I: pbuilder: network access will be disabled during build I: Current time: Fri Dec 31 19:17:48 +14 2021 I: pbuilder-time-stamp: 1640927868 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.XCMG9JTj/trustedkeys.kbx': General error gpgv: Signature made Sun Nov 15 19:42:58 2020 +14 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./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/84714/tmp/hooks/D01_modify_environment starting debug: Running on ionos1-amd64. I: Changing host+domainname to test build reproducibility I: Adding a custom variable just for the fun of it... I: Changing /bin/sh to bash Removing 'diversion of /bin/sh to /bin/sh.distrib by dash' Adding 'diversion of /bin/sh to /bin/sh.distrib by bash' Removing 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by dash' Adding 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by bash' I: Setting pbuilder2's login shell to /bin/bash I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other I: user script /srv/workspace/pbuilder/84714/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/84714/tmp/hooks/D02_print_environment starting I: set BASH=/bin/sh BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:hostcomplete:interactive_comments:progcomp:promptvars:sourcepath BASH_ALIASES=() BASH_ARGC=() BASH_ARGV=() BASH_CMDS=() BASH_LINENO=([0]="12" [1]="0") BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") BASH_VERSINFO=([0]="5" [1]="1" [2]="4" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") BASH_VERSION='5.1.4(1)-release' BUILDDIR=/build BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=amd64 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=15' DIRSTACK=() DISTRIBUTION= EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=x86_64 HOST_ARCH=amd64 IFS=' ' INVOCATION_ID=6347dc01c08444a2b3d9c7ae63ec5d45 LANG=C LANGUAGE=et_EE:et LC_ALL=C MACHTYPE=x86_64-pc-linux-gnu MAIL=/var/mail/root OPTERR=1 OPTIND=1 OSTYPE=linux-gnu PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path PBCURRENTCOMMANDLINEOPERATION=build PBUILDER_OPERATION=build PBUILDER_PKGDATADIR=/usr/share/pbuilder PBUILDER_PKGLIBDIR=/usr/lib/pbuilder PBUILDER_SYSCONFDIR=/etc PIPESTATUS=([0]="0") POSIXLY_CORRECT=y PPID=84714 PS4='+ ' PWD=/ SHELL=/bin/bash SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix SHLVL=3 SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/tmp.Ra1BglCY9r/pbuilderrc_hskl --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.Ra1BglCY9r/b2 --logfile b2/build.log pbbam_1.6.0+dfsg-2.dsc' SUDO_GID=110 SUDO_UID=105 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://78.137.99.97:3128 I: uname -a Linux i-capture-the-hostname 5.10.0-10-amd64 #1 SMP Debian 5.10.84-1 (2021-12-08) x86_64 GNU/Linux I: ls -l /bin total 5476 -rwxr-xr-x 1 root root 1234376 Aug 5 10:25 bash -rwxr-xr-x 3 root root 38984 Jul 21 2020 bunzip2 -rwxr-xr-x 3 root root 38984 Jul 21 2020 bzcat lrwxrwxrwx 1 root root 6 Jul 21 2020 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2225 Jul 21 2020 bzdiff lrwxrwxrwx 1 root root 6 Jul 21 2020 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4877 Sep 5 2019 bzexe lrwxrwxrwx 1 root root 6 Jul 21 2020 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3775 Jul 21 2020 bzgrep -rwxr-xr-x 3 root