I: pbuilder: network access will be disabled during build I: Current time: Wed Jul 28 17:26:48 +14 2021 I: pbuilder-time-stamp: 1627442808 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 [discosnp_4.4.4-1.dsc] I: copying [./discosnp_4.4.4.orig.tar.gz] I: copying [./discosnp_4.4.4-1.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/tmp/dpkg-verify-sig.ZXj534_A/trustedkeys.kbx': General error gpgv: Signature made Fri Oct 2 02:57:13 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 ./discosnp_4.4.4-1.dsc dpkg-source: info: extracting discosnp in discosnp-4.4.4 dpkg-source: info: unpacking discosnp_4.4.4.orig.tar.gz dpkg-source: info: unpacking discosnp_4.4.4-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying use_debian_packaged_gatb-core.patch dpkg-source: info: applying no_install_to_wrong_dir.patch dpkg-source: info: applying path_to_readme_file_names.patch dpkg-source: info: applying spelling.patch dpkg-source: info: applying adapt_test_scripts.patch dpkg-source: info: applying 2to3.patch dpkg-source: info: applying shell_syntax.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/1640/tmp/hooks/D01_modify_environment starting debug: Running on codethink12-arm64. I: Changing host+domainname to test build reproducibility I: Adding a custom variable just for the fun of it... I: Changing /bin/sh to bash 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/1640/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/1640/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]="aarch64-unknown-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=arm64 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=8' DIRSTACK=() DISTRIBUTION= EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/var/lib/jenkins HOSTNAME=i-capture-the-hostname HOSTTYPE=aarch64 HOST_ARCH=arm64 IFS=' ' LANG=C LANGUAGE=nl_BE:nl LC_ALL=C MACHTYPE=aarch64-unknown-linux-gnu MAIL=/var/mail/root OPTERR=1 OPTIND=1 OSTYPE=linux-gnu PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path PBCURRENTCOMMANDLINEOPERATION=build PBUILDER_OPERATION=build PBUILDER_PKGDATADIR=/usr/share/pbuilder PBUILDER_PKGLIBDIR=/usr/lib/pbuilder PBUILDER_SYSCONFDIR=/etc PIPESTATUS=([0]="0") POSIXLY_CORRECT=y PPID=1640 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.aSuJDEWlXj/pbuilderrc_RmLZ --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.aSuJDEWlXj/b2 --logfile b2/build.log --extrapackages usrmerge discosnp_4.4.4-1.dsc' SUDO_GID=117 SUDO_UID=110 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root USERNAME=root _='I: set' http_proxy=http://192.168.101.16:3128 I: uname -a Linux i-capture-the-hostname 4.15.0-151-generic #157-Ubuntu SMP Fri Jul 9 21:03:48 UTC 2021 aarch64 GNU/Linux I: ls -l /bin total 5252 -rwxr-xr-x 1 root root 1282512 Jun 22 16:26 bash -rwxr-xr-x 3 root root 34808 Jul 21 2020 bunzip2 -rwxr-xr-x 3 root root 34808 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 34808 Jul 21 2020 bzip2 -rwxr-xr-x 1 root root 14264 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 39832 Sep 23 2020 cat -rwxr-xr-x 1 root root 64512 Sep 23 2020 chgrp -rwxr-xr-x 1 root root 60368 Sep 23 2020 chmod -rwxr-xr-x 1 root root 64528 Sep 23 2020 chown -rwxr-xr-x 1 root root 138896 Sep 23 2020 cp -rwxr-xr-x 1 root root 129544 Dec 11 2020 dash -rwxr-xr-x 1 root root 101384 Sep 23 2020 date -rwxr-xr-x 1 root root 80984 Sep 23 2020 dd -rwxr-xr-x 1 root root 89824 Sep 23 2020 df -rwxr-xr-x 1 root root 143088 Sep 23 2020 dir -rwxr-xr-x 1 root root 76152 Feb 8 04:38 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 35632 Sep 23 2020 echo -rwxr-xr-x 1 root root 28 Nov 10 2020 egrep -rwxr-xr-x 1 root root 31512 Sep 23 2020 false -rwxr-xr-x 1 root root 28 Nov 10 2020 fgrep -rwxr-xr-x 1 root root 64856 Feb 8 04:38 findmnt -rwsr-xr-x 1 root root 34824 Feb 27 06:12 fusermount -rwxr-xr-x 1 root root 178400 Nov 10 2020 grep -rwxr-xr-x 2 root root 2346 Mar 3 13:30 gunzip -rwxr-xr-x 1 root root 6376 Mar 3 13:30 gzexe -rwxr-xr-x 1 root root 93744 Mar 3 13:30 gzip -rwxr-xr-x 1 root root 18440 Nov 8 2019 hostname -rwxr-xr-x 1 root root 68720 Sep 23 2020 ln -rwxr-xr-x 1 root root 52720 Feb 8 2020 login -rwxr-xr-x 1 root root 143088 Sep 23 2020 ls -rwxr-xr-x 1 root root 161960 Feb 8 04:38 lsblk -rwxr-xr-x 1 root root 85200 Sep 23 2020 mkdir -rwxr-xr-x 1 root root 68744 Sep 23 2020 mknod -rwxr-xr-x 1 root root 43976 Sep 23 2020 mktemp -rwxr-xr-x 1 root root 51368 Feb 8 04:38 more -rwsr-xr-x 1 root root 51360 Feb 8 04:38 mount -rwxr-xr-x 1 root root 14496 Feb 8 04:38 mountpoint -rwxr-xr-x 1 root root 134808 Sep 23 2020 mv lrwxrwxrwx 1 root root 8 Nov 8 2019 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Apr 19 05:38 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 35720 Sep 23 2020 pwd lrwxrwxrwx 1 root root 4 Jun 22 16:26 rbash -> bash -rwxr-xr-x 1 root root 43872 Sep 23 2020 readlink -rwxr-xr-x 1 root root 68592 Sep 23 2020 rm -rwxr-xr-x 1 root root 43880 Sep 23 2020 rmdir -rwxr-xr-x 1 root root 19208 Sep 28 2020 run-parts -rwxr-xr-x 1 root root 114016 Dec 23 2018 sed lrwxrwxrwx 1 root root 4 Jul 28 17:27 sh -> bash lrwxrwxrwx 1 root root 4 Jul 27 23:25 sh.distrib -> dash -rwxr-xr-x 1 root root 35656 Sep 23 2020 sleep -rwxr-xr-x 1 root root 72640 Sep 23 2020 stty -rwsr-xr-x 1 root root 67776 Feb 8 04:38 su -rwxr-xr-x 1 root root 35672 Sep 23 2020 sync -rwxr-xr-x 1 root root 535768 Feb 17 23:55 tar -rwxr-xr-x 1 root root 10568 Sep 28 2020 tempfile -rwxr-xr-x 1 root root 89120 Sep 23 2020 touch -rwxr-xr-x 1 root root 31512 Sep 23 2020 true -rwxr-xr-x 1 root root 14264 Feb 27 06:12 ulockmgr_server -rwsr-xr-x 1 root root 30880 Feb 8 04:38 umount -rwxr-xr-x 1 root root 35640 Sep 23 2020 uname -rwxr-xr-x 2 root root 2346 Mar 3 13:30 uncompress -rwxr-xr-x 1 root root 143088 Sep 23 2020 vdir -rwxr-xr-x 1 root root 59584 Feb 8 04:38 wdctl lrwxrwxrwx 1 root root 8 Nov 8 2019 ypdomainname -> hostname -rwxr-xr-x 1 root root 1984 Mar 3 13:30 zcat -rwxr-xr-x 1 root root 1678 Mar 3 13:30 zcmp -rwxr-xr-x 1 root root 5880 Mar 3 13:30 zdiff -rwxr-xr-x 1 root root 29 Mar 3 13:30 zegrep -rwxr-xr-x 1 root root 29 Mar 3 13:30 zfgrep -rwxr-xr-x 1 root root 2081 Mar 3 13:30 zforce -rwxr-xr-x 1 root root 7585 Mar 3 13:30 zgrep -rwxr-xr-x 1 root root 2206 Mar 3 13:30 zless -rwxr-xr-x 1 root root 1842 Mar 3 13:30 zmore -rwxr-xr-x 1 root root 4553 Mar 3 13:30 znew I: user script /srv/workspace/pbuilder/1640/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: arm64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), dh-python, python3, cmake, libgatbcore-dev, libboost-dev, libhdf5-dev, zlib1g-dev dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19646 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 dh-python; however: Package dh-python is not installed. pbuilder-satisfydepends-dummy depends on python3; however: Package python3 is not installed. pbuilder-satisfydepends-dummy depends on cmake; however: Package cmake is not installed. pbuilder-satisfydepends-dummy depends on libgatbcore-dev; however: Package libgatbcore-dev is not installed. pbuilder-satisfydepends-dummy depends on libboost-dev; however: Package libboost-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. