Tue May 2 00:41:20 UTC 2023 I: starting to build hinge/bookworm/arm64 on jenkins on '2023-05-02 00:41' Tue May 2 00:41:20 UTC 2023 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/arm64_20/25076/console.log Tue May 2 00:41:20 UTC 2023 I: Downloading source for bookworm/hinge=0.5.0-7 --2023-05-02 00:41:20-- http://cdn-fastly.deb.debian.org/debian/pool/main/h/hinge/hinge_0.5.0-7.dsc Connecting to 78.137.99.97:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2141 (2.1K) [text/prs.lines.tag] Saving to: ‘hinge_0.5.0-7.dsc’ 0K .. 100% 314K=0.007s 2023-05-02 00:41:20 (314 KB/s) - ‘hinge_0.5.0-7.dsc’ saved [2141/2141] Tue May 2 00:41:20 UTC 2023 I: hinge_0.5.0-7.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: hinge Binary: hinge Architecture: any Version: 0.5.0-7 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille Homepage: https://github.com/HingeAssembler/HINGE Standards-Version: 4.6.0 Vcs-Browser: https://salsa.debian.org/med-team/hinge Vcs-Git: https://salsa.debian.org/med-team/hinge.git Build-Depends: debhelper-compat (= 13), cmake, libspdlog-dev, libboost-dev, libboost-graph-dev, libhdf5-dev, zlib1g-dev, pandoc, python3, daligner, dazzdb, dascrubber, python3-numpy, python3-ujson, python3-colormap, python3-pbcore, python3-networkx, python3-matplotlib Package-List: hinge deb science optional arch=any Checksums-Sha1: 751c608f0632b1b29d4fc7876382a7b304c211df 477385 hinge_0.5.0.orig.tar.gz a8004e4e2e056797c310e57d218a7d725124c1ee 19920 hinge_0.5.0-7.debian.tar.xz Checksums-Sha256: e0d03e2f23eaab14123f9f74c6c069441770985ab0fdfb2c41c83e524794fdbe 477385 hinge_0.5.0.orig.tar.gz 9baddb2ec5ef3c96442d70346259261b6a08695f64b37ba76ba99e7d3fa2880b 19920 hinge_0.5.0-7.debian.tar.xz Files: 7c63320a86b69048cf778d96322054d2 477385 hinge_0.5.0.orig.tar.gz 433f4b05d5367799527688e52ef75c2a 19920 hinge_0.5.0-7.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCgAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAmHC0noRHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtEgow//Tlc17NxfLxYFUGupw+5lI2Iq8RE5E6uV qeTxZ0LvsEs2sLqLjwFd+UsXBA5AUSQiIhvgXzjRgVISArH8eDzWduQCJN4aZgCy i067KdNO1bZKJPaiqvPcqmrQBIee/QT5vzAfCxfyZ+wrV0h7kPLmMYNeex9nMQLk 8mF4j3VMpQuaApDtDjDZxqdAqMQ/lAK7wpWnRUiDXlEFtAfdG+rJ8Sa5d+KKv60S j5AXAjHHK3KIE0GWJdXMOrmGXt7OkTsQo31mo+7afTNK74p1gTBD26CEp/FyxDBO HulAEo9G4W4/pOb4k2cPz0Xo7UQbXJHJNZdiPcuO+CfMyhWGJxFP1npH6k3siKLP Mr3TWSUgh3Gwv/ToOAajdFMcmdstmnX04PRZwo97wqfuPACm4Qzv55ZCkptNIQZ9 E+besSTdJoScr+54D0ctGH9M1aiwY6ts5Xs1e12ivoGdtW2XcpI+XtphER41aeIF O4ZK4x/2PFLpcNO/zq0FGV832b/JEWDVnMDJywKimsY4fjjFUiJe27E+yocBKUnq o2hid+m2qOI5qA92CTzdbOPJ36jZY+M7Nv+Ud70R2zpTaKe+xoUIQUbt7PUq0Mq4 pUGfYhCBTcb3ZalaGyUkh77C9WdutIU5d+msh6yMpS0sX3jgwlnzqEgkwifMKpvS PfWehSebjTM= =Mw2v -----END PGP SIGNATURE----- Tue May 2 00:41:20 UTC 2023 I: Checking whether the package is not for us Tue May 2 00:41:20 UTC 2023 I: Starting 1st build on remote node codethink13-arm64.debian.net. Tue May 2 00:41:20 UTC 2023 I: Preparing to do remote build '1' on codethink13-arm64.debian.net. Tue May 2 00:52:09 UTC 2023 I: Deleting $TMPDIR on codethink13-arm64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Mon May 1 12:41:26 -12 2023 I: pbuilder-time-stamp: 1682988086 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bookworm-reproducible-base.tgz] tar: ./bin: time stamp 2024-05-28 04:48:56 is 33926849.82732886 s in the future tar: ./dev/null: time stamp 2024-05-28 04:48:25 is 33926818.82648448 s in the future tar: ./dev/zero: time stamp 2024-05-28 04:48:25 is 33926818.82639074 s in the future tar: ./dev/full: time stamp 2024-05-28 04:48:25 is 33926818.82632956 s in the future tar: ./dev/random: time stamp 2024-05-28 04:48:25 is 33926818.82626938 s in the future tar: ./dev/urandom: time stamp 2024-05-28 04:48:25 is 33926818.82620992 s in the future tar: ./dev/tty: time stamp 2024-05-28 04:48:25 is 33926818.82615182 s in the future tar: ./dev/console: time stamp 2024-05-28 04:48:25 is 33926818.82609422 s in the future tar: ./dev/pts: time stamp 2024-05-28 04:48:25 is 33926818.8260287 s in the future tar: ./dev/ptmx: time stamp 2024-05-28 04:48:25 is 33926818.8259757 s in the future tar: ./etc/apt/sources.list: time stamp 2024-05-28 04:50:35 is 33926948.825446 s in the future tar: ./etc/apt/apt.conf.d/80proxy: time stamp 2024-05-28 04:50:35 is 33926948.82532628 s in the future tar: ./etc/apt/apt.conf.d: time stamp 2024-05-28 04:50:35 is 33926948.82509334 s in the future tar: ./etc/apt/trusted.gpg.d: time stamp 2024-06-01 04:30:05 is 34271318.82307044 s in the future tar: ./etc/apt: time stamp 2024-05-28 04:50:35 is 33926948.8229996 s in the future tar: ./etc/default: time stamp 2024-05-28 04:48:54 is 33926847.82109584 s in the future tar: ./etc/dpkg/origins/default: time stamp 2024-05-28 04:48:26 is 33926819.8208843 s in the future tar: ./etc/dpkg/origins: time stamp 2024-05-28 04:48:49 is 33926842.82084042 s in the future tar: ./etc/dpkg/dpkg.cfg.d/02speedup: time stamp 2024-05-28 04:50:35 is 33926948.82068804 s in the future tar: ./etc/dpkg/dpkg.cfg.d: time stamp 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future tar: ./usr/share/locale/af: time stamp 2024-05-28 04:48:14 is 33926794.8688653 s in the future tar: ./usr/share/locale/zh_TW/LC_TIME: time stamp 2024-05-28 04:48:34 is 33926814.86882886 s in the future tar: ./usr/share/locale/zh_TW: time stamp 2024-05-28 04:48:14 is 33926794.86879322 s in the future tar: ./usr/share/locale/zh_CN/LC_TIME: time stamp 2024-05-28 04:48:34 is 33926814.86875766 s in the future tar: ./usr/share/locale/zh_CN: time stamp 2024-05-28 04:48:14 is 33926794.86872308 s in the future tar: ./usr/share/locale/vi/LC_TIME: time stamp 2024-05-28 04:48:34 is 33926814.86867854 s in the future tar: ./usr/share/locale/vi: time stamp 2024-05-28 04:48:14 is 33926794.868638 s in the future tar: ./usr/share/locale/uk/LC_TIME: time stamp 2024-05-28 04:48:34 is 33926814.86859838 s in the future tar: ./usr/share/locale/uk: time stamp 2024-05-28 04:48:14 is 33926794.86855738 s in the future tar: ./usr/share/locale/tr/LC_TIME: time stamp 2024-05-28 04:48:34 is 33926814.86851478 s in the future tar: ./usr/share/locale/tr: time stamp 2024-05-28 04:48:14 is 33926794.86847266 s in the future tar: ./usr/share/locale/sv/LC_TIME: time stamp 2024-05-28 04:48:34 is 33926814.8684296 s in the future tar: ./usr/share/locale/sv: time stamp 2024-05-28 04:48:14 is 33926794.86839304 s in the future tar: ./usr/share/locale/sl/LC_TIME: time stamp 2024-05-28 04:48:34 is 33926814.86835952 s in the future tar: ./usr/share/locale/sl: time stamp 2024-05-28 04:48:14 is 33926794.86832942 s in the future tar: ./usr/share/locale/sk/LC_TIME: time stamp 2024-05-28 04:48:34 is 33926814.86829622 s in the future tar: ./usr/share/locale/sk: time stamp 2024-05-28 04:48:14 is 33926794.86825864 s in the future tar: ./usr/share/locale/ru/LC_TIME: time stamp 2024-05-28 04:48:34 is 33926814.86821226 s in the future tar: ./usr/share/locale/ru: time stamp 2024-05-28 04:48:14 is 33926794.86817318 s in the future tar: ./usr/share/locale/ro/LC_TIME: time stamp 2024-05-28 04:48:34 is 33926814.8681298 s in the future tar: ./usr/share/locale/ro: time stamp 2024-05-28 04:48:14 is 33926794.8632323 s in the future tar: ./usr/share/locale/pt_BR/LC_TIME: time stamp 2024-05-28 04:48:34 is 33926814.8631774 s in the future tar: ./usr/share/locale/pt_BR: time stamp 2024-05-28 04:48:14 is 33926794.86314664 s in the future tar: ./usr/share/locale/pt/LC_TIME: time stamp 2024-05-28 04:48:34 is 33926814.86311486 s in the future tar: ./usr/share/locale/pt: time stamp 2024-05-28 04:48:14 is 33926794.86308382 s in the future tar: ./usr/share/locale/pl/LC_TIME: time stamp 2024-05-28 04:48:34 is 33926814.86305106 s in the future tar: ./usr/share/locale/pl: time stamp 2024-05-28 04:48:14 is 33926794.86302136 s in the future tar: ./usr/share/locale/nl/LC_TIME: time stamp 2024-05-28 04:48:34 is 33926814.86299076 s in the future tar: ./usr/share/locale/nl: time stamp 2024-05-28 04:48:14 is 33926794.86296078 s in the future tar: ./usr/share/locale/nb/LC_TIME: time stamp 2024-05-28 04:48:34 is 33926814.86292712 s in the future tar: ./usr/share/locale/nb: time stamp 2024-05-28 04:48:14 is 33926794.86289434 s in the future tar: ./usr/share/locale/lt/LC_TIME: time stamp 2024-05-28 04:48:34 is 33926814.86286134 s in the future tar: ./usr/share/locale/lt: time stamp 2024-05-28 04:48:14 is 33926794.86282844 s in the future tar: ./usr/share/locale/ko/LC_TIME: time stamp 2024-05-28 04:48:34 is 33926814.86279676 s in the future tar: ./usr/share/locale/ko: time stamp 2024-05-28 04:48:14 is 33926794.86276746 s in the future tar: ./usr/share/locale/ja/LC_TIME: time stamp 2024-05-28 04:48:34 is 33926814.86273534 s in the future tar: ./usr/share/locale/ja: time stamp 2024-05-28 04:48:14 is 33926794.86270324 s in the future tar: ./usr/share/locale/it/LC_TIME: time stamp 2024-05-28 04:48:34 is 33926814.8626706 s in the future tar: ./usr/share/locale/it: time stamp 2024-05-28 04:48:14 is 33926794.8626383 s in the future tar: ./usr/share/locale/hu/LC_TIME: time stamp 2024-05-28 04:48:34 is 33926814.86260456 s in the future tar: ./usr/share/locale/hu: time stamp 2024-05-28 04:48:14 is 33926794.86257382 s in the future tar: ./usr/share/locale/gl/LC_TIME: time stamp 2024-05-28 04:48:34 is 33926814.86254266 s in the future tar: ./usr/share/locale/gl: time stamp 2024-05-28 04:48:14 is 33926794.862513 s in the future tar: ./usr/share/locale/fr/LC_TIME: time stamp 2024-05-28 04:48:34 is 33926814.86247994 s in the future tar: ./usr/share/locale/fr: time stamp 2024-05-28 04:48:14 is 33926794.8624485 s in the future tar: ./usr/share/locale/fi/LC_TIME: time stamp 2024-05-28 04:48:34 is 33926814.8624171 s in the future tar: ./usr/share/locale/fi: time stamp 2024-05-28 04:48:14 is 33926794.86238808 s in the future tar: ./usr/share/locale/eu/LC_TIME: time stamp 2024-05-28 04:48:34 is 33926814.86235786 s in the future tar: ./usr/share/locale/eu: time stamp 2024-05-28 04:48:14 is 33926794.8623284 s in the future tar: ./usr/share/locale/es/LC_TIME: time stamp 2024-05-28 04:48:34 is 33926814.8622978 s in the future tar: ./usr/share/locale/es: time stamp 2024-05-28 04:48:14 is 33926794.86226886 s in the future tar: ./usr/share/locale/el/LC_TIME: time stamp 2024-05-28 04:48:34 is 33926814.86223904 s in the future tar: ./usr/share/locale/el: time stamp 2024-05-28 04:48:14 is 33926794.86221004 s in the future tar: ./usr/share/locale/de/LC_TIME: time stamp 2024-05-28 04:48:34 is 33926814.8621806 s in the future tar: ./usr/share/locale/de: time stamp 2024-05-28 04:48:14 is 33926794.86215214 s in the future tar: ./usr/share/locale/da/LC_TIME: time stamp 2024-05-28 04:48:34 is 33926814.86212192 s in the future tar: ./usr/share/locale/da: time stamp 2024-05-28 04:48:14 is 33926794.86209314 s in the future tar: ./usr/share/locale/cs/LC_TIME: time stamp 2024-05-28 04:48:34 is 33926814.86206034 s in the future tar: ./usr/share/locale/cs: time stamp 2024-05-28 04:48:14 is 33926794.86203068 s in the future tar: ./usr/share/locale/ca/LC_TIME: time stamp 2024-05-28 04:48:34 is 33926814.86200044 s in the future tar: ./usr/share/locale/ca: time stamp 2024-05-28 04:48:14 is 33926794.86196936 s in the future tar: ./usr/share/locale/bg/LC_TIME: time stamp 2024-05-28 04:48:34 is 33926814.86193938 s in the future tar: ./usr/share/locale/bg: time stamp 2024-05-28 04:48:14 is 33926794.86191006 s in the future tar: ./usr/lib/apt/planners: time stamp 2024-05-28 04:48:31 is 33926811.8470993 s in the future tar: ./usr/lib/apt: time stamp 2024-05-28 04:48:31 is 33926811.84699588 s in the future tar: ./usr/lib/aarch64-linux-gnu/perl/cross-config-5.36.0: time stamp 2024-05-28 04:48:42 is 33926822.8469627 s in the future tar: ./usr/lib/aarch64-linux-gnu/perl: time stamp 2024-05-28 04:48:21 is 33926801.84693216 s in the future tar: ./usr: time stamp 2024-05-28 04:48:26 is 33926806.84687764 s in the future tar: ./etc/systemd/system/multi-user.target.wants: time stamp 2024-05-28 04:48:51 is 33926831.84683296 s in the future tar: ./etc/systemd/system/timers.target.wants: time stamp 2024-05-28 04:48:53 is 33926833.8468008 s in the future tar: ./etc/systemd/system: time stamp 2024-05-28 04:48:51 is 33926831.84677352 s in the future tar: ./etc/rcS.d: time stamp 2024-05-28 04:48:49 is 33926829.84673484 s in the future tar: ./etc/rc6.d: time stamp 2024-05-28 04:48:49 is 33926829.84670736 s in the future tar: ./etc/rc0.d: time stamp 2024-05-28 04:48:49 is 33926829.84667996 s in the future 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 [hinge_0.5.0-7.dsc] I: copying [./hinge_0.5.0.orig.tar.gz] I: copying [./hinge_0.5.0-7.debian.tar.xz] I: Extracting source gpgv: Signature made Tue Dec 21 19:23:38 2021 -12 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./hinge_0.5.0-7.dsc: no acceptable signature found dpkg-source: info: extracting hinge in hinge-0.5.0 dpkg-source: info: unpacking hinge_0.5.0.orig.tar.gz dpkg-source: info: unpacking hinge_0.5.0-7.