root 38984 Jul 21 2020 bzip2 -rwxr-xr-x 1 root root 18424 Jul 21 2020 bzip2recover lrwxrwxrwx 1 root root 6 Jul 21 2020 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Jul 21 2020 bzmore -rwxr-xr-x 1 root root 43936 Sep 24 2020 cat -rwxr-xr-x 1 root root 72672 Sep 24 2020 chgrp -rwxr-xr-x 1 root root 64448 Sep 24 2020 chmod -rwxr-xr-x 1 root root 72672 Sep 24 2020 chown -rwxr-xr-x 1 root root 151168 Sep 24 2020 cp -rwxr-xr-x 1 root root 125560 Dec 11 2020 dash -rwxr-xr-x 1 root root 113664 Sep 24 2020 date -rwxr-xr-x 1 root root 80968 Sep 24 2020 dd -rwxr-xr-x 1 root root 93936 Sep 24 2020 df -rwxr-xr-x 1 root root 147176 Sep 24 2020 dir -rwxr-xr-x 1 root root 84440 Jul 29 09:09 dmesg lrwxrwxrwx 1 root root 8 Nov 8 2019 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Nov 8 2019 domainname -> hostname -rwxr-xr-x 1 root root 39712 Sep 24 2020 echo -rwxr-xr-x 1 root root 28 Nov 10 2020 egrep -rwxr-xr-x 1 root root 39680 Sep 24 2020 false -rwxr-xr-x 1 root root 28 Nov 10 2020 fgrep -rwxr-xr-x 1 root root 69032 Jul 29 09:09 findmnt -rwsr-xr-x 1 root root 34896 Feb 27 2021 fusermount -rwxr-xr-x 1 root root 203072 Nov 10 2020 grep -rwxr-xr-x 2 root root 2346 Mar 3 2021 gunzip -rwxr-xr-x 1 root root 6376 Mar 3 2021 gzexe -rwxr-xr-x 1 root root 98048 Mar 3 2021 gzip -rwxr-xr-x 1 root root 22600 Nov 8 2019 hostname -rwxr-xr-x 1 root root 72840 Sep 24 2020 ln -rwxr-xr-x 1 root root 56952 Feb 8 2020 login -rwxr-xr-x 1 root root 147176 Sep 24 2020 ls -rwxr-xr-x 1 root root 149736 Jul 29 09:09 lsblk -rwxr-xr-x 1 root root 85184 Sep 24 2020 mkdir -rwxr-xr-x 1 root root 76896 Sep 24 2020 mknod -rwxr-xr-x 1 root root 48064 Sep 24 2020 mktemp -rwxr-xr-x 1 root root 59632 Jul 29 09:09 more -rwsr-xr-x 1 root root 55528 Jul 29 09:09 mount -rwxr-xr-x 1 root root 18664 Jul 29 09:09 mountpoint -rwxr-xr-x 1 root root 147080 Sep 24 2020 mv lrwxrwxrwx 1 root root 8 Nov 8 2019 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Apr 19 2021 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 43872 Sep 24 2020 pwd lrwxrwxrwx 1 root root 4 Aug 5 10:25 rbash -> bash -rwxr-xr-x 1 root root 52032 Sep 24 2020 readlink -rwxr-xr-x 1 root root 72704 Sep 24 2020 rm -rwxr-xr-x 1 root root 52032 Sep 24 2020 rmdir -rwxr-xr-x 1 root root 27472 Sep 28 2020 run-parts -rwxr-xr-x 1 root root 122224 Dec 23 2018 sed lrwxrwxrwx 1 root root 4 Dec 31 19:19 sh -> bash lrwxrwxrwx 1 root root 4 Dec 21 23:25 sh.distrib -> dash -rwxr-xr-x 1 root root 43808 Sep 24 2020 sleep -rwxr-xr-x 1 root root 84928 Sep 24 2020 stty -rwsr-xr-x 1 root root 71912 Jul 29 09:09 su -rwxr-xr-x 1 root root 39744 Sep 24 2020 sync -rwxr-xr-x 1 root root 531928 Feb 17 2021 tar -rwxr-xr-x 1 root root 14456 Sep 28 2020 tempfile -rwxr-xr-x 1 root root 101408 Sep 24 2020 touch -rwxr-xr-x 1 root root 39680 Sep 24 2020 true -rwxr-xr-x 1 root root 14328 Feb 27 2021 ulockmgr_server -rwsr-xr-x 1 root root 35040 Jul 29 09:09 umount -rwxr-xr-x 1 root root 39744 Sep 24 2020 uname -rwxr-xr-x 2 root root 2346 Mar 3 2021 uncompress -rwxr-xr-x 1 root root 147176 Sep 24 2020 vdir -rwxr-xr-x 1 root root 63744 Jul 29 09:09 wdctl lrwxrwxrwx 1 root root 8 Nov 8 2019 ypdomainname -> hostname -rwxr-xr-x 1 root root 1984 Mar 3 2021 zcat -rwxr-xr-x 1 root root 1678 Mar 3 2021 zcmp -rwxr-xr-x 1 root root 5880 Mar 3 2021 zdiff -rwxr-xr-x 1 root root 29 Mar 3 2021 zegrep -rwxr-xr-x 1 root root 29 Mar 3 2021 zfgrep -rwxr-xr-x 1 root root 2081 Mar 3 2021 zforce -rwxr-xr-x 1 root root 7585 Mar 3 2021 zgrep -rwxr-xr-x 1 root root 2206 Mar 3 2021 zless -rwxr-xr-x 1 root root 1842 Mar 3 2021 zmore -rwxr-xr-x 1 root root 4553 Mar 3 2021 znew I: user script /srv/workspace/pbuilder/84714/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 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 ... 19655 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 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 55.5 MB of archives. After unpacking 309 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bullseye/main amd64 bsdextrautils amd64 2.36.1-8 [145 kB] Get: 2 http://deb.debian.org/debian bullseye/main amd64 libuchardet0 amd64 0.0.7-1 [67.8 kB] Get: 3 http://deb.debian.org/debian bullseye/main amd64 groff-base amd64 1.22.4-6 [936 kB] Get: 4 http://deb.debian.org/debian bullseye/main amd64 libpipeline1 amd64 1.5.3-1 [34.3 kB] Get: 5 http://deb.debian.org/debian bullseye/main amd64 man-db amd64 2.9.4-2 [1354 kB] Get: 6 http://deb.debian.org/debian bullseye/main amd64 libpython3.9-minimal amd64 3.9.2-1 [801 kB] Get: 7 http://deb.debian.org/debian bullseye/main amd64 libexpat1 amd64 2.2.10-2 [96.9 kB] Get: 8 http://deb.debian.org/debian bullseye/main amd64 python3.9-minimal amd64 3.9.2-1 [1955 kB] Get: 9 http://deb.debian.org/debian bullseye/main amd64 python3-minimal amd64 3.9.2-3 [38.2 kB] Get: 10 http://deb.debian.org/debian bullseye/main amd64 media-types all 4.0.0 [30.3 kB] Get: 11 http://deb.debian.org/debian bullseye/main amd64 libmpdec3 amd64 2.5.1-1 [87.7 kB] Get: 12 http://deb.debian.org/debian bullseye/main amd64 readline-common all 8.1-1 [73.7 kB] Get: 13 http://deb.debian.org/debian bullseye/main amd64 libreadline8 amd64 8.1-1 [169 kB] Get: 14 http://deb.debian.org/debian bullseye/main amd64 libpython3.9-stdlib amd64 3.9.2-1 [1684 kB] Get: 15 http://deb.debian.org/debian bullseye/main amd64 python3.9 amd64 3.9.2-1 [466 kB] Get: 16 http://deb.debian.org/debian bullseye/main amd64 libpython3-stdlib amd64 3.9.2-3 [21.4 kB] Get: 17 http://deb.debian.org/debian bullseye/main amd64 python3 amd64 3.9.2-3 [37.9 kB] Get: 18 http://deb.debian.org/debian bullseye/main amd64 libncurses6 amd64 6.2+20201114-2 [102 kB] Get: 19 http://deb.debian.org/debian bullseye/main amd64 libprocps8 amd64 2:3.3.17-5 [63.9 kB] Get: 20 http://deb.debian.org/debian bullseye/main amd64 procps amd64 2:3.3.17-5 [502 kB] Get: 21 http://deb.debian.org/debian bullseye/main amd64 sensible-utils all 0.0.14 [14.8 kB] Get: 22 http://deb.debian.org/debian bullseye/main amd64 libmagic-mgc amd64 1:5.39-3 [273 kB] Get: 23 http://deb.debian.org/debian bullseye/main amd64 libmagic1 amd64 1:5.39-3 [126 kB] Get: 24 http://deb.debian.org/debian bullseye/main amd64 file amd64 1:5.39-3 [69.1 kB] Get: 25 http://deb.debian.org/debian bullseye/main amd64 gettext-base amd64 0.21-4 [175 kB] Get: 26 http://deb.debian.org/debian bullseye/main amd64 libsigsegv2 amd64 2.13-1 [34.8 kB] Get: 27 http://deb.debian.org/debian bullseye/main amd64 m4 amd64 1.4.18-5 [204 kB] Get: 28 http://deb.debian.org/debian bullseye/main amd64 autoconf