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} cmake{a} cmake-data{a} debhelper{a} dh-autoreconf{a} dh-python{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} hdf5-helpers{a} intltool-debian{a} libaec-dev{a} libaec0{a} libarchive-zip-perl{a} libarchive13{a} libboost-dev{a} libboost1.74-dev{a} libbrotli1{a} libcurl4{a} libdebhelper-perl{a} libelf1{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libgatbcore-dev{a} libgatbcore3{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} libicu67{a} libjpeg-dev{a} libjpeg62-turbo{a} libjpeg62-turbo-dev{a} libjsoncpp24{a} libldap-2.4-2{a} libmagic-mgc{a} libmagic1{a} libmpdec3{a} libncurses6{a} libnghttp2-14{a} libpipeline1{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} libssh2-1{a} libsub-override-perl{a} libsz2{a} libtool{a} libuchardet0{a} libuv1{a} libxml2{a} m4{a} man-db{a} media-types{a} po-debconf{a} procps{a} python3{a} python3-distutils{a} python3-lib2to3{a} python3-minimal{a} python3.9{a} python3.9-minimal{a} readline-common{a} sensible-utils{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: ca-certificates curl libarchive-cpio-perl libgpm2 libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules lynx psmisc publicsuffix wget 0 packages upgraded, 84 newly installed, 0 to remove and 0 not upgraded. Need to get 51.8 MB of archives. After unpacking 381 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bullseye/main arm64 bsdextrautils arm64 2.36.1-7 [141 kB] Get: 2 http://deb.debian.org/debian bullseye/main arm64 libuchardet0 arm64 0.0.7-1 [67.9 kB] Get: 3 http://deb.debian.org/debian bullseye/main arm64 groff-base arm64 1.22.4-6 [883 kB] Get: 4 http://deb.debian.org/debian bullseye/main arm64 libpipeline1 arm64 1.5.3-1 [33.0 kB] Get: 5 http://deb.debian.org/debian bullseye/main arm64 man-db arm64 2.9.4-2 [1336 kB] Get: 6 http://deb.debian.org/debian bullseye/main arm64 libpython3.9-minimal arm64 3.9.2-1 [797 kB] Get: 7 http://deb.debian.org/debian bullseye/main arm64 libexpat1 arm64 2.2.10-2 [83.1 kB] Get: 8 http://deb.debian.org/debian bullseye/main arm64 python3.9-minimal arm64 3.9.2-1 [1884 kB] Get: 9 http://deb.debian.org/debian bullseye/main arm64 python3-minimal arm64 3.9.2-3 [38.2 kB] Get: 10 http://deb.debian.org/debian bullseye/main arm64 media-types all 4.0.0 [30.3 kB] Get: 11 http://deb.debian.org/debian bullseye/main arm64 libmpdec3 arm64 2.5.1-1 [84.4 kB] Get: 12 http://deb.debian.org/debian bullseye/main arm64 readline-common all 8.1-1 [73.7 kB] Get: 13 http://deb.debian.org/debian bullseye/main arm64 libreadline8 arm64 8.1-1 [160 kB] Get: 14 http://deb.debian.org/debian bullseye/main arm64 libpython3.9-stdlib arm64 3.9.2-1 [1658 kB] Get: 15 http://deb.debian.org/debian bullseye/main arm64 python3.9 arm64 3.9.2-1 [466 kB] Get: 16 http://deb.debian.org/debian bullseye/main arm64 libpython3-stdlib arm64 3.9.2-3 [21.4 kB] Get: 17 http://deb.debian.org/debian bullseye/main arm64 python3 arm64 3.9.2-3 [37.9 kB] Get: 18 http://deb.debian.org/debian bullseye/main arm64 libncurses6 arm64 6.2+20201114-2 [93.2 kB] Get: 19 http://deb.debian.org/debian bullseye/main arm64 libprocps8 arm64 2:3.3.17-5 [61.9 kB] Get: 20 http://deb.debian.org/debian bullseye/main arm64 procps arm64 2:3.3.17-5 [497 kB] Get: 21 http://deb.debian.org/debian bullseye/main arm64 sensible-utils all 0.0.14 [14.8 kB] Get: 22 http://deb.debian.org/debian bullseye/main arm64 libmagic-mgc arm64 1:5.39-3 [273 kB] Get: 23 http://deb.debian.org/debian bullseye/main arm64 libmagic1 arm64 1:5.39-3 [121 kB] Get: 24 http://deb.debian.org/debian bullseye/main arm64 file arm64 1:5.39-3 [69.1 kB] Get: 25 http://deb.debian.org/debian bullseye/main arm64 gettext-base arm64 0.21-4 [173 kB] Get: 26 http://deb.debian.org/debian bullseye/main arm64 libsigsegv2 arm64 2.13-1 [34.7 kB] Get: 27 http://deb.debian.org/debian bullseye/main arm64 m4 arm64 1.4.18-5 [199 kB] Get: 28 http://deb.debian.org/debian bullseye/main arm64 autoconf all 2.69-14 [313 kB] Get: 29 http://deb.debian.org/debian bullseye/main arm64 autotools-dev all 20180224.1+nmu1 [77.1 kB] Get: 30 http://deb.debian.org/debian bullseye/main arm64 automake all 1:1.16.3-2 [814 kB] Get: 31 http://deb.debian.org/debian bullseye/main arm64 autopoint all 0.21-4 [510 kB] Get: 32 http://deb.debian.org/debian bullseye/main arm64 cmake-data all 3.18.4-2 [1725 kB] Get: 33 http://deb.debian.org/debian bullseye/main arm64 libicu67 arm64 67.1-7 [8467 kB] Get: 34 http://deb.debian.org/debian bullseye/main arm64 libxml2 arm64 2.9.10+dfsg-6.7 [629 kB] Get: 35 http://deb.debian.org/debian bullseye/main arm64 libarchive13 arm64 3.4.3-2+b1 [320 kB] Get: 36 http://deb.debian.org/debian bullseye/main arm64 libbrotli1 arm64 1.0.9-2+b2 [267 kB] Get: 37 http://deb.debian.org/debian bullseye/main arm64 libsasl2-modules-db arm64 2.1.27+dfsg-2.1 [69.3 kB] Get: 38 http://deb.debian.org/debian bullseye/main arm64 libsasl2-2 arm64 2.1.27+dfsg-2.1 [105 kB] Get: 39 http://deb.debian.org/debian bullseye/main arm64 libldap-2.4-2 arm64 2.4.57+dfsg-3 [222 kB] Get: 40 http://deb.debian.org/debian bullseye/main arm64 libnghttp2-14 arm64 1.43.0-1 [73.8 kB] Get: 41 http://deb.debian.org/debian bullseye/main arm64 libpsl5 arm64 0.21.0-1.2 [57.1 kB] Get: 42 http://deb.debian.org/debian bullseye/main arm64 librtmp1 arm64 2.4+20151223.gitfa8646d.1-2+b2 [59.4 kB] Get: 43 http://deb.debian.org/debian bullseye/main arm64 libssh2-1 arm64 1.9.0-2 [150 kB] Get: 44 http://deb.debian.org/debian bullseye/main arm64 libcurl4 arm64 7.74.0-1.3+b1 [321 kB] Get: 45 http://deb.debian.org/debian bullseye/main arm64 libjsoncpp24 arm64 1.9.4-4 [72.5 kB] Get: 46 http://deb.debian.org/debian bullseye/main arm64 librhash0 arm64 1.4.1-2 [127 kB] Get: 47 http://deb.debian.org/debian bullseye/main arm64 libuv1 arm64 1.40.0-2 [126 kB] Get: 48 http://deb.debian.org/debian bullseye/main arm64 cmake arm64 3.18.4-2 [3673 kB] Get: 49 http://deb.debian.org/debian bullseye/main arm64 libdebhelper-perl all 13.3.4 [189 kB] Get: 50 http://deb.debian.org/debian bullseye/main arm64 libtool all 2.4.6-15 [513 kB] Get: 51 http://deb.debian.org/debian bullseye/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 52 