Wed Jul 7 01:19:05 UTC 2021 I: starting to build pbbam/bullseye/arm64 on jenkins on '2021-07-07 01:18' Wed Jul 7 01:19:05 UTC 2021 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/arm64_26/47712/console.log Wed Jul 7 01:19:05 UTC 2021 I: Downloading source for bullseye/pbbam=1.6.0+dfsg-2 --2021-07-07 01:19:05-- http://cdn-fastly.deb.debian.org/debian/pool/main/p/pbbam/pbbam_1.6.0+dfsg-2.dsc Connecting to 78.137.99.97:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2320 (2.3K) Saving to: ‘pbbam_1.6.0+dfsg-2.dsc’ 0K .. 100% 153M=0s 2021-07-07 01:19:05 (153 MB/s) - ‘pbbam_1.6.0+dfsg-2.dsc’ saved [2320/2320] Wed Jul 7 01:19:05 UTC 2021 I: pbbam_1.6.0+dfsg-2.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: pbbam Binary: pbbamtools, libpbbam1.6.0, libpbbam-dev Architecture: any Version: 1.6.0+dfsg-2 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille Homepage: http://pbbam.readthedocs.org/en/latest/index.html Standards-Version: 4.5.0 Vcs-Browser: https://salsa.debian.org/med-team/pbbam Vcs-Git: https://salsa.debian.org/med-team/pbbam.git Testsuite: autopkgtest Testsuite-Triggers: @builddeps@ Build-Depends: debhelper-compat (= 13), dh-exec, d-shlibs, meson, pkg-config, cmake, libboost-dev, zlib1g-dev, libssl-dev, libhts-dev, libpbcopper-dev (>= 1.8.0), python3-cram, libgtest-dev , samtools Package-List: libpbbam-dev deb libdevel optional arch=any libpbbam1.6.0 deb libs optional arch=any pbbamtools deb science optional arch=any Checksums-Sha1: e740c1f990df3d13ec095532762bde1169c94a5e 7800396 pbbam_1.6.0+dfsg.orig.tar.xz 422f37eb3dcf06f1c4ecccb9f3d307d456aa5c31 8564 pbbam_1.6.0+dfsg-2.debian.tar.xz Checksums-Sha256: 4bc779fae88939e23feca7f25aa51f385aec413133db44e77d255eb7fef23464 7800396 pbbam_1.6.0+dfsg.orig.tar.xz cce8bc2a2e779c69676586df5e477aa378f38a798b684f603477e6a751848f46 8564 pbbam_1.6.0+dfsg-2.debian.tar.xz Files: 8d5eb5ecbf34520ee16c869e85abf2c6 7800396 pbbam_1.6.0+dfsg.orig.tar.xz 5a51c1bd41a19e9b7f66192020d96bea 8564 pbbam_1.6.0+dfsg-2.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCgAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAl+wv+IRHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtEI6A/+Ooj1WeszLyGf0Xk7qHCd+U2GCfIo3v1l OscOUAySITJl0rE4RpZwC7R0yqSeto/BFi6/6wiysKvVpwfkEq1qClb/3VmJJa3V 1XhQKN1UZ/Qs5Pm4TowoIU7oL0A1mkAEjOOxrgk8na8asrN6fKC5hBXNgMnFAYt5 ClPqVjGZdP0U30w6wK5x0stfOOp+ZEjEU1cOQA5aFsTGxY/mdbVIIiSU5lRaz2W2 RJEsjsEojwBF182/4rLXfQkCdTjUAsudXx2JRAo/3Oj+gCVQ0UhKuPQ8GSfwG14D h9AHhtp62ExLsRF0tD7GQESVwxrKSqpkJ7ZR0ptoPioMuagYAzr9y2Zn8dqlYIVH S4kuoxjh9r9iKqXJbjLorneJVfm7UN7zCUhzgPrKYywCefJ3k5qWZyjI6DQq+dm8 +xoH0Swu7eWIF/y1EZJaAETE6/akCBF+kk2G7zM1rOtKcm5SEVnBcn8VcVDmDF95 VWdNZkMChJ4QUx2FL7jTVIIuRm3K04wtv2B1aaef4PbyfkWgSKw3BZxA/CzEdV3z 6GrG3fGvWoSh+aDlF//gxb6CFXclqMEOuoUZn8qwtOop7S5oREB322+ilErdp82C i/mh3svgAPh7IMZWKY+CU5REor1Lzb9DW1Kqn20BgllYj+eVg93Dtc4WP8/BLRpv iJHiGplozYY= =/YpP -----END PGP SIGNATURE----- Wed Jul 7 01:19:06 UTC 2021 I: Checking whether the package is not for us Wed Jul 7 01:19:06 UTC 2021 I: Starting 1st build on remote node codethink15-arm64.debian.net. Wed Jul 7 01:19:06 UTC 2021 I: Preparing to do remote build '1' on codethink15-arm64.debian.net. Wed Jul 7 01:43:30 UTC 2021 I: Deleting $TMPDIR on codethink15-arm64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Mon Aug 8 19:42:09 -12 2022 I: pbuilder-time-stamp: 1660030929 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 [pbbam_1.6.0+dfsg-2.dsc] I: copying [./pbbam_1.6.0+dfsg.orig.tar.xz] I: copying [./pbbam_1.6.0+dfsg-2.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/tmp/dpkg-verify-sig.ZvFDI33o/trustedkeys.kbx': General error gpgv: Signature made Sat Nov 14 17:42:58 2020 -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 ./pbbam_1.6.0+dfsg-2.dsc dpkg-source: info: extracting pbbam in pbbam-1.6.0+dfsg dpkg-source: info: unpacking pbbam_1.6.0+dfsg.orig.tar.xz dpkg-source: info: unpacking pbbam_1.6.0+dfsg-2.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying use_debian_packaged_python3-cram.patch dpkg-source: info: applying python3.patch dpkg-source: info: applying results_with_latest_samtools.patch dpkg-source: info: applying boost_optional.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/9897/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,-fixfilepath 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='9897' 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.5mjbqnlGle/pbuilderrc_hBKy --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.5mjbqnlGle/b1 --logfile b1/build.log pbbam_1.6.0+dfsg-2.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 codethink15-arm64 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 21 2021 bash -rwxr-xr-x 3 root root 34808 Jul 20 2020 bunzip2 -rwxr-xr-x 3 root root 34808 Jul 20 2020 bzcat lrwxrwxrwx 1 root root 6 Jul 20 2020 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2225 Jul 20 2020 bzdiff lrwxrwxrwx 1 root root 6 Jul 20 2020 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4877 Sep 4 2019 bzexe lrwxrwxrwx 1 root root 6 Jul 20 2020 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3775 Jul 20 2020 bzgrep -rwxr-xr-x 3 root root 34808 Jul 20 2020 bzip2 -rwxr-xr-x 1 root root 14264 Jul 20 2020 bzip2recover lrwxrwxrwx 1 root root 6 Jul 20 2020 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Jul 20 2020 bzmore -rwxr-xr-x 1 root root 39832 Sep 22 2020 cat -rwxr-xr-x 1 root root 64512 Sep 22 2020 chgrp -rwxr-xr-x 1 root root 60368 Sep 22 2020 chmod -rwxr-xr-x 1 root root 64528 Sep 22 2020 chown -rwxr-xr-x 1 root root 138896 Sep 22 2020 cp -rwxr-xr-x 1 root root 129544 Dec 10 2020 dash -rwxr-xr-x 1 root root 101384 Sep 22 2020 date -rwxr-xr-x 1 root root 80984 Sep 22 2020 dd -rwxr-xr-x 1 root root 89824 Sep 22 2020 df -rwxr-xr-x 1 root root 143088 Sep 22 2020 dir -rwxr-xr-x 1 root root 76152 Feb 7 2021 dmesg lrwxrwxrwx 1 root root 8 Nov 6 2019 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Nov 6 2019 domainname -> hostname -rwxr-xr-x 1 root root 35632 Sep 22 2020 echo -rwxr-xr-x 1 root root 28 Nov 9 2020 egrep -rwxr-xr-x 1 root root 31512 Sep 22 2020 false -rwxr-xr-x 1 root root 28 Nov 9 2020 fgrep -rwxr-xr-x 1 root root 64856 Feb 7 2021 findmnt -rwsr-xr-x 1 root root 34824 Feb 26 2021 fusermount -rwxr-xr-x 1 root root 178400 Nov 9 2020 grep -rwxr-xr-x 2 root root 2346 Mar 2 2021 gunzip -rwxr-xr-x 1 root root 6376 Mar 2 2021 gzexe -rwxr-xr-x 1 root root 93744 Mar 2 2021 gzip -rwxr-xr-x 1 root root 18440 Nov 6 2019 hostname -rwxr-xr-x 1 root root 68720 Sep 22 2020 ln -rwxr-xr-x 1 root root 52720 Feb 7 2020 login -rwxr-xr-x 1 root root 143088 Sep 22 2020 ls -rwxr-xr-x 1 root root 161960 Feb 7 2021 lsblk -rwxr-xr-x 1 root root 85200 Sep 22 2020 mkdir -rwxr-xr-x 1 root root 68744 Sep 22 2020 mknod -rwxr-xr-x 1 root root 43976 Sep 22 2020 mktemp -rwxr-xr-x 1 root root 51368 Feb 7 2021 more -rwsr-xr-x 1 root root 51360 Feb 7 2021 mount -rwxr-xr-x 1 root root 14496 Feb 7 2021 mountpoint -rwxr-xr-x 1 root root 134808 Sep 22 2020 mv lrwxrwxrwx 1 root root 8 Nov 6 2019 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Apr 18 2021 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 35720 Sep 22 2020 pwd lrwxrwxrwx 1 root root 4 Jun 21 2021 rbash -> bash -rwxr-xr-x 1 root root 43872 Sep 22 2020 readlink -rwxr-xr-x 1 root root 68592 Sep 22 2020 rm -rwxr-xr-x 1 root root 43880 Sep 22 2020 rmdir -rwxr-xr-x 1 root root 19208 Sep 27 2020 run-parts -rwxr-xr-x 1 root root 114016 Dec 22 2018 sed lrwxrwxrwx 1 root root 4 Aug 8 03:47 sh -> dash -rwxr-xr-x 1 root root 35656 Sep 22 2020 sleep -rwxr-xr-x 1 root root 72640 Sep 22 2020 stty -rwsr-xr-x 1 root root 67776 Feb 7 2021 su -rwxr-xr-x 1 root root 35672 Sep 22 2020 sync -rwxr-xr-x 1 root root 535768 Feb 16 2021 tar -rwxr-xr-x 1 root root 10568 Sep 27 2020 tempfile -rwxr-xr-x 1 root root 89120 Sep 22 2020 touch -rwxr-xr-x 1 root root 31512 Sep 22 2020 true -rwxr-xr-x 1 root root 14264 Feb 26 2021 ulockmgr_server -rwsr-xr-x 1 root root 30880 Feb 7 2021 umount -rwxr-xr-x 1 root root 35640 Sep 22 2020 uname -rwxr-xr-x 2 root root 2346 Mar 2 2021 uncompress -rwxr-xr-x 1 root root 143088 Sep 22 2020 vdir -rwxr-xr-x 1 root root 59584 Feb 7 2021 wdctl lrwxrwxrwx 1 root root 8 Nov 6 2019 ypdomainname -> hostname -rwxr-xr-x 1 root root 1984 Mar 2 2021 zcat -rwxr-xr-x 1 root root 1678 Mar 2 2021 zcmp -rwxr-xr-x 1 root root 5880 Mar 2 2021 zdiff -rwxr-xr-x 1 root root 29 Mar 2 2021 zegrep -rwxr-xr-x 1 root root 29 Mar 2 2021 zfgrep -rwxr-xr-x 1 root root 2081 Mar 2 2021 zforce -rwxr-xr-x 1 root root 7585 Mar 2 2021 zgrep -rwxr-xr-x 1 root root 2206 Mar 2 2021 zless -rwxr-xr-x 1 root root 1842 Mar 2 2021 zmore -rwxr-xr-x 1 root root 4553 Mar 2 2021 znew I: user script /srv/workspace/pbuilder/9897/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: arm64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), dh-exec, d-shlibs, meson, pkg-config, cmake, libboost-dev, zlib1g-dev, libssl-dev, libhts-dev, libpbcopper-dev (>= 1.8.0), python3-cram, libgtest-dev, samtools dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19646 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on dh-exec; however: Package dh-exec is not installed. pbuilder-satisfydepends-dummy depends on d-shlibs; however: Package d-shlibs is not installed. pbuilder-satisfydepends-dummy depends on meson; however: Package meson is not installed. pbuilder-satisfydepends-dummy depends on pkg-config; however: Package pkg-config is not installed. pbuilder-satisfydepends-dummy depends on cmake; however: Package cmake is not installed. pbuilder-satisfydepends-dummy depends on libboost-dev; however: Package libboost-dev is not installed. pbuilder-satisfydepends-dummy depends on zlib1g-dev; however: Package zlib1g-dev is not installed. pbuilder-satisfydepends-dummy depends on libssl-dev; however: Package libssl-dev is not installed. pbuilder-satisfydepends-dummy depends on libhts-dev; however: Package libhts-dev is not installed. pbuilder-satisfydepends-dummy depends on libpbcopper-dev (>= 1.8.0); however: Package libpbcopper-dev is not installed. pbuilder-satisfydepends-dummy depends on python3-cram; however: Package python3-cram is not installed. pbuilder-satisfydepends-dummy depends on libgtest-dev; however: Package libgtest-dev is not installed. pbuilder-satisfydepends-dummy depends on samtools; however: Package samtools 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} d-shlibs{a} debhelper{a} dh-autoreconf{a} dh-exec{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} googletest{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libarchive13{a} libboost-dev{a} libboost1.74-dev{a} libbrotli1{a} libcurl3-gnutls{a} libcurl4{a} libcurl4-gnutls-dev{a} libdebhelper-perl{a} libdeflate-dev{a} libdeflate0{a} libelf1{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libglib2.0-0{a} libgtest-dev{a} libhts-dev{a} libhts3{a} libicu67{a} libjsoncpp24{a} libldap-2.4-2{a} liblzma-dev{a} libmagic-mgc{a} libmagic1{a} libmpdec3{a} libncurses6{a} libnghttp2-14{a} libpbcopper-dev{a} libpbcopper1.8.0{a} libpipeline1{a} libprocps8{a} libpsl5{a} libpython3-stdlib{a} libpython3.9-minimal{a} libpython3.9-stdlib{a} libreadline8{a} librhash0{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsigsegv2{a} libssh2-1{a} libssl-dev{a} libsub-override-perl{a} libtool{a} libuchardet0{a} libuv1{a} libxml2{a} m4{a} man-db{a} media-types{a} meson{a} ninja-build{a} pkg-config{a} po-debconf{a} procps{a} python3{a} python3-cram{a} python3-minimal{a} python3-pkg-resources{a} python3.9{a} python3.9-minimal{a} readline-common{a} samtools{a} sensible-utils{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: