I: pbuilder: network access will be disabled during build I: Current time: Sat Mar 7 14:08:40 -12 2026 I: pbuilder-time-stamp: 1772935720 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: 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 dpkg-source: warning: cannot verify inline signature for ./hinge_0.5.0-7.dsc: unsupported subcommand 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/493925/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='amd64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 ' DISTRIBUTION='unstable' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='23dcd373dcc744b7bce2cb8085020542' 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='493925' 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.J79CUbbg/pbuilderrc_OQfm --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.J79CUbbg/b1 --logfile b1/build.log hinge_0.5.0-7.dsc' SUDO_GID='111' SUDO_UID='106' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://213.165.73.152:3128' I: uname -a Linux ionos15-amd64 6.12.9+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.9-1~bpo12+1 (2025-01-19) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Nov 22 2024 /bin -> usr/bin I: user script /srv/workspace/pbuilder/493925/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), 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 ... 19840 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} cmake{a} cmake-data{a} comerr-dev{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-dejavu-mono{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} krb5-multidev{a} libaec-dev{a} libaec0{a} libarchive-zip-perl{a} libarchive13t64{a} libblas3{a} libboost-dev{a} libboost-graph-dev{a} libboost-graph1.83-dev{a} libboost-graph1.83.0{a} libboost-regex1.83-dev{a} libboost-regex1.83.0{a} libboost-serialization1.83-dev{a} libboost-serialization1.83.0{a} libboost-test1.83-dev{a} libboost-test1.83.0{a} libboost1.83-dev{a} libbrotli-dev{a} libbrotli1{a} libcairo2{a} libcom-err2{a} libcurl3t64-gnutls{a} libcurl4-openssl-dev{a} libcurl4t64{a} libdebhelper-perl{a} libdeflate0{a} libdouble-conversion3{a} libelf1t64{a} libevent-2.1-7t64{a} libexpat1{a} libffi8{a} libfile-stripnondeterminism-perl{a} libfmt-dev{a} libfmt10{a} libfontconfig1{a} libfontenc1{a} libfreetype6{a} libfribidi0{a} libgcrypt20{a} libgfortran5{a} libglib2.0-0t64{a} libgmp-dev{a} libgmpxx4ldbl{a} libgnutls-dane0t64{a} libgnutls-openssl27t64{a} libgnutls28-dev{a} libgnutls30t64{a} libgpg-error0{a} libgraphite2-3{a} libgssapi-krb5-2{a} libgssrpc4t64{a} libharfbuzz0b{a} libhdf5-310{a} libhdf5-cpp-310{a} libhdf5-dev{a} libhdf5-fortran-310{a} libhdf5-hl-310{a} libhdf5-hl-cpp-310{a} libhdf5-hl-fortran-310{a} libhts3t64{a} libhtscodecs2{a} libicu-dev{a} libicu72{a} libidn2-0{a} libidn2-dev{a} libimagequant0{a} libjbig0{a} libjpeg-dev{a} libjpeg62-turbo{a} libjpeg62-turbo-dev{a} libjs-jquery{a} libjs-jquery-ui{a} libjsoncpp26{a} libk5crypto3{a} libkadm5clnt-mit12{a} libkadm5srv-mit12{a} libkdb5-10t64{a} libkeyutils1{a} libkrb5-3{a} libkrb5-dev{a} libkrb5support0{a} liblapack3{a} liblbfgsb0{a} liblcms2-2{a} libldap-dev{a} libldap2{a} liblerc4{a} liblua5.4-0{a} libmagic-mgc{a} libmagic1t64{a} libnghttp2-14{a} libnghttp2-dev{a} libnghttp3-9{a} libngtcp2-16{a} libngtcp2-crypto-gnutls8{a} libnuma1{a} libopenjp2-7{a} libp11-kit-dev{a} libp11-kit0{a} libpipeline1{a} libpixman-1-0{a} libpkgconf3{a} libpng16-16t64{a} libproc2-0{a} libpsl-dev{a} libpsl5t64{a} libpython3-stdlib{a} libpython3.13-minimal{a} libpython3.13-stdlib{a} libqhull-r8.0{a} libraqm0{a} libreadline8t64{a} librhash1{a} librtmp-dev{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsharpyuv0{a} libspdlog-dev{a} libspdlog1.15{a} libssh2-1-dev{a} libssh2-1t64{a} libssl-dev{a} libsz2{a} libtasn1-6{a} libtasn1-6-dev{a} libtcl8.6{a} libtiff6{a} libtk8.6{a} libtool{a} libuchardet0{a} libunbound8{a} libunistring5{a} libuv1t64{a} libwebp7{a} libwebpdemux2{a} libwebpmux3{a} libx11-6{a} libx11-data{a} libxau6{a} libxcb-render0{a} libxcb-shm0{a} libxcb1{a} libxdmcp6{a} libxext6{a} libxft2{a} libxml2{a} libxrender1{a} libxslt1.1{a} libxss1{a} libyaml-0-2{a} libzstd-dev{a} m4{a} man-db{a} media-types{a} netbase{a} nettle-dev{a} pandoc{a} pandoc-data{a} pkgconf{a} pkgconf-bin{a} po-debconf{a} procps{a} python-matplotlib-data{a} python3{a} python3-attr{a} python3-autocommand{a} python3-biopython{a} python3-brotli{a} python3-cairo{a} python3-chardet{a} python3-colormap{a} python3-contourpy{a} python3-cycler{a} python3-dateutil{a} python3-decorator{a} python3-fonttools{a} python3-freetype{a} python3-fs{a} python3-inflect{a} python3-jaraco.context{a} python3-jaraco.functools{a} python3-kiwisolver{a} python3-lxml{a} python3-lz4{a} python3-matplotlib{a} python3-minimal{a} python3-more-itertools{a} python3-mpmath{a} python3-networkx{a} python3-numpy{a} python3-numpy-dev{a} python3-packaging{a} python3-pbcore{a} python3-pil{a} python3-pil.imagetk{a} python3-pkg-resources{a} python3-platformdirs{a} python3-pyparsing{a} python3-pysam{a} python3-reportlab{a} python3-rlpycairo{a} python3-scipy{a} python3-sympy{a} python3-tk{a} python3-typeguard{a} python3-typing-extensions{a} python3-tz{a} python3-ufolib2{a} python3-ujson{a} python3-unicodedata2{a} python3.12-tk{a} python3.13{a} python3.13-minimal{a} python3.13-tk{a} readline-common{a} sensible-utils{a} sgml-base{a} tk8.6-blt2.5{a} tzdata{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 fonts-dejavu-extra isympy-common javascript-common krb5-locales libarchive-cpio-perl libglib2.0-data libgpg-error-l10n libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules libtasn1-doc linux-sysctl-defaults lynx ncbi-blast+ psmisc publicsuffix python-biopython-doc python3-bs4 python3-cssselect python3-gdal python3-h5py python3-html5lib python3-olefile python3-pooch python3-pydot python3-pygraphviz python3-yaml shared-mime-info wget xdg-user-dirs 0 packages upgraded, 255 newly installed, 0 to remove and 0 not upgraded. Need to get 227 MB of archives. After unpacking 1194 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main amd64 libpython3.13-minimal amd64 3.13.1-3+b1 [859 kB] Get: 2 http://deb.debian.org/debian unstable/main amd64 libexpat1 amd64 2.6.4-1 [106 kB] Get: 3 http://deb.debian.org/debian unstable/main amd64 python3.13-minimal amd64 3.13.1-3+b1 [2203 kB] Get: 4 http://deb.debian.org/debian unstable/main amd64 python3-minimal amd64 3.13.1-2 [27.0 kB] Get: 5 http://deb.debian.org/debian unstable/main amd64 media-types all 10.1.0 [26.9 kB] Get: 6 http://deb.debian.org/debian unstable/main amd64 netbase all 6.4 [12.8 kB] Get: 7 http://deb.debian.org/debian unstable/main amd64 tzdata all 2025a-1 [259 kB] Get: 8 http://deb.debian.org/debian unstable/main amd64 libffi8 amd64 3.4.6-1 [23.6 kB] Get: 9 http://deb.debian.org/debian unstable/main amd64 readline-common all 8.2-6 [69.4 kB] Get: 10 http://deb.debian.org/debian unstable/main amd64 libreadline8t64 amd64 8.2-6 [169 kB] Get: 11 http://deb.debian.org/debian unstable/main amd64 libpython3.13-stdlib amd64 3.13.1-3+b1 [1973 kB] Get: 12 http://deb.debian.org/debian unstable/main amd64 python3.13 amd64 3.13.1-3+b1 [740 kB] Get: 13 http://deb.debian.org/debian unstable/main amd64 libpython3-stdlib amd64 3.13.1-2 [9952 B] Get: 14 http://deb.debian.org/debian unstable/main amd64 python3 amd64 3.13.1-2 [28.0 kB] Get: 15 http://deb.debian.org/debian unstable/main amd64 sgml-base all 1.31 [15.4 kB] Get: 16 http://deb.debian.org/debian unstable/main amd64 libproc2-0 amd64 2:4.0.4-7 [64.9 kB] Get: 17 http://deb.debian.org/debian unstable/main amd64 procps amd64 2:4.0.4-7 [878 kB] Get: 18 http://deb.debian.org/debian unstable/main amd64 sensible-utils all 0.0.24 [24.8 kB] Get: 19 http://deb.debian.org/debian unstable/main amd64 libmagic-mgc amd64 1:5.45-3+b1 [314 kB] Get: 20 http://deb.debian.org/debian unstable/main amd64 libmagic1t64 amd64 1:5.45-3+b1 [108 kB] Get: 21 