I: pbuilder: network access will be disabled during build I: Current time: Wed Aug 10 14:44:32 +14 2022 I: pbuilder-time-stamp: 1660092272 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 [sniffles_1.0.12b+ds-1.dsc] I: copying [./sniffles_1.0.12b+ds.orig.tar.xz] I: copying [./sniffles_1.0.12b+ds-1.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/tmp/dpkg-verify-sig.iLrVs7DK/trustedkeys.kbx': General error gpgv: Signature made Sat Nov 28 12:37:57 2020 +14 gpgv: using RSA key 84C1977A89E7EFED3E5CA62E2FD8BEDAC020EED1 gpgv: issuer "moeller@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./sniffles_1.0.12b+ds-1.dsc dpkg-source: info: extracting sniffles in sniffles-1.0.12b+ds dpkg-source: info: unpacking sniffles_1.0.12b+ds.orig.tar.xz dpkg-source: info: unpacking sniffles_1.0.12b+ds-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying external-libs.patch dpkg-source: info: applying no-extra-binary.patch dpkg-source: info: applying stoppingRecursion.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/25168/tmp/hooks/D01_modify_environment starting debug: Running on codethink9-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/25168/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/25168/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=25168 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.mz3wB1nMBD/pbuilderrc_eRYP --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.mz3wB1nMBD/b2 --logfile b2/build.log --extrapackages usrmerge sniffles_1.0.12b+ds-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 4.15.0-147-generic #151-Ubuntu SMP Fri Jun 18 19:18:37 UTC 2021 aarch64 GNU/Linux I: ls -l /bin total 5252 -rwxr-xr-x 1 root root 1282512 Jun 22 2021 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 2021 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 2021 findmnt -rwsr-xr-x 1 root root 34824 Feb 27 2021 fusermount -rwxr-xr-x 1 root root 178400 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 93744 Mar 3 2021 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 2021 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 2021 more -rwsr-xr-x 1 root root 51360 Feb 8 2021 mount -rwxr-xr-x 1 root root 14496 Feb 8 2021 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 2021 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 35720 Sep 23 2020 pwd lrwxrwxrwx 1 root root 4 Jun 22 2021 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 Aug 10 14:44 sh -> bash lrwxrwxrwx 1 root root 4 Aug 9 05:47 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 2021 su -rwxr-xr-x 1 root root 35672 Sep 23 2020 sync -rwxr-xr-x 1 root root 535768 Feb 17 2021 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 2021 ulockmgr_server -rwsr-xr-x 1 root root 30880 Feb 8 2021 umount -rwxr-xr-x 1 root root 35640 Sep 23 2020 uname -rwxr-xr-x 2 root root 2346 Mar 3 2021 uncompress -rwxr-xr-x 1 root root 143088 Sep 23 2020 vdir -rwxr-xr-x 1 root root 59584 Feb 8 2021 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/25168/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: arm64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), cmake, libbamtools-dev, libtclap-dev, zlib1g-dev, pandoc 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 cmake; however: Package cmake is not installed. pbuilder-satisfydepends-dummy depends on libbamtools-dev; however: Package libbamtools-dev is not installed. pbuilder-satisfydepends-dummy depends on libtclap-dev; however: Package libtclap-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. 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-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libarchive13{a} libbamtools-dev{a} libbamtools2.5.1{a} libbrotli1{a} libcmark-gfm-extensions0{a} libcmark-gfm0{a} libcurl4{a} libdebhelper-perl{a} libelf1{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libicu67{a} libjsoncpp24{a} libldap-2.4-2{a} libmagic-mgc{a} libmagic1{a} libncurses6{a} libnghttp2-14{a} libpipeline1{a} libprocps8{a} libpsl5{a} librhash0{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsigsegv2{a} libssh2-1{a} libsub-override-perl{a} libtclap-dev{a} libtool{a} libuchardet0{a} libuv1{a} libxml2{a} m4{a} man-db{a} pandoc{a} pandoc-data{a} po-debconf{a} procps{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, 58 newly installed, 0 to remove and 0 not upgraded. Need to get 50.0 MB of archives. After unpacking 295 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 libncurses6 arm64 6.2+20201114-2 [93.2 kB] Get: 7 http://deb.debian.org/debian bullseye/main arm64 libprocps8 arm64 2:3.3.17-5 [61.9 kB] Get: 8 http://deb.debian.org/debian bullseye/main arm64 procps arm64 2:3.3.17-5 [497 kB] Get: 9 http://deb.debian.org/debian bullseye/main arm64 sensible-utils all 0.0.14 [14.8 kB] Get: 10 http://deb.debian.org/debian