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying external-spdlog.patch dpkg-source: info: applying libspdlog-14.0.patch dpkg-source: info: applying libspdlog-1:1.3.0 dpkg-source: info: applying 2to3.patch dpkg-source: info: applying spdlog-1.5.0.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/21062/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='arm64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=8' DISTRIBUTION='bookworm' HOME='/var/lib/jenkins' HOST_ARCH='arm64' IFS=' ' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='21062' 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.kMHWErYB/pbuilderrc_l3qu --distribution bookworm --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.kMHWErYB/b1 --logfile b1/build.log hinge_0.5.0-7.dsc' SUDO_GID='117' SUDO_UID='110' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' USERNAME='root' _='/usr/bin/systemd-run' http_proxy='http://192.168.101.16:3128' I: uname -a Linux codethink13-arm64 4.15.0-210-generic #221-Ubuntu SMP Tue Apr 18 08:32:48 UTC 2023 aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 May 28 2024 /bin -> usr/bin I: user script /srv/workspace/pbuilder/21062/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: arm64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), cmake, libspdlog-dev, libboost-dev, libboost-graph-dev, libhdf5-dev, zlib1g-dev, pandoc, python3, daligner, dazzdb, dascrubber, python3-numpy, python3-ujson, python3-colormap, python3-pbcore, python3-networkx, python3-matplotlib dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19616 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on cmake; however: Package cmake is not installed. pbuilder-satisfydepends-dummy depends on libspdlog-dev; however: Package libspdlog-dev is not installed. pbuilder-satisfydepends-dummy depends on libboost-dev; however: Package libboost-dev is not installed. pbuilder-satisfydepends-dummy depends on libboost-graph-dev; however: Package libboost-graph-dev is not installed. pbuilder-satisfydepends-dummy depends on libhdf5-dev; however: Package libhdf5-dev is not installed. pbuilder-satisfydepends-dummy depends on zlib1g-dev; however: Package zlib1g-dev is not installed. pbuilder-satisfydepends-dummy depends on pandoc; however: Package pandoc is not installed. pbuilder-satisfydepends-dummy depends on python3; however: Package python3 is not installed. pbuilder-satisfydepends-dummy depends on daligner; however: Package daligner is not installed. pbuilder-satisfydepends-dummy depends on dazzdb; however: Package dazzdb is not installed. pbuilder-satisfydepends-dummy depends on dascrubber; however: Package dascrubber is not installed. pbuilder-satisfydepends-dummy depends on python3-numpy; however: Package python3-numpy is not installed. pbuilder-satisfydepends-dummy depends on python3-ujson; however: Package python3-ujson is not installed. pbuilder-satisfydepends-dummy depends on python3-colormap; however: Package python3-colormap is not installed. pbuilder-satisfydepends-dummy depends on python3-pbcore; however: Package python3-pbcore is not installed. pbuilder-satisfydepends-dummy depends on python3-networkx; however: Package python3-networkx is not installed. pbuilder-satisfydepends-dummy depends on python3-matplotlib; however: Package python3-matplotlib 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} blt{a} bsdextrautils{a} catch2{a} cmake{a} cmake-data{a} daligner{a} dascrubber{a} dazzdb{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} fontconfig-config{a} fonts-dejavu-core{a} fonts-lyx{a} fonts-urw-base35{a} gettext{a} gettext-base{a} groff-base{a} hdf5-helpers{a} icu-devtools{a} intltool-debian{a} libaec-dev{a} libaec0{a} libarchive-zip-perl{a} libarchive13{a} libblas3{a} libboost-dev{a} libboost-graph-dev{a} libboost-graph1.74-dev{a} libboost-graph1.74.0{a} libboost-regex1.74-dev{a} libboost-regex1.74.0{a} libboost-serialization1.74-dev{a} libboost-serialization1.74.0{a} libboost-test1.74-dev{a} libboost-test1.74.0{a} libboost1.74-dev{a} libbrotli1{a} libbsd0{a} libcurl3-gnutls{a} libcurl4{a} libcurl4-openssl-dev{a} libdebhelper-perl{a} libdeflate0{a} libdouble-conversion3{a} libelf1{a} libexpat1{a} libexpat1-dev{a} libfile-stripnondeterminism-perl{a} libfmt-dev{a} libfmt9{a} libfontconfig1{a} libfontenc1{a} libfreetype6{a} libfribidi0{a} libgfortran5{a} libglib2.0-0{a} libgraphite2-3{a} libharfbuzz0b{a} libhdf5-103-1{a} libhdf5-cpp-103-1{a} libhdf5-dev{a} libhdf5-fortran-102{a} libhdf5-hl-100{a} libhdf5-hl-cpp-100{a} libhdf5-hl-fortran-100{a} libhts3{a} libhtscodecs2{a} libicu-dev{a} libicu72{a} libimagequant0{a} libjbig0{a} libjpeg-dev{a} libjpeg62-turbo{a} libjpeg62-turbo-dev{a} libjs-jquery{a} libjs-jquery-ui{a} libjs-sphinxdoc{a} libjs-underscore{a} libjsoncpp25{a} liblapack3{a} liblbfgsb0{a} liblcms2-2{a} libldap-2.5-0{a} liblerc4{a} liblua5.3-0{a} libmagic-mgc{a} libmagic1{a} libnghttp2-14{a} libopenblas-dev{a} libopenblas-pthread-dev{a} libopenblas0{a} libopenblas0-pthread{a} libopenjp2-7{a} libpipeline1{a} libpng16-16{a} libproc2-0{a} libpsl5{a} libpython3-all-dev{a} libpython3-dev{a} libpython3-stdlib{a} libpython3.11{a} libpython3.11-dev{a} libpython3.11-minimal{a} libpython3.11-stdlib{a} libqhull-r8.0{a} libraqm0{a} libreadline8{a} librhash0{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libspdlog-dev{a} libspdlog1.10{a} libssh2-1{a} libssl-dev{a} libsub-override-perl{a} libsz2{a} libtcl8.6{a} libtiff6{a} libtk8.6{a} libtool{a} libuchardet0{a} libuv1{a} libwebp7{a} libwebpdemux2{a} libwebpmux3{a} libx11-6{a} libx11-data{a} libxau6{a} libxcb1{a} libxdmcp6{a} libxext6{a} libxft2{a} libxml2{a} libxrender1{a} libxsimd-dev{a} libxslt1.1{a} libxss1{a} libyaml-0-2{a} m4{a} man-db{a} media-types{a} pandoc{a} pandoc-data{a} po-debconf{a} procps{a} python-matplotlib-data{a} python3{a} python3-all{a} python3-all-dev{a} python3-appdirs{a} python3-attr{a} python3-beniget{a} python3-biopython{a} python3-brotli{a} python3-colorama{a} python3-colorlog{a} python3-colormap{a} python3-contourpy{a} python3-cycler{a} python3-dateutil{a} python3-decorator{a} python3-dev{a} python3-distutils{a} python3-easydev{a} python3-fonttools{a} python3-fs{a} python3-gast{a} python3-kiwisolver{a} python3-lib2to3{a} python3-lxml{a} python3-lz4{a} python3-matplotlib{a} python3-minimal{a} python3-mpmath{a} python3-networkx{a} python3-numpy{a} python3-packaging{a} python3-pbcore{a} python3-pexpect{a} python3-pil{a} python3-pil.imagetk{a} python3-pkg-resources{a} python3-ply{a} python3-ptyprocess{a} python3-pyparsing{a} python3-pysam{a} python3-pythran{a} python3-renderpm{a} python3-reportlab{a} python3-reportlab-accel{a} python3-scipy{a} python3-six{a} python3-sympy{a} python3-tk{a} python3-tz{a} python3-ufolib2{a} python3-ujson{a} python3.11{a} python3.11-dev{a} python3.11-minimal{a} readline-common{a} sensible-utils{a} sgml-base{a} tk8.6-blt2.5{a} unicode-data{a} w3c-sgml-lib{a} x11-common{a} xfonts-encodings{a} xfonts-utils{a} xml-core{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: ca-certificates curl isympy-common javascript-common libarchive-cpio-perl libglib2.0-data libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules lynx ncbi-blast+ psmisc publicsuffix python-biopython-doc python3-bs4 python3-gdal python3-h5py python3-html5lib python3-olefile python3-pydot python3-pygraphviz python3-yaml shared-mime-info wget xdg-user-dirs 0 packages upgraded, 219 newly installed, 0 to remove and 0 not upgraded. Need to get 194 MB of archives. After unpacking 1059 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bookworm/main arm64 libpython3.11-minimal arm64 3.11.2-6 [806 kB] Get: 2 http://deb.debian.org/debian bookworm/main arm64 libexpat1 arm64 2.5.0-1 [84.8 kB] Get: 3 http://deb.debian.org/debian bookworm/main arm64 python3.11-minimal arm64 3.11.2-6 [1858 kB] Get: 4 http://deb.debian.org/debian bookworm/main arm64 python3-minimal arm64 3.11.2-1+b1 [26.3 kB] Get: 5 http://deb.debian.org/debian bookworm/main arm64 media-types all 10.0.0 [26.1 kB] Get: 6 http://deb.debian.org/debian bookworm/main arm64 readline-common all 8.2-1.3 [69.0 kB] Get: 7 http://deb.debian.org/debian bookworm/main arm64 libreadline8 arm64 8.2-1.3 [155 kB] Get: 8 http://deb.debian.org/debian bookworm/main arm64 libpython3.11-stdlib arm64 3.11.2-6 [1747 kB] Get: 9 http://deb.debian.org/debian bookworm/main arm64 python3.11 arm64 3.11.2-6 [572 kB] Get: 10 http://deb.debian.org/debian bookworm/main arm64 libpython3-stdlib arm64 3.11.2-1+b1 [9296 B] Get: 11 http://deb.debian.org/debian bookworm/main arm64 python3 arm64 3.11.2-1+b1 [26.3 kB] Get: 12 http://deb.debian.org/debian bookworm/main arm64 sgml-base all 1.31 [15.4 kB] Get: 13 http://deb.debian.org/debian bookworm/main arm64 libproc2-0 arm64 2:4.0.2-3 [60.1 kB] Get: 14 http://deb.debian.org/debian bookworm/main arm64 procps arm64 2:4.0.2-3 [698 kB] Get: 15 http://deb.debian.org/debian bookworm/main arm64 sensible-utils all 0.0.17+nmu1 [19.0 kB] Get: 16 http://deb.debian.org/debian bookworm/main arm64 libmagic-mgc arm64 1:5.44-3 [305 kB] Get: 17 http://deb.debian.org/debian bookworm/main arm64 libmagic1 arm64 1:5.44-3 [98.5 kB] Get: 18 http://deb.debian.org/debian bookworm/main arm64 file arm64 1:5.44-3 [42.5 kB] Get: 19 http://deb.debian.org/debian bookworm/main arm64 gettext-base arm64 0.21-12 [159 kB] Get: 20 http://deb.debian.org/debian bookworm/main arm64 libuchardet0 arm64 0.0.7-1 [67.9 kB] Get: 21 http://deb.debian.org/debian bookworm/main arm64 groff-base arm64 1.22.4-10 [861 kB] Get: 22 http://deb.debian.org/debian bookworm/main arm64 bsdextrautils arm64 2.38.1-5+b1 [86.9 kB] Get: 23 http://deb.debian.org/debian bookworm/main arm64 libpipeline1 arm64 1.5.7-1 [36.4 kB] Get: 24 http://deb.debian.org/debian bookworm/main arm64 man-db arm64 2.11.2-2 [1369 kB] Get: 25 http://deb.debian.org/debian bookworm/main arm64 m4 arm64 1.4.19-3 [276 kB] Get: 26 http://deb.debian.org/debian bookworm/main arm64 autoconf all 2.71-3 [332 kB] Get: 27 http://deb.debian.org/debian bookworm/main arm64 autotools-dev all 20220109.1 [51.6 kB] Get: 28 http://deb.debian.org/debian bookworm/main arm64 automake all 1:1.16.5-1.3 [823 kB] Get: 29 http://deb.debian.org/debian bookworm/main arm64 autopoint all 0.21-12 [495 kB] Get: 30 http://deb.debian.org/debian bookworm/main arm64 libtcl8.6 arm64 8.6.13+dfsg-2 [973 kB] Get: 31 http://deb.debian.org/debian bookworm/main arm64 libbrotli1 arm64 1.0.9-2+b6 [269 kB] Get: 32 http://deb.debian.org/debian bookworm/main arm64 libpng16-16 arm64 1.6.39-2 [269 kB] Get: 33 http://deb.debian.org/debian bookworm/main arm64 libfreetype6 arm64 2.12.1+dfsg-4 [369 kB] Get: 34 http://deb.debian.org/debian bookworm/main arm64 fonts-dejavu-core all 2.37-6 [1068 kB] Get: 35 http://deb.debian.org/debian bookworm/main arm64 libfontenc1 arm64 1:1.1.4-1 [23.6 kB] Get: 36 http://deb.debian.org/debian bookworm/main arm64 x11-common all 1:7.7+23 [252 kB] Get: 37 http://deb.debian.org/debian bookworm/main arm64 xfonts-encodings all 1:1.0.4-2.2 [577 kB] Get: 38 http://deb.debian.org/debian bookworm/main arm64 xfonts-utils arm64 1:7.7+6 [85.6 kB] Get: 39 http://deb.debian.org/debian bookworm/main arm64 fonts-urw-base35 all 20200910-7 [10.8 MB] Get: 40 http://deb.debian.org/debian bookworm/main arm64 fontconfig-config arm64 2.14.1-4 [315 kB] Get: 41 http://deb.debian.org/debian bookworm/main arm64 libfontconfig1 arm64 2.14.1-4 [381 kB] Get: 42 http://deb.debian.org/debian bookworm/main arm64 libxau6 