http://deb.debian.org/debian unstable/main amd64 file amd64 1:5.45-3+b1 [43.3 kB] Get: 22 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 0.23.1-1 [243 kB] Get: 23 http://deb.debian.org/debian unstable/main amd64 libuchardet0 amd64 0.0.8-1+b2 [68.9 kB] Get: 24 http://deb.debian.org/debian unstable/main amd64 groff-base amd64 1.23.0-7 [1185 kB] Get: 25 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.40.4-2 [92.1 kB] Get: 26 http://deb.debian.org/debian unstable/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get: 27 http://deb.debian.org/debian unstable/main amd64 man-db amd64 2.13.0-1 [1420 kB] Get: 28 http://deb.debian.org/debian unstable/main amd64 m4 amd64 1.4.19-5 [294 kB] Get: 29 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.72-3 [493 kB] Get: 30 http://deb.debian.org/debian unstable/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 31 http://deb.debian.org/debian unstable/main amd64 automake all 1:1.17-3 [862 kB] Get: 32 http://deb.debian.org/debian unstable/main amd64 autopoint all 0.23.1-1 [770 kB] Get: 33 http://deb.debian.org/debian unstable/main amd64 libtcl8.6 amd64 8.6.16+dfsg-1 [1042 kB] Get: 34 http://deb.debian.org/debian unstable/main amd64 libbrotli1 amd64 1.1.0-2+b6 [302 kB] Get: 35 http://deb.debian.org/debian unstable/main amd64 libpng16-16t64 amd64 1.6.46-4 [284 kB] Get: 36 http://deb.debian.org/debian unstable/main amd64 libfreetype6 amd64 2.13.3+dfsg-1 [452 kB] Get: 37 http://deb.debian.org/debian unstable/main amd64 fonts-dejavu-mono all 2.37-8 [489 kB] Get: 38 http://deb.debian.org/debian unstable/main amd64 fonts-dejavu-core all 2.37-8 [840 kB] Get: 39 http://deb.debian.org/debian unstable/main amd64 libfontenc1 amd64 1:1.1.8-1+b2 [23.3 kB] Get: 40 http://deb.debian.org/debian unstable/main amd64 x11-common all 1:7.7+24 [217 kB] Get: 41 http://deb.debian.org/debian unstable/main amd64 xfonts-encodings all 1:1.0.4-2.2 [577 kB] Get: 42 http://deb.debian.org/debian unstable/main amd64 xfonts-utils amd64 1:7.7+7 [93.3 kB] Get: 43 http://deb.debian.org/debian unstable/main amd64 fonts-urw-base35 all 20200910-8 [10.8 MB] Get: 44 http://deb.debian.org/debian unstable/main amd64 fontconfig-config amd64 2.15.0-2 [317 kB] Get: 45 http://deb.debian.org/debian unstable/main amd64 libfontconfig1 amd64 2.15.0-2 [391 kB] Get: 46 http://deb.debian.org/debian unstable/main amd64 libxau6 amd64 1:1.0.11-1 [20.4 kB] Get: 47 http://deb.debian.org/debian unstable/main amd64 libxdmcp6 amd64 1:1.1.5-1 [27.8 kB] Get: 48 http://deb.debian.org/debian unstable/main amd64 libxcb1 amd64 1.17.0-2+b1 [144 kB] Get: 49 http://deb.debian.org/debian unstable/main amd64 libx11-data all 2:1.8.10-2 [337 kB] Get: 50 http://deb.debian.org/debian unstable/main amd64 libx11-6 amd64 2:1.8.10-2 [813 kB] Get: 51 http://deb.debian.org/debian unstable/main amd64 libxrender1 amd64 1:0.9.10-1.1+b4 [27.8 kB] Get: 52 http://deb.debian.org/debian unstable/main amd64 libxft2 amd64 2.3.6-1+b4 [54.5 kB] Get: 53 http://deb.debian.org/debian unstable/main amd64 libxext6 amd64 2:1.3.4-1+b3 [50.4 kB] Get: 54 http://deb.debian.org/debian unstable/main amd64 libxss1 amd64 1:1.2.3-1+b3 [17.0 kB] Get: 55 http://deb.debian.org/debian unstable/main amd64 libtk8.6 amd64 8.6.16-1 [793 kB] Get: 56 http://deb.debian.org/debian unstable/main amd64 tk8.6-blt2.5 amd64 2.5.3+dfsg-7 [586 kB] Get: 57 http://deb.debian.org/debian unstable/main amd64 blt amd64 2.5.3+dfsg-7 [6024 B] Get: 58 http://deb.debian.org/debian unstable/main amd64 cmake-data all 3.31.5-1 [2267 kB] Get: 59 http://deb.debian.org/debian unstable/main amd64 libicu72 amd64 72.1-6 [9421 kB] Get: 60 http://deb.debian.org/debian unstable/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.2+b1 [699 kB] Get: 61 http://deb.debian.org/debian unstable/main amd64 libarchive13t64 amd64 3.7.4-1.1 [349 kB] Get: 62 http://deb.debian.org/debian unstable/main amd64 libkrb5support0 amd64 1.21.3-4 [32.8 kB] Get: 63 http://deb.debian.org/debian unstable/main amd64 libcom-err2 amd64 1.47.2-1 [24.0 kB] Get: 64 http://deb.debian.org/debian unstable/main amd64 libk5crypto3 amd64 1.21.3-4 [80.9 kB] Get: 65 http://deb.debian.org/debian unstable/main amd64 libkeyutils1 amd64 1.6.3-4 [9092 B] Get: 66 http://deb.debian.org/debian unstable/main amd64 libkrb5-3 amd64 1.21.3-4 [326 kB] Get: 67 http://deb.debian.org/debian unstable/main amd64 libgssapi-krb5-2 amd64 1.21.3-4 [138 kB] Get: 68 http://deb.debian.org/debian unstable/main amd64 libunistring5 amd64 1.3-1 [476 kB] Get: 69 http://deb.debian.org/debian unstable/main amd64 libidn2-0 amd64 2.3.7-2+b1 [129 kB] Get: 70 http://deb.debian.org/debian unstable/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-8+b1 [19.9 kB] Get: 71 http://deb.debian.org/debian unstable/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-8+b1 [57.6 kB] Get: 72 http://deb.debian.org/debian unstable/main amd64 libldap2 amd64 2.6.9+dfsg-1 [192 kB] Get: 73 http://deb.debian.org/debian unstable/main amd64 libnghttp2-14 amd64 1.64.0-1 [75.5 kB] Get: 74 http://deb.debian.org/debian unstable/main amd64 libpsl5t64 amd64 0.21.2-1.1+b1 [57.2 kB] Get: 75 http://deb.debian.org/debian unstable/main amd64 libp11-kit0 amd64 0.25.5-3 [425 kB] Get: 76 http://deb.debian.org/debian unstable/main amd64 libtasn1-6 amd64 4.19.0-3+b3 [49.5 kB] Get: 77 http://deb.debian.org/debian unstable/main amd64 libgnutls30t64 amd64 3.8.8-2 [1454 kB] Get: 78 http://deb.debian.org/debian unstable/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b5 [58.8 kB] Get: 79 http://deb.debian.org/debian unstable/main amd64 libssh2-1t64 amd64 1.11.1-1 [245 kB] Get: 80 http://deb.debian.org/debian unstable/main amd64 libcurl4t64 amd64 8.11.1-1+b1 [352 kB] Get: 81 http://deb.debian.org/debian unstable/main amd64 libjsoncpp26 amd64 1.9.6-3 [81.7 kB] Get: 82 http://deb.debian.org/debian unstable/main amd64 librhash1 amd64 1.4.5-1 [132 kB] Get: 83 http://deb.debian.org/debian unstable/main amd64 libuv1t64 amd64 1.48.0-7 [148 kB] Get: 84 http://deb.debian.org/debian unstable/main amd64 cmake amd64 3.31.5-1 [12.0 MB] Get: 85 http://deb.debian.org/debian unstable/main amd64 comerr-dev amd64 2.1-1.47.2-1 [55.7 kB] Get: 86 http://deb.debian.org/debian unstable/main amd64 daligner amd64 1.0+git20240119.335105d-3 [242 kB] Get: 87 http://deb.debian.org/debian unstable/main amd64 dascrubber amd64 1.1-4 [168 kB] Get: 88 http://deb.debian.org/debian unstable/main amd64 dazzdb amd64 1.0+git20240115.be65e59-1 [227 kB] Get: 89 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 13.24.1 [90.9 kB] Get: 90 http://deb.debian.org/debian unstable/main amd64 libtool all 2.5.4-3 [539 kB] Get: 91 http://deb.debian.org/debian unstable/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 92 http://deb.debian.org/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 93 http://deb.debian.org/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.14.1-1 [19.6 kB] Get: 94 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.14.1-1 [8584 B] Get: 95 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.192-4 [189 kB] Get: 96 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get: 97 http://deb.debian.org/debian unstable/main amd64 gettext amd64 0.23.1-1 [1680 kB] Get: 98 http://deb.