (2024-11-22) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 4 21:30 /bin -> usr/bin I: user script /srv/workspace/pbuilder/1763354/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: arm64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 12), cmake, libdivsufsort-dev, libboost-dev, libseqan2-dev (= 2.5.0~rc3+dfsg-1), libtclap-dev, libhts-dev dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 20083 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 (= 12); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on cmake; however: Package cmake is not installed. pbuilder-satisfydepends-dummy depends on libdivsufsort-dev; however: Package libdivsufsort-dev is not installed. pbuilder-satisfydepends-dummy depends on libboost-dev; however: Package libboost-dev is not installed. pbuilder-satisfydepends-dummy depends on libseqan2-dev (= 2.5.0~rc3+dfsg-1); however: Package libseqan2-dev is not installed. pbuilder-satisfydepends-dummy depends on libtclap-dev; however: Package libtclap-dev is not installed. pbuilder-satisfydepends-dummy depends on libhts-dev; however: Package libhts-dev is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} cmake{a} cmake-data{a} comerr-dev{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} krb5-multidev{a} libarchive-zip-perl{a} libarchive13t64{a} libboost-dev{a} libboost1.83-dev{a} libbrotli-dev{a} libbrotli1{a} libbz2-dev{a} libcom-err2{a} libcurl3t64-gnutls{a} libcurl4-gnutls-dev{a} libcurl4t64{a} libdebhelper-perl{a} libdeflate-dev{a} libdeflate0{a} libdivsufsort-dev{a} libdivsufsort3{a} libelf1t64{a} libevent-2.1-7t64{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libgmp-dev{a} libgmpxx4ldbl{a} libgnutls-dane0t64{a} libgnutls-openssl27t64{a} libgnutls28-dev{a} libgssapi-krb5-2{a} libgssrpc4t64{a} libhts-dev{a} libhts3t64{a} libhtscodecs2{a} libicu72{a} libidn2-dev{a} libjsoncpp26{a} libk5crypto3{a} libkadm5clnt-mit12{a} libkadm5srv-mit12{a} libkdb5-10t64{a} libkeyutils1{a} libkrb5-3{a} libkrb5-dev{a} libkrb5support0{a} libldap-2.5-0{a} libldap-dev{a} liblzma-dev{a} libmagic-mgc{a} libmagic1t64{a} libnghttp2-14{a} libnghttp2-dev{a} libnghttp3-9{a} libnghttp3-dev{a} libngtcp2-16{a} libngtcp2-crypto-gnutls-dev{a} libngtcp2-crypto-gnutls8{a} libngtcp2-dev{a} libp11-kit-dev{a} libpipeline1{a} libpkgconf3{a} libproc2-0{a} libpsl-dev{a} libpsl5t64{a} librhash1{a} librtmp-dev{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libssh2-1-dev{a} libssh2-1t64{a} libssl-dev{a} libtasn1-6-dev{a} libtclap-dev{a} libtool{a} libuchardet0{a} libunbound8{a} libuv1t64{a} libxml2{a} libzstd-dev{a} m4{a} man-db{a} nettle-dev{a} pkgconf{a} pkgconf-bin{a} po-debconf{a} procps{a} sensible-utils{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 libtasn1-doc linux-sysctl-defaults lynx psmisc publicsuffix wget 0 packages upgraded, 103 newly installed, 0 to remove and 0 not upgraded. Need to get 64.8 MB of archives. After unpacking 370 MB will be used. The following packages have unmet dependencies: pbuilder-satisfydepends-dummy : Depends: libseqan2-dev (= 2.5.0~rc3+dfsg-1) but it is not going to be installed The following actions will resolve these dependencies: Install the following packages: 1) libseqan2-dev [2.5.0~rc3+dfsg-1 (experimental)] The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} cmake{a} cmake-data{a} comerr-dev{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} krb5-multidev{a} libarchive-zip-perl{a} libarchive13t64{a} libboost-dev{a} libboost1.83-dev{a} libbrotli-dev{a} libbrotli1{a} libbz2-dev{a} libcom-err2{a} libcurl3t64-gnutls{a} libcurl4-gnutls-dev{a} libcurl4t64{a} libdebhelper-perl{a} libdeflate-dev{a} libdeflate0{a} libdivsufsort-dev{a} libdivsufsort3{a} libelf1t64{a} libevent-2.1-7t64{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libgmp-dev{a} libgmpxx4ldbl{a} libgnutls-dane0t64{a} libgnutls-openssl27t64{a} libgnutls28-dev{a} libgssapi-krb5-2{a} libgssrpc4t64{a} libhts-dev{a} libhts3t64{a} libhtscodecs2{a} libicu72{a} libidn2-dev{a} libjsoncpp26{a} libk5crypto3{a} libkadm5clnt-mit12{a} libkadm5srv-mit12{a} libkdb5-10t64{a} libkeyutils1{a} libkrb5-3{a} libkrb5-dev{a} libkrb5support0{a} libldap-2.5-0{a} libldap-dev{a} liblzma-dev{a} libmagic-mgc{a} libmagic1t64{a} libnghttp2-14{a} libnghttp2-dev{a} libnghttp3-9{a} libnghttp3-dev{a} libngtcp2-16{a} libngtcp2-crypto-gnutls-dev{a} libngtcp2-crypto-gnutls8{a} libngtcp2-dev{a} libp11-kit-dev{a} libpipeline1{a} libpkgconf3{a} libproc2-0{a} libpsl-dev{a} libpsl5t64{a} librhash1{a} librtmp-dev{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libseqan2-dev{a} libssh2-1-dev{a} libssh2-1t64{a} libssl-dev{a} libtasn1-6-dev{a} libtclap-dev{a} libtool{a} libuchardet0{a} libunbound8{a} libuv1t64{a} libxml2{a} libzstd-dev{a} m4{a} man-db{a} nettle-dev{a} pkgconf{a} pkgconf-bin{a} po-debconf{a} procps{a} sensible-utils{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 libtasn1-doc linux-sysctl-defaults lynx psmisc publicsuffix wget 0 packages upgraded, 104 newly installed, 0 to remove and 0 not upgraded. Need to get 66.0 MB of archives. After unpacking 383 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main arm64 libproc2-0 arm64 2:4.0.4-6 [62.3 kB] Get: 2 http://deb.debian.org/debian unstable/main arm64 procps arm64 2:4.0.4-6 [872 kB] Get: 3 http://deb.debian.org/debian unstable/main arm64 sensible-utils all 0.0.24 [24.8 kB] Get: 4 http://deb.debian.org/debian unstable/main arm64 libmagic-mgc arm64 1:5.45-3+b1 [314 kB] Get: 5 http://deb.debian.org/debian unstable/main arm64 libmagic1t64 arm64 1:5.45-3+b1 [102 kB] Get: 6 http://deb.debian.org/debian unstable/main arm64 file arm64 1:5.45-3+b1 [43.4 kB] Get: 7 http://deb.debian.org/debian unstable/main arm64 gettext-base arm64 0.22.5-2 [198 kB] Get: 8 http://deb.debian.org/debian unstable/main arm64 libuchardet0 arm64 0.0.8-1+b2 [69.2 kB] Get: 9 http://deb.debian.org/debian unstable/main arm64 groff-base arm64 1.23.0-5 [1129 kB] Get: 10 http://deb.debian.org/debian unstable/main arm64 bsdextrautils arm64 2.40.2-11 [91.2 kB] Get: 11 http://deb.debian.org/debian unstable/main arm64 libpipeline1 arm64 1.5.8-1 [40.2 kB] Get: 12 http://deb.debian.org/debian unstable/main arm64 man-db arm64 2.13.0-1 [1404 kB] Get: 13 http://deb.debian.org/debian unstable/main arm64 m4 arm64 1.4.19-4 [277 kB] Get: 14 http://deb.debian.org/debian unstable/main arm64 autoconf all 2.72-3 [493 kB] Get: 15 http://deb.debian.org/debian unstable/main arm64 autotools-dev all 20220109.1 [51.6 kB] Get: 16 http://deb.debian.org/debian unstable/main arm64 automake all 1:1.16.5-1.3 [823 kB] Get: 17 http://deb.debian.org/debian unstable/main arm64 autopoint all 0.22.5-2 [723 kB] Get: 18 http://deb.debian.org/debian unstable/main arm64 cmake-data all 3.31.1-1 [2267 kB] Get: 19 http://deb.debian.org/debian unstable/main arm64 libicu72 arm64 72.1-5+b1 [9239 kB] Get: 20 http://deb.debian.org/debian unstable/main arm64 libxml2 arm64 2.12.7+dfsg+really2.9.14-0.2+b1 [630 kB] Get: 21 http://deb.debian.org/debian unstable/main arm64 libarchive13t64 arm64 3.7.4-1.1 [323 kB] Get: 22 http://deb.debian.org/debian unstable/main arm64 libbrotli1 arm64 1.1.0-2+b6 [297 kB] Get: 23 http://deb.debian.org/debian unstable/main arm64 libkrb5support0 arm64 1.21.3-3 [32.1 kB] Get: 24 http://deb.debian.org/debian unstable/main arm64 libcom-err2 arm64 1.47.1-1+b1 [23.1 kB] Get: 25 http://deb.debian.org/debian unstable/main arm64 libk5crypto3 arm64 1.21.3-3 [80.8 kB] Get: 26 http://deb.debian.org/debian unstable/main arm64 libkeyutils1 arm64 1.6.3-4 [9352 B] Get: 27 http://deb.debian.org/debian unstable/main arm64 libkrb5-3 arm64 1.21.3-3 [310 kB] Get: 28 http://deb.debian.org/debian unstable/main arm64 libgssapi-krb5-2 arm64 1.21.3-3 [126 kB] Get: 29 http://deb.debian.org/debian unstable/main arm64 libsasl2-modules-db arm64 2.1.28+dfsg1-8 [20.0 kB] Get: 30 http://deb.debian.org/debian unstable/main arm64 libsasl2-2 arm64 2.1.28+dfsg1-8 [55.4 kB] Get: 31 http://deb.debian.org/debian unstable/main arm64 libldap-2.5-0 arm64 2.5.18+dfsg-3+b1 [175 kB] Get: 32 http://deb.debian.org/debian unstable/main arm64 libnghttp2-14 arm64 1.64.0-1 [71.3 kB] Get: 33 http://deb.debian.org/debian unstable/main arm64 libpsl5t64 arm64 0.21.2-1.1+b1 [57.1 kB] Get: 34 http://deb.debian.org/debian unstable/main arm64 librtmp1 arm64 2.4+20151223.gitfa8646d.1-2+b5 [56.8 kB] Get: 35 http://deb.debian.org/debian unstable/main arm64 libssh2-1t64 arm64 1.11.1-1 [235 kB] Get: 36 http://deb.debian.org/debian unstable/main arm64 libcurl4t64 arm64 8.11.0-1 [322 kB] Get: 37 http://deb.debian.org/debian unstable/main arm64 libexpat1 arm64 2.6.4-1 [90.7 kB] Get: 38 http://deb.debian.org/debian unstable/main arm64 libjsoncpp26 arm64 1.9.6-3 [72.9 kB] Get: 39 http://deb.debian.org/debian unstable/main arm64 librhash1 arm64 1.4.5-1 [129 kB] Get: 40 http://deb.debian.org/debian unstable/main arm64 libuv1t64 arm64 1.48.0-7 [143 kB] Get: 41 http://deb.debian.org/debian unstable/main arm64 cmake arm64 3.31.1-1 [9873 kB] Get: 42 http://deb.debian.org/debian unstable/main arm64 comerr-dev arm64 2.1-1.47.1-1+b1 [55.1 kB] Get: 43 http://deb.debian.org/debian unstable/main arm64 libdebhelper-perl all 13.20 [89.7 kB] Get: 44 http://deb.debian.org/debian unstable/main arm64 libtool all 2.4.7-8 [517 kB] Get: 45 http://deb.debian.org/debian unstable/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 46 http://deb.debian.org/debian unstable/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 47 http://deb.debian.org/debian unstable/main arm64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 48 http://deb.debian.org/debian unstable/main arm64 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 49 http://deb.debian.org/debian unstable/main arm64 libelf1t64 arm64 0.192-4 [189 kB] Get: 50 http://deb.debian.org/debian unstable/main arm64 dwz arm64 0.15-1+b1 [102 kB] Get: 51 http://deb.debian.org/debian unstable/main arm64 gettext arm64 0.22.5-2 [1532 kB] Get: 52 http://deb.debian.org/debian unstable/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 53 http://deb.debian.org/debian unstable/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 54 http://deb.debian.org/debian unstable/main arm64 debhelper all 13.20 [915 kB] Get: 55 http://deb.debian.org/debian unstable/main arm64 libgssrpc4t64 arm64 1.21.3-3 [56.7 kB] Get: 56 http://deb.debian.org/debian unstable/main arm64 libkadm5clnt-mit12 arm64 1.21.3-3 [40.3 kB] Get: 57 http://deb.debian.org/debian unstable/main arm64 libkdb5-10t64 arm64 1.21.3-3 [40.8 kB] Get: 58 http://deb.debian.org/debian unstable/main arm64 libkadm5srv-mit12 arm64 1.21.3-3 [52.2 kB] Get: 59 http://deb.debian.org/debian unstable/main arm64 krb5-multidev arm64 1.21.3-3 [126 kB] Get: 60 http://deb.debian.org/debian unstable/main arm64 libboost1.83-dev arm64 1.83.0-3.2+b1 [10.6 MB] Get: 61 http://deb.debian.org/debian unstable/main arm64 libboost-dev arm64 1.83.0.2+b2 [3828 B] Get: 62 http://deb.debian.org/debian unstable/main arm64 libbrotli-dev arm64 1.1.0-2+b6 [308 kB] Get: 63 http://deb.debian.org/debian unstable/main arm64 libbz2-dev arm64 1.0.8-6 [31.9 kB] Get: 64 http://deb.debian.org/debian unstable/main arm64 libnghttp3-9 arm64 1.4.0-1+b1 [59.6 kB] Get: 65 http://deb.debian.org/debian unstable/main arm64 libngtcp2-16 arm64 1.6.0-1 [112 kB] Get: 66 http://deb.debian.org/debian unstable/main arm64 libngtcp2-crypto-gnutls8 arm64 1.6.0-1 [18.5 kB] Get: 67 http://deb.debian.org/debian unstable/main arm64 libcurl3t64-gnutls arm64 8.11.0-1 [331 kB] Get: 68 http://deb.debian.org/debian unstable/main arm64 libevent-2.1-7t64 arm64 2.1.12-stable-10+b1 [170 kB] Get: 69 http://deb.debian.org/debian unstable/main arm64 libunbound8 arm64 1.22.0-1 [553 kB] Get: 70 http://deb.debian.org/debian unstable/main arm64 libgnutls-dane0t64 arm64 3.8.8-2 [446 kB] Get: 71 http://deb.debian.org/debian unstable/main arm64 libgnutls-openssl27t64 arm64 3.8.8-2 [446 kB] Get: 72 http://deb.debian.org/debian unstable/main arm64 libidn2-dev arm64 2.3.7-2+b1 [122 kB] Get: 73 http://deb.debian.org/debian unstable/main arm64 libp11-kit-dev arm64 0.25.5-2+b1 [208 kB] Get: 74 http://deb.debian.org/debian unstable/main arm64 libtasn1-6-dev arm64 4.19.0-3+b3 [96.5 kB] Get: 75 http://deb.debian.org/debian unstable/main arm64 libgmpxx4ldbl arm64 2:6.3.0+dfsg-2+b2 [329 kB] Get: 76 http://deb.debian.org/debian unstable/main arm64 libgmp-dev arm64 2:6.3.0+dfsg-2+b2 [621 kB] Get: 77 http://deb.debian.org/debian unstable/main arm64 nettle-dev arm64 3.10-1+b1 [1324 kB] Get: 78 http://deb.debian.org/debian unstable/main arm64 libgnutls28-dev arm64 3.8.8-2 [1404 kB] Get: 79 http://deb.debian.org/debian unstable/main arm64 libkrb5-dev arm64 1.21.3-3 [15.8 kB] Get: 80 http://deb.debian.org/debian unstable/main arm64 libldap-dev arm64 2.5.18+dfsg-3+b1 [300 kB] Get: 81 http://deb.debian.org/debian unstable/main arm64 libpkgconf3 arm64 1.8.1-4 [35.3 kB] Get: 82 http://deb.debian.org/debian unstable/main arm64 pkgconf-bin arm64 1.8.1-4 [29.6 kB] Get: 83 http://deb.debian.org/debian unstable/main arm64 pkgconf arm64 1.8.1-4 [26.1 kB] Get: 84 http://deb.debian.org/debian unstable/main arm64 libnghttp2-dev arm64 1.64.0-1 [112 kB] Get: 85 http://deb.debian.org/debian unstable/main arm64 libnghttp3-dev arm64 1.4.0-1+b1 [85.2 kB] Get: 86 http://deb.debian.org/debian unstable/main arm64 libngtcp2-crypto-gnutls-dev arm64 1.6.0-1 [23.7 kB] Get: 87 http://deb.debian.org/debian unstable/main arm64 libngtcp2-dev arm64 1.6.0-1 [165 kB] Get: 88 http://deb.debian.org/debian unstable/main arm64 libpsl-dev arm64 0.21.2-1.1+b1 [77.9 kB] Get: 89 http://deb.debian.org/debian unstable/main arm64 zlib1g-dev arm64 1:1.3.dfsg+really1.3.1-1+b1 [917 kB] Get: 90 http://deb.debian.org/debian unstable/main arm64 librtmp-dev arm64 2.4+20151223.gitfa8646d.1-2+b5 [67.5 kB] Get: 91 http://deb.debian.org/debian unstable/main arm64 libssl-dev arm64 3.3.2-2 [3185 kB] Get: 92 http://deb.debian.org/debian unstable/main arm64 libssh2-1-dev arm64 1.11.1-1 [388 kB] Get: 93 http://deb.debian.org/debian unstable/main arm64 libzstd-dev arm64 1.5.6+dfsg-1+b1 [329 kB] Get: 94 http://deb.debian.org/debian unstable/main arm64 libcurl4-gnutls-dev arm64 8.11.0-1 [459 kB] Get: 95 http://deb.debian.org/debian unstable/main arm64 libdeflate0 arm64 1.22-1 [42.2 kB] Get: 96 http://deb.debian.org/debian unstable/main arm64 libdeflate-dev arm64 1.22-1 [51.2 kB] Get: 97 http://deb.debian.org/debian unstable/main arm64 libdivsufsort3 arm64 2.0.1-6+b1 [39.9 kB] Get: 98 http://deb.debian.org/debian unstable/main arm64 libdivsufsort-dev arm64 2.0.1-6+b1 [19.1 kB] Get: 99 http://deb.debian.org/debian unstable/main arm64 libhtscodecs2 arm64 1.6.1-1 [74.6 kB] Get: 100 http://deb.debian.org/debian unstable/main arm64 libhts3t64 arm64 1.20+ds-2 [420 kB] Get: 101 http://deb.debian.org/debian unstable/main arm64 liblzma-dev arm64 5.6.3-1+b1 [312 kB] Get: 102 http://deb.debian.org/debian unstable/main arm64 libhts-dev arm64 1.20+ds-2 [1626 kB] Get: 103 http://deb.debian.org/debian experimental/main arm64 libseqan2-dev all 2.5.0~rc3+dfsg-1 [1222 kB] Get: 104 http://deb.debian.org/debian unstable/main arm64 libtclap-dev arm64 1.2.5-1+b1 [3359 kB] Fetched 66.0 MB in 1s (109 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libproc2-0:arm64. (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 ... 20083 files and directories currently installed.) Preparing to unpack .../000-libproc2-0_2%3a4.0.4-6_arm64.deb ... Unpacking libproc2-0:arm64 (2:4.0.4-6) ... Selecting previously unselected package procps. Preparing to unpack .../001-procps_2%3a4.0.4-6_arm64.deb ... Unpacking procps (2:4.0.4-6) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../002-sensible-utils_0.0.24_all.deb ... 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Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/reproducible-path/sibelia-3.0.7+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 > ../sibelia_3.0.7+dfsg-4_source.changes dpkg-buildpackage: info: source package sibelia dpkg-buildpackage: info: source version 3.0.7+dfsg-4 dpkg-buildpackage: info: source distribution experimental dpkg-buildpackage: info: source changed by Michael R. Crusoe dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 debian/rules clean dh clean --sourcedirectory=src dh_auto_clean -O--sourcedirectory=src dh_autoreconf_clean -O--sourcedirectory=src dh_clean -O--sourcedirectory=src debian/rules binary dh binary --sourcedirectory=src dh_update_autotools_config -O--sourcedirectory=src dh_autoreconf -O--sourcedirectory=src dh_auto_configure -O--sourcedirectory=src cd obj-aarch64-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 "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/aarch64-linux-gnu ../src 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 CXX compiler identification is GNU 14.2.0 -- 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 -- Configuring done (0.6s) -- 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_FIND_USE_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/sibelia-3.0.7+dfsg/obj-aarch64-linux-gnu dh_auto_build -O--sourcedirectory=src cd obj-aarch64-linux-gnu && make -j12 "INSTALL=install --strip-program=true" VERBOSE=1 make[1]: Entering directory '/build/reproducible-path/sibelia-3.0.7+dfsg/obj-aarch64-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/sibelia-3.0.7+dfsg/src -B/build/reproducible-path/sibelia-3.0.7+dfsg/obj-aarch64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/sibelia-3.0.7+dfsg/obj-aarch64-linux-gnu/CMakeFiles /build/reproducible-path/sibelia-3.0.7+dfsg/obj-aarch64-linux-gnu//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/build/reproducible-path/sibelia-3.0.7+dfsg/obj-aarch64-linux-gnu' make -f CMakeFiles/Sibelia.dir/build.make CMakeFiles/Sibelia.dir/depend make[3]: Entering directory '/build/reproducible-path/sibelia-3.0.7+dfsg/obj-aarch64-linux-gnu' cd /build/reproducible-path/sibelia-3.0.7+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sibelia-3.0.7+dfsg/src /build/reproducible-path/sibelia-3.0.7+dfsg/src 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-ffile-prefix-map=/build/reproducible-path/sibelia-3.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -MD -MT CMakeFiles/Sibelia.dir/bulgeremoval.cpp.o -MF CMakeFiles/Sibelia.dir/bulgeremoval.cpp.o.d -o CMakeFiles/Sibelia.dir/bulgeremoval.cpp.o -c /build/reproducible-path/sibelia-3.0.7+dfsg/src/bulgeremoval.cpp [ 35%] Building CXX object CMakeFiles/Sibelia.dir/indexedsequence.cpp.o /usr/bin/c++ -I/build/reproducible-path/sibelia-3.0.7+dfsg/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/sibelia-3.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -MD -MT CMakeFiles/Sibelia.dir/postprocessor.cpp.o -MF CMakeFiles/Sibelia.dir/postprocessor.cpp.o.d -o CMakeFiles/Sibelia.dir/postprocessor.cpp.o -c 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CMakeFiles/Sibelia.dir/outputgenerator.cpp.o -MF CMakeFiles/Sibelia.dir/outputgenerator.cpp.o.d -o CMakeFiles/Sibelia.dir/outputgenerator.cpp.o -c /build/reproducible-path/sibelia-3.0.7+dfsg/src/outputgenerator.cpp /usr/bin/c++ -I/build/reproducible-path/sibelia-3.0.7+dfsg/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/sibelia-3.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -MD -MT CMakeFiles/Sibelia.dir/blockinstance.cpp.o -MF CMakeFiles/Sibelia.dir/blockinstance.cpp.o.d -o CMakeFiles/Sibelia.dir/blockinstance.cpp.o -c /build/reproducible-path/sibelia-3.0.7+dfsg/src/blockinstance.cpp /usr/bin/c++ -I/build/reproducible-path/sibelia-3.0.7+dfsg/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/sibelia-3.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -MD -MT CMakeFiles/Sibelia.dir/dnasequence.cpp.o -MF CMakeFiles/Sibelia.dir/dnasequence.cpp.o.d -o CMakeFiles/Sibelia.dir/dnasequence.cpp.o -c /build/reproducible-path/sibelia-3.0.7+dfsg/src/dnasequence.cpp [ 45%] Building CXX object CMakeFiles/Sibelia.dir/sibelia.cpp.o [ 50%] Building CXX object CMakeFiles/Sibelia.dir/fasta.cpp.o [ 55%] Building CXX object CMakeFiles/Sibelia.dir/edge.cpp.o /usr/bin/c++ -I/build/reproducible-path/sibelia-3.0.7+dfsg/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/sibelia-3.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -MD -MT CMakeFiles/Sibelia.dir/fasta.cpp.o -MF CMakeFiles/Sibelia.dir/fasta.cpp.o.d -o CMakeFiles/Sibelia.dir/fasta.cpp.o -c /build/reproducible-path/sibelia-3.0.7+dfsg/src/fasta.cpp /usr/bin/c++ -I/build/reproducible-path/sibelia-3.0.7+dfsg/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/sibelia-3.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -MD -MT CMakeFiles/Sibelia.dir/sibelia.cpp.o -MF CMakeFiles/Sibelia.dir/sibelia.cpp.o.d -o CMakeFiles/Sibelia.dir/sibelia.cpp.o -c /build/reproducible-path/sibelia-3.0.7+dfsg/src/sibelia.cpp /usr/bin/c++ -I/build/reproducible-path/sibelia-3.0.7+dfsg/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/sibelia-3.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -MD -MT CMakeFiles/Sibelia.dir/edge.cpp.o -MF CMakeFiles/Sibelia.dir/edge.cpp.o.d -o CMakeFiles/Sibelia.dir/edge.cpp.o -c /build/reproducible-path/sibelia-3.0.7+dfsg/src/edge.cpp [ 60%] Building CXX object CMakeFiles/Sibelia.dir/bifurcationstorage.cpp.o /usr/bin/c++ -I/build/reproducible-path/sibelia-3.0.7+dfsg/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/sibelia-3.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -MD -MT CMakeFiles/Sibelia.dir/bifurcationstorage.cpp.o -MF CMakeFiles/Sibelia.dir/bifurcationstorage.cpp.o.d -o CMakeFiles/Sibelia.dir/bifurcationstorage.cpp.o -c /build/reproducible-path/sibelia-3.0.7+dfsg/src/bifurcationstorage.cpp In file included from /usr/include/boost/bind/detail/requires_cxx11.hpp:9, from /usr/include/boost/bind/bind.hpp:24, from /usr/include/boost/bind.hpp:29, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:31, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/blockinstance.h:10, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/blockfinder.h:10, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/blockfinder.cpp:7: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/bind/detail/requires_cxx11.hpp:9, from /usr/include/boost/bind/bind.hpp:24, from /usr/include/boost/bind.hpp:29, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:31, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/blockinstance.h:10, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/blockinstance.cpp:7: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/bind/detail/requires_cxx11.hpp:9, from /usr/include/boost/bind/bind.hpp:24, from /usr/include/boost/bind.hpp:29, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:31, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/fasta.h:10, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/dnasequence.h:10, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/dnasequence.cpp:7: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/bind/detail/requires_cxx11.hpp:9, from /usr/include/boost/bind/bind.hpp:24, from /usr/include/boost/bind.hpp:29, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:31, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/blockinstance.h:10, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/blockfinder.h:10, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/bulgeremoval.cpp:7: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/bind/detail/requires_cxx11.hpp:9, from /usr/include/boost/bind/bind.hpp:24, from /usr/include/boost/bind.hpp:29, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:31, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/blockinstance.h:10, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/blockfinder.h:10, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/edge.cpp:7: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/bind/detail/requires_cxx11.hpp:9, from /usr/include/boost/bind/bind.hpp:24, from /usr/include/boost/bind.hpp:29, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:31, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/blockinstance.h:10, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/blockfinder.h:10, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/util.h:10, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/outputgenerator.h:10, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/outputgenerator.cpp:9: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/bind/detail/requires_cxx11.hpp:9, from /usr/include/boost/bind/bind.hpp:24, from /usr/include/boost/bind.hpp:29, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:31, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/fasta.h:10, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/dnasequence.h:10, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/hashing.h:10, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/indexedsequence.h:10, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/indexedsequence.cpp:7: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/bind/detail/requires_cxx11.hpp:9, from /usr/include/boost/bind/bind.hpp:24, from /usr/include/boost/bind.hpp:29, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:31, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/blockinstance.h:10, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/blockfinder.h:10, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/util.h:10, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/util.cpp:7: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/bind/detail/requires_cxx11.hpp:9, from /usr/include/boost/bind/bind.hpp:24, from /usr/include/boost/bind.hpp:29, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:31, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/fasta.h:10, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/dnasequence.h:10, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/bifurcationstorage.h:11, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/bifurcationstorage.cpp:7: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/bind/detail/requires_cxx11.hpp:9, from /usr/include/boost/bind/bind.hpp:24, from /usr/include/boost/bind.hpp:29, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:31, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/fasta.h:10, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/fasta.cpp:7: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:104:51: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 104 | struct FancyIterator: public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/14/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/14/string:47, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:12: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/sibelia-3.0.7+dfsg/src/dnasequence.h:12, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/blockinstance.h:11: /build/reproducible-path/sibelia-3.0.7+dfsg/src/unrolledlist.h:36:45: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 36 | class iterator: public std::iterator | ^~~~~~~~ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:104:51: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 104 | struct FancyIterator: public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/14/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/14/string:47, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:12: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/sibelia-3.0.7+dfsg/src/dnasequence.h:51:51: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 51 | class StrandIterator: public std::iterator | ^~~~~~~~ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:104:51: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 104 | struct FancyIterator: public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/14/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/14/string:47, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:12: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/sibelia-3.0.7+dfsg/src/dnasequence.h:12, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/blockinstance.h:11: /build/reproducible-path/sibelia-3.0.7+dfsg/src/unrolledlist.h:36:45: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 36 | class iterator: public std::iterator | ^~~~~~~~ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/sibelia-3.0.7+dfsg/src/dnasequence.h:12: /build/reproducible-path/sibelia-3.0.7+dfsg/src/unrolledlist.h:36:45: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 36 | class iterator: public std::iterator | ^~~~~~~~ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/sibelia-3.0.7+dfsg/src/dnasequence.h:51:51: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 51 | class StrandIterator: public std::iterator | ^~~~~~~~ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:104:51: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 104 | struct FancyIterator: public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/14/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/14/string:47, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:12: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/sibelia-3.0.7+dfsg/src/dnasequence.h:51:51: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 51 | class StrandIterator: public std::iterator | ^~~~~~~~ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/sibelia-3.0.7+dfsg/src/dnasequence.h:12: /build/reproducible-path/sibelia-3.0.7+dfsg/src/unrolledlist.h:36:45: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 36 | class iterator: public std::iterator | ^~~~~~~~ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:104:51: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 104 | struct FancyIterator: public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/14/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/14/string:47, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:12: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/sibelia-3.0.7+dfsg/src/dnasequence.h:51:51: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 51 | class StrandIterator: public std::iterator | ^~~~~~~~ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/sibelia-3.0.7+dfsg/src/dnasequence.h:12, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/blockinstance.h:11: /build/reproducible-path/sibelia-3.0.7+dfsg/src/unrolledlist.h:36:45: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 36 | class iterator: public std::iterator | ^~~~~~~~ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/sibelia-3.0.7+dfsg/src/dnasequence.h:51:51: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 51 | class StrandIterator: public std::iterator | ^~~~~~~~ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:104:51: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 104 | struct FancyIterator: public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/14/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/14/string:47, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:12: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/sibelia-3.0.7+dfsg/src/dnasequence.h:12, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/blockinstance.h:11: /build/reproducible-path/sibelia-3.0.7+dfsg/src/unrolledlist.h:36:45: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 36 | class iterator: public std::iterator | ^~~~~~~~ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:104:51: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 104 | struct FancyIterator: public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/14/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/14/string:47, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:12: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/sibelia-3.0.7+dfsg/src/blockfinder.h:11: /build/reproducible-path/sibelia-3.0.7+dfsg/src/indexedsequence.h:37:22: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 37 | std::auto_ptr sequence_; | ^~~~~~~~ In file included from /usr/include/c++/14/memory:78, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:20: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ /build/reproducible-path/sibelia-3.0.7+dfsg/src/indexedsequence.h:38:22: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 38 | std::auto_ptr bifStorage_; | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ /build/reproducible-path/sibelia-3.0.7+dfsg/src/dnasequence.h:51:51: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 51 | class StrandIterator: public std::iterator | ^~~~~~~~ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/sibelia-3.0.7+dfsg/src/dnasequence.h:12, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/blockinstance.h:11: /build/reproducible-path/sibelia-3.0.7+dfsg/src/unrolledlist.h:36:45: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 36 | class iterator: public std::iterator | ^~~~~~~~ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/sibelia-3.0.7+dfsg/src/dnasequence.h:51:51: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 51 | class StrandIterator: public std::iterator | ^~~~~~~~ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:104:51: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 104 | struct FancyIterator: public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/14/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/14/string:47, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:12: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/sibelia-3.0.7+dfsg/src/dnasequence.h:12, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/blockinstance.h:11: /build/reproducible-path/sibelia-3.0.7+dfsg/src/unrolledlist.h:36:45: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 36 | class iterator: public std::iterator | ^~~~~~~~ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/sibelia-3.0.7+dfsg/src/indexedsequence.h:37:22: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 37 | std::auto_ptr sequence_; | ^~~~~~~~ In file included from /usr/include/c++/14/memory:78, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:20: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ /build/reproducible-path/sibelia-3.0.7+dfsg/src/indexedsequence.h:38:22: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 38 | std::auto_ptr bifStorage_; | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ /build/reproducible-path/sibelia-3.0.7+dfsg/src/dnasequence.h:51:51: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 51 | class StrandIterator: public std::iterator | ^~~~~~~~ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:104:51: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 104 | struct FancyIterator: public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/14/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/14/string:47, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:12: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/sibelia-3.0.7+dfsg/src/dnasequence.h:12: /build/reproducible-path/sibelia-3.0.7+dfsg/src/unrolledlist.h:36:45: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 36 | class iterator: public std::iterator | ^~~~~~~~ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/sibelia-3.0.7+dfsg/src/dnasequence.h:51:51: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 51 | class StrandIterator: public std::iterator | ^~~~~~~~ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/sibelia-3.0.7+dfsg/src/blockfinder.h:11: /build/reproducible-path/sibelia-3.0.7+dfsg/src/indexedsequence.h:37:22: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 37 | std::auto_ptr sequence_; | ^~~~~~~~ In file included from /usr/include/c++/14/memory:78, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:20: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ /build/reproducible-path/sibelia-3.0.7+dfsg/src/indexedsequence.h:38:22: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 38 | std::auto_ptr bifStorage_; | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from /build/reproducible-path/sibelia-3.0.7+dfsg/src/blockfinder.h:11: /build/reproducible-path/sibelia-3.0.7+dfsg/src/indexedsequence.h:37:22: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 37 | std::auto_ptr sequence_; | ^~~~~~~~ In file included from /usr/include/c++/14/memory:78, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:20: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ /build/reproducible-path/sibelia-3.0.7+dfsg/src/indexedsequence.h:38:22: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 38 | std::auto_ptr bifStorage_; | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from /build/reproducible-path/sibelia-3.0.7+dfsg/src/blockfinder.h:11: /build/reproducible-path/sibelia-3.0.7+dfsg/src/indexedsequence.h:37:22: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 37 | std::auto_ptr sequence_; | ^~~~~~~~ In file included from /usr/include/c++/14/memory:78, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:20: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ /build/reproducible-path/sibelia-3.0.7+dfsg/src/indexedsequence.h:38:22: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 38 | std::auto_ptr bifStorage_; | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from /build/reproducible-path/sibelia-3.0.7+dfsg/src/blockfinder.h:11: /build/reproducible-path/sibelia-3.0.7+dfsg/src/indexedsequence.h:37:22: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 37 | std::auto_ptr sequence_; | ^~~~~~~~ In file included from /usr/include/c++/14/memory:78, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:20: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ /build/reproducible-path/sibelia-3.0.7+dfsg/src/indexedsequence.h:38:22: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 38 | std::auto_ptr bifStorage_; | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:104:51: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 104 | struct FancyIterator: public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/14/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/14/string:47, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:12: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 65%] Building CXX object CMakeFiles/Sibelia.dir/serialization.cpp.o /usr/bin/c++ -I/build/reproducible-path/sibelia-3.0.7+dfsg/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/sibelia-3.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -MD -MT CMakeFiles/Sibelia.dir/serialization.cpp.o -MF CMakeFiles/Sibelia.dir/serialization.cpp.o.d -o CMakeFiles/Sibelia.dir/serialization.cpp.o -c /build/reproducible-path/sibelia-3.0.7+dfsg/src/serialization.cpp [ 70%] Building CXX object CMakeFiles/Sibelia.dir/synteny.cpp.o /usr/bin/c++ -I/build/reproducible-path/sibelia-3.0.7+dfsg/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/sibelia-3.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -MD -MT CMakeFiles/Sibelia.dir/synteny.cpp.o -MF CMakeFiles/Sibelia.dir/synteny.cpp.o.d -o CMakeFiles/Sibelia.dir/synteny.cpp.o -c /build/reproducible-path/sibelia-3.0.7+dfsg/src/synteny.cpp [ 75%] Building CXX object CMakeFiles/Sibelia.dir/test/unrolledlisttest.cpp.o /usr/bin/c++ -I/build/reproducible-path/sibelia-3.0.7+dfsg/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/sibelia-3.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -MD -MT CMakeFiles/Sibelia.dir/test/unrolledlisttest.cpp.o -MF CMakeFiles/Sibelia.dir/test/unrolledlisttest.cpp.o.d -o CMakeFiles/Sibelia.dir/test/unrolledlisttest.cpp.o -c /build/reproducible-path/sibelia-3.0.7+dfsg/src/test/unrolledlisttest.cpp [ 80%] Building CXX object CMakeFiles/Sibelia.dir/platform.cpp.o /usr/bin/c++ -I/build/reproducible-path/sibelia-3.0.7+dfsg/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/sibelia-3.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -MD -MT CMakeFiles/Sibelia.dir/platform.cpp.o -MF CMakeFiles/Sibelia.dir/platform.cpp.o.d -o CMakeFiles/Sibelia.dir/platform.cpp.o -c /build/reproducible-path/sibelia-3.0.7+dfsg/src/platform.cpp [ 85%] Building CXX object CMakeFiles/Sibelia.dir/stranditerator.cpp.o /usr/bin/c++ -I/build/reproducible-path/sibelia-3.0.7+dfsg/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/sibelia-3.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -MD -MT CMakeFiles/Sibelia.dir/stranditerator.cpp.o -MF CMakeFiles/Sibelia.dir/stranditerator.cpp.o.d -o CMakeFiles/Sibelia.dir/stranditerator.cpp.o -c /build/reproducible-path/sibelia-3.0.7+dfsg/src/stranditerator.cpp [ 90%] Building CXX object CMakeFiles/Sibelia.dir/vertexenumeration.cpp.o /usr/bin/c++ -I/build/reproducible-path/sibelia-3.0.7+dfsg/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/sibelia-3.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -MD -MT CMakeFiles/Sibelia.dir/vertexenumeration.cpp.o -MF CMakeFiles/Sibelia.dir/vertexenumeration.cpp.o.d -o CMakeFiles/Sibelia.dir/vertexenumeration.cpp.o -c /build/reproducible-path/sibelia-3.0.7+dfsg/src/vertexenumeration.cpp In file included from /usr/include/boost/bind/detail/requires_cxx11.hpp:9, from /usr/include/boost/bind/bind.hpp:24, from /usr/include/boost/bind.hpp:29, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:31, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/blockinstance.h:10, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/blockfinder.h:10, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/serialization.cpp:7: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/bind/detail/requires_cxx11.hpp:9, from /usr/include/boost/bind/bind.hpp:24, from /usr/include/boost/bind.hpp:29, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/test/../common.h:31, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/test/unrolledlisttest.h:10, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/test/unrolledlisttest.cpp:7: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/bind/detail/requires_cxx11.hpp:9, from /usr/include/boost/bind/bind.hpp:24, from /usr/include/boost/bind.hpp:29, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:31, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/blockinstance.h:10, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/blockfinder.h:10, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/synteny.cpp:9: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/sibelia-3.0.7+dfsg/src/test/../common.h:104:51: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 104 | struct FancyIterator: public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/14/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/14/string:47, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/test/../common.h:12: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/sibelia-3.0.7+dfsg/src/test/unrolledlisttest.h:11: /build/reproducible-path/sibelia-3.0.7+dfsg/src/test/../unrolledlist.h:36:45: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 36 | class iterator: public std::iterator | ^~~~~~~~ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:104:51: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 104 | struct FancyIterator: public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/14/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/14/string:47, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:12: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/sibelia-3.0.7+dfsg/src/dnasequence.h:12, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/blockinstance.h:11: /build/reproducible-path/sibelia-3.0.7+dfsg/src/unrolledlist.h:36:45: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 36 | class iterator: public std::iterator | ^~~~~~~~ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/sibelia-3.0.7+dfsg/src/dnasequence.h:51:51: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 51 | class StrandIterator: public std::iterator | ^~~~~~~~ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 95%] Building CXX object CMakeFiles/Sibelia.dir/resource.cpp.o /usr/bin/c++ -I/build/reproducible-path/sibelia-3.0.7+dfsg/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/sibelia-3.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -MD -MT CMakeFiles/Sibelia.dir/resource.cpp.o -MF CMakeFiles/Sibelia.dir/resource.cpp.o.d -o CMakeFiles/Sibelia.dir/resource.cpp.o -c /build/reproducible-path/sibelia-3.0.7+dfsg/src/resource.cpp /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:104:51: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 104 | struct FancyIterator: public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/14/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/14/string:47, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:12: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/sibelia-3.0.7+dfsg/src/dnasequence.h:12, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/blockinstance.h:11: /build/reproducible-path/sibelia-3.0.7+dfsg/src/unrolledlist.h:36:45: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 36 | class iterator: public std::iterator | ^~~~~~~~ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/sibelia-3.0.7+dfsg/src/dnasequence.h:51:51: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 51 | class StrandIterator: public std::iterator | ^~~~~~~~ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/sibelia-3.0.7+dfsg/src/blockfinder.h:11: /build/reproducible-path/sibelia-3.0.7+dfsg/src/indexedsequence.h:37:22: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 37 | std::auto_ptr sequence_; | ^~~~~~~~ In file included from /usr/include/c++/14/memory:78, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:20: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ /build/reproducible-path/sibelia-3.0.7+dfsg/src/indexedsequence.h:38:22: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 38 | std::auto_ptr bifStorage_; | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from /build/reproducible-path/sibelia-3.0.7+dfsg/src/blockfinder.h:11: /build/reproducible-path/sibelia-3.0.7+dfsg/src/indexedsequence.h:37:22: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 37 | std::auto_ptr sequence_; | ^~~~~~~~ In file included from /usr/include/c++/14/memory:78, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:20: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ /build/reproducible-path/sibelia-3.0.7+dfsg/src/indexedsequence.h:38:22: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 38 | std::auto_ptr bifStorage_; | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from /usr/include/boost/bind/detail/requires_cxx11.hpp:9, from /usr/include/boost/bind/bind.hpp:24, from /usr/include/boost/bind.hpp:29, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:31, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/fasta.h:10, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/postprocessor.h:13, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/postprocessor.cpp:9: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/bind/detail/requires_cxx11.hpp:9, from /usr/include/boost/bind/bind.hpp:24, from /usr/include/boost/bind.hpp:29, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:31, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/platform.h:10, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/platform.cpp:7: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/bind/detail/requires_cxx11.hpp:9, from /usr/include/boost/bind/bind.hpp:24, from /usr/include/boost/bind.hpp:29, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:31, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/fasta.h:10, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/dnasequence.h:10, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/stranditerator.cpp:7: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:104:51: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 104 | struct FancyIterator: public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/14/bits/stl_algobase.h:65, from /usr/include/c++/14/algorithm:60, from /usr/include/seqan/align.h:53, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/postprocessor.h:10: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/sibelia-3.0.7+dfsg/src/dnasequence.h:12, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/blockinstance.h:11, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/postprocessor.h:14: /build/reproducible-path/sibelia-3.0.7+dfsg/src/unrolledlist.h:36:45: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 36 | class iterator: public std::iterator | ^~~~~~~~ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/sibelia-3.0.7+dfsg/src/dnasequence.h:51:51: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 51 | class StrandIterator: public std::iterator | ^~~~~~~~ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /usr/include/boost/bind/detail/requires_cxx11.hpp:9, from /usr/include/boost/bind/bind.hpp:24, from /usr/include/boost/bind.hpp:29, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:31, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/fasta.h:10, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/dnasequence.h:10, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/hashing.h:10, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/indexedsequence.h:10, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/vertexenumeration.cpp:7: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:104:51: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 104 | struct FancyIterator: public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/14/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/14/string:47, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:12: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /usr/include/boost/bind/detail/requires_cxx11.hpp:9, from /usr/include/boost/bind/bind.hpp:24, from /usr/include/boost/bind.hpp:29, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:31, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/fasta.h:10, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/postprocessor.h:13, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/sibelia.cpp:8: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:104:51: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 104 | struct FancyIterator: public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/14/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/14/string:47, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:12: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/sibelia-3.0.7+dfsg/src/dnasequence.h:12: /build/reproducible-path/sibelia-3.0.7+dfsg/src/unrolledlist.h:36:45: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 36 | class iterator: public std::iterator | ^~~~~~~~ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/sibelia-3.0.7+dfsg/src/dnasequence.h:51:51: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 51 | class StrandIterator: public std::iterator | ^~~~~~~~ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:104:51: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 104 | struct FancyIterator: public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/14/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/14/string:47, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:12: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/sibelia-3.0.7+dfsg/src/dnasequence.h:12: /build/reproducible-path/sibelia-3.0.7+dfsg/src/unrolledlist.h:36:45: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 36 | class iterator: public std::iterator | ^~~~~~~~ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/sibelia-3.0.7+dfsg/src/dnasequence.h:51:51: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 51 | class StrandIterator: public std::iterator | ^~~~~~~~ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/sibelia-3.0.7+dfsg/src/indexedsequence.h:37:22: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 37 | std::auto_ptr sequence_; | ^~~~~~~~ In file included from /usr/include/c++/14/memory:78, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:20: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ /build/reproducible-path/sibelia-3.0.7+dfsg/src/indexedsequence.h:38:22: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 38 | std::auto_ptr bifStorage_; | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from /usr/include/boost/bind/detail/requires_cxx11.hpp:9, from /usr/include/boost/bind/bind.hpp:24, from /usr/include/boost/bind.hpp:29, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:31, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/resource.h:6, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/resource.cpp:6: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:104:51: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 104 | struct FancyIterator: public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/14/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/14/string:47, from /usr/include/tclap/SwitchArg.h:29, from /usr/include/tclap/CmdLine.h:27, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/sibelia.cpp:7: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/sibelia-3.0.7+dfsg/src/dnasequence.h:12, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/blockinstance.h:11, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/postprocessor.h:14: /build/reproducible-path/sibelia-3.0.7+dfsg/src/unrolledlist.h:36:45: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 36 | class iterator: public std::iterator | ^~~~~~~~ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/sibelia-3.0.7+dfsg/src/dnasequence.h:51:51: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 51 | class StrandIterator: public std::iterator | ^~~~~~~~ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/sibelia-3.0.7+dfsg/src/blockfinder.h:11, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/util.h:10, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/sibelia.cpp:9: /build/reproducible-path/sibelia-3.0.7+dfsg/src/indexedsequence.h:37:22: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 37 | std::auto_ptr sequence_; | ^~~~~~~~ In file included from /usr/include/c++/14/memory:78, from /usr/include/seqan/basic/test_system.h:53, from /usr/include/seqan/basic.h:65, from /usr/include/seqan/align.h:55, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/postprocessor.h:10: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ /build/reproducible-path/sibelia-3.0.7+dfsg/src/indexedsequence.h:38:22: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 38 | std::auto_ptr bifStorage_; | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ /build/reproducible-path/sibelia-3.0.7+dfsg/src/sibelia.cpp: In function ‘int main(int, char**)’: /build/reproducible-path/sibelia-3.0.7+dfsg/src/sibelia.cpp:239:22: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 239 | std::auto_ptr finder(inRAM.isSet() ? new SyntenyFinder::BlockFinder(chrList) : new SyntenyFinder::BlockFinder(chrList, tempDir)); | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:104:51: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 104 | struct FancyIterator: public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/14/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/14/string:47, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:12: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [100%] Linking CXX executable Sibelia /usr/bin/cmake -E cmake_link_script CMakeFiles/Sibelia.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/sibelia-3.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file,CMakeFiles/Sibelia.dir/link.d CMakeFiles/Sibelia.dir/sibelia.cpp.o CMakeFiles/Sibelia.dir/postprocessor.cpp.o CMakeFiles/Sibelia.dir/indexedsequence.cpp.o CMakeFiles/Sibelia.dir/util.cpp.o CMakeFiles/Sibelia.dir/outputgenerator.cpp.o CMakeFiles/Sibelia.dir/blockfinder.cpp.o CMakeFiles/Sibelia.dir/blockinstance.cpp.o CMakeFiles/Sibelia.dir/bifurcationstorage.cpp.o CMakeFiles/Sibelia.dir/bulgeremoval.cpp.o CMakeFiles/Sibelia.dir/dnasequence.cpp.o CMakeFiles/Sibelia.dir/edge.cpp.o CMakeFiles/Sibelia.dir/fasta.cpp.o CMakeFiles/Sibelia.dir/serialization.cpp.o CMakeFiles/Sibelia.dir/synteny.cpp.o CMakeFiles/Sibelia.dir/test/unrolledlisttest.cpp.o CMakeFiles/Sibelia.dir/platform.cpp.o CMakeFiles/Sibelia.dir/stranditerator.cpp.o CMakeFiles/Sibelia.dir/vertexenumeration.cpp.o CMakeFiles/Sibelia.dir/resource.cpp.o -o Sibelia -ldivsufsort make[3]: Leaving directory '/build/reproducible-path/sibelia-3.0.7+dfsg/obj-aarch64-linux-gnu' [100%] Built target Sibelia make[2]: Leaving directory '/build/reproducible-path/sibelia-3.0.7+dfsg/obj-aarch64-linux-gnu' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/sibelia-3.0.7+dfsg/obj-aarch64-linux-gnu/CMakeFiles 0 make[1]: Leaving directory '/build/reproducible-path/sibelia-3.0.7+dfsg/obj-aarch64-linux-gnu' debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/sibelia-3.0.7+dfsg' dh_auto_test --no-parallel make[1]: Leaving directory '/build/reproducible-path/sibelia-3.0.7+dfsg' create-stamp debian/debhelper-build-stamp dh_testroot -O--sourcedirectory=src dh_prep -O--sourcedirectory=src 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Installing: /build/reproducible-path/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/C-Sibelia/Staphylococcus_aureus/README.txt -- Installing: /build/reproducible-path/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/C-Sibelia/Staphylococcus_aureus/NCTC8325.fasta -- Installing: /build/reproducible-path/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/C-Sibelia/Staphylococcus_aureus/variant.vcf -- Installing: /build/reproducible-path/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/Sibelia -- Installing: /build/reproducible-path/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/Sibelia/Helicobacter_pylori -- Installing: /build/reproducible-path/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/Sibelia/Helicobacter_pylori/genomes_permutations.txt -- Installing: /build/reproducible-path/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/Sibelia/Helicobacter_pylori/circos -- Installing: /build/reproducible-path/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/Sibelia/Helicobacter_pylori/circos/circos.image.conf -- Installing: /build/reproducible-path/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/Sibelia/Helicobacter_pylori/circos/circos.highlight2.txt -- Installing: /build/reproducible-path/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/Sibelia/Helicobacter_pylori/circos/circos.sequences.txt -- Installing: /build/reproducible-path/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/Sibelia/Helicobacter_pylori/circos/circos.highlight4.txt -- Installing: /build/reproducible-path/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/Sibelia/Helicobacter_pylori/circos/circos.highlight1.txt -- Installing: /build/reproducible-path/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/Sibelia/Helicobacter_pylori/circos/circos.highlight.txt -- Installing: /build/reproducible-path/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/Sibelia/Helicobacter_pylori/circos/circos.png -- Installing: /build/reproducible-path/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/Sibelia/Helicobacter_pylori/circos/circos.highlight3.txt -- Installing: /build/reproducible-path/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/Sibelia/Helicobacter_pylori/circos/circos.segdup.txt -- Installing: /build/reproducible-path/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/Sibelia/Helicobacter_pylori/circos/circos.svg -- Installing: /build/reproducible-path/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/Sibelia/Helicobacter_pylori/circos/circos.conf -- Installing: /build/reproducible-path/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/Sibelia/Helicobacter_pylori/coverage_report.txt -- Installing: /build/reproducible-path/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/Sibelia/Helicobacter_pylori/Helicobacter_pylori.fasta -- Installing: /build/reproducible-path/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/Sibelia/Helicobacter_pylori/blocks_coords.txt -- Installing: /build/reproducible-path/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/Sibelia/Helicobacter_pylori/README.txt -- Installing: /build/reproducible-path/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/Sibelia/Helicobacter_pylori/d3_blocks_diagram.html -- Installing: /build/reproducible-path/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/Sibelia/Staphylococcus_aureus -- Installing: /build/reproducible-path/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/Sibelia/Staphylococcus_aureus/genomes_permutations.txt -- Installing: /build/reproducible-path/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/Sibelia/Staphylococcus_aureus/circos -- Installing: /build/reproducible-path/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/Sibelia/Staphylococcus_aureus/circos/circos.image.conf -- Installing: /build/reproducible-path/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/Sibelia/Staphylococcus_aureus/circos/circos.sequences.txt -- Installing: /build/reproducible-path/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/Sibelia/Staphylococcus_aureus/circos/circos.highlight.txt -- Installing: /build/reproducible-path/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/Sibelia/Staphylococcus_aureus/circos/circos.png -- Installing: /build/reproducible-path/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/Sibelia/Staphylococcus_aureus/circos/circos.segdup.txt -- Installing: /build/reproducible-path/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/Sibelia/Staphylococcus_aureus/circos/circos.svg -- Installing: /build/reproducible-path/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/Sibelia/Staphylococcus_aureus/circos/circos.conf -- Installing: /build/reproducible-path/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/Sibelia/Staphylococcus_aureus/coverage_report.txt -- Installing: /build/reproducible-path/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/Sibelia/Staphylococcus_aureus/blocks_coords.txt -- Installing: /build/reproducible-path/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/Sibelia/Staphylococcus_aureus/README.txt -- Installing: /build/reproducible-path/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/Sibelia/Staphylococcus_aureus/Staphylococcus.fasta -- Installing: /build/reproducible-path/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/Sibelia/Staphylococcus_aureus/d3_blocks_diagram.html -- Installing: /build/reproducible-path/sibelia-3.0.7+dfsg/debian/tmp/usr/bin/C-Sibelia.py -- Installing: /build/reproducible-path/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/utils -- Installing: /build/reproducible-path/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/utils/hidemappedcontigs.py -- Installing: /build/reproducible-path/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/utils/sortsequences.py -- Installing: /build/reproducible-path/sibelia-3.0.7+dfsg/debian/tmp/usr/lib/Sibelia make[1]: Leaving directory '/build/reproducible-path/sibelia-3.0.7+dfsg/obj-aarch64-linux-gnu' debian/rules override_dh_install make[1]: Entering directory '/build/reproducible-path/sibelia-3.0.7+dfsg' dh_install find debian -name LICENSE.txt -delete find debian -name INSTALL.md -delete make[1]: Leaving directory '/build/reproducible-path/sibelia-3.0.7+dfsg' dh_installdocs -O--sourcedirectory=src dh_installchangelogs -O--sourcedirectory=src debian/rules override_dh_installman-arch make[1]: Entering directory '/build/reproducible-path/sibelia-3.0.7+dfsg' dh_installman -a mv debian/sibelia/usr/share/man/py/man1/C-Sibelia.1 debian/sibelia/usr/share/man/man1/C-Sibelia.py.1 rm -rf debian/sibelia/usr/share/man/py make[1]: Leaving directory '/build/reproducible-path/sibelia-3.0.7+dfsg' dh_installman -O--sourcedirectory=src -Nsibelia dh_installinit -O--sourcedirectory=src dh_installsystemduser -O--sourcedirectory=src dh_lintian -O--sourcedirectory=src dh_perl -O--sourcedirectory=src dh_link -O--sourcedirectory=src dh_strip_nondeterminism -O--sourcedirectory=src dh_compress -O--sourcedirectory=src dh_fixperms -O--sourcedirectory=src dh_missing -O--sourcedirectory=src dh_dwz -O--sourcedirectory=src dh_strip -O--sourcedirectory=src dh_makeshlibs -O--sourcedirectory=src dh_shlibdeps -O--sourcedirectory=src dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 from: /lib/ld-linux-aarch64.so.1 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 to: /lib/ld-linux-aarch64.so.1.usr-is-merged dh_installdeb -O--sourcedirectory=src dh_gencontrol -O--sourcedirectory=src dh_md5sums -O--sourcedirectory=src dh_builddeb -O--sourcedirectory=src dpkg-deb: building package 'sibelia-dbgsym' in '../sibelia-dbgsym_3.0.7+dfsg-4_arm64.deb'. dpkg-deb: building package 'sibelia' in '../sibelia_3.0.7+dfsg-4_arm64.deb'. dpkg-deb: building package 'sibelia-examples' in '../sibelia-examples_3.0.7+dfsg-4_all.deb'. dpkg-genbuildinfo --build=binary -O../sibelia_3.0.7+dfsg-4_arm64.buildinfo dpkg-genchanges --build=binary -O../sibelia_3.0.7+dfsg-4_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/1763354 and its subdirectories I: Current time: Mon Nov 25 13:53:26 -12 2024 I: pbuilder-time-stamp: 1732586006 Tue Nov 26 01:53:28 UTC 2024 I: 1st build successful. Starting 2nd build on remote node codethink01-arm64.debian.net. Tue Nov 26 01:53:28 UTC 2024 I: Preparing to do remote build '2' on codethink01-arm64.debian.net. Tue Nov 26 01:53:28 UTC 2024 - checking /var/lib/jenkins/offline_nodes if codethink01-arm64.debian.net is marked as down. Tue Nov 26 01:53:28 UTC 2024 - checking via ssh if codethink01-arm64.debian.net is up. removed '/tmp/read-only-fs-test-tZZHbb' ==================================================================================== Mon Dec 29 08:16:30 UTC 2025 - running /srv/jenkins/bin/reproducible_build.sh (for job /srv/jenkins/bin/reproducible_build.sh) on codethink01-arm64, called using "2 sibelia experimental /srv/reproducible-results/rbuild-debian/r-b-build.Jw2wMKXd 3.0.7+dfsg-4" as arguments. Mon Dec 29 08:16:30 UTC 2025 - actually running "reproducible_build.sh" (md5sum 68e686e434c9ab7bc3ec047d8b309cbc) as "/tmp/jenkins-script-0mzA3Y7v" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Mon Dec 29 08:16:30 UTC 2025 I: Downloading source for experimental/sibelia=3.0.7+dfsg-4 Reading package lists... NOTICE: 'sibelia' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/sibelia.git Please use: git clone https://salsa.debian.org/med-team/sibelia.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 4846 kB of source archives. Get:1 http://deb.debian.org/debian experimental/main sibelia 3.0.7+dfsg-4 (dsc) [2156 B] Get:2 http://deb.debian.org/debian experimental/main sibelia 3.0.7+dfsg-4 (tar) [4833 kB] Get:3 http://deb.debian.org/debian experimental/main sibelia 3.0.7+dfsg-4 (diff) [10.9 kB] Fetched 4846 kB in 0s (93.8 MB/s) Download complete and in download only mode Reading package lists... NOTICE: 'sibelia' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/sibelia.git Please use: git clone https://salsa.debian.org/med-team/sibelia.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 4846 kB of source archives. Get:1 http://deb.debian.org/debian experimental/main sibelia 3.0.7+dfsg-4 (dsc) [2156 B] Get:2 http://deb.debian.org/debian experimental/main sibelia 3.0.7+dfsg-4 (tar) [4833 kB] Get:3 http://deb.debian.org/debian experimental/main sibelia 3.0.7+dfsg-4 (diff) [10.9 kB] Fetched 4846 kB in 0s (93.8 MB/s) Download complete and in download only mode ============================================================================= Re-Building sibelia in experimental on arm64 on codethink01-arm64 now. Date: Mon Dec 29 08:16:30 GMT 2025 Date UTC: Mon Dec 29 08:16:30 UTC 2025 ============================================================================= ++ mktemp -t pbuilderrc_XXXX --tmpdir=/srv/reproducible-results/rbuild-debian/r-b-build.Jw2wMKXd + local TMPCFG=/srv/reproducible-results/rbuild-debian/r-b-build.Jw2wMKXd/pbuilderrc_IkMa + case ${ARCH} in + case $ARCH in + locale=nl_BE + language=nl + case "${SUITE}" in + reproducible_buildflags=+all + extra_deb_build_options= + case "${SRCPACKAGE}" in + cat + echo BUILDDIR=/build/reproducible-path + '[' sibelia = debian-installer -o sibelia = debian-installer-netboot-images ']' + pbuilder_options=() + local pbuilder_options + DEBBUILDOPTS=-b + BINARYTARGET= + '[' sibelia = u-boot ']' + case "${SRCPACKAGE}" in + PBUILDERTIMEOUT=24 + local PRESULT=0 + sudo timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.Jw2wMKXd/pbuilderrc_IkMa --distribution experimental --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/experimental-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.Jw2wMKXd/b2 --logfile b2/build.log sibelia_3.0.7+dfsg-4.dsc W: /root/.pbuilderrc does not exist I: Logging to b2/build.log I: pbuilder: network access will be disabled during build I: Current time: Mon Dec 29 22:16:30 +14 2025 I: pbuilder-time-stamp: 1766996190 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/experimental-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 [sibelia_3.0.7+dfsg-4.dsc] I: copying [./sibelia_3.0.7+dfsg.orig.tar.xz] I: copying [./sibelia_3.0.7+dfsg-4.debian.tar.xz] I: Extracting source gpgv: Signature made Mon Nov 25 14:29:08 2024 gpgv: using RSA key 724D609337113C710550D7473C26763F6C67E6E2 gpgv: issuer "crusoe@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./sibelia_3.0.7+dfsg-4.dsc: no acceptable signature found dpkg-source: info: extracting sibelia in sibelia-3.0.7+dfsg dpkg-source: info: unpacking sibelia_3.0.7+dfsg.orig.tar.xz dpkg-source: info: unpacking sibelia_3.0.7+dfsg-4.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying use_debian_packaged_libdivsufsort.patch dpkg-source: info: applying use_debian_packaged_lagan.patch dpkg-source: info: applying snpeff_is_removed.patch dpkg-source: info: applying 2to3.patch dpkg-source: info: applying 0005-Upgrade-to-SeqAn-2.5.0.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/3116528/tmp/hooks/D01_modify_environment starting debug: Running on codethink01-arm64. I: Changing host+domainname to test build reproducibility I: Adding a custom variable just for the fun of it... I: Changing /bin/sh to bash '/bin/sh' -> '/bin/bash' lrwxrwxrwx 1 root root 9 Dec 29 08:16 /bin/sh -> /bin/bash I: Setting pbuilder2's login shell to /bin/bash I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other I: user script /srv/workspace/pbuilder/3116528/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/3116528/tmp/hooks/D02_print_environment starting I: set BASH=/bin/sh BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath BASH_ALIASES=() BASH_ARGC=() BASH_ARGV=() BASH_CMDS=() BASH_LINENO=([0]="12" [1]="0") BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") BASH_VERSINFO=([0]="5" [1]="2" [2]="32" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu") BASH_VERSION='5.2.32(1)-release' BUILDDIR=/build/reproducible-path BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=arm64 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' DIRSTACK=() DISTRIBUTION=experimental EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=aarch64 HOST_ARCH=arm64 IFS=' ' INVOCATION_ID=2827dba685cc443ab2e446158a93094f LANG=C LANGUAGE=nl_BE:nl LC_ALL=C MACHTYPE=aarch64-unknown-linux-gnu MAIL=/var/mail/root OPTERR=1 OPTIND=1 OSTYPE=linux-gnu PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path PBCURRENTCOMMANDLINEOPERATION=build PBUILDER_OPERATION=build PBUILDER_PKGDATADIR=/usr/share/pbuilder PBUILDER_PKGLIBDIR=/usr/lib/pbuilder PBUILDER_SYSCONFDIR=/etc PIPESTATUS=([0]="0") POSIXLY_CORRECT=y PPID=3116528 PS4='+ ' PWD=/ SHELL=/bin/bash SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix SHLVL=3 SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.Jw2wMKXd/pbuilderrc_IkMa --distribution experimental --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/experimental-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.Jw2wMKXd/b2 --logfile b2/build.log sibelia_3.0.7+dfsg-4.dsc' SUDO_GID=109 SUDO_UID=104 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://192.168.101.4:3128 I: uname -a Linux i-capture-the-hostname 6.1.0-28-cloud-arm64 #1 SMP Debian 6.1.119-1 (2024-11-22) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Nov 22 2024 /bin -> usr/bin I: user script /srv/workspace/pbuilder/3116528/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: arm64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 12), cmake, libdivsufsort-dev, libboost-dev, libseqan2-dev (= 2.5.0~rc3+dfsg-1), libtclap-dev, libhts-dev dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 20083 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 (= 12); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on cmake; however: Package cmake is not installed. pbuilder-satisfydepends-dummy depends on libdivsufsort-dev; however: Package libdivsufsort-dev is not installed. pbuilder-satisfydepends-dummy depends on libboost-dev; however: Package libboost-dev is not installed. pbuilder-satisfydepends-dummy depends on libseqan2-dev (= 2.5.0~rc3+dfsg-1); however: Package libseqan2-dev is not installed. pbuilder-satisfydepends-dummy depends on libtclap-dev; however: Package libtclap-dev is not installed. pbuilder-satisfydepends-dummy depends on libhts-dev; however: Package libhts-dev is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} cmake{a} cmake-data{a} comerr-dev{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} krb5-multidev{a} libarchive-zip-perl{a} libarchive13t64{a} libboost-dev{a} libboost1.83-dev{a} libbrotli-dev{a} libbrotli1{a} libbz2-dev{a} libcom-err2{a} libcurl3t64-gnutls{a} libcurl4-gnutls-dev{a} libcurl4t64{a} libdebhelper-perl{a} libdeflate-dev{a} libdeflate0{a} libdivsufsort-dev{a} libdivsufsort3{a} libelf1t64{a} libevent-2.1-7t64{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libgmp-dev{a} libgmpxx4ldbl{a} libgnutls-dane0t64{a} libgnutls-openssl27t64{a} libgnutls28-dev{a} libgssapi-krb5-2{a} libgssrpc4t64{a} libhts-dev{a} libhts3t64{a} libhtscodecs2{a} libicu72{a} libidn2-dev{a} libjsoncpp26{a} libk5crypto3{a} libkadm5clnt-mit12{a} libkadm5srv-mit12{a} libkdb5-10t64{a} libkeyutils1{a} libkrb5-3{a} libkrb5-dev{a} libkrb5support0{a} libldap-2.5-0{a} libldap-dev{a} liblzma-dev{a} libmagic-mgc{a} libmagic1t64{a} libnghttp2-14{a} libnghttp2-dev{a} libnghttp3-9{a} libnghttp3-dev{a} libngtcp2-16{a} libngtcp2-crypto-gnutls-dev{a} libngtcp2-crypto-gnutls8{a} libngtcp2-dev{a} libp11-kit-dev{a} libpipeline1{a} libpkgconf3{a} libproc2-0{a} libpsl-dev{a} libpsl5t64{a} librhash1{a} librtmp-dev{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libssh2-1-dev{a} libssh2-1t64{a} libssl-dev{a} libtasn1-6-dev{a} libtclap-dev{a} libtool{a} libuchardet0{a} libunbound8{a} libuv1t64{a} libxml2{a} libzstd-dev{a} m4{a} man-db{a} nettle-dev{a} pkgconf{a} pkgconf-bin{a} po-debconf{a} procps{a} sensible-utils{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 libtasn1-doc linux-sysctl-defaults lynx psmisc publicsuffix wget 0 packages upgraded, 103 newly installed, 0 to remove and 0 not upgraded. Need to get 64.8 MB of archives. After unpacking 370 MB will be used. The following packages have unmet dependencies: pbuilder-satisfydepends-dummy : Depends: libseqan2-dev (= 2.5.0~rc3+dfsg-1) but it is not going to be installed The following actions will resolve these dependencies: Install the following packages: 1) libseqan2-dev [2.5.0~rc3+dfsg-1 (experimental)] The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} cmake{a} cmake-data{a} comerr-dev{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} krb5-multidev{a} libarchive-zip-perl{a} libarchive13t64{a} libboost-dev{a} libboost1.83-dev{a} libbrotli-dev{a} libbrotli1{a} libbz2-dev{a} libcom-err2{a} libcurl3t64-gnutls{a} libcurl4-gnutls-dev{a} libcurl4t64{a} libdebhelper-perl{a} libdeflate-dev{a} libdeflate0{a} libdivsufsort-dev{a} libdivsufsort3{a} libelf1t64{a} libevent-2.1-7t64{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libgmp-dev{a} libgmpxx4ldbl{a} libgnutls-dane0t64{a} libgnutls-openssl27t64{a} libgnutls28-dev{a} libgssapi-krb5-2{a} libgssrpc4t64{a} libhts-dev{a} libhts3t64{a} libhtscodecs2{a} libicu72{a} libidn2-dev{a} libjsoncpp26{a} libk5crypto3{a} libkadm5clnt-mit12{a} libkadm5srv-mit12{a} libkdb5-10t64{a} libkeyutils1{a} libkrb5-3{a} libkrb5-dev{a} libkrb5support0{a} libldap-2.5-0{a} libldap-dev{a} liblzma-dev{a} libmagic-mgc{a} libmagic1t64{a} libnghttp2-14{a} libnghttp2-dev{a} libnghttp3-9{a} libnghttp3-dev{a} libngtcp2-16{a} libngtcp2-crypto-gnutls-dev{a} libngtcp2-crypto-gnutls8{a} libngtcp2-dev{a} libp11-kit-dev{a} libpipeline1{a} libpkgconf3{a} libproc2-0{a} libpsl-dev{a} libpsl5t64{a} librhash1{a} librtmp-dev{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libseqan2-dev{a} libssh2-1-dev{a} libssh2-1t64{a} libssl-dev{a} libtasn1-6-dev{a} libtclap-dev{a} libtool{a} libuchardet0{a} libunbound8{a} libuv1t64{a} libxml2{a} libzstd-dev{a} m4{a} man-db{a} nettle-dev{a} pkgconf{a} pkgconf-bin{a} po-debconf{a} procps{a} sensible-utils{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 libtasn1-doc linux-sysctl-defaults lynx psmisc publicsuffix wget 0 packages upgraded, 104 newly installed, 0 to remove and 0 not upgraded. Need to get 66.0 MB of archives. After unpacking 383 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main arm64 libproc2-0 arm64 2:4.0.4-6 [62.3 kB] Get: 2 http://deb.debian.org/debian unstable/main arm64 procps arm64 2:4.0.4-6 [872 kB] Get: 3 http://deb.debian.org/debian unstable/main arm64 sensible-utils all 0.0.24 [24.8 kB] Get: 4 http://deb.debian.org/debian unstable/main arm64 libmagic-mgc arm64 1:5.45-3+b1 [314 kB] Get: 5 http://deb.debian.org/debian unstable/main arm64 libmagic1t64 arm64 1:5.45-3+b1 [102 kB] Get: 6 http://deb.debian.org/debian unstable/main arm64 file arm64 1:5.45-3+b1 [43.4 kB] Get: 7 http://deb.debian.org/debian unstable/main arm64 gettext-base arm64 0.22.5-2 [198 kB] Get: 8 http://deb.debian.org/debian unstable/main arm64 libuchardet0 arm64 0.0.8-1+b2 [69.2 kB] Get: 9 http://deb.debian.org/debian unstable/main arm64 groff-base arm64 1.23.0-5 [1129 kB] Get: 10 http://deb.debian.org/debian unstable/main arm64 bsdextrautils arm64 2.40.2-11 [91.2 kB] Get: 11 http://deb.debian.org/debian unstable/main arm64 libpipeline1 arm64 1.5.8-1 [40.2 kB] Get: 12 http://deb.debian.org/debian unstable/main arm64 man-db arm64 2.13.0-1 [1404 kB] Get: 13 http://deb.debian.org/debian unstable/main arm64 m4 arm64 1.4.19-4 [277 kB] Get: 14 http://deb.debian.org/debian unstable/main arm64 autoconf all 2.72-3 [493 kB] Get: 15 http://deb.debian.org/debian unstable/main arm64 autotools-dev all 20220109.1 [51.6 kB] Get: 16 http://deb.debian.org/debian unstable/main arm64 automake all 1:1.16.5-1.3 [823 kB] Get: 17 http://deb.debian.org/debian unstable/main arm64 autopoint all 0.22.5-2 [723 kB] Get: 18 http://deb.debian.org/debian unstable/main arm64 cmake-data all 3.31.1-1 [2267 kB] Get: 19 http://deb.debian.org/debian unstable/main arm64 libicu72 arm64 72.1-5+b1 [9239 kB] Get: 20 http://deb.debian.org/debian unstable/main arm64 libxml2 arm64 2.12.7+dfsg+really2.9.14-0.2+b1 [630 kB] Get: 21 http://deb.debian.org/debian unstable/main arm64 libarchive13t64 arm64 3.7.4-1.1 [323 kB] Get: 22 http://deb.debian.org/debian unstable/main arm64 libbrotli1 arm64 1.1.0-2+b6 [297 kB] Get: 23 http://deb.debian.org/debian unstable/main arm64 libkrb5support0 arm64 1.21.3-3 [32.1 kB] Get: 24 http://deb.debian.org/debian unstable/main arm64 libcom-err2 arm64 1.47.1-1+b1 [23.1 kB] Get: 25 http://deb.debian.org/debian unstable/main arm64 libk5crypto3 arm64 1.21.3-3 [80.8 kB] Get: 26 http://deb.debian.org/debian unstable/main arm64 libkeyutils1 arm64 1.6.3-4 [9352 B] Get: 27 http://deb.debian.org/debian unstable/main arm64 libkrb5-3 arm64 1.21.3-3 [310 kB] Get: 28 http://deb.debian.org/debian unstable/main arm64 libgssapi-krb5-2 arm64 1.21.3-3 [126 kB] Get: 29 http://deb.debian.org/debian unstable/main arm64 libsasl2-modules-db arm64 2.1.28+dfsg1-8 [20.0 kB] Get: 30 http://deb.debian.org/debian unstable/main arm64 libsasl2-2 arm64 2.1.28+dfsg1-8 [55.4 kB] Get: 31 http://deb.debian.org/debian unstable/main arm64 libldap-2.5-0 arm64 2.5.18+dfsg-3+b1 [175 kB] Get: 32 http://deb.debian.org/debian unstable/main arm64 libnghttp2-14 arm64 1.64.0-1 [71.3 kB] Get: 33 http://deb.debian.org/debian unstable/main arm64 libpsl5t64 arm64 0.21.2-1.1+b1 [57.1 kB] Get: 34 http://deb.debian.org/debian unstable/main arm64 librtmp1 arm64 2.4+20151223.gitfa8646d.1-2+b5 [56.8 kB] Get: 35 http://deb.debian.org/debian unstable/main arm64 libssh2-1t64 arm64 1.11.1-1 [235 kB] Get: 36 http://deb.debian.org/debian unstable/main arm64 libcurl4t64 arm64 8.11.0-1 [322 kB] Get: 37 http://deb.debian.org/debian unstable/main arm64 libexpat1 arm64 2.6.4-1 [90.7 kB] Get: 38 http://deb.debian.org/debian unstable/main arm64 libjsoncpp26 arm64 1.9.6-3 [72.9 kB] Get: 39 http://deb.debian.org/debian unstable/main arm64 librhash1 arm64 1.4.5-1 [129 kB] Get: 40 http://deb.debian.org/debian unstable/main arm64 libuv1t64 arm64 1.48.0-7 [143 kB] Get: 41 http://deb.debian.org/debian unstable/main arm64 cmake arm64 3.31.1-1 [9873 kB] Get: 42 http://deb.debian.org/debian unstable/main arm64 comerr-dev arm64 2.1-1.47.1-1+b1 [55.1 kB] Get: 43 http://deb.debian.org/debian unstable/main arm64 libdebhelper-perl all 13.20 [89.7 kB] Get: 44 http://deb.debian.org/debian unstable/main arm64 libtool all 2.4.7-8 [517 kB] Get: 45 http://deb.debian.org/debian unstable/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 46 http://deb.debian.org/debian unstable/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 47 http://deb.debian.org/debian unstable/main arm64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 48 http://deb.debian.org/debian unstable/main arm64 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 49 http://deb.debian.org/debian unstable/main arm64 libelf1t64 arm64 0.192-4 [189 kB] Get: 50 http://deb.debian.org/debian unstable/main arm64 dwz arm64 0.15-1+b1 [102 kB] Get: 51 http://deb.debian.org/debian unstable/main arm64 gettext arm64 0.22.5-2 [1532 kB] Get: 52 http://deb.debian.org/debian unstable/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 53 http://deb.debian.org/debian unstable/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 54 http://deb.debian.org/debian unstable/main arm64 debhelper all 13.20 [915 kB] Get: 55 http://deb.debian.org/debian unstable/main arm64 libgssrpc4t64 arm64 1.21.3-3 [56.7 kB] Get: 56 http://deb.debian.org/debian unstable/main arm64 libkadm5clnt-mit12 arm64 1.21.3-3 [40.3 kB] Get: 57 http://deb.debian.org/debian unstable/main arm64 libkdb5-10t64 arm64 1.21.3-3 [40.8 kB] Get: 58 http://deb.debian.org/debian unstable/main arm64 libkadm5srv-mit12 arm64 1.21.3-3 [52.2 kB] Get: 59 http://deb.debian.org/debian unstable/main arm64 krb5-multidev arm64 1.21.3-3 [126 kB] Get: 60 http://deb.debian.org/debian unstable/main arm64 libboost1.83-dev arm64 1.83.0-3.2+b1 [10.6 MB] Get: 61 http://deb.debian.org/debian unstable/main arm64 libboost-dev arm64 1.83.0.2+b2 [3828 B] Get: 62 http://deb.debian.org/debian unstable/main arm64 libbrotli-dev arm64 1.1.0-2+b6 [308 kB] Get: 63 http://deb.debian.org/debian unstable/main arm64 libbz2-dev arm64 1.0.8-6 [31.9 kB] Get: 64 http://deb.debian.org/debian unstable/main arm64 libnghttp3-9 arm64 1.4.0-1+b1 [59.6 kB] Get: 65 http://deb.debian.org/debian unstable/main arm64 libngtcp2-16 arm64 1.6.0-1 [112 kB] Get: 66 http://deb.debian.org/debian unstable/main arm64 libngtcp2-crypto-gnutls8 arm64 1.6.0-1 [18.5 kB] Get: 67 http://deb.debian.org/debian unstable/main arm64 libcurl3t64-gnutls arm64 8.11.0-1 [331 kB] Get: 68 http://deb.debian.org/debian unstable/main arm64 libevent-2.1-7t64 arm64 2.1.12-stable-10+b1 [170 kB] Get: 69 http://deb.debian.org/debian unstable/main arm64 libunbound8 arm64 1.22.0-1 [553 kB] Get: 70 http://deb.debian.org/debian unstable/main arm64 libgnutls-dane0t64 arm64 3.8.8-2 [446 kB] Get: 71 http://deb.debian.org/debian unstable/main arm64 libgnutls-openssl27t64 arm64 3.8.8-2 [446 kB] Get: 72 http://deb.debian.org/debian unstable/main arm64 libidn2-dev arm64 2.3.7-2+b1 [122 kB] Get: 73 http://deb.debian.org/debian unstable/main arm64 libp11-kit-dev arm64 0.25.5-2+b1 [208 kB] Get: 74 http://deb.debian.org/debian unstable/main arm64 libtasn1-6-dev arm64 4.19.0-3+b3 [96.5 kB] Get: 75 http://deb.debian.org/debian unstable/main arm64 libgmpxx4ldbl arm64 2:6.3.0+dfsg-2+b2 [329 kB] Get: 76 http://deb.debian.org/debian unstable/main arm64 libgmp-dev arm64 2:6.3.0+dfsg-2+b2 [621 kB] Get: 77 http://deb.debian.org/debian unstable/main arm64 nettle-dev arm64 3.10-1+b1 [1324 kB] Get: 78 http://deb.debian.org/debian unstable/main arm64 libgnutls28-dev arm64 3.8.8-2 [1404 kB] Get: 79 http://deb.debian.org/debian unstable/main arm64 libkrb5-dev arm64 1.21.3-3 [15.8 kB] Get: 80 http://deb.debian.org/debian unstable/main arm64 libldap-dev arm64 2.5.18+dfsg-3+b1 [300 kB] Get: 81 http://deb.debian.org/debian unstable/main arm64 libpkgconf3 arm64 1.8.1-4 [35.3 kB] Get: 82 http://deb.debian.org/debian unstable/main arm64 pkgconf-bin arm64 1.8.1-4 [29.6 kB] Get: 83 http://deb.debian.org/debian unstable/main arm64 pkgconf arm64 1.8.1-4 [26.1 kB] Get: 84 http://deb.debian.org/debian unstable/main arm64 libnghttp2-dev arm64 1.64.0-1 [112 kB] Get: 85 http://deb.debian.org/debian unstable/main arm64 libnghttp3-dev arm64 1.4.0-1+b1 [85.2 kB] Get: 86 http://deb.debian.org/debian unstable/main arm64 libngtcp2-crypto-gnutls-dev arm64 1.6.0-1 [23.7 kB] Get: 87 http://deb.debian.org/debian unstable/main arm64 libngtcp2-dev arm64 1.6.0-1 [165 kB] Get: 88 http://deb.debian.org/debian unstable/main arm64 libpsl-dev arm64 0.21.2-1.1+b1 [77.9 kB] Get: 89 http://deb.debian.org/debian unstable/main arm64 zlib1g-dev arm64 1:1.3.dfsg+really1.3.1-1+b1 [917 kB] Get: 90 http://deb.debian.org/debian unstable/main arm64 librtmp-dev arm64 2.4+20151223.gitfa8646d.1-2+b5 [67.5 kB] Get: 91 http://deb.debian.org/debian unstable/main arm64 libssl-dev arm64 3.3.2-2 [3185 kB] Get: 92 http://deb.debian.org/debian unstable/main arm64 libssh2-1-dev arm64 1.11.1-1 [388 kB] Get: 93 http://deb.debian.org/debian unstable/main arm64 libzstd-dev arm64 1.5.6+dfsg-1+b1 [329 kB] Get: 94 http://deb.debian.org/debian unstable/main arm64 libcurl4-gnutls-dev arm64 8.11.0-1 [459 kB] Get: 95 http://deb.debian.org/debian unstable/main arm64 libdeflate0 arm64 1.22-1 [42.2 kB] Get: 96 http://deb.debian.org/debian unstable/main arm64 libdeflate-dev arm64 1.22-1 [51.2 kB] Get: 97 http://deb.debian.org/debian unstable/main arm64 libdivsufsort3 arm64 2.0.1-6+b1 [39.9 kB] Get: 98 http://deb.debian.org/debian unstable/main arm64 libdivsufsort-dev arm64 2.0.1-6+b1 [19.1 kB] Get: 99 http://deb.debian.org/debian unstable/main arm64 libhtscodecs2 arm64 1.6.1-1 [74.6 kB] Get: 100 http://deb.debian.org/debian unstable/main arm64 libhts3t64 arm64 1.20+ds-2 [420 kB] Get: 101 http://deb.debian.org/debian unstable/main arm64 liblzma-dev arm64 5.6.3-1+b1 [312 kB] Get: 102 http://deb.debian.org/debian unstable/main arm64 libhts-dev arm64 1.20+ds-2 [1626 kB] Get: 103 http://deb.debian.org/debian experimental/main arm64 libseqan2-dev all 2.5.0~rc3+dfsg-1 [1222 kB] Get: 104 http://deb.debian.org/debian unstable/main arm64 libtclap-dev arm64 1.2.5-1+b1 [3359 kB] Fetched 66.0 MB in 1s (125 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libproc2-0:arm64. (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 ... 20083 files and directories currently installed.) Preparing to unpack .../000-libproc2-0_2%3a4.0.4-6_arm64.deb ... Unpacking libproc2-0:arm64 (2:4.0.4-6) ... Selecting previously unselected package procps. Preparing to unpack .../001-procps_2%3a4.0.4-6_arm64.deb ... Unpacking procps (2:4.0.4-6) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../002-sensible-utils_0.0.24_all.deb ... Unpacking sensible-utils (0.0.24) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../003-libmagic-mgc_1%3a5.45-3+b1_arm64.deb ... Unpacking libmagic-mgc (1:5.45-3+b1) ... Selecting previously unselected package libmagic1t64:arm64. Preparing to unpack .../004-libmagic1t64_1%3a5.45-3+b1_arm64.deb ... Unpacking libmagic1t64:arm64 (1:5.45-3+b1) ... Selecting previously unselected package file. Preparing to unpack .../005-file_1%3a5.45-3+b1_arm64.deb ... Unpacking file (1:5.45-3+b1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../006-gettext-base_0.22.5-2_arm64.deb ... Unpacking gettext-base (0.22.5-2) ... Selecting previously unselected package libuchardet0:arm64. Preparing to unpack .../007-libuchardet0_0.0.8-1+b2_arm64.deb ... Unpacking libuchardet0:arm64 (0.0.8-1+b2) ... Selecting previously unselected package groff-base. Preparing to unpack .../008-groff-base_1.23.0-5_arm64.deb ... Unpacking groff-base (1.23.0-5) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../009-bsdextrautils_2.40.2-11_arm64.deb ... Unpacking bsdextrautils (2.40.2-11) ... Selecting previously unselected package libpipeline1:arm64. Preparing to unpack .../010-libpipeline1_1.5.8-1_arm64.deb ... Unpacking libpipeline1:arm64 (1.5.8-1) ... Selecting previously unselected package man-db. Preparing to unpack .../011-man-db_2.13.0-1_arm64.deb ... Unpacking man-db (2.13.0-1) ... Selecting previously unselected package m4. Preparing to unpack .../012-m4_1.4.19-4_arm64.deb ... Unpacking m4 (1.4.19-4) ... Selecting previously unselected package autoconf. Preparing to unpack .../013-autoconf_2.72-3_all.deb ... Unpacking autoconf (2.72-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../014-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. 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Building tag database... -> Finished parsing the build-deps I: Building the package I: user script /srv/workspace/pbuilder/3116528/tmp/hooks/A99_set_merged_usr starting Not re-configuring usrmerge for experimental I: user script /srv/workspace/pbuilder/3116528/tmp/hooks/A99_set_merged_usr finished hostname: Name or service not known I: Running cd /build/reproducible-path/sibelia-3.0.7+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../sibelia_3.0.7+dfsg-4_source.changes dpkg-buildpackage: info: source package sibelia dpkg-buildpackage: info: source version 3.0.7+dfsg-4 dpkg-buildpackage: info: source distribution experimental dpkg-buildpackage: info: source changed by Michael R. Crusoe dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 debian/rules clean dh clean --sourcedirectory=src dh_auto_clean -O--sourcedirectory=src dh_autoreconf_clean -O--sourcedirectory=src dh_clean -O--sourcedirectory=src debian/rules binary dh binary --sourcedirectory=src dh_update_autotools_config -O--sourcedirectory=src dh_autoreconf -O--sourcedirectory=src dh_auto_configure -O--sourcedirectory=src cd obj-aarch64-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 "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/aarch64-linux-gnu ../src 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 CXX compiler identification is GNU 14.2.0 -- 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 -- Configuring done (0.5s) -- 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_FIND_USE_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/sibelia-3.0.7+dfsg/obj-aarch64-linux-gnu dh_auto_build -O--sourcedirectory=src cd obj-aarch64-linux-gnu && make -j12 "INSTALL=install --strip-program=true" VERBOSE=1 make[1]: Entering directory '/build/reproducible-path/sibelia-3.0.7+dfsg/obj-aarch64-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/sibelia-3.0.7+dfsg/src -B/build/reproducible-path/sibelia-3.0.7+dfsg/obj-aarch64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/sibelia-3.0.7+dfsg/obj-aarch64-linux-gnu/CMakeFiles /build/reproducible-path/sibelia-3.0.7+dfsg/obj-aarch64-linux-gnu//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/build/reproducible-path/sibelia-3.0.7+dfsg/obj-aarch64-linux-gnu' make -f CMakeFiles/Sibelia.dir/build.make CMakeFiles/Sibelia.dir/depend make[3]: Entering directory '/build/reproducible-path/sibelia-3.0.7+dfsg/obj-aarch64-linux-gnu' cd /build/reproducible-path/sibelia-3.0.7+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sibelia-3.0.7+dfsg/src /build/reproducible-path/sibelia-3.0.7+dfsg/src /build/reproducible-path/sibelia-3.0.7+dfsg/obj-aarch64-linux-gnu /build/reproducible-path/sibelia-3.0.7+dfsg/obj-aarch64-linux-gnu /build/reproducible-path/sibelia-3.0.7+dfsg/obj-aarch64-linux-gnu/CMakeFiles/Sibelia.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/sibelia-3.0.7+dfsg/obj-aarch64-linux-gnu' make -f CMakeFiles/Sibelia.dir/build.make CMakeFiles/Sibelia.dir/build make[3]: Entering directory '/build/reproducible-path/sibelia-3.0.7+dfsg/obj-aarch64-linux-gnu' [ 5%] Building CXX object CMakeFiles/Sibelia.dir/sibelia.cpp.o /usr/bin/c++ -I/build/reproducible-path/sibelia-3.0.7+dfsg/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/sibelia-3.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -MD -MT CMakeFiles/Sibelia.dir/sibelia.cpp.o -MF CMakeFiles/Sibelia.dir/sibelia.cpp.o.d -o CMakeFiles/Sibelia.dir/sibelia.cpp.o 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-ffile-prefix-map=/build/reproducible-path/sibelia-3.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -MD -MT CMakeFiles/Sibelia.dir/outputgenerator.cpp.o -MF CMakeFiles/Sibelia.dir/outputgenerator.cpp.o.d -o CMakeFiles/Sibelia.dir/outputgenerator.cpp.o -c /build/reproducible-path/sibelia-3.0.7+dfsg/src/outputgenerator.cpp [ 30%] Building CXX object CMakeFiles/Sibelia.dir/blockfinder.cpp.o /usr/bin/c++ -I/build/reproducible-path/sibelia-3.0.7+dfsg/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/sibelia-3.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -MD -MT CMakeFiles/Sibelia.dir/blockfinder.cpp.o -MF CMakeFiles/Sibelia.dir/blockfinder.cpp.o.d -o CMakeFiles/Sibelia.dir/blockfinder.cpp.o -c /build/reproducible-path/sibelia-3.0.7+dfsg/src/blockfinder.cpp [ 35%] Building CXX object CMakeFiles/Sibelia.dir/blockinstance.cpp.o /usr/bin/c++ -I/build/reproducible-path/sibelia-3.0.7+dfsg/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/sibelia-3.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -MD -MT CMakeFiles/Sibelia.dir/blockinstance.cpp.o -MF CMakeFiles/Sibelia.dir/blockinstance.cpp.o.d -o CMakeFiles/Sibelia.dir/blockinstance.cpp.o -c /build/reproducible-path/sibelia-3.0.7+dfsg/src/blockinstance.cpp [ 40%] Building CXX object CMakeFiles/Sibelia.dir/bifurcationstorage.cpp.o /usr/bin/c++ -I/build/reproducible-path/sibelia-3.0.7+dfsg/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/sibelia-3.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -MD -MT CMakeFiles/Sibelia.dir/bifurcationstorage.cpp.o -MF CMakeFiles/Sibelia.dir/bifurcationstorage.cpp.o.d -o CMakeFiles/Sibelia.dir/bifurcationstorage.cpp.o -c /build/reproducible-path/sibelia-3.0.7+dfsg/src/bifurcationstorage.cpp [ 45%] Building CXX object CMakeFiles/Sibelia.dir/bulgeremoval.cpp.o /usr/bin/c++ -I/build/reproducible-path/sibelia-3.0.7+dfsg/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/sibelia-3.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -MD -MT CMakeFiles/Sibelia.dir/bulgeremoval.cpp.o -MF CMakeFiles/Sibelia.dir/bulgeremoval.cpp.o.d -o CMakeFiles/Sibelia.dir/bulgeremoval.cpp.o -c /build/reproducible-path/sibelia-3.0.7+dfsg/src/bulgeremoval.cpp [ 50%] Building CXX object CMakeFiles/Sibelia.dir/dnasequence.cpp.o /usr/bin/c++ -I/build/reproducible-path/sibelia-3.0.7+dfsg/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/sibelia-3.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -MD -MT CMakeFiles/Sibelia.dir/dnasequence.cpp.o -MF CMakeFiles/Sibelia.dir/dnasequence.cpp.o.d -o CMakeFiles/Sibelia.dir/dnasequence.cpp.o -c /build/reproducible-path/sibelia-3.0.7+dfsg/src/dnasequence.cpp [ 55%] Building CXX object CMakeFiles/Sibelia.dir/edge.cpp.o /usr/bin/c++ -I/build/reproducible-path/sibelia-3.0.7+dfsg/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/sibelia-3.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -MD -MT CMakeFiles/Sibelia.dir/edge.cpp.o -MF CMakeFiles/Sibelia.dir/edge.cpp.o.d -o CMakeFiles/Sibelia.dir/edge.cpp.o -c /build/reproducible-path/sibelia-3.0.7+dfsg/src/edge.cpp [ 60%] Building CXX object CMakeFiles/Sibelia.dir/fasta.cpp.o /usr/bin/c++ -I/build/reproducible-path/sibelia-3.0.7+dfsg/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/sibelia-3.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -MD -MT CMakeFiles/Sibelia.dir/fasta.cpp.o -MF CMakeFiles/Sibelia.dir/fasta.cpp.o.d -o CMakeFiles/Sibelia.dir/fasta.cpp.o -c /build/reproducible-path/sibelia-3.0.7+dfsg/src/fasta.cpp In file included from /usr/include/boost/bind/detail/requires_cxx11.hpp:9, from /usr/include/boost/bind/bind.hpp:24, from /usr/include/boost/bind.hpp:29, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:31, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/blockinstance.h:10, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/blockfinder.h:10, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/util.h:10, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/outputgenerator.h:10, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/outputgenerator.cpp:9: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/bind/detail/requires_cxx11.hpp:9, from /usr/include/boost/bind/bind.hpp:24, from /usr/include/boost/bind.hpp:29, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:31, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/blockinstance.h:10, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/blockfinder.h:10, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/blockfinder.cpp:7: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/bind/detail/requires_cxx11.hpp:9, from /usr/include/boost/bind/bind.hpp:24, from /usr/include/boost/bind.hpp:29, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:31, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/fasta.h:10, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/dnasequence.h:10, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/hashing.h:10, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/indexedsequence.h:10, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/indexedsequence.cpp:7: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/bind/detail/requires_cxx11.hpp:9, from /usr/include/boost/bind/bind.hpp:24, from /usr/include/boost/bind.hpp:29, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:31, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/fasta.h:10, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/dnasequence.h:10, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/bifurcationstorage.h:11, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/bifurcationstorage.cpp:7: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/bind/detail/requires_cxx11.hpp:9, from /usr/include/boost/bind/bind.hpp:24, from /usr/include/boost/bind.hpp:29, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:31, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/blockinstance.h:10, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/blockinstance.cpp:7: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/bind/detail/requires_cxx11.hpp:9, from /usr/include/boost/bind/bind.hpp:24, from /usr/include/boost/bind.hpp:29, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:31, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/blockinstance.h:10, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/blockfinder.h:10, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/util.h:10, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/util.cpp:7: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/bind/detail/requires_cxx11.hpp:9, from /usr/include/boost/bind/bind.hpp:24, from /usr/include/boost/bind.hpp:29, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:31, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/blockinstance.h:10, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/blockfinder.h:10, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/bulgeremoval.cpp:7: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:104:51: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 104 | struct FancyIterator: public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/14/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/14/string:47, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:12: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/sibelia-3.0.7+dfsg/src/dnasequence.h:12: /build/reproducible-path/sibelia-3.0.7+dfsg/src/unrolledlist.h:36:45: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 36 | class