ca-certificates curl libarchive-cpio-perl libglib2.0-data libgpm2 libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules lynx psmisc publicsuffix shared-mime-info wget xdg-user-dirs 0 packages upgraded, 85 newly installed, 0 to remove and 0 not upgraded. Need to get 52.5 MB of archives. After unpacking 304 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bullseye/main arm64 bsdextrautils arm64 2.36.1-7 [141 kB] Get: 2 http://deb.debian.org/debian bullseye/main arm64 libuchardet0 arm64 0.0.7-1 [67.9 kB] Get: 3 http://deb.debian.org/debian bullseye/main arm64 groff-base arm64 1.22.4-6 [883 kB] Get: 4 http://deb.debian.org/debian bullseye/main arm64 libpipeline1 arm64 1.5.3-1 [33.0 kB] Get: 5 http://deb.debian.org/debian bullseye/main arm64 man-db arm64 2.9.4-2 [1336 kB] Get: 6 http://deb.debian.org/debian bullseye/main arm64 libpython3.9-minimal arm64 3.9.2-1 [797 kB] Get: 7 http://deb.debian.org/debian bullseye/main arm64 libexpat1 arm64 2.2.10-2 [83.1 kB] Get: 8 http://deb.debian.org/debian bullseye/main arm64 python3.9-minimal arm64 3.9.2-1 [1884 kB] Get: 9 http://deb.debian.org/debian bullseye/main arm64 python3-minimal arm64 3.9.2-3 [38.2 kB] Get: 10 http://deb.debian.org/debian bullseye/main arm64 media-types all 4.0.0 [30.3 kB] Get: 11 http://deb.debian.org/debian bullseye/main arm64 libmpdec3 arm64 2.5.1-1 [84.4 kB] Get: 12 http://deb.debian.org/debian bullseye/main arm64 readline-common all 8.1-1 [73.7 kB] Get: 13 http://deb.debian.org/debian bullseye/main arm64 libreadline8 arm64 8.1-1 [160 kB] Get: 14 http://deb.debian.org/debian bullseye/main arm64 libpython3.9-stdlib arm64 3.9.2-1 [1658 kB] Get: 15 http://deb.debian.org/debian bullseye/main arm64 python3.9 arm64 3.9.2-1 [466 kB] Get: 16 http://deb.debian.org/debian bullseye/main arm64 libpython3-stdlib arm64 3.9.2-3 [21.4 kB] Get: 17 http://deb.debian.org/debian bullseye/main arm64 python3 arm64 3.9.2-3 [37.9 kB] Get: 18 http://deb.debian.org/debian bullseye/main arm64 libncurses6 arm64 6.2+20201114-2 [93.2 kB] Get: 19 http://deb.debian.org/debian bullseye/main arm64 libprocps8 arm64 2:3.3.17-5 [61.9 kB] Get: 20 http://deb.debian.org/debian bullseye/main arm64 procps arm64 2:3.3.17-5 [497 kB] Get: 21 http://deb.debian.org/debian bullseye/main arm64 sensible-utils all 0.0.14 [14.8 kB] Get: 22 http://deb.debian.org/debian bullseye/main arm64 libmagic-mgc arm64 1:5.39-3 [273 kB] Get: 23 http://deb.debian.org/debian bullseye/main arm64 libmagic1 arm64 1:5.39-3 [121 kB] Get: 24 http://deb.debian.org/debian bullseye/main arm64 file arm64 1:5.39-3 [69.1 kB] Get: 25 http://deb.debian.org/debian bullseye/main arm64 gettext-base arm64 0.21-4 [173 kB] Get: 26 http://deb.debian.org/debian bullseye/main arm64 libsigsegv2 arm64 2.13-1 [34.7 kB] Get: 27 http://deb.debian.org/debian bullseye/main arm64 m4 arm64 1.4.18-5 [199 kB] Get: 28 http://deb.debian.org/debian bullseye/main arm64 autoconf all 2.69-14 [313 kB] Get: 29 http://deb.debian.org/debian bullseye/main arm64 autotools-dev all 20180224.1+nmu1 [77.1 kB] Get: 30 http://deb.debian.org/debian bullseye/main arm64 automake all 1:1.16.3-2 [814 kB] Get: 31 http://deb.debian.org/debian bullseye/main arm64 autopoint all 0.21-4 [510 kB] Get: 32 http://deb.debian.org/debian bullseye/main arm64 cmake-data all 3.18.4-2 [1725 kB] Get: 33 http://deb.debian.org/debian bullseye/main arm64 libicu67 arm64 67.1-7 [8467 kB] Get: 34 http://deb.debian.org/debian bullseye/main arm64 libxml2 arm64 2.9.10+dfsg-6.7 [629 kB] Get: 35 http://deb.debian.org/debian bullseye/main arm64 libarchive13 arm64 3.4.3-2+b1 [320 kB] Get: 36 http://deb.debian.org/debian bullseye/main arm64 libbrotli1 arm64 1.0.9-2+b2 [267 kB] Get: 37 http://deb.debian.org/debian bullseye/main arm64 libsasl2-modules-db arm64 2.1.27+dfsg-2.1 [69.3 kB] Get: 38 http://deb.debian.org/debian bullseye/main arm64 libsasl2-2 arm64 2.1.27+dfsg-2.1 [105 kB] Get: 39 http://deb.debian.org/debian bullseye/main arm64 libldap-2.4-2 arm64 2.4.57+dfsg-3 [222 kB] Get: 40 http://deb.debian.org/debian bullseye/main arm64 libnghttp2-14 arm64 1.43.0-1 [73.8 kB] Get: 41 http://deb.debian.org/debian bullseye/main arm64 libpsl5 arm64 0.21.0-1.2 [57.1 kB] Get: 42 http://deb.debian.org/debian bullseye/main arm64 librtmp1 arm64 2.4+20151223.gitfa8646d.1-2+b2 [59.4 kB] Get: 43 http://deb.debian.org/debian bullseye/main arm64 libssh2-1 arm64 1.9.0-2 [150 kB] Get: 44 http://deb.debian.org/debian bullseye/main arm64 libcurl4 arm64 7.74.0-1.3 [320 kB] Get: 45 http://deb.debian.org/debian bullseye/main arm64 libjsoncpp24 arm64 1.9.4-4 [72.5 kB] Get: 46 http://deb.debian.org/debian bullseye/main arm64 librhash0 arm64 1.4.1-2 [127 kB] Get: 47 http://deb.debian.org/debian bullseye/main arm64 libuv1 arm64 1.40.0-1 [126 kB] Get: 48 http://deb.debian.org/debian bullseye/main arm64 cmake arm64 3.18.4-2 [3673 kB] Get: 49 http://deb.debian.org/debian bullseye/main arm64 d-shlibs all 0.98 [17.9 kB] Get: 50 http://deb.debian.org/debian bullseye/main arm64 libdebhelper-perl all 13.3.4 [189 kB] Get: 51 http://deb.debian.org/debian bullseye/main arm64 libtool all 2.4.6-15 [513 kB] Get: 52 http://deb.debian.org/debian bullseye/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 53 http://deb.debian.org/debian bullseye/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 54 http://deb.debian.org/debian bullseye/main arm64 libsub-override-perl all 0.09-2 [10.2 kB] Get: 55 http://deb.debian.org/debian bullseye/main arm64 libfile-stripnondeterminism-perl all 1.11.0-1 [25.6 kB] Get: 56 http://deb.debian.org/debian bullseye/main arm64 dh-strip-nondeterminism all 1.11.0-1 [15.3 kB] Get: 57 http://deb.debian.org/debian bullseye/main arm64 libelf1 arm64 0.183-1 [164 kB] Get: 58 http://deb.debian.org/debian bullseye/main arm64 dwz arm64 0.13+20210201-1 [155 kB] Get: 59 http://deb.debian.org/debian bullseye/main arm64 gettext arm64 0.21-4 [1261 kB] Get: 60 http://deb.debian.org/debian bullseye/main arm64 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 61 http://deb.debian.org/debian bullseye/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 62 http://deb.debian.org/debian bullseye/main arm64 debhelper all 13.3.4 [1049 kB] Get: 63 http://deb.debian.org/debian bullseye/main arm64 dh-exec arm64 0.23.2 [26.2 kB] Get: 64 http://deb.debian.org/debian bullseye/main arm64 googletest all 1.10.0.20201025-1.1 [629 kB] Get: 65 http://deb.debian.org/debian bullseye/main arm64 libboost1.74-dev arm64 1.74.0-9 [9534 kB] Get: 66 http://deb.debian.org/debian bullseye/main arm64 libboost-dev arm64 1.74.0.3 [4548 B] Get: 67 http://deb.debian.org/debian bullseye/main arm64 libcurl3-gnutls arm64 7.74.0-1.3 [317 kB] Get: 68 http://deb.debian.org/debian bullseye/main arm64 libcurl4-gnutls-dev arm64 7.74.0-1.3 [419 kB] Get: 69 http://deb.debian.org/debian bullseye/main arm64 libdeflate0 arm64 1.7-1 [47.7 kB] Get: 70 http://deb.debian.org/debian bullseye/main arm64 libdeflate-dev arm64 1.7-1 [44.5 kB] Get: 71 http://deb.debian.org/debian bullseye/main arm64 libglib2.0-0 arm64 2.66.8-1 [1286 kB] Get: 72 http://deb.debian.org/debian bullseye/main arm64 libgtest-dev arm64 1.10.0.20201025-1.1 [221 kB] Get: 73 http://deb.debian.org/debian bullseye/main arm64 libhts3 arm64 1.11-4 [346 kB] Get: 74 http://deb.debian.org/debian bullseye/main arm64 liblzma-dev arm64 5.2.5-2 [227 kB] Get: 75 http://deb.debian.org/debian bullseye/main arm64 zlib1g-dev arm64 1:1.2.11.dfsg-2 [189 kB] Get: 76 http://deb.debian.org/debian bullseye/main arm64 libhts-dev arm64 1.11-4 [3856 kB] Get: 77 http://deb.debian.org/debian bullseye/main arm64 libpbcopper1.8.0 arm64 1.8.0+dfsg-2+b1 [371 kB] Get: 78 http://deb.debian.org/debian bullseye/main arm64 libpbcopper-dev arm64 1.8.0+dfsg-2+b1 [640 kB] Get: 79 http://deb.debian.org/debian bullseye/main arm64 libssl-dev arm64 1.1.1k-1 [1689 kB] Get: 80 http://deb.debian.org/debian bullseye/main arm64 ninja-build arm64 1.10.1-1 [107 kB] Get: 81 http://deb.debian.org/debian bullseye/main arm64 python3-pkg-resources all 52.0.0-4 [190 kB] Get: 82 http://deb.debian.org/debian bullseye/main arm64 meson all 0.56.2-1 [437 kB] Get: 83 http://deb.debian.org/debian bullseye/main arm64 pkg-config arm64 0.29.2-1 [63.6 kB] Get: 84 http://deb.debian.org/debian bullseye/main arm64 python3-cram all 0.7-4 [17.3 kB] Get: 85 http://deb.debian.org/debian bullseye/main arm64 samtools arm64 1.11-1 [526 kB] Fetched 52.5 MB in 1s (43.8 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package bsdextrautils. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19646 files and directories currently installed.) Preparing to unpack .../0-bsdextrautils_2.36.1-7_arm64.deb ... Unpacking bsdextrautils (2.36.1-7) ... Selecting previously unselected package libuchardet0:arm64. Preparing to unpack .../1-libuchardet0_0.0.7-1_arm64.deb ... Unpacking libuchardet0:arm64 (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../2-groff-base_1.22.4-6_arm64.deb ... 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Selecting previously unselected package python3-minimal. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 20513 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.9.2-3_arm64.deb ... Unpacking python3-minimal (3.9.2-3) ... Selecting previously unselected package media-types. Preparing to unpack .../1-media-types_4.0.0_all.deb ... Unpacking media-types (4.0.0) ... Selecting previously unselected package libmpdec3:arm64. 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Selecting previously unselected package python3. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 20934 files and directories currently installed.) Preparing to unpack .../00-python3_3.9.2-3_arm64.deb ... Unpacking python3 (3.9.2-3) ... Selecting previously unselected package libncurses6:arm64. Preparing to unpack .../01-libncurses6_6.2+20201114-2_arm64.deb ... Unpacking libncurses6:arm64 (6.2+20201114-2) ... Selecting previously unselected package libprocps8:arm64. 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Unpacking gettext-base (0.21-4) ... Selecting previously unselected package libsigsegv2:arm64. Preparing to unpack .../09-libsigsegv2_2.13-1_arm64.deb ... Unpacking libsigsegv2:arm64 (2.13-1) ... Selecting previously unselected package m4. Preparing to unpack .../10-m4_1.4.18-5_arm64.deb ... Unpacking m4 (1.4.18-5) ... Selecting previously unselected package autoconf. Preparing to unpack .../11-autoconf_2.69-14_all.deb ... Unpacking autoconf (2.69-14) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../12-autotools-dev_20180224.1+nmu1_all.deb ... Unpacking autotools-dev (20180224.1+nmu1) ... Selecting previously unselected package automake. Preparing to unpack .../13-automake_1%3a1.16.3-2_all.deb ... Unpacking automake (1:1.16.3-2) ... Selecting previously unselected package autopoint. Preparing to unpack .../14-autopoint_0.21-4_all.deb ... Unpacking autopoint (0.21-4) ... Selecting previously unselected package cmake-data. 