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 99 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 100 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.24.1 [920 kB] Get: 101 http://deb.debian.org/debian unstable/main amd64 fonts-lyx all 2.4.3-1 [190 kB] Get: 102 http://deb.debian.org/debian unstable/main amd64 hdf5-helpers amd64 1.14.5+repack-3 [26.6 kB] Get: 103 http://deb.debian.org/debian unstable/main amd64 icu-devtools amd64 72.1-6 [210 kB] Get: 104 http://deb.debian.org/debian unstable/main amd64 libgssrpc4t64 amd64 1.21.3-4 [60.0 kB] Get: 105 http://deb.debian.org/debian unstable/main amd64 libkadm5clnt-mit12 amd64 1.21.3-4 [42.2 kB] Get: 106 http://deb.debian.org/debian unstable/main amd64 libkdb5-10t64 amd64 1.21.3-4 [42.4 kB] Get: 107 http://deb.debian.org/debian unstable/main amd64 libkadm5srv-mit12 amd64 1.21.3-4 [54.2 kB] Get: 108 http://deb.debian.org/debian unstable/main amd64 krb5-multidev amd64 1.21.3-4 [126 kB] Get: 109 http://deb.debian.org/debian unstable/main amd64 libaec0 amd64 1.1.3-1+b1 [23.8 kB] Get: 110 http://deb.debian.org/debian unstable/main amd64 libsz2 amd64 1.1.3-1+b1 [8080 B] Get: 111 http://deb.debian.org/debian unstable/main amd64 libaec-dev amd64 1.1.3-1+b1 [21.5 kB] Get: 112 http://deb.debian.org/debian unstable/main amd64 libblas3 amd64 3.12.1-2 [160 kB] Get: 113 http://deb.debian.org/debian unstable/main amd64 libboost1.83-dev amd64 1.83.0-4 [10.6 MB] Get: 114 http://deb.debian.org/debian unstable/main amd64 libboost-dev amd64 1.83.0.2+b2 [3836 B] Get: 115 http://deb.debian.org/debian unstable/main amd64 libboost-graph1.83.0 amd64 1.83.0-4 [359 kB] Get: 116 http://deb.debian.org/debian unstable/main amd64 libboost-regex1.83.0 amd64 1.83.0-4 [330 kB] Get: 117 http://deb.debian.org/debian unstable/main amd64 libicu-dev amd64 72.1-6 [10.4 MB] Get: 118 http://deb.debian.org/debian unstable/main amd64 libboost-regex1.83-dev amd64 1.83.0-4 [346 kB] Get: 119 http://deb.debian.org/debian unstable/main amd64 libboost-serialization1.83.0 amd64 1.83.0-4 [333 kB] Get: 120 http://deb.debian.org/debian unstable/main amd64 libboost-serialization1.83-dev amd64 1.83.0-4 [373 kB] Get: 121 http://deb.debian.org/debian unstable/main amd64 libboost-test1.83.0 amd64 1.83.0-4 [471 kB] Get: 122 http://deb.debian.org/debian unstable/main amd64 libboost-test1.83-dev amd64 1.83.0-4 [541 kB] Get: 123 http://deb.debian.org/debian unstable/main amd64 libboost-graph1.83-dev amd64 1.83.0-4 [383 kB] Get: 124 http://deb.debian.org/debian unstable/main amd64 libboost-graph-dev amd64 1.83.0.2+b2 [3700 B] Get: 125 http://deb.debian.org/debian unstable/main amd64 libbrotli-dev amd64 1.1.0-2+b6 [316 kB] Get: 126 http://deb.debian.org/debian unstable/main amd64 libpixman-1-0 amd64 0.44.0-3 [248 kB] Get: 127 http://deb.debian.org/debian unstable/main amd64 libxcb-render0 amd64 1.17.0-2+b1 [115 kB] Get: 128 http://deb.debian.org/debian unstable/main amd64 libxcb-shm0 amd64 1.17.0-2+b1 [105 kB] Get: 129 http://deb.debian.org/debian unstable/main amd64 libcairo2 amd64 1.18.2-2 [535 kB] Get: 130 http://deb.debian.org/debian unstable/main amd64 libnghttp3-9 amd64 1.6.0-2 [64.8 kB] Get: 131 http://deb.debian.org/debian unstable/main amd64 libngtcp2-16 amd64 1.9.1-1 [119 kB] Get: 132 http://deb.debian.org/debian unstable/main amd64 libngtcp2-crypto-gnutls8 amd64 1.9.1-1 [18.5 kB] Get: 133 http://deb.debian.org/debian unstable/main amd64 libcurl3t64-gnutls amd64 8.11.1-1+b1 [360 kB] Get: 134 http://deb.debian.org/debian unstable/main amd64 libidn2-dev amd64 2.3.7-2+b1 [123 kB] Get: 135 http://deb.debian.org/debian unstable/main amd64 libkrb5-dev amd64 1.21.3-4 [15.9 kB] Get: 136 http://deb.debian.org/debian unstable/main amd64 libldap-dev amd64 2.6.9+dfsg-1 [307 kB] Get: 137 http://deb.debian.org/debian unstable/main amd64 libpkgconf3 amd64 1.8.1-4 [36.4 kB] Get: 138 http://deb.debian.org/debian unstable/main amd64 pkgconf-bin amd64 1.8.1-4 [30.2 kB] Get: 139 http://deb.debian.org/debian unstable/main amd64 pkgconf amd64 1.8.1-4 [26.2 kB] Get: 140 http://deb.debian.org/debian unstable/main amd64 libnghttp2-dev amd64 1.64.0-1 [115 kB] Get: 141 http://deb.debian.org/debian unstable/main amd64 libpsl-dev amd64 0.21.2-1.1+b1 [77.6 kB] Get: 142 http://deb.debian.org/debian unstable/main amd64 libgmpxx4ldbl amd64 2:6.3.0+dfsg-3 [329 kB] Get: 143 http://deb.debian.org/debian unstable/main amd64 libgmp-dev amd64 2:6.3.0+dfsg-3 [642 kB] Get: 144 http://deb.debian.org/debian unstable/main amd64 libevent-2.1-7t64 amd64 2.1.12-stable-10+b1 [182 kB] Get: 145 http://deb.debian.org/debian unstable/main amd64 libunbound8 amd64 1.22.0-1+b1 [598 kB] Get: 146 http://deb.debian.org/debian unstable/main amd64 libgnutls-dane0t64 amd64 3.8.8-2 [449 kB] Get: 147 http://deb.debian.org/debian unstable/main amd64 libgnutls-openssl27t64 amd64 3.8.8-2 [449 kB] Get: 148 http://deb.debian.org/debian unstable/main amd64 libp11-kit-dev amd64 0.25.5-3 [208 kB] Get: 149 http://deb.debian.org/debian unstable/main amd64 libtasn1-6-dev amd64 4.19.0-3+b3 [98.9 kB] Get: 150 http://deb.debian.org/debian unstable/main amd64 nettle-dev amd64 3.10-1+b1 [1317 kB] Get: 151 http://deb.debian.org/debian unstable/main amd64 libgnutls28-dev amd64 3.8.8-2 [1391 kB] Get: 152 http://deb.debian.org/debian unstable/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1+b1 [920 kB] Get: 153 http://deb.debian.org/debian unstable/main amd64 librtmp-dev amd64 2.4+20151223.gitfa8646d.1-2+b5 [68.0 kB] Get: 154 http://deb.debian.org/debian unstable/main amd64 libssl-dev amd64 3.4.0-2 [2790 kB] Get: 155 http://deb.debian.org/debian unstable/main amd64 libssh2-1-dev amd64 1.11.1-1 [393 kB] Get: 156 http://deb.debian.org/debian unstable/main amd64 libzstd-dev amd64 1.5.6+dfsg-2 [365 kB] Get: 157 http://deb.debian.org/debian unstable/main amd64 libcurl4-openssl-dev amd64 8.11.1-1+b1 [463 kB] Get: 158 http://deb.debian.org/debian unstable/main amd64 libdeflate0 amd64 1.23-1+b1 [47.5 kB] Get: 159 http://deb.debian.org/debian unstable/main amd64 libdouble-conversion3 amd64 3.3.0-1+b3 [41.9 kB] Get: 160 http://deb.debian.org/debian unstable/main amd64 libfmt10 amd64 10.1.1+ds1-4 [127 kB] Get: 161 http://deb.debian.org/debian unstable/main amd64 libfmt-dev amd64 10.1.1+ds1-4 [177 kB] Get: 162 http://deb.debian.org/debian unstable/main amd64 libfribidi0 amd64 1.0.16-1 [26.5 kB] Get: 163 http://deb.debian.org/debian unstable/main amd64 libgpg-error0 amd64 1.51-3 [82.2 kB] Get: 164 http://deb.debian.org/debian unstable/main amd64 libgcrypt20 amd64 1.11.0-7 [843 kB] Get: 165 http://deb.debian.org/debian unstable/main amd64 libgfortran5 amd64 14.2.0-16 [836 kB] Get: 166 http://deb.debian.org/debian unstable/main amd64 libglib2.0-0t64 amd64 2.82.4-2 [1502 kB] Get: 167 http://deb.debian.org/debian unstable/main amd64 libgraphite2-3 amd64 1.3.14-2+b1 [75.4 kB] Get: 168 http://deb.debian.org/debian unstable/main amd64 libharfbuzz0b amd64 10.2.0-1 [479 kB] Get: 169 http://deb.debian.org/debian unstable/main amd64 libhdf5-310 amd64 1.14.5+repack-3 [1344 kB] Get: 170 http://deb.debian.org/debian unstable/main amd64 libhdf5-cpp-310 amd64 1.14.5+repack-3 [133 kB] Get: 171 http://deb.debian.org/debian unstable/main amd64 libhdf5-fortran-310 amd64 1.14.5+repack-3 [111 kB] Get: 172 http://deb.debian.org/debian unstable/main amd64 libhdf5-hl-310 amd64 1.14.5+repack-3 [69.3 kB] Get: 173 http://deb.debian.org/debian unstable/main amd64 libhdf5-hl-fortran-310 amd64 1.14.5+repack-3 [43.9 kB] Get: 174 http://deb.debian.org/debian unstable/main amd64 libhdf5-hl-cpp-310 amd64 1.14.5+repack-3 [24.4 kB] Get: 175 http://deb.debian.org/debian unstable/main amd64 libjpeg62-turbo amd64 1:2.1.5-3+b1 [168 kB] Get: 176 http://deb.debian.org/debian unstable/main amd64 libjpeg62-turbo-dev amd64 1:2.1.5-3+b1 [292 kB] Get: 177 http://deb.debian.org/debian unstable/main amd64 libjpeg-dev amd64 1:2.1.5-3+b1 [72.2 kB] Get: 178 http://deb.debian.org/debian unstable/main amd64 libhdf5-dev amd64 1.14.5+repack-3 [3165 kB] Get: 179 http://deb.debian.org/debian unstable/main amd64 libhtscodecs2 amd64 1.6.1-1 [95.6 kB] Get: 180 http://deb.debian.org/debian unstable/main amd64 libhts3t64 amd64 1.20+ds-2 [455 kB] Get: 181 http://deb.debian.org/debian unstable/main amd64 libimagequant0 amd64 2.18.0-1+b2 [35.2 kB] Get: 182 http://deb.debian.org/debian unstable/main amd64 libjbig0 amd64 2.1-6.1+b2 [32.1 kB] Get: 183 http://deb.debian.org/debian unstable/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get: 184 http://deb.debian.org/debian unstable/main amd64 libjs-jquery-ui all 1.13.2+dfsg-1 [250 kB] Get: 185 http://deb.debian.org/debian