I: pbuilder: network access will be disabled during build I: Current time: Fri Jul 24 14:08:57 -12 2020 I: pbuilder-time-stamp: 1595642937 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/buster-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_1.0.11+ds-1.dsc] I: copying [./sniffles_1.0.11+ds.orig.tar.xz] I: copying [./sniffles_1.0.11+ds-1.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/var/lib/jenkins/.gnupg/trustedkeys.kbx': General error gpgv: Signature made Fri Feb 1 02:32:16 2019 -12 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 ./sniffles_1.0.11+ds-1.dsc dpkg-source: info: extracting sniffles in sniffles-1.0.11+ds dpkg-source: info: unpacking sniffles_1.0.11+ds.orig.tar.xz dpkg-source: info: unpacking sniffles_1.0.11+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 I: using fakeroot in build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/24438/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='arm64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=8' DISTRIBUTION='' HOME='/var/lib/jenkins' HOST_ARCH='arm64' IFS=' ' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='24438' PS1='# ' PS2='> ' PS4='+ ' PWD='/' SHELL='/bin/bash' SHLVL='2' SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/tmp.iUDbZF9QEq/pbuilderrc_Kudn --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/buster-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.iUDbZF9QEq/b1 --logfile b1/build.log sniffles_1.0.11+ds-1.dsc' SUDO_GID='117' SUDO_UID='110' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' USERNAME='root' _='/usr/bin/systemd-run' http_proxy='http://192.168.101.16:3128' I: uname -a Linux codethink-sled10-arm64 4.4.0-186-generic #216-Ubuntu SMP Wed Jul 1 05:35:21 UTC 2020 aarch64 GNU/Linux I: ls -l /bin total 4928 -rwxr-xr-x 1 root root 1216928 Apr 17 2019 bash -rwxr-xr-x 3 root root 34808 Jul 10 2019 bunzip2 -rwxr-xr-x 3 root root 34808 Jul 10 2019 bzcat lrwxrwxrwx 1 root root 6 Jul 10 2019 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2227 Jul 10 2019 bzdiff lrwxrwxrwx 1 root root 6 Jul 10 2019 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4877 Jun 24 2019 bzexe lrwxrwxrwx 1 root root 6 Jul 10 2019 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3641 Jul 10 2019 bzgrep -rwxr-xr-x 3 root root 34808 Jul 10 2019 bzip2 -rwxr-xr-x 1 root root 14264 Jul 10 2019 bzip2recover lrwxrwxrwx 1 root root 6 Jul 10 2019 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Jul 10 2019 bzmore -rwxr-xr-x 1 root root 35576 Feb 28 2019 cat -rwxr-xr-x 1 root root 60256 Feb 28 2019 chgrp -rwxr-xr-x 1 root root 56096 Feb 28 2019 chmod -rwxr-xr-x 1 root root 64368 Feb 28 2019 chown -rwxr-xr-x 1 root root 134632 Feb 28 2019 cp -rwxr-xr-x 1 root root 129536 Jan 17 2019 dash -rwxr-xr-x 1 root root 97136 Feb 28 2019 date -rwxr-xr-x 1 root root 76736 Feb 28 2019 dd -rwxr-xr-x 1 root root 93752 Feb 28 2019 df -rwxr-xr-x 1 root root 138848 Feb 28 2019 dir -rwxr-xr-x 1 root root 75984 Jan 9 2019 dmesg lrwxrwxrwx 1 root root 8 Sep 26 2018 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Sep 26 2018 domainname -> hostname -rwxr-xr-x 1 root root 31368 Feb 28 2019 echo -rwxr-xr-x 1 root root 28 Jan 7 2019 egrep -rwxr-xr-x 1 root root 27256 Feb 28 2019 false -rwxr-xr-x 1 root root 28 Jan 7 2019 fgrep -rwxr-xr-x 1 root root 68792 Jan 9 2019 findmnt -rwsr-xr-x 1 root root 34824 Apr 22 07:38 fusermount -rwxr-xr-x 1 root root 174304 Jan 7 2019 grep -rwxr-xr-x 2 root root 2345 Jan 5 2019 gunzip -rwxr-xr-x 1 root root 6375 Jan 5 2019 gzexe -rwxr-xr-x 1 root root 89656 Jan 5 2019 gzip -rwxr-xr-x 1 root root 18440 Sep 26 2018 hostname -rwxr-xr-x 1 root root 64472 Feb 28 2019 ln -rwxr-xr-x 1 root root 52544 Jul 26 2018 login -rwxr-xr-x 1 root root 138848 Feb 28 2019 ls -rwxr-xr-x 1 root root 108552 Jan 9 2019 lsblk -rwxr-xr-x 1 root root 76840 Feb 28 2019 mkdir -rwxr-xr-x 1 root root 64480 Feb 28 2019 mknod -rwxr-xr-x 1 root root 39736 Feb 28 2019 mktemp -rwxr-xr-x 1 root root 38840 Jan 9 2019 more -rwsr-xr-x 1 root root 47112 Jan 9 2019 mount -rwxr-xr-x 1 root root 14344 Jan 9 2019 mountpoint -rwxr-xr-x 1 root root 138736 Feb 28 2019 mv lrwxrwxrwx 1 root root 8 Sep 26 2018 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Feb 14 2019 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 35560 Feb 28 2019 pwd lrwxrwxrwx 1 root root 4 Apr 17 2019 rbash -> bash -rwxr-xr-x 1 root root 43712 Feb 28 2019 readlink -rwxr-xr-x 1 root root 68440 Feb 28 2019 rm -rwxr-xr-x 1 root root 39624 Feb 28 2019 rmdir -rwxr-xr-x 1 root root 19144 Jan 21 2019 run-parts -rwxr-xr-x 1 root root 114016 Dec 22 2018 sed lrwxrwxrwx 1 root root 4 Jul 23 20:26 sh -> dash -rwxr-xr-x 1 root root 31384 Feb 28 2019 sleep -rwxr-xr-x 1 root root 