arm64 1:1.0.9-1 [19.7 kB] Get: 43 http://deb.debian.org/debian bookworm/main arm64 libbsd0 arm64 0.11.7-2 [115 kB] Get: 44 http://deb.debian.org/debian bookworm/main arm64 libxdmcp6 arm64 1:1.1.2-3 [25.4 kB] Get: 45 http://deb.debian.org/debian bookworm/main arm64 libxcb1 arm64 1.15-1 [143 kB] Get: 46 http://deb.debian.org/debian bookworm/main arm64 libx11-data all 2:1.8.4-2 [292 kB] Get: 47 http://deb.debian.org/debian bookworm/main arm64 libx11-6 arm64 2:1.8.4-2 [736 kB] Get: 48 http://deb.debian.org/debian bookworm/main arm64 libxrender1 arm64 1:0.9.10-1.1 [32.0 kB] Get: 49 http://deb.debian.org/debian bookworm/main arm64 libxft2 arm64 2.3.6-1 [58.7 kB] Get: 50 http://deb.debian.org/debian bookworm/main arm64 libxext6 arm64 2:1.3.4-1+b1 [51.7 kB] Get: 51 http://deb.debian.org/debian bookworm/main arm64 libxss1 arm64 1:1.2.3-1 [17.8 kB] Get: 52 http://deb.debian.org/debian bookworm/main arm64 libtk8.6 arm64 8.6.13-2 [729 kB] Get: 53 http://deb.debian.org/debian bookworm/main arm64 tk8.6-blt2.5 arm64 2.5.3+dfsg-4.1 [540 kB] Get: 54 http://deb.debian.org/debian bookworm/main arm64 blt arm64 2.5.3+dfsg-4.1 [14.9 kB] Get: 55 http://deb.debian.org/debian bookworm/main arm64 catch2 arm64 2.13.10-1 [447 kB] Get: 56 http://deb.debian.org/debian bookworm/main arm64 libicu72 arm64 72.1-3 [9204 kB] Get: 57 http://deb.debian.org/debian bookworm/main arm64 libxml2 arm64 2.9.14+dfsg-1.2 [620 kB] Get: 58 http://deb.debian.org/debian bookworm/main arm64 libarchive13 arm64 3.6.2-1 [316 kB] Get: 59 http://deb.debian.org/debian bookworm/main arm64 libsasl2-modules-db arm64 2.1.28+dfsg-10 [20.8 kB] Get: 60 http://deb.debian.org/debian bookworm/main arm64 libsasl2-2 arm64 2.1.28+dfsg-10 [58.0 kB] Get: 61 http://deb.debian.org/debian bookworm/main arm64 libldap-2.5-0 arm64 2.5.13+dfsg-5 [171 kB] Get: 62 http://deb.debian.org/debian bookworm/main arm64 libnghttp2-14 arm64 1.52.0-1 [67.9 kB] Get: 63 http://deb.debian.org/debian bookworm/main arm64 libpsl5 arm64 0.21.2-1 [58.6 kB] Get: 64 http://deb.debian.org/debian bookworm/main arm64 librtmp1 arm64 2.4+20151223.gitfa8646d.1-2+b2 [59.4 kB] Get: 65 http://deb.debian.org/debian bookworm/main arm64 libssh2-1 arm64 1.10.0-3+b1 [172 kB] Get: 66 http://deb.debian.org/debian bookworm/main arm64 libcurl4 arm64 7.88.1-9 [362 kB] Get: 67 http://deb.debian.org/debian bookworm/main arm64 libjsoncpp25 arm64 1.9.5-4 [72.3 kB] Get: 68 http://deb.debian.org/debian bookworm/main arm64 librhash0 arm64 1.4.3-3 [131 kB] Get: 69 http://deb.debian.org/debian bookworm/main arm64 libuv1 arm64 1.44.2-1 [133 kB] Get: 70 http://deb.debian.org/debian bookworm/main arm64 cmake-data all 3.25.1-1 [2026 kB] Get: 71 http://deb.debian.org/debian bookworm/main arm64 cmake arm64 3.25.1-1 [6806 kB] Get: 72 http://deb.debian.org/debian bookworm/main arm64 daligner arm64 1.0+git20221215.bd26967-1 [203 kB] Get: 73 http://deb.debian.org/debian bookworm/main arm64 dascrubber arm64 1.1-4 [145 kB] Get: 74 http://deb.debian.org/debian bookworm/main arm64 dazzdb arm64 1.0+git20221215.aad3a46-1 [196 kB] Get: 75 http://deb.debian.org/debian bookworm/main arm64 libdebhelper-perl all 13.11.4 [81.2 kB] Get: 76 http://deb.debian.org/debian bookworm/main arm64 libtool all 2.4.7-5 [517 kB] Get: 77 http://deb.debian.org/debian bookworm/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 78 http://deb.debian.org/debian bookworm/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 79 http://deb.debian.org/debian bookworm/main arm64 libsub-override-perl all 0.09-4 [9304 B] Get: 80 http://deb.debian.org/debian bookworm/main arm64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 81 http://deb.debian.org/debian bookworm/main arm64 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 82 http://deb.debian.org/debian bookworm/main arm64 libelf1 arm64 0.188-2.1 [173 kB] Get: 83 http://deb.debian.org/debian bookworm/main arm64 dwz arm64 0.15-1 [101 kB] Get: 84 http://deb.debian.org/debian bookworm/main arm64 gettext arm64 0.21-12 [1248 kB] Get: 85 http://deb.debian.org/debian bookworm/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 86 http://deb.debian.org/debian bookworm/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 87 http://deb.debian.org/debian bookworm/main arm64 debhelper all 13.11.4 [942 kB] Get: 88 http://deb.debian.org/debian bookworm/main arm64 fonts-lyx all 2.3.7-1 [186 kB] Get: 89 http://deb.debian.org/debian bookworm/main arm64 hdf5-helpers arm64 1.10.8+repack1-1 [27.9 kB] Get: 90 http://deb.debian.org/debian bookworm/main arm64 icu-devtools arm64 72.1-3 [192 kB] Get: 91 http://deb.debian.org/debian bookworm/main arm64 libaec0 arm64 1.0.6-1+b1 [19.9 kB] Get: 92 http://deb.debian.org/debian bookworm/main arm64 libsz2 arm64 1.0.6-1+b1 [7740 B] Get: 93 http://deb.debian.org/debian bookworm/main arm64 libaec-dev arm64 1.0.6-1+b1 [18.7 kB] Get: 94 http://deb.debian.org/debian bookworm/main arm64 libblas3 arm64 3.11.0-2 [91.4 kB] Get: 95 http://deb.debian.org/debian bookworm/main arm64 libboost1.74-dev arm64 1.74.0+ds1-20 [9510 kB] Get: 96 http://deb.debian.org/debian bookworm/main arm64 libboost-dev arm64 1.74.0.3 [4548 B] Get: 97 http://deb.debian.org/debian bookworm/main arm64 libboost-regex1.74.0 arm64 1.74.0+ds1-20 [448 kB] Get: 98 http://deb.debian.org/debian bookworm/main arm64 libboost-graph1.74.0 arm64 1.74.0+ds1-20 [292 kB] Get: 99 http://deb.debian.org/debian bookworm/main arm64 libicu-dev arm64 72.1-3 [10.2 MB] Get: 100 http://deb.debian.org/debian bookworm/main arm64 libboost-regex1.74-dev arm64 1.74.0+ds1-20 [525 kB] Get: 101 http://deb.debian.org/debian bookworm/main arm64 libboost-serialization1.74.0 arm64 1.74.0+ds1-20 [308 kB] Get: 102 http://deb.debian.org/debian bookworm/main arm64 libboost-serialization1.74-dev arm64 1.74.0+ds1-20 [357 kB] Get: 103 http://deb.debian.org/debian bookworm/main arm64 libboost-test1.74.0 arm64 1.74.0+ds1-20 [424 kB] Get: 104 http://deb.debian.org/debian bookworm/main arm64 libboost-test1.74-dev arm64 1.74.0+ds1-20 [513 kB] Get: 105 http://deb.debian.org/debian bookworm/main arm64 libboost-graph1.74-dev arm64 1.74.0+ds1-20 [315 kB] Get: 106 http://deb.debian.org/debian bookworm/main arm64 libboost-graph-dev arm64 1.74.0.3 [4436 B] Get: 107 http://deb.debian.org/debian bookworm/main arm64 libcurl3-gnutls arm64 7.88.1-9 [357 kB] Get: 108 http://deb.debian.org/debian bookworm/main arm64 libcurl4-openssl-dev arm64 7.88.1-9 [471 kB] Get: 109 http://deb.debian.org/debian bookworm/main arm64 libdeflate0 arm64 1.14-1 [54.3 kB] Get: 110 http://deb.debian.org/debian bookworm/main arm64 libdouble-conversion3 arm64 3.2.1-1 [37.6 kB] Get: 111 http://deb.debian.org/debian bookworm/main arm64 libexpat1-dev arm64 2.5.0-1 [135 kB] Get: 112 http://deb.debian.org/debian bookworm/main arm64 libfmt9 arm64 9.1.0+ds1-2 [107 kB] Get: 113 http://deb.debian.org/debian bookworm/main arm64 libfmt-dev arm64 9.1.0+ds1-2 [171 kB] Get: 114 http://deb.debian.org/debian bookworm/main arm64 libfribidi0 arm64 1.0.8-2.1 [64.9 kB] Get: 115 http://deb.debian.org/debian bookworm/main arm64 libgfortran5 arm64 12.2.0-14 [340 kB] Get: 116 http://deb.debian.org/debian bookworm/main arm64 libglib2.0-0 arm64 2.74.6-2 [1310 kB] Get: 117 http://deb.debian.org/debian bookworm/main arm64 libgraphite2-3 arm64 1.3.14-1 [75.6 kB] Get: 118 http://deb.debian.org/debian bookworm/main arm64 libharfbuzz0b arm64 6.0.0+dfsg-3 [1914 kB] Get: 119 http://deb.debian.org/debian bookworm/main arm64 libhdf5-103-1 arm64 1.10.8+repack1-1 [1037 kB] Get: 120 http://deb.debian.org/debian bookworm/main arm64 libhdf5-cpp-103-1 arm64 1.10.8+repack1-1 [119 kB] Get: 121 http://deb.debian.org/debian bookworm/main arm64 libhdf5-fortran-102 arm64 1.10.8+repack1-1 [91.1 kB] Get: 122 http://deb.debian.org/debian bookworm/main arm64 libhdf5-hl-100 arm64 1.10.8+repack1-1 [64.0 kB] Get: 123 http://deb.debian.org/debian bookworm/main arm64 libhdf5-hl-fortran-100 arm64 1.10.8+repack1-1 [42.7 kB] Get: 124 http://deb.debian.org/debian bookworm/main arm64 libhdf5-hl-cpp-100 arm64 1.10.8+repack1-1 [25.4 kB] Get: 125 http://deb.debian.org/debian bookworm/main arm64 zlib1g-dev arm64 1:1.2.13.dfsg-1 [913 kB] Get: 126 http://deb.debian.org/debian bookworm/main arm64 libjpeg62-turbo arm64 1:2.1.5-2 [171 kB] Get: 127 http://deb.debian.org/debian bookworm/main arm64 libjpeg62-turbo-dev arm64 1:2.1.5-2 [292 kB] Get: 128 http://deb.debian.org/debian bookworm/main arm64 libjpeg-dev arm64 1:2.1.5-2 [71.8 kB] Get: 129 http://deb.debian.org/debian bookworm/main arm64 libssl-dev arm64 3.0.8-1 [2296 kB] Get: 130 http://deb.debian.org/debian bookworm/main arm64 libhdf5-dev arm64 1.10.8+repack1-1 [2654 kB] Get: 131 http://deb.debian.org/debian bookworm/main arm64 libhtscodecs2 arm64 1.3.0-4 [70.5 kB] Get: 132 http://deb.debian.org/debian bookworm/main arm64 libhts3 arm64 1.16+ds-3 [392 kB] Get: 133 http://deb.debian.org/debian bookworm/main arm64 libimagequant0 arm64 2.17.0-1 [31.3 kB] Get: 134 http://deb.debian.org/debian bookworm/main arm64 libjbig0 arm64 2.1-6.1 [30.0 kB] Get: 135 http://deb.debian.org/debian bookworm/main arm64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get: 136 http://deb.debian.org/debian bookworm/main arm64 libjs-jquery-ui all 1.13.2+dfsg-1 [250 kB] Get: 137 http://deb.debian.org/debian bookworm/main arm64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB] Get: 138 http://deb.debian.org/debian bookworm/main arm64 libjs-sphinxdoc all 5.3.0-4 [130 kB] Get: 139 http://deb.debian.org/debian bookworm/main arm64 libopenblas0-pthread arm64 0.3.21+ds-4 [4532 kB] Get: 140 http://deb.debian.org/debian bookworm/main arm64 liblapack3 arm64 3.11.0-2 [1664 kB] Get: 141 http://deb.debian.org/debian bookworm/main arm64 liblbfgsb0 arm64 3.0+dfsg.4-1 [24.9 kB] Get: 142 http://deb.debian.org/debian bookworm/main arm64 liblcms2-2 arm64 2.14-2 [143 kB] Get: 143 http://deb.debian.org/debian bookworm/main arm64 liblerc4 arm64 4.0.0+ds-2 [138 kB] Get: 144 http://deb.debian.org/debian bookworm/main arm64 liblua5.3-0 arm64 5.3.6-2 [110 kB] Get: 145 http://deb.debian.org/debian bookworm/main arm64 libopenblas0 arm64 0.3.21+ds-4 [32.6 kB] Get: 146 http://deb.debian.org/debian bookworm/main arm64 libopenblas-pthread-dev arm64 0.3.21+ds-4 [3169 kB] Get: 147 http://deb.debian.org/debian bookworm/main arm64 libopenblas-dev arm64 0.3.21+ds-4 [44.9 kB] Get: 148 http://deb.debian.org/debian bookworm/main arm64 libopenjp2-7 arm64 2.5.0-1+b1 [176 kB] Get: 149 http://deb.debian.org/debian bookworm/main arm64 libpython3.11 arm64 3.11.2-6 [1841 kB] Get: 150 http://deb.debian.org/debian bookworm/main arm64 libpython3.11-dev arm64 3.11.2-6 [4395 kB] Get: 151 http://deb.debian.org/debian bookworm/main arm64 libpython3-dev arm64 3.11.2-1+b1 [9564 B] Get: 152 http://deb.debian.org/debian bookworm/main arm64 libpython3-all-dev arm64 3.11.2-1+b1 [1068 B] Get: 153 http://deb.debian.org/debian bookworm/main arm64 libqhull-r8.0 arm64 2020.2-5 [230 kB] Get: 154 http://deb.debian.org/debian bookworm/main arm64 libraqm0 arm64 0.7.0-4.1 [10.4 kB] Get: 155 http://deb.debian.org/debian bookworm/main arm64 libspdlog1.10 arm64 1:1.10.0+ds-0.4 [119 kB] Get: 156 http://deb.debian.org/debian bookworm/main arm64 libspdlog-dev arm64 1:1.10.0+ds-0.4 [209 kB] Get: 157 http://deb.debian.org/debian bookworm/main arm64 libwebp7 arm64 1.2.4-0.1 [259 kB] Get: 158 http://deb.debian.org/debian bookworm/main arm64 libtiff6 arm64 4.5.0-5 [300 kB] Get: 159 http://deb.debian.org/debian bookworm/main arm64 libwebpdemux2 arm64 1.2.4-0.1 [99.1 kB] Get: 160 http://deb.debian.org/debian bookworm/main arm64 libwebpmux3 arm64 1.2.4-0.1 [109 kB] Get: 161 http://deb.debian.org/debian bookworm/main arm64 libxsimd-dev arm64 8.1.0-7 [88.8 kB] Get: 162 http://deb.debian.org/debian bookworm/main arm64 libxslt1.1 arm64 1.1.35-1 [231 kB] Get: 163 http://deb.debian.org/debian bookworm/main arm64 libyaml-0-2 arm64 0.2.5-1 [50.4 kB] Get: 164 http://deb.debian.org/debian bookworm/main arm64 pandoc-data all 2.17.1.1-1.1 [417 kB] Get: 165 http://deb.debian.org/debian bookworm/main arm64 pandoc arm64 2.17.1.1-1.1 [29.0 MB] Get: 166 http://deb.debian.org/debian bookworm/main arm64 python-matplotlib-data all 3.6.3-1 [2744 kB] Get: 167 http://deb.debian.org/debian bookworm/main arm64 