unstable/main amd64 liblapack3 amd64 3.12.1-2 [2452 kB] Get: 186 http://deb.debian.org/debian unstable/main amd64 liblbfgsb0 amd64 3.0+dfsg.4-1+b2 [29.4 kB] Get: 187 http://deb.debian.org/debian unstable/main amd64 liblcms2-2 amd64 2.16-2 [160 kB] Get: 188 http://deb.debian.org/debian unstable/main amd64 liblerc4 amd64 4.0.0+ds-5 [183 kB] Get: 189 http://deb.debian.org/debian unstable/main amd64 liblua5.4-0 amd64 5.4.7-1+b2 [147 kB] Get: 190 http://deb.debian.org/debian unstable/main amd64 libnuma1 amd64 2.0.18-1+b1 [22.3 kB] Get: 191 http://deb.debian.org/debian unstable/main amd64 libopenjp2-7 amd64 2.5.3-1 [204 kB] Get: 192 http://deb.debian.org/debian unstable/main amd64 libqhull-r8.0 amd64 2020.2-6+b2 [248 kB] Get: 193 http://deb.debian.org/debian unstable/main amd64 libraqm0 amd64 0.10.2-1 [13.9 kB] Get: 194 http://deb.debian.org/debian unstable/main amd64 libsharpyuv0 amd64 1.5.0-0.1 [116 kB] Get: 195 http://deb.debian.org/debian unstable/main amd64 libspdlog1.15 amd64 1:1.15.0+ds-2+b1 [108 kB] Get: 196 http://deb.debian.org/debian unstable/main amd64 libspdlog-dev amd64 1:1.15.0+ds-2+b1 [89.6 kB] Get: 197 http://deb.debian.org/debian unstable/main amd64 libwebp7 amd64 1.5.0-0.1 [318 kB] Get: 198 http://deb.debian.org/debian unstable/main amd64 libtiff6 amd64 4.5.1+git230720-5 [324 kB] Get: 199 http://deb.debian.org/debian unstable/main amd64 libwebpdemux2 amd64 1.5.0-0.1 [113 kB] Get: 200 http://deb.debian.org/debian unstable/main amd64 libwebpmux3 amd64 1.5.0-0.1 [126 kB] Get: 201 http://deb.debian.org/debian unstable/main amd64 libxslt1.1 amd64 1.1.35-1.1+b1 [233 kB] Get: 202 http://deb.debian.org/debian unstable/main amd64 libyaml-0-2 amd64 0.2.5-2 [52.5 kB] Get: 203 http://deb.debian.org/debian unstable/main amd64 pandoc-data all 3.1.11.1-3 [459 kB] Get: 204 http://deb.debian.org/debian unstable/main amd64 pandoc amd64 3.1.11.1+ds-2 [26.4 MB] Get: 205 http://deb.debian.org/debian unstable/main amd64 python-matplotlib-data all 3.8.3-3 [2731 kB] Get: 206 http://deb.debian.org/debian unstable/main amd64 python3-attr all 24.3.0-1 [68.8 kB] Get: 207 http://deb.debian.org/debian unstable/main amd64 python3-autocommand all 2.2.2-3 [13.6 kB] Get: 208 http://deb.debian.org/debian unstable/main amd64 python3-numpy-dev amd64 1:2.2.2+ds-2 [138 kB] Get: 209 http://deb.debian.org/debian unstable/main amd64 python3-numpy amd64 1:2.2.2+ds-2 [7507 kB] Get: 210 http://deb.debian.org/debian unstable/main amd64 python3-chardet all 5.2.0+dfsg-2 [108 kB] Get: 211 http://deb.debian.org/debian unstable/main amd64 python3.12-tk amd64 3.12.8-5+b1 [113 kB] Get: 212 http://deb.debian.org/debian unstable/main amd64 python3.13-tk amd64 3.13.1-3+b1 [104 kB] Get: 213 http://deb.debian.org/debian unstable/main amd64 python3-tk amd64 3.13.1-1 [9464 B] Get: 214 http://deb.debian.org/debian unstable/main amd64 python3-pil.imagetk amd64 11.1.0-4 [81.4 kB] Get: 215 http://deb.debian.org/debian unstable/main amd64 python3-pil amd64 11.1.0-4 [528 kB] Get: 216 http://deb.debian.org/debian unstable/main amd64 python3-cairo amd64 1.26.1-2+b1 [130 kB] Get: 217 http://deb.debian.org/debian unstable/main amd64 python3-freetype all 2.5.1-1 [89.3 kB] Get: 218 http://deb.debian.org/debian unstable/main amd64 python3-rlpycairo all 0.3.0-3 [9904 B] Get: 219 http://deb.debian.org/debian unstable/main amd64 python3-reportlab all 4.2.5-1 [1117 kB] Get: 220 http://deb.debian.org/debian unstable/main amd64 xml-core all 0.19 [20.1 kB] Get: 221 http://deb.debian.org/debian unstable/main amd64 w3c-sgml-lib all 1.3-3 [273 kB] Get: 222 http://deb.debian.org/debian unstable/main amd64 python3-biopython amd64 1.85+dfsg-1 [1674 kB] Get: 223 http://deb.debian.org/debian unstable/main amd64 python3-brotli amd64 1.1.0-2+b6 [321 kB] Get: 224 http://deb.debian.org/debian unstable/main amd64 python3-dateutil all 2.9.0-3 [79.3 kB] Get: 225 http://deb.debian.org/debian unstable/main amd64 python3-pyparsing all 3.1.2-1 [146 kB] Get: 226 http://deb.debian.org/debian unstable/main amd64 python3-contourpy amd64 1.3.1-1 [264 kB] Get: 227 http://deb.debian.org/debian unstable/main amd64 python3-cycler all 0.12.1-1 [9496 B] Get: 228 http://deb.debian.org/debian unstable/main amd64 python3-tz all 2024.2-1 [31.0 kB] Get: 229 http://deb.debian.org/debian unstable/main amd64 python3-platformdirs all 4.3.6-1 [16.6 kB] Get: 230 http://deb.debian.org/debian unstable/main amd64 python3-fs all 2.4.16-6 [95.1 kB] Get: 231 http://deb.debian.org/debian unstable/main amd64 python3-lxml amd64 5.3.0-1+b1 [1676 kB] Get: 232 http://deb.debian.org/debian unstable/main amd64 python3-lz4 amd64 4.4.0+dfsg-1 [25.5 kB] Get: 233 http://deb.debian.org/debian unstable/main amd64 python3-decorator all 5.1.1-5 [15.1 kB] Get: 234 http://deb.debian.org/debian unstable/main amd64 python3-scipy amd64 1.14.1-4 [20.5 MB] Get: 235 http://deb.debian.org/debian unstable/main amd64 python3-mpmath all 1.3.0-1 [419 kB] Get: 236 http://deb.debian.org/debian unstable/main amd64 python3-sympy all 1.13.3-1 [4147 kB] Get: 237 http://deb.debian.org/debian unstable/main amd64 python3-ufolib2 all 0.17.0+dfsg1-1 [33.0 kB] Get: 238 http://deb.debian.org/debian unstable/main amd64 python3-unicodedata2 amd64 15.1.0+ds-1+b3 [299 kB] Get: 239 http://deb.debian.org/debian unstable/main amd64 unicode-data all 15.1.0-1 [8547 kB] Get: 240 http://deb.debian.org/debian unstable/main amd64 python3-fonttools amd64 4.55.3-2 [1633 kB] Get: 241 http://deb.debian.org/debian unstable/main amd64 python3-kiwisolver amd64 1.4.7-3 [76.9 kB] Get: 242 http://deb.debian.org/debian unstable/main amd64 python3-packaging all 24.2-1 [55.3 kB] Get: 243 http://deb.debian.org/debian unstable/main amd64 python3-matplotlib amd64 3.8.3-3+b3 [5650 kB] Get: 244 http://deb.debian.org/debian unstable/main amd64 python3-colormap all 1.3.0-1 [17.6 kB] Get: 245 http://deb.debian.org/debian unstable/main amd64 python3-more-itertools all 10.6.0-1 [65.3 kB] Get: 246 http://deb.debian.org/debian unstable/main amd64 python3-typing-extensions all 4.12.2-2 [73.0 kB] Get: 247 http://deb.debian.org/debian unstable/main amd64 python3-typeguard all 4.4.1-1 [37.0 kB] Get: 248 http://deb.debian.org/debian unstable/main amd64 python3-inflect all 7.3.1-2 [32.4 kB] Get: 249 http://deb.debian.org/debian unstable/main amd64 python3-jaraco.context all 6.0.0-1 [7984 B] Get: 250 http://deb.debian.org/debian unstable/main amd64 python3-jaraco.functools all 4.1.0-1 [12.0 kB] Get: 251 http://deb.debian.org/debian unstable/main amd64 python3-pkg-resources all 75.6.0-1 [222 kB] Get: 252 http://deb.debian.org/debian unstable/main amd64 python3-networkx all 3.2.1-5 [13.0 MB] Get: 253 http://deb.debian.org/debian unstable/main amd64 python3-pysam amd64 0.22.1+ds-2+b2 [4412 kB] Get: 254 http://deb.debian.org/debian unstable/main amd64 python3-pbcore all 2.1.2+dfsg-10 [2831 kB] Get: 255 http://deb.debian.org/debian unstable/main amd64 python3-ujson amd64 5.10.0-1+b3 [25.5 kB] Fetched 227 MB in 6s (38.5 MB/s) Preconfiguring 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Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8 to /lib/x86_64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8.2 to /lib/x86_64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8 to /lib/x86_64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8.2 to /lib/x86_64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:amd64 (8.2-6) ... Selecting previously unselected package libpython3.13-stdlib:amd64. Preparing to unpack .../7-libpython3.13-stdlib_3.13.1-3+b1_amd64.deb ... Unpacking libpython3.13-stdlib:amd64 (3.13.1-3+b1) ... Selecting previously unselected package python3.13. Preparing to unpack .../8-python3.13_3.13.1-3+b1_amd64.deb ... Unpacking python3.13 (3.13.1-3+b1) ... 