https://launchpad.net/ubuntu/+source/pbbam/1.6.0+dfsg-2/+build/20314170 RUN: /usr/share/launchpad-buildd/bin/builder-prep Kernel version: Linux lcy01-amd64-029 4.15.0-124-generic #127-Ubuntu SMP Fri Nov 6 10:54:43 UTC 2020 x86_64 Buildd toolchain package versions: launchpad-buildd_193~468~ubuntu18.04.1 python3-lpbuildd_193~468~ubuntu18.04.1 sbuild_0.75.0-1ubuntu1 bzr-builder_0.7.3+bzr174~ppa13~ubuntu16.04.1 bzr_2.7.0+bzr6622-10 git-build-recipe_0.3.6~git201906051340.ff11471~ubuntu18.04.1 git_1:2.17.1-1ubuntu0.7 dpkg-dev_1.19.0.5ubuntu2.3 python-debian_0.1.32 python3-debian_0.1.32. Syncing the system clock with the buildd NTP service... 19 Nov 11:33:04 ntpdate[1677]: adjust time server 10.211.37.1 offset 0.000328 sec RUN: /usr/share/launchpad-buildd/bin/in-target unpack-chroot --backend=chroot --series=hirsute --arch=amd64 PACKAGEBUILD-20314170 --image-type chroot /home/buildd/filecache-default/720a8366e1260e086c1691fe6381a3f2b1c21d81 Creating target for build PACKAGEBUILD-20314170 RUN: /usr/share/launchpad-buildd/bin/in-target mount-chroot --backend=chroot --series=hirsute --arch=amd64 PACKAGEBUILD-20314170 Starting target for build PACKAGEBUILD-20314170 RUN: /usr/share/launchpad-buildd/bin/in-target override-sources-list --backend=chroot --series=hirsute --arch=amd64 PACKAGEBUILD-20314170 'deb http://ftpmaster.internal/ubuntu hirsute main universe' 'deb http://ftpmaster.internal/ubuntu hirsute-security main universe' 'deb http://ftpmaster.internal/ubuntu hirsute-updates main universe' 'deb http://ftpmaster.internal/ubuntu hirsute-proposed main universe' Overriding sources.list in build-PACKAGEBUILD-20314170 RUN: /usr/share/launchpad-buildd/bin/in-target update-debian-chroot --backend=chroot --series=hirsute --arch=amd64 PACKAGEBUILD-20314170 Updating target for build PACKAGEBUILD-20314170 Get:1 http://ftpmaster.internal/ubuntu hirsute InRelease [267 kB] Get:2 http://ftpmaster.internal/ubuntu hirsute-security InRelease [88.4 kB] Get:3 http://ftpmaster.internal/ubuntu hirsute-updates InRelease [88.4 kB] Get:4 http://ftpmaster.internal/ubuntu hirsute-proposed InRelease [118 kB] Get:5 http://ftpmaster.internal/ubuntu hirsute/main amd64 Packages [1386 kB] Get:6 http://ftpmaster.internal/ubuntu hirsute/main Translation-en [509 kB] Get:7 http://ftpmaster.internal/ubuntu hirsute/universe amd64 Packages [12.8 MB] Get:8 http://ftpmaster.internal/ubuntu hirsute/universe Translation-en [5334 kB] Get:9 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 Packages [215 kB] Get:10 http://ftpmaster.internal/ubuntu hirsute-proposed/main Translation-en [80.3 kB] Get:11 http://ftpmaster.internal/ubuntu hirsute-proposed/universe amd64 Packages [1775 kB] Get:12 http://ftpmaster.internal/ubuntu hirsute-proposed/universe Translation-en [604 kB] Fetched 23.3 MB in 10s (2439 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages were automatically installed and are no longer required: libperl5.30 perl-modules-5.30 Use 'sudo apt autoremove' to remove them. The following NEW packages will be installed: libperl5.32 perl-modules-5.32 The following packages will be upgraded: apt base-files base-passwd bash binutils binutils-common binutils-x86-64-linux-gnu bsdutils coreutils cpp-10 dash dpkg dpkg-dev fakeroot g++-10 gcc-10 gcc-10-base grep libapparmor1 libapt-pkg6.0 libasan6 libatomic1 libaudit-common libaudit1 libbinutils libblkid1 libc-bin libc-dev-bin libc6 libc6-dev libcap2 libcc1-0 libcrypt-dev libcrypt1 libcryptsetup12 libctf-nobfd0 libctf0 libdebconfclient0 libdpkg-perl libfakeroot libgcc-10-dev libgcc-s1 libgcrypt20 libgomp1 libgssapi-krb5-2 libidn2-0 libip4tc2 libitm1 libk5crypto3 libkrb5-3 libkrb5support0 liblsan0 libmount1 libmpc3 libncurses6 libncursesw6 libnpth0 libquadmath0 libreadline8 libseccomp2 libselinux1 libsemanage-common libsemanage1 libsmartcols1 libstdc++-10-dev libstdc++6 libsystemd0 libtinfo6 libtirpc-common libtirpc-dev libtirpc3 libtsan0 libubsan1 libudev1 libuuid1 linux-libc-dev mount ncurses-base ncurses-bin perl perl-base readline-common systemd systemd-sysv systemd-timesyncd sysvinit-utils tzdata util-linux 88 upgraded, 2 newly installed, 0 to remove and 0 not upgraded. Need to get 245 MB of archives. After this operation, 928 MB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu hirsute/main amd64 libcrypt-dev amd64 1:4.4.17-1ubuntu1 [105 kB] Get:2 http://ftpmaster.internal/ubuntu hirsute/main amd64 libcrypt1 amd64 1:4.4.17-1ubuntu1 [78.8 kB] Get:3 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 libc6-dev amd64 2.32-0ubuntu5 [2128 kB] Get:4 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 libc-dev-bin amd64 2.32-0ubuntu5 [30.9 kB] Get:5 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 linux-libc-dev amd64 5.8.0-30.32+21.04.2 [1139 kB] Get:6 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 libtirpc-common all 1.2.6-3 [7444 B] Get:7 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 libk5crypto3 amd64 1.17-10ubuntu1 [79.2 kB] Get:8 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 libgssapi-krb5-2 amd64 1.17-10ubuntu1 [121 kB] Get:9 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 libkrb5-3 amd64 1.17-10ubuntu1 [332 kB] Get:10 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 libkrb5support0 amd64 1.17-10ubuntu1 [30.7 kB] Get:11 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 libtirpc-dev amd64 1.2.6-3 [184 kB] Get:12 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 libtirpc3 amd64 1.2.6-3 [77.2 kB] Get:13 http://ftpmaster.internal/ubuntu hirsute/main amd64 libcc1-0 amd64 10.2.0-17ubuntu1 [41.1 kB] Get:14 http://ftpmaster.internal/ubuntu hirsute/main amd64 gcc-10-base amd64 10.2.0-17ubuntu1 [19.5 kB] Get:15 http://ftpmaster.internal/ubuntu hirsute/main amd64 libgcc-s1 amd64 10.2.0-17ubuntu1 [41.7 kB] Get:16 http://ftpmaster.internal/ubuntu hirsute/main amd64 libgomp1 amd64 10.2.0-17ubuntu1 [102 kB] Get:17 http://ftpmaster.internal/ubuntu hirsute/main amd64 libitm1 amd64 10.2.0-17ubuntu1 [26.3 kB] Get:18 http://ftpmaster.internal/ubuntu hirsute/main amd64 libatomic1 amd64 10.2.0-17ubuntu1 [9284 B] Get:19 http://ftpmaster.internal/ubuntu hirsute/main amd64 libasan6 amd64 10.2.0-17ubuntu1 [344 kB] Get:20 http://ftpmaster.internal/ubuntu hirsute/main amd64 liblsan0 amd64 10.2.0-17ubuntu1 [144 kB] Get:21 http://ftpmaster.internal/ubuntu hirsute/main amd64 libtsan0 amd64 10.2.0-17ubuntu1 [319 kB] Get:22 http://ftpmaster.internal/ubuntu hirsute/main amd64 libubsan1 amd64 10.2.0-17ubuntu1 [136 kB] Get:23 http://ftpmaster.internal/ubuntu hirsute/main amd64 libquadmath0 amd64 10.2.0-17ubuntu1 [146 kB] Get:24 http://ftpmaster.internal/ubuntu hirsute/main amd64 g++-10 amd64 10.2.0-17ubuntu1 [70.1 MB] Get:25 http://ftpmaster.internal/ubuntu hirsute/main amd64 libstdc++-10-dev amd64 10.2.0-17ubuntu1 [1750 kB] Get:26 http://ftpmaster.internal/ubuntu hirsute/main amd64 libgcc-10-dev amd64 10.2.0-17ubuntu1 [2345 kB] Get:27 http://ftpmaster.internal/ubuntu hirsute/main amd64 gcc-10 amd64 10.2.0-17ubuntu1 [72.0 MB] Get:28 http://ftpmaster.internal/ubuntu hirsute/main amd64 cpp-10 amd64 10.2.0-17ubuntu1 [63.4 MB] Get:29 http://ftpmaster.internal/ubuntu hirsute/main amd64 libstdc++6 amd64 10.2.0-17ubuntu1 [502 kB] Get:30 http://ftpmaster.internal/ubuntu hirsute/main amd64 libmpc3 amd64 1.2.0-1 [44.3 kB] Get:31 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 libctf-nobfd0 amd64 2.35.1-3ubuntu1 [48.4 kB] Get:32 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 libctf0 amd64 2.35.1-3ubuntu1 [47.6 kB] Get:33 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 libbinutils amd64 2.35.1-3ubuntu1 [481 kB] Get:34 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 binutils-common amd64 2.35.1-3ubuntu1 [212 kB] Get:35 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 binutils amd64 2.35.1-3ubuntu1 [3380 B] Get:36 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 binutils-x86-64-linux-gnu amd64 2.35.1-3ubuntu1 [1648 kB] Get:37 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 libc6 amd64 2.32-0ubuntu5 [2684 kB] Get:38 http://ftpmaster.internal/ubuntu hirsute/main amd64 base-files amd64 11ubuntu16 [60.5 kB] Get:39 http://ftpmaster.internal/ubuntu hirsute/main amd64 bash amd64 5.1~rc2-1ubuntu1 [680 kB] Get:40 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 bsdutils amd64 1:2.36.1-1ubuntu1 [86.8 kB] Get:41 http://ftpmaster.internal/ubuntu hirsute/main amd64 coreutils amd64 8.32-4ubuntu1 [1352 kB] Get:42 http://ftpmaster.internal/ubuntu hirsute/main amd64 dpkg amd64 1.20.5ubuntu3 [1172 kB] Get:43 http://ftpmaster.internal/ubuntu hirsute/main amd64 dash amd64 0.5.11+git20200708+dd9ef66+really0.5.10.2-0ubuntu1 [86.8 kB] Get:44 http://ftpmaster.internal/ubuntu hirsute/main amd64 grep amd64 3.6-1 [155 kB] Get:45 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 libncursesw6 amd64 6.2+20200918-1 [132 kB] Get:46 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 libncurses6 amd64 6.2+20200918-1 [102 kB] Get:47 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 libtinfo6 amd64 6.2+20200918-1 [87.3 kB] Get:48 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 ncurses-bin amd64 6.2+20200918-1 [173 kB] Get:49 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 perl-modules-5.32 all 5.32.0-5 [2754 kB] Get:50 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 libperl5.32 amd64 5.32.0-5 [4044 kB] Get:51 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 perl amd64 5.32.0-5 [225 kB] Get:52 