all 2.69-14 [313 kB] Get: 29 http://deb.debian.org/debian bullseye/main amd64 autotools-dev all 20180224.1+nmu1 [77.1 kB] Get: 30 http://deb.debian.org/debian bullseye/main amd64 automake all 1:1.16.3-2 [814 kB] Get: 31 http://deb.debian.org/debian bullseye/main amd64 autopoint all 0.21-4 [510 kB] Get: 32 http://deb.debian.org/debian bullseye/main amd64 cmake-data all 3.18.4-2+deb11u1 [1725 kB] Get: 33 http://deb.debian.org/debian bullseye/main amd64 libicu67 amd64 67.1-7 [8622 kB] Get: 34 http://deb.debian.org/debian bullseye/main amd64 libxml2 amd64 2.9.10+dfsg-6.7 [693 kB] Get: 35 http://deb.debian.org/debian bullseye/main amd64 libarchive13 amd64 3.4.3-2+b1 [343 kB] Get: 36 http://deb.debian.org/debian bullseye/main amd64 libbrotli1 amd64 1.0.9-2+b2 [279 kB] Get: 37 http://deb.debian.org/debian bullseye/main amd64 libsasl2-modules-db amd64 2.1.27+dfsg-2.1 [69.1 kB] Get: 38 http://deb.debian.org/debian bullseye/main amd64 libsasl2-2 amd64 2.1.27+dfsg-2.1 [106 kB] Get: 39 http://deb.debian.org/debian bullseye/main amd64 libldap-2.4-2 amd64 2.4.57+dfsg-3 [232 kB] Get: 40 http://deb.debian.org/debian bullseye/main amd64 libnghttp2-14 amd64 1.43.0-1 [77.1 kB] Get: 41 http://deb.debian.org/debian bullseye/main amd64 libpsl5 amd64 0.21.0-1.2 [57.3 kB] Get: 42 http://deb.debian.org/debian bullseye/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b2 [60.8 kB] Get: 43 http://deb.debian.org/debian bullseye/main amd64 libssh2-1 amd64 1.9.0-2 [156 kB] Get: 44 http://deb.debian.org/debian bullseye/main amd64 libcurl4 amd64 7.74.0-1.3+deb11u1 [341 kB] Get: 45 http://deb.debian.org/debian bullseye/main amd64 libjsoncpp24 amd64 1.9.4-4 [78.9 kB] Get: 46 http://deb.debian.org/debian bullseye/main amd64 librhash0 amd64 1.4.1-2 [129 kB] Get: 47 http://deb.debian.org/debian bullseye/main amd64 libuv1 amd64 1.40.0-2 [132 kB] Get: 48 http://deb.debian.org/debian bullseye/main amd64 cmake amd64 3.18.4-2+deb11u1 [5593 kB] Get: 49 http://deb.debian.org/debian bullseye/main amd64 d-shlibs all 0.98 [17.9 kB] Get: 50 http://deb.debian.org/debian bullseye/main amd64 libdebhelper-perl all 13.3.4 [189 kB] Get: 51 http://deb.debian.org/debian bullseye/main amd64 libtool all 2.4.6-15 [513 kB] Get: 52 http://deb.debian.org/debian bullseye/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 53 http://deb.debian.org/debian bullseye/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 54 http://deb.debian.org/debian bullseye/main amd64 libsub-override-perl all 0.09-2 [10.2 kB] Get: 55 http://deb.debian.org/debian bullseye/main amd64 libfile-stripnondeterminism-perl all 1.12.0-1 [26.3 kB] Get: 56 http://deb.debian.org/debian bullseye/main amd64 dh-strip-nondeterminism all 1.12.0-1 [15.4 kB] Get: 57 http://deb.debian.org/debian bullseye/main amd64 libelf1 amd64 0.183-1 [165 kB] Get: 58 http://deb.debian.org/debian bullseye/main amd64 dwz amd64 0.13+20210201-1 [175 kB] Get: 59 http://deb.debian.org/debian bullseye/main amd64 gettext amd64 0.21-4 [1311 kB] Get: 60 http://deb.debian.org/debian bullseye/main amd64 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 61 http://deb.debian.org/debian bullseye/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 62 http://deb.debian.org/debian bullseye/main amd64 debhelper