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Setting up libcurl4-openssl-dev:amd64 (8.11.1-1+b1) ... Setting up libhdf5-hl-cpp-310:amd64 (1.14.5+repack-3) ... Setting up libhdf5-hl-fortran-310:amd64 (1.14.5+repack-3) ... Setting up libhdf5-dev (1.14.5+repack-3) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/pkgconfig/hdf5-serial.pc to provide /usr/lib/x86_64-linux-gnu/pkgconfig/hdf5.pc (hdf5.pc) in auto mode Setting up python3-fonttools (4.55.3-2) ... Setting up python3-ufolib2 (0.17.0+dfsg1-1) ... Setting up python3-matplotlib (3.8.3-3+b3) ... Setting up python3-colormap (1.3.0-1) ... Processing triggers for libc-bin (2.40-6) ... Processing triggers for sgml-base (1.31) ... Setting up w3c-sgml-lib (1.3-3) ... Setting up python3-biopython (1.85+dfsg-1) ... Setting up python3-pbcore (2.1.2+dfsg-10) ... Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/reproducible-path/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 amd64 debian/rules clean dh clean dh_clean debian/rules binary dh binary dh_update_autotools_config dh_autoreconf dh_auto_configure cd obj-x86_64-linux-gnu && DEB_PYTHON_INSTALL_LAYOUT=deb PKG_CONFIG=/usr/bin/pkg-config cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=None -DCMAKE_INSTALL_SYSCONFDIR=/etc -DCMAKE_INSTALL_LOCALSTATEDIR=/var -DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON -DCMAKE_FIND_USE_PACKAGE_REGISTRY=OFF -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON -DFETCHCONTENT_FULLY_DISCONNECTED=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run -DCMAKE_SKIP_INSTALL_ALL_DEPENDENCY=ON "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/x86_64-linux-gnu .. CMake Deprecation Warning at CMakeLists.txt:1 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- The C compiler identification is GNU 14.2.0 -- The CXX compiler identification is GNU 14.2.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/cc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done CMake Deprecation Warning at src/CMakeLists.txt:1 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. CMake Deprecation Warning at src/lib/CMakeLists.txt:1 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- Found ZLIB: /usr/lib/x86_64-linux-gnu/libz.so (found version "1.3.1") CMake Deprecation Warning at src/filter/CMakeLists.txt:1 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. CMake Deprecation Warning at src/maximal/CMakeLists.txt:1 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. CMake Deprecation Warning at src/consensus/CMakeLists.txt:1 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. CMake Deprecation Warning at src/layout/CMakeLists.txt:1 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. CMake Warning (dev) at src/layout/CMakeLists.txt:5 (FIND_PACKAGE): Policy CMP0167 is not set: The FindBoost module is removed. Run "cmake --help-policy CMP0167" for policy details. Use the cmake_policy command to set the policy and suppress this warning. This warning is for project developers. Use -Wno-dev to suppress it. -- Found Boost: /usr/lib/x86_64-linux-gnu/cmake/Boost-1.83.0/BoostConfig.cmake (found version "1.83.0") found components: graph CMake Deprecation Warning at src/test/CMakeLists.txt:1 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- Configuring done (0.5s) 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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/hinge-0.5.0/src/layout/hinging.cpp This warning is for project developers. Use -Wno-dev to suppress it. -- Generating done (0.0s) CMake Warning: Manually-specified variables were not used by the project: CMAKE_EXPORT_NO_PACKAGE_REGISTRY CMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY CMAKE_INSTALL_LIBDIR CMAKE_INSTALL_LOCALSTATEDIR CMAKE_INSTALL_RUNSTATEDIR CMAKE_INSTALL_SYSCONFDIR FETCHCONTENT_FULLY_DISCONNECTED -- Build files have been written to: /build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu dh_auto_build cd obj-x86_64-linux-gnu && make -j42 "INSTALL=install --strip-program=true" VERBOSE=1 make[1]: Entering directory '/build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/hinge-0.5.0 -B/build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu/CMakeFiles /build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu' make -f bin/CMakeFiles/man.dir/build.make bin/CMakeFiles/man.dir/depend make -f bin/lib/CMakeFiles/ini.dir/build.make bin/lib/CMakeFiles/ini.dir/depend make -f bin/lib/CMakeFiles/DB.dir/build.make bin/lib/CMakeFiles/DB.dir/depend make -f bin/lib/CMakeFiles/LA.dir/build.make bin/lib/CMakeFiles/LA.dir/depend make[3]: Entering directory '/build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu' cd /build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hinge-0.5.0 /build/reproducible-path/hinge-0.5.0/src /build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu /build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu/bin /build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu/bin/CMakeFiles/man.dir/DependInfo.cmake "--color=" make -f bin/lib/CMakeFiles/PAF.dir/build.make bin/lib/CMakeFiles/PAF.dir/depend make -f bin/lib/CMakeFiles/kmer_lookup.dir/build.make bin/lib/CMakeFiles/kmer_lookup.dir/depend make[3]: Entering directory '/build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu' cd /build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hinge-0.5.0 /build/reproducible-path/hinge-0.5.0/src/lib /build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu /build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu/bin/lib /build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu/bin/lib/CMakeFiles/DB.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu' cd /build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hinge-0.5.0 /build/reproducible-path/hinge-0.5.0/src/lib /build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu /build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu/bin/lib /build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu/bin/lib/CMakeFiles/ini.dir/DependInfo.cmake "--color=" make -f bin/lib/CMakeFiles/DW_banded.dir/build.make bin/lib/CMakeFiles/DW_banded.dir/depend make[3]: Entering directory '/build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu' cd /build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hinge-0.5.0 /build/reproducible-path/hinge-0.5.0/src/lib /build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu /build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu/bin/lib /build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu/bin/lib/CMakeFiles/LA.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu' cd /build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hinge-0.5.0 /build/reproducible-path/hinge-0.5.0/src/lib /build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu /build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu/bin/lib /build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu/bin/lib/CMakeFiles/PAF.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu' cd /build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hinge-0.5.0 /build/reproducible-path/hinge-0.5.0/src/lib /build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu /build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu/bin/lib /build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu/bin/lib/CMakeFiles/kmer_lookup.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu' cd /build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hinge-0.5.0 /build/reproducible-path/hinge-0.5.0/src/lib /build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu /build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu/bin/lib /build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu/bin/lib/CMakeFiles/DW_banded.