http://deb.debian.org/debian bullseye/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 53 http://deb.debian.org/debian bullseye/main arm64 libsub-override-perl all 0.09-2 [10.2 kB] Get: 54 http://deb.debian.org/debian bullseye/main arm64 libfile-stripnondeterminism-perl all 1.12.0-1 [26.3 kB] Get: 55 http://deb.debian.org/debian bullseye/main arm64 dh-strip-nondeterminism all 1.12.0-1 [15.4 kB] Get: 56 http://deb.debian.org/debian bullseye/main arm64 libelf1 arm64 0.183-1 [164 kB] Get: 57 http://deb.debian.org/debian bullseye/main arm64 dwz arm64 0.13+20210201-1 [155 kB] Get: 58 http://deb.debian.org/debian bullseye/main arm64 gettext arm64 0.21-4 [1261 kB] Get: 59 http://deb.debian.org/debian bullseye/main arm64 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 60 http://deb.debian.org/debian bullseye/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 61 http://deb.debian.org/debian bullseye/main arm64 debhelper all 13.3.4 [1049 kB] Get: 62 http://deb.debian.org/debian bullseye/main arm64 python3-lib2to3 all 3.9.2-1 [77.8 kB] Get: 63 http://deb.debian.org/debian bullseye/main arm64 python3-distutils all 3.9.2-1 [143 kB] Get: 64 http://deb.debian.org/debian bullseye/main arm64 dh-python all 4.20201102+nmu1 [99.4 kB] Get: 65 http://deb.debian.org/debian bullseye/main arm64 hdf5-helpers arm64 1.10.6+repack-4 [40.4 kB] Get: 66 http://deb.debian.org/debian bullseye/main arm64 libaec0 arm64 1.0.4-1 [19.8 kB] Get: 67 http://deb.debian.org/debian bullseye/main arm64 libsz2 arm64 1.0.4-1 [6736 B] Get: 68 http://deb.debian.org/debian bullseye/main arm64 libaec-dev arm64 1.0.4-1 [18.2 kB] Get: 69 http://deb.debian.org/debian bullseye/main arm64 libboost1.74-dev arm64 1.74.0-9 [9534 kB] Get: 70 http://deb.debian.org/debian bullseye/main arm64 libboost-dev arm64 1.74.0.3 [4548 B] Get: 71 http://deb.debian.org/debian bullseye/main arm64 libgatbcore3 arm64 1.4.2+dfsg-6 [1561 kB] Get: 72 http://deb.debian.org/debian bullseye/main arm64 libgatbcore-dev arm64 1.4.2+dfsg-6 [4039 kB] Get: 73 http://deb.debian.org/debian bullseye/main arm64 libgfortran5 arm64 10.2.1-6 [333 kB] Get: 74 http://deb.debian.org/debian bullseye/main arm64 libhdf5-103-1 arm64 1.10.6+repack-4 [1032 kB] Get: 75 http://deb.debian.org/debian bullseye/main arm64 libhdf5-cpp-103-1 arm64 1.10.6+repack-4 [131 kB] Get: 76 http://deb.debian.org/debian bullseye/main arm64 libhdf5-fortran-102 arm64 1.10.6+repack-4 [103 kB] Get: 77 http://deb.debian.org/debian bullseye/main arm64 libhdf5-hl-100 arm64 1.10.6+repack-4 [78.6 kB] Get: 78 http://deb.debian.org/debian bullseye/main arm64 libhdf5-hl-fortran-100 arm64 1.10.6+repack-4 [55.0 kB] Get: 79 http://deb.debian.org/debian bullseye/main arm64 libhdf5-hl-cpp-100 arm64 1.10.6+repack-4 [37.6 kB] Get: 80 http://deb.debian.org/debian bullseye/main arm64 zlib1g-dev arm64 1:1.2.11.dfsg-2 [189 kB] Get: 81 http://deb.debian.org/debian bullseye/main arm64 libjpeg62-turbo arm64 1:2.0.6-4 [133 kB] Get: 82 http://deb.debian.org/debian bullseye/main arm64 libjpeg62-turbo-dev arm64 1:2.0.6-4 [255 kB] Get: 83 http://deb.debian.org/debian bullseye/main arm64 libjpeg-dev arm64 1:2.0.6-4 [67.8 kB] Get: 84 http://deb.debian.org/debian bullseye/main arm64 libhdf5-dev arm64 1.10.6+repack-4 [2535 kB] Fetched 51.8 MB in 1s (42.4 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package bsdextrautils. 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Selecting previously unselected package libhdf5-dev. Preparing to unpack .../67-libhdf5-dev_1.10.6+repack-4_arm64.deb ... Unpacking libhdf5-dev (1.10.6+repack-4) ... Setting up media-types (4.0.0) ... Setting up libpipeline1:arm64 (1.5.3-1) ... Setting up libpsl5:arm64 (0.21.0-1.2) ... Setting up libboost1.74-dev:arm64 (1.74.0-9) ... Setting up bsdextrautils (2.36.1-7) ... update-alternatives: using /usr/bin/write.ul to provide /usr/bin/write (write) in auto mode Setting up hdf5-helpers (1.10.6+repack-4) ... Setting up libicu67:arm64 (67.1-7) ... Setting up libmagic-mgc (1:5.39-3) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.3.4) ... Setting up libbrotli1:arm64 (1.0.9-2+b2) ... Setting up libnghttp2-14:arm64 (1.43.0-1) ... Setting up libmagic1:arm64 (1:5.39-3) ... Setting up gettext-base (0.21-4) ... Setting up file (1:5.39-3) ... Setting up libaec0:arm64 (1.0.4-1) ... Setting up libsasl2-modules-db:arm64 (2.1.27+dfsg-2.1) ... Setting up autotools-dev (20180224.1+nmu1) ... Setting up libuv1:arm64 (1.40.0-2) ... Setting up libjpeg62-turbo:arm64 (1:2.0.6-4) ... Setting up libjpeg62-turbo-dev:arm64 (1:2.0.6-4) ... Setting up librtmp1:arm64 (2.4+20151223.gitfa8646d.1-2+b2) ... Setting up libncurses6:arm64 (6.2+20201114-2) ... Setting up libsigsegv2:arm64 (2.13-1) ... Setting up autopoint (0.21-4) ... Setting up libsasl2-2:arm64 (2.1.27+dfsg-2.1) ... Setting up libgfortran5:arm64 (10.2.1-6) ... Setting up libgatbcore3:arm64 (1.4.2+dfsg-6) ... Setting up libjsoncpp24:arm64 (1.9.4-4) ... Setting up zlib1g-dev:arm64 (1:1.2.11.dfsg-2) ... Setting up sensible-utils (0.0.14) ... Setting up librhash0:arm64 (1.4.1-2) ... Setting up libuchardet0:arm64 (0.0.7-1) ... Setting up libmpdec3:arm64 (2.5.1-1) ... Setting up libsub-override-perl (0.09-2) ... Setting up libssh2-1:arm64 (1.9.0-2) ... Setting up cmake-data (3.18.4-2) ... Setting up libboost-dev:arm64 (1.74.0.3) ... Setting up libelf1:arm64 (0.183-1) ... Setting up readline-common (8.1-1) ... Setting up libxml2:arm64 (2.9.10+dfsg-6.7) ... Setting up libprocps8:arm64 (2:3.3.17-5) ... Setting up libsz2:arm64 (1.0.4-1) ... Setting up libfile-stripnondeterminism-perl (1.12.0-1) ... Setting up gettext (0.21-4) ... Setting up libtool (2.4.6-15) ... Setting up libarchive13:arm64 (3.4.3-2+b1) ... Setting up libreadline8:arm64 (8.1-1) ... Setting up libaec-dev:arm64 (1.0.4-1) ... Setting up libjpeg-dev:arm64 (1:2.0.6-4) ... Setting up libldap-2.4-2:arm64 (2.4.57+dfsg-3) ... Setting up m4 (1.4.18-5) ... Setting up intltool-debian (0.35.0+20060710.5) ... Setting up libgatbcore-dev:arm64 (1.4.2+dfsg-6) ... Setting up autoconf (2.69-14) ... Setting up dh-strip-nondeterminism (1.12.0-1) ... Setting up libhdf5-103-1:arm64 (1.10.6+repack-4) ... Setting up dwz (0.13+20210201-1) ... Setting up groff-base (1.22.4-6) ... Setting up procps (2:3.3.17-5) ... Setting up libhdf5-cpp-103-1:arm64 (1.10.6+repack-4) ... Setting up libcurl4:arm64 (7.74.0-1.3+b1) ... Setting up libpython3.9-stdlib:arm64 (3.9.2-1) ... Setting up libpython3-stdlib:arm64 (3.9.2-3) ... Setting up libhdf5-hl-100:arm64 (1.10.6+repack-4) ... Setting up automake (1:1.16.3-2) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up po-debconf (1.0.21+nmu1) ... Setting up man-db (2.9.4-2) ... Not building database; man-db/auto-update is not 'true'. Setting up dh-autoreconf (20) ... Setting up libhdf5-hl-cpp-100:arm64 (1.10.6+repack-4) ... Setting up libhdf5-fortran-102:arm64 (1.10.6+repack-4) ... Setting up cmake (3.18.4-2) ... Setting up libhdf5-hl-fortran-100:arm64 (1.10.6+repack-4) ... Setting up python3.9 (3.9.2-1) ... Setting up debhelper (13.3.4) ... Setting up python3 (3.9.2-3) ... Setting up libhdf5-dev (1.10.6+repack-4) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/pkgconfig/hdf5-serial.pc to provide /usr/lib/aarch64-linux-gnu/pkgconfig/hdf5.pc (hdf5.pc) in auto mode Setting up python3-lib2to3 (3.9.2-1) ... Setting up python3-distutils (3.9.2-1) ... Setting up dh-python (4.20201102+nmu1) ... Processing triggers for libc-bin (2.31-13) ... 