all 13.3.4 [1049 kB] Get: 63 http://deb.debian.org/debian bullseye/main amd64 dh-exec amd64 0.23.2 [26.6 kB] Get: 64 http://deb.debian.org/debian bullseye/main amd64 googletest all 1.10.0.20201025-1.1 [629 kB] Get: 65 http://deb.debian.org/debian bullseye/main amd64 libboost1.74-dev amd64 1.74.0-9 [9534 kB] Get: 66 http://deb.debian.org/debian bullseye/main amd64 libboost-dev amd64 1.74.0.3 [4548 B] Get: 67 http://deb.debian.org/debian bullseye/main amd64 libcurl3-gnutls amd64 7.74.0-1.3+deb11u1 [338 kB] Get: 68 http://deb.debian.org/debian bullseye/main amd64 libcurl4-gnutls-dev amd64 7.74.0-1.3+deb11u1 [429 kB] Get: 69 http://deb.debian.org/debian bullseye/main amd64 libdeflate0 amd64 1.7-1 [53.1 kB] Get: 70 http://deb.debian.org/debian bullseye/main amd64 libdeflate-dev amd64 1.7-1 [46.9 kB] Get: 71 http://deb.debian.org/debian bullseye/main amd64 libglib2.0-0 amd64 2.66.8-1 [1370 kB] Get: 72 http://deb.debian.org/debian bullseye/main amd64 libgtest-dev amd64 1.10.0.20201025-1.1 [226 kB] Get: 73 http://deb.debian.org/debian bullseye/main amd64 libhts3 amd64 1.11-4 [378 kB] Get: 74 http://deb.debian.org/debian bullseye/main amd64 liblzma-dev amd64 5.2.5-2 [229 kB] Get: 75 http://deb.debian.org/debian bullseye/main amd64 zlib1g-dev amd64 1:1.2.11.dfsg-2 [190 kB] Get: 76 http://deb.debian.org/debian bullseye/main amd64 libhts-dev amd64 1.11-4 [3858 kB] Get: 77 http://deb.debian.org/debian bullseye/main amd64 libpbcopper1.8.0 amd64 1.8.0+dfsg-2+b1 [452 kB] Get: 78 http://deb.debian.org/debian bullseye/main amd64 libpbcopper-dev amd64 1.8.0+dfsg-2+b1 [707 kB] Get: 79 http://deb.debian.org/debian bullseye/main amd64 libssl-dev amd64 1.1.1k-1+deb11u1 [1810 kB] Get: 80 http://deb.debian.org/debian bullseye/main amd64 ninja-build amd64 1.10.1-1 [112 kB] Get: 81 http://deb.debian.org/debian bullseye/main amd64 python3-pkg-resources all 52.0.0-4 [190 kB] Get: 82 http://deb.debian.org/debian bullseye/main amd64 meson all 0.56.2-1 [437 kB] Get: 83 http://deb.debian.org/debian bullseye/main amd64 pkg-config amd64 0.29.2-1 [65.1 kB] Get: 84 http://deb.debian.org/debian bullseye/main amd64 python3-cram all 0.7-4 [17.3 kB] Get: 85 http://deb.debian.org/debian bullseye/main amd64 samtools amd64 1.11-1 [545 kB] Fetched 55.5 MB in 2s (30.4 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package bsdextrautils. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19655 files and directories currently installed.) Preparing to unpack .../0-bsdextrautils_2.36.1-8_amd64.deb ... Unpacking bsdextrautils (2.36.1-8) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../1-libuchardet0_0.0.7-1_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../2-groff-base_1.22.4-6_amd64.deb ... 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Building tag database... -> Finished parsing the build-deps I: Building the package hostname: Name or service not known I: Running cd /build/pbbam-1.6.0+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../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 amd64 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-x86_64-linux-gnu && LC_ALL=C.UTF-8 meson .. --wrap-mode=nodownload --buildtype=plain --prefix=/usr --sysconfdir=/etc --localstatedir=/var --libdir=lib/x86_64-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-x86_64-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: x86_64 Host machine cpu: x86_64 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-x86_64-linux-gnu && LC_ALL=C.UTF-8 ninja -j15 -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 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-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 [6/228] 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_BamReader.cpp.o -MF tests/pbbam_test.p/src_test_BamReader.cpp.o.d -o tests/pbbam_test.p/src_test_BamReader.cpp.o -c ../tests/src/test_BamReader.cpp [7/228] 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_BedReader.cpp.o -MF tests/pbbam_test.p/src_test_BedReader.cpp.o.d -o tests/pbbam_test.p/src_test_BedReader.cpp.o -c ../tests/src/test_BedReader.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_BedWriter.cpp.o -MF tests/pbbam_test.p/src_test_BedWriter.cpp.o.d -o tests/pbbam_test.p/src_test_BedWriter.cpp.o -c ../tests/src/test_BedWriter.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 -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tests/pbbam_test.p/src_test_AlignmentPrinter.cpp.o -MF tests/pbbam_test.p/src_test_AlignmentPrinter.cpp.o.d -o tests/pbbam_test.p/src_test_AlignmentPrinter.cpp.o -c ../tests/src/test_AlignmentPrinter.cpp [10/228] 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 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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 src/libpbbam.so.1.6.0.p/vcf_VcfReader.cpp.o src/libpbbam.so.1.6.0.p/vcf_VcfSort.cpp.o src/libpbbam.so.1.6.0.p/vcf_VcfVariant.cpp.o src/libpbbam.so.1.6.0.p/vcf_VcfWriter.cpp.o src/libpbbam.so.1.6.0.p/pugixml_pugixml.cpp.o src/libpbbam.so.1.6.0.p/meson-generated_.._PbbamVersion.cpp.o -Wl,--as-needed -Wl,--no-undefined -shared -fPIC -Wl,--start-group -Wl,-soname,libpbbam.so.1.6.0 -g -O2 -fdebug-prefix-map=/build/pbbam-1.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -pthread /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libhts.so /usr/lib/x86_64-linux-gnu/libpbcopper.so -Wl,--end-group [155/228] 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_FastqReader.cpp.o -MF tests/pbbam_test.p/src_test_FastqReader.cpp.o.d -o tests/pbbam_test.p/src_test_FastqReader.cpp.o -c ../tests/src/test_FastqReader.cpp [156/228] /usr/bin/meson --internal symbolextractor /build/pbbam-1.6.0+dfsg/obj-x86_64-linux-gnu src/libpbbam.so.1.6.0 src/libpbbam.so.1.6.0 src/libpbbam.so.1.6.0.p/libpbbam.so.1.6.0.symbols [157/228] 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_FastaSequenceQuery.cpp.o -MF tests/pbbam_test.p/src_test_FastaSequenceQuery.cpp.o.d -o tests/pbbam_test.p/src_test_FastaSequenceQuery.cpp.o -c ../tests/src/test_FastaSequenceQuery.cpp [158/228] 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_CompositeBamReaders.cpp.o -MF tests/pbbam_test.p/src_test_CompositeBamReaders.cpp.o.d -o tests/pbbam_test.p/src_test_CompositeBamReaders.cpp.o -c ../tests/src/test_CompositeBamReaders.cpp [159/228] c++ -Itests/pbbam_test.p -Itests -I../tests -Iinclude -I../include 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../tests/src/test_VcfHeader.cpp [185/228] /usr/bin/python3 ../tests/scripts/generate_data.py /build/pbbam-1.6.0+dfsg/tests/data /build/pbbam-1.6.0+dfsg/obj-x86_64-linux-gnu/tests Generating test data in /build/pbbam-1.6.0+dfsg/obj-x86_64-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. 