I: pbuilder: network access will be disabled during build I: Current time: Tue Dec 28 05:39:33 +14 2021 I: pbuilder-time-stamp: 1640619573 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bullseye-reproducible-base.tgz] I: copying local configuration 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_0.5.0-6.dsc] I: copying [./hinge_0.5.0.orig.tar.gz] I: copying [./hinge_0.5.0-6.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/tmp/dpkg-verify-sig.oIntJ27s/trustedkeys.kbx': General error gpgv: Signature made Fri Mar 20 07:26:36 2020 +14 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./hinge_0.5.0-6.dsc 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_0.5.0-6.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/641354/tmp/hooks/D01_modify_environment starting debug: Running on ionos1-amd64. I: Changing host+domainname to test build reproducibility I: Adding a custom variable just for the fun of it... I: Changing /bin/sh to bash Removing 'diversion of /bin/sh to /bin/sh.distrib by dash' Adding 'diversion of /bin/sh to /bin/sh.distrib by bash' Removing 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by dash' Adding 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by bash' I: Setting pbuilder2's login shell to /bin/bash I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other I: user script /srv/workspace/pbuilder/641354/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/641354/tmp/hooks/D02_print_environment starting I: set BASH=/bin/sh BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:hostcomplete:interactive_comments:progcomp:promptvars:sourcepath BASH_ALIASES=() BASH_ARGC=() BASH_ARGV=() BASH_CMDS=() BASH_LINENO=([0]="12" [1]="0") BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") BASH_VERSINFO=([0]="5" [1]="1" [2]="4" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") BASH_VERSION='5.1.4(1)-release' BUILDDIR=/build BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=amd64 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=15' DIRSTACK=() DISTRIBUTION= EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=x86_64 HOST_ARCH=amd64 IFS=' ' INVOCATION_ID=6d1192de1b3c48378b056bf09afa51c3 LANG=C LANGUAGE=et_EE:et LC_ALL=C MACHTYPE=x86_64-pc-linux-gnu MAIL=/var/mail/root OPTERR=1 OPTIND=1 OSTYPE=linux-gnu PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path PBCURRENTCOMMANDLINEOPERATION=build PBUILDER_OPERATION=build PBUILDER_PKGDATADIR=/usr/share/pbuilder PBUILDER_PKGLIBDIR=/usr/lib/pbuilder PBUILDER_SYSCONFDIR=/etc PIPESTATUS=([0]="0") POSIXLY_CORRECT=y PPID=641354 PS4='+ ' PWD=/ SHELL=/bin/bash SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix SHLVL=3 SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/tmp.KoKOAwD13J/pbuilderrc_74zm --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.KoKOAwD13J/b2 --logfile b2/build.log hinge_0.5.0-6.dsc' SUDO_GID=110 SUDO_UID=105 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://78.137.99.97:3128 I: uname -a Linux i-capture-the-hostname 5.10.0-10-amd64 #1 SMP Debian 5.10.84-1 (2021-12-08) x86_64 GNU/Linux I: ls -l /bin total 5476 -rwxr-xr-x 1 root root 1234376 Aug 5 10:25 bash -rwxr-xr-x 3 root root 38984 Jul 21 2020 bunzip2 -rwxr-xr-x 3 root root 38984 Jul 21 2020 bzcat lrwxrwxrwx 1 root root 6 Jul 21 2020 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2225 Jul 21 2020 bzdiff lrwxrwxrwx 1 root root 6 Jul 21 2020 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4877 Sep 5 2019 bzexe lrwxrwxrwx 1 root root 6 Jul 21 2020 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3775 Jul 21 2020 bzgrep -rwxr-xr-x 3 root root 38984 Jul 21 2020 bzip2 -rwxr-xr-x 1 root root 18424 Jul 21 2020 bzip2recover lrwxrwxrwx 1 root root 6 Jul 21 2020 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Jul 21 2020 bzmore -rwxr-xr-x 1 root root 43936 Sep 24 2020 cat -rwxr-xr-x 1 root root 72672 Sep 24 2020 chgrp -rwxr-xr-x 1 root root 64448 Sep 24 2020 chmod -rwxr-xr-x 1 root root 72672 Sep 24 2020 chown -rwxr-xr-x 1 root root 151168 Sep 24 2020 cp -rwxr-xr-x 1 root root 125560 Dec 11 2020 dash -rwxr-xr-x 1 root root 113664 Sep 24 2020 date -rwxr-xr-x 1 root root 80968 Sep 24 2020 dd -rwxr-xr-x 1 root root 93936 Sep 24 2020 df -rwxr-xr-x 1 root root 147176 Sep 24 2020 dir -rwxr-xr-x 1 root root 84440 Jul 29 09:09 dmesg lrwxrwxrwx 1 root root 8 Nov 8 2019 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Nov 8 2019 domainname -> hostname -rwxr-xr-x 1 root root 39712 Sep 24 2020 echo -rwxr-xr-x 1 root root 28 Nov 10 2020 egrep -rwxr-xr-x 1 root root 39680 Sep 24 2020 false -rwxr-xr-x 1 root root 28 Nov 10 2020 fgrep -rwxr-xr-x 1 root root 69032 Jul 29 09:09 findmnt -rwsr-xr-x 1 root root 34896 Feb 27 2021 fusermount -rwxr-xr-x 1 root root 203072 Nov 10 2020 grep -rwxr-xr-x 2 root root 2346 Mar 3 2021 gunzip -rwxr-xr-x 1 root root 6376 Mar 3 2021 gzexe -rwxr-xr-x 1 root root 98048 Mar 3 2021 gzip -rwxr-xr-x 1 root root 22600 Nov 8 2019 hostname -rwxr-xr-x 1 root root 72840 Sep 24 2020 ln -rwxr-xr-x 1 root root 56952 Feb 8 2020 login -rwxr-xr-x 1 root root 147176 Sep 24 2020 ls -rwxr-xr-x 1 root root 149736 Jul 29 09:09 lsblk -rwxr-xr-x 1 root root 85184 Sep 24 2020 mkdir -rwxr-xr-x 1 root root 76896 Sep 24 2020 mknod -rwxr-xr-x 1 root root 48064 Sep 24 2020 mktemp -rwxr-xr-x 1 root root 59632 Jul 29 09:09 more -rwsr-xr-x 1 root root 55528 Jul 29 09:09 mount -rwxr-xr-x 1 root root 18664 Jul 29 09:09 mountpoint -rwxr-xr-x 1 root root 147080 Sep 24 2020 mv lrwxrwxrwx 1 root root 8 Nov 8 2019 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Apr 19 2021 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 43872 Sep 24 2020 pwd lrwxrwxrwx 1 root root 4 Aug 5 10:25 rbash -> bash -rwxr-xr-x 1 root root 52032 Sep 24 2020 readlink -rwxr-xr-x 1 root root 72704 Sep 24 2020 rm -rwxr-xr-x 1 root root 52032 Sep 24 2020 rmdir -rwxr-xr-x 1 root root 27472 Sep 28 2020 run-parts -rwxr-xr-x 1 root root 122224 Dec 23 2018 sed lrwxrwxrwx 1 root root 4 Dec 28 05:39 sh -> bash lrwxrwxrwx 1 root root 4 Dec 21 23:25 sh.distrib -> dash -rwxr-xr-x 1 root root 43808 Sep 24 2020 sleep -rwxr-xr-x 1 root root 84928 Sep 24 2020 stty -rwsr-xr-x 1 root root 71912 Jul 29 09:09 su -rwxr-xr-x 1 root root 39744 Sep 24 2020 sync -rwxr-xr-x 1 root root 531928 Feb 17 2021 tar -rwxr-xr-x 1 root root 14456 Sep 28 2020 tempfile -rwxr-xr-x 1 root root 101408 Sep 24 2020 touch -rwxr-xr-x 1 root root 39680 Sep 24 2020 true -rwxr-xr-x 1 root root 14328 Feb 27 2021 ulockmgr_server -rwsr-xr-x 1 root root 35040 Jul 29 09:09 umount -rwxr-xr-x 1 root root 39744 Sep 24 2020 uname -rwxr-xr-x 2 root root 2346 Mar 3 2021 uncompress -rwxr-xr-x 1 root root 147176 Sep 24 2020 vdir -rwxr-xr-x 1 root root 63744 Jul 29 09:09 wdctl lrwxrwxrwx 1 root root 8 Nov 8 2019 ypdomainname -> hostname -rwxr-xr-x 1 root root 1984 Mar 3 2021 zcat -rwxr-xr-x 1 root root 1678 Mar 3 2021 zcmp -rwxr-xr-x 1 root root 5880 Mar 3 2021 zdiff -rwxr-xr-x 1 root root 29 Mar 3 2021 zegrep -rwxr-xr-x 1 root root 29 Mar 3 2021 zfgrep -rwxr-xr-x 1 root root 2081 Mar 3 2021 zforce -rwxr-xr-x 1 root root 7585 Mar 3 2021 zgrep -rwxr-xr-x 1 root root 2206 Mar 3 2021 zless -rwxr-xr-x 1 root root 1842 Mar 3 2021 zmore -rwxr-xr-x 1 root root 4553 Mar 3 2021 znew I: user script /srv/workspace/pbuilder/641354/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 (= 12), 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 ... 