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu' make -f bin/lib/CMakeFiles/kmer_lookup.dir/build.make bin/lib/CMakeFiles/kmer_lookup.dir/build make[3]: Leaving directory '/build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu' make -f bin/CMakeFiles/man.dir/build.make bin/CMakeFiles/man.dir/build make[3]: Leaving directory '/build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu' make -f bin/lib/CMakeFiles/ini.dir/build.make bin/lib/CMakeFiles/ini.dir/build make -f bin/lib/CMakeFiles/DB.dir/build.make bin/lib/CMakeFiles/DB.dir/build make -f bin/lib/CMakeFiles/LA.dir/build.make bin/lib/CMakeFiles/LA.dir/build make[3]: Entering directory '/build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu' make -f bin/lib/CMakeFiles/PAF.dir/build.make bin/lib/CMakeFiles/PAF.dir/build make -f bin/lib/CMakeFiles/DW_banded.dir/build.make bin/lib/CMakeFiles/DW_banded.dir/build make[3]: Entering directory '/build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu' [ 13%] Building CXX object bin/lib/CMakeFiles/ini.dir/INIReader.cpp.o [ 13%] Generating hinge.1 [ 13%] Building C object bin/lib/CMakeFiles/ini.dir/ini.c.o [ 17%] Building C object bin/lib/CMakeFiles/LA.dir/align.c.o [ 17%] Building C object bin/lib/CMakeFiles/DB.dir/QV.c.o [ 20%] Building C object bin/lib/CMakeFiles/PAF.dir/paf.c.o [ 27%] Building C object bin/lib/CMakeFiles/DB.dir/DB.c.o [ 27%] Building C object bin/lib/CMakeFiles/kmer_lookup.dir/kmer_lookup.c.o [ 31%] Building C object bin/lib/CMakeFiles/DW_banded.dir/DW_banded.c.o cd /build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu/bin && /usr/bin/pandoc --from markdown --to man -s /build/reproducible-path/hinge-0.5.0/src/hinge.1.md -o hinge.1 cd /build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu/bin/lib && /usr/bin/cc -I/build/reproducible-path/hinge-0.5.0/src/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hinge-0.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/hinge-0.5.0/src/lib/ini.c cd /build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu/bin/lib && /usr/bin/cc -I/build/reproducible-path/hinge-0.5.0/src/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hinge-0.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/hinge-0.5.0/src/lib/QV.c cd /build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu/bin/lib && /usr/bin/cc -I/build/reproducible-path/hinge-0.5.0/src/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hinge-0.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/hinge-0.5.0/src/lib/align.c cd /build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu/bin/lib && /usr/bin/cc -I/build/reproducible-path/hinge-0.5.0/src/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hinge-0.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/hinge-0.5.0/src/lib/paf.c cd /build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu/bin/lib && /usr/bin/c++ -I/build/reproducible-path/hinge-0.5.0/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/hinge-0.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/hinge-0.5.0/src/lib/INIReader.cpp cd /build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu/bin/lib && /usr/bin/cc -I/build/reproducible-path/hinge-0.5.0/src/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hinge-0.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/hinge-0.5.0/src/lib/kmer_lookup.c cd /build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu/bin/lib && /usr/bin/cc -I/build/reproducible-path/hinge-0.5.0/src/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hinge-0.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/hinge-0.5.0/src/lib/DB.c cd /build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu/bin/lib && /usr/bin/cc -I/build/reproducible-path/hinge-0.5.0/src/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hinge-0.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/hinge-0.5.0/src/lib/DW_banded.c make[3]: Leaving directory '/build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu' [ 31%] Built target man /build/reproducible-path/hinge-0.5.0/src/lib/DB.c: In function 'Load_QVs': /build/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu/bin/lib && /usr/bin/cmake -P CMakeFiles/PAF.dir/cmake_clean_target.cmake cd /build/reproducible-path/hinge-0.5.0/obj-x86_64-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 /usr/bin/ranlib libPAF.a make[3]: Leaving directory '/build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu' [ 34%] Built target PAF [ 37%] Linking C static library libDW_banded.a cd /build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu/bin/lib && /usr/bin/cmake -P CMakeFiles/DW_banded.dir/cmake_clean_target.cmake cd /build/reproducible-path/hinge-0.5.0/obj-x86_64-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/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu' [ 37%] Built target DW_banded /build/reproducible-path/hinge-0.5.0/src/lib/DB.c: In function 'Open_DB': /build/reproducible-path/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/reproducible-path/hinge-0.5.0/src/lib/DB.c:525:29: /build/reproducible-path/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/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu/bin/lib && /usr/bin/cmake -P CMakeFiles/kmer_lookup.dir/cmake_clean_target.cmake cd /build/reproducible-path/hinge-0.5.0/obj-x86_64-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/reproducible-path/hinge-0.5.0/obj-x86_64-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/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu' cd /build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hinge-0.5.0 /build/reproducible-path/hinge-0.5.0/src/lib /build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu /build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu/bin/lib /build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu/bin/lib/CMakeFiles/falcon.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu' make -f bin/lib/CMakeFiles/falcon.dir/build.make bin/lib/CMakeFiles/falcon.dir/build make[3]: Entering directory '/build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu' [ 44%] Building C object bin/lib/CMakeFiles/falcon.dir/falcon.c.o cd /build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu/bin/lib && /usr/bin/cc -I/build/reproducible-path/hinge-0.5.0/src/include -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/hinge-0.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/hinge-0.5.0/src/lib/falcon.c [ 48%] Linking C static library libfalcon.a cd /build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu/bin/lib && /usr/bin/cmake -P CMakeFiles/falcon.dir/cmake_clean_target.cmake /build/reproducible-path/hinge-0.5.0/src/lib/DB.c: In function 'Read_All_Sequences': /build/reproducible-path/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/reproducible-path/hinge-0.5.0/src/lib/DB.c:1564:18: /build/reproducible-path/hinge-0.5.0/src/lib/DB.c:84:12: note: returned from 'malloc' 84 | if ((p = malloc(size)) == NULL) | ^~~~~~~~~~~~ cd /build/reproducible-path/hinge-0.5.0/obj-x86_64-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/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu' [ 48%] Built target falcon [ 51%] Linking C static library libDB.a cd /build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu/bin/lib && /usr/bin/cmake -P CMakeFiles/DB.dir/cmake_clean_target.cmake cd /build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu/bin/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/DB.dir/link.txt --verbose=1 [ 55%] Linking CXX static library libini.a cd /build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu/bin/lib && /usr/bin/cmake -P CMakeFiles/ini.dir/cmake_clean_target.cmake cd /build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu/bin/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/ini.