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 perl-base amd64 5.32.0-5 [1562 kB] Get:53 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 util-linux amd64 2.36.1-1ubuntu1 [1073 kB] Get:54 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 libdebconfclient0 amd64 0.255ubuntu1 [6184 B] Get:55 http://ftpmaster.internal/ubuntu hirsute/main amd64 base-passwd amd64 3.5.48 [47.5 kB] Get:56 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 libc-bin amd64 2.32-0ubuntu5 [622 kB] Get:57 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 ncurses-base all 6.2+20200918-1 [18.7 kB] Get:58 http://ftpmaster.internal/ubuntu hirsute/main amd64 sysvinit-utils amd64 2.96-5ubuntu1 [20.8 kB] Get:59 http://ftpmaster.internal/ubuntu hirsute/main amd64 libgcrypt20 amd64 1.8.7-2ubuntu1 [424 kB] Get:60 http://ftpmaster.internal/ubuntu hirsute/main amd64 systemd-sysv amd64 246.6-2ubuntu1 [10.3 kB] Get:61 http://ftpmaster.internal/ubuntu hirsute/main amd64 systemd-timesyncd amd64 246.6-2ubuntu1 [28.2 kB] Get:62 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 libapparmor1 amd64 3.0.0-0ubuntu4 [35.9 kB] Get:63 http://ftpmaster.internal/ubuntu hirsute/main amd64 libaudit-common all 1:2.8.5-3ubuntu2 [4092 B] Get:64 http://ftpmaster.internal/ubuntu hirsute/main amd64 libaudit1 amd64 1:2.8.5-3ubuntu2 [39.5 kB] Get:65 http://ftpmaster.internal/ubuntu hirsute/main amd64 libcap2 amd64 1:2.44-1 [17.2 kB] Get:66 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 libblkid1 amd64 2.36.1-1ubuntu1 [132 kB] Get:67 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 libuuid1 amd64 2.36.1-1ubuntu1 [21.5 kB] Get:68 http://ftpmaster.internal/ubuntu hirsute/main amd64 libcryptsetup12 amd64 2:2.3.4-1ubuntu1 [195 kB] Get:69 http://ftpmaster.internal/ubuntu hirsute/main amd64 libidn2-0 amd64 2.3.0-4 [52.4 kB] Get:70 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 libip4tc2 amd64 1.8.5-3ubuntu4 [18.7 kB] Get:71 http://ftpmaster.internal/ubuntu hirsute/main amd64 libselinux1 amd64 3.1-2build1 [69.4 kB] Get:72 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 libmount1 amd64 2.36.1-1ubuntu1 [147 kB] Get:73 http://ftpmaster.internal/ubuntu hirsute/main amd64 libseccomp2 amd64 2.4.3-1ubuntu5 [42.0 kB] Get:74 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 mount amd64 2.36.1-1ubuntu1 [121 kB] Get:75 http://ftpmaster.internal/ubuntu hirsute/main amd64 systemd amd64 246.6-2ubuntu1 [4165 kB] Get:76 http://ftpmaster.internal/ubuntu hirsute/main amd64 libsystemd0 amd64 246.6-2ubuntu1 [273 kB] Get:77 http://ftpmaster.internal/ubuntu hirsute/main amd64 libudev1 amd64 246.6-2ubuntu1 [67.6 kB] Get:78 http://ftpmaster.internal/ubuntu hirsute/main amd64 libapt-pkg6.0 amd64 2.1.11 [848 kB] Get:79 http://ftpmaster.internal/ubuntu hirsute/main amd64 apt amd64 2.1.11 [1305 kB] Get:80 http://ftpmaster.internal/ubuntu hirsute/main amd64 libsemanage-common all 3.1-1build1 [10.1 kB] Get:81 http://ftpmaster.internal/ubuntu hirsute/main amd64 libsemanage1 amd64 3.1-1build1 [87.2 kB] Get:82 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 libsmartcols1 amd64 2.36.1-1ubuntu1 [94.7 kB] Get:83 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 readline-common all 8.1~rc2-2 [54.1 kB] Get:84 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 libreadline8 amd64 8.1~rc2-2 [137 kB] Get:85 http://ftpmaster.internal/ubuntu hirsute/main amd64 tzdata all 2020d-1ubuntu1 [293 kB] Get:86 http://ftpmaster.internal/ubuntu hirsute/main amd64 dpkg-dev all 1.20.5ubuntu3 [758 kB] Get:87 http://ftpmaster.internal/ubuntu hirsute/main amd64 libdpkg-perl all 1.20.5ubuntu3 [232 kB] Get:88 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 libfakeroot amd64 1.25.3-1.1 [26.8 kB] Get:89 http://ftpmaster.internal/ubuntu hirsute-proposed/main amd64 fakeroot amd64 1.25.3-1.1 [62.9 kB] Get:90 http://ftpmaster.internal/ubuntu hirsute/main amd64 libnpth0 amd64 1.6-3 [8220 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 245 MB in 11s (23.0 MB/s) (Reading database ... 12980 files and directories currently installed.) 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Initializing machine ID from random generator. Setting up systemd-timesyncd (246.6-2ubuntu1) ... Setting up systemd-sysv (246.6-2ubuntu1) ... Processing triggers for libc-bin (2.32-0ubuntu5) ... RUN: /usr/share/launchpad-buildd/bin/sbuild-package PACKAGEBUILD-20314170 amd64 hirsute-proposed -c chroot:build-PACKAGEBUILD-20314170 --arch=amd64 --dist=hirsute-proposed --nolog -A pbbam_1.6.0+dfsg-2.dsc Initiating build PACKAGEBUILD-20314170 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 4.15.0-124-generic #127-Ubuntu SMP Fri Nov 6 10:54:43 UTC 2020 x86_64 sbuild (Debian sbuild) 0.75.0 (21 Mar 2018) on lcy01-amd64-029.buildd +==============================================================================+ | pbbam 1.6.0+dfsg-2 (amd64) Thu, 19 Nov 2020 11:34:42 +0000 | +==============================================================================+ Package: pbbam Version: 1.6.0+dfsg-2 Source Version: 1.6.0+dfsg-2 Distribution: hirsute-proposed Machine Architecture: amd64 Host Architecture: amd64 Build Architecture: amd64 Build Type: binary I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-20314170/chroot-autobuild' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- pbbam_1.6.0+dfsg-2.dsc exists in .; copying to chroot I: NOTICE: Log filtering will replace 'build/pbbam-HLLEMr/pbbam-1.6.0+dfsg' with '<>' I: NOTICE: Log filtering will replace 'build/pbbam-HLLEMr' with '<>' +------------------------------------------------------------------------------+ | Install build-essential | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: build-essential, fakeroot Filtered Build-Depends: build-essential, fakeroot dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/<>/resolver-gcXXLg/apt_archive/sbuild-build-depends-core-dummy.deb'. dpkg-scanpackages: warning: Packages in archive but missing from override file: dpkg-scanpackages: warning: sbuild-build-depends-core-dummy dpkg-scanpackages: info: Wrote 1 entries to output Packages file. Ign:1 copy:/<>/resolver-gcXXLg/apt_archive ./ InRelease Get:2 copy:/<>/resolver-gcXXLg/apt_archive ./ Release [957 B] Ign:3 copy:/<>/resolver-gcXXLg/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-gcXXLg/apt_archive ./ Sources [349 B] Get:5 copy:/<>/resolver-gcXXLg/apt_archive ./ Packages [433 B] Fetched 1739 B in 0s (91.7 kB/s) Reading package lists... Reading package lists... Install core build dependencies (apt-based resolver) ---------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following packages were automatically installed and are no longer required: libperl5.30 perl-modules-5.30 Use 'apt autoremove' to remove them. The following NEW packages will be installed: sbuild-build-depends-core-dummy 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 856 B of archives. After this operation, 0 B of additional disk space will be used. Get:1 copy:/<>/resolver-gcXXLg/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [856 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 856 B in 0s (0 B/s) Selecting previously unselected package sbuild-build-depends-core-dummy. (Reading database ... 14902 files and directories currently installed.) Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_amd64.deb ... Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ... Setting up sbuild-build-depends-core-dummy (0.invalid.0) ... +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (amd64 included in any) +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged 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 Filtered 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 dpkg-deb: building package 'sbuild-build-depends-pbbam-dummy' in '/<>/resolver-gcXXLg/apt_archive/sbuild-build-depends-pbbam-dummy.deb'. dpkg-scanpackages: warning: Packages in archive but missing from override file: dpkg-scanpackages: warning: sbuild-build-depends-core-dummy sbuild-build-depends-pbbam-dummy dpkg-scanpackages: info: Wrote 2 entries to output Packages file. Ign:1 copy:/<>/resolver-gcXXLg/apt_archive ./ InRelease Get:2 copy:/<>/resolver-gcXXLg/apt_archive ./ Release [963 B] Ign:3 copy:/<>/resolver-gcXXLg/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-gcXXLg/apt_archive ./ Sources [593 B] Get:5 copy:/<>/resolver-gcXXLg/apt_archive ./ Packages [664 B] Fetched 2220 B in 0s (105 kB/s) Reading package lists... Reading package lists... Install pbbam build dependencies (apt-based resolver) ----------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following packages were automatically installed and are no longer required: libperl5.30 perl-modules-5.30 Use 'apt autoremove' to remove them. The following additional packages will be installed: autoconf automake autopoint autotools-dev bsdextrautils cmake cmake-data d-shlibs debhelper dh-autoreconf dh-exec dh-strip-nondeterminism dwz file gettext gettext-base googletest groff-base intltool-debian libarchive-zip-perl libarchive13 libasn1-8-heimdal libboost-dev libboost1.71-dev libbrotli1 libcroco3 libcurl3-gnutls libcurl4 libcurl4-gnutls-dev libdebhelper-perl libdeflate-dev libdeflate0 libelf1 libexpat1 libfile-stripnondeterminism-perl libglib2.0-0 libgssapi3-heimdal libgtest-dev libhcrypto4-heimdal libheimbase1-heimdal libheimntlm0-heimdal libhts-dev libhts3 libhx509-5-heimdal libicu67 libjsoncpp1 libkrb5-26-heimdal libldap-2.4-2 liblzma-dev libmagic-mgc libmagic1 libnghttp2-14 libpbcopper-dev