19655 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 12); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on cmake; however: Package cmake is not installed. pbuilder-satisfydepends-dummy depends on 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} bsdextrautils{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} fonts-lyx{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} libcmark-gfm-extensions0{a} libcmark-gfm0{a} libcurl3-gnutls{a} libcurl4{a} libdebhelper-perl{a} libdeflate0{a} libdouble-conversion3{a} libelf1{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libfmt-dev{a} libfmt7{a} libfreetype6{a} libgfortran5{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} libicu-dev{a} libicu67{a} libimagequant0{a} libjbig0{a} libjpeg-dev{a} libjpeg62-turbo{a} libjpeg62-turbo-dev{a} libjs-jquery{a} libjs-jquery-ui{a} libjsoncpp24{a} liblapack3{a} liblcms2-2{a} libldap-2.4-2{a} libmagic-mgc{a} libmagic1{a} libmd0{a} libmpdec3{a} libncurses6{a} libnghttp2-14{a} libpipeline1{a} libpng16-16{a} libprocps8{a} libpsl5{a} libpython3-stdlib{a} libpython3.9-minimal{a} libpython3.9-stdlib{a} libreadline8{a} librhash0{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsigsegv2{a} libspdlog-dev{a} libspdlog1{a} libssh2-1{a} libsub-override-perl{a} libsz2{a} libtiff5{a} libtool{a} libuchardet0{a} libuv1{a} libwebp6{a} libwebpdemux2{a} libwebpmux3{a} libxau6{a} libxcb1{a} libxdmcp6{a} libxml2{a} m4{a} mailcap{a} man-db{a} media-types{a} mime-support{a} pandoc{a} pandoc-data{a} po-debconf{a} procps{a} python-matplotlib-data{a} python3{a} python3-appdirs{a} python3-biopython{a} python3-colorama{a} python3-colorlog{a} python3-colormap{a} python3-cycler{a} python3-dateutil{a} python3-decorator{a} python3-easydev{a} python3-kiwisolver{a} python3-matplotlib{a} python3-minimal{a} python3-networkx{a} python3-numpy{a} python3-pbcore{a} python3-pexpect{a} python3-pil{a} python3-pkg-resources{a} python3-ptyprocess{a} python3-pyparsing{a} python3-pysam{a} python3-reportlab{a} python3-reportlab-accel{a} python3-six{a} python3-ujson{a} python3.9{a} python3.9-minimal{a} readline-common{a} sensible-utils{a} ttf-bitstream-vera{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: ca-certificates curl javascript-common libarchive-cpio-perl libgpm2 libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules lynx ncbi-blast+ psmisc publicsuffix python-biopython-doc python3-gdal python3-h5py python3-olefile python3-pydot python3-pygraphviz python3-renderpm python3-scipy python3-tk python3-yaml wget 0 packages upgraded, 152 newly installed, 0 to remove and 0 not upgraded. Need to get 108 MB of archives. After unpacking 618 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bullseye/main amd64 bsdextrautils amd64 2.36.1-8 [145 kB] Get: 2 http://deb.debian.org/debian bullseye/main amd64 libuchardet0 amd64 0.0.7-1 [67.8 kB] Get: 3 http://deb.debian.org/debian bullseye/main amd64 groff-base amd64 1.22.4-6 [936 kB] Get: 4 http://deb.debian.org/debian bullseye/main amd64 libpipeline1 amd64 1.5.3-1 [34.3 kB] Get: 5 http://deb.debian.org/debian bullseye/main amd64 man-db amd64 2.9.4-2 [1354 kB] Get: 6 http://deb.debian.org/debian bullseye/main amd64 libpython3.9-minimal amd64 3.9.2-1 [801 kB] Get: 7 http://deb.debian.org/debian bullseye/main amd64 libexpat1 amd64 2.2.10-2 [96.9 kB] Get: 8 http://deb.debian.org/debian bullseye/main amd64 python3.9-minimal amd64 3.9.2-1 [1955 kB] Get: 9 http://deb.debian.org/debian bullseye/main amd64 python3-minimal amd64 3.9.2-3 [38.2 kB] Get: 10 http://deb.debian.org/debian bullseye/main amd64 media-types all 4.0.0 [30.3 kB] Get: 11 http://deb.debian.org/debian bullseye/main amd64 mailcap all 3.69 [31.7 kB] Get: 12 http://deb.debian.org/debian bullseye/main amd64 mime-support all 3.66 [10.9 kB] Get: 13 http://deb.debian.org/debian bullseye/main amd64 libmpdec3 amd64 2.5.1-1 [87.7 kB] Get: 14 http://deb.debian.org/debian bullseye/main amd64 readline-common all 8.1-1 [73.7 kB] Get: 15 http://deb.debian.org/debian bullseye/main amd64 libreadline8 amd64 8.1-1 [169 kB] Get: 16 http://deb.debian.org/debian bullseye/main amd64 libpython3.9-stdlib amd64 3.9.2-1 [1684 kB] Get: 17 http://deb.debian.org/debian bullseye/main amd64 python3.9 amd64 3.9.2-1 [466 kB] Get: 18 http://deb.debian.org/debian bullseye/main amd64 libpython3-stdlib amd64 3.9.2-3 [21.4 kB] Get: 19 http://deb.debian.org/debian bullseye/main amd64 python3 amd64 3.9.2-3 [37.9 kB] Get: 20 http://deb.debian.org/debian bullseye/main amd64 libncurses6 amd64 6.2+20201114-2 [102 kB] Get: 21 http://deb.debian.org/debian bullseye/main amd64 libprocps8 amd64 2:3.3.17-5 [63.9 kB] Get: 22 http://deb.debian.org/debian bullseye/main amd64 procps amd64 2:3.3.17-5 [502 kB] Get: 23 http://deb.debian.org/debian bullseye/main amd64 sensible-utils all 0.0.14 [14.8 kB] Get: 24 http://deb.debian.org/debian bullseye/main amd64 libmagic-mgc amd64 1:5.39-3 [273 kB] Get: 25 http://deb.debian.org/debian bullseye/main amd64 libmagic1 amd64 1:5.39-3 [126 kB] Get: 26 http://deb.debian.org/debian bullseye/main amd64 file amd64 1:5.39-3 [69.1 kB] Get: 27 http://deb.debian.org/debian bullseye/main amd64 gettext-base amd64 0.21-4 [175 kB] Get: 28 http://deb.debian.org/debian bullseye/main amd64 libsigsegv2 amd64 2.13-1 [34.8 kB] Get: 29 http://deb.debian.org/debian bullseye/main amd64 m4 amd64 1.4.18-5 [204 kB] Get: 30 http://deb.debian.org/debian bullseye/main amd64 autoconf all 2.69-14 [313 kB] Get: 31 http://deb.debian.org/debian bullseye/main amd64 autotools-dev all 20180224.1+nmu1 [77.1 kB] Get: 32 http://deb.debian.org/debian bullseye/main amd64 automake all 1:1.16.3-2 [814 kB] Get: 33 http://deb.debian.org/debian bullseye/main amd64 autopoint all 0.21-4 [510 kB] Get: 34 http://deb.debian.org/debian bullseye/main amd64 cmake-data all 3.18.4-2+deb11u1 [1725 kB] Get: 35 http://deb.debian.org/debian bullseye/main amd64 libicu67 amd64 67.1-7 [8622 kB] Get: 36 http://deb.debian.org/debian bullseye/main amd64 libxml2 amd64 2.9.10+dfsg-6.7 [693 kB] Get: 37 http://deb.debian.org/debian bullseye/main amd64 libarchive13 amd64 3.4.3-2+b1 [343 kB] Get: 38 http://deb.debian.org/debian bullseye/main amd64 libbrotli1 amd64 1.0.9-2+b2 [279 kB] Get: 39 http://deb.debian.org/debian bullseye/main amd64 libsasl2-modules-db amd64 2.1.27+dfsg-2.1 [69.1 kB] Get: 40 http://deb.debian.org/debian bullseye/main amd64 libsasl2-2 amd64 2.1.27+dfsg-2.1 [106 kB] Get: 41 http://deb.debian.org/debian bullseye/main amd64 libldap-2.4-2 amd64 2.4.57+dfsg-3 [232 kB] Get: 42 http://deb.debian.org/debian bullseye/main amd64 libnghttp2-14 amd64 1.43.0-1 [77.1 kB] Get: 43 http://deb.debian.org/debian bullseye/main amd64 libpsl5 amd64 0.21.0-1.2 [57.3 kB] Get: 44 http://deb.debian.org/debian bullseye/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b2 [60.8 kB] Get: 45 http://deb.debian.org/debian bullseye/main amd64 libssh2-1 amd64 1.9.0-2 [156 kB] Get: 46 http://deb.debian.org/debian bullseye/main amd64 libcurl4 amd64 7.74.0-1.3+deb11u1 [341 kB] Get: 47 http://deb.debian.org/debian bullseye/main amd64 libjsoncpp24 amd64 1.9.4-4 [78.9 kB] Get: 48 http://deb.debian.org/debian bullseye/main amd64 librhash0 amd64 1.4.1-2 [129 kB] Get: 49 http://deb.debian.org/debian bullseye/main amd64 libuv1 amd64 1.40.0-2 [132 kB] Get: 50 http://deb.debian.org/debian bullseye/main amd64 cmake amd64 3.18.4-2+deb11u1 [5593 kB] Get: 51 http://deb.debian.org/debian bullseye/main amd64 daligner amd64 1.0+git20200727.ed40ce5-3 [205 kB] Get: 52 http://deb.debian.org/debian bullseye/main amd64 dascrubber amd64 1.1-2 [169 kB] Get: 53 http://deb.debian.org/debian bullseye/main amd64 dazzdb amd64 1.0+git20201103.8d98c37-1+deb11u1 [210 kB] Get: 54 http://deb.debian.org/debian bullseye/main amd64 libdebhelper-perl all 13.3.4 [189 kB] Get: 55 http://deb.debian.org/debian bullseye/main amd64 libtool all 2.4.6-15 [513 kB] Get: 56 http://deb.debian.org/debian bullseye/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 57 http://deb.debian.org/debian bullseye/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 58 http://deb.debian.org/debian bullseye/main amd64 libsub-override-perl all 0.09-2 [10.2 kB] Get: 59 http://deb.debian.org/debian bullseye/main amd64 libfile-stripnondeterminism-perl all 1.12.0-1 [26.3 kB] Get: 60 http://deb.debian.org/debian bullseye/main amd64 dh-strip-nondeterminism all 1.12.0-1 [15.4 kB] Get: 61 http://deb.debian.org/debian bullseye/main amd64 libelf1 amd64 0.183-1 [165 kB] Get: 62 http://deb.debian.org/debian bullseye/main