iterator: public std::iterator | ^~~~~~~~ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /usr/include/boost/bind/detail/requires_cxx11.hpp:9, from /usr/include/boost/bind/bind.hpp:24, from /usr/include/boost/bind.hpp:29, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:31, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/blockinstance.h:10, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/blockfinder.h:10, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/edge.cpp:7: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/sibelia-3.0.7+dfsg/src/dnasequence.h:51:51: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 51 | class StrandIterator: public std::iterator | ^~~~~~~~ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:104:51: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 104 | struct FancyIterator: public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/14/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/14/string:47, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:12: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/sibelia-3.0.7+dfsg/src/dnasequence.h:12, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/blockinstance.h:11: /build/reproducible-path/sibelia-3.0.7+dfsg/src/unrolledlist.h:36:45: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 36 | class iterator: public std::iterator | ^~~~~~~~ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/sibelia-3.0.7+dfsg/src/dnasequence.h:51:51: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 51 | class StrandIterator: public std::iterator | ^~~~~~~~ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/sibelia-3.0.7+dfsg/src/indexedsequence.h:37:22: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 37 | std::auto_ptr sequence_; | ^~~~~~~~ In file included from /usr/include/c++/14/memory:78, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:20: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ /build/reproducible-path/sibelia-3.0.7+dfsg/src/indexedsequence.h:38:22: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 38 | std::auto_ptr bifStorage_; | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from /usr/include/boost/bind/detail/requires_cxx11.hpp:9, from /usr/include/boost/bind/bind.hpp:24, from /usr/include/boost/bind.hpp:29, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:31, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/fasta.h:10, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/dnasequence.h:10, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/dnasequence.cpp:7: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/sibelia-3.0.7+dfsg/src/blockfinder.h:11: /build/reproducible-path/sibelia-3.0.7+dfsg/src/indexedsequence.h:37:22: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 37 | std::auto_ptr sequence_; | ^~~~~~~~ In file included from /usr/include/c++/14/memory:78, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:20: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ /build/reproducible-path/sibelia-3.0.7+dfsg/src/indexedsequence.h:38:22: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 38 | std::auto_ptr bifStorage_; | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:104:51: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 104 | struct FancyIterator: public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/14/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/14/string:47, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:12: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/sibelia-3.0.7+dfsg/src/dnasequence.h:12, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/blockinstance.h:11: /build/reproducible-path/sibelia-3.0.7+dfsg/src/unrolledlist.h:36:45: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 36 | class iterator: public std::iterator | ^~~~~~~~ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:104:51: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 104 | struct FancyIterator: public std::iterator | ^~~~~~~~ /build/reproducible-path/sibelia-3.0.7+dfsg/src/dnasequence.h:51:51: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 51 | class StrandIterator: public std::iterator | ^~~~~~~~ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /usr/include/c++/14/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/14/string:47, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:12: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/sibelia-3.0.7+dfsg/src/dnasequence.h:12: /build/reproducible-path/sibelia-3.0.7+dfsg/src/unrolledlist.h:36:45: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 36 | class iterator: public std::iterator | ^~~~~~~~ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/sibelia-3.0.7+dfsg/src/dnasequence.h:51:51: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 51 | class StrandIterator: public std::iterator | ^~~~~~~~ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:104:51: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 104 | struct FancyIterator: public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/14/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/14/string:47, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:12: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/sibelia-3.0.7+dfsg/src/dnasequence.h:12, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/blockinstance.h:11: /build/reproducible-path/sibelia-3.0.7+dfsg/src/unrolledlist.h:36:45: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 36 | class iterator: public std::iterator | ^~~~~~~~ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/sibelia-3.0.7+dfsg/src/dnasequence.h:51:51: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 51 | class StrandIterator: public std::iterator | ^~~~~~~~ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /usr/include/boost/bind/detail/requires_cxx11.hpp:9, from /usr/include/boost/bind/bind.hpp:24, from /usr/include/boost/bind.hpp:29, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:31, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/fasta.h:10, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/fasta.cpp:7: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/sibelia-3.0.7+dfsg/src/blockfinder.h:11: /build/reproducible-path/sibelia-3.0.7+dfsg/src/indexedsequence.h:37:22: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 37 | std::auto_ptr sequence_; | ^~~~~~~~ In file included from /usr/include/c++/14/memory:78, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:20: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ /build/reproducible-path/sibelia-3.0.7+dfsg/src/indexedsequence.h:38:22: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 38 | std::auto_ptr bifStorage_; | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:104:51: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 104 | struct FancyIterator: public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/14/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/14/string:47, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:12: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/sibelia-3.0.7+dfsg/src/dnasequence.h:12, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/blockinstance.h:11: /build/reproducible-path/sibelia-3.0.7+dfsg/src/unrolledlist.h:36:45: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 36 | class iterator: public std::iterator | ^~~~~~~~ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/sibelia-3.0.7+dfsg/src/dnasequence.h:51:51: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 51 | class StrandIterator: public std::iterator | ^~~~~~~~ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:104:51: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 104 | struct FancyIterator: public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/14/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/14/string:47, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:12: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/sibelia-3.0.7+dfsg/src/blockfinder.h:11: /build/reproducible-path/sibelia-3.0.7+dfsg/src/indexedsequence.h:37:22: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 37 | std::auto_ptr sequence_; | ^~~~~~~~ In file included from /usr/include/c++/14/memory:78, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:20: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ /build/reproducible-path/sibelia-3.0.7+dfsg/src/indexedsequence.h:38:22: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 38 | std::auto_ptr bifStorage_; | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from /build/reproducible-path/sibelia-3.0.7+dfsg/src/dnasequence.h:12, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/blockinstance.h:11: /build/reproducible-path/sibelia-3.0.7+dfsg/src/unrolledlist.h:36:45: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 36 | class iterator: public std::iterator | ^~~~~~~~ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/sibelia-3.0.7+dfsg/src/dnasequence.h:51:51: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 51 | class StrandIterator: public std::iterator | ^~~~~~~~ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:104:51: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 104 | struct FancyIterator: public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/14/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/14/string:47, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:12: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/sibelia-3.0.7+dfsg/src/dnasequence.h:12, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/blockinstance.h:11: /build/reproducible-path/sibelia-3.0.7+dfsg/src/unrolledlist.h:36:45: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 36 | class iterator: public std::iterator | ^~~~~~~~ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/sibelia-3.0.7+dfsg/src/dnasequence.h:51:51: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 51 | class StrandIterator: public std::iterator | ^~~~~~~~ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:104:51: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 104 | struct FancyIterator: public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/14/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/14/string:47, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:12: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/sibelia-3.0.7+dfsg/src/dnasequence.h:12: /build/reproducible-path/sibelia-3.0.7+dfsg/src/unrolledlist.h:36:45: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 36 | class iterator: public std::iterator | ^~~~~~~~ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/sibelia-3.0.7+dfsg/src/blockfinder.h:11: /build/reproducible-path/sibelia-3.0.7+dfsg/src/indexedsequence.h:37:22: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 37 | std::auto_ptr sequence_; | ^~~~~~~~ In file included from /usr/include/c++/14/memory:78, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:20: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ /build/reproducible-path/sibelia-3.0.7+dfsg/src/indexedsequence.h:38:22: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 38 | std::auto_ptr bifStorage_; | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ /build/reproducible-path/sibelia-3.0.7+dfsg/src/dnasequence.h:51:51: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 51 | class StrandIterator: public std::iterator | ^~~~~~~~ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:104:51: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 104 | struct FancyIterator: public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/14/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/14/string:47, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:12: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/sibelia-3.0.7+dfsg/src/blockfinder.h:11: /build/reproducible-path/sibelia-3.0.7+dfsg/src/indexedsequence.h:37:22: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 37 | std::auto_ptr sequence_; | ^~~~~~~~ In file included from /usr/include/c++/14/memory:78, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:20: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ /build/reproducible-path/sibelia-3.0.7+dfsg/src/indexedsequence.h:38:22: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 38 | std::auto_ptr bifStorage_; | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ [ 65%] Building CXX object CMakeFiles/Sibelia.dir/serialization.cpp.o /usr/bin/c++ -I/build/reproducible-path/sibelia-3.0.7+dfsg/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/sibelia-3.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -MD -MT CMakeFiles/Sibelia.dir/serialization.cpp.o -MF CMakeFiles/Sibelia.dir/serialization.cpp.o.d -o CMakeFiles/Sibelia.dir/serialization.cpp.o -c /build/reproducible-path/sibelia-3.0.7+dfsg/src/serialization.cpp [ 70%] Building CXX object CMakeFiles/Sibelia.dir/synteny.cpp.o /usr/bin/c++ -I/build/reproducible-path/sibelia-3.0.7+dfsg/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/sibelia-3.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -MD -MT CMakeFiles/Sibelia.dir/synteny.cpp.o -MF CMakeFiles/Sibelia.dir/synteny.cpp.o.d -o CMakeFiles/Sibelia.dir/synteny.cpp.o -c /build/reproducible-path/sibelia-3.0.7+dfsg/src/synteny.cpp [ 75%] Building CXX object CMakeFiles/Sibelia.dir/test/unrolledlisttest.cpp.o /usr/bin/c++ -I/build/reproducible-path/sibelia-3.0.7+dfsg/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/sibelia-3.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -MD -MT CMakeFiles/Sibelia.dir/test/unrolledlisttest.cpp.o -MF CMakeFiles/Sibelia.dir/test/unrolledlisttest.cpp.o.d -o CMakeFiles/Sibelia.dir/test/unrolledlisttest.cpp.o -c /build/reproducible-path/sibelia-3.0.7+dfsg/src/test/unrolledlisttest.cpp [ 80%] Building CXX object CMakeFiles/Sibelia.dir/platform.cpp.o /usr/bin/c++ -I/build/reproducible-path/sibelia-3.0.7+dfsg/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/sibelia-3.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -MD -MT CMakeFiles/Sibelia.dir/platform.cpp.o -MF CMakeFiles/Sibelia.dir/platform.cpp.o.d -o CMakeFiles/Sibelia.dir/platform.cpp.o -c /build/reproducible-path/sibelia-3.0.7+dfsg/src/platform.cpp [ 85%] Building CXX object CMakeFiles/Sibelia.dir/stranditerator.cpp.o /usr/bin/c++ -I/build/reproducible-path/sibelia-3.0.7+dfsg/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/sibelia-3.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -MD -MT CMakeFiles/Sibelia.dir/stranditerator.cpp.o -MF CMakeFiles/Sibelia.dir/stranditerator.cpp.o.d -o CMakeFiles/Sibelia.dir/stranditerator.cpp.o -c /build/reproducible-path/sibelia-3.0.7+dfsg/src/stranditerator.cpp [ 90%] Building CXX object CMakeFiles/Sibelia.dir/vertexenumeration.cpp.o /usr/bin/c++ -I/build/reproducible-path/sibelia-3.0.7+dfsg/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/sibelia-3.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -MD -MT CMakeFiles/Sibelia.dir/vertexenumeration.cpp.o -MF CMakeFiles/Sibelia.dir/vertexenumeration.cpp.o.d -o CMakeFiles/Sibelia.dir/vertexenumeration.cpp.o -c /build/reproducible-path/sibelia-3.0.7+dfsg/src/vertexenumeration.cpp In file included from /usr/include/boost/bind/detail/requires_cxx11.hpp:9, from /usr/include/boost/bind/bind.hpp:24, from /usr/include/boost/bind.hpp:29, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:31, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/fasta.h:10, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/postprocessor.h:13, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/sibelia.cpp:8: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/bind/detail/requires_cxx11.hpp:9, from /usr/include/boost/bind/bind.hpp:24, from /usr/include/boost/bind.hpp:29, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:31, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/blockinstance.h:10, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/blockfinder.h:10, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/serialization.cpp:7: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:104:51: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 104 | struct FancyIterator: public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/14/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/14/string:47, from /usr/include/tclap/SwitchArg.h:29, from /usr/include/tclap/CmdLine.h:27, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/sibelia.cpp:7: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/sibelia-3.0.7+dfsg/src/dnasequence.h:12, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/blockinstance.h:11, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/postprocessor.h:14: /build/reproducible-path/sibelia-3.0.7+dfsg/src/unrolledlist.h:36:45: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 36 | class iterator: public std::iterator | ^~~~~~~~ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /usr/include/boost/bind/detail/requires_cxx11.hpp:9, from /usr/include/boost/bind/bind.hpp:24, from /usr/include/boost/bind.hpp:29, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:31, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/blockinstance.h:10, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/blockfinder.h:10, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/synteny.cpp:9: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/sibelia-3.0.7+dfsg/src/dnasequence.h:51:51: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 51 | class StrandIterator: public std::iterator | ^~~~~~~~ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 95%] Building CXX object CMakeFiles/Sibelia.dir/resource.cpp.o /usr/bin/c++ -I/build/reproducible-path/sibelia-3.0.7+dfsg/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/sibelia-3.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -MD -MT CMakeFiles/Sibelia.dir/resource.cpp.o -MF CMakeFiles/Sibelia.dir/resource.cpp.o.d -o CMakeFiles/Sibelia.dir/resource.cpp.o -c /build/reproducible-path/sibelia-3.0.7+dfsg/src/resource.cpp In file included from /usr/include/boost/bind/detail/requires_cxx11.hpp:9, from /usr/include/boost/bind/bind.hpp:24, from /usr/include/boost/bind.hpp:29, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/test/../common.h:31, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/test/unrolledlisttest.h:10, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/test/unrolledlisttest.cpp:7: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/sibelia-3.0.7+dfsg/src/blockfinder.h:11, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/util.h:10, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/sibelia.cpp:9: /build/reproducible-path/sibelia-3.0.7+dfsg/src/indexedsequence.h:37:22: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 37 | std::auto_ptr sequence_; | ^~~~~~~~ In file included from /usr/include/c++/14/memory:78, from /usr/include/seqan/basic/test_system.h:53, from /usr/include/seqan/basic.h:65, from /usr/include/seqan/align.h:55, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/postprocessor.h:10: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ /build/reproducible-path/sibelia-3.0.7+dfsg/src/indexedsequence.h:38:22: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 38 | std::auto_ptr bifStorage_; | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:104:51: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 104 | struct FancyIterator: public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/14/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/14/string:47, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:12: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/sibelia-3.0.7+dfsg/src/dnasequence.h:12, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/blockinstance.h:11: /build/reproducible-path/sibelia-3.0.7+dfsg/src/unrolledlist.h:36:45: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 36 | class iterator: public std::iterator | ^~~~~~~~ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/sibelia-3.0.7+dfsg/src/dnasequence.h:51:51: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 51 | class StrandIterator: public std::iterator | ^~~~~~~~ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/sibelia-3.0.7+dfsg/src/sibelia.cpp: In function ‘int main(int, char**)’: /build/reproducible-path/sibelia-3.0.7+dfsg/src/sibelia.cpp:239:22: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 239 | std::auto_ptr finder(inRAM.isSet() ? new SyntenyFinder::BlockFinder(chrList) : new SyntenyFinder::BlockFinder(chrList, tempDir)); | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from /build/reproducible-path/sibelia-3.0.7+dfsg/src/blockfinder.h:11: /build/reproducible-path/sibelia-3.0.7+dfsg/src/indexedsequence.h:37:22: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 37 | std::auto_ptr sequence_; | ^~~~~~~~ In file included from /usr/include/c++/14/memory:78, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:20: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ /build/reproducible-path/sibelia-3.0.7+dfsg/src/indexedsequence.h:38:22: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 38 | std::auto_ptr bifStorage_; | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from /usr/include/boost/bind/detail/requires_cxx11.hpp:9, from /usr/include/boost/bind/bind.hpp:24, from /usr/include/boost/bind.hpp:29, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:31, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/platform.h:10, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/platform.cpp:7: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:104:51: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 104 | struct FancyIterator: public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/14/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/14/string:47, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:12: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/sibelia-3.0.7+dfsg/src/dnasequence.h:12, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/blockinstance.h:11: /build/reproducible-path/sibelia-3.0.7+dfsg/src/unrolledlist.h:36:45: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 36 | class iterator: public std::iterator | ^~~~~~~~ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/sibelia-3.0.7+dfsg/src/dnasequence.h:51:51: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 51 | class StrandIterator: public std::iterator | ^~~~~~~~ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/sibelia-3.0.7+dfsg/src/blockfinder.h:11: /build/reproducible-path/sibelia-3.0.7+dfsg/src/indexedsequence.h:37:22: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 37 | std::auto_ptr sequence_; | ^~~~~~~~ In file included from /usr/include/c++/14/memory:78, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:20: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ /build/reproducible-path/sibelia-3.0.7+dfsg/src/indexedsequence.h:38:22: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 38 | std::auto_ptr bifStorage_; | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from /usr/include/boost/bind/detail/requires_cxx11.hpp:9, from /usr/include/boost/bind/bind.hpp:24, from /usr/include/boost/bind.hpp:29, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:31, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/fasta.h:10, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/dnasequence.h:10, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/hashing.h:10, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/indexedsequence.h:10, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/vertexenumeration.cpp:7: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/sibelia-3.0.7+dfsg/src/test/../common.h:104:51: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 104 | struct FancyIterator: public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/14/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/14/string:47, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/test/../common.h:12: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/sibelia-3.0.7+dfsg/src/test/unrolledlisttest.h:11: /build/reproducible-path/sibelia-3.0.7+dfsg/src/test/../unrolledlist.h:36:45: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 36 | class iterator: public std::iterator | ^~~~~~~~ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /usr/include/boost/bind/detail/requires_cxx11.hpp:9, from /usr/include/boost/bind/bind.hpp:24, from /usr/include/boost/bind.hpp:29, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:31, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/fasta.h:10, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/postprocessor.h:13, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/postprocessor.cpp:9: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:104:51: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 104 | struct FancyIterator: public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/14/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/14/string:47, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:12: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /usr/include/boost/bind/detail/requires_cxx11.hpp:9, from /usr/include/boost/bind/bind.hpp:24, from /usr/include/boost/bind.hpp:29, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:31, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/fasta.h:10, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/dnasequence.h:10, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/stranditerator.cpp:7: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:104:51: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 104 | struct FancyIterator: public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/14/bits/stl_algobase.h:65, from /usr/include/c++/14/algorithm:60, from /usr/include/seqan/align.h:53, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/postprocessor.h:10: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/sibelia-3.0.7+dfsg/src/dnasequence.h:12, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/blockinstance.h:11, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/postprocessor.h:14: /build/reproducible-path/sibelia-3.0.7+dfsg/src/unrolledlist.h:36:45: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 36 | class iterator: public std::iterator | ^~~~~~~~ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/sibelia-3.0.7+dfsg/src/dnasequence.h:51:51: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 51 | class StrandIterator: public std::iterator | ^~~~~~~~ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:104:51: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 104 | struct FancyIterator: public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/14/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/14/string:47, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:12: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/sibelia-3.0.7+dfsg/src/dnasequence.h:12: /build/reproducible-path/sibelia-3.0.7+dfsg/src/unrolledlist.h:36:45: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 36 | class iterator: public std::iterator | ^~~~~~~~ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/sibelia-3.0.7+dfsg/src/dnasequence.h:51:51: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 51 | class StrandIterator: public std::iterator | ^~~~~~~~ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/sibelia-3.0.7+dfsg/src/indexedsequence.h:37:22: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 37 | std::auto_ptr sequence_; | ^~~~~~~~ In file included from /usr/include/c++/14/memory:78, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:20: /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ /build/reproducible-path/sibelia-3.0.7+dfsg/src/indexedsequence.h:38:22: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 38 | std::auto_ptr bifStorage_; | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:104:51: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 104 | struct FancyIterator: public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/14/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/14/string:47, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:12: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/sibelia-3.0.7+dfsg/src/dnasequence.h:12: /build/reproducible-path/sibelia-3.0.7+dfsg/src/unrolledlist.h:36:45: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 36 | class iterator: public std::iterator | ^~~~~~~~ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/sibelia-3.0.7+dfsg/src/dnasequence.h:51:51: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 51 | class StrandIterator: public std::iterator | ^~~~~~~~ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /usr/include/boost/bind/detail/requires_cxx11.hpp:9, from /usr/include/boost/bind/bind.hpp:24, from /usr/include/boost/bind.hpp:29, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:31, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/resource.h:6, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/resource.cpp:6: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:104:51: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 104 | struct FancyIterator: public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/14/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/14/string:47, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:12: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [100%] Linking CXX executable Sibelia /usr/bin/cmake -E cmake_link_script CMakeFiles/Sibelia.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/sibelia-3.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file,CMakeFiles/Sibelia.dir/link.d CMakeFiles/Sibelia.dir/sibelia.cpp.o CMakeFiles/Sibelia.dir/postprocessor.cpp.o CMakeFiles/Sibelia.dir/indexedsequence.cpp.o CMakeFiles/Sibelia.dir/util.cpp.o CMakeFiles/Sibelia.dir/outputgenerator.cpp.o CMakeFiles/Sibelia.dir/blockfinder.cpp.o CMakeFiles/Sibelia.dir/blockinstance.cpp.o CMakeFiles/Sibelia.dir/bifurcationstorage.cpp.o CMakeFiles/Sibelia.dir/bulgeremoval.cpp.o CMakeFiles/Sibelia.dir/dnasequence.cpp.o CMakeFiles/Sibelia.dir/edge.cpp.o CMakeFiles/Sibelia.dir/fasta.cpp.o CMakeFiles/Sibelia.dir/serialization.cpp.o CMakeFiles/Sibelia.dir/synteny.cpp.o CMakeFiles/Sibelia.dir/test/unrolledlisttest.cpp.o CMakeFiles/Sibelia.dir/platform.cpp.o CMakeFiles/Sibelia.dir/stranditerator.cpp.o CMakeFiles/Sibelia.dir/vertexenumeration.cpp.o CMakeFiles/Sibelia.dir/resource.cpp.o -o Sibelia -ldivsufsort make[3]: Leaving directory '/build/reproducible-path/sibelia-3.0.7+dfsg/obj-aarch64-linux-gnu' [100%] Built target Sibelia make[2]: Leaving directory '/build/reproducible-path/sibelia-3.0.7+dfsg/obj-aarch64-linux-gnu' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/sibelia-3.0.7+dfsg/obj-aarch64-linux-gnu/CMakeFiles 0 make[1]: Leaving directory '/build/reproducible-path/sibelia-3.0.7+dfsg/obj-aarch64-linux-gnu' debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/sibelia-3.0.7+dfsg' dh_auto_test --no-parallel make[1]: Leaving directory '/build/reproducible-path/sibelia-3.0.7+dfsg' create-stamp debian/debhelper-build-stamp dh_testroot -O--sourcedirectory=src dh_prep -O--sourcedirectory=src dh_auto_install -O--sourcedirectory=src cd obj-aarch64-linux-gnu && make -j12 install DESTDIR=/build/reproducible-path/sibelia-3.0.7\+dfsg/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/reproducible-path/sibelia-3.0.7+dfsg/obj-aarch64-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/sibelia-3.0.7+dfsg/src -B/build/reproducible-path/sibelia-3.0.7+dfsg/obj-aarch64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/sibelia-3.0.7+dfsg/obj-aarch64-linux-gnu/CMakeFiles /build/reproducible-path/sibelia-3.0.7+dfsg/obj-aarch64-linux-gnu//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/build/reproducible-path/sibelia-3.0.7+dfsg/obj-aarch64-linux-gnu' make -f CMakeFiles/Sibelia.dir/build.make CMakeFiles/Sibelia.dir/depend make[3]: Entering directory '/build/reproducible-path/sibelia-3.0.7+dfsg/obj-aarch64-linux-gnu' cd /build/reproducible-path/sibelia-3.0.7+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/sibelia-3.0.7+dfsg/src /build/reproducible-path/sibelia-3.0.7+dfsg/src /build/reproducible-path/sibelia-3.0.7+dfsg/obj-aarch64-linux-gnu /build/reproducible-path/sibelia-3.0.7+dfsg/obj-aarch64-linux-gnu /build/reproducible-path/sibelia-3.0.7+dfsg/obj-aarch64-linux-gnu/CMakeFiles/Sibelia.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/sibelia-3.0.7+dfsg/obj-aarch64-linux-gnu' make -f CMakeFiles/Sibelia.dir/build.make CMakeFiles/Sibelia.dir/build make[3]: Entering directory '/build/reproducible-path/sibelia-3.0.7+dfsg/obj-aarch64-linux-gnu' make[3]: Nothing to be done for 'CMakeFiles/Sibelia.dir/build'. make[3]: Leaving directory '/build/reproducible-path/sibelia-3.0.7+dfsg/obj-aarch64-linux-gnu' [100%] Built target Sibelia make[2]: Leaving directory '/build/reproducible-path/sibelia-3.0.7+dfsg/obj-aarch64-linux-gnu' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/sibelia-3.0.7+dfsg/obj-aarch64-linux-gnu/CMakeFiles 0 make -f CMakeFiles/Makefile2 preinstall make[2]: Entering directory '/build/reproducible-path/sibelia-3.0.7+dfsg/obj-aarch64-linux-gnu' make[2]: Nothing to be done for 'preinstall'. make[2]: Leaving directory '/build/reproducible-path/sibelia-3.0.7+dfsg/obj-aarch64-linux-gnu' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "Release" -- Installing: /build/reproducible-path/sibelia-3.0.7+dfsg/debian/tmp/usr/bin/Sibelia -- Installing: /build/reproducible-path/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/NEWS.md -- Installing: /build/reproducible-path/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/ANNOTATION.md -- Installing: /build/reproducible-path/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/README.md -- Installing: /build/reproducible-path/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/USAGE.md -- Installing: /build/reproducible-path/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/INSTALL.md -- Installing: /build/reproducible-path/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/SIBELIA.md -- Installing: /build/reproducible-path/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/C-SIBELIA.md -- Installing: /build/reproducible-path/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/LICENSE.txt -- Installing: /build/reproducible-path/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples -- Installing: /build/reproducible-path/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/C-Sibelia -- Installing: /build/reproducible-path/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/C-Sibelia/Staphylococcus_aureus -- Installing: /build/reproducible-path/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/C-Sibelia/Staphylococcus_aureus/RN4220.fasta -- Installing: /build/reproducible-path/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/C-Sibelia/Staphylococcus_aureus/README.txt -- Installing: 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/build/reproducible-path/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/Sibelia/Helicobacter_pylori/circos/circos.highlight2.txt -- Installing: /build/reproducible-path/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/Sibelia/Helicobacter_pylori/circos/circos.sequences.txt -- Installing: /build/reproducible-path/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/Sibelia/Helicobacter_pylori/circos/circos.highlight4.txt -- Installing: /build/reproducible-path/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/Sibelia/Helicobacter_pylori/circos/circos.highlight1.txt -- Installing: /build/reproducible-path/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/Sibelia/Helicobacter_pylori/circos/circos.highlight.txt -- Installing: /build/reproducible-path/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/Sibelia/Helicobacter_pylori/circos/circos.png -- Installing: 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/build/reproducible-path/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/Sibelia/Helicobacter_pylori/blocks_coords.txt -- Installing: /build/reproducible-path/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/Sibelia/Helicobacter_pylori/README.txt -- Installing: /build/reproducible-path/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/Sibelia/Helicobacter_pylori/d3_blocks_diagram.html -- Installing: /build/reproducible-path/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/Sibelia/Staphylococcus_aureus -- Installing: /build/reproducible-path/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/Sibelia/Staphylococcus_aureus/genomes_permutations.txt -- Installing: /build/reproducible-path/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/Sibelia/Staphylococcus_aureus/circos -- Installing: 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/build/reproducible-path/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/Sibelia/Staphylococcus_aureus/circos/circos.conf -- Installing: /build/reproducible-path/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/Sibelia/Staphylococcus_aureus/coverage_report.txt -- Installing: /build/reproducible-path/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/Sibelia/Staphylococcus_aureus/blocks_coords.txt -- Installing: /build/reproducible-path/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/Sibelia/Staphylococcus_aureus/README.txt -- Installing: /build/reproducible-path/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/Sibelia/Staphylococcus_aureus/Staphylococcus.fasta -- Installing: /build/reproducible-path/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/doc/examples/Sibelia/Staphylococcus_aureus/d3_blocks_diagram.html -- Installing: /build/reproducible-path/sibelia-3.0.7+dfsg/debian/tmp/usr/bin/C-Sibelia.py -- Installing: /build/reproducible-path/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/utils -- Installing: /build/reproducible-path/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/utils/hidemappedcontigs.py -- Installing: /build/reproducible-path/sibelia-3.0.7+dfsg/debian/tmp/usr/share/Sibelia/utils/sortsequences.py -- Installing: /build/reproducible-path/sibelia-3.0.7+dfsg/debian/tmp/usr/lib/Sibelia make[1]: Leaving directory '/build/reproducible-path/sibelia-3.0.7+dfsg/obj-aarch64-linux-gnu' debian/rules override_dh_install make[1]: Entering directory '/build/reproducible-path/sibelia-3.0.7+dfsg' dh_install find debian -name LICENSE.txt -delete find debian -name INSTALL.md -delete make[1]: Leaving directory '/build/reproducible-path/sibelia-3.0.7+dfsg' dh_installdocs -O--sourcedirectory=src dh_installchangelogs -O--sourcedirectory=src debian/rules override_dh_installman-arch make[1]: Entering directory '/build/reproducible-path/sibelia-3.0.7+dfsg' dh_installman -a mv debian/sibelia/usr/share/man/py/man1/C-Sibelia.1 debian/sibelia/usr/share/man/man1/C-Sibelia.py.1 rm -rf debian/sibelia/usr/share/man/py make[1]: Leaving directory '/build/reproducible-path/sibelia-3.0.7+dfsg' dh_installman -O--sourcedirectory=src -Nsibelia dh_installinit -O--sourcedirectory=src dh_installsystemduser -O--sourcedirectory=src dh_lintian -O--sourcedirectory=src dh_perl -O--sourcedirectory=src dh_link -O--sourcedirectory=src dh_strip_nondeterminism -O--sourcedirectory=src dh_compress -O--sourcedirectory=src dh_fixperms -O--sourcedirectory=src dh_missing -O--sourcedirectory=src dh_dwz -O--sourcedirectory=src dh_strip -O--sourcedirectory=src dh_makeshlibs -O--sourcedirectory=src dh_shlibdeps -O--sourcedirectory=src dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 from: /lib/ld-linux-aarch64.so.1 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 to: /lib/ld-linux-aarch64.so.1.usr-is-merged dh_installdeb -O--sourcedirectory=src dh_gencontrol -O--sourcedirectory=src dh_md5sums -O--sourcedirectory=src dh_builddeb -O--sourcedirectory=src dpkg-deb: building package 'sibelia' in '../sibelia_3.0.7+dfsg-4_arm64.deb'. dpkg-deb: building package 'sibelia-dbgsym' in '../sibelia-dbgsym_3.0.7+dfsg-4_arm64.deb'. dpkg-deb: building package 'sibelia-examples' in '../sibelia-examples_3.0.7+dfsg-4_all.deb'. dpkg-genbuildinfo --build=binary -O../sibelia_3.0.7+dfsg-4_arm64.buildinfo dpkg-genchanges --build=binary -O../sibelia_3.0.7+dfsg-4_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: user script /srv/workspace/pbuilder/3116528/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/3116528/tmp/hooks/B01_cleanup finished 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/3116528 and its subdirectories I: Current time: Mon Dec 29 22:18:50 +14 2025 I: pbuilder-time-stamp: 1766996330 + false + set +x Mon Dec 29 08:18:50 UTC 2025 I: Signing ./b2/sibelia_3.0.7+dfsg-4_arm64.buildinfo as sibelia_3.0.7+dfsg-4_arm64.buildinfo.asc Mon Dec 29 08:18:50 UTC 2025 I: Signed ./b2/sibelia_3.0.7+dfsg-4_arm64.buildinfo as ./b2/sibelia_3.0.7+dfsg-4_arm64.buildinfo.asc Mon Dec 29 08:18:50 UTC 2025 - build #2 for sibelia/experimental/arm64 on codethink01-arm64 done. Starting cleanup. All cleanup done. Mon Dec 29 08:18:50 UTC 2025 - reproducible_build.sh stopped running as /tmp/jenkins-script-0mzA3Y7v, removing. /srv/reproducible-results/rbuild-debian/r-b-build.Jw2wMKXd: total 160 drwxr-xr-x 2 jenkins jenkins 4096 Nov 26 01:53 b1 drwxr-xr-x 2 jenkins jenkins 4096 Nov 26 01:55 b2 -rw------- 1 jenkins jenkins 143705 Nov 26 01:53 rbuildlog.dtL9asS -rw-r--r-- 1 jenkins jenkins 2156 Nov 25 14:32 sibelia_3.0.7+dfsg-4.dsc /srv/reproducible-results/rbuild-debian/r-b-build.Jw2wMKXd/b1: total 11644 -rw-r--r-- 1 jenkins jenkins 140092 Nov 26 01:53 build.log -rw-r--r-- 1 jenkins jenkins 3696536 Nov 26 01:53 sibelia-dbgsym_3.0.7+dfsg-4_arm64.deb -rw-r--r-- 1 jenkins jenkins 7704828 Nov 26 01:53 sibelia-examples_3.0.7+dfsg-4_all.deb -rw-r--r-- 1 jenkins jenkins 10944 Nov 26 01:53 sibelia_3.0.7+dfsg-4.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 2156 Nov 26 01:53 sibelia_3.0.7+dfsg-4.dsc -rw-r--r-- 1 jenkins jenkins 7882 Nov 26 01:53 sibelia_3.0.7+dfsg-4_arm64.buildinfo -rw-r--r-- 1 jenkins jenkins 8764 Nov 26 01:53 sibelia_3.0.7+dfsg-4_arm64.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 1867 Nov 26 01:53 sibelia_3.0.7+dfsg-4_arm64.changes -rw-r--r-- 1 jenkins jenkins 299476 Nov 26 01:53 sibelia_3.0.7+dfsg-4_arm64.deb -rw-r--r-- 1 jenkins jenkins 1368 Nov 26 01:53 sibelia_3.0.7+dfsg-4_source.changes /srv/reproducible-results/rbuild-debian/r-b-build.Jw2wMKXd/b2: total 11644 -rw-r--r-- 1 jenkins jenkins 142041 Nov 26 01:55 build.log -rw-r--r-- 1 jenkins jenkins 3696536 Nov 26 01:55 sibelia-dbgsym_3.0.7+dfsg-4_arm64.deb -rw-r--r-- 1 jenkins jenkins 7704828 Nov 26 01:55 sibelia-examples_3.0.7+dfsg-4_all.deb -rw-r--r-- 1 jenkins jenkins 10944 Nov 26 01:55 sibelia_3.0.7+dfsg-4.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 2156 Nov 26 01:55 sibelia_3.0.7+dfsg-4.dsc -rw-r--r-- 1 jenkins jenkins 7882 Nov 26 01:55 sibelia_3.0.7+dfsg-4_arm64.buildinfo -rw-r--r-- 1 jenkins jenkins 8764 Nov 26 01:55 sibelia_3.0.7+dfsg-4_arm64.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 1867 Nov 26 01:55 sibelia_3.0.7+dfsg-4_arm64.changes -rw-r--r-- 1 jenkins jenkins 299476 Nov 26 01:55 sibelia_3.0.7+dfsg-4_arm64.deb -rw-r--r-- 1 jenkins jenkins 1368 Nov 26 01:55 sibelia_3.0.7+dfsg-4_source.changes Tue Nov 26 01:55:51 UTC 2024 I: Deleting $TMPDIR on codethink01-arm64.debian.net. Tue Nov 26 01:55:52 UTC 2024 I: sibelia_3.0.7+dfsg-4_arm64.changes: Format: 1.8 Date: Mon, 25 Nov 2024 15:20:04 +0100 Source: sibelia Binary: sibelia sibelia-dbgsym sibelia-examples Architecture: arm64 all Version: 3.0.7+dfsg-4 Distribution: experimental Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Michael R. Crusoe Description: sibelia - comparative genomics tool sibelia-examples - comparative genomics tool (example data) Changes: sibelia (3.0.7+dfsg-4) experimental; urgency=medium . * Team upload. * d/control: Experimental rebuild using the 3rd release candidate of SeqAn 2.5.0 * Added patch for the explicit seqan2 namespace. Checksums-Sha1: e3ae6db55806caf3d41090fe428b418f842d5012 3696536 sibelia-dbgsym_3.0.7+dfsg-4_arm64.deb 7aed54e21532633ea3b22f9e77f5cc2dc52e7acf 7704828 sibelia-examples_3.0.7+dfsg-4_all.deb 144201f5d0986782dce8bbeaee16a514c397178a 7882 sibelia_3.0.7+dfsg-4_arm64.buildinfo f2a97ca437b852097078ac7ef28635d08701d56f 299476 sibelia_3.0.7+dfsg-4_arm64.deb Checksums-Sha256: 6d7117e3a5010be81e6dfe19b2ff28178463ad24646a4687723095747ee32901 3696536 sibelia-dbgsym_3.0.7+dfsg-4_arm64.deb 17f6747c72bba28119e5207d3df6a87b6b6885960b9091f2e10b0ceeddd8e966 7704828 sibelia-examples_3.0.7+dfsg-4_all.deb 5de1b46ccaca3e8b808cd4e0c579cc0ca0115bbf2c4abeb5a83bc67513a90672 7882 sibelia_3.0.7+dfsg-4_arm64.buildinfo e718226c626693d58ee3950bf7eb9fe5e28ca4a3e099bb9cc59b6add67a86625 299476 sibelia_3.0.7+dfsg-4_arm64.deb Files: 57a289f6a18a54e5cb8429fe9cb36c89 3696536 debug optional sibelia-dbgsym_3.0.7+dfsg-4_arm64.deb 3a43e52488f008b9e6ab16aad211184e 7704828 science optional sibelia-examples_3.0.7+dfsg-4_all.deb 589f32062ac977f9a9304765f2fc3284 7882 science optional sibelia_3.0.7+dfsg-4_arm64.buildinfo 238922933485a764bc0c54e5cb9932d3 299476 science optional sibelia_3.0.7+dfsg-4_arm64.deb Diff of the two buildlogs: -- --- b1/build.log 2024-11-26 01:53:27.698329134 +0000 +++ b2/build.log 2024-11-26 01:55:51.143857497 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Mon Nov 25 13:51:10 -12 2024 -I: pbuilder-time-stamp: 1732585870 +I: Current time: Mon Dec 29 22:16:30 +14 2025 +I: pbuilder-time-stamp: 1766996190 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/experimental-reproducible-base.tgz] I: copying local configuration @@ -32,52 +32,84 @@ dpkg-source: info: applying 0005-Upgrade-to-SeqAn-2.5.0.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/1763354/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/3116528/tmp/hooks/D01_modify_environment starting +debug: Running on codethink01-arm64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Dec 29 08:16 /bin/sh -> /bin/bash +I: Setting pbuilder2's login shell to /bin/bash +I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other +I: user script /srv/workspace/pbuilder/3116528/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/3116528/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='arm64' - DEBIAN_FRONTEND='noninteractive' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="32" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu") + BASH_VERSION='5.2.32(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=arm64 + DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' - DISTRIBUTION='experimental' - HOME='/root' - HOST_ARCH='arm64' + DIRSTACK=() + DISTRIBUTION=experimental + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=aarch64 + HOST_ARCH=arm64 IFS=' ' - INVOCATION_ID='b3d452d9c6b640c7907b6cff8d400475' - 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='1763354' - PS1='# ' - PS2='> ' + INVOCATION_ID=2827dba685cc443ab2e446158a93094f + LANG=C + LANGUAGE=nl_BE:nl + LC_ALL=C + MACHTYPE=aarch64-unknown-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=3116528 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.Jw2wMKXd/pbuilderrc_7ddl --distribution experimental --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/experimental-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.Jw2wMKXd/b1 --logfile b1/build.log sibelia_3.0.7+dfsg-4.dsc' - SUDO_GID='109' - SUDO_UID='104' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://192.168.101.4:3128' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.Jw2wMKXd/pbuilderrc_IkMa --distribution experimental --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/experimental-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.Jw2wMKXd/b2 --logfile b2/build.log sibelia_3.0.7+dfsg-4.dsc' + SUDO_GID=109 + SUDO_UID=104 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://192.168.101.4:3128 I: uname -a - Linux codethink02-arm64 6.1.0-28-cloud-arm64 #1 SMP Debian 6.1.119-1 (2024-11-22) aarch64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-28-cloud-arm64 #1 SMP Debian 6.1.119-1 (2024-11-22) aarch64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Aug 4 21:30 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/1763354/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Nov 22 2024 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/3116528/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -244,7 +276,7 @@ Get: 102 http://deb.debian.org/debian unstable/main arm64 libhts-dev arm64 1.20+ds-2 [1626 kB] Get: 103 http://deb.debian.org/debian experimental/main arm64 libseqan2-dev all 2.5.0~rc3+dfsg-1 [1222 kB] Get: 104 http://deb.debian.org/debian unstable/main arm64 libtclap-dev arm64 1.2.5-1+b1 [3359 kB] -Fetched 66.0 MB in 1s (109 MB/s) +Fetched 66.0 MB in 1s (125 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libproc2-0:arm64. (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 ... 20083 files and directories currently installed.) @@ -675,7 +707,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/sibelia-3.0.7+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 > ../sibelia_3.0.7+dfsg-4_source.changes +I: user script /srv/workspace/pbuilder/3116528/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for experimental +I: user script /srv/workspace/pbuilder/3116528/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/sibelia-3.0.7+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../sibelia_3.0.7+dfsg-4_source.changes dpkg-buildpackage: info: source package sibelia dpkg-buildpackage: info: source version 3.0.7+dfsg-4 dpkg-buildpackage: info: source distribution experimental @@ -708,7 +744,7 @@ -- Check for working CXX compiler: /usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done --- Configuring done (0.6s) +-- Configuring done (0.5s) -- Generating done (0.0s) CMake Warning: Manually-specified variables were not used by the project: @@ -737,37 +773,39 @@ make[3]: Leaving directory '/build/reproducible-path/sibelia-3.0.7+dfsg/obj-aarch64-linux-gnu' make -f CMakeFiles/Sibelia.dir/build.make CMakeFiles/Sibelia.dir/build make[3]: Entering directory '/build/reproducible-path/sibelia-3.0.7+dfsg/obj-aarch64-linux-gnu' -[ 5%] Building CXX object CMakeFiles/Sibelia.dir/util.cpp.o -/usr/bin/c++ -I/build/reproducible-path/sibelia-3.0.7+dfsg/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/sibelia-3.