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Unpacking libssh2-1:arm64 (1.9.0-2) ... Selecting previously unselected package libcurl4:arm64. Preparing to unpack .../27-libcurl4_7.74.0-1.3_arm64.deb ... Unpacking libcurl4:arm64 (7.74.0-1.3) ... Selecting previously unselected package libjsoncpp24:arm64. Preparing to unpack .../28-libjsoncpp24_1.9.4-4_arm64.deb ... Unpacking libjsoncpp24:arm64 (1.9.4-4) ... Selecting previously unselected package librhash0:arm64. Preparing to unpack .../29-librhash0_1.4.1-2_arm64.deb ... Unpacking librhash0:arm64 (1.4.1-2) ... Selecting previously unselected package libuv1:arm64. Preparing to unpack .../30-libuv1_1.40.0-1_arm64.deb ... Unpacking libuv1:arm64 (1.40.0-1) ... Selecting previously unselected package cmake. Preparing to unpack .../31-cmake_3.18.4-2_arm64.deb ... Unpacking cmake (3.18.4-2) ... Selecting previously unselected package d-shlibs. Preparing to unpack .../32-d-shlibs_0.98_all.deb ... Unpacking d-shlibs (0.98) ... Selecting previously unselected package libdebhelper-perl. 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Selecting previously unselected package liblzma-dev:arm64. Preparing to unpack .../57-liblzma-dev_5.2.5-2_arm64.deb ... Unpacking liblzma-dev:arm64 (5.2.5-2) ... Selecting previously unselected package zlib1g-dev:arm64. Preparing to unpack .../58-zlib1g-dev_1%3a1.2.11.dfsg-2_arm64.deb ... Unpacking zlib1g-dev:arm64 (1:1.2.11.dfsg-2) ... Selecting previously unselected package libhts-dev:arm64. Preparing to unpack .../59-libhts-dev_1.11-4_arm64.deb ... Unpacking libhts-dev:arm64 (1.11-4) ... Selecting previously unselected package libpbcopper1.8.0:arm64. Preparing to unpack .../60-libpbcopper1.8.0_1.8.0+dfsg-2+b1_arm64.deb ... Unpacking libpbcopper1.8.0:arm64 (1.8.0+dfsg-2+b1) ... Selecting previously unselected package libpbcopper-dev:arm64. Preparing to unpack .../61-libpbcopper-dev_1.8.0+dfsg-2+b1_arm64.deb ... Unpacking libpbcopper-dev:arm64 (1.8.0+dfsg-2+b1) ... Selecting previously unselected package libssl-dev:arm64. Preparing to unpack .../62-libssl-dev_1.1.1k-1_arm64.deb ... 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Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/pbbam-1.6.0+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../pbbam_1.6.0+dfsg-2_source.changes dpkg-buildpackage: info: source package pbbam dpkg-buildpackage: info: source version 1.6.0+dfsg-2 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 debian/rules clean dh clean --buildsystem=meson debian/rules override_dh_auto_clean make[1]: Entering directory '/build/pbbam-1.6.0+dfsg' dh_auto_clean find -name "*.deb.t" -delete rm -f -r /build/pbbam-1.6.0+dfsg/gendata make[1]: Leaving directory '/build/pbbam-1.6.0+dfsg' dh_autoreconf_clean -O--buildsystem=meson dh_clean -O--buildsystem=meson debian/rules binary dh binary --buildsystem=meson dh_update_autotools_config -O--buildsystem=meson dh_autoreconf -O--buildsystem=meson dh_auto_configure -O--buildsystem=meson cd obj-aarch64-linux-gnu && LC_ALL=C.UTF-8 meson .. --wrap-mode=nodownload --buildtype=plain --prefix=/usr --sysconfdir=/etc --localstatedir=/var --libdir=lib/aarch64-linux-gnu The Meson build system Version: 0.56.2 Source dir: /build/pbbam-1.6.0+dfsg Build dir: /build/pbbam-1.6.0+dfsg/obj-aarch64-linux-gnu Build type: native build Project name: PacBioBAM Project version: 1.6.0 Using 'CXXFLAGS' from environment with value: '-g -O2 -fdebug-prefix-map=/build/pbbam-1.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security' Using 'LDFLAGS' from environment with value: '-Wl,-z,relro -Wl,-z,now' Using 'CPPFLAGS' from environment with value: '-Wdate-time -D_FORTIFY_SOURCE=2' C++ compiler for the host machine: c++ (gcc 10.2.1 "c++ (Debian 10.2.1-6) 10.2.1 20210110") C++ linker for the host machine: c++ ld.bfd 2.35.2 Using 'CXXFLAGS' from environment with value: '-g -O2 -fdebug-prefix-map=/build/pbbam-1.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security' Using 'LDFLAGS' from environment with value: '-Wl,-z,relro -Wl,-z,now' Using 'CPPFLAGS' from environment with value: '-Wdate-time -D_FORTIFY_SOURCE=2' Host machine cpu family: aarch64 Host machine cpu: aarch64 Compiler for C++ supports arguments -Wduplicated-cond: YES Compiler for C++ supports arguments -Wduplicated-branches: YES Compiler for C++ supports arguments -Wlogical-op: YES Compiler for C++ supports arguments -Wrestrict: YES Compiler for C++ supports arguments -Wnull-dereference: YES Compiler for C++ supports arguments -Wuseless-cast: YES Compiler for C++ supports arguments -Wdouble-promotion: YES Compiler for C++ supports arguments -Wshadow: YES Compiler for C++ supports arguments -Wformat=1: YES Run-time dependency threads found: YES Found pkg-config: /usr/bin/pkg-config (0.29.2) Run-time dependency Boost found: YES 1.74.0 (/usr/include) Run-time dependency zlib found: YES 1.2.11 Run-time dependency htslib found: YES 1.11-4 Run-time dependency pbcopper found: YES 1.8.0 Configuring PbbamVersion.cpp using configuration Configuring LibraryVersion.h using configuration Program python3 found: YES (/usr/bin/python3) Program tools/check-formatting found: YES (/build/pbbam-1.6.0+dfsg/tools/check-formatting) Program tools/check-eof found: YES (/build/pbbam-1.6.0+dfsg/tools/check-eof) Program cram3 found: YES (/usr/bin/cram3) Run-time dependency GTest found: YES 1.10.0 Configuring group.fofn using configuration Configuring PbbamTestData.h using configuration Configuring synthetic_movie_all.subreadset.xml using configuration Configuring Bam2SamVersion.h using configuration Configuring bam2sam.t using configuration Configuring PbIndexVersion.h using configuration Configuring PbIndexDumpVersion.h using configuration Configuring pbindexdump_json.t using configuration Configuring pbindexdump_cpp.t using configuration Configuring PbMergeVersion.h using configuration Configuring pbmerge_pacbio_ordering.t using configuration Configuring pbmerge_aligned_ordering.t using configuration Configuring pbmerge_mixed_ordering.t using configuration Configuring pbmerge_dataset.t using configuration Configuring pbmerge_fofn.t using configuration Configuring PbBamifyVersion.h using configuration Program samtools found: YES (/usr/bin/samtools) Configuring pbbamify.t using configuration Configuring CcsKineticsBystrandifyVersion.h using configuration Build targets in project: 12 Option buildtype is: plain [default: release] Found ninja-1.10.1 at /usr/bin/ninja dh_auto_build -O--buildsystem=meson cd obj-aarch64-linux-gnu && LC_ALL=C.UTF-8 ninja -j8 -v [1/228] /usr/bin/meson --internal vcstagger ../src/LibraryGitHash.h.in src/LibraryGitHash.h 1.6.0 /build/pbbam-1.6.0+dfsg/src @PBBAM_GIT_SHA1@ '(.*)' /build/pbbam-1.6.0+dfsg/src/git describe --always '--dirty=*' [2/228] /usr/bin/meson --internal vcstagger ../src/PbbamGitHash.cpp.in src/PbbamGitHash.cpp 1.6.0 /build/pbbam-1.6.0+dfsg/src @PBBAM_GIT_SHA1@ '(.*)' /build/pbbam-1.6.0+dfsg/src/git describe --always '--dirty=*' [3/228] c++ -Isrc/libpbbam.so.1.6.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbbam-1.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.1.6.0.p/meson-generated_.._PbbamGitHash.cpp.o -MF src/libpbbam.so.1.6.0.p/meson-generated_.._PbbamGitHash.cpp.o.d -o src/libpbbam.so.1.6.0.p/meson-generated_.._PbbamGitHash.cpp.o -c src/PbbamGitHash.cpp [4/228] c++ -Isrc/libpbbam.so.1.6.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbbam-1.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.1.6.0.p/BaiIndexCache.cpp.o -MF src/libpbbam.so.1.6.0.p/BaiIndexCache.cpp.o.d -o src/libpbbam.so.1.6.0.p/BaiIndexCache.cpp.o -c ../src/BaiIndexCache.cpp [5/228] c++ -Isrc/libpbbam.so.1.6.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbbam-1.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.1.6.0.p/AlignmentPrinter.cpp.o -MF src/libpbbam.so.1.6.0.p/AlignmentPrinter.cpp.o.d -o src/libpbbam.so.1.6.0.p/AlignmentPrinter.cpp.o -c ../src/AlignmentPrinter.cpp [6/228] c++ -Isrc/libpbbam.so.1.6.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbbam-1.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.1.6.0.p/BamFile.cpp.o -MF src/libpbbam.so.1.6.0.p/BamFile.cpp.o.d -o src/libpbbam.so.1.6.0.p/BamFile.cpp.o -c ../src/BamFile.cpp [7/228] c++ -Isrc/libpbbam.so.1.6.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbbam-1.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.1.6.0.p/BaiIndexedBamReader.cpp.o -MF src/libpbbam.so.1.6.0.p/BaiIndexedBamReader.cpp.o.d -o src/libpbbam.so.1.6.0.p/BaiIndexedBamReader.cpp.o -c ../src/BaiIndexedBamReader.cpp [8/228] c++ -Itests/pbbam_test.p -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbbam-1.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_ALL_NO_LIB -DGTEST_HAS_PTHREAD=1 -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tests/pbbam_test.p/src_test_BamRecordImplTags.cpp.o -MF tests/pbbam_test.p/src_test_BamRecordImplTags.cpp.o.d -o tests/pbbam_test.p/src_test_BamRecordImplTags.cpp.o -c ../tests/src/test_BamRecordImplTags.cpp [9/228] c++ -Itests/pbbam_test.p -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbbam-1.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_ALL_NO_LIB -DGTEST_HAS_PTHREAD=1 -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict 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c++ -Isrc/libpbbam.so.1.6.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbbam-1.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.1.6.0.p/BamReader.cpp.o -MF src/libpbbam.so.1.6.0.p/BamReader.cpp.o.d -o src/libpbbam.so.1.6.0.p/BamReader.cpp.o -c ../src/BamReader.cpp [12/228] c++ -Isrc/libpbbam.so.1.6.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbbam-1.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security 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-I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbbam-1.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_ALL_NO_LIB -DGTEST_HAS_PTHREAD=1 -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tests/pbbam_test.p/src_test_BamHeader.cpp.o -MF tests/pbbam_test.p/src_test_BamHeader.cpp.o.d -o tests/pbbam_test.p/src_test_BamHeader.cpp.o -c ../tests/src/test_BamHeader.cpp [134/228] c++ -Itests/pbbam_test.p -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbbam-1.