72480 Feb 28 2019 stty -rwsr-xr-x 1 root root 59424 Jan 9 2019 su -rwxr-xr-x 1 root root 31416 Feb 28 2019 sync -rwxr-xr-x 1 root root 449416 Apr 23 2019 tar -rwxr-xr-x 1 root root 10560 Jan 21 2019 tempfile -rwxr-xr-x 1 root root 88968 Feb 28 2019 touch -rwxr-xr-x 1 root root 27256 Feb 28 2019 true -rwxr-xr-x 1 root root 14264 Apr 22 07:38 ulockmgr_server -rwsr-xr-x 1 root root 30728 Jan 9 2019 umount -rwxr-xr-x 1 root root 31384 Feb 28 2019 uname -rwxr-xr-x 2 root root 2345 Jan 5 2019 uncompress -rwxr-xr-x 1 root root 138848 Feb 28 2019 vdir -rwxr-xr-x 1 root root 34824 Jan 9 2019 wdctl -rwxr-xr-x 1 root root 946 Jan 21 2019 which lrwxrwxrwx 1 root root 8 Sep 26 2018 ypdomainname -> hostname -rwxr-xr-x 1 root root 1983 Jan 5 2019 zcat -rwxr-xr-x 1 root root 1677 Jan 5 2019 zcmp -rwxr-xr-x 1 root root 5879 Jan 5 2019 zdiff -rwxr-xr-x 1 root root 29 Jan 5 2019 zegrep -rwxr-xr-x 1 root root 29 Jan 5 2019 zfgrep -rwxr-xr-x 1 root root 2080 Jan 5 2019 zforce -rwxr-xr-x 1 root root 7584 Jan 5 2019 zgrep -rwxr-xr-x 1 root root 2205 Jan 5 2019 zless -rwxr-xr-x 1 root root 1841 Jan 5 2019 zmore -rwxr-xr-x 1 root root 4552 Jan 5 2019 znew I: user script /srv/workspace/pbuilder/24438/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 (>= 12~), 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 ... 19168 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 (>= 12~); however: Package debhelper 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} bsdmainutils{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} libbsd0{a} libcroco3{a} libcurl4{a} libelf1{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libglib2.0-0{a} libgssapi-krb5-2{a} libicu63{a} libjsoncpp1{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} libldap-2.4-2{a} libldap-common{a} liblua5.1-0{a} libmagic-mgc{a} libmagic1{a} libncurses6{a} libnghttp2-14{a} libpipeline1{a} libprocps7{a} libpsl5{a} librhash0{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsigsegv2{a} libssh2-1{a} libssl1.1{a} libtclap-dev{a} libtool{a} libuchardet0{a} libuv1{a} libxml2{a} libyaml-0-2{a} lsb-base{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 krb5-locales libarchive-cpio-perl libglib2.0-data libgpm2 libltdl-dev libmail-sendmail-perl libsasl2-modules lynx psmisc publicsuffix shared-mime-info wget xdg-user-dirs 0 packages upgraded, 66 newly installed, 0 to remove and 0 not upgraded. Need to get 46.6 MB of archives. After unpacking 249 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian buster/main arm64 libbsd0 arm64 0.9.1-2 [97.4 kB] Get: 2 http://deb.debian.org/debian buster/main arm64 bsdmainutils arm64 11.1.2+b1 [185 kB] Get: 3 http://deb.debian.org/debian buster/main arm64 libuchardet0 arm64 0.0.6-3 [65.0 kB] Get: 4 http://deb.debian.org/debian buster/main arm64 groff-base arm64 1.22.4-3 [869 kB] Get: 5 http://deb.debian.org/debian buster/main arm64 libpipeline1 arm64 1.5.1-2 [29.8 kB] Get: 6 http://deb.debian.org/debian buster/main arm64 man-db arm64 2.8.5-2 [1258 kB] Get: 7 http://deb.debian.org/debian buster/main arm64 libncurses6 arm64 6.1+20181013-2+deb10u2 [92.6 kB] Get: 8 http://deb.debian.org/debian buster/main arm64 libprocps7 arm64 2:3.3.15-2 [58.0 kB] Get: 9 http://deb.debian.org/debian buster/main arm64 lsb-base all 10.2019051400 [28.4 kB] Get: 10 http://deb.debian.org/debian buster/main arm64 procps arm64 2:3.3.15-2 [245 kB] Get: 11 http://deb.debian.org/debian buster/main arm64 sensible-utils all 0.0.12 [15.8 kB] Get: 12 http://deb.debian.org/debian buster/main arm64 libmagic-mgc arm64 1:5.35-4+deb10u1 [242 kB] Get: 13 http://deb.debian.org/debian buster/main arm64 libmagic1 arm64 1:5.35-4+deb10u1 [115 kB] Get: 14 http://deb.debian.org/debian buster/main arm64 file arm64 1:5.35-4+deb10u1 [66.4 kB] Get: 15 http://deb.debian.org/debian buster/main arm64 gettext-base arm64 0.19.8.1-9 [120 kB] Get: 16 http://deb.debian.org/debian buster/main arm64 libsigsegv2 arm64 2.12-2 [32.3 kB] Get: 17 http://deb.debian.org/debian buster/main arm64 m4 arm64 1.4.18-2 [198 kB] Get: 18 http://deb.debian.org/debian buster/main arm64 autoconf all 2.69-11 [341 kB] Get: 19 http://deb.debian.org/debian buster/main arm64 autotools-dev all 20180224.1 [77.0 kB] Get: 20 http://deb.debian.org/debian buster/main arm64 automake all 1:1.16.1-4 [771 kB] Get: 21 http://deb.debian.org/debian buster/main arm64 autopoint all 0.19.8.1-9 [434 kB] Get: 22 http://deb.debian.org/debian buster/main arm64 cmake-data all 3.13.4-1 [1476 kB] Get: 23 http://deb.debian.org/debian buster/main arm64 libicu63 arm64 63.1-6+deb10u1 [8151 kB] Get: 24 http://deb.debian.org/debian buster/main arm64 libxml2 arm64 2.9.4+dfsg1-7+b3 [623 kB] Get: 25 http://deb.debian.org/debian buster/main arm64 libarchive13 