amd64 dwz amd64 0.13+20210201-1 [175 kB] Get: 63 http://deb.debian.org/debian bullseye/main amd64 gettext amd64 0.21-4 [1311 kB] Get: 64 http://deb.debian.org/debian bullseye/main amd64 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 65 http://deb.debian.org/debian bullseye/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 66 http://deb.debian.org/debian bullseye/main amd64 debhelper all 13.3.4 [1049 kB] Get: 67 http://deb.debian.org/debian bullseye/main amd64 fonts-lyx all 2.3.6-1 [205 kB] Get: 68 http://deb.debian.org/debian bullseye/main amd64 hdf5-helpers amd64 1.10.6+repack-4+deb11u1 [40.4 kB] Get: 69 http://deb.debian.org/debian bullseye/main amd64 icu-devtools amd64 67.1-7 [201 kB] Get: 70 http://deb.debian.org/debian bullseye/main amd64 libaec0 amd64 1.0.4-1 [20.3 kB] Get: 71 http://deb.debian.org/debian bullseye/main amd64 libsz2 amd64 1.0.4-1 [6760 B] Get: 72 http://deb.debian.org/debian bullseye/main amd64 libaec-dev amd64 1.0.4-1 [18.7 kB] Get: 73 http://deb.debian.org/debian bullseye/main amd64 libblas3 amd64 3.9.0-3 [153 kB] Get: 74 http://deb.debian.org/debian bullseye/main amd64 libboost1.74-dev amd64 1.74.0-9 [9534 kB] Get: 75 http://deb.debian.org/debian bullseye/main amd64 libboost-dev amd64 1.74.0.3 [4548 B] Get: 76 http://deb.debian.org/debian bullseye/main amd64 libboost-regex1.74.0 amd64 1.74.0-9 [516 kB] Get: 77 http://deb.debian.org/debian bullseye/main amd64 libboost-graph1.74.0 amd64 1.74.0-9 [326 kB] Get: 78 http://deb.debian.org/debian bullseye/main amd64 libicu-dev amd64 67.1-7 [9597 kB] Get: 79 http://deb.debian.org/debian bullseye/main amd64 libboost-regex1.74-dev amd64 1.74.0-9 [588 kB] Get: 80 http://deb.debian.org/debian bullseye/main amd64 libboost-serialization1.74.0 amd64 1.74.0-9 [340 kB] Get: 81 http://deb.debian.org/debian bullseye/main amd64 libboost-serialization1.74-dev amd64 1.74.0-9 [383 kB] Get: 82 http://deb.debian.org/debian bullseye/main amd64 libboost-test1.74.0 amd64 1.74.0-9 [472 kB] Get: 83 http://deb.debian.org/debian bullseye/main amd64 libboost-test1.74-dev amd64 1.74.0-9 [547 kB] Get: 84 http://deb.debian.org/debian bullseye/main amd64 libboost-graph1.74-dev amd64 1.74.0-9 [346 kB] Get: 85 http://deb.debian.org/debian bullseye/main amd64 libboost-graph-dev amd64 1.74.0.3 [4436 B] Get: 86 http://deb.debian.org/debian bullseye/main amd64 libmd0 amd64 1.0.3-3 [28.0 kB] Get: 87 http://deb.debian.org/debian bullseye/main amd64 libbsd0 amd64 0.11.3-1 [108 kB] Get: 88 http://deb.debian.org/debian bullseye/main amd64 libcmark-gfm0 amd64 0.29.0.gfm.0-6 [117 kB] Get: 89 http://deb.debian.org/debian bullseye/main amd64 libcmark-gfm-extensions0 amd64 0.29.0.gfm.0-6 [46.1 kB] Get: 90 http://deb.debian.org/debian bullseye/main amd64 libcurl3-gnutls amd64 7.74.0-1.3+deb11u1 [338 kB] Get: 91 http://deb.debian.org/debian bullseye/main amd64 libdeflate0 amd64 1.7-1 [53.1 kB] Get: 92 http://deb.debian.org/debian bullseye/main amd64 libdouble-conversion3 amd64 3.1.5-6.1 [41.0 kB] Get: 93 http://deb.debian.org/debian bullseye/main amd64 libfmt7 amd64 7.1.3+ds1-5 [110 kB] Get: 94 http://deb.debian.org/debian bullseye/main amd64 libfmt-dev amd64 7.1.3+ds1-5 [142 kB] Get: 95 http://deb.debian.org/debian bullseye/main amd64 libpng16-16 amd64 1.6.37-3 [294 kB] Get: 96 http://deb.debian.org/debian bullseye/main amd64 libfreetype6 amd64 2.10.4+dfsg-1 [418 kB] Get: 97 http://deb.debian.org/debian bullseye/main amd64 libgfortran5 amd64 10.2.1-6 [727 kB] Get: 98 http://deb.debian.org/debian bullseye/main amd64 libhdf5-103-1 amd64 1.10.6+repack-4+deb11u1 [1189 kB] Get: 99 http://deb.debian.org/debian bullseye/main amd64 libhdf5-cpp-103-1 amd64 1.10.6+repack-4+deb11u1 [141 kB] Get: 100 http://deb.debian.org/debian bullseye/main amd64 libhdf5-fortran-102 amd64 1.10.6+repack-4+deb11u1 [105 kB] Get: 101 http://deb.debian.org/debian bullseye/main amd64 libhdf5-hl-100 amd64 1.10.6+repack-4+deb11u1 [81.8 kB] Get: 102 http://deb.debian.org/debian bullseye/main amd64 libhdf5-hl-fortran-100 amd64 1.10.6+repack-4+deb11u1 [56.8 kB] Get: 103 http://deb.debian.org/debian bullseye/main amd64 libhdf5-hl-cpp-100 amd64 1.10.6+repack-4+deb11u1 [37.7 kB] Get: 104 http://deb.debian.org/debian bullseye/main amd64 zlib1g-dev amd64 1:1.2.11.dfsg-2 [190 kB] Get: 105 http://deb.debian.org/debian bullseye/main amd64 libjpeg62-turbo amd64 1:2.0.6-4 [151 kB] Get: 106 http://deb.debian.org/debian bullseye/main amd64 libjpeg62-turbo-dev amd64 1:2.0.6-4 [278 kB] Get: 107 http://deb.debian.org/debian bullseye/main amd64 libjpeg-dev amd64 1:2.0.6-4 [67.8 kB] Get: 108 http://deb.debian.org/debian bullseye/main amd64 libhdf5-dev amd64 1.10.6+repack-4+deb11u1 [2438 kB] Get: 109 http://deb.debian.org/debian bullseye/main amd64 libhts3 amd64 1.11-4 [378 kB] Get: 110 http://deb.debian.org/debian bullseye/main amd64 libimagequant0 amd64 2.12.2-1.1 [32.5 kB] Get: 111 http://deb.debian.org/debian bullseye/main amd64 libjbig0 amd64 2.1-3.1+b2 [31.0 kB] Get: 112 http://deb.debian.org/debian bullseye/main amd64 libjs-jquery all 3.5.1+dfsg+~3.5.5-7 [315 kB] Get: 113 http://deb.debian.org/debian bullseye/main amd64 libjs-jquery-ui all 1.12.1+dfsg-8+deb11u1 [232 kB] Get: 114 http://deb.debian.org/debian bullseye/main amd64 liblapack3 amd64 3.9.0-3 [2166 kB] Get: 115 http://deb.debian.org/debian bullseye/main amd64 liblcms2-2 amd64 2.12~rc1-2 [150 kB] Get: 116 http://deb.debian.org/debian bullseye/main amd64 libspdlog1 amd64 1:1.8.1+ds-2.1 [89.7 kB] Get: 117 http://deb.debian.org/debian bullseye/main amd64 libspdlog-dev amd64 1:1.8.1+ds-2.1 [177 kB] Get: 118 http://deb.debian.org/debian bullseye/main amd64 libwebp6 amd64 0.6.1-2.1 [258 kB] Get: 119 http://deb.debian.org/debian bullseye/main amd64 libtiff5 amd64 4.2.0-1 [289 kB] Get: 120 http://deb.debian.org/debian bullseye/main amd64 libwebpdemux2 amd64 0.6.1-2.1 [87.7 kB] Get: 121 http://deb.debian.org/debian bullseye/main amd64 libwebpmux3 amd64 0.6.1-2.1 [97.6 kB] Get: 122 http://deb.debian.org/debian bullseye/main amd64 libxau6 amd64 1:1.0.9-1 [19.7 kB] Get: 123 http://deb.debian.org/debian bullseye/main amd64 libxdmcp6 amd64 1:1.1.2-3 [26.3 kB] Get: 124 http://deb.debian.org/debian bullseye/main amd64 libxcb1 amd64 1.14-3 [140 kB] Get: 125 http://deb.debian.org/debian bullseye/main amd64 pandoc-data all 2.9.2.1-1 [376 kB] Get: 126 http://deb.debian.org/debian bullseye/main amd64 pandoc amd64 2.9.2.1-1+b1 [18.5 MB] Get: 127 http://deb.debian.org/debian bullseye/main amd64 ttf-bitstream-vera all 1.10-8.1 [223 kB] Get: 128 http://deb.debian.org/debian bullseye/main amd64 python-matplotlib-data all 3.3.4-1 [4153 kB] Get: 129 http://deb.debian.org/debian bullseye/main amd64 python3-appdirs all 1.4.4-1 [12.7 kB] Get: 130 http://deb.debian.org/debian bullseye/main amd64 python3-pkg-resources all 52.0.0-4 [190 kB] Get: 131 http://deb.debian.org/debian bullseye/main amd64 python3-numpy amd64 1:1.19.5-1 [2693 kB] Get: 132 http://deb.debian.org/debian bullseye/main amd64 python3-reportlab-accel amd64 3.5.59-2 [39.1 kB] Get: 133 http://deb.debian.org/debian bullseye/main amd64 python3-pil amd64 8.1.2+dfsg-0.3 [445 kB] Get: 134 http://deb.debian.org/debian bullseye/main amd64 python3-reportlab all 3.5.59-2 [575 kB] Get: 135 http://deb.debian.org/debian bullseye/main amd64 python3-biopython amd64 1.78+dfsg-4 [1402 kB] Get: 136 http://deb.debian.org/debian bullseye/main amd64 python3-colorama all 0.4.4-1 [28.5 kB] Get: 137 http://deb.debian.org/debian bullseye/main amd64 python3-colorlog all 4.7.2-1 [25.6 kB] Get: 138 http://deb.debian.org/debian bullseye/main amd64 python3-six all 1.16.0-2 [17.5 kB] Get: 139 http://deb.debian.org/debian bullseye/main amd64 python3-dateutil all 2.8.1-6 [79.2 kB] Get: 140 http://deb.debian.org/debian bullseye/main amd64 python3-pyparsing all 2.4.7-1 [109 kB] Get: 141 http://deb.debian.org/debian bullseye/main amd64 python3-cycler all 0.10.0-3 [8084 B] Get: 142 http://deb.debian.org/debian bullseye/main amd64 