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 Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: libfile-find-rule-perl libnumber-compare-perl libtext-glob-perl The following NEW packages will be installed: libfile-find-rule-perl libnumber-compare-perl libtext-glob-perl usrmerge 0 upgraded, 4 newly installed, 0 to remove and 0 not upgraded. Need to get 59.5 kB of archives. After this operation, 157 kB of additional disk space will be used. Get:1 http://deb.debian.org/debian bullseye/main arm64 libnumber-compare-perl all 0.03-1.1 [6956 B] Get:2 http://deb.debian.org/debian bullseye/main arm64 libtext-glob-perl all 0.11-1 [8888 B] Get:3 http://deb.debian.org/debian bullseye/main arm64 libfile-find-rule-perl all 0.34-1 [30.6 kB] Get:4 http://deb.debian.org/debian bullseye/main arm64 usrmerge all 25 [13.0 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 59.5 kB in 0s (1496 kB/s) Selecting previously unselected package libnumber-compare-perl. (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 ... 41709 files and directories currently installed.) Preparing to unpack .../libnumber-compare-perl_0.03-1.1_all.deb ... Unpacking libnumber-compare-perl (0.03-1.1) ... Selecting previously unselected package libtext-glob-perl. Preparing to unpack .../libtext-glob-perl_0.11-1_all.deb ... Unpacking libtext-glob-perl (0.11-1) ... Selecting previously unselected package libfile-find-rule-perl. Preparing to unpack .../libfile-find-rule-perl_0.34-1_all.deb ... Unpacking libfile-find-rule-perl (0.34-1) ... Selecting previously unselected package usrmerge. Preparing to unpack .../archives/usrmerge_25_all.deb ... Unpacking usrmerge (25) ... Setting up libtext-glob-perl (0.11-1) ... Setting up libnumber-compare-perl (0.03-1.1) ... Setting up libfile-find-rule-perl (0.34-1) ... Setting up usrmerge (25) ... The system has been successfully converted. Processing triggers for man-db (2.9.4-2) ... Not building database; man-db/auto-update is not 'true'. I: Building the package hostname: Temporary failure in name resolution I: Running cd /build/discosnp-4.4.4/ && 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 > ../discosnp_4.4.4-1_source.changes dpkg-buildpackage: info: source package discosnp dpkg-buildpackage: info: source version 4.4.4-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 debian/rules clean dh clean --with python3 dh_clean debian/rules binary dh binary --with python3 dh_update_autotools_config dh_autoreconf dh_auto_configure cd obj-aarch64-linux-gnu && cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=None -DCMAKE_INSTALL_SYSCONFDIR=/etc -DCMAKE_INSTALL_LOCALSTATEDIR=/var -DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run -DCMAKE_SKIP_INSTALL_ALL_DEPENDENCY=ON "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/aarch64-linux-gnu .. -- The C compiler identification is GNU 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 -- gatb-core is here '/build/discosnp-4.4.4/thirdparty/gatb-core' CMake Warning (dev) at /usr/lib/aarch64-linux-gnu/cmake/GatbCore.cmake:39 (add_subdirectory): The source directory /build/discosnp-4.4.4/thirdparty/gatb-core does not contain a CMakeLists.txt file. CMake does not support this case but it used to work accidentally and is being allowed for compatibility. Policy CMP0014 is not set: Input directories must have CMakeLists.txt. Run "cmake --help-policy CMP0014" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): CMakeLists.txt:47 (include) This warning is for project developers. Use -Wno-dev to suppress it. -- Configuring done -- Generating done CMake Warning: Manually-specified variables were not used by the project: CMAKE_EXPORT_NO_PACKAGE_REGISTRY CMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY -- Build files have been written to: /build/discosnp-4.4.4/obj-aarch64-linux-gnu dh_auto_build cd obj-aarch64-linux-gnu && make -j8 "INSTALL=install --strip-program=true" VERBOSE=1 make[1]: Entering directory '/build/discosnp-4.4.4/obj-aarch64-linux-gnu' /usr/bin/cmake -S/build/discosnp-4.4.4 -B/build/discosnp-4.4.4/obj-aarch64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/discosnp-4.4.4/obj-aarch64-linux-gnu/CMakeFiles /build/discosnp-4.4.4/obj-aarch64-linux-gnu//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/build/discosnp-4.4.4/obj-aarch64-linux-gnu' make -f tools/kissnp2/CMakeFiles/kissnp2.dir/build.make tools/kissnp2/CMakeFiles/kissnp2.dir/depend make[3]: Entering directory '/build/discosnp-4.4.4/obj-aarch64-linux-gnu' cd /build/discosnp-4.4.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/discosnp-4.4.4 /build/discosnp-4.4.4/tools/kissnp2 /build/discosnp-4.4.4/obj-aarch64-linux-gnu /build/discosnp-4.4.4/obj-aarch64-linux-gnu/tools/kissnp2 /build/discosnp-4.4.4/obj-aarch64-linux-gnu/tools/kissnp2/CMakeFiles/kissnp2.dir/DependInfo.cmake --color= make -f tools/kissreads2/CMakeFiles/kissreads2.dir/build.make tools/kissreads2/CMakeFiles/kissreads2.dir/depend make[3]: Entering directory '/build/discosnp-4.4.4/obj-aarch64-linux-gnu' cd /build/discosnp-4.4.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/discosnp-4.4.4 /build/discosnp-4.4.4/tools/kissreads2 /build/discosnp-4.4.4/obj-aarch64-linux-gnu /build/discosnp-4.4.4/obj-aarch64-linux-gnu/tools/kissreads2 /build/discosnp-4.4.4/obj-aarch64-linux-gnu/tools/kissreads2/CMakeFiles/kissreads2.dir/DependInfo.cmake --color= make -f tools/QHC/CMakeFiles/quick_hierarchical_clustering.dir/build.make tools/QHC/CMakeFiles/quick_hierarchical_clustering.dir/depend make[3]: Entering directory '/build/discosnp-4.4.4/obj-aarch64-linux-gnu' cd /build/discosnp-4.4.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/discosnp-4.4.4 /build/discosnp-4.4.4/tools/QHC /build/discosnp-4.4.4/obj-aarch64-linux-gnu /build/discosnp-4.4.4/obj-aarch64-linux-gnu/tools/QHC /build/discosnp-4.4.4/obj-aarch64-linux-gnu/tools/QHC/CMakeFiles/quick_hierarchical_clustering.dir/DependInfo.cmake --color= make -f tools/read_file_names/CMakeFiles/read_file_names.dir/build.make tools/read_file_names/CMakeFiles/read_file_names.dir/depend make[3]: Entering directory '/build/discosnp-4.4.4/obj-aarch64-linux-gnu' cd /build/discosnp-4.4.