libpbcopper1.8.0 libpipeline1 libpsl5 libpython3-stdlib libpython3.8-minimal libpython3.8-stdlib librhash0 libroken18-heimdal librtmp1 libsasl2-2 libsasl2-modules-db libsigsegv2 libssh-4 libssl-dev libsub-override-perl libtool libuchardet0 libuv1 libwind0-heimdal libxml2 m4 man-db meson mime-support ninja-build pkg-config po-debconf python3 python3-cram python3-minimal python3-pkg-resources python3.8 python3.8-minimal samtools zlib1g-dev Suggested packages: autoconf-archive gnu-standards autoconf-doc cmake-doc dh-make gettext-doc libasprintf-dev libgettextpo-dev groff lrzip libboost-doc libboost1.71-doc libboost-atomic1.71-dev libboost-chrono1.71-dev libboost-container1.71-dev libboost-context1.71-dev libboost-contract1.71-dev libboost-coroutine1.71-dev libboost-date-time1.71-dev libboost-exception1.71-dev libboost-fiber1.71-dev libboost-filesystem1.71-dev libboost-graph1.71-dev libboost-graph-parallel1.71-dev libboost-iostreams1.71-dev libboost-locale1.71-dev libboost-log1.71-dev libboost-math1.71-dev libboost-mpi1.71-dev libboost-mpi-python1.71-dev libboost-numpy1.71-dev libboost-program-options1.71-dev libboost-python1.71-dev libboost-random1.71-dev libboost-regex1.71-dev libboost-serialization1.71-dev libboost-stacktrace1.71-dev libboost-system1.71-dev libboost-test1.71-dev libboost-thread1.71-dev libboost-timer1.71-dev libboost-type-erasure1.71-dev libboost-wave1.71-dev libboost1.71-tools-dev libmpfrc++-dev libntl-dev libcurl4-doc libgnutls28-dev libidn11-dev libkrb5-dev libldap2-dev librtmp-dev libssh2-1-dev liblzma-doc libssl-doc libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc apparmor less www-browser libmail-box-perl python3-doc python3-tk python3-venv python3-setuptools python3.8-venv python3.8-doc binfmt-support cwltool Recommended packages: curl | wget | lynx libarchive-cpio-perl libglib2.0-data shared-mime-info xdg-user-dirs libldap-common publicsuffix libsasl2-modules libltdl-dev libmail-sendmail-perl The following NEW packages will be installed: autoconf automake autopoint autotools-dev bsdextrautils cmake cmake-data d-shlibs debhelper dh-autoreconf dh-exec dh-strip-nondeterminism dwz file gettext gettext-base googletest groff-base intltool-debian libarchive-zip-perl libarchive13 libasn1-8-heimdal libboost-dev libboost1.71-dev libbrotli1 libcroco3 libcurl3-gnutls libcurl4 libcurl4-gnutls-dev libdebhelper-perl libdeflate-dev libdeflate0 libelf1 libexpat1 libfile-stripnondeterminism-perl libglib2.0-0 libgssapi3-heimdal libgtest-dev libhcrypto4-heimdal libheimbase1-heimdal libheimntlm0-heimdal libhts-dev libhts3 libhx509-5-heimdal libicu67 libjsoncpp1 libkrb5-26-heimdal libldap-2.4-2 liblzma-dev libmagic-mgc libmagic1 libnghttp2-14 libpbcopper-dev libpbcopper1.8.0 libpipeline1 libpsl5 libpython3-stdlib libpython3.8-minimal libpython3.8-stdlib librhash0 libroken18-heimdal librtmp1 libsasl2-2 libsasl2-modules-db libsigsegv2 libssh-4 libssl-dev libsub-override-perl libtool libuchardet0 libuv1 libwind0-heimdal libxml2 m4 man-db meson mime-support ninja-build pkg-config po-debconf python3 python3-cram python3-minimal python3-pkg-resources python3.8 python3.8-minimal samtools sbuild-build-depends-pbbam-dummy zlib1g-dev 0 upgraded, 89 newly installed, 0 to remove and 0 not upgraded. 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http://ftpmaster.internal/ubuntu hirsute/main amd64 dh-exec amd64 0.23.2 [25.0 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 51.0 MB in 1s (51.5 MB/s) Selecting previously unselected package libpython3.8-minimal:amd64. (Reading database ... 14902 files and directories currently installed.) Preparing to unpack .../libpython3.8-minimal_3.8.6-1_amd64.deb ... Unpacking libpython3.8-minimal:amd64 (3.8.6-1) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../libexpat1_2.2.10-1_amd64.deb ... Unpacking libexpat1:amd64 (2.2.10-1) ... Selecting previously unselected package python3.8-minimal. Preparing to unpack .../python3.8-minimal_3.8.6-1_amd64.deb ... Unpacking python3.8-minimal (3.8.6-1) ... Setting up libpython3.8-minimal:amd64 (3.8.6-1) ... Setting up libexpat1:amd64 (2.2.10-1) ... Setting up python3.8-minimal (3.8.6-1) ... Selecting previously unselected package python3-minimal. (Reading database ... 15193 files and directories currently installed.) Preparing to unpack .../python3-minimal_3.8.6-1_amd64.deb ... Unpacking python3-minimal (3.8.6-1) ... Selecting previously unselected package mime-support. Preparing to unpack .../mime-support_3.64ubuntu1_all.deb ... 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Not building database; man-db/auto-update is not 'true'. Created symlink /etc/systemd/system/timers.target.wants/man-db.timer → /lib/systemd/system/man-db.timer. Setting up intltool-debian (0.35.0+20060710.5) ... Setting up libkrb5-26-heimdal:amd64 (7.7.0+dfsg-2) ... Setting up po-debconf (1.0.21) ... Setting up libheimntlm0-heimdal:amd64 (7.7.0+dfsg-2) ... Setting up libgssapi3-heimdal:amd64 (7.7.0+dfsg-2) ... Setting up libldap-2.4-2:amd64 (2.4.53+dfsg-1ubuntu5) ... Setting up libcurl3-gnutls:amd64 (7.72.0-1ubuntu1) ... Setting up libcurl4-gnutls-dev:amd64 (7.72.0-1ubuntu1) ... Setting up libcurl4:amd64 (7.72.0-1ubuntu1) ... Setting up libhts3:amd64 (1.11-2) ... Setting up libhts-dev:amd64 (1.11-2) ... Setting up samtools (1.11-1) ... Setting up cmake (3.18.4-1ubuntu1) ... Setting up debhelper (13.2.1ubuntu1) ... Setting up dh-exec (0.23.2) ... Setting up dh-autoreconf (19) ... Setting up sbuild-build-depends-pbbam-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.32-0ubuntu5) ... +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 4.15.0-124-generic amd64 (x86_64) Toolchain package versions: binutils_2.35.1-3ubuntu1 dpkg-dev_1.20.5ubuntu3 g++-10_10.2.0-17ubuntu1 gcc-10_10.2.0-17ubuntu1 libc6-dev_2.32-0ubuntu5 libstdc++-10-dev_10.2.0-17ubuntu1 libstdc++6_10.2.0-17ubuntu1 linux-libc-dev_5.8.0-30.32+21.04.2 Package versions: adduser_3.118ubuntu2 advancecomp_2.1-2.1build1 apt_2.1.11 autoconf_2.69-11.1 automake_1:1.16.2-4ubuntu1 autopoint_0.19.8.1-10build1 autotools-dev_20180224.1 base-files_11ubuntu16 base-passwd_3.5.48 bash_5.1~rc2-1ubuntu1 binutils_2.35.1-3ubuntu1 binutils-common_2.35.1-3ubuntu1 binutils-x86-64-linux-gnu_2.35.1-3ubuntu1 bsdextrautils_2.36.1-1ubuntu1 bsdutils_1:2.36.1-1ubuntu1 build-essential_12.8ubuntu3 bzip2_1.0.8-4ubuntu2 ca-certificates_20200601 cmake_3.18.4-1ubuntu1 cmake-data_3.18.4-1ubuntu1 coreutils_8.32-4ubuntu1 cpp_4:10.2.0-1ubuntu1 cpp-10_10.2.0-17ubuntu1 d-shlibs_0.95 dash_0.5.11+git20200708+dd9ef66+really0.5.10.2-0ubuntu1 debconf_1.5.74 debhelper_13.2.1ubuntu1 debianutils_4.11.2 dh-autoreconf_19 dh-exec_0.23.2 dh-strip-nondeterminism_1.9.0-1 diffutils_1:3.7-3ubuntu1 dpkg_1.20.5ubuntu3 dpkg-dev_1.20.5ubuntu3 dwz_0.13-5 e2fsprogs_1.45.6-1ubuntu1 fakeroot_1.25.3-1.1 file_1:5.38-5 findutils_4.7.0-1ubuntu2 g++_4:10.2.0-1ubuntu1 g++-10_10.2.0-17ubuntu1 gcc_4:10.2.0-1ubuntu1 gcc-10_10.2.0-17ubuntu1 gcc-10-base_10.2.0-17ubuntu1 gettext_0.19.8.1-10build1 gettext-base_0.19.8.1-10build1 googletest_1.10.0.20201025-1 gpg_2.2.20-1ubuntu1 gpg-agent_2.2.20-1ubuntu1 gpgconf_2.2.20-1ubuntu1 gpgv_2.2.20-1ubuntu1 grep_3.6-1 groff-base_1.22.4-5 gzip_1.10-2ubuntu1 hostname_3.23 init_1.58 init-system-helpers_1.58 intltool-debian_0.35.0+20060710.5 libacl1_2.2.53-8 libapparmor1_3.0.0-0ubuntu4 libapt-pkg6.0_2.1.11 libarchive-zip-perl_1.68-1 libarchive13_3.4.3-2 libargon2-1_0~20171227-0.2build20.10.0 libasan6_10.2.0-17ubuntu1 libasn1-8-heimdal_7.7.0+dfsg-2 libassuan0_2.5.3-7.1 libatomic1_10.2.0-17ubuntu1 libattr1_1:2.4.48-5 libaudit-common_1:2.8.5-3ubuntu2 libaudit1_1:2.8.5-3ubuntu2 libbinutils_2.35.1-3ubuntu1 libblkid1_2.36.1-1ubuntu1 libboost-dev_1.71.0.0ubuntu4 libboost1.71-dev_1.71.0-6ubuntu10 libbrotli1_1.0.9-2build1 libbz2-1.0_1.0.8-4ubuntu2 libc-bin_2.32-0ubuntu5 libc-dev-bin_2.32-0ubuntu5 libc6_2.32-0ubuntu5 libc6-dev_2.32-0ubuntu5 libcap-ng0_0.7.9-2.2 libcap2_1:2.44-1 libcc1-0_10.2.0-17ubuntu1 libcom-err2_1.45.6-1ubuntu1 libcroco3_0.6.13-1 libcrypt-dev_1:4.4.17-1ubuntu1 libcrypt1_1:4.4.17-1ubuntu1 libcryptsetup12_2:2.3.4-1ubuntu1 libctf-nobfd0_2.35.1-3ubuntu1 libctf0_2.35.1-3ubuntu1 libcurl3-gnutls_7.72.0-1ubuntu1 libcurl4_7.72.0-1ubuntu1 libcurl4-gnutls-dev_7.72.0-1ubuntu1 libdb5.3_5.3.28+dfsg1-0.6ubuntu3 libdebconfclient0_0.255ubuntu1 libdebhelper-perl_13.2.1ubuntu1 libdeflate-dev_1.6-1 libdeflate0_1.6-1 libdevmapper1.02.1_2:1.02.167-1ubuntu3 libdpkg-perl_1.20.5ubuntu3 libelf1_0.182-1 libexpat1_2.2.10-1 libext2fs2_1.45.6-1ubuntu1 libfakeroot_1.25.3-1.1 libffi8ubuntu1_3.4~20200819gead65ca871-0ubuntu3 libfile-stripnondeterminism-perl_1.9.0-1 libgcc-10-dev_10.2.0-17ubuntu1 libgcc-s1_10.2.0-17ubuntu1 libgcrypt20_1.8.7-2ubuntu1 libgdbm-compat4_1.18.1-5.1 libgdbm6_1.18.1-5.1 libglib2.0-0_2.66.2-1 libgmp10_2:6.2.0+dfsg-6ubuntu1 libgnutls30_3.6.15-4ubuntu2 libgomp1_10.2.0-17ubuntu1 libgpg-error0_1.38-2 libgssapi-krb5-2_1.17-10ubuntu1 libgssapi3-heimdal_7.7.0+dfsg-2 libgtest-dev_1.10.0.20201025-1 libhcrypto4-heimdal_7.7.0+dfsg-2 libheimbase1-heimdal_7.7.0+dfsg-2 libheimntlm0-heimdal_7.7.0+dfsg-2 libhogweed6_3.6-2 libhts-dev_1.11-2 libhts3_1.11-2 libhx509-5-heimdal_7.7.0+dfsg-2 libicu67_67.1-4 libidn2-0_2.3.0-4 libip4tc2_1.8.5-3ubuntu4 libisl22_0.22.1-1 libitm1_10.2.0-17ubuntu1 libjson-c5_0.15-1 libjsoncpp1_1.7.4-3.1ubuntu2 libk5crypto3_1.17-10ubuntu1 libkeyutils1_1.6.1-2ubuntu1 libkmod2_27+20200310-2ubuntu1 libkrb5-26-heimdal_7.7.0+dfsg-2 libkrb5-3_1.17-10ubuntu1 libkrb5support0_1.17-10ubuntu1 