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time 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src/libpbbam.so.1.6.0.p/BaiIndexedBamReader.cpp.o src/libpbbam.so.1.6.0.p/BamFile.cpp.o src/libpbbam.so.1.6.0.p/BamFileMerger.cpp.o src/libpbbam.so.1.6.0.p/BamHeader.cpp.o src/libpbbam.so.1.6.0.p/BamReader.cpp.o src/libpbbam.so.1.6.0.p/BamRecord.cpp.o src/libpbbam.so.1.6.0.p/BamRecordImpl.cpp.o src/libpbbam.so.1.6.0.p/BamRecordTags.cpp.o src/libpbbam.so.1.6.0.p/BamRecordView.cpp.o src/libpbbam.so.1.6.0.p/BamTagCodec.cpp.o src/libpbbam.so.1.6.0.p/BamWriter.cpp.o src/libpbbam.so.1.6.0.p/BgzipFastaWriter.cpp.o src/libpbbam.so.1.6.0.p/BgzipFastqWriter.cpp.o src/libpbbam.so.1.6.0.p/BgzipWriter.cpp.o src/libpbbam.so.1.6.0.p/ChemistryTable.cpp.o src/libpbbam.so.1.6.0.p/CollectionMetadata.cpp.o src/libpbbam.so.1.6.0.p/Compare.cpp.o src/libpbbam.so.1.6.0.p/CompositeBamReader.cpp.o src/libpbbam.so.1.6.0.p/CompositeFastaReader.cpp.o src/libpbbam.so.1.6.0.p/Config.cpp.o src/libpbbam.so.1.6.0.p/DataSet.cpp.o src/libpbbam.so.1.6.0.p/DataSetBaseTypes.cpp.o src/libpbbam.so.1.6.0.p/DataSetElement.cpp.o src/libpbbam.so.1.6.0.p/DataSetIO.cpp.o src/libpbbam.so.1.6.0.p/DataSetTypes.cpp.o src/libpbbam.so.1.6.0.p/DataSetXsd.cpp.o src/libpbbam.so.1.6.0.p/EntireFileQuery.cpp.o src/libpbbam.so.1.6.0.p/ErrnoReason.cpp.o src/libpbbam.so.1.6.0.p/FaiIndex.cpp.o src/libpbbam.so.1.6.0.p/FaiZmwChunker.cpp.o src/libpbbam.so.1.6.0.p/FastaCache.cpp.o src/libpbbam.so.1.6.0.p/FastaReader.cpp.o src/libpbbam.so.1.6.0.p/FastaSequence.cpp.o src/libpbbam.so.1.6.0.p/FastaSequenceQuery.cpp.o src/libpbbam.so.1.6.0.p/FastaWriter.cpp.o src/libpbbam.so.1.6.0.p/FastqReader.cpp.o src/libpbbam.so.1.6.0.p/FastqSequence.cpp.o src/libpbbam.so.1.6.0.p/FastqWriter.cpp.o src/libpbbam.so.1.6.0.p/FileProducer.cpp.o src/libpbbam.so.1.6.0.p/FileUtils.cpp.o src/libpbbam.so.1.6.0.p/FofnReader.cpp.o src/libpbbam.so.1.6.0.p/FormatUtils.cpp.o src/libpbbam.so.1.6.0.p/GenomicIntervalQuery.cpp.o src/libpbbam.so.1.6.0.p/IFastaWriter.cpp.o src/libpbbam.so.1.6.0.p/IFastqWriter.cpp.o src/libpbbam.so.1.6.0.p/IndexedBamWriter.cpp.o src/libpbbam.so.1.6.0.p/IndexedFastaReader.cpp.o src/libpbbam.so.1.6.0.p/IndexedFastqBgzfReader.cpp.o src/libpbbam.so.1.6.0.p/IndexedFastqReader.cpp.o src/libpbbam.so.1.6.0.p/IndexedFastqTextReader.cpp.o src/libpbbam.so.1.6.0.p/IndexedFastqReaderImpl.cpp.o src/libpbbam.so.1.6.0.p/IRecordWriter.cpp.o src/libpbbam.so.1.6.0.p/KSeqReader.cpp.o src/libpbbam.so.1.6.0.p/LibraryInfo.cpp.o src/libpbbam.so.1.6.0.p/MD5.cpp.o src/libpbbam.so.1.6.0.p/MemoryUtils.cpp.o src/libpbbam.so.1.6.0.p/PbiBuilder.cpp.o src/libpbbam.so.1.6.0.p/PbiFile.cpp.o src/libpbbam.so.1.6.0.p/PbiFilter.cpp.o src/libpbbam.so.1.6.0.p/PbiFilterQuery.cpp.o src/libpbbam.so.1.6.0.p/PbiFilterTypes.cpp.o src/libpbbam.so.1.6.0.p/PbiIndexedBamReader.cpp.o src/libpbbam.so.1.6.0.p/PbiIndexIO.cpp.o src/libpbbam.so.1.6.0.p/PbiRawData.cpp.o src/libpbbam.so.1.6.0.p/ProgramInfo.cpp.o src/libpbbam.so.1.6.0.p/ReadGroupInfo.cpp.o src/libpbbam.so.1.6.0.p/RecordType.cpp.o src/libpbbam.so.1.6.0.p/RunMetadata.cpp.o src/libpbbam.so.1.6.0.p/RunMetadataParser.cpp.o src/libpbbam.so.1.6.0.p/SamReader.cpp.o src/libpbbam.so.1.6.0.p/SamTagCodec.cpp.o src/libpbbam.so.1.6.0.p/SamWriter.cpp.o src/libpbbam.so.1.6.0.p/SequenceInfo.cpp.o src/libpbbam.so.1.6.0.p/StringUtilities.cpp.o src/libpbbam.so.1.6.0.p/Tag.cpp.o src/libpbbam.so.1.6.0.p/TagCollection.cpp.o src/libpbbam.so.1.6.0.p/TextFileReader.cpp.o src/libpbbam.so.1.6.0.p/TextFileWriter.cpp.o src/libpbbam.so.1.6.0.p/Validator.cpp.o src/libpbbam.so.1.6.0.p/ValidationErrors.cpp.o src/libpbbam.so.1.6.0.p/ValidationException.cpp.o src/libpbbam.so.1.6.0.p/Version.cpp.o src/libpbbam.so.1.6.0.p/VirtualZmwBamRecord.cpp.o src/libpbbam.so.1.6.0.p/VirtualZmwCompositeReader.cpp.o src/libpbbam.so.1.6.0.p/VirtualZmwReader.cpp.o src/libpbbam.so.1.6.0.p/VirtualRegion.cpp.o src/libpbbam.so.1.6.0.p/VirtualRegionTypeMap.cpp.o src/libpbbam.so.1.6.0.p/XmlReader.cpp.o src/libpbbam.so.1.6.0.p/XmlWriter.cpp.o src/libpbbam.so.1.6.0.p/WhitelistedZmwReadStitcher.cpp.o src/libpbbam.so.1.6.0.p/ZmwChunkedFastaReader.cpp.o src/libpbbam.so.1.6.0.p/ZmwChunkedFastqReader.cpp.o src/libpbbam.so.1.6.0.p/ZmwChunkedFastxBgzfReader.cpp.o src/libpbbam.so.1.6.0.p/ZmwChunkedFastxReaderImpl.cpp.o src/libpbbam.so.1.6.0.p/ZmwChunkedFastxTextReader.cpp.o src/libpbbam.so.1.6.0.p/ZmwGroupQuery.cpp.o src/libpbbam.so.1.6.0.p/ZmwReadStitcher.cpp.o src/libpbbam.so.1.6.0.p/ZmwQuery.cpp.o src/libpbbam.so.1.6.0.p/ZmwTypeMap.cpp.o src/libpbbam.so.1.6.0.p/bed_BedReader.cpp.o src/libpbbam.so.1.6.0.p/bed_BedWriter.cpp.o src/libpbbam.so.1.6.0.p/ccs_CCSPbiBuilder.cpp.o src/libpbbam.so.1.6.0.p/ccs_CCSRecord.cpp.o src/libpbbam.so.1.6.0.p/ccs_CCSRecordFormat.cpp.o src/libpbbam.so.1.6.0.p/ccs_CCSRecordReader.cpp.o src/libpbbam.so.1.6.0.p/ccs_CCSRecordWriter.cpp.o src/libpbbam.so.1.6.0.p/vcf_VcfFile.cpp.o src/libpbbam.so.1.6.0.p/vcf_VcfFormat.cpp.o src/libpbbam.so.1.6.0.p/vcf_VcfHeader.cpp.o src/libpbbam.so.1.6.0.p/vcf_VcfHeaderTypes.cpp.o src/libpbbam.so.1.6.0.p/vcf_VcfQuery.cpp.o 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-Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tests/pbbam_test.p/src_test_VcfVariant.cpp.o -MF tests/pbbam_test.p/src_test_VcfVariant.cpp.o.d -o tests/pbbam_test.p/src_test_VcfVariant.cpp.o -c ../tests/src/test_VcfVariant.cpp [190/228] c++ -Itests/pbbam_test.p -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbbam-1.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_ALL_NO_LIB -DGTEST_HAS_PTHREAD=1 -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tests/pbbam_test.p/src_test_VcfWriter.cpp.o -MF tests/pbbam_test.p/src_test_VcfWriter.cpp.o.d -o tests/pbbam_test.p/src_test_VcfWriter.cpp.o -c ../tests/src/test_VcfWriter.cpp [191/228] /usr/bin/python3 ../tests/scripts/generate_data.py /build/pbbam-1.6.0+dfsg/tests/data /build/pbbam-1.6.0+dfsg/obj-aarch64-linux-gnu/tests Generating test data in /build/pbbam-1.6.0+dfsg/obj-aarch64-linux-gnu/tests - Creating file: truncated.bam...done. - Creating file: chunking_emptyfilters.subreadset.xml...done. - Creating file: chunking_missingfilters.subreadset.xml...done. - Creating file: normal.fa...done. - Creating file: normal.fq...done. - Creating symlink: aligned.bam...done. - Creating symlink: aligned.bam.bai...done. - Creating symlink: aligned.bam.pbi...done. - Creating symlink: aligned2.bam...done. - Creating symlink: aligned2.bam.bai...done. - Creating symlink: aligned2.bam.pbi...done. - Creating symlink: m150404_101626_42267_c100807920800000001823174110291514_s1_p0.1.subreads.bam...done. - Creating symlink: m150404_101626_42267_c100807920800000001823174110291514_s1_p0.1.subreads.bam.pbi...done. - Creating symlink: m150404_101626_42267_c100807920800000001823174110291514_s1_p0.2.subreads.bam...done. - Creating symlink: m150404_101626_42267_c100807920800000001823174110291514_s1_p0.2.subreads.bam.pbi...done. - Creating symlink: m150404_101626_42267_c100807920800000001823174110291514_s1_p0.3.subreads.bam...done. - Creating symlink: m150404_101626_42267_c100807920800000001823174110291514_s1_p0.3.subreads.bam.pbi...done. - Creating symlink: missing_pbi.bam...done. [192/228] c++ -Itests/zero_byte_check/zero_byte_check.p -Itests/zero_byte_check -I../tests/zero_byte_check -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbbam-1.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_ALL_NO_LIB -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tests/zero_byte_check/zero_byte_check.p/main.cpp.o -MF tests/zero_byte_check/zero_byte_check.p/main.cpp.o.d -o tests/zero_byte_check/zero_byte_check.p/main.cpp.o -c ../tests/zero_byte_check/main.cpp [193/228] c++ -o tests/zero_byte_check/zero_byte_check tests/zero_byte_check/zero_byte_check.p/main.cpp.o -Wl,--as-needed -Wl,--no-undefined -g -O2 -fdebug-prefix-map=/build/pbbam-1.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Wl,--start-group src/libpbbam.so.1.6.0 /usr/lib/aarch64-linux-gnu/libhts.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/libpbcopper.so -Wl,--end-group '-Wl,-rpath,$ORIGIN/../../src' -Wl,-rpath-link,/build/pbbam-1.6.0+dfsg/obj-aarch64-linux-gnu/src [194/228] c++ -Itests/pbbam_test.p -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbbam-1.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_ALL_NO_LIB -DGTEST_HAS_PTHREAD=1 -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tests/pbbam_test.p/src_test_ZmwChunkedFastxReader.cpp.o -MF tests/pbbam_test.p/src_test_ZmwChunkedFastxReader.cpp.o.d -o tests/pbbam_test.p/src_test_ZmwChunkedFastxReader.cpp.o -c ../tests/src/test_ZmwChunkedFastxReader.cpp [195/228] c++ -Itools/bam2sam.p -Itools -I../tools -Iinclude -I../include -I../tools/bam2sam -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbbam-1.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tools/bam2sam.p/bam2sam_src_main.cpp.o -MF tools/bam2sam.p/bam2sam_src_main.cpp.o.d -o tools/bam2sam.p/bam2sam_src_main.cpp.o -c ../tools/bam2sam/src/main.cpp [196/228] c++ -Itests/pbbam_test.p -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbbam-1.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_ALL_NO_LIB -DGTEST_HAS_PTHREAD=1 -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tests/pbbam_test.p/src_test_PbiFilter.cpp.o -MF tests/pbbam_test.p/src_test_PbiFilter.cpp.o.d -o tests/pbbam_test.p/src_test_PbiFilter.cpp.o -c ../tests/src/test_PbiFilter.cpp [197/228] c++ -Itests/pbbam_test.p -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbbam-1.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_ALL_NO_LIB -DGTEST_HAS_PTHREAD=1 -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tests/pbbam_test.p/src_test_WhitelistedZmwReadStitcher.cpp.o -MF tests/pbbam_test.p/src_test_WhitelistedZmwReadStitcher.cpp.o.d -o tests/pbbam_test.p/src_test_WhitelistedZmwReadStitcher.cpp.o -c ../tests/src/test_WhitelistedZmwReadStitcher.cpp [198/228] c++ -Itools/bam2sam.p -Itools -I../tools -Iinclude -I../include -I../tools/bam2sam -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbbam-1.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tools/bam2sam.p/bam2sam_src_Bam2SamSettings.cpp.o -MF tools/bam2sam.p/bam2sam_src_Bam2SamSettings.cpp.o.d -o tools/bam2sam.p/bam2sam_src_Bam2SamSettings.cpp.o -c ../tools/bam2sam/src/Bam2SamSettings.cpp [199/228] c++ -Itools/pbindex.p -Itools -I../tools -Iinclude -I../include -I../tools/pbindex -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbbam-1.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_ALL_NO_LIB -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tools/pbindex.p/pbindex_src_main.cpp.o -MF tools/pbindex.p/pbindex_src_main.cpp.o.d -o tools/pbindex.p/pbindex_src_main.cpp.o -c ../tools/pbindex/src/main.cpp [200/228] c++ -Itools/pbindex.p -Itools -I../tools -Iinclude -I../include -I../tools/pbindex -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbbam-1.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_ALL_NO_LIB -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tools/pbindex.p/pbindex_src_PbIndexWorkflow.cpp.o -MF tools/pbindex.p/pbindex_src_PbIndexWorkflow.cpp.o.d -o tools/pbindex.p/pbindex_src_PbIndexWorkflow.cpp.o -c ../tools/pbindex/src/PbIndexWorkflow.cpp [201/228] c++ -Itools/pbindex.p -Itools -I../tools -Iinclude -I../include -I../tools/pbindex -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbbam-1.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_ALL_NO_LIB -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tools/pbindex.p/pbindex_src_PbIndexSettings.cpp.o -MF tools/pbindex.p/pbindex_src_PbIndexSettings.cpp.o.d -o tools/pbindex.p/pbindex_src_PbIndexSettings.cpp.o -c ../tools/pbindex/src/PbIndexSettings.cpp [202/228] c++ -Itests/pbbam_test.p -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbbam-1.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_ALL_NO_LIB -DGTEST_HAS_PTHREAD=1 -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tests/pbbam_test.p/src_test_ZmwQuery.cpp.o -MF tests/pbbam_test.p/src_test_ZmwQuery.cpp.o.d -o tests/pbbam_test.p/src_test_ZmwQuery.cpp.o -c ../tests/src/test_ZmwQuery.cpp [203/228] c++ -Itools/bam2sam.p -Itools -I../tools -Iinclude -I../include -I../tools/bam2sam -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbbam-1.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tools/bam2sam.p/bam2sam_src_Bam2SamWorkflow.cpp.o -MF tools/bam2sam.p/bam2sam_src_Bam2SamWorkflow.cpp.o.d -o tools/bam2sam.p/bam2sam_src_Bam2SamWorkflow.cpp.o -c ../tools/bam2sam/src/Bam2SamWorkflow.cpp [204/228] c++ -o tools/pbindex tools/pbindex.p/pbindex_src_main.cpp.o tools/pbindex.p/pbindex_src_PbIndexSettings.cpp.o tools/pbindex.p/pbindex_src_PbIndexWorkflow.cpp.o -Wl,--as-needed -Wl,--no-undefined -g -O2 -fdebug-prefix-map=/build/pbbam-1.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Wl,--start-group src/libpbbam.so.1.6.0 /usr/lib/aarch64-linux-gnu/libhts.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/libpbcopper.so -Wl,--end-group '-Wl,-rpath,$ORIGIN/../src' -Wl,-rpath-link,/build/pbbam-1.6.0+dfsg/obj-aarch64-linux-gnu/src [205/228] c++ -o tools/bam2sam tools/bam2sam.p/bam2sam_src_main.cpp.o tools/bam2sam.p/bam2sam_src_Bam2SamSettings.cpp.o tools/bam2sam.p/bam2sam_src_Bam2SamWorkflow.cpp.o -Wl,--as-needed -Wl,--no-undefined -g -O2 -fdebug-prefix-map=/build/pbbam-1.