arm64 3.3.3-4+deb10u1 [291 kB] Get: 26 http://deb.debian.org/debian buster/main arm64 libkeyutils1 arm64 1.6-6 [14.9 kB] Get: 27 http://deb.debian.org/debian buster/main arm64 libkrb5support0 arm64 1.17-3 [64.7 kB] Get: 28 http://deb.debian.org/debian buster/main arm64 libk5crypto3 arm64 1.17-3 [122 kB] Get: 29 http://deb.debian.org/debian buster/main arm64 libssl1.1 arm64 1.1.1d-0+deb10u3 [1382 kB] Get: 30 http://deb.debian.org/debian buster/main arm64 libkrb5-3 arm64 1.17-3 [353 kB] Get: 31 http://deb.debian.org/debian buster/main arm64 libgssapi-krb5-2 arm64 1.17-3 [150 kB] Get: 32 http://deb.debian.org/debian buster/main arm64 libsasl2-modules-db arm64 2.1.27+dfsg-1+deb10u1 [69.3 kB] Get: 33 http://deb.debian.org/debian buster/main arm64 libsasl2-2 arm64 2.1.27+dfsg-1+deb10u1 [105 kB] Get: 34 http://deb.debian.org/debian buster/main arm64 libldap-common all 2.4.47+dfsg-3+deb10u2 [89.7 kB] Get: 35 http://deb.debian.org/debian buster/main arm64 libldap-2.4-2 arm64 2.4.47+dfsg-3+deb10u2 [216 kB] Get: 36 http://deb.debian.org/debian buster/main arm64 libnghttp2-14 arm64 1.36.0-2+deb10u1 [81.9 kB] Get: 37 http://deb.debian.org/debian buster/main arm64 libpsl5 arm64 0.20.2-2 [53.6 kB] Get: 38 http://deb.debian.org/debian buster/main arm64 librtmp1 arm64 2.4+20151223.gitfa8646d.1-2 [55.7 kB] Get: 39 http://deb.debian.org/debian buster/main arm64 libssh2-1 arm64 1.8.0-2.1 [135 kB] Get: 40 http://deb.debian.org/debian buster/main arm64 libcurl4 arm64 7.64.0-4+deb10u1 [312 kB] Get: 41 http://deb.debian.org/debian buster/main arm64 libexpat1 arm64 2.2.6-2+deb10u1 [85.4 kB] Get: 42 http://deb.debian.org/debian buster/main arm64 libjsoncpp1 arm64 1.7.4-3 [71.0 kB] Get: 43 http://deb.debian.org/debian buster/main arm64 librhash0 arm64 1.3.8-1 [121 kB] Get: 44 http://deb.debian.org/debian buster/main arm64 libuv1 arm64 1.24.1-1 [105 kB] Get: 45 http://deb.debian.org/debian buster/main arm64 cmake arm64 3.13.4-1 [3046 kB] Get: 46 http://deb.debian.org/debian buster/main arm64 libtool all 2.4.6-9 [547 kB] Get: 47 http://deb.debian.org/debian buster/main arm64 dh-autoreconf all 19 [16.9 kB] Get: 48 http://deb.debian.org/debian buster/main arm64 libarchive-zip-perl all 1.64-1 [96.8 kB] Get: 49 http://deb.debian.org/debian buster/main arm64 libfile-stripnondeterminism-perl all 1.1.2-1 [19.8 kB] Get: 50 http://deb.debian.org/debian buster/main arm64 dh-strip-nondeterminism all 1.1.2-1 [13.0 kB] Get: 51 http://deb.debian.org/debian buster/main arm64 libelf1 arm64 0.176-1.1 [160 kB] Get: 52 http://deb.debian.org/debian buster/main arm64 dwz arm64 0.12-3 [71.7 kB] Get: 53 http://deb.debian.org/debian buster/main arm64 libglib2.0-0 arm64 2.58.3-2+deb10u2 [1185 kB] Get: 54 http://deb.debian.org/debian buster/main arm64 libcroco3 arm64 0.6.12-3 [140 kB] Get: 55 http://deb.debian.org/debian buster/main arm64 gettext arm64 0.19.8.1-9 [1261 kB] Get: 56 http://deb.debian.org/debian buster/main arm64 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 57 http://deb.debian.org/debian buster/main arm64 po-debconf all 1.0.21 [248 kB] Get: 58 http://deb.debian.org/debian buster/main arm64 debhelper all 12.1.1 [1016 kB] Get: 59 http://deb.debian.org/debian buster/main arm64 libbamtools2.5.1 arm64 2.5.1+dfsg-3 [149 kB] Get: 60 http://deb.debian.org/debian buster/main arm64 libbamtools-dev arm64 2.5.1+dfsg-3 [21.8 kB] Get: 61 http://deb.debian.org/debian buster/main arm64 liblua5.1-0 arm64 5.1.5-8.1+b2 [97.2 kB] Get: 62 http://deb.debian.org/debian buster/main arm64 libtclap-dev arm64 1.2.2-1 [139 kB] Get: 63 http://deb.debian.org/debian buster/main arm64 libyaml-0-2 arm64 0.2.1-1 [41.4 kB] Get: 64 http://deb.debian.org/debian buster/main arm64 pandoc-data all 2.2.1-3 [329 kB] Get: 65 http://deb.debian.org/debian buster/main arm64 pandoc arm64 2.2.1-3+b2 [18.3 MB] Get: 66 http://deb.debian.org/debian buster/main arm64 zlib1g-dev arm64 1:1.2.11.dfsg-1 [210 kB] Fetched 46.6 MB in 8s (6146 kB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libbsd0:arm64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19168 files and directories currently installed.) Preparing to unpack .../00-libbsd0_0.9.1-2_arm64.deb ... Unpacking libbsd0:arm64 (0.9.1-2) ... Selecting previously unselected package bsdmainutils. Preparing to unpack .../01-bsdmainutils_11.1.2+b1_arm64.deb ... Unpacking bsdmainutils (11.1.2+b1) ... Selecting previously unselected package libuchardet0:arm64. Preparing to unpack .../02-libuchardet0_0.0.6-3_arm64.deb ... Unpacking libuchardet0:arm64 (0.0.6-3) ... Selecting previously unselected package groff-base. Preparing to unpack .../03-groff-base_1.22.4-3_arm64.deb ... Unpacking groff-base (1.22.4-3) ... Selecting previously unselected package