bullseye/main arm64 libmagic-mgc arm64 1:5.39-3 [273 kB] Get: 11 http://deb.debian.org/debian bullseye/main arm64 libmagic1 arm64 1:5.39-3 [121 kB] Get: 12 http://deb.debian.org/debian bullseye/main arm64 file arm64 1:5.39-3 [69.1 kB] Get: 13 http://deb.debian.org/debian bullseye/main arm64 gettext-base arm64 0.21-4 [173 kB] Get: 14 http://deb.debian.org/debian bullseye/main arm64 libsigsegv2 arm64 2.13-1 [34.7 kB] Get: 15 http://deb.debian.org/debian bullseye/main arm64 m4 arm64 1.4.18-5 [199 kB] Get: 16 http://deb.debian.org/debian bullseye/main arm64 autoconf all 2.69-14 [313 kB] Get: 17 http://deb.debian.org/debian bullseye/main arm64 autotools-dev all 20180224.1+nmu1 [77.1 kB] Get: 18 http://deb.debian.org/debian bullseye/main arm64 automake all 1:1.16.3-2 [814 kB] Get: 19 http://deb.debian.org/debian bullseye/main arm64 autopoint all 0.21-4 [510 kB] Get: 20 http://deb.debian.org/debian bullseye/main arm64 cmake-data all 3.18.4-2 [1725 kB] Get: 21 http://deb.debian.org/debian bullseye/main arm64 libicu67 arm64 67.1-7 [8467 kB] Get: 22 http://deb.debian.org/debian bullseye/main arm64 libxml2 arm64 2.9.10+dfsg-6.7 [629 kB] Get: 23 http://deb.debian.org/debian bullseye/main arm64 libarchive13 arm64 3.4.3-2+b1 [320 kB] Get: 24 http://deb.debian.org/debian bullseye/main arm64 libbrotli1 arm64 1.0.9-2+b2 [267 kB] Get: 25 http://deb.debian.org/debian bullseye/main arm64 libsasl2-modules-db arm64 2.1.27+dfsg-2.1 [69.3 kB] Get: 26 http://deb.debian.org/debian bullseye/main arm64 libsasl2-2 arm64 2.1.27+dfsg-2.1 [105 kB] Get: 27 http://deb.debian.org/debian bullseye/main arm64 libldap-2.4-2 arm64 2.4.57+dfsg-3 [222 kB] Get: 28 http://deb.debian.org/debian bullseye/main arm64 libnghttp2-14 arm64 1.43.0-1 [73.8 kB] Get: 29 http://deb.debian.org/debian bullseye/main arm64 libpsl5 arm64 0.21.0-1.2 [57.1 kB] Get: 30 http://deb.debian.org/debian bullseye/main arm64 librtmp1 arm64 2.4+20151223.gitfa8646d.1-2+b2 [59.4 kB] Get: 31 http://deb.debian.org/debian bullseye/main arm64 libssh2-1 arm64 1.9.0-2 [150 kB] Get: 32 http://deb.debian.org/debian bullseye/main arm64 libcurl4 arm64 7.74.0-1.3+b1 [321 kB] Get: 33 http://deb.debian.org/debian bullseye/main arm64 libexpat1 arm64 2.2.10-2 [83.1 kB] Get: 34 http://deb.debian.org/debian bullseye/main arm64 libjsoncpp24 arm64 1.9.4-4 [72.5 kB] Get: 35 http://deb.debian.org/debian bullseye/main arm64 librhash0 arm64 1.4.1-2 [127 kB] Get: 36 http://deb.debian.org/debian bullseye/main arm64 libuv1 arm64 1.40.0-1 [126 kB] Get: 37 http://deb.debian.org/debian bullseye/main arm64 cmake arm64 3.18.4-2 [3673 kB] Get: 38 http://deb.debian.org/debian bullseye/main arm64 libdebhelper-perl all 13.3.4 [189 kB] Get: 39 http://deb.debian.org/debian bullseye/main arm64 libtool all 2.4.6-15 [513 kB] Get: 40 http://deb.debian.org/debian bullseye/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 41 http://deb.debian.org/debian bullseye/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 42 http://deb.debian.org/debian bullseye/main arm64 libsub-override-perl all 0.09-2 [10.2 kB] Get: 43 http://deb.debian.org/debian bullseye/main arm64 libfile-stripnondeterminism-perl all 1.11.0-1 [25.6 kB] Get: 44 http://deb.debian.org/debian bullseye/main arm64 dh-strip-nondeterminism all 1.11.0-1 [15.3 kB] Get: 45 http://deb.debian.org/debian bullseye/main arm64 libelf1 arm64 0.183-1 [164 kB] Get: 46 http://deb.debian.org/debian bullseye/main arm64 dwz arm64 0.13+20210201-1 [155 kB] Get: 47 http://deb.debian.org/debian bullseye/main arm64 gettext arm64 0.21-4 [1261 kB] Get: 48 http://deb.debian.org/debian bullseye/main arm64 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 49 http://deb.debian.org/debian bullseye/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 50 http://deb.debian.org/debian bullseye/main arm64 debhelper all 13.3.4 [1049 kB] Get: 51 http://deb.debian.org/debian bullseye/main arm64 libbamtools2.5.1 arm64 2.5.1+dfsg-9 [142 kB] Get: 52 http://deb.debian.org/debian bullseye/main arm64 libbamtools-dev arm64 2.5.1+dfsg-9 [197 kB] Get: 53 http://deb.debian.org/debian bullseye/main arm64 libcmark-gfm0 arm64 0.29.0.gfm.0-6 [108 kB] Get: 54 http://deb.debian.org/debian bullseye/main arm64 libcmark-gfm-extensions0 arm64 0.29.0.gfm.0-6 [45.4 kB] Get: 55 http://deb.debian.org/debian bullseye/main arm64 libtclap-dev arm64 1.2.3-1 [143 kB] Get: 56 http://deb.debian.org/debian bullseye/main arm64 pandoc-data all 2.9.2.1-1 [376 kB] Get: 57 http://deb.debian.org/debian bullseye/main arm64 pandoc arm64 2.9.2.1-1+b1 [22.8 MB] Get: 58 http://deb.debian.org/debian bullseye/main arm64 zlib1g-dev arm64 1:1.2.11.dfsg-2 [189 kB] Fetched 50.0 MB in 1s (58.7 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 ... 