python3-lib2to3 all 3.11.2-2 [76.2 kB] Get: 168 http://deb.debian.org/debian bookworm/main arm64 python3-distutils all 3.11.2-2 [131 kB] Get: 169 http://deb.debian.org/debian bookworm/main arm64 python3-all arm64 3.11.2-1+b1 [1064 B] Get: 170 http://deb.debian.org/debian bookworm/main arm64 python3.11-dev arm64 3.11.2-6 [617 kB] Get: 171 http://deb.debian.org/debian bookworm/main arm64 python3-dev arm64 3.11.2-1+b1 [26.2 kB] Get: 172 http://deb.debian.org/debian bookworm/main arm64 python3-all-dev arm64 3.11.2-1+b1 [1076 B] Get: 173 http://deb.debian.org/debian bookworm/main arm64 python3-appdirs all 1.4.4-3 [13.0 kB] Get: 174 http://deb.debian.org/debian bookworm/main arm64 python3-attr all 22.2.0-1 [65.4 kB] Get: 175 http://deb.debian.org/debian bookworm/main arm64 python3-gast all 0.5.2-2 [9364 B] Get: 176 http://deb.debian.org/debian bookworm/main arm64 python3-beniget all 0.4.1-3 [9920 B] Get: 177 http://deb.debian.org/debian bookworm/main arm64 python3-pkg-resources all 66.1.1-1 [296 kB] Get: 178 http://deb.debian.org/debian bookworm/main arm64 python3-numpy arm64 1:1.24.2-1 [4751 kB] Get: 179 http://deb.debian.org/debian bookworm/main arm64 python3-renderpm arm64 3.6.12-1+b1 [73.5 kB] Get: 180 http://deb.debian.org/debian bookworm/main arm64 python3-reportlab-accel arm64 3.6.12-1+b1 [38.4 kB] Get: 181 http://deb.debian.org/debian bookworm/main arm64 python3-tk arm64 3.11.2-2 [97.7 kB] Get: 182 http://deb.debian.org/debian bookworm/main arm64 python3-pil.imagetk arm64 9.4.0-1.1+b1 [74.4 kB] Get: 183 http://deb.debian.org/debian bookworm/main arm64 python3-pil arm64 9.4.0-1.1+b1 [452 kB] Get: 184 http://deb.debian.org/debian bookworm/main arm64 python3-reportlab all 3.6.12-1 [564 kB] Get: 185 http://deb.debian.org/debian bookworm/main arm64 xml-core all 0.18+nmu1 [23.8 kB] Get: 186 http://deb.debian.org/debian bookworm/main arm64 w3c-sgml-lib all 1.3-3 [273 kB] Get: 187 http://deb.debian.org/debian bookworm/main arm64 python3-biopython arm64 1.80+dfsg-4+b1 [1580 kB] Get: 188 http://deb.debian.org/debian bookworm/main arm64 python3-brotli arm64 1.0.9-2+b6 [281 kB] Get: 189 http://deb.debian.org/debian bookworm/main arm64 python3-colorama all 0.4.6-2 [36.8 kB] Get: 190 http://deb.debian.org/debian bookworm/main arm64 python3-colorlog all 6.7.0-1 [26.5 kB] Get: 191 http://deb.debian.org/debian bookworm/main arm64 python3-six all 1.16.0-4 [17.5 kB] Get: 192 http://deb.debian.org/debian bookworm/main arm64 python3-dateutil all 2.8.2-2 [78.3 kB] Get: 193 http://deb.debian.org/debian bookworm/main arm64 python3-pyparsing all 3.0.9-1 [138 kB] Get: 194 http://deb.debian.org/debian bookworm/main arm64 python3-contourpy arm64 1.0.7-1+b1 [154 kB] Get: 195 http://deb.debian.org/debian bookworm/main arm64 python3-cycler all 0.11.0-1 [8020 B] Get: 196 http://deb.debian.org/debian bookworm/main arm64 python3-decorator all 5.1.1-3 [14.9 kB] Get: 197 http://deb.debian.org/debian bookworm/main arm64 python3-ply all 3.11-5 [65.8 kB] Get: 198 http://deb.debian.org/debian bookworm/main arm64 python3-pythran arm64 0.11.0+ds-7 [427 kB] Get: 199 http://deb.debian.org/debian bookworm/main arm64 python3-scipy arm64 1.10.1-2 [14.2 MB] Get: 200 http://deb.debian.org/debian bookworm/main arm64 python3-ufolib2 all 0.14.0+dfsg1-1 [34.3 kB] Get: 201 http://deb.debian.org/debian bookworm/main arm64 python3-mpmath all 1.2.1-2 [418 kB] Get: 202 http://deb.debian.org/debian bookworm/main arm64 python3-sympy all 1.11.1-1 [4358 kB] Get: 203 http://deb.debian.org/debian bookworm/main arm64 python3-tz all 2022.7.1-3 [30.1 kB] Get: 204 http://deb.debian.org/debian bookworm/main arm64 python3-fs all 2.4.16-2 [95.2 kB] Get: 205 http://deb.debian.org/debian bookworm/main arm64 python3-lxml arm64 4.9.2-1+b1 [1074 kB] Get: 206 http://deb.debian.org/debian bookworm/main arm64 python3-lz4 arm64 4.0.2+dfsg-1+b2 [25.0 kB] Get: 207 http://deb.debian.org/debian bookworm/main arm64 unicode-data all 15.0.0-1 [7984 kB] Get: 208 http://deb.debian.org/debian bookworm/main arm64 python3-fonttools arm64 4.38.0-1+b1 [990 kB] Get: 209 http://deb.debian.org/debian bookworm/main arm64 python3-kiwisolver arm64 1.4.4-1+b1 [55.4 kB] Get: 210 http://deb.debian.org/debian bookworm/main arm64 python3-packaging all 23.0-1 [32.5 kB] Get: 211 http://deb.debian.org/debian bookworm/main arm64 python3-matplotlib arm64 3.6.3-1+b1 [6774 kB] Get: 212 http://deb.debian.org/debian bookworm/main arm64 python3-ptyprocess all 0.7.0-5 [14.7 kB] Get: 213 http://deb.debian.org/debian bookworm/main arm64 python3-pexpect all 4.8.0-4 [52.9 kB] Get: 214 http://deb.debian.org/debian bookworm/main arm64 python3-easydev all 0.12.0+dfsg-4 [35.0 kB] Get: 215 http://deb.debian.org/debian bookworm/main arm64 python3-colormap all 1.0.4-3 [15.4 kB] Get: 216 http://deb.debian.org/debian bookworm/main arm64 python3-networkx all 2.8.8-1 [1425 kB] Get: 217 http://deb.debian.org/debian bookworm/main arm64 python3-pysam arm64 0.20.0+ds-3+b1 [1493 kB] Get: 218 http://deb.debian.org/debian bookworm/main arm64 python3-pbcore all 2.1.2+dfsg-5 [2830 kB] Get: 219 http://deb.debian.org/debian bookworm/main arm64 python3-ujson arm64 5.7.0-1 [23.7 kB] Fetched 194 MB in 13s (15.2 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.11-minimal: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 ... 19616 files and directories currently installed.) Preparing to unpack .../libpython3.11-minimal_3.11.2-6_arm64.deb ... Unpacking libpython3.11-minimal:arm64 (3.11.2-6) ... Selecting previously unselected package libexpat1:arm64. Preparing to unpack .../libexpat1_2.5.0-1_arm64.deb ... Unpacking libexpat1:arm64 (2.5.0-1) ... Selecting previously unselected package python3.11-minimal. Preparing to unpack .../python3.11-minimal_3.11.2-6_arm64.deb ... Unpacking python3.11-minimal (3.11.2-6) ... Setting up libpython3.11-minimal:arm64 (3.11.2-6) ... Setting up libexpat1:arm64 (2.5.0-1) ... Setting up python3.11-minimal (3.11.2-6) ... Selecting previously unselected package python3-minimal. (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 ... 19932 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.11.2-1+b1_arm64.deb ... Unpacking python3-minimal (3.11.2-1+b1) ... Selecting previously unselected package media-types. Preparing to unpack .../1-media-types_10.0.0_all.deb ... Unpacking media-types (10.0.0) ... Selecting previously unselected package readline-common. Preparing to unpack .../2-readline-common_8.2-1.3_all.deb ... Unpacking readline-common (8.2-1.3) ... Selecting previously unselected package libreadline8:arm64. Preparing to unpack .../3-libreadline8_8.2-1.3_arm64.deb ... Unpacking libreadline8:arm64 (8.2-1.3) ... Selecting previously unselected package libpython3.11-stdlib:arm64. Preparing to unpack .../4-libpython3.11-stdlib_3.11.2-6_arm64.deb ... Unpacking libpython3.11-stdlib:arm64 (3.11.2-6) ... Selecting previously unselected package python3.11. Preparing to unpack .../5-python3.11_3.11.2-6_arm64.deb ... Unpacking python3.11 (3.11.2-6) ... Selecting previously unselected package libpython3-stdlib:arm64. Preparing to unpack .../6-libpython3-stdlib_3.11.2-1+b1_arm64.deb ... Unpacking libpython3-stdlib:arm64 (3.11.2-1+b1) ... Setting up python3-minimal (3.11.2-1+b1) ... Selecting previously unselected package python3. (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 ... 20366 files and directories currently installed.) Preparing to unpack .../000-python3_3.11.2-1+b1_arm64.deb ... Unpacking python3 (3.11.2-1+b1) ... Selecting previously unselected package sgml-base. Preparing to unpack .../001-sgml-base_1.31_all.deb ... Unpacking sgml-base (1.31) ... Selecting previously unselected package libproc2-0:arm64. Preparing to unpack .../002-libproc2-0_2%3a4.0.2-3_arm64.deb ... Unpacking libproc2-0:arm64 (2:4.0.2-3) ... Selecting previously unselected package procps. Preparing to unpack .../003-procps_2%3a4.0.2-3_arm64.deb ... Unpacking procps (2:4.0.2-3) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../004-sensible-utils_0.0.17+nmu1_all.deb ... Unpacking sensible-utils (0.0.17+nmu1) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../005-libmagic-mgc_1%3a5.44-3_arm64.deb ... Unpacking libmagic-mgc (1:5.44-3) ... Selecting previously unselected package libmagic1:arm64. Preparing to unpack .../006-libmagic1_1%3a5.44-3_arm64.deb ... Unpacking libmagic1:arm64 (1:5.44-3) ... Selecting previously unselected package file. Preparing to unpack .../007-file_1%3a5.44-3_arm64.deb ... Unpacking file (1:5.44-3) ... Selecting previously unselected package gettext-base. 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Selecting previously unselected package libpng16-16:arm64. Preparing to unpack .../021-libpng16-16_1.6.39-2_arm64.deb ... Unpacking libpng16-16:arm64 (1.6.39-2) ... Selecting previously unselected package libfreetype6:arm64. Preparing to unpack .../022-libfreetype6_2.12.1+dfsg-4_arm64.deb ... Unpacking libfreetype6:arm64 (2.12.1+dfsg-4) ... Selecting previously unselected package fonts-dejavu-core. Preparing to unpack .../023-fonts-dejavu-core_2.37-6_all.deb ... Unpacking fonts-dejavu-core (2.37-6) ... Selecting previously unselected package libfontenc1:arm64. Preparing to unpack .../024-libfontenc1_1%3a1.1.4-1_arm64.deb ... Unpacking libfontenc1:arm64 (1:1.1.4-1) ... Selecting previously unselected package x11-common. Preparing to unpack .../025-x11-common_1%3a7.7+23_all.deb ... Unpacking x11-common (1:7.7+23) ... Selecting previously unselected package xfonts-encodings. Preparing to unpack .../026-xfonts-encodings_1%3a1.0.4-2.2_all.deb ... 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Unpacking intltool-debian (0.35.0+20060710.6) ... Selecting previously unselected package po-debconf. Preparing to unpack .../075-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../076-debhelper_13.11.4_all.deb ... Unpacking debhelper (13.11.4) ... Selecting previously unselected package fonts-lyx. Preparing to unpack .../077-fonts-lyx_2.3.7-1_all.deb ... Unpacking fonts-lyx (2.3.7-1) ... Selecting previously unselected package hdf5-helpers. Preparing to unpack .../078-hdf5-helpers_1.10.8+repack1-1_arm64.deb ... Unpacking hdf5-helpers (1.10.8+repack1-1) ... Selecting previously unselected package icu-devtools. Preparing to unpack .../079-icu-devtools_72.1-3_arm64.deb ... Unpacking icu-devtools (72.1-3) ... Selecting previously unselected package libaec0:arm64. Preparing to unpack .../080-libaec0_1.0.6-1+b1_arm64.deb ... Unpacking libaec0:arm64 (1.0.6-1+b1) ... 