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/usr/lib/x86_64-linux-gnu/libpbcopper.so -Wl,--end-group '-Wl,-rpath,$ORIGIN/../src' -Wl,-rpath-link,/build/pbbam-1.6.0+dfsg/obj-x86_64-linux-gnu/src [214/228] 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 [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_PbBamifySettings.cpp.o -MF tools/pbbamify.p/pbbamify_src_PbBamifySettings.cpp.o.d -o tools/pbbamify.p/pbbamify_src_PbBamifySettings.cpp.o -c ../tools/pbbamify/src/PbBamifySettings.cpp [216/228] 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 tools/ccs-kinetics-bystrandify.p/ccs-kinetics-bystrandify_src_main.cpp.o -c ../tools/ccs-kinetics-bystrandify/src/main.cpp [217/228] 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 [218/228] 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_CcsKineticsBystrandifySettings.cpp.o -MF tools/ccs-kinetics-bystrandify.p/ccs-kinetics-bystrandify_src_CcsKineticsBystrandifySettings.cpp.o.d -o tools/ccs-kinetics-bystrandify.p/ccs-kinetics-bystrandify_src_CcsKineticsBystrandifySettings.cpp.o -c ../tools/ccs-kinetics-bystrandify/src/CcsKineticsBystrandifySettings.cpp [219/228] 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_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 [220/228] 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 [221/228] 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_PbBamifyWorkflow.cpp.o -MF tools/pbbamify.p/pbbamify_src_PbBamifyWorkflow.cpp.o.d -o tools/pbbamify.p/pbbamify_src_PbBamifyWorkflow.cpp.o -c ../tools/pbbamify/src/PbBamifyWorkflow.cpp [222/228] 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 [223/228] 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/x86_64-linux-gnu/libhts.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libpbcopper.so -Wl,--end-group '-Wl,-rpath,$ORIGIN/../src' -Wl,-rpath-link,/build/pbbam-1.6.0+dfsg/obj-x86_64-linux-gnu/src [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/x86_64-linux-gnu/libhts.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libpbcopper.so -Wl,--end-group '-Wl,-rpath,$ORIGIN/../src' -Wl,-rpath-link,/build/pbbam-1.6.0+dfsg/obj-x86_64-linux-gnu/src [225/228] c++ -Itools/ccs-kinetics-bystrandify.p -Itools -I../tools -Iinclude -I../include -I../tools/ccs-kinetics-bystrandify -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/build/pbbam-1.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_ALL_NO_LIB -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tools/ccs-kinetics-bystrandify.p/ccs-kinetics-bystrandify_src_CcsKineticsBystrandifyWorkflow.cpp.o -MF tools/ccs-kinetics-bystrandify.p/ccs-kinetics-bystrandify_src_CcsKineticsBystrandifyWorkflow.cpp.o.d -o tools/ccs-kinetics-bystrandify.p/ccs-kinetics-bystrandify_src_CcsKineticsBystrandifyWorkflow.cpp.o -c ../tools/ccs-kinetics-bystrandify/src/CcsKineticsBystrandifyWorkflow.cpp [226/228] c++ -o tools/ccs-kinetics-bystrandify tools/ccs-kinetics-bystrandify.p/ccs-kinetics-bystrandify_src_main.cpp.o tools/ccs-kinetics-bystrandify.p/ccs-kinetics-bystrandify_src_CcsKineticsBystrandifySettings.cpp.o tools/ccs-kinetics-bystrandify.p/ccs-kinetics-bystrandify_src_CcsKineticsBystrandifyWorkflow.cpp.o -Wl,--as-needed -Wl,--no-undefined -g -O2 -fdebug-prefix-map=/build/pbbam-1.