19646 files and directories currently installed.) Preparing to unpack .../00-bsdextrautils_2.36.1-7_arm64.deb ... Unpacking bsdextrautils (2.36.1-7) ... Selecting previously unselected package libuchardet0:arm64. Preparing to unpack .../01-libuchardet0_0.0.7-1_arm64.deb ... Unpacking libuchardet0:arm64 (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../02-groff-base_1.22.4-6_arm64.deb ... Unpacking groff-base (1.22.4-6) ... Selecting previously unselected package libpipeline1:arm64. Preparing to unpack .../03-libpipeline1_1.5.3-1_arm64.deb ... Unpacking libpipeline1:arm64 (1.5.3-1) ... Selecting previously unselected package man-db. Preparing to unpack .../04-man-db_2.9.4-2_arm64.deb ... Unpacking man-db (2.9.4-2) ... Selecting previously unselected package libncurses6:arm64. Preparing to unpack .../05-libncurses6_6.2+20201114-2_arm64.deb ... Unpacking libncurses6:arm64 (6.2+20201114-2) ... Selecting previously unselected package libprocps8:arm64. Preparing to unpack .../06-libprocps8_2%3a3.3.17-5_arm64.deb ... Unpacking libprocps8:arm64 (2:3.3.17-5) ... Selecting previously unselected package procps. Preparing to unpack .../07-procps_2%3a3.3.17-5_arm64.deb ... Unpacking procps (2:3.3.17-5) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../08-sensible-utils_0.0.14_all.deb ... Unpacking sensible-utils (0.0.14) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../09-libmagic-mgc_1%3a5.39-3_arm64.deb ... Unpacking libmagic-mgc (1:5.39-3) ... Selecting previously unselected package libmagic1:arm64. Preparing to unpack .../10-libmagic1_1%3a5.39-3_arm64.deb ... Unpacking libmagic1:arm64 (1:5.39-3) ... Selecting previously unselected package file. Preparing to unpack .../11-file_1%3a5.39-3_arm64.deb ... Unpacking file (1:5.39-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../12-gettext-base_0.21-4_arm64.deb ... Unpacking gettext-base (0.21-4) ... Selecting previously unselected package libsigsegv2:arm64. Preparing to unpack .../13-libsigsegv2_2.13-1_arm64.deb ... Unpacking libsigsegv2:arm64 (2.13-1) ... Selecting previously unselected package m4. Preparing to unpack .../14-m4_1.4.18-5_arm64.deb ... Unpacking m4 (1.4.18-5) ... Selecting previously unselected package autoconf. Preparing to unpack .../15-autoconf_2.69-14_all.deb ... 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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 libbamtools2.5.1:arm64 (2.5.1+dfsg-9) ... Setting up autopoint (0.21-4) ... Setting up libcmark-gfm0:arm64 (0.29.0.gfm.0-6) ... Setting up libsasl2-2:arm64 (2.1.27+dfsg-2.1) ... Setting up libtclap-dev (1.2.3-1) ... 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 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 pandoc-data (2.9.2.1-1) ... Setting up libelf1:arm64 (0.183-1) ... Setting up libxml2:arm64 (2.9.10+dfsg-6.7) ... Setting up libprocps8:arm64 (2:3.3.17-5) ... Setting up libfile-stripnondeterminism-perl (1.11.0-1) ... Setting up gettext (0.21-4) ... Setting up libtool (2.4.6-15) ... Setting up libarchive13:arm64 (3.4.3-2+b1) ... Setting up libldap-2.4-2:arm64 (2.4.57+dfsg-3) ... Setting up m4 (1.4.18-5) ... Setting up libcmark-gfm-extensions0:arm64 (0.29.0.gfm.0-6) ... Setting up intltool-debian (0.35.0+20060710.5) ... Setting up pandoc (2.9.2.1-1+b1) ... Setting up libbamtools-dev:arm64 (2.5.1+dfsg-9) ... Setting up autoconf (2.69-14) ... Setting up dh-strip-nondeterminism (1.11.0-1) ... 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 libcurl4:arm64 (7.74.0-1.3+b1) ... 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 cmake (3.18.4-2) ... Setting up debhelper (13.3.4) ... Processing triggers for libc-bin (2.31-12) ... 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 (3035 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 ... 25222 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/sniffles-1.0.12b+ds/ && 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 > ../sniffles_1.0.12b+ds-1_source.changes dpkg-buildpackage: info: source package sniffles dpkg-buildpackage: info: source version 1.0.12b+ds-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Steffen Moeller dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/build/sniffles-1.0.12b+ds' dh_auto_clean find -name "*.mk" -delete rm -rf bin rm -f \ makefile \ debian/sniffles.1 \ test.vcf \ make[1]: Leaving directory '/build/sniffles-1.0.12b+ds' dh_clean debian/rules binary dh binary dh_update_autotools_config dh_autoreconf debian/rules override_dh_auto_configure make[1]: Entering directory '/build/sniffles-1.0.12b+ds' dh_auto_configure -- \ -DCMAKE_INCLUDE_PATH="/usr/include/bamtools" 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 -DCMAKE_INCLUDE_PATH=/usr/include/bamtools .. -- 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 OpenMP_C: -fopenmp (found version "4.5") -- Found OpenMP_CXX: -fopenmp (found version "4.5") -- Found