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Setting up media-types (10.0.0) ... Setting up libpipeline1:arm64 (1.5.7-1) ... Setting up libgraphite2-3:arm64 (1.3.14-1) ... Setting up liblcms2-2:arm64 (2.14-2) ... Setting up catch2 (2.13.10-1) ... Setting up libxau6:arm64 (1:1.0.9-1) ... Setting up libdouble-conversion3:arm64 (3.2.1-1) ... Setting up libpsl5:arm64 (0.21.2-1) ... Setting up libboost1.74-dev:arm64 (1.74.0+ds1-20) ... Setting up libicu72:arm64 (72.1-3) ... Setting up liblerc4:arm64 (4.0.0+ds-2) ... Setting up bsdextrautils (2.38.1-5+b1) ... Setting up hdf5-helpers (1.10.8+repack1-1) ... Setting up libmagic-mgc (1:5.44-3) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libyaml-0-2:arm64 (0.2.5-1) ... Setting up libglib2.0-0:arm64 (2.74.6-2) ... No schema files found: doing nothing. Setting up dascrubber (1.1-4) ... Setting up fonts-lyx (2.3.7-1) ... Setting up libdebhelper-perl (13.11.4) ... Setting up libbrotli1:arm64 (1.0.9-2+b6) ... Setting up x11-common (1:7.7+23) ... invoke-rc.d: could not determine current runlevel Setting up X socket directories... /tmp/.X11-unix /tmp/.ICE-unix. Setting up libnghttp2-14:arm64 (1.52.0-1) ... Setting up libmagic1:arm64 (1:5.44-3) ... Setting up libdeflate0:arm64 (1.14-1) ... Setting up gettext-base (0.21-12) ... Setting up m4 (1.4.19-3) ... Setting up libqhull-r8.0:arm64 (2020.2-5) ... Setting up file (1:5.44-3) ... Setting up libjbig0:arm64 (2.1-6.1) ... Setting up libaec0:arm64 (1.0.6-1+b1) ... Setting up libsasl2-modules-db:arm64 (2.1.28+dfsg-10) ... Setting up unicode-data (15.0.0-1) ... Setting up dazzdb (1.0+git20221215.aad3a46-1) ... Setting up libxsimd-dev:arm64 (8.1.0-7) ... Setting up libfontenc1:arm64 (1:1.1.4-1) ... Setting up autotools-dev (20220109.1) ... Setting up libblas3:arm64 (3.11.0-2) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/aarch64-linux-gnu/libblas.so.3 (libblas.so.3-aarch64-linux-gnu) in auto mode Setting up libuv1:arm64 (1.44.2-1) ... Setting up libexpat1-dev:arm64 (2.5.0-1) ... Setting up libboost-test1.74.0:arm64 (1.74.0+ds1-20) ... Setting up libjpeg62-turbo:arm64 (1:2.1.5-2) ... Setting up libx11-data (2:1.8.4-2) ... Setting up libjpeg62-turbo-dev:arm64 (1:2.1.5-2) ... Setting up librtmp1:arm64 (2.4+20151223.gitfa8646d.1-2+b2) ... Setting up xfonts-encodings (1:1.0.4-2.2) ... Setting up libfribidi0:arm64 (1.0.8-2.1) ... Setting up libboost-regex1.74.0:arm64 (1.74.0+ds1-20) ... Setting up libimagequant0:arm64 (2.17.0-1) ... Setting up libproc2-0:arm64 (2:4.0.2-3) ... Setting up libssl-dev:arm64 (3.0.8-1) ... Setting up libpng16-16:arm64 (1.6.39-2) ... Setting up libboost-graph1.74.0:arm64 (1.74.0+ds1-20) ... Setting up libtcl8.6:arm64 (8.6.13+dfsg-2) ... Setting up autopoint (0.21-12) ... Setting up libjsoncpp25:arm64 (1.9.5-4) ... Setting up icu-devtools (72.1-3) ... Setting up fonts-dejavu-core (2.37-6) ... Setting up libsasl2-2:arm64 (2.1.28+dfsg-10) ... Setting up libgfortran5:arm64 (12.2.0-14) ... Setting up autoconf (2.71-3) ... Setting up libwebp7:arm64 (1.2.4-0.1) ... Setting up libfmt9:arm64 (9.1.0+ds1-2) ... Setting up libboost-serialization1.74.0:arm64 (1.74.0+ds1-20) ... Setting up zlib1g-dev:arm64 (1:1.2.13.dfsg-1) ... Setting up sensible-utils (0.0.17+nmu1) ... Setting up librhash0:arm64 (1.4.3-3) ... Setting up libtiff6:arm64 (4.5.0-5) ... Setting up libuchardet0:arm64 (0.0.7-1) ... Setting up liblua5.3-0:arm64 (5.3.6-2) ... Setting up procps (2:4.0.2-3) ... Setting up daligner (1.0+git20221215.bd26967-1) ... Setting up libopenjp2-7:arm64 (2.5.0-1+b1) ... Setting up libsub-override-perl (0.09-4) ... Setting up libssh2-1:arm64 (1.10.0-3+b1) ... Setting up sgml-base (1.31) ... Setting up cmake-data (3.25.1-1) ... Setting up libboost-dev:arm64 (1.74.0.3) ... Setting up pandoc-data (2.17.1.1-1.1) ... Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Setting up libboost-test1.74-dev:arm64 (1.74.0+ds1-20) ... Setting up python-matplotlib-data (3.6.3-1) ... Setting up libwebpmux3:arm64 (1.2.4-0.1) ... Setting up libbsd0:arm64 (0.11.7-2) ... Setting up libelf1:arm64 (0.188-2.1) ... Setting up readline-common (8.2-1.3) ... Setting up libicu-dev:arm64 (72.1-3) ... Setting up libxml2:arm64 (2.9.14+dfsg-1.2) ... Setting up libsz2:arm64 (1.0.6-1+b1) ... Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... Setting up libspdlog1.10:arm64 (1:1.10.0+ds-0.4) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.13.1-1) ... Setting up libxdmcp6:arm64 (1:1.1.2-3) ... Setting up liblapack3:arm64 (3.11.0-2) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/aarch64-linux-gnu/liblapack.so.3 (liblapack.so.3-aarch64-linux-gnu) in auto mode Setting up libxcb1:arm64 (1.15-1) ... Setting up gettext (0.21-12) ... Setting up libopenblas0-pthread:arm64 (0.3.21+ds-4) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/openblas-pthread/libblas.so.3 to provide /usr/lib/aarch64-linux-gnu/libblas.so.3 (libblas.so.3-aarch64-linux-gnu) in auto mode update-alternatives: using /usr/lib/aarch64-linux-gnu/openblas-pthread/liblapack.so.3 to provide /usr/lib/aarch64-linux-gnu/liblapack.so.3 (liblapack.so.3-aarch64-linux-gnu) in auto mode update-alternatives: using /usr/lib/aarch64-linux-gnu/openblas-pthread/libopenblas.so.0 to provide /usr/lib/aarch64-linux-gnu/libopenblas.so.0 (libopenblas.so.0-aarch64-linux-gnu) in auto mode Setting up libtool (2.4.7-5) ... Setting up libarchive13:arm64 (3.6.2-1) ... Setting up fontconfig-config (2.14.1-4) ... Setting up libwebpdemux2:arm64 (1.2.4-0.1) ... Setting up libreadline8:arm64 (8.2-1.3) ... Setting up libaec-dev:arm64 (1.0.6-1+b1) ... Setting up libjpeg-dev:arm64 (1:2.1.5-2) ... Setting up libldap-2.5-0:arm64 (2.5.13+dfsg-5) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up libjs-jquery-ui (1.13.2+dfsg-1) ... Setting up pandoc (2.17.1.1-1.1) ... Setting up libfreetype6:arm64 (2.12.1+dfsg-4) ... Setting up libfmt-dev:arm64 (9.1.0+ds1-2) ... Setting up libjs-sphinxdoc (5.3.0-4) ... Setting up libboost-serialization1.74-dev:arm64 (1.74.0+ds1-20) ... Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up dwz (0.15-1) ... Setting up libboost-regex1.74-dev:arm64 (1.74.0+ds1-20) ... Setting up libopenblas0:arm64 (0.3.21+ds-4) ... Setting up groff-base (1.22.4-10) ... Setting up xml-core (0.18+nmu1) ... Setting up libxslt1.1:arm64 (1.1.35-1) ... Setting up libcurl4:arm64 (7.88.1-9) ... Setting up libx11-6:arm64 (2:1.8.4-2) ... Setting up libharfbuzz0b:arm64 (6.0.0+dfsg-3) ... Setting up libfontconfig1:arm64 (2.14.1-4) ... Setting up liblbfgsb0:arm64 (3.0+dfsg.4-1) ... Setting up libopenblas-pthread-dev:arm64 (0.3.21+ds-4) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/openblas-pthread/libblas.so to provide /usr/lib/aarch64-linux-gnu/libblas.so (libblas.so-aarch64-linux-gnu) in auto mode update-alternatives: using /usr/lib/aarch64-linux-gnu/openblas-pthread/liblapack.so to provide /usr/lib/aarch64-linux-gnu/liblapack.so (liblapack.so-aarch64-linux-gnu) in auto mode update-alternatives: using /usr/lib/aarch64-linux-gnu/openblas-pthread/libopenblas.so to provide /usr/lib/aarch64-linux-gnu/libopenblas.so (libopenblas.so-aarch64-linux-gnu) in auto mode Setting up libxrender1:arm64 (1:0.9.10-1.1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libpython3.11-stdlib:arm64 (3.11.2-6) ... Setting up libxext6:arm64 (2:1.3.4-1+b1) ... Setting up libcurl3-gnutls:arm64 (7.88.1-9) ... Setting up xfonts-utils (1:7.7+6) ... Setting up libspdlog-dev:arm64 (1:1.10.0+ds-0.4) ... Setting up man-db (2.11.2-2) ... Not building database; man-db/auto-update is not 'true'. Setting up libopenblas-dev:arm64 (0.3.21+ds-4) ... Setting up libcurl4-openssl-dev:arm64 (7.88.1-9) ... Setting up libboost-graph1.74-dev:arm64 (1.74.0+ds1-20) ... Setting up libraqm0:arm64 (0.7.0-4.1) ... Setting up libhdf5-103-1:arm64 (1.10.8+repack1-1) ... Setting up libhdf5-cpp-103-1:arm64 (1.10.8+repack1-1) ... Setting up cmake (3.25.1-1) ... Setting up libxss1:arm64 (1:1.2.3-1) ... Setting up libpython3-stdlib:arm64 (3.11.2-1+b1) ... Setting up libhdf5-hl-100:arm64 (1.10.8+repack1-1) ... Setting up libboost-graph-dev:arm64 (1.74.0.3) ... Setting up python3.11 (3.11.2-6) ... Setting up libxft2:arm64 (2.3.6-1) ... Setting up libhts3:arm64 (1.16+ds-3) ... Setting up libpython3.11:arm64 (3.11.2-6) ... Setting up libtk8.6:arm64 (8.6.13-2) ... Setting up debhelper (13.11.4) ... Setting up python3 (3.11.2-1+b1) ... Setting up fonts-urw-base35 (20200910-7) ... Setting up python3-ujson:arm64 (5.7.0-1) ... Setting up python3-tz (2022.7.1-3) ... Setting up python3-six (1.16.0-4) ... Setting up python3-decorator (5.1.1-3) ... Setting up libhdf5-hl-cpp-100:arm64 (1.10.8+repack1-1) ... Setting up python3-packaging (23.0-1) ... Setting up python3-pyparsing (3.0.9-1) ... Setting up libpython3.11-dev:arm64 (3.11.2-6) ... Setting up python3-brotli (1.0.9-2+b6) ... Setting up python3-cycler (0.11.0-1) ... Setting up python3-reportlab-accel:arm64 (3.6.12-1+b1) ... Setting up python3-kiwisolver (1.4.4-1+b1) ... Setting up libhdf5-fortran-102:arm64 (1.10.8+repack1-1) ... Setting up python3-lxml:arm64 (4.9.2-1+b1) ... Setting up libhdf5-hl-fortran-100:arm64 (1.10.8+repack1-1) ... Setting up python3-dateutil (2.8.2-2) ... Setting up python3-mpmath (1.2.1-2) ... Setting up python3-lib2to3 (3.11.2-2) ... Setting up python3-appdirs (1.4.4-3) ... Setting up python3-ptyprocess (0.7.0-5) ... Setting up python3-pkg-resources (66.1.1-1) ... Setting up python3-distutils (3.11.2-2) ... Setting up python3-sympy (1.11.1-1) ... Setting up python3-attr (22.2.0-1) ... Setting up tk8.6-blt2.5 (2.5.3+dfsg-4.1) ... Setting up python3-pysam (0.20.0+ds-3+b1) ... Setting up libpython3-dev:arm64 (3.11.2-1+b1) ... Setting up python3-renderpm:arm64 (3.6.12-1+b1) ... Setting up python3-colorama (0.4.6-2) ... Setting up python3-colorlog (6.7.0-1) ... Setting up python3-lz4 (4.0.2+dfsg-1+b2) ... Setting up python3.11-dev (3.11.2-6) ... Setting up blt (2.5.3+dfsg-4.1) ... Setting up python3-ply (3.11-5) ... Setting up python3-gast (0.5.2-2) ... Setting up python3-all (3.11.2-1+b1) ... Setting up python3-tk:arm64 (3.11.2-2) ... Setting up python3-networkx (2.8.8-1) ... Setting up python3-fs (2.4.16-2) ... Setting up python3-beniget (0.4.1-3) ... Setting up libpython3-all-dev:arm64 (3.11.2-1+b1) ... Setting up python3-pexpect (4.8.0-4) ... Setting up python3-dev (3.11.2-1+b1) ... Setting up libhdf5-dev (1.10.8+repack1-1) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/pkgconfig/hdf5-serial.pc to provide /usr/lib/aarch64-linux-gnu/pkgconfig/hdf5.pc (hdf5.pc) in auto mode Setting up python3-numpy (1:1.24.2-1) ... Setting up python3-contourpy (1.0.7-1+b1) ... Setting up python3-all-dev (3.11.2-1+b1) ... Setting up python3-easydev (0.12.0+dfsg-4) ... Setting up python3-pythran (0.11.0+ds-7) ... Setting up python3-scipy (1.10.1-2) ... Setting up python3-pil:arm64 (9.4.0-1.1+b1) ... Setting up python3-pil.imagetk:arm64 (9.4.0-1.1+b1) ... Setting up python3-ufolib2 (0.14.0+dfsg1-1) ... Setting up python3-reportlab (3.6.12-1) ... Setting up python3-fonttools (4.38.0-1+b1) ... Setting up python3-matplotlib (3.6.3-1+b1) ... Setting up python3-colormap (1.0.4-3) ... Processing triggers for libc-bin (2.36-9) ... Processing triggers for sgml-base (1.31) ... Setting up w3c-sgml-lib (1.3-3) ... Setting up python3-biopython (1.80+dfsg-4+b1) ... Setting up python3-pbcore (2.1.2+dfsg-5) ... Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/hinge-0.5.0/ && 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 > ../hinge_0.5.0-7_source.changes dpkg-buildpackage: info: source package hinge dpkg-buildpackage: info: source version 0.5.0-7 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 debian/rules clean dh clean dh_clean debian/rules binary dh binary dh_update_autotools_config dh_autoreconf dh_auto_configure cd obj-aarch64-linux-gnu && cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=None -DCMAKE_INSTALL_SYSCONFDIR=/etc -DCMAKE_INSTALL_LOCALSTATEDIR=/var -DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON -DCMAKE_FIND_USE_PACKAGE_REGISTRY=OFF -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON -DFETCHCONTENT_FULLY_DISCONNECTED=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run -DCMAKE_SKIP_INSTALL_ALL_DEPENDENCY=ON "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/aarch64-linux-gnu .. -- The C compiler identification is GNU 12.2.0 -- The CXX compiler identification is GNU 12.2.