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/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu' [ 55%] Built target DB /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/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu' [ 55%] Built target ini [ 58%] Linking C static library libLA.a cd /build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu/bin/lib && /usr/bin/cmake -P CMakeFiles/LA.dir/cmake_clean_target.cmake cd /build/reproducible-path/hinge-0.5.0/obj-x86_64-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/reproducible-path/hinge-0.5.0/obj-x86_64-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/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu' cd /build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hinge-0.5.0 /build/reproducible-path/hinge-0.5.0/src/lib /build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu /build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu/bin/lib /build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu/bin/lib/CMakeFiles/LAInterface.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu' make -f bin/lib/CMakeFiles/LAInterface.dir/build.make bin/lib/CMakeFiles/LAInterface.dir/build make[3]: Entering directory '/build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu' [ 62%] Building CXX object bin/lib/CMakeFiles/LAInterface.dir/LAInterface.cpp.o cd /build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu/bin/lib && /usr/bin/c++ -I/build/reproducible-path/hinge-0.5.0/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/hinge-0.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/hinge-0.5.0/src/lib/LAInterface.cpp /build/reproducible-path/hinge-0.5.0/src/lib/LAInterface.cpp: In member function 'void LAInterface::getOverlapw(std::vector&, int, int)': /build/reproducible-path/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/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu/bin/lib && /usr/bin/cmake -P CMakeFiles/LAInterface.dir/cmake_clean_target.cmake cd /build/reproducible-path/hinge-0.5.0/obj-x86_64-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/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu' [ 65%] Built target LAInterface make -f bin/filter/CMakeFiles/Reads_filter.dir/build.make bin/filter/CMakeFiles/Reads_filter.dir/depend make -f bin/maximal/CMakeFiles/get_maximal_reads.dir/build.make bin/maximal/CMakeFiles/get_maximal_reads.dir/depend make -f bin/consensus/CMakeFiles/draft_assembly.dir/build.make bin/consensus/CMakeFiles/draft_assembly.dir/depend make -f bin/consensus/CMakeFiles/consensus.dir/build.make bin/consensus/CMakeFiles/consensus.dir/depend make[3]: Entering directory '/build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu' cd /build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hinge-0.5.0 /build/reproducible-path/hinge-0.5.0/src/filter /build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu /build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu/bin/filter /build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu/bin/filter/CMakeFiles/Reads_filter.dir/DependInfo.cmake "--color=" make -f bin/layout/CMakeFiles/hinging.dir/build.make bin/layout/CMakeFiles/hinging.dir/depend make[3]: Entering directory '/build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu' cd /build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hinge-0.5.0 /build/reproducible-path/hinge-0.5.0/src/maximal /build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu /build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu/bin/maximal /build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu/bin/maximal/CMakeFiles/get_maximal_reads.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu' cd /build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hinge-0.5.0 /build/reproducible-path/hinge-0.5.0/src/consensus /build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu /build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu/bin/consensus /build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu/bin/consensus/CMakeFiles/draft_assembly.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu' cd /build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hinge-0.5.0 /build/reproducible-path/hinge-0.5.0/src/consensus /build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu /build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu/bin/consensus /build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu/bin/consensus/CMakeFiles/consensus.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu' cd /build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/hinge-0.5.0 /build/reproducible-path/hinge-0.5.0/src/layout /build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu /build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu/bin/layout /build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu/bin/layout/CMakeFiles/hinging.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu' make -f bin/filter/CMakeFiles/Reads_filter.dir/build.make bin/filter/CMakeFiles/Reads_filter.dir/build make[3]: Leaving directory '/build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu' make -f bin/consensus/CMakeFiles/draft_assembly.dir/build.make bin/consensus/CMakeFiles/draft_assembly.dir/build make -f bin/consensus/CMakeFiles/consensus.dir/build.make bin/consensus/CMakeFiles/consensus.dir/build make[3]: Entering directory '/build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu' make -f bin/layout/CMakeFiles/hinging.dir/build.make bin/layout/CMakeFiles/hinging.dir/build make[3]: Entering directory '/build/reproducible-path/hinge-0.5.0/obj-x86_64-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/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu' [ 72%] Building CXX object bin/consensus/CMakeFiles/draft_assembly.dir/draft.cpp.o [ 72%] Building CXX object bin/consensus/CMakeFiles/consensus.dir/consensus.cpp.o [ 75%] Building CXX object bin/filter/CMakeFiles/Reads_filter.dir/filter.cpp.o cd /build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu/bin/consensus && /usr/bin/c++ -DSPDLOG_FMT_EXTERNAL -I/build/reproducible-path/hinge-0.5.0/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/hinge-0.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/hinge-0.5.0/src/consensus/consensus.cpp cd /build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu/bin/consensus && /usr/bin/c++ -DSPDLOG_FMT_EXTERNAL -I/build/reproducible-path/hinge-0.5.0/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/hinge-0.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/hinge-0.5.0/src/consensus/draft.cpp cd /build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu/bin/filter && /usr/bin/c++ -DSPDLOG_FMT_EXTERNAL -I/build/reproducible-path/hinge-0.5.0/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/hinge-0.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/hinge-0.5.0/src/filter/filter.cpp [ 79%] Building CXX object bin/layout/CMakeFiles/hinging.dir/hinging.cpp.o [ 82%] Building CXX object bin/maximal/CMakeFiles/get_maximal_reads.dir/maximal.cpp.o cd /build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu/bin/layout && /usr/bin/c++ -DBOOST_GRAPH_NO_LIB -DBOOST_REGEX_NO_LIB -DSPDLOG_FMT_EXTERNAL -I/build/reproducible-path/hinge-0.5.0/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/hinge-0.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/hinge-0.5.0/src/layout/hinging.cpp cd /build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu/bin/maximal && /usr/bin/c++ -DSPDLOG_FMT_EXTERNAL -I/build/reproducible-path/hinge-0.5.0/src/include -g -O2 -ffile-prefix-map=/build/reproducible-path/hinge-0.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/hinge-0.5.0/src/maximal/maximal.cpp [ 86%] Linking CXX executable consensus cd /build/reproducible-path/hinge-0.5.0/obj-x86_64-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/reproducible-path/hinge-0.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/consensus.dir/link.d 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/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu' [ 86%] Built target consensus [ 89%] Linking CXX executable get_maximal_reads cd /build/reproducible-path/hinge-0.5.0/obj-x86_64-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/reproducible-path/hinge-0.