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Wl,--start-group /usr/lib/aarch64-linux-gnu/libhts.so -pthread /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/libpbcopper.so -Wl,--end-group [206/228] c++ -Itests/pbbam_test.p -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbbam-1.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_ALL_NO_LIB -DGTEST_HAS_PTHREAD=1 -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tests/pbbam_test.p/src_test_Tags.cpp.o -MF tests/pbbam_test.p/src_test_Tags.cpp.o.d -o tests/pbbam_test.p/src_test_Tags.cpp.o -c ../tests/src/test_Tags.cpp [207/228] c++ -Itools/pbindexdump.p -Itools -I../tools -Iinclude -I../include -I../tools/pbindexdump -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbbam-1.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_ALL_NO_LIB -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tools/pbindexdump.p/pbindexdump_src_PbIndexDumpWorkflow.cpp.o -MF tools/pbindexdump.p/pbindexdump_src_PbIndexDumpWorkflow.cpp.o.d -o tools/pbindexdump.p/pbindexdump_src_PbIndexDumpWorkflow.cpp.o -c ../tools/pbindexdump/src/PbIndexDumpWorkflow.cpp [208/228] c++ -Itools/pbindexdump.p -Itools -I../tools -Iinclude -I../include -I../tools/pbindexdump -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbbam-1.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_ALL_NO_LIB -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tools/pbindexdump.p/pbindexdump_src_main.cpp.o -MF tools/pbindexdump.p/pbindexdump_src_main.cpp.o.d -o tools/pbindexdump.p/pbindexdump_src_main.cpp.o -c ../tools/pbindexdump/src/main.cpp [209/228] c++ -Itools/pbmerge.p -Itools -I../tools -Iinclude -I../include -I../tools/pbmerge -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbbam-1.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_ALL_NO_LIB -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tools/pbmerge.p/pbmerge_src_main.cpp.o -MF tools/pbmerge.p/pbmerge_src_main.cpp.o.d -o tools/pbmerge.p/pbmerge_src_main.cpp.o -c ../tools/pbmerge/src/main.cpp [210/228] c++ -Itools/pbindexdump.p -Itools -I../tools -Iinclude -I../include -I../tools/pbindexdump -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbbam-1.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_ALL_NO_LIB -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tools/pbindexdump.p/pbindexdump_src_PbIndexDumpSettings.cpp.o -MF tools/pbindexdump.p/pbindexdump_src_PbIndexDumpSettings.cpp.o.d -o tools/pbindexdump.p/pbindexdump_src_PbIndexDumpSettings.cpp.o -c ../tools/pbindexdump/src/PbIndexDumpSettings.cpp [211/228] c++ -Itools/pbindexdump.p -Itools -I../tools -Iinclude -I../include -I../tools/pbindexdump -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbbam-1.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 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-fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbbam-1.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_ALL_NO_LIB -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tools/pbmerge.p/pbmerge_src_PbMergeWorkflow.cpp.o -MF tools/pbmerge.p/pbmerge_src_PbMergeWorkflow.cpp.o.d -o tools/pbmerge.p/pbmerge_src_PbMergeWorkflow.cpp.o -c ../tools/pbmerge/src/PbMergeWorkflow.cpp [215/228] c++ -Itools/pbbamify.p -Itools -I../tools -Iinclude -I../include -I../tools/pbbamify -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbbam-1.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_ALL_NO_LIB -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tools/pbbamify.p/pbbamify_src_main.cpp.o -MF tools/pbbamify.p/pbbamify_src_main.cpp.o.d -o tools/pbbamify.p/pbbamify_src_main.cpp.o -c ../tools/pbbamify/src/main.cpp [216/228] c++ -o tools/pbmerge tools/pbmerge.p/pbmerge_src_main.cpp.o tools/pbmerge.p/pbmerge_src_PbMergeSettings.cpp.o tools/pbmerge.p/pbmerge_src_PbMergeWorkflow.cpp.o -Wl,--as-needed -Wl,--no-undefined -g -O2 -fdebug-prefix-map=/build/pbbam-1.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Wl,--start-group src/libpbbam.so.1.6.0 /usr/lib/aarch64-linux-gnu/libhts.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/libpbcopper.so -Wl,--end-group '-Wl,-rpath,$ORIGIN/../src' -Wl,-rpath-link,/build/pbbam-1.6.0+dfsg/obj-aarch64-linux-gnu/src [217/228] c++ -Itests/pbbam_test.p -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbbam-1.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_ALL_NO_LIB -DGTEST_HAS_PTHREAD=1 -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tests/pbbam_test.p/src_test_ZmwReadStitcher.cpp.o -MF tests/pbbam_test.p/src_test_ZmwReadStitcher.cpp.o.d -o tests/pbbam_test.p/src_test_ZmwReadStitcher.cpp.o -c ../tests/src/test_ZmwReadStitcher.cpp [218/228] c++ -Itools/pbindexdump.p -Itools -I../tools -Iinclude -I../include -I../tools/pbindexdump -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbbam-1.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_ALL_NO_LIB -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tools/pbindexdump.p/pbindexdump_src_JsonFormatter.cpp.o -MF tools/pbindexdump.p/pbindexdump_src_JsonFormatter.cpp.o.d -o tools/pbindexdump.p/pbindexdump_src_JsonFormatter.cpp.o -c ../tools/pbindexdump/src/JsonFormatter.cpp [219/228] c++ -o tools/pbindexdump tools/pbindexdump.p/pbindexdump_src_CppFormatter.cpp.o tools/pbindexdump.p/pbindexdump_src_JsonFormatter.cpp.o tools/pbindexdump.p/pbindexdump_src_PbIndexDumpSettings.cpp.o tools/pbindexdump.p/pbindexdump_src_PbIndexDumpWorkflow.cpp.o tools/pbindexdump.p/pbindexdump_src_main.cpp.o -Wl,--as-needed -Wl,--no-undefined -g -O2 -fdebug-prefix-map=/build/pbbam-1.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Wl,--start-group src/libpbbam.so.1.6.0 /usr/lib/aarch64-linux-gnu/libhts.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/libpbcopper.so -Wl,--end-group '-Wl,-rpath,$ORIGIN/../src' -Wl,-rpath-link,/build/pbbam-1.6.0+dfsg/obj-aarch64-linux-gnu/src [220/228] c++ -Itools/ccs-kinetics-bystrandify.p -Itools -I../tools -Iinclude -I../include -I../tools/ccs-kinetics-bystrandify -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbbam-1.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_ALL_NO_LIB -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tools/ccs-kinetics-bystrandify.p/ccs-kinetics-bystrandify_src_main.cpp.o -MF tools/ccs-kinetics-bystrandify.p/ccs-kinetics-bystrandify_src_main.cpp.o.d -o 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-Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbbam-1.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_ALL_NO_LIB -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tools/pbbamify.p/pbbamify_src_QueryLookup.cpp.o -MF tools/pbbamify.p/pbbamify_src_QueryLookup.cpp.o.d -o tools/pbbamify.p/pbbamify_src_QueryLookup.cpp.o -c ../tools/pbbamify/src/QueryLookup.cpp [224/228] c++ -o tools/pbbamify tools/pbbamify.p/pbbamify_src_main.cpp.o tools/pbbamify.p/pbbamify_src_PbBamifySettings.cpp.o tools/pbbamify.p/pbbamify_src_PbBamifyWorkflow.cpp.o tools/pbbamify.p/pbbamify_src_QueryLookup.cpp.o -Wl,--as-needed -Wl,--no-undefined -g -O2 -fdebug-prefix-map=/build/pbbam-1.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Wl,--start-group src/libpbbam.so.1.6.0 /usr/lib/aarch64-linux-gnu/libhts.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/libpbcopper.so -Wl,--end-group '-Wl,-rpath,$ORIGIN/../src' -Wl,-rpath-link,/build/pbbam-1.6.0+dfsg/obj-aarch64-linux-gnu/src [225/228] c++ -Itools/ccs-kinetics-bystrandify.p -Itools -I../tools -Iinclude -I../include -I../tools/ccs-kinetics-bystrandify -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbbam-1.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_ALL_NO_LIB -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tools/ccs-kinetics-bystrandify.p/ccs-kinetics-bystrandify_src_CcsKineticsBystrandifyWorkflow.cpp.o -MF tools/ccs-kinetics-bystrandify.p/ccs-kinetics-bystrandify_src_CcsKineticsBystrandifyWorkflow.cpp.o.d -o 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-I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbbam-1.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_ALL_NO_LIB -DGTEST_HAS_PTHREAD=1 -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tests/pbbam_test.p/src_test_Version.cpp.o -MF tests/pbbam_test.p/src_test_Version.cpp.o.d -o tests/pbbam_test.p/src_test_Version.cpp.o -c ../tests/src/test_Version.cpp [228/228] c++ -o tests/pbbam_test tests/pbbam_test.p/src_test_AlignmentPrinter.cpp.o tests/pbbam_test.p/src_test_BamFile.cpp.o tests/pbbam_test.p/src_test_BamHeader.cpp.o tests/pbbam_test.p/src_test_BamReader.cpp.o tests/pbbam_test.p/src_test_BamRecord.cpp.o tests/pbbam_test.p/src_test_BamRecordClipping.cpp.o tests/pbbam_test.p/src_test_BamRecordImplCore.cpp.o tests/pbbam_test.p/src_test_BamRecordImplTags.cpp.o tests/pbbam_test.p/src_test_BamRecordImplVariableData.cpp.o tests/pbbam_test.p/src_test_BamRecordMapping.cpp.o tests/pbbam_test.p/src_test_BamWriter.cpp.o tests/pbbam_test.p/src_test_BedReader.cpp.o tests/pbbam_test.p/src_test_BedWriter.cpp.o tests/pbbam_test.p/src_test_BgzipFastaWriter.cpp.o tests/pbbam_test.p/src_test_BgzipFastqWriter.cpp.o tests/pbbam_test.p/src_test_BgzipWriter.cpp.o tests/pbbam_test.p/src_test_CCSPbiBuilder.cpp.o tests/pbbam_test.p/src_test_CCSRecord.cpp.o tests/pbbam_test.p/src_test_CCSRecordIO.cpp.o tests/pbbam_test.p/src_test_CollectionMetadata.cpp.o tests/pbbam_test.p/src_test_Compare.cpp.o tests/pbbam_test.p/src_test_CompositeBamReaders.cpp.o tests/pbbam_test.p/src_test_DataSetCore.cpp.o tests/pbbam_test.p/src_test_DataSetGenomicIntervals.cpp.o tests/pbbam_test.p/src_test_DataSetIO.cpp.o tests/pbbam_test.p/src_test_DataSetQuery.cpp.o tests/pbbam_test.p/src_test_DataSetXsd.cpp.o tests/pbbam_test.p/src_test_EndToEnd.cpp.o tests/pbbam_test.p/src_test_EntireFileQuery.cpp.o tests/pbbam_test.p/src_test_FaiIndex.cpp.o tests/pbbam_test.p/src_test_FaiZmwChunker.cpp.o tests/pbbam_test.p/src_test_FastaCache.cpp.o tests/pbbam_test.p/src_test_FastaReader.cpp.o tests/pbbam_test.p/src_test_FastaSequence.cpp.o tests/pbbam_test.p/src_test_FastaSequenceQuery.cpp.o tests/pbbam_test.p/src_test_FastaWriter.cpp.o tests/pbbam_test.p/src_test_FastqReader.cpp.o tests/pbbam_test.p/src_test_FastqSequence.cpp.o tests/pbbam_test.p/src_test_FastqWriter.cpp.o tests/pbbam_test.p/src_test_FileUtils.cpp.o tests/pbbam_test.p/src_test_GenomicIntervalQuery.cpp.o tests/pbbam_test.p/src_test_IndexedBamWriter.cpp.o tests/pbbam_test.p/src_test_IndexedFastaReader.cpp.o tests/pbbam_test.p/src_test_IndexedFastqReader.cpp.o tests/pbbam_test.p/src_test_LongCigar.cpp.o tests/pbbam_test.p/src_test_PacBioIndex.cpp.o tests/pbbam_test.p/src_test_PbiFilter.cpp.o tests/pbbam_test.p/src_test_PbiFilterQuery.cpp.o tests/pbbam_test.p/src_test_QualityValues.cpp.o tests/pbbam_test.p/src_test_Pulse2BaseCache.cpp.o tests/pbbam_test.p/src_test_ReadGroupInfo.cpp.o tests/pbbam_test.p/src_test_RunMetadata.cpp.o tests/pbbam_test.p/src_test_SamIO.cpp.o tests/pbbam_test.p/src_test_SequenceUtils.cpp.o tests/pbbam_test.p/src_test_StringUtils.cpp.o tests/pbbam_test.p/src_test_Tags.cpp.o tests/pbbam_test.p/src_test_TextFileReader.cpp.o tests/pbbam_test.p/src_test_TextFileWriter.cpp.o tests/pbbam_test.p/src_test_TimeUtils.cpp.o tests/pbbam_test.p/src_test_Validator.cpp.o tests/pbbam_test.p/src_test_VcfFile.cpp.o tests/pbbam_test.p/src_test_VcfFormat.cpp.o tests/pbbam_test.p/src_test_VcfHeader.cpp.o tests/pbbam_test.p/src_test_VcfReader.cpp.o tests/pbbam_test.p/src_test_VcfSort.cpp.o tests/pbbam_test.p/src_test_VcfQuery.cpp.o tests/pbbam_test.p/src_test_VcfVariant.cpp.o tests/pbbam_test.p/src_test_VcfWriter.cpp.o tests/pbbam_test.p/src_test_Version.cpp.o tests/pbbam_test.p/src_test_WhitelistedZmwReadStitcher.cpp.o tests/pbbam_test.p/src_test_ZmwChunkedFastxReader.cpp.o tests/pbbam_test.p/src_test_ZmwReadStitcher.cpp.o tests/pbbam_test.p/src_test_ZmwQuery.cpp.o -Wl,--as-needed -Wl,--no-undefined -g -O2 -fdebug-prefix-map=/build/pbbam-1.