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Wl,--start-group src/libpbbam.so.1.6.0 /usr/lib/x86_64-linux-gnu/libhts.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libpbcopper.so -Wl,--end-group '-Wl,-rpath,$ORIGIN/../src' -Wl,-rpath-link,/build/pbbam-1.6.0+dfsg/obj-x86_64-linux-gnu/src [227/228] 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 [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/x86_64-linux-gnu/libgtest_main.a -lpthread /usr/lib/x86_64-linux-gnu/libgtest.a /usr/lib/x86_64-linux-gnu/libhts.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libpbcopper.so -Wl,--end-group '-Wl,-rpath,$ORIGIN/../src' -Wl,-rpath-link,/build/pbbam-1.6.0+dfsg/obj-x86_64-linux-gnu/src debian/rules override_dh_auto_test make[1]: Entering directory '/build/pbbam-1.6.0+dfsg' sed \ -e 's/$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-x86_64-linux-gnu && LC_ALL=C.UTF-8 meson .. --wrap-mode=nodownload --buildtype=plain --prefix=/usr --sysconfdir=/etc --localstatedir=/var --libdir=lib/x86_64-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:/i/capture/the/path" 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-x86_64-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-x86_64-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: x86_64 Host machine cpu: x86_64 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 PbbamGitHash.cpp with a custom command [3/14] Generating LibraryGitHash.h 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/x86_64-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-x86_64-linux-gnu/meson-private/pbbam.pc to /build/pbbam-1.6.0+dfsg/debian/tmp/usr/lib/x86_64-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/x86_64-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/x86_64-linux-gnu install -d -m 755 debian/libpbbam1.6.0/usr/lib/x86_64-linux-gnu mv debian/tmp/usr/lib/x86_64-linux-gnu/libpbbam.so debian/libpbbam-dev/usr/lib/x86_64-linux-gnu mv /build/pbbam-1.6.0+dfsg/debian/tmp/usr/lib/x86_64-linux-gnu/libpbbam.so.1.6.0 debian/libpbbam1.6.0/usr/lib/x86_64-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/x86_64-linux-gnu/pkgconfig mv debian/tmp/usr/lib/*/pkgconfig/*.pc debian/libpbbam-dev/usr/lib/x86_64-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_amd64.deb'. dpkg-deb: building package 'libpbbam1.6.0-dbgsym' in '../libpbbam1.6.0-dbgsym_1.6.0+dfsg-2_amd64.deb'. dpkg-deb: building package 'pbbamtools-dbgsym' in '../pbbamtools-dbgsym_1.6.0+dfsg-2_amd64.deb'. dpkg-deb: building package 'libpbbam1.6.0' in '../libpbbam1.6.0_1.6.0+dfsg-2_amd64.deb'. dpkg-deb: building package 'libpbbam-dev' in '../libpbbam-dev_1.6.0+dfsg-2_amd64.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../pbbam_1.6.0+dfsg-2_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: user script /srv/workspace/pbuilder/84714/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/84714/tmp/hooks/B01_cleanup finished I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/84714 and its subdirectories I: Current time: Fri Dec 31 19:31:43 +14 2021 I: pbuilder-time-stamp: 1640928703