python3-kiwisolver amd64 1.3.1-1+b1 [55.7 kB] Get: 143 http://deb.debian.org/debian bullseye/main amd64 python3-matplotlib amd64 3.3.4-1 [4163 kB] Get: 144 http://deb.debian.org/debian bullseye/main amd64 python3-ptyprocess all 0.7.0-1 [13.6 kB] Get: 145 http://deb.debian.org/debian bullseye/main amd64 python3-pexpect all 4.8.0-2 [54.9 kB] Get: 146 http://deb.debian.org/debian bullseye/main amd64 python3-easydev all 0.10.1+dfsg-1 [37.9 kB] Get: 147 http://deb.debian.org/debian bullseye/main amd64 python3-colormap all 1.0.3-1 [15.2 kB] Get: 148 http://deb.debian.org/debian bullseye/main amd64 python3-decorator all 4.4.2-2 [15.8 kB] Get: 149 http://deb.debian.org/debian bullseye/main amd64 python3-networkx all 2.5+ds-2 [900 kB] Get: 150 http://deb.debian.org/debian bullseye/main amd64 python3-pysam amd64 0.15.4+ds-3+b2 [1536 kB] Get: 151 http://deb.debian.org/debian bullseye/main amd64 python3-pbcore all 1.7.1+git20200430.a127b1e+dfsg-1 [2881 kB] Get: 152 http://deb.debian.org/debian bullseye/main amd64 python3-ujson amd64 4.0.2-1 [21.8 kB] Fetched 108 MB in 3s (41.8 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package bsdextrautils. (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 ... 19655 files and directories currently installed.) Preparing to unpack .../0-bsdextrautils_2.36.1-8_amd64.deb ... Unpacking bsdextrautils (2.36.1-8) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../1-libuchardet0_0.0.7-1_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../2-groff-base_1.22.4-6_amd64.deb ... Unpacking groff-base (1.22.4-6) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../3-libpipeline1_1.5.3-1_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.3-1) ... Selecting previously unselected package man-db. Preparing to unpack .../4-man-db_2.9.4-2_amd64.deb ... Unpacking man-db (2.9.4-2) ... Selecting previously unselected package libpython3.9-minimal:amd64. Preparing to unpack .../5-libpython3.9-minimal_3.9.2-1_amd64.deb ... Unpacking libpython3.9-minimal:amd64 (3.9.2-1) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../6-libexpat1_2.2.10-2_amd64.deb ... Unpacking libexpat1:amd64 (2.2.10-2) ... Selecting previously unselected package python3.9-minimal. Preparing to unpack .../7-python3.9-minimal_3.9.2-1_amd64.deb ... Unpacking python3.9-minimal (3.9.2-1) ... Setting up libpython3.9-minimal:amd64 (3.9.2-1) ... Setting up libexpat1:amd64 (2.2.10-2) ... Setting up python3.9-minimal (3.9.2-1) ... 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 ... 20522 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.9.2-3_amd64.deb ... Unpacking python3-minimal (3.9.2-3) ... Selecting previously unselected package media-types. Preparing to unpack .../1-media-types_4.0.0_all.deb ... Unpacking media-types (4.0.0) ... Selecting previously unselected package mailcap. Preparing to unpack .../2-mailcap_3.69_all.deb ... Unpacking mailcap (3.69) ... Selecting previously unselected package mime-support. Preparing to unpack .../3-mime-support_3.66_all.deb ... Unpacking mime-support (3.66) ... Selecting previously unselected package libmpdec3:amd64. Preparing to unpack .../4-libmpdec3_2.5.1-1_amd64.deb ... Unpacking libmpdec3:amd64 (2.5.1-1) ... Selecting previously unselected package readline-common. Preparing to unpack .../5-readline-common_8.1-1_all.deb ... Unpacking readline-common (8.1-1) ... Selecting previously unselected package libreadline8:amd64. Preparing to unpack .../6-libreadline8_8.1-1_amd64.deb ... Unpacking libreadline8:amd64 (8.1-1) ... Selecting previously unselected package libpython3.9-stdlib:amd64. Preparing to unpack .../7-libpython3.9-stdlib_3.9.2-1_amd64.deb ... Unpacking libpython3.9-stdlib:amd64 (3.9.2-1) ... Selecting previously unselected package python3.9. Preparing to unpack .../8-python3.9_3.9.2-1_amd64.deb ... Unpacking python3.9 (3.9.2-1) ... Selecting previously unselected package libpython3-stdlib:amd64. Preparing to unpack .../9-libpython3-stdlib_3.9.2-3_amd64.deb ... Unpacking libpython3-stdlib:amd64 (3.9.2-3) ... Setting up python3-minimal (3.9.2-3) ... 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 ... 20967 files and directories currently installed.) Preparing to unpack .../000-python3_3.9.2-3_amd64.deb ... Unpacking python3 (3.9.2-3) ... Selecting previously unselected package libncurses6:amd64. Preparing to unpack .../001-libncurses6_6.2+20201114-2_amd64.deb ... Unpacking libncurses6:amd64 (6.2+20201114-2) ... Selecting previously unselected package libprocps8:amd64. Preparing to unpack .../002-libprocps8_2%3a3.3.17-5_amd64.deb ... Unpacking libprocps8:amd64 (2:3.3.17-5) ... Selecting previously unselected package procps. Preparing to unpack .../003-procps_2%3a3.3.17-5_amd64.deb ... Unpacking procps (2:3.3.17-5) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../004-sensible-utils_0.0.14_all.deb ... Unpacking sensible-utils (0.0.14) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../005-libmagic-mgc_1%3a5.39-3_amd64.deb ... Unpacking libmagic-mgc (1:5.39-3) ... Selecting previously unselected package libmagic1:amd64. Preparing to unpack .../006-libmagic1_1%3a5.39-3_amd64.deb ... Unpacking libmagic1:amd64 (1:5.39-3) ... 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Building tag database... -> Finished parsing the build-deps I: Building the package hostname: Name or service not known I: Running cd /build/hinge-0.5.0/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../hinge_0.5.0-6_source.changes dpkg-buildpackage: info: source package hinge dpkg-buildpackage: info: source version 0.5.0-6 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 && 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_PACKAGE_NO_PACKAGE_REGISTRY=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/x86_64-linux-gnu .. -- The C compiler identification is GNU 10.2.1 -- The CXX compiler identification is GNU 10.2.1 -- 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/x86_64-linux-gnu/libz.so (found version "1.2.11") -- Found Boost: /usr/lib/x86_64-linux-gnu/cmake/Boost-1.74.0/BoostConfig.cmake (found version "1.74.0") found components: graph -- Configuring done -- Generating done CMake Warning: Manually-specified variables were not used by the project: CMAKE_EXPORT_NO_PACKAGE_REGISTRY CMAKE_INSTALL_LIBDIR CMAKE_INSTALL_LOCALSTATEDIR CMAKE_INSTALL_RUNSTATEDIR CMAKE_INSTALL_SYSCONFDIR -- Build files have been written to: /build/hinge-0.5.0/obj-x86_64-linux-gnu dh_auto_build cd obj-x86_64-linux-gnu && make -j15 "INSTALL=install --strip-program=true" VERBOSE=1 make[1]: Entering directory '/build/hinge-0.5.0/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/hinge-0.5.0 -B/build/hinge-0.5.0/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/hinge-0.5.0/obj-x86_64-linux-gnu/CMakeFiles /build/hinge-0.5.0/obj-x86_64-linux-gnu//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/build/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/DW_banded.dir/build.make bin/lib/CMakeFiles/DW_banded.dir/depend make -f bin/lib/CMakeFiles/DB.dir/build.make bin/lib/CMakeFiles/DB.dir/depend make[3]: Entering directory '/build/hinge-0.5.0/obj-x86_64-linux-gnu' cd /build/hinge-0.5.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hinge-0.5.0 /build/hinge-0.5.0/src /build/hinge-0.5.0/obj-x86_64-linux-gnu /build/hinge-0.5.0/obj-x86_64-linux-gnu/bin /build/hinge-0.5.0/obj-x86_64-linux-gnu/bin/CMakeFiles/man.dir/DependInfo.cmake --color= make -f bin/lib/CMakeFiles/LA.dir/build.make bin/lib/CMakeFiles/LA.dir/depend 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-x86_64-linux-gnu' cd /build/hinge-0.5.0/obj-x86_64-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-x86_64-linux-gnu /build/hinge-0.5.0/obj-x86_64-linux-gnu/bin/lib /build/hinge-0.5.0/obj-x86_64-linux-gnu/bin/lib/CMakeFiles/ini.dir/DependInfo.cmake --color= make -f bin/lib/CMakeFiles/kmer_lookup.dir/build.make bin/lib/CMakeFiles/kmer_lookup.dir/depend make[3]: Entering directory '/build/hinge-0.5.0/obj-x86_64-linux-gnu' cd /build/hinge-0.5.0/obj-x86_64-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-x86_64-linux-gnu /build/hinge-0.5.0/obj-x86_64-linux-gnu/bin/lib /build/hinge-0.5.0/obj-x86_64-linux-gnu/bin/lib/CMakeFiles/DW_banded.