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Wl,--start-group src/libpbbam.so.1.6.0 /usr/lib/aarch64-linux-gnu/libgtest_main.a -lpthread /usr/lib/aarch64-linux-gnu/libgtest.a /usr/lib/aarch64-linux-gnu/libhts.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/libpbcopper.so -Wl,--end-group '-Wl,-rpath,$ORIGIN/../src' -Wl,-rpath-link,/build/pbbam-1.6.0+dfsg/obj-aarch64-linux-gnu/src debian/rules override_dh_auto_test make[1]: Entering directory '/build/pbbam-1.6.0+dfsg' sed \ -e 's/$BAM2SAM/samtools view/g' \ -e 's/\-\-header\-only/-H/g' \ -e 's/\-\-no\-header//g' \ -e 's|@PacBioBAM_BinDir@/||g' \ -e 's|$TOOLS_BIN/||g' \ -e 's|@PacBioBAM_TestsDir@|/build/pbbam-1.6.0+dfsg/tests|g' \ -e 's|@PacBioBAM_VERSION@|1.6.0+dfsg|g' \ -e 's|@GeneratedTestDataDir@|/build/pbbam-1.6.0+dfsg/gendata|g' \ -e '/@PG/s|+dfsg||g' \ -e 's/$SAMTOOLS/samtools/g' \ tests/src/cram/pbbamify.t.in > tests/src/cram/pbbamify.deb.t sed \ -e 's/$BAM2SAM/samtools view/g' \ -e 's/\-\-header\-only/-H/g' \ -e 's/\-\-no\-header//g' \ -e 's|@PacBioBAM_BinDir@/||g' \ -e 's|$TOOLS_BIN/||g' \ -e 's|@PacBioBAM_TestsDir@|/build/pbbam-1.6.0+dfsg/tests|g' \ -e 's|@PacBioBAM_VERSION@|1.6.0+dfsg|g' \ -e 's|@GeneratedTestDataDir@|/build/pbbam-1.6.0+dfsg/gendata|g' \ -e '/@PG/s|+dfsg||g' \ -e 's/$SAMTOOLS/samtools/g' \ tests/src/cram/pbindexdump_cpp.t.in > tests/src/cram/pbindexdump_cpp.deb.t sed \ -e 's/$BAM2SAM/samtools view/g' \ -e 's/\-\-header\-only/-H/g' \ -e 's/\-\-no\-header//g' \ -e 's|@PacBioBAM_BinDir@/||g' \ -e 's|$TOOLS_BIN/||g' \ -e 's|@PacBioBAM_TestsDir@|/build/pbbam-1.6.0+dfsg/tests|g' \ -e 's|@PacBioBAM_VERSION@|1.6.0+dfsg|g' \ -e 's|@GeneratedTestDataDir@|/build/pbbam-1.6.0+dfsg/gendata|g' \ -e '/@PG/s|+dfsg||g' \ -e 's/$SAMTOOLS/samtools/g' \ tests/src/cram/pbindexdump_json.t.in > tests/src/cram/pbindexdump_json.deb.t sed \ -e 's/$BAM2SAM/samtools view/g' \ -e 's/\-\-header\-only/-H/g' \ -e 's/\-\-no\-header//g' \ -e 's|@PacBioBAM_BinDir@/||g' \ -e 's|$TOOLS_BIN/||g' \ -e 's|@PacBioBAM_TestsDir@|/build/pbbam-1.6.0+dfsg/tests|g' \ -e 's|@PacBioBAM_VERSION@|1.6.0+dfsg|g' \ -e 's|@GeneratedTestDataDir@|/build/pbbam-1.6.0+dfsg/gendata|g' \ -e '/@PG/s|+dfsg||g' \ -e 's/$SAMTOOLS/samtools/g' \ tests/src/cram/pbmerge_aligned_ordering.t.in > tests/src/cram/pbmerge_aligned_ordering.deb.t sed \ -e 's/$BAM2SAM/samtools view/g' \ -e 's/\-\-header\-only/-H/g' \ -e 's/\-\-no\-header//g' \ -e 's|@PacBioBAM_BinDir@/||g' \ -e 's|$TOOLS_BIN/||g' \ -e 's|@PacBioBAM_TestsDir@|/build/pbbam-1.6.0+dfsg/tests|g' \ -e 's|@PacBioBAM_VERSION@|1.6.0+dfsg|g' \ -e 's|@GeneratedTestDataDir@|/build/pbbam-1.6.0+dfsg/gendata|g' \ -e '/@PG/s|+dfsg||g' \ -e 's/$SAMTOOLS/samtools/g' \ tests/src/cram/pbmerge_dataset.t.in > tests/src/cram/pbmerge_dataset.deb.t sed \ -e 's/$BAM2SAM/samtools view/g' \ -e 's/\-\-header\-only/-H/g' \ -e 's/\-\-no\-header//g' \ -e 's|@PacBioBAM_BinDir@/||g' \ -e 's|$TOOLS_BIN/||g' \ -e 's|@PacBioBAM_TestsDir@|/build/pbbam-1.6.0+dfsg/tests|g' \ -e 's|@PacBioBAM_VERSION@|1.6.0+dfsg|g' \ -e 's|@GeneratedTestDataDir@|/build/pbbam-1.6.0+dfsg/gendata|g' \ -e '/@PG/s|+dfsg||g' \ -e 's/$SAMTOOLS/samtools/g' \ tests/src/cram/pbmerge_fofn.t.in > tests/src/cram/pbmerge_fofn.deb.t sed \ -e 's/$BAM2SAM/samtools view/g' \ -e 's/\-\-header\-only/-H/g' \ -e 's/\-\-no\-header//g' \ -e 's|@PacBioBAM_BinDir@/||g' \ -e 's|$TOOLS_BIN/||g' \ -e 's|@PacBioBAM_TestsDir@|/build/pbbam-1.6.0+dfsg/tests|g' \ -e 's|@PacBioBAM_VERSION@|1.6.0+dfsg|g' \ -e 's|@GeneratedTestDataDir@|/build/pbbam-1.6.0+dfsg/gendata|g' \ -e '/@PG/s|+dfsg||g' \ -e 's/$SAMTOOLS/samtools/g' \ tests/src/cram/pbmerge_mixed_ordering.t.in > tests/src/cram/pbmerge_mixed_ordering.deb.t sed \ -e 's/$BAM2SAM/samtools view/g' \ -e 's/\-\-header\-only/-H/g' \ -e 's/\-\-no\-header//g' \ -e 's|@PacBioBAM_BinDir@/||g' \ -e 's|$TOOLS_BIN/||g' \ -e 's|@PacBioBAM_TestsDir@|/build/pbbam-1.6.0+dfsg/tests|g' \ -e 's|@PacBioBAM_VERSION@|1.6.0+dfsg|g' \ -e 's|@GeneratedTestDataDir@|/build/pbbam-1.6.0+dfsg/gendata|g' \ -e '/@PG/s|+dfsg||g' \ -e 's/$SAMTOOLS/samtools/g' \ tests/src/cram/pbmerge_pacbio_ordering.t.in > tests/src/cram/pbmerge_pacbio_ordering.deb.t dh_auto_configure -O--buildsystem=meson cd obj-aarch64-linux-gnu && LC_ALL=C.UTF-8 meson .. --wrap-mode=nodownload --buildtype=plain --prefix=/usr --sysconfdir=/etc --localstatedir=/var --libdir=lib/aarch64-linux-gnu Directory already configured. Just run your build command (e.g. ninja) and Meson will regenerate as necessary. If ninja fails, run "ninja reconfigure" or "meson --reconfigure" to force Meson to regenerate. If build failures persist, run "meson setup --wipe" to rebuild from scratch using the same options as passed when configuring the build. To change option values, run "meson configure" instead. mkdir -p /build/pbbam-1.6.0+dfsg/gendata python3 tests/scripts/generate_data.py /build/pbbam-1.6.0+dfsg/tests/data /build/pbbam-1.6.0+dfsg/gendata Generating test data in /build/pbbam-1.6.0+dfsg/gendata - Creating file: truncated.bam...done. - Creating file: chunking_emptyfilters.subreadset.xml...done. - Creating file: chunking_missingfilters.subreadset.xml...done. - Creating file: normal.fa...done. - Creating file: normal.fq...done. - Creating symlink: aligned.bam...done. - Creating symlink: aligned.bam.bai...done. - Creating symlink: aligned.bam.pbi...done. - Creating symlink: aligned2.bam...done. - Creating symlink: aligned2.bam.bai...done. - Creating symlink: aligned2.bam.pbi...done. - Creating symlink: m150404_101626_42267_c100807920800000001823174110291514_s1_p0.1.subreads.bam...done. - Creating symlink: m150404_101626_42267_c100807920800000001823174110291514_s1_p0.1.subreads.bam.pbi...done. - Creating symlink: m150404_101626_42267_c100807920800000001823174110291514_s1_p0.2.subreads.bam...done. - Creating symlink: m150404_101626_42267_c100807920800000001823174110291514_s1_p0.2.subreads.bam.pbi...done. - Creating symlink: m150404_101626_42267_c100807920800000001823174110291514_s1_p0.3.subreads.bam...done. - Creating symlink: m150404_101626_42267_c100807920800000001823174110291514_s1_p0.3.subreads.bam.pbi...done. - Creating symlink: missing_pbi.bam...done. # Fix broken PATH synthetic_movie_all_path=`find $PWD -name synthetic_movie_all.subreadset.xml` ; \ sed -i -e "s?.GENERATEDDATADIR/synthetic_movie_all.subreadset.xml?${synthetic_movie_all_path}?" tests/src/cram/pbbamify* BINDIR=`dirname $(find $PWD -name pbmerge -type f -executable)`; \ LIBDIR=`find $PWD -name lib -type d`; \ PATH="$BINDIR:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" LD_LIBRARY_PATH="$LIBDIR:" \ cram3 -v --preserve-env tests/src/cram/pbbamify.deb.t tests/src/cram/pbindexdump_cpp.deb.t tests/src/cram/pbindexdump_json.deb.t tests/src/cram/pbmerge_aligned_ordering.deb.t tests/src/cram/pbmerge_dataset.deb.t tests/src/cram/pbmerge_fofn.deb.t tests/src/cram/pbmerge_mixed_ordering.deb.t tests/src/cram/pbmerge_pacbio_ordering.deb.t tests/src/cram/pbbamify.deb.t: passed tests/src/cram/pbindexdump_cpp.deb.t: passed tests/src/cram/pbindexdump_json.deb.t: passed tests/src/cram/pbmerge_aligned_ordering.deb.t: passed tests/src/cram/pbmerge_dataset.deb.t: passed tests/src/cram/pbmerge_fofn.deb.t: passed tests/src/cram/pbmerge_mixed_ordering.deb.t: passed tests/src/cram/pbmerge_pacbio_ordering.deb.t: passed # Ran 8 tests, 0 skipped, 0 failed. make[1]: Leaving directory '/build/pbbam-1.6.0+dfsg' create-stamp debian/debhelper-build-stamp dh_testroot -O--buildsystem=meson dh_prep -O--buildsystem=meson dh_auto_install -O--buildsystem=meson cd obj-aarch64-linux-gnu && DESTDIR=/build/pbbam-1.6.0\+dfsg/debian/tmp LC_ALL=C.UTF-8 ninja install [0/1] Regenerating build files. The Meson build system Version: 0.56.2 Source dir: /build/pbbam-1.6.0+dfsg Build dir: /build/pbbam-1.6.0+dfsg/obj-aarch64-linux-gnu Build type: native build Project name: PacBioBAM Project version: 1.6.0 C++ compiler for the host machine: c++ (gcc 10.2.1 "c++ (Debian 10.2.1-6) 10.2.1 20210110") C++ linker for the host machine: c++ ld.bfd 2.35.2 Host machine cpu family: aarch64 Host machine cpu: aarch64 Compiler for C++ supports arguments -Wduplicated-cond: YES (cached) Compiler for C++ supports arguments -Wduplicated-branches: YES (cached) Compiler for C++ supports arguments -Wlogical-op: YES (cached) Compiler for C++ supports arguments -Wrestrict: YES (cached) Compiler for C++ supports arguments -Wnull-dereference: YES (cached) Compiler for C++ supports arguments -Wuseless-cast: YES (cached) Compiler for C++ supports arguments -Wdouble-promotion: YES (cached) Compiler for C++ supports arguments -Wshadow: YES (cached) Compiler for C++ supports arguments -Wformat=1: YES (cached) Dependency threads found: YES unknown (cached) Dependency boost found: YES 1.74.0 (cached) Dependency zlib found: YES 1.2.11 (cached) Dependency htslib found: YES 1.11-4 (cached) Dependency pbcopper found: YES 1.8.0 (cached) Configuring PbbamVersion.cpp using configuration Configuring LibraryVersion.h using configuration Program python3 found: YES (/usr/bin/python3) Program tools/check-formatting found: YES (/build/pbbam-1.6.0+dfsg/tools/check-formatting) Program tools/check-eof found: YES (/build/pbbam-1.6.0+dfsg/tools/check-eof) Program cram3 found: YES (/usr/bin/cram3) Dependency gtest found: YES 1.10.0 (cached) Configuring group.fofn using configuration Configuring PbbamTestData.h using configuration Configuring synthetic_movie_all.subreadset.xml using configuration Configuring Bam2SamVersion.h using configuration Configuring bam2sam.t using configuration Configuring PbIndexVersion.h using configuration Configuring PbIndexDumpVersion.h using configuration Configuring pbindexdump_json.t using configuration Configuring pbindexdump_cpp.t using configuration Configuring PbMergeVersion.h using configuration Configuring pbmerge_pacbio_ordering.t using configuration Configuring pbmerge_aligned_ordering.t using configuration Configuring pbmerge_mixed_ordering.t using configuration Configuring pbmerge_dataset.t using configuration Configuring pbmerge_fofn.t using configuration Configuring PbBamifyVersion.h using configuration Program samtools found: YES (/usr/bin/samtools) Configuring pbbamify.t using configuration Configuring CcsKineticsBystrandifyVersion.h using configuration Build targets in project: 12 Option buildtype is: plain [default: release] Found ninja-1.10.1 at /usr/bin/ninja [1/15] Generating pbbam_generate_data with a custom command [2/15] Generating LibraryGitHash.h with a custom command [3/14] Generating PbbamGitHash.cpp with a custom command [3/4] Installing files. Installing src/libpbbam.so.1.6.0 to /build/pbbam-1.6.0+dfsg/debian/tmp/usr/lib/aarch64-linux-gnu Installing tools/bam2sam to /build/pbbam-1.6.0+dfsg/debian/tmp/usr/bin Installing tools/pbindex to /build/pbbam-1.6.0+dfsg/debian/tmp/usr/bin Installing tools/pbindexdump to /build/pbbam-1.6.0+dfsg/debian/tmp/usr/bin Installing tools/pbmerge to /build/pbbam-1.6.0+dfsg/debian/tmp/usr/bin Installing