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/discosnp-4.4.4 /build/discosnp-4.4.4/tools/read_file_names /build/discosnp-4.4.4/obj-aarch64-linux-gnu /build/discosnp-4.4.4/obj-aarch64-linux-gnu/tools/read_file_names /build/discosnp-4.4.4/obj-aarch64-linux-gnu/tools/read_file_names/CMakeFiles/read_file_names.dir/DependInfo.cmake --color= make -f tools/create_coverage_h5_file/CMakeFiles/create_coverage_h5_file.dir/build.make tools/create_coverage_h5_file/CMakeFiles/create_coverage_h5_file.dir/depend make[3]: Entering directory '/build/discosnp-4.4.4/obj-aarch64-linux-gnu' cd /build/discosnp-4.4.4/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/discosnp-4.4.4 /build/discosnp-4.4.4/tools/create_coverage_h5_file /build/discosnp-4.4.4/obj-aarch64-linux-gnu /build/discosnp-4.4.4/obj-aarch64-linux-gnu/tools/create_coverage_h5_file /build/discosnp-4.4.4/obj-aarch64-linux-gnu/tools/create_coverage_h5_file/CMakeFiles/create_coverage_h5_file.dir/DependInfo.cmake --color= Dependee "/build/discosnp-4.4.4/obj-aarch64-linux-gnu/tools/QHC/CMakeFiles/quick_hierarchical_clustering.dir/DependInfo.cmake" is newer than depender "/build/discosnp-4.4.4/obj-aarch64-linux-gnu/tools/QHC/CMakeFiles/quick_hierarchical_clustering.dir/depend.internal". Dependee "/build/discosnp-4.4.4/obj-aarch64-linux-gnu/tools/QHC/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/discosnp-4.4.4/obj-aarch64-linux-gnu/tools/QHC/CMakeFiles/quick_hierarchical_clustering.dir/depend.internal". Scanning dependencies of target quick_hierarchical_clustering make[3]: Leaving directory '/build/discosnp-4.4.4/obj-aarch64-linux-gnu' make -f tools/QHC/CMakeFiles/quick_hierarchical_clustering.dir/build.make tools/QHC/CMakeFiles/quick_hierarchical_clustering.dir/build make[3]: Entering directory '/build/discosnp-4.4.4/obj-aarch64-linux-gnu' Dependee "/build/discosnp-4.4.4/obj-aarch64-linux-gnu/tools/kissnp2/CMakeFiles/kissnp2.dir/DependInfo.cmake" is newer than depender "/build/discosnp-4.4.4/obj-aarch64-linux-gnu/tools/kissnp2/CMakeFiles/kissnp2.dir/depend.internal". Dependee "/build/discosnp-4.4.4/obj-aarch64-linux-gnu/tools/kissnp2/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/discosnp-4.4.4/obj-aarch64-linux-gnu/tools/kissnp2/CMakeFiles/kissnp2.dir/depend.internal". Scanning dependencies of target kissnp2 make[3]: Leaving directory '/build/discosnp-4.4.4/obj-aarch64-linux-gnu' make -f tools/kissnp2/CMakeFiles/kissnp2.dir/build.make tools/kissnp2/CMakeFiles/kissnp2.dir/build Dependee "/build/discosnp-4.4.4/obj-aarch64-linux-gnu/tools/read_file_names/CMakeFiles/read_file_names.dir/DependInfo.cmake" is newer than depender "/build/discosnp-4.4.4/obj-aarch64-linux-gnu/tools/read_file_names/CMakeFiles/read_file_names.dir/depend.internal". Dependee "/build/discosnp-4.4.4/obj-aarch64-linux-gnu/tools/read_file_names/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/discosnp-4.4.4/obj-aarch64-linux-gnu/tools/read_file_names/CMakeFiles/read_file_names.dir/depend.internal". Dependee "/build/discosnp-4.4.4/obj-aarch64-linux-gnu/tools/kissreads2/CMakeFiles/kissreads2.dir/DependInfo.cmake" is newer than depender "/build/discosnp-4.4.4/obj-aarch64-linux-gnu/tools/kissreads2/CMakeFiles/kissreads2.dir/depend.internal". Dependee "/build/discosnp-4.4.4/obj-aarch64-linux-gnu/tools/kissreads2/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/discosnp-4.4.4/obj-aarch64-linux-gnu/tools/kissreads2/CMakeFiles/kissreads2.dir/depend.internal". Scanning dependencies of target read_file_names make[3]: Leaving directory '/build/discosnp-4.4.4/obj-aarch64-linux-gnu' make[3]: Entering directory '/build/discosnp-4.4.4/obj-aarch64-linux-gnu' make -f tools/read_file_names/CMakeFiles/read_file_names.dir/build.make tools/read_file_names/CMakeFiles/read_file_names.dir/build Scanning dependencies of target kissreads2 make[3]: Entering directory '/build/discosnp-4.4.4/obj-aarch64-linux-gnu' Dependee "/build/discosnp-4.4.4/obj-aarch64-linux-gnu/tools/create_coverage_h5_file/CMakeFiles/create_coverage_h5_file.dir/DependInfo.cmake" is newer than depender "/build/discosnp-4.4.4/obj-aarch64-linux-gnu/tools/create_coverage_h5_file/CMakeFiles/create_coverage_h5_file.dir/depend.internal". Dependee "/build/discosnp-4.4.4/obj-aarch64-linux-gnu/tools/create_coverage_h5_file/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/discosnp-4.4.4/obj-aarch64-linux-gnu/tools/create_coverage_h5_file/CMakeFiles/create_coverage_h5_file.dir/depend.internal". Scanning dependencies of target create_coverage_h5_file make[3]: Leaving directory '/build/discosnp-4.4.4/obj-aarch64-linux-gnu' make -f tools/create_coverage_h5_file/CMakeFiles/create_coverage_h5_file.dir/build.make tools/create_coverage_h5_file/CMakeFiles/create_coverage_h5_file.dir/build make[3]: Leaving directory '/build/discosnp-4.4.4/obj-aarch64-linux-gnu' make -f tools/kissreads2/CMakeFiles/kissreads2.dir/build.make tools/kissreads2/CMakeFiles/kissreads2.dir/build [ 4%] Building CXX object tools/QHC/CMakeFiles/quick_hierarchical_clustering.dir/src/quick_hierarchical_clustering.cpp.o make[3]: Entering directory '/build/discosnp-4.4.4/obj-aarch64-linux-gnu' make[3]: Entering directory '/build/discosnp-4.4.4/obj-aarch64-linux-gnu' cd /build/discosnp-4.4.4/obj-aarch64-linux-gnu/tools/QHC && /usr/bin/c++ -I/build/discosnp-4.4.4/tools/QHC/src -g -O2 -fdebug-prefix-map=/build/discosnp-4.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/quick_hierarchical_clustering.dir/src/quick_hierarchical_clustering.cpp.o -c /build/discosnp-4.4.4/tools/QHC/src/quick_hierarchical_clustering.cpp [ 13%] Building CXX object tools/kissnp2/CMakeFiles/kissnp2.dir/src/Bubble.cpp.o [ 21%] Building CXX object tools/read_file_names/CMakeFiles/read_file_names.dir/src/get_read_file_names.cpp.o [ 21%] Building CXX object tools/kissnp2/CMakeFiles/kissnp2.dir/src/Filter.cpp.o cd /build/discosnp-4.4.4/obj-aarch64-linux-gnu/tools/read_file_names && /usr/bin/c++ -I/build/discosnp-4.4.4/tools/read_file_names/src -g -O2 -fdebug-prefix-map=/build/discosnp-4.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/read_file_names.dir/src/get_read_file_names.cpp.o -c /build/discosnp-4.4.4/tools/read_file_names/src/get_read_file_names.cpp cd /build/discosnp-4.4.4/obj-aarch64-linux-gnu/tools/kissnp2 && /usr/bin/c++ -I/build/discosnp-4.4.4/tools/kissnp2/src -g -O2 -fdebug-prefix-map=/build/discosnp-4.