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/cc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Found ZLIB: /usr/lib/aarch64-linux-gnu/libz.so (found version "1.2.13") -- Found Boost: /usr/lib/aarch64-linux-gnu/cmake/Boost-1.74.0/BoostConfig.cmake (found version "1.74.0") found components: graph -- Configuring done CMake Warning (dev) at src/filter/CMakeLists.txt:4 (add_executable): Policy CMP0115 is not set: Source file extensions must be explicit. Run "cmake --help-policy CMP0115" for policy details. Use the cmake_policy command to set the policy and suppress this warning. File: /build/hinge-0.5.0/src/filter/filter.cpp This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at src/maximal/CMakeLists.txt:4 (add_executable): Policy CMP0115 is not set: Source file extensions must be explicit. Run "cmake --help-policy CMP0115" for policy details. Use the cmake_policy command to set the policy and suppress this warning. File: /build/hinge-0.5.0/src/maximal/maximal.cpp This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at src/consensus/CMakeLists.txt:4 (add_executable): Policy CMP0115 is not set: Source file extensions must be explicit. Run "cmake --help-policy CMP0115" for policy details. Use the cmake_policy command to set the policy and suppress this warning. File: /build/hinge-0.5.0/src/consensus/draft.cpp This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at src/layout/CMakeLists.txt:9 (add_executable): Policy CMP0115 is not set: Source file extensions must be explicit. Run "cmake --help-policy CMP0115" for policy details. Use the cmake_policy command to set the policy and suppress this warning. File: /build/hinge-0.5.0/src/layout/hinging.cpp This warning is for project developers. Use -Wno-dev to suppress it. -- Generating done CMake Warning: Manually-specified variables were not used by the project: CMAKE_EXPORT_NO_PACKAGE_REGISTRY CMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY CMAKE_INSTALL_LIBDIR CMAKE_INSTALL_LOCALSTATEDIR CMAKE_INSTALL_RUNSTATEDIR CMAKE_INSTALL_SYSCONFDIR FETCHCONTENT_FULLY_DISCONNECTED -- Build files have been written to: /build/hinge-0.5.0/obj-aarch64-linux-gnu dh_auto_build cd obj-aarch64-linux-gnu && make -j8 "INSTALL=install --strip-program=true" VERBOSE=1 make[1]: Entering directory '/build/hinge-0.5.0/obj-aarch64-linux-gnu' /usr/bin/cmake -S/build/hinge-0.5.0 -B/build/hinge-0.5.0/obj-aarch64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/hinge-0.5.0/obj-aarch64-linux-gnu/CMakeFiles /build/hinge-0.5.0/obj-aarch64-linux-gnu//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/build/hinge-0.5.0/obj-aarch64-linux-gnu' make -f 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bin/lib/CMakeFiles/DB.dir/depend make[3]: Entering directory '/build/hinge-0.5.0/obj-aarch64-linux-gnu' cd /build/hinge-0.5.0/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hinge-0.5.0 /build/hinge-0.5.0/src/lib /build/hinge-0.5.0/obj-aarch64-linux-gnu /build/hinge-0.5.0/obj-aarch64-linux-gnu/bin/lib /build/hinge-0.5.0/obj-aarch64-linux-gnu/bin/lib/CMakeFiles/DB.dir/DependInfo.cmake --color= make -f bin/lib/CMakeFiles/LA.dir/build.make bin/lib/CMakeFiles/LA.dir/depend make[3]: Entering directory '/build/hinge-0.5.0/obj-aarch64-linux-gnu' cd /build/hinge-0.5.0/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hinge-0.5.0 /build/hinge-0.5.0/src/lib /build/hinge-0.5.0/obj-aarch64-linux-gnu /build/hinge-0.5.0/obj-aarch64-linux-gnu/bin/lib /build/hinge-0.5.0/obj-aarch64-linux-gnu/bin/lib/CMakeFiles/LA.dir/DependInfo.cmake --color= make -f bin/lib/CMakeFiles/PAF.dir/build.make bin/lib/CMakeFiles/PAF.dir/depend make[3]: Entering directory '/build/hinge-0.5.0/obj-aarch64-linux-gnu' cd /build/hinge-0.5.0/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hinge-0.5.0 /build/hinge-0.5.0/src/lib /build/hinge-0.5.0/obj-aarch64-linux-gnu /build/hinge-0.5.0/obj-aarch64-linux-gnu/bin/lib /build/hinge-0.5.0/obj-aarch64-linux-gnu/bin/lib/CMakeFiles/PAF.dir/DependInfo.cmake --color= make -f bin/lib/CMakeFiles/kmer_lookup.dir/build.make bin/lib/CMakeFiles/kmer_lookup.dir/depend make[3]: Leaving directory '/build/hinge-0.5.0/obj-aarch64-linux-gnu' make[3]: Entering directory '/build/hinge-0.5.0/obj-aarch64-linux-gnu' cd /build/hinge-0.5.0/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hinge-0.5.0 /build/hinge-0.5.0/src/lib /build/hinge-0.5.0/obj-aarch64-linux-gnu /build/hinge-0.5.0/obj-aarch64-linux-gnu/bin/lib /build/hinge-0.5.0/obj-aarch64-linux-gnu/bin/lib/CMakeFiles/kmer_lookup.dir/DependInfo.cmake --color= make -f bin/CMakeFiles/man.dir/build.make bin/CMakeFiles/man.dir/build make[3]: Entering directory '/build/hinge-0.5.0/obj-aarch64-linux-gnu' make -f bin/lib/CMakeFiles/DW_banded.dir/build.make bin/lib/CMakeFiles/DW_banded.dir/depend make[3]: Entering directory '/build/hinge-0.5.0/obj-aarch64-linux-gnu' cd /build/hinge-0.5.0/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hinge-0.5.0 /build/hinge-0.5.0/src/lib /build/hinge-0.5.0/obj-aarch64-linux-gnu /build/hinge-0.5.0/obj-aarch64-linux-gnu/bin/lib /build/hinge-0.5.0/obj-aarch64-linux-gnu/bin/lib/CMakeFiles/DW_banded.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/hinge-0.5.0/obj-aarch64-linux-gnu' make -f bin/lib/CMakeFiles/ini.dir/build.make bin/lib/CMakeFiles/ini.dir/build make[3]: Entering directory '/build/hinge-0.5.0/obj-aarch64-linux-gnu' [ 3%] Generating hinge.1 make[3]: Leaving directory '/build/hinge-0.5.0/obj-aarch64-linux-gnu' make -f bin/lib/CMakeFiles/DB.dir/build.make bin/lib/CMakeFiles/DB.dir/build make[3]: Leaving directory '/build/hinge-0.5.0/obj-aarch64-linux-gnu' make[3]: Entering directory '/build/hinge-0.5.0/obj-aarch64-linux-gnu' make -f bin/lib/CMakeFiles/kmer_lookup.dir/build.make bin/lib/CMakeFiles/kmer_lookup.dir/build cd /build/hinge-0.5.0/obj-aarch64-linux-gnu/bin && /usr/bin/pandoc --from markdown --to man -s /build/hinge-0.5.0/src/hinge.1.md -o hinge.1 make[3]: Leaving directory '/build/hinge-0.5.0/obj-aarch64-linux-gnu' make[3]: Entering directory '/build/hinge-0.5.0/obj-aarch64-linux-gnu' make -f bin/lib/CMakeFiles/DW_banded.dir/build.make bin/lib/CMakeFiles/DW_banded.dir/build make[3]: Entering directory '/build/hinge-0.5.0/obj-aarch64-linux-gnu' [ 6%] Building C object bin/lib/CMakeFiles/ini.dir/ini.c.o make[3]: Leaving directory '/build/hinge-0.5.0/obj-aarch64-linux-gnu' make[3]: Leaving directory '/build/hinge-0.5.0/obj-aarch64-linux-gnu' make -f bin/lib/CMakeFiles/LA.dir/build.make bin/lib/CMakeFiles/LA.dir/build cd /build/hinge-0.5.0/obj-aarch64-linux-gnu/bin/lib && /usr/bin/cc -I/build/hinge-0.5.0/src/include -g -O2 -ffile-prefix-map=/build/hinge-0.5.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -MD -MT bin/lib/CMakeFiles/ini.dir/ini.c.o -MF CMakeFiles/ini.dir/ini.c.o.d -o CMakeFiles/ini.dir/ini.c.o -c /build/hinge-0.5.0/src/lib/ini.c make[3]: Entering directory '/build/hinge-0.5.0/obj-aarch64-linux-gnu' make -f bin/lib/CMakeFiles/PAF.dir/build.make bin/lib/CMakeFiles/PAF.dir/build [ 10%] Building C object bin/lib/CMakeFiles/DB.dir/DB.c.o make[3]: Entering directory '/build/hinge-0.5.0/obj-aarch64-linux-gnu' [ 13%] Building CXX object bin/lib/CMakeFiles/ini.dir/INIReader.cpp.o cd /build/hinge-0.5.0/obj-aarch64-linux-gnu/bin/lib && /usr/bin/cc -I/build/hinge-0.5.0/src/include -g -O2 -ffile-prefix-map=/build/hinge-0.5.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -MD -MT bin/lib/CMakeFiles/DB.dir/DB.c.o -MF CMakeFiles/DB.dir/DB.c.o.d -o CMakeFiles/DB.dir/DB.c.o -c /build/hinge-0.5.0/src/lib/DB.c cd /build/hinge-0.5.0/obj-aarch64-linux-gnu/bin/lib && /usr/bin/c++ -I/build/hinge-0.5.0/src/include -g -O2 -ffile-prefix-map=/build/hinge-0.5.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -fopenmp -MD -MT bin/lib/CMakeFiles/ini.dir/INIReader.cpp.o -MF CMakeFiles/ini.dir/INIReader.cpp.o.d -o CMakeFiles/ini.dir/INIReader.cpp.o -c /build/hinge-0.5.0/src/lib/INIReader.cpp [ 17%] Building C object bin/lib/CMakeFiles/kmer_lookup.dir/kmer_lookup.c.o cd /build/hinge-0.5.0/obj-aarch64-linux-gnu/bin/lib && /usr/bin/cc -I/build/hinge-0.5.0/src/include -g -O2 -ffile-prefix-map=/build/hinge-0.5.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -MD -MT bin/lib/CMakeFiles/kmer_lookup.dir/kmer_lookup.c.o -MF CMakeFiles/kmer_lookup.dir/kmer_lookup.c.o.d -o CMakeFiles/kmer_lookup.dir/kmer_lookup.c.o -c /build/hinge-0.5.0/src/lib/kmer_lookup.c [ 20%] Building C object bin/lib/CMakeFiles/DW_banded.dir/DW_banded.c.o cd /build/hinge-0.5.0/obj-aarch64-linux-gnu/bin/lib && /usr/bin/cc -I/build/hinge-0.5.0/src/include -g -O2 -ffile-prefix-map=/build/hinge-0.5.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -MD -MT bin/lib/CMakeFiles/DW_banded.dir/DW_banded.c.o -MF CMakeFiles/DW_banded.dir/DW_banded.c.o.d -o CMakeFiles/DW_banded.dir/DW_banded.c.o -c /build/hinge-0.5.0/src/lib/DW_banded.c [ 24%] Building C object bin/lib/CMakeFiles/PAF.dir/paf.c.o cd /build/hinge-0.5.0/obj-aarch64-linux-gnu/bin/lib && /usr/bin/cc -I/build/hinge-0.5.0/src/include -g -O2 -ffile-prefix-map=/build/hinge-0.5.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -MD -MT bin/lib/CMakeFiles/PAF.dir/paf.c.o -MF CMakeFiles/PAF.dir/paf.c.o.d -o CMakeFiles/PAF.dir/paf.c.o -c /build/hinge-0.5.0/src/lib/paf.c [ 27%] Building C object bin/lib/CMakeFiles/LA.dir/align.c.o cd /build/hinge-0.5.0/obj-aarch64-linux-gnu/bin/lib && /usr/bin/cc -I/build/hinge-0.5.0/src/include -g -O2 -ffile-prefix-map=/build/hinge-0.5.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -MD -MT bin/lib/CMakeFiles/LA.dir/align.c.o -MF CMakeFiles/LA.dir/align.c.o.d -o CMakeFiles/LA.dir/align.c.o -c /build/hinge-0.5.0/src/lib/align.c make[3]: Leaving directory '/build/hinge-0.5.0/obj-aarch64-linux-gnu' [ 27%] Built target man [ 31%] Building C object bin/lib/CMakeFiles/DB.dir/QV.c.o cd /build/hinge-0.5.0/obj-aarch64-linux-gnu/bin/lib && /usr/bin/cc -I/build/hinge-0.5.0/src/include -g -O2 -ffile-prefix-map=/build/hinge-0.5.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -MD -MT bin/lib/CMakeFiles/DB.dir/QV.c.o -MF CMakeFiles/DB.dir/QV.c.o.d -o CMakeFiles/DB.dir/QV.c.o -c /build/hinge-0.5.0/src/lib/QV.c /build/hinge-0.5.0/src/lib/DB.c: In function 'Load_QVs': /build/hinge-0.5.0/src/lib/DB.c:916:9: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 916 | fscanf(istub,DB_NFILE,&nfiles); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/hinge-0.5.0/src/lib/DB.c:920:13: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 920 | { fscanf(istub,DB_FDATA,&last,fname,prolog); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/hinge-0.5.0/src/lib/DB.c:925:13: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 925 | { fscanf(istub,DB_FDATA,&last,fname,prolog); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 34%] Linking C static library libPAF.a cd /build/hinge-0.5.0/obj-aarch64-linux-gnu/bin/lib && /usr/bin/cmake -P CMakeFiles/PAF.dir/cmake_clean_target.cmake cd /build/hinge-0.5.0/obj-aarch64-linux-gnu/bin/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/PAF.dir/link.txt --verbose=1 /usr/bin/ar qc libPAF.a CMakeFiles/PAF.dir/paf.c.o /build/hinge-0.5.0/src/lib/kmer_lookup.c: In function 'find_best_aln_range': /build/hinge-0.5.0/src/lib/kmer_lookup.c:347:14: warning: argument 1 range [18446744071562067968, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 347 | q_coor = calloc( km_ptr->count, sizeof(seq_coor_t) ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/hinge-0.5.0/src/lib/kmer_lookup.c:56: /usr/include/stdlib.h:556:14: note: in a call to allocation function 'calloc' declared here 556 | extern void *calloc (size_t __nmemb, size_t __size) | ^~~~~~ /build/hinge-0.5.0/src/lib/kmer_lookup.c:348:14: warning: argument 1 range [18446744071562067968, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 348 | t_coor = calloc( km_ptr->count, sizeof(seq_coor_t) ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/stdlib.h:556:14: note: in a call to allocation function 'calloc' declared here 556 | extern void *calloc (size_t __nmemb, size_t __size) | ^~~~~~ /usr/bin/ranlib libPAF.a make[3]: Leaving directory '/build/hinge-0.5.0/obj-aarch64-linux-gnu' [ 34%] Built target PAF [ 37%] Linking C static library libDW_banded.a cd /build/hinge-0.5.0/obj-aarch64-linux-gnu/bin/lib && /usr/bin/cmake -P CMakeFiles/DW_banded.dir/cmake_clean_target.cmake cd /build/hinge-0.5.0/obj-aarch64-linux-gnu/bin/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/DW_banded.dir/link.txt --verbose=1 /usr/bin/ar qc libDW_banded.a CMakeFiles/DW_banded.dir/DW_banded.c.o /usr/bin/ranlib libDW_banded.a make[3]: Leaving directory '/build/hinge-0.5.0/obj-aarch64-linux-gnu' [ 37%] Built target DW_banded /build/hinge-0.5.0/src/lib/DB.c: In function 'Open_DB': /build/hinge-0.5.0/src/lib/DB.c:533:11: warning: 'free' called on pointer 'p' with nonzero offset 40 [-Wfree-nonheap-object] 533 | free(reads); | ^~~~~~~~~~~ In function 'Malloc', inlined from 'Open_DB' at /build/hinge-0.5.0/src/lib/DB.c:525:29: /build/hinge-0.5.0/src/lib/DB.c:84:12: note: returned from 'malloc' 84 | if ((p = malloc(size)) == NULL) | ^~~~~~~~~~~~ [ 41%] Linking C static library libkmer_lookup.a cd /build/hinge-0.5.0/obj-aarch64-linux-gnu/bin/lib && /usr/bin/cmake -P CMakeFiles/kmer_lookup.dir/cmake_clean_target.cmake cd /build/hinge-0.5.0/obj-aarch64-linux-gnu/bin/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/kmer_lookup.dir/link.txt --verbose=1 /usr/bin/ar qc libkmer_lookup.a CMakeFiles/kmer_lookup.dir/kmer_lookup.c.o /usr/bin/ranlib libkmer_lookup.a make[3]: Leaving directory '/build/hinge-0.5.0/obj-aarch64-linux-gnu' [ 41%] Built target kmer_lookup make -f bin/lib/CMakeFiles/falcon.dir/build.make bin/lib/CMakeFiles/falcon.dir/depend make[3]: Entering directory '/build/hinge-0.5.0/obj-aarch64-linux-gnu' cd /build/hinge-0.5.0/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hinge-0.5.0 /build/hinge-0.5.0/src/lib /build/hinge-0.5.0/obj-aarch64-linux-gnu /build/hinge-0.5.0/obj-aarch64-linux-gnu/bin/lib /build/hinge-0.5.0/obj-aarch64-linux-gnu/bin/lib/CMakeFiles/falcon.