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -MD -MT CMakeFiles/Sibelia.dir/util.cpp.o -MF CMakeFiles/Sibelia.dir/util.cpp.o.d -o CMakeFiles/Sibelia.dir/util.cpp.o -c /build/reproducible-path/sibelia-3.0.7+dfsg/src/util.cpp +[ 5%] Building CXX object CMakeFiles/Sibelia.dir/sibelia.cpp.o +/usr/bin/c++ -I/build/reproducible-path/sibelia-3.0.7+dfsg/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/sibelia-3.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -MD -MT CMakeFiles/Sibelia.dir/sibelia.cpp.o -MF CMakeFiles/Sibelia.dir/sibelia.cpp.o.d -o CMakeFiles/Sibelia.dir/sibelia.cpp.o -c /build/reproducible-path/sibelia-3.0.7+dfsg/src/sibelia.cpp [ 10%] Building CXX object CMakeFiles/Sibelia.dir/postprocessor.cpp.o -[ 15%] Building CXX object CMakeFiles/Sibelia.dir/blockfinder.cpp.o -[ 20%] Building CXX object CMakeFiles/Sibelia.dir/outputgenerator.cpp.o -[ 25%] Building CXX object CMakeFiles/Sibelia.dir/blockinstance.cpp.o -[ 30%] Building CXX object CMakeFiles/Sibelia.dir/bulgeremoval.cpp.o -/usr/bin/c++ -I/build/reproducible-path/sibelia-3.0.7+dfsg/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/sibelia-3.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -MD -MT CMakeFiles/Sibelia.dir/blockfinder.cpp.o -MF CMakeFiles/Sibelia.dir/blockfinder.cpp.o.d -o CMakeFiles/Sibelia.dir/blockfinder.cpp.o -c /build/reproducible-path/sibelia-3.0.7+dfsg/src/blockfinder.cpp -/usr/bin/c++ -I/build/reproducible-path/sibelia-3.0.7+dfsg/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/sibelia-3.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -MD -MT CMakeFiles/Sibelia.dir/bulgeremoval.cpp.o -MF CMakeFiles/Sibelia.dir/bulgeremoval.cpp.o.d -o CMakeFiles/Sibelia.dir/bulgeremoval.cpp.o -c /build/reproducible-path/sibelia-3.0.7+dfsg/src/bulgeremoval.cpp -[ 35%] Building CXX object CMakeFiles/Sibelia.dir/indexedsequence.cpp.o /usr/bin/c++ -I/build/reproducible-path/sibelia-3.0.7+dfsg/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/sibelia-3.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -MD -MT CMakeFiles/Sibelia.dir/postprocessor.cpp.o -MF CMakeFiles/Sibelia.dir/postprocessor.cpp.o.d -o CMakeFiles/Sibelia.dir/postprocessor.cpp.o -c /build/reproducible-path/sibelia-3.0.7+dfsg/src/postprocessor.cpp +[ 15%] Building CXX object CMakeFiles/Sibelia.dir/indexedsequence.cpp.o /usr/bin/c++ -I/build/reproducible-path/sibelia-3.0.7+dfsg/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/sibelia-3.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -MD -MT CMakeFiles/Sibelia.dir/indexedsequence.cpp.o -MF CMakeFiles/Sibelia.dir/indexedsequence.cpp.o.d -o CMakeFiles/Sibelia.dir/indexedsequence.cpp.o -c /build/reproducible-path/sibelia-3.0.7+dfsg/src/indexedsequence.cpp -[ 40%] Building CXX object CMakeFiles/Sibelia.dir/dnasequence.cpp.o +[ 20%] Building CXX object CMakeFiles/Sibelia.dir/outputgenerator.cpp.o +[ 25%] Building CXX object CMakeFiles/Sibelia.dir/util.cpp.o +/usr/bin/c++ -I/build/reproducible-path/sibelia-3.0.7+dfsg/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/sibelia-3.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -MD -MT CMakeFiles/Sibelia.dir/util.cpp.o -MF CMakeFiles/Sibelia.dir/util.cpp.o.d -o CMakeFiles/Sibelia.dir/util.cpp.o -c /build/reproducible-path/sibelia-3.0.7+dfsg/src/util.cpp /usr/bin/c++ -I/build/reproducible-path/sibelia-3.0.7+dfsg/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/sibelia-3.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -MD -MT CMakeFiles/Sibelia.dir/outputgenerator.cpp.o -MF CMakeFiles/Sibelia.dir/outputgenerator.cpp.o.d -o CMakeFiles/Sibelia.dir/outputgenerator.cpp.o -c /build/reproducible-path/sibelia-3.0.7+dfsg/src/outputgenerator.cpp +[ 30%] Building CXX object CMakeFiles/Sibelia.dir/blockfinder.cpp.o +/usr/bin/c++ -I/build/reproducible-path/sibelia-3.0.7+dfsg/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/sibelia-3.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -MD -MT CMakeFiles/Sibelia.dir/blockfinder.cpp.o -MF CMakeFiles/Sibelia.dir/blockfinder.cpp.o.d -o CMakeFiles/Sibelia.dir/blockfinder.cpp.o -c /build/reproducible-path/sibelia-3.0.7+dfsg/src/blockfinder.cpp +[ 35%] Building CXX object CMakeFiles/Sibelia.dir/blockinstance.cpp.o /usr/bin/c++ -I/build/reproducible-path/sibelia-3.0.7+dfsg/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/sibelia-3.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -MD -MT CMakeFiles/Sibelia.dir/blockinstance.cpp.o -MF CMakeFiles/Sibelia.dir/blockinstance.cpp.o.d -o CMakeFiles/Sibelia.dir/blockinstance.cpp.o -c /build/reproducible-path/sibelia-3.0.7+dfsg/src/blockinstance.cpp +[ 40%] Building CXX object CMakeFiles/Sibelia.dir/bifurcationstorage.cpp.o +/usr/bin/c++ -I/build/reproducible-path/sibelia-3.0.7+dfsg/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/sibelia-3.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -MD -MT CMakeFiles/Sibelia.dir/bifurcationstorage.cpp.o -MF 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-D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -MD -MT CMakeFiles/Sibelia.dir/fasta.cpp.o -MF CMakeFiles/Sibelia.dir/fasta.cpp.o.d -o CMakeFiles/Sibelia.dir/fasta.cpp.o -c /build/reproducible-path/sibelia-3.0.7+dfsg/src/fasta.cpp In file included from /usr/include/boost/bind/detail/requires_cxx11.hpp:9, from /usr/include/boost/bind/bind.hpp:24, from /usr/include/boost/bind.hpp:29, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:31, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/blockinstance.h:10, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/blockfinder.h:10, - from /build/reproducible-path/sibelia-3.0.7+dfsg/src/blockfinder.cpp:7: + from /build/reproducible-path/sibelia-3.0.7+dfsg/src/util.h:10, + from /build/reproducible-path/sibelia-3.0.7+dfsg/src/outputgenerator.h:10, + from /build/reproducible-path/sibelia-3.0.7+dfsg/src/outputgenerator.cpp:9: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ @@ -776,7 +814,8 @@ from /usr/include/boost/bind.hpp:29, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:31, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/blockinstance.h:10, - from /build/reproducible-path/sibelia-3.0.7+dfsg/src/blockinstance.cpp:7: + from /build/reproducible-path/sibelia-3.0.7+dfsg/src/blockfinder.h:10, + from /build/reproducible-path/sibelia-3.0.7+dfsg/src/blockfinder.cpp:7: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ @@ -786,7 +825,9 @@ from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:31, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/fasta.h:10, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/dnasequence.h:10, - from /build/reproducible-path/sibelia-3.0.7+dfsg/src/dnasequence.cpp:7: + from /build/reproducible-path/sibelia-3.0.7+dfsg/src/hashing.h:10, + from /build/reproducible-path/sibelia-3.0.7+dfsg/src/indexedsequence.h:10, + from /build/reproducible-path/sibelia-3.0.7+dfsg/src/indexedsequence.cpp:7: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ @@ -794,9 +835,10 @@ from /usr/include/boost/bind/bind.hpp:24, from /usr/include/boost/bind.hpp:29, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:31, - from /build/reproducible-path/sibelia-3.0.7+dfsg/src/blockinstance.h:10, - from /build/reproducible-path/sibelia-3.0.7+dfsg/src/blockfinder.h:10, - from /build/reproducible-path/sibelia-3.0.7+dfsg/src/bulgeremoval.cpp:7: + from /build/reproducible-path/sibelia-3.0.7+dfsg/src/fasta.h:10, + from /build/reproducible-path/sibelia-3.0.7+dfsg/src/dnasequence.h:10, + from /build/reproducible-path/sibelia-3.0.7+dfsg/src/bifurcationstorage.h:11, + from /build/reproducible-path/sibelia-3.0.7+dfsg/src/bifurcationstorage.cpp:7: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ @@ -805,8 +847,7 @@ from /usr/include/boost/bind.hpp:29, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:31, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/blockinstance.h:10, - from /build/reproducible-path/sibelia-3.0.7+dfsg/src/blockfinder.h:10, - from /build/reproducible-path/sibelia-3.0.7+dfsg/src/edge.cpp:7: + from /build/reproducible-path/sibelia-3.0.7+dfsg/src/blockinstance.cpp:7: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ @@ -817,20 +858,7 @@ from /build/reproducible-path/sibelia-3.0.7+dfsg/src/blockinstance.h:10, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/blockfinder.h:10, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/util.h:10, - from /build/reproducible-path/sibelia-3.0.7+dfsg/src/outputgenerator.h:10, - from /build/reproducible-path/sibelia-3.0.7+dfsg/src/outputgenerator.cpp:9: -/usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ - 36 | BOOST_PRAGMA_MESSAGE( - | ^~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/boost/bind/detail/requires_cxx11.hpp:9, - from /usr/include/boost/bind/bind.hpp:24, - from /usr/include/boost/bind.hpp:29, - from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:31, - from /build/reproducible-path/sibelia-3.0.7+dfsg/src/fasta.h:10, - from /build/reproducible-path/sibelia-3.0.7+dfsg/src/dnasequence.h:10, - from /build/reproducible-path/sibelia-3.0.7+dfsg/src/hashing.h:10, - from /build/reproducible-path/sibelia-3.0.7+dfsg/src/indexedsequence.h:10, - from /build/reproducible-path/sibelia-3.0.7+dfsg/src/indexedsequence.cpp:7: + from /build/reproducible-path/sibelia-3.0.7+dfsg/src/util.cpp:7: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ @@ -840,28 +868,7 @@ from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:31, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/blockinstance.h:10, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/blockfinder.h:10, - from /build/reproducible-path/sibelia-3.0.7+dfsg/src/util.h:10, - from /build/reproducible-path/sibelia-3.0.7+dfsg/src/util.cpp:7: -/usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ - 36 | BOOST_PRAGMA_MESSAGE( - | ^~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/boost/bind/detail/requires_cxx11.hpp:9, - from /usr/include/boost/bind/bind.hpp:24, - from /usr/include/boost/bind.hpp:29, - from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:31, - from /build/reproducible-path/sibelia-3.0.7+dfsg/src/fasta.h:10, - from /build/reproducible-path/sibelia-3.0.7+dfsg/src/dnasequence.h:10, - from /build/reproducible-path/sibelia-3.0.7+dfsg/src/bifurcationstorage.h:11, - from /build/reproducible-path/sibelia-3.0.7+dfsg/src/bifurcationstorage.cpp:7: -/usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ - 36 | BOOST_PRAGMA_MESSAGE( - | ^~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/boost/bind/detail/requires_cxx11.hpp:9, - from /usr/include/boost/bind/bind.hpp:24, - from /usr/include/boost/bind.hpp:29, - from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:31, - from /build/reproducible-path/sibelia-3.0.7+dfsg/src/fasta.h:10, - from /build/reproducible-path/sibelia-3.0.7+dfsg/src/fasta.cpp:7: + from /build/reproducible-path/sibelia-3.0.7+dfsg/src/bulgeremoval.cpp:7: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ @@ -874,23 +881,23 @@ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -In file included from /build/reproducible-path/sibelia-3.0.7+dfsg/src/dnasequence.h:12, - from /build/reproducible-path/sibelia-3.0.7+dfsg/src/blockinstance.h:11: +In file included from /build/reproducible-path/sibelia-3.0.7+dfsg/src/dnasequence.h:12: /build/reproducible-path/sibelia-3.0.7+dfsg/src/unrolledlist.h:36:45: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 36 | class iterator: public std::iterator | ^~~~~~~~ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -/build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:104:51: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] - 104 | struct FancyIterator: public std::iterator - | ^~~~~~~~ -In file included from /usr/include/c++/14/bits/stl_iterator_base_funcs.h:66, - from /usr/include/c++/14/string:47, - from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:12: -/usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ +In file included from /usr/include/boost/bind/detail/requires_cxx11.hpp:9, + from /usr/include/boost/bind/bind.hpp:24, + from /usr/include/boost/bind.hpp:29, + from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:31, + from /build/reproducible-path/sibelia-3.0.7+dfsg/src/blockinstance.h:10, + from /build/reproducible-path/sibelia-3.0.7+dfsg/src/blockfinder.h:10, + from /build/reproducible-path/sibelia-3.0.7+dfsg/src/edge.cpp:7: +/usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ + 36 | BOOST_PRAGMA_MESSAGE( + | ^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/sibelia-3.0.7+dfsg/src/dnasequence.h:51:51: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 51 | class StrandIterator: public std::iterator | ^~~~~~~~ @@ -914,19 +921,51 @@ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -In file included from /build/reproducible-path/sibelia-3.0.7+dfsg/src/dnasequence.h:12: -/build/reproducible-path/sibelia-3.0.7+dfsg/src/unrolledlist.h:36:45: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] - 36 | class iterator: public std::iterator - | ^~~~~~~~ -/usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ /build/reproducible-path/sibelia-3.0.7+dfsg/src/dnasequence.h:51:51: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 51 | class StrandIterator: public std::iterator | ^~~~~~~~ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +/build/reproducible-path/sibelia-3.0.7+dfsg/src/indexedsequence.h:37:22: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] + 37 | std::auto_ptr sequence_; + | ^~~~~~~~ +In file included from /usr/include/c++/14/memory:78, + from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:20: +/usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here + 59 | template class auto_ptr; + | ^~~~~~~~ +/build/reproducible-path/sibelia-3.0.7+dfsg/src/indexedsequence.h:38:22: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] + 38 | std::auto_ptr bifStorage_; + | ^~~~~~~~ +/usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here + 59 | template class auto_ptr; + | ^~~~~~~~ +In file included from /usr/include/boost/bind/detail/requires_cxx11.hpp:9, + from /usr/include/boost/bind/bind.hpp:24, + from /usr/include/boost/bind.hpp:29, + from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:31, + from /build/reproducible-path/sibelia-3.0.7+dfsg/src/fasta.h:10, + from /build/reproducible-path/sibelia-3.0.7+dfsg/src/dnasequence.h:10, + from /build/reproducible-path/sibelia-3.0.7+dfsg/src/dnasequence.cpp:7: +/usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ + 36 | BOOST_PRAGMA_MESSAGE( + | ^~~~~~~~~~~~~~~~~~~~ +In file included from /build/reproducible-path/sibelia-3.0.7+dfsg/src/blockfinder.h:11: +/build/reproducible-path/sibelia-3.0.7+dfsg/src/indexedsequence.h:37:22: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] + 37 | std::auto_ptr sequence_; + | ^~~~~~~~ +In file included from /usr/include/c++/14/memory:78, + from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:20: +/usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here + 59 | template class auto_ptr; + | ^~~~~~~~ +/build/reproducible-path/sibelia-3.0.7+dfsg/src/indexedsequence.h:38:22: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] + 38 | std::auto_ptr bifStorage_; + | ^~~~~~~~ +/usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here + 59 | template class auto_ptr; + | ^~~~~~~~ /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:104:51: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 104 | struct FancyIterator: public std::iterator | ^~~~~~~~ @@ -936,13 +975,8 @@ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -/build/reproducible-path/sibelia-3.0.7+dfsg/src/dnasequence.h:51:51: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] - 51 | class StrandIterator: public std::iterator - | ^~~~~~~~ -/usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -In file included from /build/reproducible-path/sibelia-3.0.7+dfsg/src/dnasequence.h:12: +In file included from /build/reproducible-path/sibelia-3.0.7+dfsg/src/dnasequence.h:12, + from /build/reproducible-path/sibelia-3.0.7+dfsg/src/blockinstance.h:11: /build/reproducible-path/sibelia-3.0.7+dfsg/src/unrolledlist.h:36:45: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 36 | class iterator: public std::iterator | ^~~~~~~~ @@ -952,20 +986,19 @@ /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:104:51: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 104 | struct FancyIterator: public std::iterator | ^~~~~~~~ -In file included from /usr/include/c++/14/bits/stl_iterator_base_funcs.h:66, - from /usr/include/c++/14/string:47, - from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:12: -/usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ /build/reproducible-path/sibelia-3.0.7+dfsg/src/dnasequence.h:51:51: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 51 | class StrandIterator: public std::iterator | ^~~~~~~~ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -In file included from /build/reproducible-path/sibelia-3.0.7+dfsg/src/dnasequence.h:12, - from /build/reproducible-path/sibelia-3.0.7+dfsg/src/blockinstance.h:11: +In file included from /usr/include/c++/14/bits/stl_iterator_base_funcs.h:66, + from /usr/include/c++/14/string:47, + from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:12: +/usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +In file included from /build/reproducible-path/sibelia-3.0.7+dfsg/src/dnasequence.h:12: /build/reproducible-path/sibelia-3.0.7+dfsg/src/unrolledlist.h:36:45: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 36 | class iterator: public std::iterator | ^~~~~~~~ @@ -995,15 +1028,21 @@ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -/build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:104:51: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] - 104 | struct FancyIterator: public std::iterator +/build/reproducible-path/sibelia-3.0.7+dfsg/src/dnasequence.h:51:51: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] + 51 | class StrandIterator: public std::iterator | ^~~~~~~~ -In file included from /usr/include/c++/14/bits/stl_iterator_base_funcs.h:66, - from /usr/include/c++/14/string:47, - from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:12: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +In file included from /usr/include/boost/bind/detail/requires_cxx11.hpp:9, + from /usr/include/boost/bind/bind.hpp:24, + from /usr/include/boost/bind.hpp:29, + from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:31, + from /build/reproducible-path/sibelia-3.0.7+dfsg/src/fasta.h:10, + from /build/reproducible-path/sibelia-3.0.7+dfsg/src/fasta.cpp:7: +/usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ + 36 | BOOST_PRAGMA_MESSAGE( + | ^~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/sibelia-3.0.7+dfsg/src/blockfinder.h:11: /build/reproducible-path/sibelia-3.0.7+dfsg/src/indexedsequence.h:37:22: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 37 | std::auto_ptr sequence_; @@ -1019,9 +1058,12 @@ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ -/build/reproducible-path/sibelia-3.0.7+dfsg/src/dnasequence.h:51:51: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] - 51 | class StrandIterator: public std::iterator +/build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:104:51: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] + 104 | struct FancyIterator: public std::iterator | ^~~~~~~~ +In file included from /usr/include/c++/14/bits/stl_iterator_base_funcs.h:66, + from /usr/include/c++/14/string:47, + from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:12: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -1048,14 +1090,7 @@ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -In file included from /build/reproducible-path/sibelia-3.0.7+dfsg/src/dnasequence.h:12, - from /build/reproducible-path/sibelia-3.0.7+dfsg/src/blockinstance.h:11: -/build/reproducible-path/sibelia-3.0.7+dfsg/src/unrolledlist.h:36:45: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] - 36 | class iterator: public std::iterator - | ^~~~~~~~ -/usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ +In file included from /build/reproducible-path/sibelia-3.0.7+dfsg/src/blockfinder.h:11: /build/reproducible-path/sibelia-3.0.7+dfsg/src/indexedsequence.h:37:22: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 37 | std::auto_ptr sequence_; | ^~~~~~~~ @@ -1070,6 +1105,14 @@ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ +In file included from /build/reproducible-path/sibelia-3.0.7+dfsg/src/dnasequence.h:12, + from /build/reproducible-path/sibelia-3.0.7+dfsg/src/blockinstance.h:11: +/build/reproducible-path/sibelia-3.0.7+dfsg/src/unrolledlist.h:36:45: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] + 36 | class iterator: public std::iterator + | ^~~~~~~~ +/usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ /build/reproducible-path/sibelia-3.0.7+dfsg/src/dnasequence.h:51:51: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 51 | class StrandIterator: public std::iterator | ^~~~~~~~ @@ -1085,7 +1128,8 @@ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -In file included from /build/reproducible-path/sibelia-3.0.7+dfsg/src/dnasequence.h:12: +In file included from /build/reproducible-path/sibelia-3.0.7+dfsg/src/dnasequence.h:12, + from /build/reproducible-path/sibelia-3.0.7+dfsg/src/blockinstance.h:11: /build/reproducible-path/sibelia-3.0.7+dfsg/src/unrolledlist.h:36:45: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 36 | class iterator: public std::iterator | ^~~~~~~~ @@ -1098,6 +1142,22 @@ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +/build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:104:51: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] + 104 | struct FancyIterator: public std::iterator + | ^~~~~~~~ +In file included from /usr/include/c++/14/bits/stl_iterator_base_funcs.h:66, + from /usr/include/c++/14/string:47, + from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:12: +/usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +In file included from /build/reproducible-path/sibelia-3.0.7+dfsg/src/dnasequence.h:12: +/build/reproducible-path/sibelia-3.0.7+dfsg/src/unrolledlist.h:36:45: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] + 36 | class iterator: public std::iterator + | ^~~~~~~~ +/usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ In file included from /build/reproducible-path/sibelia-3.0.7+dfsg/src/blockfinder.h:11: /build/reproducible-path/sibelia-3.0.7+dfsg/src/indexedsequence.h:37:22: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 37 | std::auto_ptr sequence_; @@ -1113,6 +1173,21 @@ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ +/build/reproducible-path/sibelia-3.0.7+dfsg/src/dnasequence.h:51:51: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] + 51 | class StrandIterator: public std::iterator + | ^~~~~~~~ +/usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +/build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:104:51: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] + 104 | struct FancyIterator: public std::iterator + | ^~~~~~~~ +In file included from /usr/include/c++/14/bits/stl_iterator_base_funcs.h:66, + from /usr/include/c++/14/string:47, + from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:12: +/usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ In file included from /build/reproducible-path/sibelia-3.0.7+dfsg/src/blockfinder.h:11: /build/reproducible-path/sibelia-3.0.7+dfsg/src/indexedsequence.h:37:22: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 37 | std::auto_ptr sequence_; @@ -1128,45 +1203,6 @@ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ -In file included from /build/reproducible-path/sibelia-3.0.7+dfsg/src/blockfinder.h:11: -/build/reproducible-path/sibelia-3.0.7+dfsg/src/indexedsequence.h:37:22: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] - 37 | std::auto_ptr sequence_; - | ^~~~~~~~ -In file included from /usr/include/c++/14/memory:78, - from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:20: -/usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here - 59 | template class auto_ptr; - | ^~~~~~~~ -/build/reproducible-path/sibelia-3.0.7+dfsg/src/indexedsequence.h:38:22: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] - 38 | std::auto_ptr bifStorage_; - | ^~~~~~~~ -/usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here - 59 | template class auto_ptr; - | ^~~~~~~~ -In file included from /build/reproducible-path/sibelia-3.0.7+dfsg/src/blockfinder.h:11: -/build/reproducible-path/sibelia-3.0.7+dfsg/src/indexedsequence.h:37:22: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] - 37 | std::auto_ptr sequence_; - | ^~~~~~~~ -In file included from /usr/include/c++/14/memory:78, - from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:20: -/usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here - 59 | template class auto_ptr; - | ^~~~~~~~ -/build/reproducible-path/sibelia-3.0.7+dfsg/src/indexedsequence.h:38:22: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] - 38 | std::auto_ptr bifStorage_; - | ^~~~~~~~ -/usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here - 59 | template class auto_ptr; - | ^~~~~~~~ -/build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:104:51: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] - 104 | struct FancyIterator: public std::iterator - | ^~~~~~~~ -In file included from /usr/include/c++/14/bits/stl_iterator_base_funcs.h:66, - from /usr/include/c++/14/string:47, - from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:12: -/usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ [ 65%] Building CXX object CMakeFiles/Sibelia.dir/serialization.cpp.o /usr/bin/c++ -I/build/reproducible-path/sibelia-3.0.7+dfsg/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/sibelia-3.