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/kissnp2.dir/src/Filter.cpp.o -c /build/discosnp-4.4.4/tools/kissnp2/src/Filter.cpp [ 8%] Building CXX object tools/create_coverage_h5_file/CMakeFiles/create_coverage_h5_file.dir/src/create_coverage_h5_file.cpp.o cd /build/discosnp-4.4.4/obj-aarch64-linux-gnu/tools/create_coverage_h5_file && /usr/bin/c++ -I/build/discosnp-4.4.4/tools/create_coverage_h5_file/src -g -O2 -fdebug-prefix-map=/build/discosnp-4.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/create_coverage_h5_file.dir/src/create_coverage_h5_file.cpp.o -c /build/discosnp-4.4.4/tools/create_coverage_h5_file/src/create_coverage_h5_file.cpp cd /build/discosnp-4.4.4/obj-aarch64-linux-gnu/tools/kissnp2 && /usr/bin/c++ -I/build/discosnp-4.4.4/tools/kissnp2/src -g -O2 -fdebug-prefix-map=/build/discosnp-4.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/kissnp2.dir/src/Bubble.cpp.o -c /build/discosnp-4.4.4/tools/kissnp2/src/Bubble.cpp [ 30%] Building CXX object tools/kissnp2/CMakeFiles/kissnp2.dir/src/main.cpp.o [ 30%] Building CXX object tools/kissnp2/CMakeFiles/kissnp2.dir/src/Kissnp2.cpp.o [ 34%] Building CXX object tools/kissreads2/CMakeFiles/kissreads2.dir/src/Kissreads2.cpp.o cd /build/discosnp-4.4.4/obj-aarch64-linux-gnu/tools/kissreads2 && /usr/bin/c++ -I/build/discosnp-4.4.4/tools/kissreads2/src -g -O2 -fdebug-prefix-map=/build/discosnp-4.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/kissreads2.dir/src/Kissreads2.cpp.o -c /build/discosnp-4.4.4/tools/kissreads2/src/Kissreads2.cpp cd /build/discosnp-4.4.4/obj-aarch64-linux-gnu/tools/kissnp2 && /usr/bin/c++ -I/build/discosnp-4.4.4/tools/kissnp2/src -g -O2 -fdebug-prefix-map=/build/discosnp-4.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/kissnp2.dir/src/main.cpp.o -c /build/discosnp-4.4.4/tools/kissnp2/src/main.cpp cd /build/discosnp-4.4.4/obj-aarch64-linux-gnu/tools/kissnp2 && /usr/bin/c++ -I/build/discosnp-4.4.4/tools/kissnp2/src -g -O2 -fdebug-prefix-map=/build/discosnp-4.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/kissnp2.dir/src/Kissnp2.cpp.o -c /build/discosnp-4.4.4/tools/kissnp2/src/Kissnp2.cpp [ 39%] Linking CXX executable ../../bin/quick_hierarchical_clustering cd /build/discosnp-4.4.4/obj-aarch64-linux-gnu/tools/QHC && /usr/bin/cmake -E cmake_link_script CMakeFiles/quick_hierarchical_clustering.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/discosnp-4.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -rdynamic CMakeFiles/quick_hierarchical_clustering.dir/src/quick_hierarchical_clustering.cpp.o -o ../../bin/quick_hierarchical_clustering -L/usr/lib/aarch64-linux-gnu/hdf5/serial -Wl,-rpath,/usr/lib/aarch64-linux-gnu/hdf5/serial: -lgatbcore -lhdf5 -lz make[3]: Leaving directory '/build/discosnp-4.4.4/obj-aarch64-linux-gnu' [ 39%] Built target quick_hierarchical_clustering [ 43%] Building CXX object tools/kissreads2/CMakeFiles/kissreads2.dir/src/commons.cpp.o cd /build/discosnp-4.4.4/obj-aarch64-linux-gnu/tools/kissreads2 && /usr/bin/c++ -I/build/discosnp-4.4.4/tools/kissreads2/src -g -O2 -fdebug-prefix-map=/build/discosnp-4.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/kissreads2.dir/src/commons.cpp.o -c /build/discosnp-4.4.4/tools/kissreads2/src/commons.cpp [ 47%] Building CXX object tools/kissreads2/CMakeFiles/kissreads2.dir/src/couple.cpp.o cd /build/discosnp-4.4.4/obj-aarch64-linux-gnu/tools/kissreads2 && /usr/bin/c++ -I/build/discosnp-4.4.4/tools/kissreads2/src -g -O2 -fdebug-prefix-map=/build/discosnp-4.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/kissreads2.dir/src/couple.cpp.o -c /build/discosnp-4.4.4/tools/kissreads2/src/couple.cpp [ 52%] Building CXX object tools/kissreads2/CMakeFiles/kissreads2.dir/src/extension_algorithm.cpp.o cd /build/discosnp-4.4.4/obj-aarch64-linux-gnu/tools/kissreads2 && /usr/bin/c++ -I/build/discosnp-4.4.4/tools/kissreads2/src -g -O2 -fdebug-prefix-map=/build/discosnp-4.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/kissreads2.dir/src/extension_algorithm.cpp.o -c /build/discosnp-4.4.4/tools/kissreads2/src/extension_algorithm.cpp [ 56%] Linking CXX executable ../../bin/read_file_names cd /build/discosnp-4.4.4/obj-aarch64-linux-gnu/tools/read_file_names && /usr/bin/cmake -E cmake_link_script CMakeFiles/read_file_names.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/discosnp-4.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -rdynamic CMakeFiles/read_file_names.dir/src/get_read_file_names.cpp.o -o ../../bin/read_file_names -L/usr/lib/aarch64-linux-gnu/hdf5/serial -Wl,-rpath,/usr/lib/aarch64-linux-gnu/hdf5/serial: -lgatbcore -lhdf5 -lz make[3]: Leaving directory '/build/discosnp-4.4.4/obj-aarch64-linux-gnu' [ 56%] Built target read_file_names [ 60%] Building CXX object tools/kissreads2/CMakeFiles/kissreads2.dir/src/fragment_index.cpp.o cd /build/discosnp-4.4.4/obj-aarch64-linux-gnu/tools/kissreads2 && /usr/bin/c++ -I/build/discosnp-4.4.4/tools/kissreads2/src -g -O2 -fdebug-prefix-map=/build/discosnp-4.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/kissreads2.dir/src/fragment_index.cpp.o -c /build/discosnp-4.4.4/tools/kissreads2/src/fragment_index.cpp [ 65%] Building CXX object tools/kissreads2/CMakeFiles/kissreads2.dir/src/fragment_info.cpp.o cd /build/discosnp-4.4.4/obj-aarch64-linux-gnu/tools/kissreads2 && /usr/bin/c++ -I/build/discosnp-4.4.4/tools/kissreads2/src -g -O2 -fdebug-prefix-map=/build/discosnp-4.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/kissreads2.dir/src/fragment_info.cpp.o -c /build/discosnp-4.4.4/tools/kissreads2/src/fragment_info.cpp [ 69%] Building CXX object tools/kissreads2/CMakeFiles/kissreads2.dir/src/interface_libchash.cpp.o cd /build/discosnp-4.4.4/obj-aarch64-linux-gnu/tools/kissreads2 && /usr/bin/c++ -I/build/discosnp-4.4.4/tools/kissreads2/src -g -O2 -fdebug-prefix-map=/build/discosnp-4.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/kissreads2.dir/src/interface_libchash.cpp.o -c /build/discosnp-4.4.4/tools/kissreads2/src/interface_libchash.cpp [ 73%] Building CXX object tools/kissreads2/CMakeFiles/kissreads2.dir/src/libchash.cpp.o cd /build/discosnp-4.4.4/obj-aarch64-linux-gnu/tools/kissreads2 && /usr/bin/c++ -I/build/discosnp-4.4.4/tools/kissreads2/src -g -O2 -fdebug-prefix-map=/build/discosnp-4.