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/hinge-0.5.0/obj-aarch64-linux-gnu' make -f bin/lib/CMakeFiles/falcon.dir/build.make bin/lib/CMakeFiles/falcon.dir/build make[3]: Entering directory '/build/hinge-0.5.0/obj-aarch64-linux-gnu' [ 44%] Building C object bin/lib/CMakeFiles/falcon.dir/falcon.c.o cd /build/hinge-0.5.0/obj-aarch64-linux-gnu/bin/lib && /usr/bin/cc -I/build/hinge-0.5.0/src/include -g -O2 -ffile-prefix-map=/build/hinge-0.5.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -MD -MT bin/lib/CMakeFiles/falcon.dir/falcon.c.o -MF CMakeFiles/falcon.dir/falcon.c.o.d -o CMakeFiles/falcon.dir/falcon.c.o -c /build/hinge-0.5.0/src/lib/falcon.c [ 48%] Linking C static library libfalcon.a cd /build/hinge-0.5.0/obj-aarch64-linux-gnu/bin/lib && /usr/bin/cmake -P CMakeFiles/falcon.dir/cmake_clean_target.cmake cd /build/hinge-0.5.0/obj-aarch64-linux-gnu/bin/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/falcon.dir/link.txt --verbose=1 /usr/bin/ar qc libfalcon.a CMakeFiles/falcon.dir/falcon.c.o /usr/bin/ranlib libfalcon.a make[3]: Leaving directory '/build/hinge-0.5.0/obj-aarch64-linux-gnu' [ 48%] Built target falcon /build/hinge-0.5.0/src/lib/DB.c: In function 'Read_All_Sequences': /build/hinge-0.5.0/src/lib/DB.c:1587:15: warning: 'free' called on pointer 'p' with nonzero offset 1 [-Wfree-nonheap-object] 1587 | free(seq); | ^~~~~~~~~ In function 'Malloc', inlined from 'Read_All_Sequences' at /build/hinge-0.5.0/src/lib/DB.c:1564:18: /build/hinge-0.5.0/src/lib/DB.c:84:12: note: returned from 'malloc' 84 | if ((p = malloc(size)) == NULL) | ^~~~~~~~~~~~ [ 51%] Linking C static library libDB.a cd /build/hinge-0.5.0/obj-aarch64-linux-gnu/bin/lib && /usr/bin/cmake -P CMakeFiles/DB.dir/cmake_clean_target.cmake cd /build/hinge-0.5.0/obj-aarch64-linux-gnu/bin/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/DB.dir/link.txt --verbose=1 /usr/bin/ar qc libDB.a CMakeFiles/DB.dir/DB.c.o CMakeFiles/DB.dir/QV.c.o /usr/bin/ranlib libDB.a make[3]: Leaving directory '/build/hinge-0.5.0/obj-aarch64-linux-gnu' [ 51%] Built target DB [ 55%] Linking CXX static library libini.a cd /build/hinge-0.5.0/obj-aarch64-linux-gnu/bin/lib && /usr/bin/cmake -P CMakeFiles/ini.dir/cmake_clean_target.cmake cd /build/hinge-0.5.0/obj-aarch64-linux-gnu/bin/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/ini.dir/link.txt --verbose=1 /usr/bin/ar qc libini.a CMakeFiles/ini.dir/ini.c.o CMakeFiles/ini.dir/INIReader.cpp.o /usr/bin/ranlib libini.a make[3]: Leaving directory '/build/hinge-0.5.0/obj-aarch64-linux-gnu' [ 55%] Built target ini [ 58%] Linking C static library libLA.a cd /build/hinge-0.5.0/obj-aarch64-linux-gnu/bin/lib && /usr/bin/cmake -P CMakeFiles/LA.dir/cmake_clean_target.cmake cd /build/hinge-0.5.0/obj-aarch64-linux-gnu/bin/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/LA.dir/link.txt --verbose=1 /usr/bin/ar qc libLA.a CMakeFiles/LA.dir/align.c.o /usr/bin/ranlib libLA.a make[3]: Leaving directory '/build/hinge-0.5.0/obj-aarch64-linux-gnu' [ 58%] Built target LA make -f bin/lib/CMakeFiles/LAInterface.dir/build.make bin/lib/CMakeFiles/LAInterface.dir/depend make[3]: Entering directory '/build/hinge-0.5.0/obj-aarch64-linux-gnu' cd /build/hinge-0.5.0/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hinge-0.5.0 /build/hinge-0.5.0/src/lib /build/hinge-0.5.0/obj-aarch64-linux-gnu /build/hinge-0.5.0/obj-aarch64-linux-gnu/bin/lib /build/hinge-0.5.0/obj-aarch64-linux-gnu/bin/lib/CMakeFiles/LAInterface.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/hinge-0.5.0/obj-aarch64-linux-gnu' make -f bin/lib/CMakeFiles/LAInterface.dir/build.make bin/lib/CMakeFiles/LAInterface.dir/build make[3]: Entering directory '/build/hinge-0.5.0/obj-aarch64-linux-gnu' [ 62%] Building CXX object bin/lib/CMakeFiles/LAInterface.dir/LAInterface.cpp.o cd /build/hinge-0.5.0/obj-aarch64-linux-gnu/bin/lib && /usr/bin/c++ -I/build/hinge-0.5.0/src/include -g -O2 -ffile-prefix-map=/build/hinge-0.5.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -fopenmp -MD -MT bin/lib/CMakeFiles/LAInterface.dir/LAInterface.cpp.o -MF CMakeFiles/LAInterface.dir/LAInterface.cpp.o.d -o CMakeFiles/LAInterface.dir/LAInterface.cpp.o -c /build/hinge-0.5.0/src/lib/LAInterface.cpp /build/hinge-0.5.0/src/lib/LAInterface.cpp: In member function 'void LAInterface::getOverlapw(std::vector&, int, int)': /build/hinge-0.5.0/src/lib/LAInterface.cpp:1666:22: warning: format '%d' expects argument of type 'int', but argument 2 has type 'int64' {aka 'long long int'} [-Wformat=] 1666 | printf("%d percent finished\n", j/(novl/100)); | ~^ ~~~~~~~~~~~~ | | | | int int64 {aka long long int} | %lld [ 65%] Linking CXX static library libLAInterface.a cd /build/hinge-0.5.0/obj-aarch64-linux-gnu/bin/lib && /usr/bin/cmake -P CMakeFiles/LAInterface.dir/cmake_clean_target.cmake cd /build/hinge-0.5.0/obj-aarch64-linux-gnu/bin/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/LAInterface.dir/link.txt --verbose=1 /usr/bin/ar qc libLAInterface.a CMakeFiles/LAInterface.dir/LAInterface.cpp.o /usr/bin/ranlib libLAInterface.a make[3]: Leaving directory '/build/hinge-0.5.0/obj-aarch64-linux-gnu' [ 65%] Built target LAInterface make -f bin/filter/CMakeFiles/Reads_filter.dir/build.make bin/filter/CMakeFiles/Reads_filter.dir/depend make[3]: Entering directory '/build/hinge-0.5.0/obj-aarch64-linux-gnu' cd /build/hinge-0.5.0/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hinge-0.5.0 /build/hinge-0.5.0/src/filter /build/hinge-0.5.0/obj-aarch64-linux-gnu /build/hinge-0.5.0/obj-aarch64-linux-gnu/bin/filter /build/hinge-0.5.0/obj-aarch64-linux-gnu/bin/filter/CMakeFiles/Reads_filter.dir/DependInfo.cmake --color= make -f bin/maximal/CMakeFiles/get_maximal_reads.dir/build.make bin/maximal/CMakeFiles/get_maximal_reads.dir/depend make[3]: Entering directory '/build/hinge-0.5.0/obj-aarch64-linux-gnu' cd /build/hinge-0.5.0/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hinge-0.5.0 /build/hinge-0.5.0/src/maximal /build/hinge-0.5.0/obj-aarch64-linux-gnu /build/hinge-0.5.0/obj-aarch64-linux-gnu/bin/maximal /build/hinge-0.5.0/obj-aarch64-linux-gnu/bin/maximal/CMakeFiles/get_maximal_reads.dir/DependInfo.cmake --color= make -f bin/consensus/CMakeFiles/draft_assembly.dir/build.make bin/consensus/CMakeFiles/draft_assembly.dir/depend make[3]: Entering directory '/build/hinge-0.5.0/obj-aarch64-linux-gnu' cd /build/hinge-0.5.0/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hinge-0.5.0 /build/hinge-0.5.0/src/consensus /build/hinge-0.5.0/obj-aarch64-linux-gnu /build/hinge-0.5.0/obj-aarch64-linux-gnu/bin/consensus /build/hinge-0.5.0/obj-aarch64-linux-gnu/bin/consensus/CMakeFiles/draft_assembly.dir/DependInfo.cmake --color= make -f bin/consensus/CMakeFiles/consensus.dir/build.make bin/consensus/CMakeFiles/consensus.dir/depend make[3]: Entering directory '/build/hinge-0.5.0/obj-aarch64-linux-gnu' cd /build/hinge-0.5.0/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hinge-0.5.0 /build/hinge-0.5.0/src/consensus /build/hinge-0.5.0/obj-aarch64-linux-gnu /build/hinge-0.5.0/obj-aarch64-linux-gnu/bin/consensus /build/hinge-0.5.0/obj-aarch64-linux-gnu/bin/consensus/CMakeFiles/consensus.dir/DependInfo.cmake --color= make -f bin/layout/CMakeFiles/hinging.dir/build.make bin/layout/CMakeFiles/hinging.dir/depend make[3]: Entering directory '/build/hinge-0.5.0/obj-aarch64-linux-gnu' cd /build/hinge-0.5.0/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hinge-0.5.0 /build/hinge-0.5.0/src/layout /build/hinge-0.5.0/obj-aarch64-linux-gnu /build/hinge-0.5.0/obj-aarch64-linux-gnu/bin/layout /build/hinge-0.5.0/obj-aarch64-linux-gnu/bin/layout/CMakeFiles/hinging.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/hinge-0.5.0/obj-aarch64-linux-gnu' make -f bin/consensus/CMakeFiles/consensus.dir/build.make bin/consensus/CMakeFiles/consensus.dir/build make[3]: Leaving directory '/build/hinge-0.5.0/obj-aarch64-linux-gnu' make[3]: Entering directory '/build/hinge-0.5.0/obj-aarch64-linux-gnu' make -f bin/maximal/CMakeFiles/get_maximal_reads.dir/build.make bin/maximal/CMakeFiles/get_maximal_reads.dir/build make[3]: Entering directory '/build/hinge-0.5.0/obj-aarch64-linux-gnu' make[3]: Leaving directory '/build/hinge-0.5.0/obj-aarch64-linux-gnu' make -f bin/layout/CMakeFiles/hinging.dir/build.make bin/layout/CMakeFiles/hinging.dir/build make[3]: Entering directory '/build/hinge-0.5.0/obj-aarch64-linux-gnu' [ 68%] Building CXX object bin/layout/CMakeFiles/hinging.dir/hinging.cpp.o cd /build/hinge-0.5.0/obj-aarch64-linux-gnu/bin/layout && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DSPDLOG_FMT_EXTERNAL -I/build/hinge-0.5.0/src/include -g -O2 -ffile-prefix-map=/build/hinge-0.5.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -fopenmp -MD -MT bin/layout/CMakeFiles/hinging.dir/hinging.cpp.o -MF CMakeFiles/hinging.dir/hinging.cpp.o.d -o CMakeFiles/hinging.dir/hinging.cpp.o -c /build/hinge-0.5.0/src/layout/hinging.cpp make[3]: Leaving directory '/build/hinge-0.5.0/obj-aarch64-linux-gnu' make[3]: Leaving directory '/build/hinge-0.5.0/obj-aarch64-linux-gnu' make -f bin/filter/CMakeFiles/Reads_filter.dir/build.make bin/filter/CMakeFiles/Reads_filter.dir/build make[3]: Entering directory '/build/hinge-0.5.0/obj-aarch64-linux-gnu' make -f bin/consensus/CMakeFiles/draft_assembly.dir/build.make bin/consensus/CMakeFiles/draft_assembly.dir/build make[3]: Entering directory '/build/hinge-0.5.0/obj-aarch64-linux-gnu' [ 72%] Building CXX object bin/filter/CMakeFiles/Reads_filter.dir/filter.cpp.o cd /build/hinge-0.5.0/obj-aarch64-linux-gnu/bin/filter && /usr/bin/c++ -DSPDLOG_FMT_EXTERNAL -I/build/hinge-0.5.0/src/include -g -O2 -ffile-prefix-map=/build/hinge-0.5.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -fopenmp -MD -MT bin/filter/CMakeFiles/Reads_filter.dir/filter.cpp.o -MF CMakeFiles/Reads_filter.dir/filter.cpp.o.d -o CMakeFiles/Reads_filter.dir/filter.cpp.o -c /build/hinge-0.5.0/src/filter/filter.cpp [ 75%] Building CXX object bin/consensus/CMakeFiles/draft_assembly.dir/draft.cpp.o cd /build/hinge-0.5.0/obj-aarch64-linux-gnu/bin/consensus && /usr/bin/c++ -DSPDLOG_FMT_EXTERNAL -I/build/hinge-0.5.0/src/include -g -O2 -ffile-prefix-map=/build/hinge-0.5.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -fopenmp -MD -MT bin/consensus/CMakeFiles/draft_assembly.dir/draft.cpp.o -MF CMakeFiles/draft_assembly.dir/draft.cpp.o.d -o CMakeFiles/draft_assembly.dir/draft.cpp.o -c /build/hinge-0.5.0/src/consensus/draft.cpp [ 79%] Building CXX object bin/maximal/CMakeFiles/get_maximal_reads.dir/maximal.cpp.o [ 82%] Building CXX object bin/consensus/CMakeFiles/consensus.dir/consensus.cpp.o cd /build/hinge-0.5.0/obj-aarch64-linux-gnu/bin/maximal && /usr/bin/c++ -DSPDLOG_FMT_EXTERNAL -I/build/hinge-0.5.0/src/include -g -O2 -ffile-prefix-map=/build/hinge-0.5.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -fopenmp -MD -MT bin/maximal/CMakeFiles/get_maximal_reads.dir/maximal.cpp.o -MF CMakeFiles/get_maximal_reads.dir/maximal.cpp.o.d -o CMakeFiles/get_maximal_reads.dir/maximal.cpp.o -c /build/hinge-0.5.0/src/maximal/maximal.cpp cd /build/hinge-0.5.0/obj-aarch64-linux-gnu/bin/consensus && /usr/bin/c++ -DSPDLOG_FMT_EXTERNAL -I/build/hinge-0.5.0/src/include -g -O2 -ffile-prefix-map=/build/hinge-0.5.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -fopenmp -MD -MT bin/consensus/CMakeFiles/consensus.dir/consensus.cpp.o -MF CMakeFiles/consensus.dir/consensus.cpp.o.d -o CMakeFiles/consensus.dir/consensus.cpp.o -c /build/hinge-0.5.0/src/consensus/consensus.cpp [ 86%] Linking CXX executable consensus cd /build/hinge-0.5.0/obj-aarch64-linux-gnu/bin/consensus && /usr/bin/cmake -E cmake_link_script CMakeFiles/consensus.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hinge-0.5.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/consensus.dir/consensus.cpp.o -o consensus -lfmt ../lib/libLAInterface.a ../lib/libfalcon.a ../lib/libini.a ../lib/libLA.a ../lib/libDB.a ../lib/libPAF.a -lz ../lib/libkmer_lookup.a ../lib/libDW_banded.a make[3]: Leaving directory '/build/hinge-0.5.0/obj-aarch64-linux-gnu' [ 86%] Built target consensus [ 89%] Linking CXX executable get_maximal_reads cd /build/hinge-0.5.0/obj-aarch64-linux-gnu/bin/maximal && /usr/bin/cmake -E cmake_link_script CMakeFiles/get_maximal_reads.