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/hinge-0.5.0/obj-x86_64-linux-gnu' cd /build/hinge-0.5.0/obj-x86_64-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-x86_64-linux-gnu /build/hinge-0.5.0/obj-x86_64-linux-gnu/bin/lib /build/hinge-0.5.0/obj-x86_64-linux-gnu/bin/lib/CMakeFiles/DB.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/hinge-0.5.0/obj-x86_64-linux-gnu' cd /build/hinge-0.5.0/obj-x86_64-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-x86_64-linux-gnu /build/hinge-0.5.0/obj-x86_64-linux-gnu/bin/lib /build/hinge-0.5.0/obj-x86_64-linux-gnu/bin/lib/CMakeFiles/LA.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/hinge-0.5.0/obj-x86_64-linux-gnu' cd /build/hinge-0.5.0/obj-x86_64-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-x86_64-linux-gnu /build/hinge-0.5.0/obj-x86_64-linux-gnu/bin/lib /build/hinge-0.5.0/obj-x86_64-linux-gnu/bin/lib/CMakeFiles/PAF.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/hinge-0.5.0/obj-x86_64-linux-gnu' cd /build/hinge-0.5.0/obj-x86_64-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-x86_64-linux-gnu /build/hinge-0.5.0/obj-x86_64-linux-gnu/bin/lib /build/hinge-0.5.0/obj-x86_64-linux-gnu/bin/lib/CMakeFiles/kmer_lookup.dir/DependInfo.cmake --color= Dependee "/build/hinge-0.5.0/obj-x86_64-linux-gnu/bin/lib/CMakeFiles/ini.dir/DependInfo.cmake" is newer than depender "/build/hinge-0.5.0/obj-x86_64-linux-gnu/bin/lib/CMakeFiles/ini.dir/depend.internal". 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Dependee "/build/hinge-0.5.0/obj-x86_64-linux-gnu/bin/lib/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/hinge-0.5.0/obj-x86_64-linux-gnu/bin/lib/CMakeFiles/kmer_lookup.dir/depend.internal". Dependee "/build/hinge-0.5.0/obj-x86_64-linux-gnu/bin/lib/CMakeFiles/PAF.dir/DependInfo.cmake" is newer than depender "/build/hinge-0.5.0/obj-x86_64-linux-gnu/bin/lib/CMakeFiles/PAF.dir/depend.internal". Dependee "/build/hinge-0.5.0/obj-x86_64-linux-gnu/bin/lib/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/hinge-0.5.0/obj-x86_64-linux-gnu/bin/lib/CMakeFiles/PAF.dir/depend.internal". make[3]: Leaving directory '/build/hinge-0.5.0/obj-x86_64-linux-gnu' Scanning dependencies of target DB Dependee "/build/hinge-0.5.0/obj-x86_64-linux-gnu/bin/lib/CMakeFiles/LA.dir/DependInfo.cmake" is newer than depender "/build/hinge-0.5.0/obj-x86_64-linux-gnu/bin/lib/CMakeFiles/LA.dir/depend.internal". Dependee "/build/hinge-0.5.0/obj-x86_64-linux-gnu/bin/lib/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/hinge-0.5.0/obj-x86_64-linux-gnu/bin/lib/CMakeFiles/LA.dir/depend.internal". Scanning dependencies of target kmer_lookup Scanning dependencies of target PAF make[3]: Leaving directory '/build/hinge-0.5.0/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/hinge-0.5.0/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/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[3]: Leaving directory '/build/hinge-0.5.0/obj-x86_64-linux-gnu' make -f bin/CMakeFiles/man.dir/build.make bin/CMakeFiles/man.dir/build make -f bin/lib/CMakeFiles/DW_banded.dir/build.make bin/lib/CMakeFiles/DW_banded.dir/build make -f bin/lib/CMakeFiles/DB.dir/build.make bin/lib/CMakeFiles/DB.dir/build Scanning dependencies of target LA make -f bin/lib/CMakeFiles/PAF.dir/build.make bin/lib/CMakeFiles/PAF.dir/build make -f bin/lib/CMakeFiles/kmer_lookup.dir/build.make bin/lib/CMakeFiles/kmer_lookup.dir/build make[3]: Entering directory '/build/hinge-0.5.0/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/hinge-0.5.0/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/hinge-0.5.0/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/hinge-0.5.0/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/hinge-0.5.0/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/hinge-0.5.0/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/hinge-0.5.0/obj-x86_64-linux-gnu' make -f bin/lib/CMakeFiles/LA.dir/build.make bin/lib/CMakeFiles/LA.dir/build make[3]: Entering directory '/build/hinge-0.5.0/obj-x86_64-linux-gnu' [ 3%] Building C object bin/lib/CMakeFiles/ini.dir/ini.c.o [ 6%] Generating hinge.1 cd /build/hinge-0.5.0/obj-x86_64-linux-gnu/bin/lib && /usr/bin/cc -I/build/hinge-0.5.0/src/include -g -O2 -fdebug-prefix-map=/build/hinge-0.5.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -o CMakeFiles/ini.dir/ini.c.o -c /build/hinge-0.5.0/src/lib/ini.c [ 10%] Building C object bin/lib/CMakeFiles/PAF.dir/paf.c.o [ 13%] Building C object bin/lib/CMakeFiles/DB.dir/QV.c.o [ 20%] Building C object bin/lib/CMakeFiles/kmer_lookup.dir/kmer_lookup.c.o [ 20%] Building C object bin/lib/CMakeFiles/DB.dir/DB.c.o cd /build/hinge-0.5.0/obj-x86_64-linux-gnu/bin && /usr/bin/pandoc --from markdown --to man -s /build/hinge-0.5.0/src/hinge.1.md -o hinge.1 cd /build/hinge-0.5.0/obj-x86_64-linux-gnu/bin/lib && /usr/bin/cc -I/build/hinge-0.5.0/src/include -g -O2 -fdebug-prefix-map=/build/hinge-0.5.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -o CMakeFiles/PAF.dir/paf.c.o -c /build/hinge-0.5.0/src/lib/paf.c [ 24%] Building C object bin/lib/CMakeFiles/LA.dir/align.c.o cd /build/hinge-0.5.0/obj-x86_64-linux-gnu/bin/lib && /usr/bin/cc -I/build/hinge-0.5.0/src/include -g -O2 -fdebug-prefix-map=/build/hinge-0.5.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -o CMakeFiles/DB.dir/DB.c.o -c /build/hinge-0.5.0/src/lib/DB.c cd /build/hinge-0.5.0/obj-x86_64-linux-gnu/bin/lib && /usr/bin/cc -I/build/hinge-0.5.0/src/include -g -O2 -fdebug-prefix-map=/build/hinge-0.5.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -o CMakeFiles/kmer_lookup.dir/kmer_lookup.c.o -c /build/hinge-0.5.0/src/lib/kmer_lookup.c cd /build/hinge-0.5.0/obj-x86_64-linux-gnu/bin/lib && /usr/bin/cc -I/build/hinge-0.5.0/src/include -g -O2 -fdebug-prefix-map=/build/hinge-0.5.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -o CMakeFiles/LA.dir/align.c.o -c /build/hinge-0.5.0/src/lib/align.c cd /build/hinge-0.5.0/obj-x86_64-linux-gnu/bin/lib && /usr/bin/cc -I/build/hinge-0.5.0/src/include -g -O2 -fdebug-prefix-map=/build/hinge-0.5.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -o CMakeFiles/DB.dir/QV.c.o -c /build/hinge-0.5.0/src/lib/QV.c [ 27%] Building C object bin/lib/CMakeFiles/DW_banded.dir/DW_banded.c.o [ 31%] Building CXX object bin/lib/CMakeFiles/ini.dir/INIReader.cpp.o cd /build/hinge-0.5.0/obj-x86_64-linux-gnu/bin/lib && /usr/bin/c++ -I/build/hinge-0.5.0/src/include -g -O2 -fdebug-prefix-map=/build/hinge-0.5.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -fopenmp -o CMakeFiles/ini.dir/INIReader.cpp.o -c /build/hinge-0.5.0/src/lib/INIReader.cpp cd /build/hinge-0.5.0/obj-x86_64-linux-gnu/bin/lib && /usr/bin/cc -I/build/hinge-0.5.0/src/include -g -O2 -fdebug-prefix-map=/build/hinge-0.5.