libldap-2.4-2_2.4.53+dfsg-1ubuntu5 liblockfile-bin_1.16-1.1 liblockfile1_1.16-1.1 liblsan0_10.2.0-17ubuntu1 liblz4-1_1.9.2-2 liblzma-dev_5.2.4-1ubuntu1 liblzma5_5.2.4-1ubuntu1 libmagic-mgc_1:5.38-5 libmagic1_1:5.38-5 libmount1_2.36.1-1ubuntu1 libmpc3_1.2.0-1 libmpfr6_4.1.0-3 libncurses6_6.2+20200918-1 libncursesw6_6.2+20200918-1 libnettle8_3.6-2 libnghttp2-14_1.41.0-3 libnpth0_1.6-3 libnsl-dev_1.3.0-0ubuntu3 libnsl2_1.3.0-0ubuntu3 libnss-nis_3.1-0ubuntu4 libnss-nisplus_1.3-0ubuntu4 libp11-kit0_0.23.21-2build1 libpam-modules_1.3.1-5ubuntu6 libpam-modules-bin_1.3.1-5ubuntu6 libpam-runtime_1.3.1-5ubuntu6 libpam0g_1.3.1-5ubuntu6 libpbcopper-dev_1.8.0+dfsg-2 libpbcopper1.8.0_1.8.0+dfsg-2 libpcre2-8-0_10.34-7 libpcre3_2:8.39-13 libperl5.30_5.30.3-4 libperl5.32_5.32.0-5 libpipeline1_1.5.3-1 libpng16-16_1.6.37-3 libprocps8_2:3.3.16-5ubuntu2 libpsl5_0.21.0-1.1ubuntu1 libpython3-stdlib_3.8.6-1 libpython3.8-minimal_3.8.6-1 libpython3.8-stdlib_3.8.6-1 libquadmath0_10.2.0-17ubuntu1 libreadline8_8.1~rc2-2 librhash0_1.4.0-1 libroken18-heimdal_7.7.0+dfsg-2 librtmp1_2.4+20151223.gitfa8646d.1-2build2 libsasl2-2_2.1.27+dfsg-2ubuntu1 libsasl2-modules-db_2.1.27+dfsg-2ubuntu1 libseccomp2_2.4.3-1ubuntu5 libselinux1_3.1-2build1 libsemanage-common_3.1-1build1 libsemanage1_3.1-1build1 libsepol1_3.1-1 libsigsegv2_2.12-2build1 libsmartcols1_2.36.1-1ubuntu1 libsqlite3-0_3.33.0-1 libss2_1.45.6-1ubuntu1 libssh-4_0.9.5-1 libssl-dev_1.1.1f-1ubuntu4 libssl1.1_1.1.1f-1ubuntu4 libstdc++-10-dev_10.2.0-17ubuntu1 libstdc++6_10.2.0-17ubuntu1 libsub-override-perl_0.09-2 libsystemd0_246.6-2ubuntu1 libtasn1-6_4.16.0-2 libtinfo6_6.2+20200918-1 libtirpc-common_1.2.6-3 libtirpc-dev_1.2.6-3 libtirpc3_1.2.6-3 libtool_2.4.6-14 libtsan0_10.2.0-17ubuntu1 libubsan1_10.2.0-17ubuntu1 libuchardet0_0.0.7-1 libudev1_246.6-2ubuntu1 libunistring2_0.9.10-4 libuuid1_2.36.1-1ubuntu1 libuv1_1.40.0-1 libwind0-heimdal_7.7.0+dfsg-2 libxml2_2.9.10+dfsg-6.2 libzstd1_1.4.5+dfsg-4 linux-libc-dev_5.8.0-30.32+21.04.2 lockfile-progs_0.1.18 login_1:4.8.1-1ubuntu6 logsave_1.45.6-1ubuntu1 lsb-base_11.1.0ubuntu2 m4_1.4.18-4 make_4.3-4ubuntu1 man-db_2.9.3-2 mawk_1.3.4.20200120-2 meson_0.56.0-1 mime-support_3.64ubuntu1 mount_2.36.1-1ubuntu1 ncurses-base_6.2+20200918-1 ncurses-bin_6.2+20200918-1 ninja-build_1.10.1-1 openssl_1.1.1f-1ubuntu4 optipng_0.7.7-1 passwd_1:4.8.1-1ubuntu6 patch_2.7.6-6 perl_5.32.0-5 perl-base_5.32.0-5 perl-modules-5.30_5.30.3-4 perl-modules-5.32_5.32.0-5 pinentry-curses_1.1.0-4build1 pkg-config_0.29.2-1ubuntu1 pkgbinarymangler_146 po-debconf_1.0.21 policyrcd-script-zg2_0.1-3 procps_2:3.3.16-5ubuntu2 python3_3.8.6-1 python3-cram_0.7-4 python3-minimal_3.8.6-1 python3-pkg-resources_50.3.0-1 python3.8_3.8.6-1 python3.8-minimal_3.8.6-1 readline-common_8.1~rc2-2 rpcsvc-proto_1.4.2-0ubuntu4 samtools_1.11-1 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-pbbam-dummy_0.invalid.0 sed_4.7-1ubuntu1 sensible-utils_0.0.13 systemd_246.6-2ubuntu1 systemd-sysv_246.6-2ubuntu1 systemd-timesyncd_246.6-2ubuntu1 sysvinit-utils_2.96-5ubuntu1 tar_1.30+dfsg-7 tzdata_2020d-1ubuntu1 ubuntu-keyring_2020.06.17.1 util-linux_2.36.1-1ubuntu1 xz-utils_5.2.4-1ubuntu1 zlib1g_1:1.2.11.dfsg-2ubuntu4 zlib1g-dev_1:1.2.11.dfsg-2ubuntu4 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- gpgv: Signature made Sun Nov 15 05:42:58 2020 UTC 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 Check disk space ---------------- Sufficient free space for build User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf DEB_BUILD_OPTIONS=parallel=4 HOME=/sbuild-nonexistent LANG=C.UTF-8 LC_ALL=C.UTF-8 LOGNAME=buildd PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games SCHROOT_ALIAS_NAME=build-PACKAGEBUILD-20314170 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-20314170 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-20314170 SCHROOT_UID=2001 SCHROOT_USER=buildd SHELL=/bin/sh TERM=unknown USER=buildd V=1 dpkg-buildpackage ----------------- dpkg-buildpackage: info: source package pbbam dpkg-buildpackage: info: source version 1.6.0+dfsg-2 dpkg-buildpackage: info: source distribution unstable 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 '/<>/pbbam-1.6.0+dfsg' dh_auto_clean find -name "*.deb.t" -delete rm -f -r /<>/pbbam-1.6.0+dfsg/gendata make[1]: Leaving directory '/<>/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: 0.56.0 Source dir: /<>/pbbam-1.6.0+dfsg Build dir: /<>/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=/<>/pbbam-1.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security' Using 'LDFLAGS' from environment with value: '-Wl,-Bsymbolic-functions -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 10.2.0 "c++ (Ubuntu 10.2.0-17ubuntu1) 10.2.0") C++ linker for the host machine: c++ ld.bfd 2.35.1 Using 'CXXFLAGS' from environment with value: '-g -O2 -fdebug-prefix-map=/<>/pbbam-1.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security' Using 'LDFLAGS' from environment with value: '-Wl,-Bsymbolic-functions -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 1.71.0 (/usr/include) Run-time dependency zlib found: YES 1.2.11 Run-time dependency htslib found: YES 1.11-2 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 (/<>/pbbam-1.6.0+dfsg/tools/check-formatting) Program tools/check-eof found: YES (/<>/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 -j4 -v [1/228] /usr/bin/meson --internal vcstagger ../src/PbbamGitHash.cpp.in src/PbbamGitHash.cpp 1.6.0 /<>/pbbam-1.6.0+dfsg/src @PBBAM_GIT_SHA1@ '(.*)' /<>/pbbam-1.6.0+dfsg/src/git describe --always '--dirty=*' [2/228] /usr/bin/meson --internal vcstagger ../src/LibraryGitHash.h.in src/LibraryGitHash.h 1.6.0 /<>/pbbam-1.6.0+dfsg/src @PBBAM_GIT_SHA1@ '(.*)' /<>/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=/<>/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=/<>/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 [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=/<>/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 [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=/<>/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 [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=/<>/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 [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=/<>/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_BamRecordImplCore.cpp.o -MF tests/pbbam_test.p/src_test_BamRecordImplCore.cpp.o.d -o tests/pbbam_test.p/src_test_BamRecordImplCore.cpp.o -c ../tests/src/test_BamRecordImplCore.cpp [9/228] 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=/<>/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/BamFileMerger.cpp.o -MF src/libpbbam.so.1.6.0.p/BamFileMerger.cpp.o.d -o src/libpbbam.so.1.6.0.p/BamFileMerger.cpp.o -c ../src/BamFileMerger.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=/<>/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 [11/228] 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=/<>/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/BamHeader.cpp.o -MF 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-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_VcfHeader.cpp.o -MF tests/pbbam_test.p/src_test_VcfHeader.cpp.o.d -o tests/pbbam_test.p/src_test_VcfHeader.cpp.o -c ../tests/src/test_VcfHeader.cpp [186/228] 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=/<>/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_VcfFormat.cpp.o -MF tests/pbbam_test.p/src_test_VcfFormat.cpp.o.d -o tests/pbbam_test.p/src_test_VcfFormat.cpp.o -c ../tests/src/test_VcfFormat.cpp [187/228] 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=/<>/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_VcfReader.cpp.o -MF tests/pbbam_test.p/src_test_VcfReader.cpp.o.d -o tests/pbbam_test.p/src_test_VcfReader.cpp.o -c ../tests/src/test_VcfReader.cpp [188/228] 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=/<>/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_VcfSort.cpp.o -MF tests/pbbam_test.p/src_test_VcfSort.cpp.o.d -o tests/pbbam_test.p/src_test_VcfSort.cpp.o -c ../tests/src/test_VcfSort.cpp [189/228] 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=/<>/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_VcfQuery.cpp.o -MF tests/pbbam_test.p/src_test_VcfQuery.cpp.o.d -o tests/pbbam_test.p/src_test_VcfQuery.cpp.o -c ../tests/src/test_VcfQuery.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=/<>/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 [191/228] 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=/<>/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 [192/228] 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=/<>/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_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 [193/228] 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=/<>/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 [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=/<>/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 [195/228] 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=/<>/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 [196/228] /usr/bin/python3 ../tests/scripts/generate_data.py /<>/pbbam-1.6.0+dfsg/tests/data /<>/pbbam-1.6.0+dfsg/obj-x86_64-linux-gnu/tests Generating test data in /<>/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. [197/228] 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=/<>/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 [198/228] 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=/<>/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 [199/228] 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=/<>/pbbam-1.