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/kissreads2.dir/src/libchash.cpp.o -c /build/discosnp-4.4.4/tools/kissreads2/src/libchash.cpp /build/discosnp-4.4.4/tools/kissreads2/src/libchash.cpp: In function 'HTItem* HashFind(HashTable*, u_long)': /build/discosnp-4.4.4/tools/kissreads2/src/libchash.cpp:188:12: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 188 | fread(&_ul, sizeof(_ul), 1, (fp)); \ | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/discosnp-4.4.4/tools/kissreads2/src/libchash.cpp:215:7: note: in expansion of macro 'READ_UL' 215 | READ_UL((ht)->fpData, cchData); \ | ^~~~~~~ /build/discosnp-4.4.4/tools/kissreads2/src/libchash.cpp:1216:4: note: in expansion of macro 'LOAD_AND_RETURN' 1216 | LOAD_AND_RETURN(ht, Find(ht, KEY_TRUNC(ht, key), NULL)); | ^~~~~~~~~~~~~~~ /build/discosnp-4.4.4/tools/kissreads2/src/libchash.cpp: In function 'HTItem* HashFindLast(HashTable*)': /build/discosnp-4.4.4/tools/kissreads2/src/libchash.cpp:188:12: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 188 | fread(&_ul, sizeof(_ul), 1, (fp)); \ | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/discosnp-4.4.4/tools/kissreads2/src/libchash.cpp:215:7: note: in expansion of macro 'READ_UL' 215 | READ_UL((ht)->fpData, cchData); \ | ^~~~~~~ /build/discosnp-4.4.4/tools/kissreads2/src/libchash.cpp:1221:4: note: in expansion of macro 'LOAD_AND_RETURN' 1221 | LOAD_AND_RETURN(ht, ht->posLastFind); | ^~~~~~~~~~~~~~~ /build/discosnp-4.4.4/tools/kissreads2/src/libchash.cpp: In function 'HTItem* HashFirstBucket(HashTable*)': /build/discosnp-4.4.4/tools/kissreads2/src/libchash.cpp:188:12: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 188 | fread(&_ul, sizeof(_ul), 1, (fp)); \ | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/discosnp-4.4.4/tools/kissreads2/src/libchash.cpp:215:7: note: in expansion of macro 'READ_UL' 215 | READ_UL((ht)->fpData, cchData); \ | ^~~~~~~ /build/discosnp-4.4.4/tools/kissreads2/src/libchash.cpp:1285:7: note: in expansion of macro 'LOAD_AND_RETURN' 1285 | { LOAD_AND_RETURN(ht, retval);} | ^~~~~~~~~~~~~~~ /build/discosnp-4.4.4/tools/kissreads2/src/libchash.cpp: In function 'HTItem* HashNextBucket(HashTable*)': /build/discosnp-4.4.4/tools/kissreads2/src/libchash.cpp:188:12: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 188 | fread(&_ul, sizeof(_ul), 1, (fp)); \ | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/discosnp-4.4.4/tools/kissreads2/src/libchash.cpp:215:7: note: in expansion of macro 'READ_UL' 215 | READ_UL((ht)->fpData, cchData); \ | ^~~~~~~ /build/discosnp-4.4.4/tools/kissreads2/src/libchash.cpp:1295:8: note: in expansion of macro 'LOAD_AND_RETURN' 1295 | {LOAD_AND_RETURN(ht, retval);} | ^~~~~~~~~~~~~~~ /build/discosnp-4.4.4/tools/kissreads2/src/libchash.cpp: In function 'HashTable* HashDoLoad(FILE*, char* (*)(FILE*, int), HashTable*)': /build/discosnp-4.4.4/tools/kissreads2/src/libchash.cpp:1402:9: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 1402 | fread(szMagicKey, 1, 4, fp); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/discosnp-4.4.4/tools/kissreads2/src/libchash.cpp:188:12: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 188 | fread(&_ul, sizeof(_ul), 1, (fp)); \ | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/discosnp-4.4.4/tools/kissreads2/src/libchash.cpp:1411:4: note: in expansion of macro 'READ_UL' 1411 | READ_UL(fp, ht->cchKey); | ^~~~~~~ /build/discosnp-4.4.4/tools/kissreads2/src/libchash.cpp:188:12: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 188 | fread(&_ul, sizeof(_ul), 1, (fp)); \ | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/discosnp-4.4.4/tools/kissreads2/src/libchash.cpp:1412:4: note: in expansion of macro 'READ_UL' 1412 | READ_UL(fp, ht->cItems); | ^~~~~~~ /build/discosnp-4.4.4/tools/kissreads2/src/libchash.cpp:188:12: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 188 | fread(&_ul, sizeof(_ul), 1, (fp)); \ | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/discosnp-4.4.4/tools/kissreads2/src/libchash.cpp:1413:4: note: in expansion of macro 'READ_UL' 1413 | READ_UL(fp, ht->cDeletedItems); | ^~~~~~~ /build/discosnp-4.4.4/tools/kissreads2/src/libchash.cpp:188:12: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 188 | fread(&_ul, sizeof(_ul), 1, (fp)); \ | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/discosnp-4.4.4/tools/kissreads2/src/libchash.cpp:1416:4: note: in expansion of macro 'READ_UL' 1416 | READ_UL(fp, cchKey); | ^~~~~~~ /build/discosnp-4.4.4/tools/kissreads2/src/libchash.cpp:1418:9: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 1418 | fread(rgchKeys, 1, cchKey, fp); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /build/discosnp-4.4.4/tools/kissreads2/src/libchash.cpp:188:12: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 188 | fread(&_ul, sizeof(_ul), 1, (fp)); \ | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/discosnp-4.4.4/tools/kissreads2/src/libchash.cpp:1423:7: note: in expansion of macro 'READ_UL' 1423 | READ_UL(fp, bck->data); /* all we need if dataRead is NULL */ | ^~~~~~~ /build/discosnp-4.4.4/tools/kissreads2/src/libchash.cpp: In function 'u_long SparseRead(FILE*, SparseBin**)': /build/discosnp-4.4.4/tools/kissreads2/src/libchash.cpp:188:12: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 188 | fread(&_ul, sizeof(_ul), 1, (fp)); \ | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/discosnp-4.4.4/tools/kissreads2/src/libchash.cpp:617:4: note: in expansion of macro 'READ_UL' 617 | READ_UL(fp, cBuckets); /* actually, cBuckets is stored */ | ^~~~~~~ /build/discosnp-4.4.4/tools/kissreads2/src/libchash.cpp:188:12: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 188 | fread(&_ul, sizeof(_ul), 1, (fp)); \ | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/discosnp-4.4.4/tools/kissreads2/src/libchash.cpp:622:3: note: in expansion of macro 'READ_UL' 622 | READ_UL(fp, (*pbinSparse)[i].bmOccupied[j]); | ^~~~~~~ [ 78%] Linking CXX executable ../../bin/create_coverage_h5_file cd /build/discosnp-4.4.4/obj-aarch64-linux-gnu/tools/create_coverage_h5_file && /usr/bin/cmake -E cmake_link_script CMakeFiles/create_coverage_h5_file.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/discosnp-4.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -rdynamic CMakeFiles/create_coverage_h5_file.dir/src/create_coverage_h5_file.cpp.o -o ../../bin/create_coverage_h5_file -L/usr/lib/aarch64-linux-gnu/hdf5/serial -Wl,-rpath,/usr/lib/aarch64-linux-gnu/hdf5/serial: -lgatbcore -lhdf5 -lz make[3]: Leaving directory '/build/discosnp-4.4.4/obj-aarch64-linux-gnu' [ 78%] Built target create_coverage_h5_file [ 82%] Building CXX object tools/kissreads2/CMakeFiles/kissreads2.dir/src/list.cpp.o cd /build/discosnp-4.4.4/obj-aarch64-linux-gnu/tools/kissreads2 && /usr/bin/c++ -I/build/discosnp-4.4.4/tools/kissreads2/src -g -O2 -fdebug-prefix-map=/build/discosnp-4.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/kissreads2.dir/src/list.cpp.o -c /build/discosnp-4.4.4/tools/kissreads2/src/list.cpp [ 86%] Building CXX object tools/kissreads2/CMakeFiles/kissreads2.dir/src/main.cpp.o cd /build/discosnp-4.4.4/obj-aarch64-linux-gnu/tools/kissreads2 && /usr/bin/c++ -I/build/discosnp-4.4.4/tools/kissreads2/src -g -O2 -fdebug-prefix-map=/build/discosnp-4.