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -o CMakeFiles/DW_banded.dir/DW_banded.c.o -c /build/hinge-0.5.0/src/lib/DW_banded.c make[3]: Leaving directory '/build/hinge-0.5.0/obj-x86_64-linux-gnu' /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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 31%] Built target man [ 34%] Linking C static library libPAF.a cd /build/hinge-0.5.0/obj-x86_64-linux-gnu/bin/lib && /usr/bin/cmake -P CMakeFiles/PAF.dir/cmake_clean_target.cmake /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:542:14: note: in a call to allocation function 'calloc' declared here 542 | 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) ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/hinge-0.5.0/src/lib/kmer_lookup.c:56: /usr/include/stdlib.h:542:14: note: in a call to allocation function 'calloc' declared here 542 | extern void *calloc (size_t __nmemb, size_t __size) | ^~~~~~ cd /build/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/hinge-0.5.0/obj-x86_64-linux-gnu' [ 34%] Built target PAF [ 37%] Linking C static library libDW_banded.a cd /build/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/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/hinge-0.5.0/obj-x86_64-linux-gnu' [ 37%] Built target DW_banded [ 41%] Linking C static library libkmer_lookup.a cd /build/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/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/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/hinge-0.5.0/obj-x86_64-linux-gnu' cd /build/hinge-0.5.0/obj-x86_64-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-x86_64-linux-gnu /build/hinge-0.5.0/obj-x86_64-linux-gnu/bin/lib /build/hinge-0.5.0/obj-x86_64-linux-gnu/bin/lib/CMakeFiles/falcon.dir/DependInfo.cmake --color= Dependee "/build/hinge-0.5.0/obj-x86_64-linux-gnu/bin/lib/CMakeFiles/falcon.dir/DependInfo.cmake" is newer than depender "/build/hinge-0.5.0/obj-x86_64-linux-gnu/bin/lib/CMakeFiles/falcon.dir/depend.internal". Dependee "/build/hinge-0.5.0/obj-x86_64-linux-gnu/bin/lib/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/hinge-0.5.0/obj-x86_64-linux-gnu/bin/lib/CMakeFiles/falcon.dir/depend.internal". Scanning dependencies of target falcon make[3]: Leaving directory '/build/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/hinge-0.5.0/obj-x86_64-linux-gnu' [ 44%] Building C object bin/lib/CMakeFiles/falcon.dir/falcon.c.o cd /build/hinge-0.5.0/obj-x86_64-linux-gnu/bin/lib && /usr/bin/cc -I/build/hinge-0.5.0/src/include -g -O2 -fdebug-prefix-map=/build/hinge-0.5.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -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-x86_64-linux-gnu/bin/lib && /usr/bin/cmake -P CMakeFiles/falcon.dir/cmake_clean_target.cmake cd /build/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/hinge-0.5.0/obj-x86_64-linux-gnu' [ 48%] Built target falcon [ 51%] Linking C static library libDB.a cd /build/hinge-0.5.0/obj-x86_64-linux-gnu/bin/lib && /usr/bin/cmake -P CMakeFiles/DB.dir/cmake_clean_target.cmake cd /build/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 /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-x86_64-linux-gnu' [ 51%] Built target DB [ 55%] Linking CXX static library libini.a cd /build/hinge-0.5.0/obj-x86_64-linux-gnu/bin/lib && /usr/bin/cmake -P CMakeFiles/ini.dir/cmake_clean_target.cmake cd /build/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 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-x86_64-linux-gnu' [ 55%] Built target ini [ 58%] Linking C static library libLA.a cd /build/hinge-0.5.0/obj-x86_64-linux-gnu/bin/lib && /usr/bin/cmake -P CMakeFiles/LA.dir/cmake_clean_target.cmake cd /build/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/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/hinge-0.5.0/obj-x86_64-linux-gnu' cd /build/hinge-0.5.0/obj-x86_64-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-x86_64-linux-gnu /build/hinge-0.5.0/obj-x86_64-linux-gnu/bin/lib /build/hinge-0.5.0/obj-x86_64-linux-gnu/bin/lib/CMakeFiles/LAInterface.dir/DependInfo.cmake --color= Dependee "/build/hinge-0.5.0/obj-x86_64-linux-gnu/bin/lib/CMakeFiles/LAInterface.dir/DependInfo.cmake" is newer than depender "/build/hinge-0.5.0/obj-x86_64-linux-gnu/bin/lib/CMakeFiles/LAInterface.dir/depend.internal". Dependee "/build/hinge-0.5.0/obj-x86_64-linux-gnu/bin/lib/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/hinge-0.5.0/obj-x86_64-linux-gnu/bin/lib/CMakeFiles/LAInterface.dir/depend.internal". Scanning dependencies of target LAInterface make[3]: Leaving directory '/build/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/hinge-0.5.0/obj-x86_64-linux-gnu' [ 62%] Building CXX object bin/lib/CMakeFiles/LAInterface.dir/LAInterface.cpp.o cd /build/hinge-0.5.0/obj-x86_64-linux-gnu/bin/lib && /usr/bin/c++ -I/build/hinge-0.5.0/src/include -g -O2 -fdebug-prefix-map=/build/hinge-0.5.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -fopenmp -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 In file included from /usr/include/string.h:495, from /build/hinge-0.5.0/src/lib/LAInterface.cpp:3: In function 'char* strncpy(char*, const char*, size_t)', inlined from 'int get_id_from_string(const char*)' at /build/hinge-0.5.0/src/lib/LAInterface.cpp:4816:12: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:34: warning: 'char* __builtin___strncpy_chk(char*, const char*, long unsigned int, long unsigned int)' specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/hinge-0.5.0/src/lib/LAInterface.cpp: In function 'int get_id_from_string(const char*)': /build/hinge-0.5.0/src/lib/LAInterface.cpp:4816:33: note: length computed here 4816 | strncpy(substr, sub1, strlen(sub1) - strlen(sub2)); | ~~~~~~^~~~~~ [ 65%] Linking CXX static library libLAInterface.a cd /build/hinge-0.5.0/obj-x86_64-linux-gnu/bin/lib && /usr/bin/cmake -P CMakeFiles/LAInterface.dir/cmake_clean_target.cmake cd /build/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/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[3]: Entering directory '/build/hinge-0.5.0/obj-x86_64-linux-gnu' cd /build/hinge-0.5.0/obj-x86_64-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-x86_64-linux-gnu /build/hinge-0.5.0/obj-x86_64-linux-gnu/bin/filter /build/hinge-0.5.0/obj-x86_64-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-x86_64-linux-gnu' cd /build/hinge-0.5.0/obj-x86_64-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-x86_64-linux-gnu /build/hinge-0.5.0/obj-x86_64-linux-gnu/bin/maximal /build/hinge-0.5.0/obj-x86_64-linux-gnu/bin/maximal/CMakeFiles/get_maximal_reads.dir/DependInfo.cmake --color= make -f bin/consensus/CMakeFiles/consensus.dir/build.make bin/consensus/CMakeFiles/consensus.dir/depend 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-x86_64-linux-gnu' cd /build/hinge-0.5.0/obj-x86_64-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-x86_64-linux-gnu /build/hinge-0.5.0/obj-x86_64-linux-gnu/bin/consensus /build/hinge-0.5.0/obj-x86_64-linux-gnu/bin/consensus/CMakeFiles/consensus.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/hinge-0.5.0/obj-x86_64-linux-gnu' cd /build/hinge-0.5.0/obj-x86_64-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-x86_64-linux-gnu /build/hinge-0.5.0/obj-x86_64-linux-gnu/bin/consensus /build/hinge-0.5.0/obj-x86_64-linux-gnu/bin/consensus/CMakeFiles/draft_assembly.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-x86_64-linux-gnu' cd /build/hinge-0.5.0/obj-x86_64-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-x86_64-linux-gnu /build/hinge-0.5.0/obj-x86_64-linux-gnu/bin/layout /build/hinge-0.5.0/obj-x86_64-linux-gnu/bin/layout/CMakeFiles/hinging.dir/DependInfo.cmake --color= Dependee "/build/hinge-0.5.0/obj-x86_64-linux-gnu/bin/maximal/CMakeFiles/get_maximal_reads.dir/DependInfo.cmake" is newer than depender "/build/hinge-0.5.0/obj-x86_64-linux-gnu/bin/maximal/CMakeFiles/get_maximal_reads.dir/depend.internal". Dependee "/build/hinge-0.5.0/obj-x86_64-linux-gnu/bin/maximal/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/hinge-0.5.0/obj-x86_64-linux-gnu/bin/maximal/CMakeFiles/get_maximal_reads.dir/depend.internal". Scanning dependencies of target get_maximal_reads make[3]: Leaving directory '/build/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 Dependee "/build/hinge-0.5.0/obj-x86_64-linux-gnu/bin/filter/CMakeFiles/Reads_filter.dir/DependInfo.cmake" is newer than depender "/build/hinge-0.5.0/obj-x86_64-linux-gnu/bin/filter/CMakeFiles/Reads_filter.dir/depend.internal". Dependee "/build/hinge-0.5.0/obj-x86_64-linux-gnu/bin/filter/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/hinge-0.5.0/obj-x86_64-linux-gnu/bin/filter/CMakeFiles/Reads_filter.dir/depend.internal". Scanning dependencies of target Reads_filter make[3]: Entering directory '/build/hinge-0.5.0/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/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 Dependee "/build/hinge-0.5.0/obj-x86_64-linux-gnu/bin/consensus/CMakeFiles/draft_assembly.dir/DependInfo.cmake" is newer than depender "/build/hinge-0.5.0/obj-x86_64-linux-gnu/bin/consensus/CMakeFiles/draft_assembly.dir/depend.internal". Dependee "/build/hinge-0.5.0/obj-x86_64-linux-gnu/bin/consensus/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/hinge-0.5.0/obj-x86_64-linux-gnu/bin/consensus/CMakeFiles/draft_assembly.dir/depend.internal". Scanning dependencies of target draft_assembly Dependee "/build/hinge-0.5.0/obj-x86_64-linux-gnu/bin/consensus/CMakeFiles/consensus.dir/DependInfo.cmake" is newer than depender "/build/hinge-0.5.0/obj-x86_64-linux-gnu/bin/consensus/CMakeFiles/consensus.dir/depend.internal". Dependee "/build/hinge-0.5.0/obj-x86_64-linux-gnu/bin/consensus/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/hinge-0.5.0/obj-x86_64-linux-gnu/bin/consensus/CMakeFiles/consensus.dir/depend.internal". Dependee "/build/hinge-0.5.0/obj-x86_64-linux-gnu/bin/layout/CMakeFiles/hinging.dir/DependInfo.cmake" is newer than depender "/build/hinge-0.5.0/obj-x86_64-linux-gnu/bin/layout/CMakeFiles/hinging.dir/depend.internal". Dependee "/build/hinge-0.5.0/obj-x86_64-linux-gnu/bin/layout/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/hinge-0.5.0/obj-x86_64-linux-gnu/bin/layout/CMakeFiles/hinging.dir/depend.internal". make[3]: Leaving directory '/build/hinge-0.5.0/obj-x86_64-linux-gnu' [ 68%] Building CXX object bin/maximal/CMakeFiles/get_maximal_reads.dir/maximal.cpp.o cd /build/hinge-0.5.0/obj-x86_64-linux-gnu/bin/maximal && /usr/bin/c++ -DSPDLOG_FMT_EXTERNAL -I/build/hinge-0.5.0/src/include -g -O2 -fdebug-prefix-map=/build/hinge-0.5.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -fopenmp -o CMakeFiles/get_maximal_reads.dir/maximal.cpp.o -c /build/hinge-0.5.0/src/maximal/maximal.cpp Scanning dependencies of target consensus make[3]: Leaving directory '/build/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[3]: Entering directory '/build/hinge-0.5.0/obj-x86_64-linux-gnu' Scanning dependencies of target hinging make[3]: Leaving directory '/build/hinge-0.5.0/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/hinge-0.5.0/obj-x86_64-linux-gnu' make -f bin/consensus/CMakeFiles/consensus.dir/build.make bin/consensus/CMakeFiles/consensus.dir/build make[3]: Entering directory '/build/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/hinge-0.5.0/obj-x86_64-linux-gnu' [ 72%] Building CXX object bin/filter/CMakeFiles/Reads_filter.dir/filter.cpp.o cd /build/hinge-0.5.0/obj-x86_64-linux-gnu/bin/filter && /usr/bin/c++ -DSPDLOG_FMT_EXTERNAL -I/build/hinge-0.5.0/src/include -g -O2 -fdebug-prefix-map=/build/hinge-0.5.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -fopenmp -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-x86_64-linux-gnu/bin/consensus && /usr/bin/c++ -DSPDLOG_FMT_EXTERNAL -I/build/hinge-0.5.0/src/include -g -O2 -fdebug-prefix-map=/build/hinge-0.5.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -fopenmp -o CMakeFiles/draft_assembly.dir/draft.cpp.o -c /build/hinge-0.5.0/src/consensus/draft.cpp [ 79%] Building CXX object bin/consensus/CMakeFiles/consensus.dir/consensus.cpp.o cd /build/hinge-0.5.0/obj-x86_64-linux-gnu/bin/consensus && /usr/bin/c++ -DSPDLOG_FMT_EXTERNAL -I/build/hinge-0.5.0/src/include -g -O2 -fdebug-prefix-map=/build/hinge-0.5.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -fopenmp -o CMakeFiles/consensus.dir/consensus.cpp.o -c /build/hinge-0.5.0/src/consensus/consensus.cpp [ 82%] Building CXX object bin/layout/CMakeFiles/hinging.dir/hinging.cpp.o cd /build/hinge-0.5.0/obj-x86_64-linux-gnu/bin/layout && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DSPDLOG_FMT_EXTERNAL -I/build/hinge-0.5.0/src/include -g -O2 -fdebug-prefix-map=/build/hinge-0.5.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++11 -fopenmp -o CMakeFiles/hinging.dir/hinging.cpp.o -c /build/hinge-0.5.0/src/layout/hinging.cpp [ 86%] Linking CXX executable consensus cd /build/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 -fdebug-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-x86_64-linux-gnu' [ 86%] Built target consensus [ 89%] Linking CXX executable get_maximal_reads cd /build/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 -fdebug-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-x86_64-linux-gnu' [ 89%] Built target get_maximal_reads [ 93%] Linking CXX executable draft_assembly cd /build/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 -fdebug-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-x86_64-linux-gnu' [ 93%] Built target draft_assembly [ 96%] Linking CXX executable Reads_filter cd /build/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 -fdebug-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-x86_64-linux-gnu' [ 96%] Built target Reads_filter [100%] Linking CXX executable hinging cd /build/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 -fdebug-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/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 make[3]: Leaving directory '/build/hinge-0.5.0/obj-x86_64-linux-gnu' [100%] Built target hinging make[2]: Leaving directory '/build/hinge-0.5.0/obj-x86_64-linux-gnu' /usr/bin/cmake -E cmake_progress_start /build/hinge-0.5.0/obj-x86_64-linux-gnu/CMakeFiles 0 make[1]: Leaving directory '/build/hinge-0.5.0/obj-x86_64-linux-gnu' dh_auto_test create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install cd obj-x86_64-linux-gnu && make -j15 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-x86_64-linux-gnu' /usr/bin/cmake -S/build/hinge-0.5.0 -B/build/hinge-0.5.0/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/hinge-0.5.0/obj-x86_64-linux-gnu/CMakeFiles /build/hinge-0.5.0/obj-x86_64-linux-gnu//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/build/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/DW_banded.dir/build.make bin/lib/CMakeFiles/DW_banded.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/hinge-0.5.0/obj-x86_64-linux-gnu' cd /build/hinge-0.5.0/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hinge-0.5.0 /build/hinge-0.5.0/src /build/hinge-0.5.0/obj-x86_64-linux-gnu /build/hinge-0.5.0/obj-x86_64-linux-gnu/bin /build/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[3]: Entering directory '/build/hinge-0.5.0/obj-x86_64-linux-gnu' cd /build/hinge-0.5.0/obj-x86_64-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-x86_64-linux-gnu /build/hinge-0.5.0/obj-x86_64-linux-gnu/bin/lib /build/hinge-0.5.0/obj-x86_64-linux-gnu/bin/lib/CMakeFiles/ini.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/hinge-0.5.0/obj-x86_64-linux-gnu' cd /build/hinge-0.5.0/obj-x86_64-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-x86_64-linux-gnu /build/hinge-0.5.0/obj-x86_64-linux-gnu/bin/lib /build/hinge-0.5.0/obj-x86_64-linux-gnu/bin/lib/CMakeFiles/DW_banded.dir/DependInfo.cmake --color= make -f bin/lib/CMakeFiles/kmer_lookup.dir/build.make bin/lib/CMakeFiles/kmer_lookup.dir/depend make[3]: Entering directory '/build/hinge-0.5.0/obj-x86_64-linux-gnu' cd /build/hinge-0.5.0/obj-x86_64-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-x86_64-linux-gnu /build/hinge-0.5.0/obj-x86_64-linux-gnu/bin/lib /build/hinge-0.5.0/obj-x86_64-linux-gnu/bin/lib/CMakeFiles/DB.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/hinge-0.5.0/obj-x86_64-linux-gnu' cd /build/hinge-0.5.0/obj-x86_64-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-x86_64-linux-gnu /build/hinge-0.5.0/obj-x86_64-linux-gnu/bin/lib /build/hinge-0.5.0/obj-x86_64-linux-gnu/bin/lib/CMakeFiles/LA.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/hinge-0.5.0/obj-x86_64-linux-gnu' cd /build/hinge-0.5.0/obj-x86_64-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-x86_64-linux-gnu /build/hinge-0.5.0/obj-x86_64-linux-gnu/bin/lib /build/hinge-0.5.0/obj-x86_64-linux-gnu/bin/lib/CMakeFiles/PAF.