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -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,/<>/pbbam-1.6.0+dfsg/obj-x86_64-linux-gnu/src [200/228] 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=/<>/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 [201/228] 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=/<>/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 [202/228] 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=/<>/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 [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=/<>/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 [204/228] 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=/<>/pbbam-1.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,--start-group /usr/lib/x86_64-linux-gnu/libhts.so -pthread /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libpbcopper.so -Wl,--end-group [205/228] 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=/<>/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 [206/228] 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=/<>/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 [207/228] 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=/<>/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 [208/228] 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 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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=/<>/pbbam-1.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -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,/<>/pbbam-1.6.0+dfsg/obj-x86_64-linux-gnu/src [213/228] 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 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../tools/ccs-kinetics-bystrandify/src/CcsKineticsBystrandifySettings.cpp [224/228] 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=/<>/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 [225/228] 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=/<>/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 [226/228] 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=/<>/pbbam-1.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -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,$ORIGIN/../src' -Wl,-rpath-link,/<>/pbbam-1.6.0+dfsg/obj-x86_64-linux-gnu/src [227/228] c++ -Itools/ccs-kinetics-bystrandify.p -Itools -I../tools -Iinclude -I../include -I../tools/ccs-kinetics-bystrandify -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++14 -g -O2 -fdebug-prefix-map=/<>/pbbam-1.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_ALL_NO_LIB -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tools/ccs-kinetics-bystrandify.p/ccs-kinetics-bystrandify_src_CcsKineticsBystrandifyWorkflow.cpp.o -MF tools/ccs-kinetics-bystrandify.p/ccs-kinetics-bystrandify_src_CcsKineticsBystrandifyWorkflow.cpp.o.d -o tools/ccs-kinetics-bystrandify.p/ccs-kinetics-bystrandify_src_CcsKineticsBystrandifyWorkflow.cpp.o -c ../tools/ccs-kinetics-bystrandify/src/CcsKineticsBystrandifyWorkflow.cpp [228/228] c++ -o tools/ccs-kinetics-bystrandify tools/ccs-kinetics-bystrandify.p/ccs-kinetics-bystrandify_src_main.cpp.o tools/ccs-kinetics-bystrandify.p/ccs-kinetics-bystrandify_src_CcsKineticsBystrandifySettings.cpp.o tools/ccs-kinetics-bystrandify.p/ccs-kinetics-bystrandify_src_CcsKineticsBystrandifyWorkflow.cpp.o -Wl,--as-needed -Wl,--no-undefined -g -O2 -fdebug-prefix-map=/<>/pbbam-1.6.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,--start-group src/libpbbam.so.1.6.0 /usr/lib/x86_64-linux-gnu/libhts.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libpbcopper.so -Wl,--end-group '-Wl,-rpath,$ORIGIN/../src' -Wl,-rpath-link,/<>/pbbam-1.6.0+dfsg/obj-x86_64-linux-gnu/src debian/rules override_dh_auto_test make[1]: Entering directory '/<>/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@|/<>/pbbam-1.6.0+dfsg/tests|g' \ -e 's|@PacBioBAM_VERSION@|1.6.0+dfsg|g' \ -e 's|@GeneratedTestDataDir@|/<>/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|$TOOLS_BIN/||g' \ -e 's|@PacBioBAM_TestsDir@|/<>/pbbam-1.6.0+dfsg/tests|g' \ -e 's|@PacBioBAM_VERSION@|1.6.0+dfsg|g' \ -e 's|@GeneratedTestDataDir@|/<>/pbbam-1.6.0+dfsg/gendata|g' \ -e '/@PG/s|+dfsg||g' \ -e 's/$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@|/<>/pbbam-1.6.0+dfsg/tests|g' \ -e 's|@PacBioBAM_VERSION@|1.6.0+dfsg|g' \ -e 's|@GeneratedTestDataDir@|/<>/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|$TOOLS_BIN/||g' \ -e 's|@PacBioBAM_TestsDir@|/<>/pbbam-1.6.0+dfsg/tests|g' \ -e 's|@PacBioBAM_VERSION@|1.6.0+dfsg|g' \ -e 's|@GeneratedTestDataDir@|/<>/pbbam-1.6.0+dfsg/gendata|g' \ -e '/@PG/s|+dfsg||g' \ -e 's/$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@|/<>/pbbam-1.6.0+dfsg/tests|g' \ -e 's|@PacBioBAM_VERSION@|1.6.0+dfsg|g' \ -e 's|@GeneratedTestDataDir@|/<>/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|$TOOLS_BIN/||g' \ -e 's|@PacBioBAM_TestsDir@|/<>/pbbam-1.6.0+dfsg/tests|g' \ -e 's|@PacBioBAM_VERSION@|1.6.0+dfsg|g' \ -e 's|@GeneratedTestDataDir@|/<>/pbbam-1.6.0+dfsg/gendata|g' \ -e '/@PG/s|+dfsg||g' \ -e 's/$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@|/<>/pbbam-1.6.0+dfsg/tests|g' \ -e 's|@PacBioBAM_VERSION@|1.6.0+dfsg|g' \ -e 's|@GeneratedTestDataDir@|/<>/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|$TOOLS_BIN/||g' \ -e 's|@PacBioBAM_TestsDir@|/<>/pbbam-1.6.0+dfsg/tests|g' \ -e 's|@PacBioBAM_VERSION@|1.6.0+dfsg|g' \ -e 's|@GeneratedTestDataDir@|/<>/pbbam-1.6.0+dfsg/gendata|g' \ -e '/@PG/s|+dfsg||g' \ -e 's/$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 /<>/pbbam-1.6.0+dfsg/gendata python3 tests/scripts/generate_data.py /<>/pbbam-1.6.0+dfsg/tests/data /<>/pbbam-1.6.0+dfsg/gendata Generating test data in /<>/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/local/sbin:/usr/local/bin:/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 '/<>/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=/<>/pbbam-1.6.0\+dfsg/debian/tmp LC_ALL=C.UTF-8 ninja install [0/1] Regenerating build files. The Meson build system Version: 0.56.0 Source dir: /<>/pbbam-1.6.0+dfsg Build dir: /<>/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 10.2.0 "c++ (Ubuntu 10.2.0-17ubuntu1) 10.2.0") C++ linker for the host machine: c++ ld.bfd 2.35.1 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 1.71.0 (cached) Dependency zlib found: YES 1.2.11 (cached) Dependency htslib found: YES 1.11-2 (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 (/<>/pbbam-1.6.0+dfsg/tools/check-formatting) Program tools/check-eof found: YES (/<>/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 /<>/pbbam-1.6.0+dfsg/debian/tmp/usr/lib/x86_64-linux-gnu Installing tools/bam2sam to /<>/pbbam-1.6.0+dfsg/debian/tmp/usr/bin Installing tools/pbindex to /<>/pbbam-1.6.0+dfsg/debian/tmp/usr/bin Installing tools/pbindexdump to /<>/pbbam-1.6.0+dfsg/debian/tmp/usr/bin Installing tools/pbmerge to /<>/pbbam-1.6.0+dfsg/debian/tmp/usr/bin Installing tools/pbbamify to /<>/pbbam-1.6.0+dfsg/debian/tmp/usr/bin Installing tools/ccs-kinetics-bystrandify to /<>/pbbam-1.6.0+dfsg/debian/tmp/usr/bin Installing /<>/pbbam-1.6.0+dfsg/include/pbbam/Accuracy.h to /<>/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /<>/pbbam-1.6.0+dfsg/include/pbbam/AlignmentPrinter.h to /<>/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /<>/pbbam-1.6.0+dfsg/include/pbbam/BaiIndexCache.h to /<>/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /<>/pbbam-1.6.0+dfsg/include/pbbam/BaiIndexedBamReader.h to /<>/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /<>/pbbam-1.6.0+dfsg/include/pbbam/BamFile.h to /<>/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /<>/pbbam-1.6.0+dfsg/include/pbbam/BamFileMerger.h to /<>/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /<>/pbbam-1.6.0+dfsg/include/pbbam/BamHeader.h to /<>/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /<>/pbbam-1.6.0+dfsg/include/pbbam/BamReader.h to /<>/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /<>/pbbam-1.6.0+dfsg/include/pbbam/BamRecord.h to /<>/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /<>/pbbam-1.6.0+dfsg/include/pbbam/BamRecordImpl.h to /<>/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /<>/pbbam-1.6.0+dfsg/include/pbbam/BamRecordTag.h to /<>/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /<>/pbbam-1.6.0+dfsg/include/pbbam/BamRecordView.h to /<>/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /<>/pbbam-1.6.0+dfsg/include/pbbam/BamTagCodec.h to /<>/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /<>/pbbam-1.6.0+dfsg/include/pbbam/BamWriter.h to /<>/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /<>/pbbam-1.6.0+dfsg/include/pbbam/BgzipFastaWriter.h to /<>/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /<>/pbbam-1.6.0+dfsg/include/pbbam/BgzipFastqWriter.h to /<>/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /<>/pbbam-1.6.0+dfsg/include/pbbam/BgzipWriter.h to /<>/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /<>/pbbam-1.6.0+dfsg/include/pbbam/Cigar.h to /<>/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /<>/pbbam-1.6.0+dfsg/include/pbbam/CigarOperation.h to /<>/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /<>/pbbam-1.6.0+dfsg/include/pbbam/ClipType.h to /<>/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /<>/pbbam-1.6.0+dfsg/include/pbbam/CollectionMetadata.h to /<>/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /<>/pbbam-1.6.0+dfsg/include/pbbam/Compare.h to /<>/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /<>/pbbam-1.6.0+dfsg/include/pbbam/CompositeBamReader.h to /<>/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /<>/pbbam-1.6.0+dfsg/include/pbbam/CompositeFastaReader.h to /<>/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /<>/pbbam-1.6.0+dfsg/include/pbbam/Config.h to /<>/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /<>/pbbam-1.6.0+dfsg/include/pbbam/DataSet.h to /<>/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /<>/pbbam-1.6.0+dfsg/include/pbbam/DataSetTypes.h to /<>/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /<>/pbbam-1.6.0+dfsg/include/pbbam/DataSetXsd.h to /<>/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /<>/pbbam-1.6.0+dfsg/include/pbbam/Deleters.h to /<>/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /<>/pbbam-1.6.0+dfsg/include/pbbam/EntireFileQuery.h to /<>/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /<>/pbbam-1.6.0+dfsg/include/pbbam/FaiIndex.h to /<>/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /<>/pbbam-1.6.0+dfsg/include/pbbam/FastaCache.h to /<>/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /<>/pbbam-1.6.0+dfsg/include/pbbam/FastaReader.h to /<>/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /<>/pbbam-1.6.0+dfsg/include/pbbam/FastaSequence.h to /<>/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /<>/pbbam-1.6.0+dfsg/include/pbbam/FastaSequenceQuery.h to /<>/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /<>/pbbam-1.6.0+dfsg/include/pbbam/FastaWriter.h to /<>/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /<>/pbbam-1.6.0+dfsg/include/pbbam/FastqReader.h to /<>/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /<>/pbbam-1.6.0+dfsg/include/pbbam/FastqSequence.h to /<>/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /<>/pbbam-1.6.0+dfsg/include/pbbam/FastqWriter.h to /<>/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /<>/pbbam-1.6.0+dfsg/include/pbbam/FormatUtils.h to /<>/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /<>/pbbam-1.6.0+dfsg/include/pbbam/FrameEncodingType.h to /<>/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /<>/pbbam-1.6.0+dfsg/include/pbbam/Frames.h to /<>/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /<>/pbbam-1.6.0+dfsg/include/pbbam/GenomicInterval.h to /<>/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /<>/pbbam-1.6.0+dfsg/include/pbbam/GenomicIntervalQuery.h to /<>/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /<>/pbbam-1.6.0+dfsg/include/pbbam/IFastaWriter.h to /<>/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /<>/pbbam-1.6.0+dfsg/include/pbbam/IFastqWriter.h to /<>/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /<>/pbbam-1.6.0+dfsg/include/pbbam/IndexedBamWriter.h to /<>/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /<>/pbbam-1.6.0+dfsg/include/pbbam/IndexedFastaReader.h to /<>/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /<>/pbbam-1.6.0+dfsg/include/pbbam/IndexedFastqReader.h to /<>/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /<>/pbbam-1.6.0+dfsg/include/pbbam/Interval.h to /<>/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /<>/pbbam-1.6.0+dfsg/include/pbbam/IRecordWriter.h to /<>/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /<>/pbbam-1.6.0+dfsg/include/pbbam/LibraryInfo.h to /<>/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /<>/pbbam-1.6.0+dfsg/include/pbbam/LocalContextFlags.h to /<>/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /<>/pbbam-1.6.0+dfsg/include/pbbam/MD5.h to /<>/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /<>/pbbam-1.6.0+dfsg/include/pbbam/MoveAppend.h to /<>/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /<>/pbbam-1.6.0+dfsg/include/pbbam/Orientation.h to /<>/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /<>/pbbam-1.6.0+dfsg/include/pbbam/PbbamVersion.h to /<>/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /<>/pbbam-1.6.0+dfsg/include/pbbam/PbiBasicTypes.h to /<>/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /<>/pbbam-1.6.0+dfsg/include/pbbam/PbiBuilder.h to /<>/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /<>/pbbam-1.6.0+dfsg/include/pbbam/PbiFile.h to /<>/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /<>/pbbam-1.6.0+dfsg/include/pbbam/PbiFilter.h to /<>/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /<>/pbbam-1.6.0+dfsg/include/pbbam/PbiFilterQuery.h to /<>/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /<>/pbbam-1.6.0+dfsg/include/pbbam/PbiFilterTypes.h to /<>/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /<>/pbbam-1.6.0+dfsg/include/pbbam/PbiIndexedBamReader.h to /<>/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /<>/pbbam-1.6.0+dfsg/include/pbbam/PbiRawData.h to /<>/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /<>/pbbam-1.6.0+dfsg/include/pbbam/Position.h to /<>/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /<>/pbbam-1.6.0+dfsg/include/pbbam/ProgramInfo.h to /<>/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /<>/pbbam-1.6.0+dfsg/include/pbbam/PulseBehavior.h to /<>/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /<>/pbbam-1.6.0+dfsg/include/pbbam/PulseExclusionReason.h to /<>/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /<>/pbbam-1.6.0+dfsg/include/pbbam/QualityValue.h to /<>/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /<>/pbbam-1.6.0+dfsg/include/pbbam/QualityValues.h to /<>/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /<>/pbbam-1.6.0+dfsg/include/pbbam/ReadGroupInfo.h to /<>/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /<>/pbbam-1.6.0+dfsg/include/pbbam/RecordType.h to /<>/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /<>/pbbam-1.6.0+dfsg/include/pbbam/RunMetadata.h to /<>/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /<>/pbbam-1.6.0+dfsg/include/pbbam/SamReader.h to /<>/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /<>/pbbam-1.6.0+dfsg/include/pbbam/SamTagCodec.h to /<>/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /<>/pbbam-1.6.0+dfsg/include/pbbam/SamWriter.h to /<>/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /<>/pbbam-1.6.0+dfsg/include/pbbam/SequenceInfo.h to /<>/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /<>/pbbam-1.6.0+dfsg/include/pbbam/SNR.h to /<>/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /<>/pbbam-1.6.0+dfsg/include/pbbam/Strand.h to /<>/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /<>/pbbam-1.6.0+dfsg/include/pbbam/StringUtilities.h to /<>/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /<>/pbbam-1.6.0+dfsg/include/pbbam/Tag.h to /<>/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /<>/pbbam-1.6.0+dfsg/include/pbbam/TagCollection.h to /<>/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /<>/pbbam-1.6.0+dfsg/include/pbbam/TextFileReader.h to /<>/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /<>/pbbam-1.6.0+dfsg/include/pbbam/TextFileWriter.h to /<>/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /<>/pbbam-1.6.0+dfsg/include/pbbam/Validator.h to /<>/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /<>/pbbam-1.6.0+dfsg/include/pbbam/ZmwGroupQuery.h to /<>/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /<>/pbbam-1.6.0+dfsg/include/pbbam/ZmwQuery.h to /<>/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /<>/pbbam-1.6.0+dfsg/include/pbbam/ZmwType.h to /<>/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /<>/pbbam-1.6.0+dfsg/include/pbbam/ZmwTypeMap.h to /<>/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam Installing /<>/pbbam-1.6.0+dfsg/include/pbbam/bed/BedReader.h to /<>/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam/bed Installing /<>/pbbam-1.6.0+dfsg/include/pbbam/bed/BedWriter.h to /<>/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam/bed Installing /<>/pbbam-1.6.0+dfsg/include/pbbam/ccs/CCSHeader.h to /<>/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam/ccs Installing /<>/pbbam-1.6.0+dfsg/include/pbbam/ccs/CCSPbiBuilder.h to /<>/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam/ccs Installing /<>/pbbam-1.6.0+dfsg/include/pbbam/ccs/CCSRecord.h to /<>/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam/ccs Installing /<>/pbbam-1.6.0+dfsg/include/pbbam/ccs/CCSRecordFormat.h to /<>/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam/ccs Installing /<>/pbbam-1.6.0+dfsg/include/pbbam/ccs/CCSRecordReader.h to /<>/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam/ccs Installing /<>/pbbam-1.6.0+dfsg/include/pbbam/ccs/CCSRecordWriter.h to /<>/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam/ccs Installing /<>/pbbam-1.6.0+dfsg/include/pbbam/exception/BundleChemistryMappingException.h to /<>/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam/exception Installing /<>/pbbam-1.6.0+dfsg/include/pbbam/exception/InvalidSequencingChemistryException.h to /<>/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam/exception Installing /<>/pbbam-1.6.0+dfsg/include/pbbam/exception/ValidationException.h to /<>/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam/exception Installing /<>/pbbam-1.6.0+dfsg/include/pbbam/internal/Compare.inl to /<>/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam/internal Installing /<>/pbbam-1.6.0+dfsg/include/pbbam/internal/CompositeBamReader.inl