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/kissreads2.dir/src/main.cpp.o -c /build/discosnp-4.4.4/tools/kissreads2/src/main.cpp [ 91%] Building CXX object tools/kissreads2/CMakeFiles/kissreads2.dir/src/outputs.cpp.o cd /build/discosnp-4.4.4/obj-aarch64-linux-gnu/tools/kissreads2 && /usr/bin/c++ -I/build/discosnp-4.4.4/tools/kissreads2/src -g -O2 -fdebug-prefix-map=/build/discosnp-4.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/kissreads2.dir/src/outputs.cpp.o -c /build/discosnp-4.4.4/tools/kissreads2/src/outputs.cpp [ 95%] Linking CXX executable ../../bin/kissnp2 cd /build/discosnp-4.4.4/obj-aarch64-linux-gnu/tools/kissnp2 && /usr/bin/cmake -E cmake_link_script CMakeFiles/kissnp2.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/discosnp-4.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -rdynamic CMakeFiles/kissnp2.dir/src/Bubble.cpp.o CMakeFiles/kissnp2.dir/src/Filter.cpp.o CMakeFiles/kissnp2.dir/src/Kissnp2.cpp.o CMakeFiles/kissnp2.dir/src/main.cpp.o -o ../../bin/kissnp2 -L/usr/lib/aarch64-linux-gnu/hdf5/serial -Wl,-rpath,/usr/lib/aarch64-linux-gnu/hdf5/serial: -lgatbcore -lhdf5 -lz make[3]: Leaving directory '/build/discosnp-4.4.4/obj-aarch64-linux-gnu' [ 95%] Built target kissnp2 [100%] Linking CXX executable ../../bin/kissreads2 cd /build/discosnp-4.4.4/obj-aarch64-linux-gnu/tools/kissreads2 && /usr/bin/cmake -E cmake_link_script CMakeFiles/kissreads2.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/discosnp-4.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -rdynamic CMakeFiles/kissreads2.dir/src/Kissreads2.cpp.o CMakeFiles/kissreads2.dir/src/commons.cpp.o CMakeFiles/kissreads2.dir/src/couple.cpp.o CMakeFiles/kissreads2.dir/src/extension_algorithm.cpp.o CMakeFiles/kissreads2.dir/src/fragment_index.cpp.o CMakeFiles/kissreads2.dir/src/fragment_info.cpp.o CMakeFiles/kissreads2.dir/src/interface_libchash.cpp.o CMakeFiles/kissreads2.dir/src/libchash.cpp.o CMakeFiles/kissreads2.dir/src/list.cpp.o CMakeFiles/kissreads2.dir/src/main.cpp.o CMakeFiles/kissreads2.dir/src/outputs.cpp.o -o ../../bin/kissreads2 -L/usr/lib/aarch64-linux-gnu/hdf5/serial -Wl,-rpath,/usr/lib/aarch64-linux-gnu/hdf5/serial: -lgatbcore -lhdf5 -lz make[3]: Leaving directory '/build/discosnp-4.4.4/obj-aarch64-linux-gnu' [100%] Built target kissreads2 make[2]: Leaving directory '/build/discosnp-4.4.4/obj-aarch64-linux-gnu' /usr/bin/cmake -E cmake_progress_start /build/discosnp-4.4.4/obj-aarch64-linux-gnu/CMakeFiles 0 make[1]: Leaving directory '/build/discosnp-4.4.4/obj-aarch64-linux-gnu' dh_auto_test create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install cd obj-aarch64-linux-gnu && make -j8 install DESTDIR=/build/discosnp-4.4.4/debian/discosnp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/discosnp-4.4.4/obj-aarch64-linux-gnu' /usr/bin/cmake -S/build/discosnp-4.4.4 -B/build/discosnp-4.4.4/obj-aarch64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 preinstall make[2]: Entering directory '/build/discosnp-4.4.4/obj-aarch64-linux-gnu' make[2]: Nothing to be done for 'preinstall'. make[2]: Leaving directory '/build/discosnp-4.4.4/obj-aarch64-linux-gnu' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "None" -- Installing: /build/discosnp-4.4.4/debian/discosnp/usr/bin/kissnp2 -- Set runtime path of "/build/discosnp-4.4.4/debian/discosnp/usr/bin/kissnp2" to "" -- Installing: /build/discosnp-4.4.4/debian/discosnp/usr/bin/kissreads2 -- Set runtime path of "/build/discosnp-4.4.4/debian/discosnp/usr/bin/kissreads2" to "" -- Installing: /build/discosnp-4.4.4/debian/discosnp/usr/bin/quick_hierarchical_clustering -- Set runtime path of "/build/discosnp-4.4.4/debian/discosnp/usr/bin/quick_hierarchical_clustering" to "" -- Installing: /build/discosnp-4.4.4/debian/discosnp/usr/bin/read_file_names -- Set runtime path of "/build/discosnp-4.4.4/debian/discosnp/usr/bin/read_file_names" to "" -- Installing: /build/discosnp-4.4.4/debian/discosnp/usr/bin/create_coverage_h5_file -- Set runtime path of "/build/discosnp-4.4.4/debian/discosnp/usr/bin/create_coverage_h5_file" to "" make[1]: Leaving directory '/build/discosnp-4.4.4/obj-aarch64-linux-gnu' debian/rules override_dh_install make[1]: Entering directory '/build/discosnp-4.4.4' dh_install mkdir -p debian/discosnp/usr/lib/discosnp/bin mv debian/discosnp/usr/bin/read_file_names debian/discosnp/usr/lib/discosnp/bin mv debian/discosnp/usr/bin/quick_hierarchical_clustering debian/discosnp/usr/lib/discosnp/bin rm -rf debian/discosnp/usr/share/discosnp/scripts/jenkins make[1]: Leaving directory '/build/discosnp-4.4.4' dh_installdocs dh_installchangelogs debian/rules override_dh_installman make[1]: Entering directory '/build/discosnp-4.4.4' dh_installman # dh_installman interprets .sh as language - just copy manpages manually cp -a debian/mans/*.sh.1 debian/discosnp/usr/share/man/man1 make[1]: Leaving directory '/build/discosnp-4.4.4' dh_python3 I: dh_python3 tools:114: replacing shebang in debian/discosnp/usr/share/discosnp/scripts/create_filtered_vcf.py I: dh_python3 tools:114: replacing shebang in debian/discosnp/usr/share/discosnp/scripts/vcf_formatting_functions.py I: dh_python3 tools:114: replacing shebang in debian/discosnp/usr/share/discosnp/scripts/k3000/K3000_common.py I: dh_python3 tools:114: replacing shebang in debian/discosnp/usr/share/discosnp/scripts/k3000/K3000_compacted_int_to_fa.py I: dh_python3 tools:114: replacing shebang in debian/discosnp/usr/share/discosnp/scripts/k3000/K3000_compacted_paths_to_fa.py I: dh_python3 tools:114: replacing shebang in debian/discosnp/usr/share/discosnp/scripts/k3000/K3000_msr_to_gfa.py I: dh_python3 tools:114: replacing shebang in debian/discosnp/usr/share/discosnp/scripts/k3000/K3000_node_ids_to_node_sequences.py I: dh_python3 tools:114: replacing shebang in debian/discosnp/usr/share/discosnp/discoSnpRAD/clustering_scripts/fasta_and_cluster_to_filtered_vcf.py dh_lintian 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 'discosnp' in '../discosnp_4.4.4-1_arm64.deb'. dpkg-deb: building package 'discosnp-dbgsym' in '../discosnp-dbgsym_4.4.4-1_arm64.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../discosnp_4.4.4-1_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: including full source code in upload I: copying local configuration I: user script /srv/workspace/pbuilder/1640/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/1640/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/1640 and its subdirectories I: Current time: Wed Jul 28 17:31:45 +14 2021 I: pbuilder-time-stamp: 1627443105