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/get_maximal_reads.dir/link.d 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/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu' [ 89%] Built target get_maximal_reads [ 93%] Linking CXX executable Reads_filter cd /build/reproducible-path/hinge-0.5.0/obj-x86_64-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/reproducible-path/hinge-0.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/Reads_filter.dir/link.d 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/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu' [ 93%] Built target Reads_filter [ 96%] Linking CXX executable draft_assembly cd /build/reproducible-path/hinge-0.5.0/obj-x86_64-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/reproducible-path/hinge-0.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/draft_assembly.dir/link.d 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/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu' [ 96%] Built target draft_assembly [100%] Linking CXX executable hinging cd /build/reproducible-path/hinge-0.5.0/obj-x86_64-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/reproducible-path/hinge-0.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/hinging.dir/link.d CMakeFiles/hinging.dir/hinging.cpp.o -o hinging -lfmt ../lib/libLAInterface.a ../lib/libini.a /usr/lib/x86_64-linux-gnu/libboost_graph.a ../lib/libLA.a ../lib/libDB.a ../lib/libPAF.a -lz /usr/lib/x86_64-linux-gnu/libboost_regex.a -licudata -licui18n -licuuc make[3]: Leaving directory '/build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu' [100%] Built target hinging make[2]: Leaving directory '/build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu/CMakeFiles 0 make[1]: Leaving directory '/build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu' dh_auto_test create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install --destdir=debian/hinge/ cd obj-x86_64-linux-gnu && make -j42 install DESTDIR=/build/reproducible-path/hinge-0.5.0/debian/hinge AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/hinge-0.5.0 -B/build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 preinstall make[2]: Entering directory '/build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu' make[2]: Nothing to be done for 'preinstall'. make[2]: Leaving directory '/build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "None" -- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge -- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/pipeline_consensus_norevcomp.py -- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/random_condensation.py -- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/create_hgraph.py -- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/pruning_and_clipping.py -- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/run_mapping3.py -- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/parse_qv.py -- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/draw_pileup_region.py -- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/draw2_pileup_w_repeat.py -- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/pileup.ipynb -- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/download_NCTC_pipeline.py -- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/condense_graph.py -- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/draw_pileup_region_find_bridges.py -- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/parse_read.py -- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/draft_assembly.py -- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/add_groundtruth_json.py -- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/draw2_pileup_region.py -- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/get_draft_annotation.py -- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/Visualise_graph.py -- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/parse_alignment.py -- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/run_mapping2.py -- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/pipeline_consensus.py -- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/parse.py -- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/condense_graph_with_gt.py -- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/correct_head.py -- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/fasta_to_fastq.py -- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/condense_graph_create_gfa_compute_n50.py -- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/create_bandage_file.py -- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/get_single_strand.py -- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/draw2_pileup.py -- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/merge_hinges.py -- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/interface_utils.py -- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/get_draft_path_norevcomp.py -- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/get_NCTC_json.py -- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/compute_n50_from_draft.py -- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/unitig.py -- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/repeat_annotate_reads.py -- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/condense_graph_annotate_clip_ends.py -- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/longest_path.py -- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/draw2.py -- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/condense_graph_and_annotate.py -- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/clip_ends.py -- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/run_mapping.py -- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/create_hgraph_nogt.py -- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/run_parse_read.py -- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/add_groundtruth.py -- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/connected.py -- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/pruning_and_clipping_nanopore.py -- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/parallel_draw.sh -- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/draft_assembly_not_perfect.py -- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/get_draft_path.py -- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/run_parse_alignment.py -- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/split_las.py -- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/pipeline_nctc.py -- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/parallel_draw_large.sh -- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/get_consensus_gfa.py -- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/share/man/man1/hinge.1 -- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/bin/hinge -- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/Reads_filter -- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/get_maximal_reads -- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/draft_assembly -- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/consensus -- Installing: /build/reproducible-path/hinge-0.5.0/debian/hinge/usr/lib/hinge/hinging make[1]: Leaving directory '/build/reproducible-path/hinge-0.5.0/obj-x86_64-linux-gnu' dh_installdocs dh_installchangelogs debian/rules override_dh_installexamples make[1]: Entering directory '/build/reproducible-path/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/reproducible-path/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-dbgsym' in '../hinge-dbgsym_0.5.0-7_amd64.deb'. dpkg-deb: building package 'hinge' in '../hinge_0.5.0-7_amd64.deb'. dpkg-genbuildinfo --build=binary -O../hinge_0.5.0-7_amd64.buildinfo dpkg-genchanges --build=binary -O../hinge_0.5.0-7_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/493925 and its subdirectories I: Current time: Sat Mar 7 14:11:56 -12 2026 I: pbuilder-time-stamp: 1772935916