to /<>/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam/internal Installing /<>/pbbam-1.6.0+dfsg/include/pbbam/internal/DataSetBaseTypes.h to /<>/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam/internal Installing /<>/pbbam-1.6.0+dfsg/include/pbbam/internal/DataSetElement.h to /<>/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam/internal Installing /<>/pbbam-1.6.0+dfsg/include/pbbam/internal/DataSetElement.inl to /<>/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam/internal Installing /<>/pbbam-1.6.0+dfsg/include/pbbam/internal/PbiBasicTypes.inl to /<>/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam/internal Installing /<>/pbbam-1.6.0+dfsg/include/pbbam/internal/PbiFilter.inl to /<>/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam/internal Installing /<>/pbbam-1.6.0+dfsg/include/pbbam/internal/PbiFilterTypes.inl to /<>/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam/internal Installing /<>/pbbam-1.6.0+dfsg/include/pbbam/internal/QueryBase.h to /<>/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam/internal Installing /<>/pbbam-1.6.0+dfsg/include/pbbam/internal/QueryBase.inl to /<>/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam/internal Installing /<>/pbbam-1.6.0+dfsg/include/pbbam/vcf/VcfVariant.h to /<>/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam/vcf Installing /<>/pbbam-1.6.0+dfsg/include/pbbam/vcf/VcfFile.h to /<>/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam/vcf Installing /<>/pbbam-1.6.0+dfsg/include/pbbam/vcf/VcfFormat.h to /<>/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam/vcf Installing /<>/pbbam-1.6.0+dfsg/include/pbbam/vcf/VcfHeader.h to /<>/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam/vcf Installing /<>/pbbam-1.6.0+dfsg/include/pbbam/vcf/VcfHeaderTypes.h to /<>/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam/vcf Installing /<>/pbbam-1.6.0+dfsg/include/pbbam/vcf/VcfReader.h to /<>/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam/vcf Installing /<>/pbbam-1.6.0+dfsg/include/pbbam/vcf/VcfSort.h to /<>/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam/vcf Installing /<>/pbbam-1.6.0+dfsg/include/pbbam/vcf/VcfQuery.h to /<>/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam/vcf Installing /<>/pbbam-1.6.0+dfsg/include/pbbam/vcf/VcfWriter.h to /<>/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam/vcf Installing /<>/pbbam-1.6.0+dfsg/include/pbbam/virtual/VirtualPolymeraseBamRecord.h to /<>/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam/virtual Installing /<>/pbbam-1.6.0+dfsg/include/pbbam/virtual/VirtualPolymeraseCompositeReader.h to /<>/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam/virtual Installing /<>/pbbam-1.6.0+dfsg/include/pbbam/virtual/VirtualPolymeraseReader.h to /<>/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam/virtual Installing /<>/pbbam-1.6.0+dfsg/include/pbbam/virtual/VirtualRegion.h to /<>/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam/virtual Installing /<>/pbbam-1.6.0+dfsg/include/pbbam/virtual/VirtualRegionType.h to /<>/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam/virtual Installing /<>/pbbam-1.6.0+dfsg/include/pbbam/virtual/VirtualRegionTypeMap.h to /<>/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam/virtual Installing /<>/pbbam-1.6.0+dfsg/include/pbbam/virtual/VirtualZmwBamRecord.h to /<>/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam/virtual Installing /<>/pbbam-1.6.0+dfsg/include/pbbam/virtual/WhitelistedZmwReadStitcher.h to /<>/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam/virtual Installing /<>/pbbam-1.6.0+dfsg/include/pbbam/virtual/ZmwReadStitcher.h to /<>/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam/virtual Installing /<>/pbbam-1.6.0+dfsg/include/pbbam/virtual/ZmwWhitelistVirtualReader.h to /<>/pbbam-1.6.0+dfsg/debian/tmp/usr/include/pbbam/virtual Installing /<>/pbbam-1.6.0+dfsg/obj-x86_64-linux-gnu/meson-private/pbbam.pc to /<>/pbbam-1.6.0+dfsg/debian/tmp/usr/lib/x86_64-linux-gnu/pkgconfig debian/rules override_dh_install make[1]: Entering directory '/<>/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 /<>/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 '/<>/pbbam-1.6.0+dfsg' dh_installdocs -O--buildsystem=meson debian/rules override_dh_installchangelogs make[1]: Entering directory '/<>/pbbam-1.6.0+dfsg' dh_installchangelogs CHANGELOG.md make[1]: Leaving directory '/<>/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 INFO: pkgstriptranslations version 146 INFO: pkgstriptranslations version 146 INFO: pkgstriptranslations version 146 pkgstriptranslations: processing pbbamtools (in debian/pbbamtools); do_strip: , oemstrip: pkgstriptranslations: processing libpbbam-dev (in debian/libpbbam-dev); do_strip: , oemstrip: pkgstriptranslations: processing libpbbam1.6.0 (in debian/libpbbam1.6.0); do_strip: , oemstrip: pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/pbbamtools/DEBIAN/control, package pbbamtools, directory debian/pbbamtools .. removing usr/share/doc/pbbamtools/changelog.gz Searching for duplicated docs in dependency libpbbam1.6.0... symlinking changelog.Debian.gz in pbbamtools to file in libpbbam1.6.0 pkgstripfiles: processing control file: debian/libpbbam1.6.0/DEBIAN/control, package libpbbam1.6.0, directory debian/libpbbam1.6.0 .. removing usr/share/doc/libpbbam1.6.0/changelog.gz pkgstripfiles: Running PNG optimization (using 4 cpus) for package pbbamtools ... INFO: pkgstripfiles: waiting for lock (libpbbam1.6.0) ... pkgstripfiles: No PNG files. dpkg-deb: building package 'pbbamtools' in '../pbbamtools_1.6.0+dfsg-2_amd64.deb'. pkgstripfiles: processing control file: debian/libpbbam-dev/DEBIAN/control, package libpbbam-dev, directory debian/libpbbam-dev .. removing usr/share/doc/libpbbam-dev/changelog.gz INFO: pkgstripfiles: waiting for lock (libpbbam-dev) ... INFO: pkgstriptranslations version 146 pkgstriptranslations: processing pbbamtools-dbgsym (in debian/.debhelper/pbbamtools/dbgsym-root); do_strip: , oemstrip: pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: Truncating usr/share/doc/libpbbam1.6.0/changelog.Debian.gz to topmost ten records pkgstripfiles: Running PNG optimization (using 4 cpus) for package libpbbam1.6.0 ... pkgstripfiles: No PNG files. dpkg-deb: building package 'libpbbam1.6.0' in '../libpbbam1.6.0_1.6.0+dfsg-2_amd64.deb'. Searching for duplicated docs in dependency libpbbam1.6.0... symlinking changelog.Debian.gz in libpbbam-dev to file in libpbbam1.6.0 pkgstripfiles: Running PNG optimization (using 4 cpus) for package libpbbam-dev ... pkgstripfiles: No PNG files. dpkg-deb: building package 'libpbbam-dev' in '../libpbbam-dev_1.6.0+dfsg-2_amd64.deb'. pkgstripfiles: processing control file: debian/.debhelper/pbbamtools/dbgsym-root/DEBIAN/control, package pbbamtools-dbgsym, directory debian/.debhelper/pbbamtools/dbgsym-root dpkg-deb: building package 'pbbamtools-dbgsym' in 'debian/.debhelper/scratch-space/build-pbbamtools/pbbamtools-dbgsym_1.6.0+dfsg-2_amd64.deb'. Renaming pbbamtools-dbgsym_1.6.0+dfsg-2_amd64.deb to pbbamtools-dbgsym_1.6.0+dfsg-2_amd64.ddeb INFO: pkgstriptranslations version 146 pkgstriptranslations: processing libpbbam1.6.0-dbgsym (in debian/.debhelper/libpbbam1.6.0/dbgsym-root); do_strip: , oemstrip: pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/.debhelper/libpbbam1.6.0/dbgsym-root/DEBIAN/control, package libpbbam1.6.0-dbgsym, directory debian/.debhelper/libpbbam1.6.0/dbgsym-root dpkg-deb: building package 'libpbbam1.6.0-dbgsym' in 'debian/.debhelper/scratch-space/build-libpbbam1.6.0/libpbbam1.6.0-dbgsym_1.6.0+dfsg-2_amd64.deb'. Renaming libpbbam1.6.0-dbgsym_1.6.0+dfsg-2_amd64.deb to libpbbam1.6.0-dbgsym_1.6.0+dfsg-2_amd64.ddeb dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary -mLaunchpad Build Daemon >../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) -------------------------------------------------------------------------------- Build finished at 2020-11-19T11:51:16Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Post Build Chroot | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ pbbam_1.6.0+dfsg-2_amd64.changes: --------------------------------- Format: 1.8 Date: Sun, 15 Nov 2020 06:31:21 +0100 Source: pbbam Binary: libpbbam-dev libpbbam1.6.0 pbbamtools Architecture: amd64 Version: 1.6.0+dfsg-2 Distribution: hirsute-proposed Urgency: medium Maintainer: Launchpad Build Daemon 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: f93760086d0d3b9179f213721657e10c7c389b8c 75520 libpbbam-dev_1.6.0+dfsg-2_amd64.deb f0699d0cf6a2296eac48171be4519d76b8bf71ec 15274356 libpbbam1.6.0-dbgsym_1.6.0+dfsg-2_amd64.ddeb 3ffc3982ed05074f51a334779067ac0bc3d5231f 672660 libpbbam1.6.0_1.6.0+dfsg-2_amd64.deb 80d337282b2ef137464cc2e3bb6a9622b5a03c45 8989 pbbam_1.6.0+dfsg-2_amd64.buildinfo 3a5e19b6614d0cf499d854841428e3741b60f377 2091564 pbbamtools-dbgsym_1.6.0+dfsg-2_amd64.ddeb b30c3087a51d44bf064a3741bf8c3753ec7eb8b8 82116 pbbamtools_1.6.0+dfsg-2_amd64.deb Checksums-Sha256: e388366f22eeae19a6418bd05d9d2ab0d61ad51431c88200334f794fa968d994 75520 libpbbam-dev_1.6.0+dfsg-2_amd64.deb d1877fdf87c1dd558d837dc15d22d6b8f6e26eac49b73891a996fa0ccfcfd2ad 15274356 libpbbam1.6.0-dbgsym_1.6.0+dfsg-2_amd64.ddeb 7f788b5e6b2c8acc8bfc595171bcce0d7dadd6d2f66cfa6ee9aa35f0402b1eb7 672660 libpbbam1.6.0_1.6.0+dfsg-2_amd64.deb bed6d8f6bfdde6a574bf1568398fb29c44790e8f0ed89614e5d98610e58788bd 8989 pbbam_1.6.0+dfsg-2_amd64.buildinfo 