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/hinge-0.5.0/obj-x86_64-linux-gnu' cd /build/hinge-0.5.0/obj-x86_64-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-x86_64-linux-gnu /build/hinge-0.5.0/obj-x86_64-linux-gnu/bin/lib /build/hinge-0.5.0/obj-x86_64-linux-gnu/bin/lib/CMakeFiles/kmer_lookup.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/hinge-0.5.0/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/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[3]: Leaving directory '/build/hinge-0.5.0/obj-x86_64-linux-gnu' make -f bin/lib/CMakeFiles/LA.dir/build.make bin/lib/CMakeFiles/LA.dir/build make -f bin/lib/CMakeFiles/PAF.dir/build.make bin/lib/CMakeFiles/PAF.dir/build make[3]: Leaving directory '/build/hinge-0.5.0/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/hinge-0.5.0/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/hinge-0.5.0/obj-x86_64-linux-gnu' make -f bin/lib/CMakeFiles/DB.dir/build.make bin/lib/CMakeFiles/DB.dir/build make[3]: Entering directory '/build/hinge-0.5.0/obj-x86_64-linux-gnu' make[3]: Nothing to be done for 'bin/lib/CMakeFiles/ini.dir/build'. make[3]: Leaving directory '/build/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/hinge-0.5.0/obj-x86_64-linux-gnu' make -f bin/lib/CMakeFiles/DW_banded.dir/build.make bin/lib/CMakeFiles/DW_banded.dir/build make -f bin/lib/CMakeFiles/kmer_lookup.dir/build.make bin/lib/CMakeFiles/kmer_lookup.dir/build make[3]: Entering directory '/build/hinge-0.5.0/obj-x86_64-linux-gnu' make[3]: Nothing to be done for 'bin/lib/CMakeFiles/LA.dir/build'. make[3]: Leaving directory '/build/hinge-0.5.0/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/hinge-0.5.0/obj-x86_64-linux-gnu' make[3]: Nothing to be done for 'bin/lib/CMakeFiles/PAF.dir/build'. make[3]: Leaving directory '/build/hinge-0.5.0/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/hinge-0.5.0/obj-x86_64-linux-gnu' make[3]: Nothing to be done for 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directory '/build/hinge-0.5.0/obj-x86_64-linux-gnu' cd /build/hinge-0.5.0/obj-x86_64-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-x86_64-linux-gnu /build/hinge-0.5.0/obj-x86_64-linux-gnu/bin/lib /build/hinge-0.5.0/obj-x86_64-linux-gnu/bin/lib/CMakeFiles/falcon.dir/DependInfo.cmake --color= 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-x86_64-linux-gnu' cd /build/hinge-0.5.0/obj-x86_64-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-x86_64-linux-gnu /build/hinge-0.5.0/obj-x86_64-linux-gnu/bin/lib /build/hinge-0.5.0/obj-x86_64-linux-gnu/bin/lib/CMakeFiles/LAInterface.dir/DependInfo.cmake --color= [ 51%] Built target man make[3]: Leaving directory '/build/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]: Leaving directory '/build/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/hinge-0.5.0/obj-x86_64-linux-gnu' make[3]: Nothing to be done for 'bin/lib/CMakeFiles/LAInterface.dir/build'. make[3]: Leaving directory '/build/hinge-0.5.0/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/hinge-0.5.0/obj-x86_64-linux-gnu' make[3]: Nothing to be done for 'bin/lib/CMakeFiles/falcon.dir/build'. make[3]: Leaving directory '/build/hinge-0.5.0/obj-x86_64-linux-gnu' [ 58%] Built target LAInterface make -f bin/filter/CMakeFiles/Reads_filter.dir/build.make bin/filter/CMakeFiles/Reads_filter.dir/depend [ 65%] Built target falcon make -f bin/maximal/CMakeFiles/get_maximal_reads.dir/build.make bin/maximal/CMakeFiles/get_maximal_reads.dir/depend 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-x86_64-linux-gnu' cd /build/hinge-0.5.0/obj-x86_64-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-x86_64-linux-gnu /build/hinge-0.5.0/obj-x86_64-linux-gnu/bin/filter /build/hinge-0.5.0/obj-x86_64-linux-gnu/bin/filter/CMakeFiles/Reads_filter.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-x86_64-linux-gnu' cd /build/hinge-0.5.0/obj-x86_64-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-x86_64-linux-gnu /build/hinge-0.5.0/obj-x86_64-linux-gnu/bin/maximal /build/hinge-0.5.0/obj-x86_64-linux-gnu/bin/maximal/CMakeFiles/get_maximal_reads.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/hinge-0.5.0/obj-x86_64-linux-gnu' cd /build/hinge-0.5.0/obj-x86_64-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-x86_64-linux-gnu /build/hinge-0.5.0/obj-x86_64-linux-gnu/bin/layout /build/hinge-0.5.0/obj-x86_64-linux-gnu/bin/layout/CMakeFiles/hinging.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/hinge-0.5.0/obj-x86_64-linux-gnu' cd /build/hinge-0.5.0/obj-x86_64-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-x86_64-linux-gnu /build/hinge-0.5.0/obj-x86_64-linux-gnu/bin/consensus /build/hinge-0.5.0/obj-x86_64-linux-gnu/bin/consensus/CMakeFiles/consensus.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-x86_64-linux-gnu' cd /build/hinge-0.5.0/obj-x86_64-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-x86_64-linux-gnu /build/hinge-0.5.0/obj-x86_64-linux-gnu/bin/consensus /build/hinge-0.5.0/obj-x86_64-linux-gnu/bin/consensus/CMakeFiles/draft_assembly.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/hinge-0.5.0/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/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 -f bin/filter/CMakeFiles/Reads_filter.dir/build.make bin/filter/CMakeFiles/Reads_filter.dir/build make[3]: Leaving directory '/build/hinge-0.5.0/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/hinge-0.5.0/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/hinge-0.5.0/obj-x86_64-linux-gnu' make[3]: Nothing to be done for 'bin/maximal/CMakeFiles/get_maximal_reads.dir/build'. make[3]: Leaving directory '/build/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 -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-x86_64-linux-gnu' make[3]: Nothing to be done for 'bin/filter/CMakeFiles/Reads_filter.dir/build'. make[3]: Leaving directory '/build/hinge-0.5.0/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/hinge-0.5.0/obj-x86_64-linux-gnu' make -f bin/consensus/CMakeFiles/consensus.dir/build.make bin/consensus/CMakeFiles/consensus.dir/build make[3]: Entering directory '/build/hinge-0.5.0/obj-x86_64-linux-gnu' make[3]: Nothing to be done for 'bin/layout/CMakeFiles/hinging.dir/build'. make[3]: Leaving directory '/build/hinge-0.5.0/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/hinge-0.5.0/obj-x86_64-linux-gnu' make[3]: Nothing to be done for 'bin/consensus/CMakeFiles/draft_assembly.dir/build'. make[3]: Leaving directory '/build/hinge-0.5.0/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/hinge-0.5.0/obj-x86_64-linux-gnu' make[3]: Nothing to be done for 'bin/consensus/CMakeFiles/consensus.dir/build'. make[3]: Leaving directory '/build/hinge-0.5.0/obj-x86_64-linux-gnu' [ 72%] Built target hinging [ 86%] Built target draft_assembly [ 86%] Built target get_maximal_reads [ 93%] Built target Reads_filter [100%] Built target consensus make[2]: Leaving directory '/build/hinge-0.5.0/obj-x86_64-linux-gnu' /usr/bin/cmake -E cmake_progress_start /build/hinge-0.5.0/obj-x86_64-linux-gnu/CMakeFiles 0 make -f CMakeFiles/Makefile2 preinstall make[2]: Entering directory '/build/hinge-0.5.0/obj-x86_64-linux-gnu' make[2]: Nothing to be done for 'preinstall'. make[2]: Leaving directory '/build/hinge-0.5.0/obj-x86_64-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-x86_64-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 dh_strip dh_makeshlibs dh_shlibdeps dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'hinge' in '../hinge_0.5.0-6_amd64.deb'. dpkg-deb: building package 'hinge-dbgsym' in '../hinge-dbgsym_0.5.0-6_amd64.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../hinge_0.5.0-6_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: user script /srv/workspace/pbuilder/641354/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/641354/tmp/hooks/B01_cleanup finished I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/641354 and its subdirectories I: Current time: Tue Dec 28 05:42:19 +14 2021 I: pbuilder-time-stamp: 1640619739