tools/pbbamify to /build/pbbam-1.6.0+dfsg/debian/tmp/usr/bin Installing tools/ccs-kinetics-bystrandify to /build/pbbam-1.6.0+dfsg/debian/tmp/usr/bin Installing /build/pbbam-1.6.0+dfsg/include/pbbam/Accuracy.h to /build/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-1.6.0+dfsg/include/pbbam/AlignmentPrinter.h to /build/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-1.6.0+dfsg/include/pbbam/BaiIndexCache.h to /build/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-1.6.0+dfsg/include/pbbam/BaiIndexedBamReader.h to /build/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-1.6.0+dfsg/include/pbbam/BamFile.h to /build/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-1.6.0+dfsg/include/pbbam/BamFileMerger.h to /build/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-1.6.0+dfsg/include/pbbam/BamHeader.h to /build/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-1.6.0+dfsg/include/pbbam/BamReader.h to /build/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-1.6.0+dfsg/include/pbbam/BamRecord.h to /build/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-1.6.0+dfsg/include/pbbam/BamRecordImpl.h to /build/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-1.6.0+dfsg/include/pbbam/BamRecordTag.h to /build/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-1.6.0+dfsg/include/pbbam/BamRecordView.h to /build/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-1.6.0+dfsg/include/pbbam/BamTagCodec.h to /build/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-1.6.0+dfsg/include/pbbam/BamWriter.h to /build/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-1.6.0+dfsg/include/pbbam/BgzipFastaWriter.h to /build/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-1.6.0+dfsg/include/pbbam/BgzipFastqWriter.h to /build/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-1.6.0+dfsg/include/pbbam/BgzipWriter.h to /build/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-1.6.0+dfsg/include/pbbam/Cigar.h to /build/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-1.6.0+dfsg/include/pbbam/CigarOperation.h to /build/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-1.6.0+dfsg/include/pbbam/ClipType.h to /build/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-1.6.0+dfsg/include/pbbam/CollectionMetadata.h to /build/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-1.6.0+dfsg/include/pbbam/Compare.h to /build/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-1.6.0+dfsg/include/pbbam/CompositeBamReader.h to /build/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-1.6.0+dfsg/include/pbbam/CompositeFastaReader.h to /build/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-1.6.0+dfsg/include/pbbam/Config.h to /build/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-1.6.0+dfsg/include/pbbam/DataSet.h to /build/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-1.6.0+dfsg/include/pbbam/DataSetTypes.h to /build/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-1.6.0+dfsg/include/pbbam/DataSetXsd.h to /build/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-1.6.0+dfsg/include/pbbam/Deleters.h to /build/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-1.6.0+dfsg/include/pbbam/EntireFileQuery.h to /build/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-1.6.0+dfsg/include/pbbam/FaiIndex.h to /build/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-1.6.0+dfsg/include/pbbam/FastaCache.h to /build/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-1.6.0+dfsg/include/pbbam/FastaReader.h to /build/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-1.6.0+dfsg/include/pbbam/FastaSequence.h to /build/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-1.6.0+dfsg/include/pbbam/FastaSequenceQuery.h to /build/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-1.6.0+dfsg/include/pbbam/FastaWriter.h to /build/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-1.6.0+dfsg/include/pbbam/FastqReader.h to /build/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-1.6.0+dfsg/include/pbbam/FastqSequence.h to /build/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-1.6.0+dfsg/include/pbbam/FastqWriter.h to /build/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-1.6.0+dfsg/include/pbbam/FormatUtils.h to /build/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-1.6.0+dfsg/include/pbbam/FrameEncodingType.h to /build/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-1.6.0+dfsg/include/pbbam/Frames.h to /build/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-1.6.0+dfsg/include/pbbam/GenomicInterval.h to /build/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-1.6.0+dfsg/include/pbbam/GenomicIntervalQuery.h to /build/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-1.6.0+dfsg/include/pbbam/IFastaWriter.h to /build/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-1.6.0+dfsg/include/pbbam/IFastqWriter.h to /build/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-1.6.0+dfsg/include/pbbam/IndexedBamWriter.h to /build/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-1.6.0+dfsg/include/pbbam/IndexedFastaReader.h to /build/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-1.6.0+dfsg/include/pbbam/IndexedFastqReader.h to /build/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-1.6.0+dfsg/include/pbbam/Interval.h to /build/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-1.6.0+dfsg/include/pbbam/IRecordWriter.h to /build/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-1.6.0+dfsg/include/pbbam/LibraryInfo.h to /build/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-1.6.0+dfsg/include/pbbam/LocalContextFlags.h to /build/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-1.6.0+dfsg/include/pbbam/MD5.h to /build/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-1.6.0+dfsg/include/pbbam/MoveAppend.h to /build/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-1.6.0+dfsg/include/pbbam/Orientation.h to /build/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-1.6.0+dfsg/include/pbbam/PbbamVersion.h to /build/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-1.6.0+dfsg/include/pbbam/PbiBasicTypes.h to /build/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-1.6.0+dfsg/include/pbbam/PbiBuilder.h to /build/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-1.6.0+dfsg/include/pbbam/PbiFile.h to /build/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-1.6.0+dfsg/include/pbbam/PbiFilter.h to /build/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-1.6.0+dfsg/include/pbbam/PbiFilterQuery.h to /build/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-1.6.0+dfsg/include/pbbam/PbiFilterTypes.h to /build/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-1.6.0+dfsg/include/pbbam/PbiIndexedBamReader.h to /build/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-1.6.0+dfsg/include/pbbam/PbiRawData.h to /build/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-1.6.0+dfsg/include/pbbam/Position.h to /build/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-1.6.0+dfsg/include/pbbam/ProgramInfo.h to /build/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-1.6.0+dfsg/include/pbbam/PulseBehavior.h to /build/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-1.6.0+dfsg/include/pbbam/PulseExclusionReason.h to /build/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-1.6.0+dfsg/include/pbbam/QualityValue.h to /build/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-1.6.0+dfsg/include/pbbam/QualityValues.h to /build/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-1.6.0+dfsg/include/pbbam/ReadGroupInfo.h to /build/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-1.6.0+dfsg/include/pbbam/RecordType.h to /build/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-1.6.0+dfsg/include/pbbam/RunMetadata.h to /build/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-1.6.0+dfsg/include/pbbam/SamReader.h to /build/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-1.6.0+dfsg/include/pbbam/SamTagCodec.h to /build/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-1.6.0+dfsg/include/pbbam/SamWriter.h to /build/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-1.6.0+dfsg/include/pbbam/SequenceInfo.h to /build/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-1.6.0+dfsg/include/pbbam/SNR.h to /build/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-1.6.0+dfsg/include/pbbam/Strand.h to /build/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-1.6.0+dfsg/include/pbbam/StringUtilities.h to /build/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-1.6.0+dfsg/include/pbbam/Tag.h to /build/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-1.6.0+dfsg/include/pbbam/TagCollection.h to /build/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-1.6.0+dfsg/include/pbbam/TextFileReader.h to /build/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-1.6.0+dfsg/include/pbbam/TextFileWriter.h to /build/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-1.6.0+dfsg/include/pbbam/Validator.h to /build/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-1.6.0+dfsg/include/pbbam/ZmwGroupQuery.h to /build/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-1.6.0+dfsg/include/pbbam/ZmwQuery.h to /build/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-1.6.0+dfsg/include/pbbam/ZmwType.h to /build/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-1.6.0+dfsg/include/pbbam/ZmwTypeMap.h to /build/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /build/pbbam-1.6.0+dfsg/include/pbbam/bed/BedReader.h to /build/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam/bed Installing /build/pbbam-1.6.0+dfsg/include/pbbam/bed/BedWriter.h to /build/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam/bed Installing /build/pbbam-1.6.0+dfsg/include/pbbam/ccs/CCSHeader.h to /build/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam/ccs Installing /build/pbbam-1.6.0+dfsg/include/pbbam/ccs/CCSPbiBuilder.h to /build/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam/ccs Installing /build/pbbam-1.6.0+dfsg/include/pbbam/ccs/CCSRecord.h to /build/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam/ccs Installing /build/pbbam-1.6.0+dfsg/include/pbbam/ccs/CCSRecordFormat.h to /build/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam/ccs Installing /build/pbbam-1.6.0+dfsg/include/pbbam/ccs/CCSRecordReader.h to /build/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam/ccs Installing /build/pbbam-1.6.0+dfsg/include/pbbam/ccs/CCSRecordWriter.h to /build/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam/ccs Installing /build/pbbam-1.6.0+dfsg/include/pbbam/exception/BundleChemistryMappingException.h to /build/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam/exception Installing /build/pbbam-1.6.0+dfsg/include/pbbam/exception/InvalidSequencingChemistryException.h to /build/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam/exception Installing /build/pbbam-1.6.0+dfsg/include/pbbam/exception/ValidationException.h to /build/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam/exception Installing /build/pbbam-1.6.0+dfsg/include/pbbam/internal/Compare.inl to /build/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam/internal Installing /build/pbbam-1.6.0+dfsg/include/pbbam/internal/CompositeBamReader.inl to /build/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam/internal Installing /build/pbbam-1.6.0+dfsg/include/pbbam/internal/DataSetBaseTypes.h