OpenMP: TRUE (found version "4.5") -- 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/sniffles-1.0.12b+ds/obj-aarch64-linux-gnu make[1]: Leaving directory '/build/sniffles-1.0.12b+ds' dh_auto_build cd obj-aarch64-linux-gnu && make -j8 "INSTALL=install --strip-program=true" VERBOSE=1 make[1]: Entering directory '/build/sniffles-1.0.12b+ds/obj-aarch64-linux-gnu' /usr/bin/cmake -S/build/sniffles-1.0.12b+ds -B/build/sniffles-1.0.12b+ds/obj-aarch64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/sniffles-1.0.12b+ds/obj-aarch64-linux-gnu/CMakeFiles /build/sniffles-1.0.12b+ds/obj-aarch64-linux-gnu//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/build/sniffles-1.0.12b+ds/obj-aarch64-linux-gnu' make -f src/CMakeFiles/sniffles.dir/build.make src/CMakeFiles/sniffles.dir/depend make[3]: Entering directory '/build/sniffles-1.0.12b+ds/obj-aarch64-linux-gnu' cd /build/sniffles-1.0.12b+ds/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sniffles-1.0.12b+ds /build/sniffles-1.0.12b+ds/src /build/sniffles-1.0.12b+ds/obj-aarch64-linux-gnu /build/sniffles-1.0.12b+ds/obj-aarch64-linux-gnu/src /build/sniffles-1.0.12b+ds/obj-aarch64-linux-gnu/src/CMakeFiles/sniffles.dir/DependInfo.cmake --color= Dependee "/build/sniffles-1.0.12b+ds/obj-aarch64-linux-gnu/src/CMakeFiles/sniffles.dir/DependInfo.cmake" is newer than depender "/build/sniffles-1.0.12b+ds/obj-aarch64-linux-gnu/src/CMakeFiles/sniffles.dir/depend.internal". 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Scanning dependencies of target sniffles make[3]: Leaving directory '/build/sniffles-1.0.12b+ds/obj-aarch64-linux-gnu' make -f src/CMakeFiles/sniffles.dir/build.make src/CMakeFiles/sniffles.dir/build make[3]: Entering directory '/build/sniffles-1.0.12b+ds/obj-aarch64-linux-gnu' [ 4%] Building CXX object src/CMakeFiles/sniffles.dir/Alignment.cpp.o [ 8%] Building CXX object src/CMakeFiles/sniffles.dir/Sniffles.cpp.o cd /build/sniffles-1.0.12b+ds/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/usr/include/bamtools -I/build/sniffles-1.0.12b+ds/src/../lib/bamtools-2.3.0/src -I/build/sniffles-1.0.12b+ds/src/../lib/tclap-1.2.1/include -g -O2 -fdebug-prefix-map=/build/sniffles-1.0.12b+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -o CMakeFiles/sniffles.dir/Alignment.cpp.o -c /build/sniffles-1.0.12b+ds/src/Alignment.cpp [ 13%] Building CXX object src/CMakeFiles/sniffles.dir/Ignore_Regions.cpp.o [ 17%] Building CXX object src/CMakeFiles/sniffles.dir/tree/Breakpoint_Tree.cpp.o [ 21%] Building CXX object src/CMakeFiles/sniffles.dir/Genotyper/Genotyper.cpp.o cd /build/sniffles-1.0.12b+ds/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/usr/include/bamtools -I/build/sniffles-1.0.12b+ds/src/../lib/bamtools-2.3.0/src -I/build/sniffles-1.0.12b+ds/src/../lib/tclap-1.2.1/include -g -O2 -fdebug-prefix-map=/build/sniffles-1.0.12b+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -o CMakeFiles/sniffles.dir/tree/Breakpoint_Tree.cpp.o -c /build/sniffles-1.0.12b+ds/src/tree/Breakpoint_Tree.cpp [ 26%] Building CXX object src/CMakeFiles/sniffles.dir/BamParser.cpp.o cd /build/sniffles-1.0.12b+ds/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/usr/include/bamtools -I/build/sniffles-1.0.12b+ds/src/../lib/bamtools-2.3.0/src -I/build/sniffles-1.0.12b+ds/src/../lib/tclap-1.2.1/include -g -O2 -fdebug-prefix-map=/build/sniffles-1.0.12b+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -o CMakeFiles/sniffles.dir/Genotyper/Genotyper.cpp.o -c /build/sniffles-1.0.12b+ds/src/Genotyper/Genotyper.cpp [ 30%] Building CXX object src/CMakeFiles/sniffles.dir/tree/Intervall_bed.cpp.o [ 34%] Building CXX object src/CMakeFiles/sniffles.dir/sub/Detect_Breakpoints.cpp.o cd /build/sniffles-1.0.12b+ds/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/usr/include/bamtools -I/build/sniffles-1.0.12b+ds/src/../lib/bamtools-2.3.0/src -I/build/sniffles-1.0.12b+ds/src/../lib/tclap-1.2.1/include -g -O2 -fdebug-prefix-map=/build/sniffles-1.0.12b+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -o CMakeFiles/sniffles.dir/BamParser.cpp.o -c /build/sniffles-1.0.12b+ds/src/BamParser.cpp cd /build/sniffles-1.0.12b+ds/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/usr/include/bamtools -I/build/sniffles-1.0.12b+ds/src/../lib/bamtools-2.3.0/src -I/build/sniffles-1.0.12b+ds/src/../lib/tclap-1.2.1/include -g -O2 -fdebug-prefix-map=/build/sniffles-1.0.12b+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -o CMakeFiles/sniffles.dir/Sniffles.cpp.o -c /build/sniffles-1.0.12b+ds/src/Sniffles.cpp cd /build/sniffles-1.0.12b+ds/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/usr/include/bamtools -I/build/sniffles-1.0.12b+ds/src/../lib/bamtools-2.3.0/src -I/build/sniffles-1.0.12b+ds/src/../lib/tclap-1.2.1/include -g -O2 -fdebug-prefix-map=/build/sniffles-1.0.12b+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -o CMakeFiles/sniffles.dir/Ignore_Regions.cpp.o -c /build/sniffles-1.0.12b+ds/src/Ignore_Regions.cpp cd /build/sniffles-1.0.12b+ds/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/usr/include/bamtools -I/build/sniffles-1.0.12b+ds/src/../lib/bamtools-2.3.0/src -I/build/sniffles-1.0.12b+ds/src/../lib/tclap-1.2.1/include -g -O2 -fdebug-prefix-map=/build/sniffles-1.0.12b+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -o CMakeFiles/sniffles.dir/tree/Intervall_bed.cpp.o -c /build/sniffles-1.0.12b+ds/src/tree/Intervall_bed.cpp cd /build/sniffles-1.0.12b+ds/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/usr/include/bamtools -I/build/sniffles-1.0.12b+ds/src/../lib/bamtools-2.3.0/src -I/build/sniffles-1.0.12b+ds/src/../lib/tclap-1.2.1/include -g -O2 -fdebug-prefix-map=/build/sniffles-1.0.12b+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -o CMakeFiles/sniffles.dir/sub/Detect_Breakpoints.cpp.o -c /build/sniffles-1.0.12b+ds/src/sub/Detect_Breakpoints.cpp [ 39%] Building CXX object src/CMakeFiles/sniffles.dir/sub/Breakpoint.cpp.o cd /build/sniffles-1.0.12b+ds/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/usr/include/bamtools -I/build/sniffles-1.0.12b+ds/src/../lib/bamtools-2.3.0/src -I/build/sniffles-1.0.12b+ds/src/../lib/tclap-1.2.1/include -g -O2 -fdebug-prefix-map=/build/sniffles-1.0.12b+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -o CMakeFiles/sniffles.dir/sub/Breakpoint.cpp.o -c /build/sniffles-1.0.12b+ds/src/sub/Breakpoint.cpp [ 43%] Building CXX object src/CMakeFiles/sniffles.dir/tree/IntervallTree.cpp.o cd /build/sniffles-1.0.12b+ds/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/usr/include/bamtools -I/build/sniffles-1.0.12b+ds/src/../lib/bamtools-2.3.0/src -I/build/sniffles-1.0.12b+ds/src/../lib/tclap-1.2.1/include -g -O2 -fdebug-prefix-map=/build/sniffles-1.0.12b+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -o CMakeFiles/sniffles.dir/tree/IntervallTree.cpp.o -c /build/sniffles-1.0.12b+ds/src/tree/IntervallTree.cpp [ 47%] Building CXX object src/CMakeFiles/sniffles.dir/tree/IntervallList.cpp.o cd /build/sniffles-1.0.12b+ds/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/usr/include/bamtools -I/build/sniffles-1.0.12b+ds/src/../lib/bamtools-2.3.0/src -I/build/sniffles-1.0.12b+ds/src/../lib/tclap-1.2.1/include -g -O2 -fdebug-prefix-map=/build/sniffles-1.0.12b+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -o CMakeFiles/sniffles.dir/tree/IntervallList.cpp.o -c /build/sniffles-1.0.12b+ds/src/tree/IntervallList.cpp /build/sniffles-1.0.12b+ds/src/Genotyper/Genotyper.cpp: In member function 'void Genotyper::update_svs_output(std::map, std::vector >)': /build/sniffles-1.0.12b+ds/src/Genotyper/Genotyper.cpp:343:8: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 343 | system(move.c_str()); | ~~~~~~^~~~~~~~~~~~~~ /build/sniffles-1.0.12b+ds/src/Genotyper/Genotyper.cpp: In member function 'void Genotyper::update_SVs2()': /build/sniffles-1.0.12b+ds/src/Genotyper/Genotyper.cpp:382:8: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 382 | system(del.c_str()); | ~~~~~~^~~~~~~~~~~~~ /build/sniffles-1.0.12b+ds/src/Genotyper/Genotyper.cpp: In member function 'void Genotyper::update_file(Breakpoint_Tree&, breakpoint_node*&)': /build/sniffles-1.0.12b+ds/src/Genotyper/Genotyper.cpp:719:8: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 719 | system(move.c_str()); | ~~~~~~^~~~~~~~~~~~~~ /build/sniffles-1.0.12b+ds/src/Genotyper/Genotyper.cpp: In member function 'void Genotyper::update_SVs()': /build/sniffles-1.0.12b+ds/src/Genotyper/Genotyper.cpp:858:8: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 858 | system(del.c_str()); | ~~~~~~^~~~~~~~~~~~~ [ 52%] Building CXX object src/CMakeFiles/sniffles.dir/realign/SWCPU.cpp.o cd /build/sniffles-1.0.12b+ds/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/usr/include/bamtools -I/build/sniffles-1.0.12b+ds/src/../lib/bamtools-2.3.0/src -I/build/sniffles-1.0.12b+ds/src/../lib/tclap-1.2.1/include -g -O2 -fdebug-prefix-map=/build/sniffles-1.0.12b+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -o CMakeFiles/sniffles.dir/realign/SWCPU.cpp.o -c /build/sniffles-1.0.12b+ds/src/realign/SWCPU.cpp /build/sniffles-1.0.12b+ds/src/realign/SWCPU.cpp: In constructor 'SWCPUCor::SWCPUCor(int)': /build/sniffles-1.0.12b+ds/src/realign/SWCPU.cpp:30:35: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] 30 | fprintf(stderr, "Allocationg: %llu\n", maxLen * sizeof(MatrixElement)); | ~~~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | | long unsigned int | long long unsigned int | %lu [ 56%] Building CXX object src/CMakeFiles/sniffles.dir/realign/Realign.cpp.o cd /build/sniffles-1.0.12b+ds/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/usr/include/bamtools -I/build/sniffles-1.0.12b+ds/src/../lib/bamtools-2.3.0/src -I/build/sniffles-1.0.12b+ds/src/../lib/tclap-1.2.1/include -g -O2 -fdebug-prefix-map=/build/sniffles-1.0.12b+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -o CMakeFiles/sniffles.dir/realign/Realign.cpp.o -c /build/sniffles-1.0.12b+ds/src/realign/Realign.cpp [ 60%] Building CXX object src/CMakeFiles/sniffles.dir/print/VCFPrinter.cpp.o cd /build/sniffles-1.0.12b+ds/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/usr/include/bamtools -I/build/sniffles-1.0.12b+ds/src/../lib/bamtools-2.3.0/src -I/build/sniffles-1.0.12b+ds/src/../lib/tclap-1.2.1/include -g -O2 -fdebug-prefix-map=/build/sniffles-1.0.12b+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -o CMakeFiles/sniffles.dir/print/VCFPrinter.cpp.o -c /build/sniffles-1.0.12b+ds/src/print/VCFPrinter.cpp [ 65%] Building CXX object src/CMakeFiles/sniffles.dir/print/BedpePrinter.cpp.o cd /build/sniffles-1.0.12b+ds/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/usr/include/bamtools -I/build/sniffles-1.0.12b+ds/src/../lib/bamtools-2.3.0/src -I/build/sniffles-1.0.12b+ds/src/../lib/tclap-1.2.1/include -g -O2 -fdebug-prefix-map=/build/sniffles-1.0.12b+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -o CMakeFiles/sniffles.dir/print/BedpePrinter.cpp.o -c /build/sniffles-1.0.12b+ds/src/print/BedpePrinter.cpp /build/sniffles-1.0.12b+ds/src/print/VCFPrinter.cpp: In member function 'virtual void VCFPrinter::print_body(Breakpoint*&, BamTools::RefVector)': /build/sniffles-1.0.12b+ds/src/print/VCFPrinter.cpp:369:22: warning: format '%i' expects argument of type 'int', but argument 3 has type 'std::__cxx11::basic_string::size_type' {aka 'long unsigned int'} [-Wformat=] 369 | fprintf(file, "%i", SV->get_sequence().size()); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | int std::__cxx11::basic_string::size_type {aka long unsigned int} | %li /build/sniffles-1.0.12b+ds/src/print/VCFPrinter.cpp:376:21: warning: format '%i' expects argument of type 'int', but argument 3 has type 'long int' [-Wformat=] 376 | fprintf(file, "%i", SV->get_length() * -1); | ~^ ~~~~~~~~~~~~~~~~~~~~~ | | | | int long int | %li /build/sniffles-1.0.12b+ds/src/print/VCFPrinter.cpp:378:21: warning: format '%i' expects argument of type 'int', but argument 3 has type 'long int' [-Wformat=] 378 | fprintf(file, "%i", SV->get_length()); | ~^ ~~~~~~~~~~~~~~~~ | | | | int long int | %li /build/sniffles-1.0.12b+ds/src/print/VCFPrinter.cpp: In member function 'virtual void VCFPrinter::print_body_recall(Breakpoint*&, BamTools::RefVector)': /build/sniffles-1.0.12b+ds/src/print/VCFPrinter.cpp:510:19: warning: format '%i' expects argument of type 'int', but argument 3 has type 'long int' [-Wformat=] 510 | fprintf(file, "%i", SV->get_length()); | ~^ ~~~~~~~~~~~~~~~~ | | | | int long int | %li /build/sniffles-1.0.12b+ds/src/print/BedpePrinter.cpp: In member function 'virtual void BedpePrinter::print_body(Breakpoint*&, BamTools::RefVector)': /build/sniffles-1.0.12b+ds/src/print/BedpePrinter.cpp:99:21: warning: format '%i' expects argument of type 'int', but argument 3 has type 'long int' [-Wformat=] 99 | fprintf(file, "%i", SV->get_length()); | ~^ ~~~~~~~~~~~~~~~~ | | | | int long int | %li /build/sniffles-1.0.12b+ds/src/print/BedpePrinter.cpp: In member function 'virtual void BedpePrinter::print_body_recall(Breakpoint*&, BamTools::RefVector)': /build/sniffles-1.0.12b+ds/src/print/BedpePrinter.cpp:123:18: warning: format '%i' expects argument of type 'int', but argument 3 has type 'long int' [-Wformat=] 123 | fprintf(file, "%i", IPrinter::calc_pos(SV->get_coordinates().start.max_pos, ref, chr)); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | int long int | %li /build/sniffles-1.0.12b+ds/src/print/BedpePrinter.cpp:130:18: warning: format '%i' expects argument of type 'int', but argument 3 has type 'long int' [-Wformat=] 130 | fprintf(file, "%i", IPrinter::calc_pos(SV->get_coordinates().stop.max_pos, ref, chr)); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | int long int | %li /build/sniffles-1.0.12b+ds/src/print/BedpePrinter.cpp:158:19: warning: format '%i' expects argument of type 'int', but argument 3 has type 'long int' [-Wformat=] 158 | fprintf(file, "%i", SV->get_length()); | ~^ ~~~~~~~~~~~~~~~~ | | | | int long int | %li [ 69%] Building CXX object src/CMakeFiles/sniffles.dir/print/IPrinter.cpp.o cd /build/sniffles-1.0.12b+ds/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/usr/include/bamtools -I/build/sniffles-1.0.12b+ds/src/../lib/bamtools-2.3.0/src -I/build/sniffles-1.0.12b+ds/src/../lib/tclap-1.2.1/include -g -O2 -fdebug-prefix-map=/build/sniffles-1.0.12b+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -o CMakeFiles/sniffles.dir/print/IPrinter.cpp.o -c /build/sniffles-1.0.12b+ds/src/print/IPrinter.cpp [ 73%] Building CXX object src/CMakeFiles/sniffles.dir/tree/BinTree.cpp.o cd /build/sniffles-1.0.12b+ds/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/usr/include/bamtools -I/build/sniffles-1.0.12b+ds/src/../lib/bamtools-2.3.0/src -I/build/sniffles-1.0.12b+ds/src/../lib/tclap-1.2.1/include -g -O2 -fdebug-prefix-map=/build/sniffles-1.0.12b+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -o CMakeFiles/sniffles.dir/tree/BinTree.cpp.o -c /build/sniffles-1.0.12b+ds/src/tree/BinTree.cpp /build/sniffles-1.0.12b+ds/src/print/IPrinter.cpp: In function 'void write_read(Alignment*, FILE*&)': /build/sniffles-1.0.12b+ds/src/print/IPrinter.cpp:21:29: warning: unknown conversion type character 'r' in format [-Wformat=] 21 | fprintf(ref_allel_reads, "%ref_plus", '\t'); | ^ /build/sniffles-1.0.12b+ds/src/print/IPrinter.cpp:21:27: warning: too many arguments for format [-Wformat-extra-args] 21 | fprintf(ref_allel_reads, "%ref_plus", '\t'); | ^~~~~~~~~~~ /build/sniffles-1.0.12b+ds/src/print/IPrinter.cpp:23:29: warning: unknown conversion type character 'r' in format [-Wformat=] 23 | fprintf(ref_allel_reads, "%ref_plus", '\t'); | ^ /build/sniffles-1.0.12b+ds/src/print/IPrinter.cpp:23:27: warning: too many arguments for format [-Wformat-extra-args] 23 | fprintf(ref_allel_reads, "%ref_plus", '\t'); | ^~~~~~~~~~~ /build/sniffles-1.0.12b+ds/src/print/IPrinter.cpp:24:29: warning: format '%i' expects argument of type 'int', but argument 3 has type 'size_t' {aka 'long unsigned int'} [-Wformat=] 24 | fprintf(ref_allel_reads, "%i", tmp_aln->getRefLength()); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~ | | | | int size_t {aka long unsigned int} | %li /build/sniffles-1.0.12b+ds/src/print/IPrinter.cpp:25:29: warning: unknown conversion type character 'r' in format [-Wformat=] 25 | fprintf(ref_allel_reads, "%ref_plus", '\t'); | ^ /build/sniffles-1.0.12b+ds/src/print/IPrinter.cpp:25:27: warning: too many arguments for format [-Wformat-extra-args] 25 | fprintf(ref_allel_reads, "%ref_plus", '\t'); | ^~~~~~~~~~~ /build/sniffles-1.0.12b+ds/src/print/IPrinter.cpp:27:30: warning: unknown conversion type character 'r' in format [-Wformat=] 27 | fprintf(ref_allel_reads, "%ref_plus", '1'); | ^ /build/sniffles-1.0.12b+ds/src/print/IPrinter.cpp:27:28: warning: too many arguments for format [-Wformat-extra-args] 27 | fprintf(ref_allel_reads, "%ref_plus", '1'); | ^~~~~~~~~~~ /build/sniffles-1.0.12b+ds/src/print/IPrinter.cpp:29:30: warning: unknown conversion type character 'r' in format [-Wformat=] 29 | fprintf(ref_allel_reads, "%ref_plus", '2'); | ^ /build/sniffles-1.0.12b+ds/src/print/IPrinter.cpp:29:28: warning: too many arguments for format [-Wformat-extra-args] 29 | fprintf(ref_allel_reads, "%ref_plus", '2'); | ^~~~~~~~~~~ /build/sniffles-1.0.12b+ds/src/print/IPrinter.cpp:31:29: warning: unknown conversion type character 'r' in format [-Wformat=] 31 | fprintf(ref_allel_reads, "%ref_plus", '\n'); | ^ /build/sniffles-1.0.12b+ds/src/print/IPrinter.cpp:31:27: warning: too many arguments for format [-Wformat-extra-args] 31 | fprintf(ref_allel_reads, "%ref_plus", '\n'); | ^~~~~~~~~~~ [ 78%] Building CXX object src/CMakeFiles/sniffles.dir/plane-sweep/PlaneSweep_slim.cpp.o cd /build/sniffles-1.0.12b+ds/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/usr/include/bamtools -I/build/sniffles-1.0.12b+ds/src/../lib/bamtools-2.3.0/src -I/build/sniffles-1.0.12b+ds/src/../lib/tclap-1.2.1/include -g -O2 -fdebug-prefix-map=/build/sniffles-1.0.12b+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -o CMakeFiles/sniffles.dir/plane-sweep/PlaneSweep_slim.cpp.o -c /build/sniffles-1.0.12b+ds/src/plane-sweep/PlaneSweep_slim.cpp [ 82%] Building CXX object src/CMakeFiles/sniffles.dir/print/NGMPrinter.cpp.o cd /build/sniffles-1.0.12b+ds/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/usr/include/bamtools -I/build/sniffles-1.0.12b+ds/src/../lib/bamtools-2.3.0/src -I/build/sniffles-1.0.12b+ds/src/../lib/tclap-1.2.1/include -g -O2 -fdebug-prefix-map=/build/sniffles-1.0.12b+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -o CMakeFiles/sniffles.dir/print/NGMPrinter.cpp.o -c /build/sniffles-1.0.12b+ds/src/print/NGMPrinter.cpp [ 86%] Building CXX object src/CMakeFiles/sniffles.dir/cluster/Cluster_SVs.cpp.o cd /build/sniffles-1.0.12b+ds/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/usr/include/bamtools -I/build/sniffles-1.0.12b+ds/src/../lib/bamtools-2.3.0/src -I/build/sniffles-1.0.12b+ds/src/../lib/tclap-1.2.1/include -g -O2 -fdebug-prefix-map=/build/sniffles-1.0.12b+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -o CMakeFiles/sniffles.dir/cluster/Cluster_SVs.cpp.o -c /build/sniffles-1.0.12b+ds/src/cluster/Cluster_SVs.cpp [ 91%] Building CXX object src/CMakeFiles/sniffles.dir/force_calling/Force_calling.cpp.o