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -MD -MT CMakeFiles/Sibelia.dir/serialization.cpp.o -MF CMakeFiles/Sibelia.dir/serialization.cpp.o.d -o CMakeFiles/Sibelia.dir/serialization.cpp.o -c /build/reproducible-path/sibelia-3.0.7+dfsg/src/serialization.cpp [ 70%] Building CXX object CMakeFiles/Sibelia.dir/synteny.cpp.o @@ -1183,18 +1219,9 @@ from /usr/include/boost/bind/bind.hpp:24, from /usr/include/boost/bind.hpp:29, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:31, - from /build/reproducible-path/sibelia-3.0.7+dfsg/src/blockinstance.h:10, - from /build/reproducible-path/sibelia-3.0.7+dfsg/src/blockfinder.h:10, - from /build/reproducible-path/sibelia-3.0.7+dfsg/src/serialization.cpp:7: -/usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ - 36 | BOOST_PRAGMA_MESSAGE( - | ^~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/boost/bind/detail/requires_cxx11.hpp:9, - from /usr/include/boost/bind/bind.hpp:24, - from /usr/include/boost/bind.hpp:29, - from /build/reproducible-path/sibelia-3.0.7+dfsg/src/test/../common.h:31, - from /build/reproducible-path/sibelia-3.0.7+dfsg/src/test/unrolledlisttest.h:10, - from /build/reproducible-path/sibelia-3.0.7+dfsg/src/test/unrolledlisttest.cpp:7: + from /build/reproducible-path/sibelia-3.0.7+dfsg/src/fasta.h:10, + from /build/reproducible-path/sibelia-3.0.7+dfsg/src/postprocessor.h:13, + from /build/reproducible-path/sibelia-3.0.7+dfsg/src/sibelia.cpp:8: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ @@ -1204,43 +1231,40 @@ from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:31, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/blockinstance.h:10, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/blockfinder.h:10, - from /build/reproducible-path/sibelia-3.0.7+dfsg/src/synteny.cpp:9: + from /build/reproducible-path/sibelia-3.0.7+dfsg/src/serialization.cpp:7: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/sibelia-3.0.7+dfsg/src/test/../common.h:104:51: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] - 104 | struct FancyIterator: public std::iterator - | ^~~~~~~~ -In file included from /usr/include/c++/14/bits/stl_iterator_base_funcs.h:66, - from /usr/include/c++/14/string:47, - from /build/reproducible-path/sibelia-3.0.7+dfsg/src/test/../common.h:12: -/usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -In file included from /build/reproducible-path/sibelia-3.0.7+dfsg/src/test/unrolledlisttest.h:11: -/build/reproducible-path/sibelia-3.0.7+dfsg/src/test/../unrolledlist.h:36:45: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] - 36 | class iterator: public std::iterator - | ^~~~~~~~ -/usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:104:51: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 104 | struct FancyIterator: public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/14/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/14/string:47, - from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:12: + from /usr/include/tclap/SwitchArg.h:29, + from /usr/include/tclap/CmdLine.h:27, + from /build/reproducible-path/sibelia-3.0.7+dfsg/src/sibelia.cpp:7: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/sibelia-3.0.7+dfsg/src/dnasequence.h:12, - from /build/reproducible-path/sibelia-3.0.7+dfsg/src/blockinstance.h:11: + from /build/reproducible-path/sibelia-3.0.7+dfsg/src/blockinstance.h:11, + from /build/reproducible-path/sibelia-3.0.7+dfsg/src/postprocessor.h:14: /build/reproducible-path/sibelia-3.0.7+dfsg/src/unrolledlist.h:36:45: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 36 | class iterator: public std::iterator | ^~~~~~~~ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +In file included from /usr/include/boost/bind/detail/requires_cxx11.hpp:9, + from /usr/include/boost/bind/bind.hpp:24, + from /usr/include/boost/bind.hpp:29, + from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:31, + from /build/reproducible-path/sibelia-3.0.7+dfsg/src/blockinstance.h:10, + from /build/reproducible-path/sibelia-3.0.7+dfsg/src/blockfinder.h:10, + from /build/reproducible-path/sibelia-3.0.7+dfsg/src/synteny.cpp:9: +/usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ + 36 | BOOST_PRAGMA_MESSAGE( + | ^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/sibelia-3.0.7+dfsg/src/dnasequence.h:51:51: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 51 | class StrandIterator: public std::iterator | ^~~~~~~~ @@ -1249,6 +1273,35 @@ | ^~~~~~~~ [ 95%] Building CXX object CMakeFiles/Sibelia.dir/resource.cpp.o /usr/bin/c++ -I/build/reproducible-path/sibelia-3.0.7+dfsg/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/sibelia-3.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -MD -MT CMakeFiles/Sibelia.dir/resource.cpp.o -MF CMakeFiles/Sibelia.dir/resource.cpp.o.d -o CMakeFiles/Sibelia.dir/resource.cpp.o -c /build/reproducible-path/sibelia-3.0.7+dfsg/src/resource.cpp +In file included from /usr/include/boost/bind/detail/requires_cxx11.hpp:9, + from /usr/include/boost/bind/bind.hpp:24, + from /usr/include/boost/bind.hpp:29, + from /build/reproducible-path/sibelia-3.0.7+dfsg/src/test/../common.h:31, + from /build/reproducible-path/sibelia-3.0.7+dfsg/src/test/unrolledlisttest.h:10, + from /build/reproducible-path/sibelia-3.0.7+dfsg/src/test/unrolledlisttest.cpp:7: +/usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ + 36 | BOOST_PRAGMA_MESSAGE( + | ^~~~~~~~~~~~~~~~~~~~ +In file included from /build/reproducible-path/sibelia-3.0.7+dfsg/src/blockfinder.h:11, + from /build/reproducible-path/sibelia-3.0.7+dfsg/src/util.h:10, + from /build/reproducible-path/sibelia-3.0.7+dfsg/src/sibelia.cpp:9: +/build/reproducible-path/sibelia-3.0.7+dfsg/src/indexedsequence.h:37:22: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] + 37 | std::auto_ptr sequence_; + | ^~~~~~~~ +In file included from /usr/include/c++/14/memory:78, + from /usr/include/seqan/basic/test_system.h:53, + from /usr/include/seqan/basic.h:65, + from /usr/include/seqan/align.h:55, + from /build/reproducible-path/sibelia-3.0.7+dfsg/src/postprocessor.h:10: +/usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here + 59 | template class auto_ptr; + | ^~~~~~~~ +/build/reproducible-path/sibelia-3.0.7+dfsg/src/indexedsequence.h:38:22: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] + 38 | std::auto_ptr bifStorage_; + | ^~~~~~~~ +/usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here + 59 | template class auto_ptr; + | ^~~~~~~~ /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:104:51: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 104 | struct FancyIterator: public std::iterator | ^~~~~~~~ @@ -1272,17 +1325,9 @@ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -In file included from /build/reproducible-path/sibelia-3.0.7+dfsg/src/blockfinder.h:11: -/build/reproducible-path/sibelia-3.0.7+dfsg/src/indexedsequence.h:37:22: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] - 37 | std::auto_ptr sequence_; - | ^~~~~~~~ -In file included from /usr/include/c++/14/memory:78, - from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:20: -/usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here - 59 | template class auto_ptr; - | ^~~~~~~~ -/build/reproducible-path/sibelia-3.0.7+dfsg/src/indexedsequence.h:38:22: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] - 38 | std::auto_ptr bifStorage_; +/build/reproducible-path/sibelia-3.0.7+dfsg/src/sibelia.cpp: In function ‘int main(int, char**)’: +/build/reproducible-path/sibelia-3.0.7+dfsg/src/sibelia.cpp:239:22: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] + 239 | std::auto_ptr finder(inRAM.isSet() ? new SyntenyFinder::BlockFinder(chrList) : new SyntenyFinder::BlockFinder(chrList, tempDir)); | ^~~~~~~~ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; @@ -1306,44 +1351,22 @@ from /usr/include/boost/bind/bind.hpp:24, from /usr/include/boost/bind.hpp:29, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:31, - from /build/reproducible-path/sibelia-3.0.7+dfsg/src/fasta.h:10, - from /build/reproducible-path/sibelia-3.0.7+dfsg/src/postprocessor.h:13, - from /build/reproducible-path/sibelia-3.0.7+dfsg/src/postprocessor.cpp:9: -/usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ - 36 | BOOST_PRAGMA_MESSAGE( - | ^~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/boost/bind/detail/requires_cxx11.hpp:9, - from /usr/include/boost/bind/bind.hpp:24, - from /usr/include/boost/bind.hpp:29, - from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:31, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/platform.h:10, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/platform.cpp:7: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/boost/bind/detail/requires_cxx11.hpp:9, - from /usr/include/boost/bind/bind.hpp:24, - from /usr/include/boost/bind.hpp:29, - from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:31, - from /build/reproducible-path/sibelia-3.0.7+dfsg/src/fasta.h:10, - from /build/reproducible-path/sibelia-3.0.7+dfsg/src/dnasequence.h:10, - from /build/reproducible-path/sibelia-3.0.7+dfsg/src/stranditerator.cpp:7: -/usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ - 36 | BOOST_PRAGMA_MESSAGE( - | ^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:104:51: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 104 | struct FancyIterator: public std::iterator | ^~~~~~~~ -In file included from /usr/include/c++/14/bits/stl_algobase.h:65, - from /usr/include/c++/14/algorithm:60, - from /usr/include/seqan/align.h:53, - from /build/reproducible-path/sibelia-3.0.7+dfsg/src/postprocessor.h:10: +In file included from /usr/include/c++/14/bits/stl_iterator_base_funcs.h:66, + from /usr/include/c++/14/string:47, + from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:12: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/sibelia-3.0.7+dfsg/src/dnasequence.h:12, - from /build/reproducible-path/sibelia-3.0.7+dfsg/src/blockinstance.h:11, - from /build/reproducible-path/sibelia-3.0.7+dfsg/src/postprocessor.h:14: + from /build/reproducible-path/sibelia-3.0.7+dfsg/src/blockinstance.h:11: /build/reproducible-path/sibelia-3.0.7+dfsg/src/unrolledlist.h:36:45: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 36 | class iterator: public std::iterator | ^~~~~~~~ @@ -1356,6 +1379,21 @@ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +In file included from /build/reproducible-path/sibelia-3.0.7+dfsg/src/blockfinder.h:11: +/build/reproducible-path/sibelia-3.0.7+dfsg/src/indexedsequence.h:37:22: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] + 37 | std::auto_ptr sequence_; + | ^~~~~~~~ +In file included from /usr/include/c++/14/memory:78, + from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:20: +/usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here + 59 | template class auto_ptr; + | ^~~~~~~~ +/build/reproducible-path/sibelia-3.0.7+dfsg/src/indexedsequence.h:38:22: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] + 38 | std::auto_ptr bifStorage_; + | ^~~~~~~~ +/usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here + 59 | template class auto_ptr; + | ^~~~~~~~ In file included from /usr/include/boost/bind/detail/requires_cxx11.hpp:9, from /usr/include/boost/bind/bind.hpp:24, from /usr/include/boost/bind.hpp:29, @@ -1368,12 +1406,19 @@ /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:104:51: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] +/build/reproducible-path/sibelia-3.0.7+dfsg/src/test/../common.h:104:51: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 104 | struct FancyIterator: public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/14/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/14/string:47, - from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:12: + from /build/reproducible-path/sibelia-3.0.7+dfsg/src/test/../common.h:12: +/usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +In file included from /build/reproducible-path/sibelia-3.0.7+dfsg/src/test/unrolledlisttest.h:11: +/build/reproducible-path/sibelia-3.0.7+dfsg/src/test/../unrolledlist.h:36:45: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] + 36 | class iterator: public std::iterator + | ^~~~~~~~ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -1383,7 +1428,7 @@ from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:31, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/fasta.h:10, from /build/reproducible-path/sibelia-3.0.7+dfsg/src/postprocessor.h:13, - from /build/reproducible-path/sibelia-3.0.7+dfsg/src/sibelia.cpp:8: + from /build/reproducible-path/sibelia-3.0.7+dfsg/src/postprocessor.cpp:9: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ @@ -1396,7 +1441,29 @@ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -In file included from /build/reproducible-path/sibelia-3.0.7+dfsg/src/dnasequence.h:12: +In file included from /usr/include/boost/bind/detail/requires_cxx11.hpp:9, + from /usr/include/boost/bind/bind.hpp:24, + from /usr/include/boost/bind.hpp:29, + from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:31, + from /build/reproducible-path/sibelia-3.0.7+dfsg/src/fasta.h:10, + from /build/reproducible-path/sibelia-3.0.7+dfsg/src/dnasequence.h:10, + from /build/reproducible-path/sibelia-3.0.7+dfsg/src/stranditerator.cpp:7: +/usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ + 36 | BOOST_PRAGMA_MESSAGE( + | ^~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:104:51: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] + 104 | struct FancyIterator: public std::iterator + | ^~~~~~~~ +In file included from /usr/include/c++/14/bits/stl_algobase.h:65, + from /usr/include/c++/14/algorithm:60, + from /usr/include/seqan/align.h:53, + from /build/reproducible-path/sibelia-3.0.7+dfsg/src/postprocessor.h:10: +/usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +In file included from /build/reproducible-path/sibelia-3.0.7+dfsg/src/dnasequence.h:12, + from /build/reproducible-path/sibelia-3.0.7+dfsg/src/blockinstance.h:11, + from /build/reproducible-path/sibelia-3.0.7+dfsg/src/postprocessor.h:14: /build/reproducible-path/sibelia-3.0.7+dfsg/src/unrolledlist.h:36:45: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 36 | class iterator: public std::iterator | ^~~~~~~~ @@ -1445,29 +1512,16 @@ /usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ -In file included from /usr/include/boost/bind/detail/requires_cxx11.hpp:9, - from /usr/include/boost/bind/bind.hpp:24, - from /usr/include/boost/bind.hpp:29, - from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:31, - from /build/reproducible-path/sibelia-3.0.7+dfsg/src/resource.h:6, - from /build/reproducible-path/sibelia-3.0.7+dfsg/src/resource.cpp:6: -/usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ - 36 | BOOST_PRAGMA_MESSAGE( - | ^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:104:51: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 104 | struct FancyIterator: public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/14/bits/stl_iterator_base_funcs.h:66, from /usr/include/c++/14/string:47, - from /usr/include/tclap/SwitchArg.h:29, - from /usr/include/tclap/CmdLine.h:27, - from /build/reproducible-path/sibelia-3.0.7+dfsg/src/sibelia.cpp:7: + from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:12: /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -In file included from /build/reproducible-path/sibelia-3.0.7+dfsg/src/dnasequence.h:12, - from /build/reproducible-path/sibelia-3.0.7+dfsg/src/blockinstance.h:11, - from /build/reproducible-path/sibelia-3.0.7+dfsg/src/postprocessor.h:14: +In file included from /build/reproducible-path/sibelia-3.0.7+dfsg/src/dnasequence.h:12: /build/reproducible-path/sibelia-3.0.7+dfsg/src/unrolledlist.h:36:45: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 36 | class iterator: public std::iterator | ^~~~~~~~ @@ -1480,33 +1534,15 @@ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -In file included from /build/reproducible-path/sibelia-3.0.7+dfsg/src/blockfinder.h:11, - from /build/reproducible-path/sibelia-3.0.7+dfsg/src/util.h:10, - from /build/reproducible-path/sibelia-3.0.7+dfsg/src/sibelia.cpp:9: -/build/reproducible-path/sibelia-3.0.7+dfsg/src/indexedsequence.h:37:22: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] - 37 | std::auto_ptr sequence_; - | ^~~~~~~~ -In file included from /usr/include/c++/14/memory:78, - from /usr/include/seqan/basic/test_system.h:53, - from /usr/include/seqan/basic.h:65, - from /usr/include/seqan/align.h:55, - from /build/reproducible-path/sibelia-3.0.7+dfsg/src/postprocessor.h:10: -/usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here - 59 | template class auto_ptr; - | ^~~~~~~~ -/build/reproducible-path/sibelia-3.0.7+dfsg/src/indexedsequence.h:38:22: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] - 38 | std::auto_ptr bifStorage_; - | ^~~~~~~~ -/usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here - 59 | template class auto_ptr; - | ^~~~~~~~ -/build/reproducible-path/sibelia-3.0.7+dfsg/src/sibelia.cpp: In function ‘int main(int, char**)’: -/build/reproducible-path/sibelia-3.0.7+dfsg/src/sibelia.cpp:239:22: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] - 239 | std::auto_ptr finder(inRAM.isSet() ? new SyntenyFinder::BlockFinder(chrList) : new SyntenyFinder::BlockFinder(chrList, tempDir)); - | ^~~~~~~~ -/usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here - 59 | template class auto_ptr; - | ^~~~~~~~ +In file included from /usr/include/boost/bind/detail/requires_cxx11.hpp:9, + from /usr/include/boost/bind/bind.hpp:24, + from /usr/include/boost/bind.hpp:29, + from /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:31, + from /build/reproducible-path/sibelia-3.0.7+dfsg/src/resource.h:6, + from /build/reproducible-path/sibelia-3.0.7+dfsg/src/resource.cpp:6: +/usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ + 36 | BOOST_PRAGMA_MESSAGE( + | ^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/sibelia-3.0.7+dfsg/src/common.h:104:51: warning: ‘template struct std::iterator’ is deprecated [-Wdeprecated-declarations] 104 | struct FancyIterator: public std::iterator | ^~~~~~~~ @@ -1649,8 +1685,8 @@ dh_gencontrol -O--sourcedirectory=src dh_md5sums -O--sourcedirectory=src dh_builddeb -O--sourcedirectory=src -dpkg-deb: building package 'sibelia-dbgsym' in '../sibelia-dbgsym_3.0.7+dfsg-4_arm64.deb'. dpkg-deb: building package 'sibelia' in '../sibelia_3.0.7+dfsg-4_arm64.deb'. +dpkg-deb: building package 'sibelia-dbgsym' in '../sibelia-dbgsym_3.0.7+dfsg-4_arm64.deb'. dpkg-deb: building package 'sibelia-examples' in '../sibelia-examples_3.0.7+dfsg-4_all.deb'. dpkg-genbuildinfo --build=binary -O../sibelia_3.0.7+dfsg-4_arm64.buildinfo dpkg-genchanges --build=binary -O../sibelia_3.0.7+dfsg-4_arm64.changes @@ -1659,12 +1695,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/3116528/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/3116528/tmp/hooks/B01_cleanup finished 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/1763354 and its subdirectories -I: Current time: Mon Nov 25 13:53:26 -12 2024 -I: pbuilder-time-stamp: 1732586006 +I: removing directory /srv/workspace/pbuilder/3116528 and its subdirectories +I: Current time: Mon Dec 29 22:18:50 +14 2025 +I: pbuilder-time-stamp: 1766996330 Compressing the 2nd log... /var/lib/jenkins/userContent/reproducible/debian/logdiffs/experimental/arm64/sibelia_3.0.7+dfsg-4.diff: 91.7% -- replaced with /var/lib/jenkins/userContent/reproducible/debian/logdiffs/experimental/arm64/sibelia_3.0.7+dfsg-4.diff.gz b2/build.log: 89.7% -- replaced with stdout Compressing the 1st log... b1/build.log: 90.1% -- replaced with stdout Tue Nov 26 01:55:53 UTC 2024 I: diffoscope 283 will be used to compare the two builds: ++ date -u +%s + DIFFOSCOPE_STAMP=/var/log/reproducible-builds/diffoscope_stamp_sibelia_experimental_arm64_1732586153 + touch /var/log/reproducible-builds/diffoscope_stamp_sibelia_experimental_arm64_1732586153 + RESULT=0 + systemd-run '--description=diffoscope on sibelia/3.0.7+dfsg-4 in experimental/arm64' --slice=rb-build-diffoscope.slice -u rb-diffoscope-arm64_16-38298 '--property=SuccessExitStatus=1 124' --user --send-sighup --pipe --wait -E TMPDIR timeout 155m nice schroot --directory /srv/reproducible-results/rbuild-debian/r-b-build.Jw2wMKXd --run-session -c jenkins-reproducible-unstable-diffoscope-90a7bb15-f838-4d84-b2c1-ed2da7481aaf -- sh -c 'export TMPDIR=/srv/reproducible-results/rbuild-debian/r-b-build.Jw2wMKXd/dbd-tmp-aOXtilI ; timeout 150m diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.Jw2wMKXd/sibelia_3.0.7+dfsg-4.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.Jw2wMKXd/sibelia_3.0.7+dfsg-4.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.Jw2wMKXd/sibelia_3.0.7+dfsg-4.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.Jw2wMKXd/b1/sibelia_3.0.7+dfsg-4_arm64.changes /srv/reproducible-results/rbuild-debian/r-b-build.Jw2wMKXd/b2/sibelia_3.0.7+dfsg-4_arm64.changes' + false + set +x Running as unit: rb-diffoscope-arm64_16-38298.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.Jw2wMKXd/sibelia_3.0.7+dfsg-4.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.Jw2wMKXd/sibelia_3.0.7+dfsg-4.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.Jw2wMKXd/sibelia_3.0.7+dfsg-4.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.Jw2wMKXd/b1/sibelia_3.0.7+dfsg-4_arm64.changes /srv/reproducible-results/rbuild-debian/r-b-build.Jw2wMKXd/b2/sibelia_3.0.7+dfsg-4_arm64.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call abc.DotChangesFile ## main (total time: 0.447s) 0.447s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.121s) 0.121s 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: 770ms CPU time consumed: 759ms _ _ _ _ ___(_) |__ ___| (_) __ _ / __| | '_ \ / _ \ | |/ _` | \__ \ | |_) | __/ | | (_| | |___/_|_.__/ \___|_|_|\__,_| Tue Nov 26 02:10:37 UTC 2024 I: diffoscope 283 found no differences in the changes files, and a .buildinfo file also exists. Tue Nov 26 02:10:37 UTC 2024 I: sibelia from experimental built successfully and reproducibly on arm64. INSERT 0 1 INSERT 0 1 DELETE 1 [2024-11-26 02:10:40] INFO: Starting at 2024-11-26 02:10:40.078241 [2024-11-26 02:10:40] INFO: Generating the pages of 1 package(s) [2024-11-26 02:10:42] CRITICAL: https://tests.reproducible-builds.org/debian/experimental/arm64/sibelia didn't produce a buildlog, even though it has been built. [2024-11-26 02:10:42] INFO: Finished at 2024-11-26 02:10:42.312487, took: 0:00:02.234256 Tue Nov 26 02:10:42 UTC 2024 - successfully updated the database and updated https://tests.reproducible-builds.org/debian/rb-pkg/experimental/arm64/sibelia.html Tue Nov 26 02:10:42 UTC 2024 I: Submitting .buildinfo files to external archives: Tue Nov 26 02:10:42 UTC 2024 I: Submitting 12K b1/sibelia_3.0.7+dfsg-4_arm64.buildinfo.asc https://buildinfo.debian.net/144201f5d0986782dce8bbeaee16a514c397178a/sibelia_3.0.7+dfsg-4_all Tue Nov 26 02:11:01 UTC 2024 I: Submitting 12K b2/sibelia_3.0.7+dfsg-4_arm64.buildinfo.asc https://buildinfo.debian.net/f68ec492698ebe17270de5a68e75c3bb1f5bbf19/sibelia_3.0.7+dfsg-4_all Tue Nov 26 02:11:28 UTC 2024 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Tue Nov 26 02:11:28 UTC 2024 I: Done submitting .buildinfo files. Tue Nov 26 02:11:28 UTC 2024 I: Removing signed sibelia_3.0.7+dfsg-4_arm64.buildinfo.asc files: removed './b1/sibelia_3.0.7+dfsg-4_arm64.buildinfo.asc' removed './b2/sibelia_3.0.7+dfsg-4_arm64.buildinfo.asc' 1732587088 arm64 experimental sibelia Starting cleanup. /var/lib/jenkins/userContent/reproducible/debian/rbuild/experimental/arm64/sibelia_3.0.7+dfsg-4.rbuild.log: 88.4% -- replaced with /var/lib/jenkins/userContent/reproducible/debian/rbuild/experimental/arm64/sibelia_3.0.7+dfsg-4.rbuild.log.gz [2024-11-26 02:11:28] INFO: Starting at 2024-11-26 02:11:28.702671 [2024-11-26 02:11:28] INFO: Generating the pages of 1 package(s) [2024-11-26 02:11:29] INFO: Finished at 2024-11-26 02:11:29.194135, took: 0:00:00.491473 All cleanup done. Tue Nov 26 02:11:29 UTC 2024 - total duration: 0h 19m 39s. Tue Nov 26 02:11:29 UTC 2024 - reproducible_build.sh stopped running as /tmp/jenkins-script-9MDkYmT7, removing. Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 20min 31.231s CPU time consumed: 9.176s