libpipeline1:arm64. Preparing to unpack .../04-libpipeline1_1.5.1-2_arm64.deb ... Unpacking libpipeline1:arm64 (1.5.1-2) ... Selecting previously unselected package man-db. Preparing to unpack .../05-man-db_2.8.5-2_arm64.deb ... Unpacking man-db (2.8.5-2) ... Selecting previously unselected package libncurses6:arm64. Preparing to unpack .../06-libncurses6_6.1+20181013-2+deb10u2_arm64.deb ... Unpacking libncurses6:arm64 (6.1+20181013-2+deb10u2) ... Selecting previously unselected package libprocps7:arm64. Preparing to unpack .../07-libprocps7_2%3a3.3.15-2_arm64.deb ... Unpacking libprocps7:arm64 (2:3.3.15-2) ... Selecting previously unselected package lsb-base. Preparing to unpack .../08-lsb-base_10.2019051400_all.deb ... Unpacking lsb-base (10.2019051400) ... Selecting previously unselected package procps. Preparing to unpack .../09-procps_2%3a3.3.15-2_arm64.deb ... Unpacking procps (2:3.3.15-2) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../10-sensible-utils_0.0.12_all.deb ... Unpacking sensible-utils (0.0.12) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../11-libmagic-mgc_1%3a5.35-4+deb10u1_arm64.deb ... Unpacking libmagic-mgc (1:5.35-4+deb10u1) ... Selecting previously unselected package libmagic1:arm64. Preparing to unpack .../12-libmagic1_1%3a5.35-4+deb10u1_arm64.deb ... Unpacking libmagic1:arm64 (1:5.35-4+deb10u1) ... Selecting previously unselected package file. Preparing to unpack .../13-file_1%3a5.35-4+deb10u1_arm64.deb ... Unpacking file (1:5.35-4+deb10u1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../14-gettext-base_0.19.8.1-9_arm64.deb ... Unpacking gettext-base (0.19.8.1-9) ... 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No schema files found: doing nothing. Setting up libssl1.1:arm64 (1.1.1d-0+deb10u3) ... Setting up libprocps7:arm64 (2:3.3.15-2) ... Setting up libnghttp2-14:arm64 (1.36.0-2+deb10u1) ... Setting up libmagic1:arm64 (1:5.35-4+deb10u1) ... Setting up gettext-base (0.19.8.1-9) ... Setting up file (1:5.35-4+deb10u1) ... Setting up libldap-common (2.4.47+dfsg-3+deb10u2) ... Setting up libicu63:arm64 (63.1-6+deb10u1) ... Setting up libkrb5support0:arm64 (1.17-3) ... Setting up libsasl2-modules-db:arm64 (2.1.27+dfsg-1+deb10u1) ... Setting up autotools-dev (20180224.1) ... Setting up libuv1:arm64 (1.24.1-1) ... Setting up librtmp1:arm64 (2.4+20151223.gitfa8646d.1-2) ... Setting up libncurses6:arm64 (6.1+20181013-2+deb10u2) ... Setting up libsigsegv2:arm64 (2.12-2) ... Setting up libbamtools2.5.1:arm64 (2.5.1+dfsg-3) ... Setting up autopoint (0.19.8.1-9) ... Setting up libk5crypto3:arm64 (1.17-3) ... Setting up libsasl2-2:arm64 (2.1.27+dfsg-1+deb10u1) ... Setting up libtclap-dev (1.2.2-1) ... Setting up zlib1g-dev:arm64 (1:1.2.11.dfsg-1) ... Setting up sensible-utils (0.0.12) ... Setting up librhash0:arm64 (1.3.8-1) ... Setting up libuchardet0:arm64 (0.0.6-3) ... Setting up procps (2:3.3.15-2) ... update-alternatives: using /usr/bin/w.procps to provide /usr/bin/w (w) in auto mode Setting up liblua5.1-0:arm64 (5.1.5-8.1+b2) ... Setting up libssh2-1:arm64 (1.8.0-2.1) ... Setting up cmake-data (3.13.4-1) ... Setting up libkrb5-3:arm64 (1.17-3) ... Setting up pandoc-data (2.2.1-3) ... Setting up libbsd0:arm64 (0.9.1-2) ... Setting up libelf1:arm64 (0.176-1.1) ... Setting up libxml2:arm64 (2.9.4+dfsg1-7+b3) ... Setting up libjsoncpp1:arm64 (1.7.4-3) ... Setting up libfile-stripnondeterminism-perl (1.1.2-1) ... Setting up libtool (2.4.6-9) ... Setting up libarchive13:arm64 (3.3.3-4+deb10u1) ... Setting up libldap-2.4-2:arm64 (2.4.47+dfsg-3+deb10u2) ... Setting up m4 (1.4.18-2) ... Setting up pandoc (2.2.1-3+b2) ... Setting up libbamtools-dev:arm64 (2.5.1+dfsg-3) ... Setting up bsdmainutils (11.1.2+b1) ... update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode Setting up libgssapi-krb5-2:arm64 (1.17-3) ... Setting up libcroco3:arm64 (0.6.12-3) ... Setting up autoconf (2.69-11) ... Setting up dwz (0.12-3) ... Setting up groff-base (1.22.4-3) ... Setting up libcurl4:arm64 (7.64.0-4+deb10u1) ... Setting up automake (1:1.16.1-4) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up gettext (0.19.8.1-9) ... Setting up man-db (2.8.5-2) ... Not building database; man-db/auto-update is not 'true'. Setting up intltool-debian (0.35.0+20060710.5) ... Setting up cmake (3.13.4-1) ... Setting up po-debconf (1.0.21) ... Setting up debhelper (12.1.1) ... Setting up dh-autoreconf (19) ... Setting up dh-strip-nondeterminism (1.1.2-1) ... Processing triggers for libc-bin (2.28-10) ... Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps Reading package lists... Building dependency tree... Reading state information... fakeroot is already the newest version (1.23-1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package I: Running cd /build/sniffles-1.0.11+ds/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b dpkg-buildpackage: info: source package sniffles dpkg-buildpackage: info: source version 1.0.11+ds-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 fakeroot debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/build/sniffles-1.0.11+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-1.0.11+ds' dh_clean debian/rules build dh build dh_update_autotools_config dh_autoreconf debian/rules override_dh_auto_configure make[1]: Entering directory '/build/sniffles-1.0.11+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 "-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 8.3.0 -- The CXX compiler identification is GNU 8.3.0 -- Check for working C compiler: /usr/bin/cc -- Check for working C compiler: /usr/bin/cc -- works -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Detecting C compile features -- Detecting C compile features - done -- Check for working CXX compiler: /usr/bin/c++ -- Check for working CXX compiler: /usr/bin/c++ -- works -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- 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-1.0.11+ds/obj-aarch64-linux-gnu make[1]: Leaving directory '/build/sniffles-1.0.11+ds' dh_auto_build cd obj-aarch64-linux-gnu && make -j8 "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/sniffles-1.0.11+ds/obj-aarch64-linux-gnu' /usr/bin/cmake -S/build/sniffles-1.0.11+ds -B/build/sniffles-1.0.11+ds/obj-aarch64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/sniffles-1.0.11+ds/obj-aarch64-linux-gnu/CMakeFiles /build/sniffles-1.0.11+ds/obj-aarch64-linux-gnu/CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/build/sniffles-1.0.11+ds/obj-aarch64-linux-gnu' make -f src/CMakeFiles/sniffles.dir/build.make src/CMakeFiles/sniffles.dir/depend make[3]: Entering directory '/build/sniffles-1.0.11+ds/obj-aarch64-linux-gnu' cd /build/sniffles-1.0.11+ds/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/sniffles-1.0.11+ds /build/sniffles-1.0.11+ds/src /build/sniffles-1.0.11+ds/obj-aarch64-linux-gnu /build/sniffles-1.0.11+ds/obj-aarch64-linux-gnu/src /build/sniffles-1.0.11+ds/obj-aarch64-linux-gnu/src/CMakeFiles/sniffles.dir/DependInfo.cmake --color= Scanning dependencies of target sniffles make[3]: Leaving directory '/build/sniffles-1.0.11+ds/obj-aarch64-linux-gnu' make -f src/CMakeFiles/sniffles.dir/build.make src/CMakeFiles/sniffles.dir/build make[3]: Entering directory '/build/sniffles-1.0.11+ds/obj-aarch64-linux-gnu' [ 4%] Building CXX object src/CMakeFiles/sniffles.dir/tree/Breakpoint_Tree.cpp.o cd /build/sniffles-1.0.11+ds/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/usr/include/bamtools -I/build/sniffles-1.0.11+ds/src/../lib/bamtools-2.3.0/src -I/build/sniffles-1.0.11+ds/src/../lib/tclap-1.2.1/include -g -O2 -ffile-prefix-map=/build/sniffles-1.0.11+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-1.0.11+ds/src/tree/Breakpoint_Tree.cpp [ 13%] Building CXX object src/CMakeFiles/sniffles.dir/Genotyper/Genotyper.cpp.o [ 13%] Building CXX object src/CMakeFiles/sniffles.dir/Alignment.cpp.o [ 17%] Building CXX object src/CMakeFiles/sniffles.dir/BamParser.cpp.o cd /build/sniffles-1.0.11+ds/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/usr/include/bamtools -I/build/sniffles-1.0.11+ds/src/../lib/bamtools-2.3.0/src -I/build/sniffles-1.0.11+ds/src/../lib/tclap-1.2.1/include -g -O2 -ffile-prefix-map=/build/sniffles-1.0.11+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-1.0.11+ds/src/Genotyper/Genotyper.cpp cd /build/sniffles-1.0.11+ds/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/usr/include/bamtools -I/build/sniffles-1.0.11+ds/src/../lib/bamtools-2.3.0/src -I/build/sniffles-1.0.11+ds/src/../lib/tclap-1.2.1/include -g -O2 -ffile-prefix-map=/build/sniffles-1.0.11+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-1.0.11+ds/src/Alignment.cpp cd /build/sniffles-1.0.11+ds/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/usr/include/bamtools -I/build/sniffles-1.0.11+ds/src/../lib/bamtools-2.3.0/src -I/build/sniffles-1.0.11+ds/src/../lib/tclap-1.2.1/include -g -O2 -ffile-prefix-map=/build/sniffles-1.0.11+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-1.0.11+ds/src/BamParser.cpp [ 21%] Building CXX object src/CMakeFiles/sniffles.dir/Sniffles.cpp.o cd /build/sniffles-1.0.11+ds/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/usr/include/bamtools -I/build/sniffles-1.0.11+ds/src/../lib/bamtools-2.3.0/src -I/build/sniffles-1.0.11+ds/src/../lib/tclap-1.2.1/include -g -O2 -ffile-prefix-map=/build/sniffles-1.0.11+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-1.0.11+ds/src/Sniffles.cpp [ 26%] Building CXX