cd /build/sniffles-1.0.12b+ds/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/usr/include/bamtools -I/build/sniffles-1.0.12b+ds/src/../lib/bamtools-2.3.0/src -I/build/sniffles-1.0.12b+ds/src/../lib/tclap-1.2.1/include -g -O2 -fdebug-prefix-map=/build/sniffles-1.0.12b+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -o CMakeFiles/sniffles.dir/force_calling/Force_calling.cpp.o -c /build/sniffles-1.0.12b+ds/src/force_calling/Force_calling.cpp /build/sniffles-1.0.12b+ds/src/cluster/Cluster_SVs.cpp: In member function 'void Cluster_SVS::update_SVs(std::vector&)': /build/sniffles-1.0.12b+ds/src/cluster/Cluster_SVs.cpp:84:8: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 84 | system(move.c_str()); | ~~~~~~^~~~~~~~~~~~~~ /build/sniffles-1.0.12b+ds/src/cluster/Cluster_SVs.cpp: In member function 'void Cluster_SVS::update_SVs()': /build/sniffles-1.0.12b+ds/src/cluster/Cluster_SVs.cpp:154:8: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 154 | system(del.c_str()); | ~~~~~~^~~~~~~~~~~~~ [ 95%] Building CXX object src/CMakeFiles/sniffles.dir/force_calling/VCF_parser.cpp.o cd /build/sniffles-1.0.12b+ds/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/usr/include/bamtools -I/build/sniffles-1.0.12b+ds/src/../lib/bamtools-2.3.0/src -I/build/sniffles-1.0.12b+ds/src/../lib/tclap-1.2.1/include -g -O2 -fdebug-prefix-map=/build/sniffles-1.0.12b+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -o CMakeFiles/sniffles.dir/force_calling/VCF_parser.cpp.o -c /build/sniffles-1.0.12b+ds/src/force_calling/VCF_parser.cpp [100%] Linking CXX executable ../../bin/sniffles-core-1.0.12/sniffles cd /build/sniffles-1.0.12b+ds/obj-aarch64-linux-gnu/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/sniffles.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/sniffles-1.0.12b+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/sniffles.dir/tree/Breakpoint_Tree.cpp.o CMakeFiles/sniffles.dir/Genotyper/Genotyper.cpp.o CMakeFiles/sniffles.dir/Alignment.cpp.o CMakeFiles/sniffles.dir/BamParser.cpp.o CMakeFiles/sniffles.dir/Sniffles.cpp.o CMakeFiles/sniffles.dir/Ignore_Regions.cpp.o CMakeFiles/sniffles.dir/tree/Intervall_bed.cpp.o CMakeFiles/sniffles.dir/sub/Detect_Breakpoints.cpp.o CMakeFiles/sniffles.dir/sub/Breakpoint.cpp.o CMakeFiles/sniffles.dir/tree/IntervallTree.cpp.o CMakeFiles/sniffles.dir/tree/IntervallList.cpp.o CMakeFiles/sniffles.dir/realign/SWCPU.cpp.o CMakeFiles/sniffles.dir/realign/Realign.cpp.o CMakeFiles/sniffles.dir/print/VCFPrinter.cpp.o CMakeFiles/sniffles.dir/print/BedpePrinter.cpp.o CMakeFiles/sniffles.dir/print/IPrinter.cpp.o CMakeFiles/sniffles.dir/tree/BinTree.cpp.o CMakeFiles/sniffles.dir/print/NGMPrinter.cpp.o CMakeFiles/sniffles.dir/plane-sweep/PlaneSweep_slim.cpp.o CMakeFiles/sniffles.dir/cluster/Cluster_SVs.cpp.o CMakeFiles/sniffles.dir/force_calling/Force_calling.cpp.o CMakeFiles/sniffles.dir/force_calling/VCF_parser.cpp.o -o ../../bin/sniffles-core-1.0.12/sniffles -lbamtools -lz make[3]: Leaving directory '/build/sniffles-1.0.12b+ds/obj-aarch64-linux-gnu' [100%] Built target sniffles make[2]: Leaving directory '/build/sniffles-1.0.12b+ds/obj-aarch64-linux-gnu' /usr/bin/cmake -E cmake_progress_start /build/sniffles-1.0.12b+ds/obj-aarch64-linux-gnu/CMakeFiles 0 make[1]: Leaving directory '/build/sniffles-1.0.12b+ds/obj-aarch64-linux-gnu' debian/rules override_dh_auto_test make[1]: Entering directory '/build/sniffles-1.0.12b+ds' bin/sniffles-*/sniffles -m test_set/reads_region.bam -v test.vcf Estimating parameter... Max dist between aln events: 4 Max diff in window: 50 Min score ratio: 2 Avg DEL ratio: 0.0432235 Avg INS ratio: 0.0740733 Start parsing... 21 Switch Chr 21 Reassessing breakpoints Continue parsing Finalizing .. Start genotype calling: Reopening Bam file for parsing coverage Finalizing .. make[1]: Leaving directory '/build/sniffles-1.0.12b+ds' create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install dh_install dh_installdocs dh_installchangelogs dh_installexamples debian/rules override_dh_installman make[1]: Entering directory '/build/sniffles-1.0.12b+ds' pandoc --from markdown --to man -s debian/sniffles.1.md -o debian/sniffles.1 dh_installman debian/sniffles.1 make[1]: Leaving directory '/build/sniffles-1.0.12b+ds' 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 'sniffles' in '../sniffles_1.0.12b+ds-1_arm64.deb'. dpkg-deb: building package 'sniffles-dbgsym' in '../sniffles-dbgsym_1.0.12b+ds-1_arm64.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../sniffles_1.0.12b+ds-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/25168/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/25168/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/25168 and its subdirectories I: Current time: Wed Aug 10 14:45:50 +14 2022 I: pbuilder-time-stamp: 1660092350