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hinge-0.5.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/get_maximal_reads.dir/maximal.cpp.o -o get_maximal_reads -lfmt ../lib/libLAInterface.a ../lib/libini.a ../lib/libLA.a ../lib/libDB.a ../lib/libPAF.a -lz make[3]: Leaving directory '/build/hinge-0.5.0/obj-aarch64-linux-gnu' [ 89%] Built target get_maximal_reads [ 93%] Linking CXX executable Reads_filter cd /build/hinge-0.5.0/obj-aarch64-linux-gnu/bin/filter && /usr/bin/cmake -E cmake_link_script CMakeFiles/Reads_filter.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hinge-0.5.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/Reads_filter.dir/filter.cpp.o -o Reads_filter -lfmt ../lib/libLAInterface.a ../lib/libini.a ../lib/libLA.a ../lib/libDB.a ../lib/libPAF.a -lz make[3]: Leaving directory '/build/hinge-0.5.0/obj-aarch64-linux-gnu' [ 93%] Built target Reads_filter [ 96%] Linking CXX executable draft_assembly cd /build/hinge-0.5.0/obj-aarch64-linux-gnu/bin/consensus && /usr/bin/cmake -E cmake_link_script CMakeFiles/draft_assembly.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hinge-0.5.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/draft_assembly.dir/draft.cpp.o -o draft_assembly -lfmt ../lib/libLAInterface.a ../lib/libini.a ../lib/libfalcon.a ../lib/libLA.a ../lib/libDB.a ../lib/libPAF.a -lz ../lib/libkmer_lookup.a ../lib/libDW_banded.a make[3]: Leaving directory '/build/hinge-0.5.0/obj-aarch64-linux-gnu' [ 96%] Built target draft_assembly [100%] Linking CXX executable hinging cd /build/hinge-0.5.0/obj-aarch64-linux-gnu/bin/layout && /usr/bin/cmake -E cmake_link_script CMakeFiles/hinging.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hinge-0.5.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/hinging.dir/hinging.cpp.o -o hinging -lfmt ../lib/libLAInterface.a ../lib/libini.a /usr/lib/aarch64-linux-gnu/libboost_graph.a ../lib/libLA.a ../lib/libDB.a ../lib/libPAF.a -lz /usr/lib/aarch64-linux-gnu/libboost_regex.a make[3]: Leaving directory '/build/hinge-0.5.0/obj-aarch64-linux-gnu' [100%] Built target hinging make[2]: Leaving directory '/build/hinge-0.5.0/obj-aarch64-linux-gnu' /usr/bin/cmake -E cmake_progress_start /build/hinge-0.5.0/obj-aarch64-linux-gnu/CMakeFiles 0 make[1]: Leaving directory '/build/hinge-0.5.0/obj-aarch64-linux-gnu' dh_auto_test create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install --destdir=debian/hinge/ cd obj-aarch64-linux-gnu && make -j8 install DESTDIR=/build/hinge-0.5.0/debian/hinge AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/hinge-0.5.0/obj-aarch64-linux-gnu' /usr/bin/cmake -S/build/hinge-0.5.0 -B/build/hinge-0.5.0/obj-aarch64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 preinstall make[2]: Entering directory '/build/hinge-0.5.0/obj-aarch64-linux-gnu' make[2]: Nothing to be done for 'preinstall'. make[2]: Leaving directory '/build/hinge-0.5.0/obj-aarch64-linux-gnu' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "None" -- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge -- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/unitig.py -- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/split_las.py -- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/run_parse_read.py -- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/run_parse_alignment.py -- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/run_mapping3.py -- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/run_mapping2.py -- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/run_mapping.py -- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/repeat_annotate_reads.py -- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/random_condensation.py -- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/pruning_and_clipping_nanopore.py -- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/pruning_and_clipping.py -- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/pipeline_nctc.py -- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/pipeline_consensus_norevcomp.py -- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/pipeline_consensus.py -- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/pileup.ipynb -- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/parse_read.py -- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/parse_qv.py -- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/parse_alignment.py -- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/parse.py -- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/parallel_draw_large.sh -- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/parallel_draw.sh -- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/merge_hinges.py -- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/longest_path.py -- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/interface_utils.py -- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/get_single_strand.py -- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/get_draft_path_norevcomp.py -- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/get_draft_path.py -- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/get_draft_annotation.py -- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/get_consensus_gfa.py -- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/get_NCTC_json.py -- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/fasta_to_fastq.py -- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/draw_pileup_region_find_bridges.py -- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/draw_pileup_region.py -- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/draw2_pileup_w_repeat.py -- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/draw2_pileup_region.py -- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/draw2_pileup.py -- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/draw2.py -- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/draft_assembly_not_perfect.py -- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/draft_assembly.py -- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/download_NCTC_pipeline.py -- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/create_hgraph_nogt.py -- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/create_hgraph.py -- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/create_bandage_file.py -- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/correct_head.py -- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/connected.py -- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/condense_graph_with_gt.py -- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/condense_graph_create_gfa_compute_n50.py -- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/condense_graph_annotate_clip_ends.py -- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/condense_graph_and_annotate.py -- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/condense_graph.py -- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/compute_n50_from_draft.py -- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/clip_ends.py -- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/add_groundtruth_json.py -- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/add_groundtruth.py -- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/Visualise_graph.py -- Installing: /build/hinge-0.5.0/debian/hinge/usr/share/man/man1/hinge.1 -- Installing: /build/hinge-0.5.0/debian/hinge/usr/bin/hinge -- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/Reads_filter -- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/get_maximal_reads -- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/draft_assembly -- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/consensus -- Installing: /build/hinge-0.5.0/debian/hinge/usr/lib/hinge/hinging make[1]: Leaving directory '/build/hinge-0.5.0/obj-aarch64-linux-gnu' dh_installdocs dh_installchangelogs debian/rules override_dh_installexamples make[1]: Entering directory '/build/hinge-0.5.0' dh_installexamples # only install nominal.ini from the utils/ directory, but preserve # the directory structure (since demo scripts expect it) mkdir -p debian/hinge/usr/share/doc/hinge/examples/utils \ && cp utils/nominal.ini debian/hinge/usr/share/doc/hinge/examples/utils make[1]: Leaving directory '/build/hinge-0.5.0' dh_installman dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'hinge' in '../hinge_0.5.0-7_arm64.deb'. dpkg-deb: building package 'hinge-dbgsym' in '../hinge-dbgsym_0.5.0-7_arm64.deb'. dpkg-genbuildinfo --build=binary -O../hinge_0.5.0-7_arm64.buildinfo dpkg-genchanges --build=binary -O../hinge_0.5.0-7_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/21062 and its subdirectories I: Current time: Mon May 1 12:52:02 -12 2023 I: pbuilder-time-stamp: 1682988722 Tue May 2 00:52:10 UTC 2023 I: 1st build successful. Starting 2nd build on remote node codethink16-arm64.debian.net. Tue May 2 00:52:10 UTC 2023 I: Preparing to do remote build '2' on codethink16-arm64.debian.net. Tue May 2 01:02:03 UTC 2023 I: Deleting $TMPDIR on codethink16-arm64.debian.net. Tue May 2 01:02:04 UTC 2023 I: hinge_0.5.0-7_arm64.changes: Format: 1.8 Date: Wed, 22 Dec 2021 08:21:12 +0100 Source: hinge Binary: hinge hinge-dbgsym Architecture: arm64 Version: 0.5.0-7 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: hinge - long read genome assembler based on hinging Changes: hinge (0.5.0-7) unstable; urgency=medium . * Packaging update * Standards-Version: 4.6.0 (routine-update) * debhelper-compat 13 (routine-update) * No tab in license text (routine-update) * No need to exclude files any more in d/copyright Checksums-Sha1: 0d1eb65c75fb44d386007d5193449da107e856be 8602104 hinge-dbgsym_0.5.0-7_arm64.deb f77fe0755b941e38595c654048a37c5937ef217e 11216 hinge_0.5.0-7_arm64.buildinfo 227bfe65c79c65341b849b180cc3280d1d86e3f8 453800 hinge_0.5.0-7_arm64.deb Checksums-Sha256: 78f86ad5b5830bcc22f33bad429d926eea51fc11de6d5780e96c344903b17b46 8602104 hinge-dbgsym_0.5.0-7_arm64.deb 6d24e7a6607d9c55f447cb0bf5561faecd4a483c20991bf2965486375b19e3c8 11216 hinge_0.5.0-7_arm64.buildinfo d78768713f7b5d0d985ee2bb9cf75ce287d78e6dfd2afca1af72dbacf1e5e55a 453800 hinge_0.5.0-7_arm64.deb Files: 4576be7f55d149fb3caa0bcaeb6725df 8602104 debug optional hinge-dbgsym_0.5.0-7_arm64.deb d030dada2c8fbd7680baac308af3cafd 11216 science optional hinge_0.5.0-7_arm64.buildinfo 2d35bcf24af5709497d5810a954946e9 453800 science optional hinge_0.5.0-7_arm64.deb Tue May 2 01:02:06 UTC 2023 I: diffoscope 241 will be used to compare the two builds: # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.kMHWErYB/hinge_0.5.0-7.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.kMHWErYB/hinge_0.5.0-7.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.kMHWErYB/hinge_0.5.0-7.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.kMHWErYB/b1/hinge_0.5.0-7_arm64.changes /srv/reproducible-results/rbuild-debian/r-b-build.kMHWErYB/b2/hinge_0.5.0-7_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: 0.478s) 0.478s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.116s) 0.116s 12 calls diffoscope.comparators.binary.FilesystemFile 0.000s 10 calls abc.DotChangesFile ## specialize (total time: 0.000s) 0.000s 1 call specialize Tue May 2 01:02:07 UTC 2023 I: diffoscope 241 found no differences in the changes files, and a .buildinfo file also exists. Tue May 2 01:02:07 UTC 2023 I: hinge from bookworm built successfully and reproducibly on arm64. Tue May 2 01:02:09 UTC 2023 I: Submitting .buildinfo files to external archives: Tue May 2 01:02:09 UTC 2023 I: Submitting 12K b1/hinge_0.5.0-7_arm64.buildinfo.asc Tue May 2 01:02:09 UTC 2023 I: Submitting 12K b2/hinge_0.5.0-7_arm64.buildinfo.asc Tue May 2 01:02:10 UTC 2023 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Tue May 2 01:02:10 UTC 2023 I: Done submitting .buildinfo files. Tue May 2 01:02:10 UTC 2023 I: Removing signed hinge_0.5.0-7_arm64.buildinfo.asc files: removed './b1/hinge_0.5.0-7_arm64.buildinfo.asc' removed './b2/hinge_0.5.0-7_arm64.buildinfo.asc'