object src/CMakeFiles/sniffles.dir/tree/Intervall_bed.cpp.o [ 30%] Building CXX object src/CMakeFiles/sniffles.dir/Ignore_Regions.cpp.o cd /build/sniffles-1.0.11+ds/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/usr/include/bamtools -I/build/sniffles-1.0.11+ds/src/../lib/bamtools-2.3.0/src -I/build/sniffles-1.0.11+ds/src/../lib/tclap-1.2.1/include -g -O2 -ffile-prefix-map=/build/sniffles-1.0.11+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-1.0.11+ds/src/tree/Intervall_bed.cpp cd /build/sniffles-1.0.11+ds/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/usr/include/bamtools -I/build/sniffles-1.0.11+ds/src/../lib/bamtools-2.3.0/src -I/build/sniffles-1.0.11+ds/src/../lib/tclap-1.2.1/include -g -O2 -ffile-prefix-map=/build/sniffles-1.0.11+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-1.0.11+ds/src/Ignore_Regions.cpp [ 34%] Building CXX object src/CMakeFiles/sniffles.dir/sub/Detect_Breakpoints.cpp.o cd /build/sniffles-1.0.11+ds/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/usr/include/bamtools -I/build/sniffles-1.0.11+ds/src/../lib/bamtools-2.3.0/src -I/build/sniffles-1.0.11+ds/src/../lib/tclap-1.2.1/include -g -O2 -ffile-prefix-map=/build/sniffles-1.0.11+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-1.0.11+ds/src/sub/Detect_Breakpoints.cpp /build/sniffles-1.0.11+ds/src/tree/Intervall_bed.cpp: In member function 'bool IntervallTree_bed::is_in(long int, Leaf*&)': /build/sniffles-1.0.11+ds/src/tree/Intervall_bed.cpp:91:1: warning: control reaches end of non-void function [-Wreturn-type] } ^ [ 39%] Building CXX object src/CMakeFiles/sniffles.dir/sub/Breakpoint.cpp.o cd /build/sniffles-1.0.11+ds/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/usr/include/bamtools -I/build/sniffles-1.0.11+ds/src/../lib/bamtools-2.3.0/src -I/build/sniffles-1.0.11+ds/src/../lib/tclap-1.2.1/include -g -O2 -ffile-prefix-map=/build/sniffles-1.0.11+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-1.0.11+ds/src/sub/Breakpoint.cpp /build/sniffles-1.0.11+ds/src/Genotyper/Genotyper.cpp: In member function 'void Genotyper::update_file(Breakpoint_Tree&, breakpoint_node*&)': /build/sniffles-1.0.11+ds/src/Genotyper/Genotyper.cpp:252:8: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result] system(move.c_str()); ~~~~~~^~~~~~~~~~~~~~ /build/sniffles-1.0.11+ds/src/Genotyper/Genotyper.cpp: In member function 'void Genotyper::update_SVs()': /build/sniffles-1.0.11+ds/src/Genotyper/Genotyper.cpp:352:8: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result] system(del.c_str()); ~~~~~~^~~~~~~~~~~~~ [ 43%] Building CXX object src/CMakeFiles/sniffles.dir/tree/IntervallTree.cpp.o cd /build/sniffles-1.0.11+ds/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/usr/include/bamtools -I/build/sniffles-1.0.11+ds/src/../lib/bamtools-2.3.0/src -I/build/sniffles-1.0.11+ds/src/../lib/tclap-1.2.1/include -g -O2 -ffile-prefix-map=/build/sniffles-1.0.11+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-1.0.11+ds/src/tree/IntervallTree.cpp [ 47%] Building CXX object src/CMakeFiles/sniffles.dir/tree/IntervallList.cpp.o cd /build/sniffles-1.0.11+ds/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/usr/include/bamtools -I/build/sniffles-1.0.11+ds/src/../lib/bamtools-2.3.0/src -I/build/sniffles-1.0.11+ds/src/../lib/tclap-1.2.1/include -g -O2 -ffile-prefix-map=/build/sniffles-1.0.11+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-1.0.11+ds/src/tree/IntervallList.cpp /build/sniffles-1.0.11+ds/src/tree/IntervallTree.cpp: In member function 'bool IntervallTree::overlaps(long int, long int, TNode*)': /build/sniffles-1.0.11+ds/src/tree/IntervallTree.cpp:141:1: warning: control reaches end of non-void function [-Wreturn-type] } ^ [ 52%] Building CXX object src/CMakeFiles/sniffles.dir/realign/SWCPU.cpp.o cd /build/sniffles-1.0.11+ds/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/usr/include/bamtools -I/build/sniffles-1.0.11+ds/src/../lib/bamtools-2.3.0/src -I/build/sniffles-1.0.11+ds/src/../lib/tclap-1.2.1/include -g -O2 -ffile-prefix-map=/build/sniffles-1.0.11+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-1.0.11+ds/src/realign/SWCPU.cpp /build/sniffles-1.0.11+ds/src/realign/SWCPU.cpp: In constructor 'SWCPUCor::SWCPUCor(int)': /build/sniffles-1.0.11+ds/src/realign/SWCPU.cpp:30:18: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=] fprintf(stderr, "Allocationg: %llu\n", maxLen * sizeof(MatrixElement)); ^~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 56%] Building CXX object src/CMakeFiles/sniffles.dir/realign/Realign.cpp.o cd /build/sniffles-1.0.11+ds/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/usr/include/bamtools -I/build/sniffles-1.0.11+ds/src/../lib/bamtools-2.3.0/src -I/build/sniffles-1.0.11+ds/src/../lib/tclap-1.2.1/include -g -O2 -ffile-prefix-map=/build/sniffles-1.0.11+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-1.0.11+ds/src/realign/Realign.cpp [ 60%] Building CXX object src/CMakeFiles/sniffles.dir/print/VCFPrinter.cpp.o cd /build/sniffles-1.0.11+ds/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/usr/include/bamtools -I/build/sniffles-1.0.11+ds/src/../lib/bamtools-2.3.0/src -I/build/sniffles-1.0.11+ds/src/../lib/tclap-1.2.1/include -g -O2 -ffile-prefix-map=/build/sniffles-1.0.11+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-1.0.11+ds/src/print/VCFPrinter.cpp [ 65%] Building CXX object src/CMakeFiles/sniffles.dir/print/BedpePrinter.cpp.o cd /build/sniffles-1.0.11+ds/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/usr/include/bamtools -I/build/sniffles-1.0.11+ds/src/../lib/bamtools-2.3.0/src -I/build/sniffles-1.0.11+ds/src/../lib/tclap-1.2.1/include -g -O2 -ffile-prefix-map=/build/sniffles-1.0.11+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-1.0.11+ds/src/print/BedpePrinter.cpp /build/sniffles-1.0.11+ds/src/print/BedpePrinter.cpp: In member function 'virtual void BedpePrinter::print_body(Breakpoint*&, BamTools::RefVector)': /build/sniffles-1.0.11+ds/src/print/BedpePrinter.cpp:38:18: warning: format '%i' expects argument of type 'int', but argument 3 has type 'long int' [-Wformat=] fprintf(file, "%i", IPrinter::calc_pos(SV->get_coordinates().start.max_pos, ref, chr)); ^~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/sniffles-1.0.11+ds/src/print/BedpePrinter.cpp:60:18: warning: format '%i' expects argument of type 'int', but argument 3 has type 'long int' [-Wformat=] fprintf(file, "%i", IPrinter::calc_pos(end_coord, ref, chr)); ^~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/sniffles-1.0.11+ds/src/print/BedpePrinter.cpp:95:19: warning: format '%i' expects argument of type 'int', but argument 3 has type 'long int' [-Wformat=] fprintf(file, "%i", SV->get_length()); ^~~~ ~~~~~~~~~~~~~~~~ /build/sniffles-1.0.11+ds/src/print/BedpePrinter.cpp: In member function 'virtual void BedpePrinter::print_body_recall(Breakpoint*&, BamTools::RefVector)': /build/sniffles-1.0.11+ds/src/print/BedpePrinter.cpp:119:16: warning: format '%i' expects argument of type 'int', but argument 3 has type 'long int' [-Wformat=] fprintf(file, "%i", IPrinter::calc_pos(SV->get_coordinates().start.max_pos, ref, chr)); ^~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/sniffles-1.0.11+ds/src/print/BedpePrinter.cpp:126:16: warning: format '%i' expects argument of type 'int', but argument 3 has type 'long int' [-Wformat=] fprintf(file, "%i", IPrinter::calc_pos(SV->get_coordinates().stop.max_pos, ref, chr)); ^~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/sniffles-1.0.11+ds/src/print/BedpePrinter.cpp:154:17: warning: format '%i' expects argument of type 'int', but argument 3 has type 'long int' [-Wformat=] fprintf(file, "%i", SV->get_length()); ^~~~ ~~~~~~~~~~~~~~~~ /build/sniffles-1.0.11+ds/src/print/VCFPrinter.cpp: In member function 'virtual void VCFPrinter::print_body(Breakpoint*&, BamTools::RefVector)': /build/sniffles-1.0.11+ds/src/print/VCFPrinter.cpp:210:19: warning: format '%i' expects argument of type 'int', but argument 3 has type 'long int' [-Wformat=] fprintf(file, "%i", SV->get_length() * -1); ^~~~ ~~~~~~~~~~~~~~~~~~~~~ /build/sniffles-1.0.11+ds/src/print/VCFPrinter.cpp:212:19: warning: format '%i' expects argument of type 'int', but argument 3 has type 'long int' [-Wformat=] fprintf(file, "%i", SV->get_length()); ^~~~ ~~~~~~~~~~~~~~~~ /build/sniffles-1.0.11+ds/src/print/VCFPrinter.cpp: In member function 'virtual void VCFPrinter::print_body_recall(Breakpoint*&, BamTools::RefVector)': /build/sniffles-1.0.11+ds/src/print/VCFPrinter.cpp:344:17: warning: format '%i' expects argument of type 'int', but argument 3 has type 'long int' [-Wformat=] fprintf(file, "%i", SV->get_length()); ^~~~ ~~~~~~~~~~~~~~~~ [ 69%] Building CXX object src/CMakeFiles/sniffles.dir/print/IPrinter.cpp.o cd /build/sniffles-1.0.11+ds/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/usr/include/bamtools -I/build/sniffles-1.0.11+ds/src/../lib/bamtools-2.3.0/src -I/build/sniffles-1.0.11+ds/src/../lib/tclap-1.2.1/include -g -O2 -ffile-prefix-map=/build/sniffles-1.0.11+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-1.0.11+ds/src/print/IPrinter.cpp [ 73%] Building CXX object src/CMakeFiles/sniffles.dir/tree/BinTree.cpp.o cd /build/sniffles-1.0.11+ds/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/usr/include/bamtools -I/build/sniffles-1.0.11+ds/src/../lib/bamtools-2.3.0/src -I/build/sniffles-1.0.11+ds/src/../lib/tclap-1.2.1/include -g -O2 -ffile-prefix-map=/build/sniffles-1.0.11+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-1.0.11+ds/src/tree/BinTree.cpp [ 78%] Building CXX object src/CMakeFiles/sniffles.dir/print/NGMPrinter.cpp.o cd /build/sniffles-1.0.11+ds/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/usr/include/bamtools -I/build/sniffles-1.0.11+ds/src/../lib/bamtools-2.3.0/src -I/build/sniffles-1.0.11+ds/src/../lib/tclap-1.2.1/include -g -O2 -ffile-prefix-map=/build/sniffles-1.0.11+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-1.0.11+ds/src/print/NGMPrinter.cpp [ 82%] Building CXX object src/CMakeFiles/sniffles.dir/plane-sweep/PlaneSweep_slim.cpp.o cd /build/sniffles-1.0.11+ds/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/usr/include/bamtools -I/build/sniffles-1.0.11+ds/src/../lib/bamtools-2.3.0/src -I/build/sniffles-1.0.11+ds/src/../lib/tclap-1.2.1/include -g -O2 -ffile-prefix-map=/build/sniffles-1.0.11+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-1.0.11+ds/src/plane-sweep/PlaneSweep_slim.cpp [ 86%] Building CXX object src/CMakeFiles/sniffles.dir/cluster/Cluster_SVs.cpp.o cd /build/sniffles-1.0.11+ds/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/usr/include/bamtools -I/build/sniffles-1.0.11+ds/src/../lib/bamtools-2.3.0/src -I/build/sniffles-1.0.11+ds/src/../lib/tclap-1.2.1/include -g -O2 -ffile-prefix-map=/build/sniffles-1.0.11+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-1.0.11+ds/src/cluster/Cluster_SVs.cpp /build/sniffles-1.0.11+ds/src/cluster/Cluster_SVs.cpp: In member function 'void Cluster_SVS::update_SVs(std::vector&)': /build/sniffles-1.0.11+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] system(move.c_str()); ~~~~~~^~~~~~~~~~~~~~ /build/sniffles-1.0.11+ds/src/cluster/Cluster_SVs.cpp: In member function 'void Cluster_SVS::update_SVs()': /build/sniffles-1.0.11+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] system(del.c_str()); ~~~~~~^~~~~~~~~~~~~ [ 91%] Building CXX object src/CMakeFiles/sniffles.dir/force_calling/Force_calling.cpp.o cd /build/sniffles-1.0.11+ds/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/usr/include/bamtools -I/build/sniffles-1.0.11+ds/src/../lib/bamtools-2.3.0/src -I/build/sniffles-1.0.11+ds/src/../lib/tclap-1.2.1/include -g -O2 -ffile-prefix-map=/build/sniffles-1.0.11+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-1.0.11+ds/src/force_calling/Force_calling.cpp [ 95%] Building CXX object src/CMakeFiles/sniffles.dir/force_calling/VCF_parser.cpp.o cd /build/sniffles-1.0.11+ds/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/usr/include/bamtools -I/build/sniffles-1.0.11+ds/src/../lib/bamtools-2.3.0/src -I/build/sniffles-1.0.11+ds/src/../lib/tclap-1.2.1/include -g -O2 -ffile-prefix-map=/build/sniffles-1.0.11+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-1.0.11+ds/src/force_calling/VCF_parser.cpp [100%] Linking CXX executable ../../bin/sniffles-core-1.0.11/sniffles cd /build/sniffles-1.0.11+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 -ffile-prefix-map=/build/sniffles-1.0.11+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-1.0.11/sniffles -lbamtools -lz make[3]: Leaving directory '/build/sniffles-1.0.11+ds/obj-aarch64-linux-gnu' [100%] Built target sniffles make[2]: Leaving directory '/build/sniffles-1.0.11+ds/obj-aarch64-linux-gnu' /usr/bin/cmake -E cmake_progress_start /build/sniffles-1.0.11+ds/obj-aarch64-linux-gnu/CMakeFiles 0 make[1]: Leaving directory '/build/sniffles-1.0.11+ds/obj-aarch64-linux-gnu' debian/rules override_dh_auto_test make[1]: Entering directory '/build/sniffles-1.0.11+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 Finalizing .. make[1]: Leaving directory '/build/sniffles-1.0.11+ds' create-stamp debian/debhelper-build-stamp fakeroot debian/rules binary dh binary dh_testroot dh_prep dh_auto_install dh_install dh_installdocs dh_installchangelogs debian/rules override_dh_installman make[1]: Entering directory '/build/sniffles-1.0.11+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-1.0.11+ds' dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_dwz dh_strip dh_makeshlibs dh_shlibdeps dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/sniffles/usr/bin/sniffles was not linked against libz.so.1 (it uses none of the library's symbols) dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'sniffles' in '../sniffles_1.0.11+ds-1_arm64.deb'. dpkg-deb: building package 'sniffles-dbgsym' in '../sniffles-dbgsym_1.0.11+ds-1_arm64.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../sniffles_1.0.11+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) I: copying local configuration I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/24438 and its subdirectories I: Current time: Fri Jul 24 14:10:22 -12 2020 I: pbuilder-time-stamp: 1595643022