to /build/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam/internal Installing /build/pbbam-1.6.0+dfsg/include/pbbam/internal/DataSetElement.h to /build/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam/internal Installing /build/pbbam-1.6.0+dfsg/include/pbbam/internal/DataSetElement.inl to /build/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam/internal Installing /build/pbbam-1.6.0+dfsg/include/pbbam/internal/PbiBasicTypes.inl to /build/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam/internal Installing /build/pbbam-1.6.0+dfsg/include/pbbam/internal/PbiFilter.inl to /build/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam/internal Installing /build/pbbam-1.6.0+dfsg/include/pbbam/internal/PbiFilterTypes.inl to /build/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam/internal Installing /build/pbbam-1.6.0+dfsg/include/pbbam/internal/QueryBase.h to /build/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam/internal Installing /build/pbbam-1.6.0+dfsg/include/pbbam/internal/QueryBase.inl to /build/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam/internal Installing /build/pbbam-1.6.0+dfsg/include/pbbam/vcf/VcfVariant.h to /build/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam/vcf Installing /build/pbbam-1.6.0+dfsg/include/pbbam/vcf/VcfFile.h to /build/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam/vcf Installing /build/pbbam-1.6.0+dfsg/include/pbbam/vcf/VcfFormat.h to /build/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam/vcf Installing /build/pbbam-1.6.0+dfsg/include/pbbam/vcf/VcfHeader.h to /build/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam/vcf Installing /build/pbbam-1.6.0+dfsg/include/pbbam/vcf/VcfHeaderTypes.h to /build/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam/vcf Installing /build/pbbam-1.6.0+dfsg/include/pbbam/vcf/VcfReader.h to /build/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam/vcf Installing /build/pbbam-1.6.0+dfsg/include/pbbam/vcf/VcfSort.h to /build/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam/vcf Installing /build/pbbam-1.6.0+dfsg/include/pbbam/vcf/VcfQuery.h to /build/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam/vcf Installing /build/pbbam-1.6.0+dfsg/include/pbbam/vcf/VcfWriter.h to /build/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam/vcf Installing /build/pbbam-1.6.0+dfsg/include/pbbam/virtual/VirtualPolymeraseBamRecord.h to /build/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam/virtual Installing /build/pbbam-1.6.0+dfsg/include/pbbam/virtual/VirtualPolymeraseCompositeReader.h to /build/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam/virtual Installing /build/pbbam-1.6.0+dfsg/include/pbbam/virtual/VirtualPolymeraseReader.h to /build/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam/virtual Installing /build/pbbam-1.6.0+dfsg/include/pbbam/virtual/VirtualRegion.h to /build/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam/virtual Installing /build/pbbam-1.6.0+dfsg/include/pbbam/virtual/VirtualRegionType.h to /build/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam/virtual Installing /build/pbbam-1.6.0+dfsg/include/pbbam/virtual/VirtualRegionTypeMap.h to /build/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam/virtual Installing /build/pbbam-1.6.0+dfsg/include/pbbam/virtual/VirtualZmwBamRecord.h to /build/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam/virtual Installing /build/pbbam-1.6.0+dfsg/include/pbbam/virtual/WhitelistedZmwReadStitcher.h to /build/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam/virtual Installing /build/pbbam-1.6.0+dfsg/include/pbbam/virtual/ZmwReadStitcher.h to /build/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam/virtual Installing /build/pbbam-1.6.0+dfsg/include/pbbam/virtual/ZmwWhitelistVirtualReader.h to /build/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam/virtual Installing /build/pbbam-1.6.0+dfsg/obj-aarch64-linux-gnu/meson-private/pbbam.pc to /build/pbbam-1.6.0+dfsg/debian/tmp/usr/lib/aarch64-linux-gnu/pkgconfig debian/rules override_dh_install make[1]: Entering directory '/build/pbbam-1.6.0+dfsg' dh_install d-shlibmove --commit \ --multiarch \ --devunversioned \ --exclude-la \ --exclude-a \ --override s/libhts2-dev/libhts-dev/ \ --override s/libpbcopper[0-9.]*-dev/libpbcopper-dev/ \ --movedev debian/tmp/usr/include/* usr/include \ --movedev "debian/tmp/usr/lib/*/pkgconfig/*.pc" usr/lib/aarch64-linux-gnu/pkgconfig \ debian/tmp/usr/lib/*/*.so Library package automatic movement utility --> libhts-dev package exists. --> libpbcopper-dev package exists. --> zlib1g-dev package exists. set -e install -d -m 755 debian/libpbbam-dev/usr/lib/aarch64-linux-gnu install -d -m 755 debian/libpbbam1.6.0/usr/lib/aarch64-linux-gnu mv debian/tmp/usr/lib/aarch64-linux-gnu/libpbbam.so debian/libpbbam-dev/usr/lib/aarch64-linux-gnu mv /build/pbbam-1.6.0+dfsg/debian/tmp/usr/lib/aarch64-linux-gnu/libpbbam.so.1.6.0 debian/libpbbam1.6.0/usr/lib/aarch64-linux-gnu PKGDEV=libpbbam-dev PKGSHL=libpbbam1.6.0 install -d -m 755 debian/libpbbam-dev/usr/include mv debian/tmp/usr/include/pbbam debian/libpbbam-dev/usr/include install -d -m 755 debian/libpbbam-dev/usr/lib/aarch64-linux-gnu/pkgconfig mv debian/tmp/usr/lib/*/pkgconfig/*.pc debian/libpbbam-dev/usr/lib/aarch64-linux-gnu/pkgconfig find debian -name "lib*.la" -delete make[1]: Leaving directory '/build/pbbam-1.6.0+dfsg' dh_installdocs -O--buildsystem=meson debian/rules override_dh_installchangelogs make[1]: Entering directory '/build/pbbam-1.6.0+dfsg' dh_installchangelogs CHANGELOG.md make[1]: Leaving directory '/build/pbbam-1.6.0+dfsg' dh_installsystemduser -O--buildsystem=meson dh_perl -O--buildsystem=meson dh_link -O--buildsystem=meson dh_strip_nondeterminism -O--buildsystem=meson dh_compress -O--buildsystem=meson dh_fixperms -O--buildsystem=meson dh_missing -O--buildsystem=meson dh_dwz -a -O--buildsystem=meson dh_strip -a -O--buildsystem=meson dh_makeshlibs -a -O--buildsystem=meson dh_shlibdeps -a -O--buildsystem=meson dh_installdeb -O--buildsystem=meson dh_gencontrol -O--buildsystem=meson dpkg-gencontrol: warning: package libpbbam-dev: substitution variable ${devlibs:Depends} unused, but is defined dh_md5sums -O--buildsystem=meson dh_builddeb -O--buildsystem=meson dpkg-deb: building package 'pbbamtools' in '../pbbamtools_1.6.0+dfsg-2_arm64.deb'. dpkg-deb: building package 'libpbbam-dev' in '../libpbbam-dev_1.6.0+dfsg-2_arm64.deb'. dpkg-deb: building package 'libpbbam1.6.0-dbgsym' in '../libpbbam1.6.0-dbgsym_1.6.0+dfsg-2_arm64.deb'. dpkg-deb: building package 'libpbbam1.6.0' in '../libpbbam1.6.0_1.6.0+dfsg-2_arm64.deb'. dpkg-deb: building package 'pbbamtools-dbgsym' in '../pbbamtools-dbgsym_1.6.0+dfsg-2_arm64.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../pbbam_1.6.0+dfsg-2_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: not including original source code in upload I: copying local configuration I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/9897 and its subdirectories I: Current time: Mon Aug 8 20:06:27 -12 2022 I: pbuilder-time-stamp: 1660032387 Wed Jul 7 01:43:31 UTC 2021 I: 1st build successful. Starting 2nd build on remote node codethink12-arm64.debian.net. Wed Jul 7 01:43:31 UTC 2021 I: Preparing to do remote build '2' on codethink12-arm64.debian.net. Wed Jul 7 01:56:29 UTC 2021 I: Deleting $TMPDIR on codethink12-arm64.debian.net. Wed Jul 7 01:56:30 UTC 2021 I: pbbam_1.6.0+dfsg-2_arm64.changes: Format: 1.8 Date: Sun, 15 Nov 2020 06:31:21 +0100 Source: pbbam Binary: libpbbam-dev libpbbam1.6.0 libpbbam1.6.0-dbgsym pbbamtools pbbamtools-dbgsym Architecture: arm64 Version: 1.6.0+dfsg-2 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: libpbbam-dev - Pacific Biosciences binary alignment/map (BAM) library (headers) libpbbam1.6.0 - Pacific Biosciences binary alignment/map (BAM) library pbbamtools - processing Pacific Biosciences binary alignment/map files Changes: pbbam (1.6.0+dfsg-2) unstable; urgency=medium . * Source-only upload Checksums-Sha1: 504a6076c73390ebb205bbce35d86b93c6007f9d 87156 libpbbam-dev_1.6.0+dfsg-2_arm64.deb 04f06a00440050cfcf4d8cda7893d3e31fd61aa0 14955220 libpbbam1.6.0-dbgsym_1.6.0+dfsg-2_arm64.deb 0d955fe2fe73d5b73cbbb40c876547013a539721 605804 libpbbam1.6.0_1.6.0+dfsg-2_arm64.deb 3f4c45d0faae74840ed3a806580bff644831bcf2 7830 pbbam_1.6.0+dfsg-2_arm64.buildinfo 62a86fb58bb1284dd4ae9fecf0ea4246b716a2d4 2069884 pbbamtools-dbgsym_1.6.0+dfsg-2_arm64.deb 9fbdc1ef4d600541fe0c8e4512289f60fedef3c7 83276 pbbamtools_1.6.0+dfsg-2_arm64.deb Checksums-Sha256: 887a7e94ae1cff233db36b3c49a8186794096bef7677c14aead1e8714138f2b2 87156 libpbbam-dev_1.6.0+dfsg-2_arm64.deb 88bfe0cb5cf905a3b84dce394c3fb75bd09f6130c2a4890ce192c5462eec7470 14955220 libpbbam1.6.0-dbgsym_1.6.0+dfsg-2_arm64.deb 34ee759511908748d9550bddf12068f542a1e87639941acf458d2f3677e9edfe 605804 libpbbam1.6.0_1.6.0+dfsg-2_arm64.deb 38a5c6ce76f598309643fec6bbcbe51c7a62dfc1f60c2fa5ef277e1390cbda6d 7830 pbbam_1.6.0+dfsg-2_arm64.buildinfo d9dbcfb787ead430cbff8f617c6c19e184dac8a815efb7b1f373f8a9350d1bc1 2069884 pbbamtools-dbgsym_1.6.0+dfsg-2_arm64.deb 54f08c4d9bdd58d333886cf04b32b30a4e3e033fc0305d35233878c8a13db504 83276 pbbamtools_1.6.0+dfsg-2_arm64.deb Files: 11d7e694a4143457dd212e14c117291b 87156 libdevel optional libpbbam-dev_1.6.0+dfsg-2_arm64.deb 2f0e4abf7b9b29a47651b0f82a98814f 14955220 debug optional libpbbam1.6.0-dbgsym_1.6.0+dfsg-2_arm64.deb 282ac6b431f515e71be743c9083443e6 605804 libs optional libpbbam1.6.0_1.6.0+dfsg-2_arm64.deb bf63a1087a68396edf01401a9cbc234a 7830 science optional pbbam_1.6.0+dfsg-2_arm64.buildinfo a339af7c307922cabe02862a89c3e088 2069884 debug optional pbbamtools-dbgsym_1.6.0+dfsg-2_arm64.deb ddd99eec39bd4f22c8bb865ed5e8f638 83276 science optional pbbamtools_1.6.0+dfsg-2_arm64.deb Wed Jul 7 01:56:34 UTC 2021 I: diffoscope 177 will be used to compare the two builds: # Profiling output for: /usr/bin/diffoscope --html /srv/reproducible-results/rbuild-debian/tmp.5mjbqnlGle/pbbam_1.6.0+dfsg-2.diffoscope.html --text /srv/reproducible-results/rbuild-debian/tmp.5mjbqnlGle/pbbam_1.6.0+dfsg-2.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/tmp.5mjbqnlGle/pbbam_1.6.0+dfsg-2.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/tmp.5mjbqnlGle/b1/pbbam_1.6.0+dfsg-2_arm64.changes /srv/reproducible-results/rbuild-debian/tmp.5mjbqnlGle/b2/pbbam_1.6.0+dfsg-2_arm64.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call abc.DotChangesFile ## main (total time: 1.331s) 1.331s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.400s) 0.400s 10 calls diffoscope.comparators.binary.FilesystemFile 0.000s 8 calls abc.DotChangesFile Wed Jul 7 01:56:38 UTC 2021 I: diffoscope 177 found no differences in the changes files, and a .buildinfo file also exists. Wed Jul 7 01:56:38 UTC 2021 I: pbbam from bullseye built successfully and reproducibly on arm64. Wed Jul 7 01:56:40 UTC 2021 I: Submitting .buildinfo files to external archives: Wed Jul 7 01:56:40 UTC 2021 I: Submitting 12K b1/pbbam_1.6.0+dfsg-2_arm64.buildinfo.asc Wed Jul 7 01:56:41 UTC 2021 I: Submitting 12K b2/pbbam_1.6.0+dfsg-2_arm64.buildinfo.asc Wed Jul 7 01:56:42 UTC 2021 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Wed Jul 7 01:56:42 UTC 2021 I: Done submitting .buildinfo files. Wed Jul 7 01:56:42 UTC 2021 I: Removing signed pbbam_1.6.0+dfsg-2_arm64.buildinfo.asc files: removed './b1/pbbam_1.6.0+dfsg-2_arm64.buildinfo.asc' removed './b2/pbbam_1.6.0+dfsg-2_arm64.buildinfo.asc'