3d70b3ba9ebab4236b104cefe4661f3090e54a23f5cdabd3688762a71fbfa81a 2091564 pbbamtools-dbgsym_1.6.0+dfsg-2_amd64.ddeb cbd0ed30691246aba6be06e5efb2b298f9829806cdcd3f91af161ee51e93cc47 82116 pbbamtools_1.6.0+dfsg-2_amd64.deb Files: a1097e993d25ae55407d3cc589cdb70d 75520 libdevel optional libpbbam-dev_1.6.0+dfsg-2_amd64.deb 25ed2eed40d44dc56d8f6029fc6f5bbb 15274356 debug optional libpbbam1.6.0-dbgsym_1.6.0+dfsg-2_amd64.ddeb bb3570500dbf6f62825c744734861d70 672660 libs optional libpbbam1.6.0_1.6.0+dfsg-2_amd64.deb 603147dea6a17fdeb62c4076ed2446cc 8989 science optional pbbam_1.6.0+dfsg-2_amd64.buildinfo 193ab7bb8aa6299527158de95b505c32 2091564 debug optional pbbamtools-dbgsym_1.6.0+dfsg-2_amd64.ddeb 8ddd0ad99e1041ad36ac5d9c30ae43ec 82116 science optional pbbamtools_1.6.0+dfsg-2_amd64.deb +------------------------------------------------------------------------------+ | Buildinfo | +------------------------------------------------------------------------------+ Format: 1.0 Source: pbbam Binary: libpbbam-dev libpbbam1.6.0 libpbbam1.6.0-dbgsym pbbamtools pbbamtools-dbgsym Architecture: amd64 Version: 1.6.0+dfsg-2 Checksums-Md5: a1097e993d25ae55407d3cc589cdb70d 75520 libpbbam-dev_1.6.0+dfsg-2_amd64.deb 25ed2eed40d44dc56d8f6029fc6f5bbb 15274356 libpbbam1.6.0-dbgsym_1.6.0+dfsg-2_amd64.ddeb bb3570500dbf6f62825c744734861d70 672660 libpbbam1.6.0_1.6.0+dfsg-2_amd64.deb 193ab7bb8aa6299527158de95b505c32 2091564 pbbamtools-dbgsym_1.6.0+dfsg-2_amd64.ddeb 8ddd0ad99e1041ad36ac5d9c30ae43ec 82116 pbbamtools_1.6.0+dfsg-2_amd64.deb Checksums-Sha1: f93760086d0d3b9179f213721657e10c7c389b8c 75520 libpbbam-dev_1.6.0+dfsg-2_amd64.deb f0699d0cf6a2296eac48171be4519d76b8bf71ec 15274356 libpbbam1.6.0-dbgsym_1.6.0+dfsg-2_amd64.ddeb 3ffc3982ed05074f51a334779067ac0bc3d5231f 672660 libpbbam1.6.0_1.6.0+dfsg-2_amd64.deb 3a5e19b6614d0cf499d854841428e3741b60f377 2091564 pbbamtools-dbgsym_1.6.0+dfsg-2_amd64.ddeb b30c3087a51d44bf064a3741bf8c3753ec7eb8b8 82116 pbbamtools_1.6.0+dfsg-2_amd64.deb Checksums-Sha256: e388366f22eeae19a6418bd05d9d2ab0d61ad51431c88200334f794fa968d994 75520 libpbbam-dev_1.6.0+dfsg-2_amd64.deb d1877fdf87c1dd558d837dc15d22d6b8f6e26eac49b73891a996fa0ccfcfd2ad 15274356 libpbbam1.6.0-dbgsym_1.6.0+dfsg-2_amd64.ddeb 7f788b5e6b2c8acc8bfc595171bcce0d7dadd6d2f66cfa6ee9aa35f0402b1eb7 672660 libpbbam1.6.0_1.6.0+dfsg-2_amd64.deb 3d70b3ba9ebab4236b104cefe4661f3090e54a23f5cdabd3688762a71fbfa81a 2091564 pbbamtools-dbgsym_1.6.0+dfsg-2_amd64.ddeb cbd0ed30691246aba6be06e5efb2b298f9829806cdcd3f91af161ee51e93cc47 82116 pbbamtools_1.6.0+dfsg-2_amd64.deb Build-Origin: Ubuntu Build-Architecture: amd64 Build-Date: Thu, 19 Nov 2020 11:51:15 +0000 Build-Path: /<>/pbbam-1.6.0+dfsg Build-Tainted-By: usr-local-has-programs Installed-Build-Depends: adduser (= 3.118ubuntu2), apt (= 2.1.11), autoconf (= 2.69-11.1), automake (= 1:1.16.2-4ubuntu1), autopoint (= 0.19.8.1-10build1), autotools-dev (= 20180224.1), base-files (= 11ubuntu16), base-passwd (= 3.5.48), bash (= 5.1~rc2-1ubuntu1), binutils (= 2.35.1-3ubuntu1), binutils-common (= 2.35.1-3ubuntu1), binutils-x86-64-linux-gnu (= 2.35.1-3ubuntu1), bsdextrautils (= 2.36.1-1ubuntu1), bsdutils (= 1:2.36.1-1ubuntu1), build-essential (= 12.8ubuntu3), bzip2 (= 1.0.8-4ubuntu2), cmake (= 3.18.4-1ubuntu1), cmake-data (= 3.18.4-1ubuntu1), coreutils (= 8.32-4ubuntu1), cpp (= 4:10.2.0-1ubuntu1), cpp-10 (= 10.2.0-17ubuntu1), d-shlibs (= 0.95), dash (= 0.5.11+git20200708+dd9ef66+really0.5.10.2-0ubuntu1), debconf (= 1.5.74), debhelper (= 13.2.1ubuntu1), debianutils (= 4.11.2), dh-autoreconf (= 19), dh-exec (= 0.23.2), dh-strip-nondeterminism (= 1.9.0-1), diffutils (= 1:3.7-3ubuntu1), dpkg (= 1.20.5ubuntu3), dpkg-dev (= 1.20.5ubuntu3), dwz (= 0.13-5), file (= 1:5.38-5), findutils (= 4.7.0-1ubuntu2), g++ (= 4:10.2.0-1ubuntu1), g++-10 (= 10.2.0-17ubuntu1), gcc (= 4:10.2.0-1ubuntu1), gcc-10 (= 10.2.0-17ubuntu1), gcc-10-base (= 10.2.0-17ubuntu1), gettext (= 0.19.8.1-10build1), gettext-base (= 0.19.8.1-10build1), googletest (= 1.10.0.20201025-1), gpgv (= 2.2.20-1ubuntu1), grep (= 3.6-1), groff-base (= 1.22.4-5), gzip (= 1.10-2ubuntu1), hostname (= 3.23), init-system-helpers (= 1.58), intltool-debian (= 0.35.0+20060710.5), libacl1 (= 2.2.53-8), libapt-pkg6.0 (= 2.1.11), libarchive-zip-perl (= 1.68-1), libarchive13 (= 3.4.3-2), libasan6 (= 10.2.0-17ubuntu1), libasn1-8-heimdal (= 7.7.0+dfsg-2), libatomic1 (= 10.2.0-17ubuntu1), libattr1 (= 1:2.4.48-5), libaudit-common (= 1:2.8.5-3ubuntu2), libaudit1 (= 1:2.8.5-3ubuntu2), libbinutils (= 2.35.1-3ubuntu1), libblkid1 (= 2.36.1-1ubuntu1), libboost-dev (= 1.71.0.0ubuntu4), libboost1.71-dev (= 1.71.0-6ubuntu10), libbrotli1 (= 1.0.9-2build1), libbz2-1.0 (= 1.0.8-4ubuntu2), libc-bin (= 2.32-0ubuntu5), libc-dev-bin (= 2.32-0ubuntu5), libc6 (= 2.32-0ubuntu5), libc6-dev (= 2.32-0ubuntu5), libcap-ng0 (= 0.7.9-2.2), libcc1-0 (= 10.2.0-17ubuntu1), libcom-err2 (= 1.45.6-1ubuntu1), libcroco3 (= 0.6.13-1), libcrypt-dev (= 1:4.4.17-1ubuntu1), libcrypt1 (= 1:4.4.17-1ubuntu1), libctf-nobfd0 (= 2.35.1-3ubuntu1), libctf0 (= 2.35.1-3ubuntu1), libcurl3-gnutls (= 7.72.0-1ubuntu1), libcurl4 (= 7.72.0-1ubuntu1), libcurl4-gnutls-dev (= 7.72.0-1ubuntu1), libdb5.3 (= 5.3.28+dfsg1-0.6ubuntu3), libdebconfclient0 (= 0.255ubuntu1), libdebhelper-perl (= 13.2.1ubuntu1), libdeflate-dev (= 1.6-1), libdeflate0 (= 1.6-1), libdpkg-perl (= 1.20.5ubuntu3), libelf1 (= 0.182-1), libexpat1 (= 2.2.10-1), libffi8ubuntu1 (= 3.4~20200819gead65ca871-0ubuntu3), libfile-stripnondeterminism-perl (= 1.9.0-1), libgcc-10-dev (= 10.2.0-17ubuntu1), libgcc-s1 (= 10.2.0-17ubuntu1), libgcrypt20 (= 1.8.7-2ubuntu1), libgdbm-compat4 (= 1.18.1-5.1), libgdbm6 (= 1.18.1-5.1), libglib2.0-0 (= 2.66.2-1), libgmp10 (= 2:6.2.0+dfsg-6ubuntu1), libgnutls30 (= 3.6.15-4ubuntu2), libgomp1 (= 10.2.0-17ubuntu1), libgpg-error0 (= 1.38-2), libgssapi-krb5-2 (= 1.17-10ubuntu1), libgssapi3-heimdal (= 7.7.0+dfsg-2), libgtest-dev (= 1.10.0.20201025-1), libhcrypto4-heimdal (= 7.7.0+dfsg-2), libheimbase1-heimdal (= 7.7.0+dfsg-2), libheimntlm0-heimdal (= 7.7.0+dfsg-2), libhogweed6 (= 3.6-2), libhts-dev (= 1.11-2), libhts3 (= 1.11-2), libhx509-5-heimdal (= 7.7.0+dfsg-2), libicu67 (= 67.1-4), libidn2-0 (= 2.3.0-4), libisl22 (= 0.22.1-1), libitm1 (= 10.2.0-17ubuntu1), libjsoncpp1 (= 1.7.4-3.1ubuntu2), libk5crypto3 (= 1.17-10ubuntu1), libkeyutils1 (= 1.6.1-2ubuntu1), libkrb5-26-heimdal (= 7.7.0+dfsg-2), libkrb5-3 (= 1.17-10ubuntu1), libkrb5support0 (= 1.17-10ubuntu1), libldap-2.4-2 (= 2.4.53+dfsg-1ubuntu5), liblsan0 (= 10.2.0-17ubuntu1), liblz4-1 (= 1.9.2-2), liblzma-dev (= 5.2.4-1ubuntu1), liblzma5 (= 5.2.4-1ubuntu1), libmagic-mgc (= 1:5.38-5), libmagic1 (= 1:5.38-5), libmount1 (= 2.36.1-1ubuntu1), libmpc3 (= 1.2.0-1), libmpfr6 (= 4.1.0-3), libncurses6 (= 6.2+20200918-1), libncursesw6 (= 6.2+20200918-1), libnettle8 (= 3.6-2), libnghttp2-14 (= 1.41.0-3), libnsl-dev (= 1.3.0-0ubuntu3), libnsl2 (= 1.3.0-0ubuntu3), libp11-kit0 (= 0.23.21-2build1), libpam-modules (= 1.3.1-5ubuntu6), libpam-modules-bin (= 1.3.1-5ubuntu6), libpam-runtime (= 1.3.1-5ubuntu6), libpam0g (= 1.3.1-5ubuntu6), libpbcopper-dev (= 1.8.0+dfsg-2), libpbcopper1.8.0 (= 1.8.0+dfsg-2), libpcre2-8-0 (= 10.34-7), libpcre3 (= 2:8.39-13), libperl5.32 (= 5.32.0-5), libpipeline1 (= 1.5.3-1), libprocps8 (= 2:3.3.16-5ubuntu2), libpsl5 (= 0.21.0-1.1ubuntu1), libpython3-stdlib (= 3.8.6-1), libpython3.8-minimal (= 3.8.6-1), libpython3.8-stdlib (= 3.8.6-1), libquadmath0 (= 10.2.0-17ubuntu1), libreadline8 (= 8.1~rc2-2), librhash0 (= 1.4.0-1), libroken18-heimdal (= 7.7.0+dfsg-2), librtmp1 (= 2.4+20151223.gitfa8646d.1-2build2), libsasl2-2 (= 2.1.27+dfsg-2ubuntu1), libsasl2-modules-db (= 2.1.27+dfsg-2ubuntu1), libseccomp2 (= 2.4.3-1ubuntu5), libselinux1 (= 3.1-2build1), libsemanage-common (= 3.1-1build1), libsemanage1 (= 3.1-1build1), libsepol1 (= 3.1-1), libsigsegv2 (= 2.12-2build1), libsmartcols1 (= 2.36.1-1ubuntu1), libsqlite3-0 (= 3.33.0-1), libssh-4 (= 0.9.5-1), libssl-dev (= 1.1.1f-1ubuntu4), libssl1.1 (= 1.1.1f-1ubuntu4), libstdc++-10-dev (= 10.2.0-17ubuntu1), libstdc++6 (= 10.2.0-17ubuntu1), libsub-override-perl (= 0.09-2), libsystemd0 (= 246.6-2ubuntu1), libtasn1-6 (= 4.16.0-2), libtinfo6 (= 6.2+20200918-1), libtirpc-common (= 1.2.6-3), libtirpc-dev (= 1.2.6-3), libtirpc3 (= 1.2.6-3), libtool (= 2.4.6-14), libtsan0 (= 10.2.0-17ubuntu1), libubsan1 (= 10.2.0-17ubuntu1), libuchardet0 (= 0.0.7-1), libudev1 (= 246.6-2ubuntu1), libunistring2 (= 0.9.10-4), libuuid1 (= 2.36.1-1ubuntu1), libuv1 (= 1.40.0-1), libwind0-heimdal (= 7.7.0+dfsg-2), libxml2 (= 2.9.10+dfsg-6.2), libzstd1 (= 1.4.5+dfsg-4), linux-libc-dev (= 5.8.0-30.32+21.04.2), login (= 1:4.8.1-1ubuntu6), lsb-base (= 11.1.0ubuntu2), m4 (= 1.4.18-4), make (= 4.3-4ubuntu1), man-db (= 2.9.3-2), mawk (= 1.3.4.20200120-2), meson (= 0.56.0-1), mime-support (= 3.64ubuntu1), ncurses-base (= 6.2+20200918-1), ncurses-bin (= 6.2+20200918-1), ninja-build (= 1.10.1-1), passwd (= 1:4.8.1-1ubuntu6), patch (= 2.7.6-6), perl (= 5.32.0-5), perl-base (= 5.32.0-5), perl-modules-5.32 (= 5.32.0-5), pkg-config (= 0.29.2-1ubuntu1), po-debconf (= 1.0.21), procps (= 2:3.3.16-5ubuntu2), python3 (= 3.8.6-1), python3-cram (= 0.7-4), python3-minimal (= 3.8.6-1), python3-pkg-resources (= 50.3.0-1), python3.8 (= 3.8.6-1), python3.8-minimal (= 3.8.6-1), readline-common (= 8.1~rc2-2), rpcsvc-proto (= 1.4.2-0ubuntu4), samtools (= 1.11-1), sed (= 4.7-1ubuntu1), sensible-utils (= 0.0.13), sysvinit-utils (= 2.96-5ubuntu1), tar (= 1.30+dfsg-7), ubuntu-keyring (= 2020.06.17.1), util-linux (= 2.36.1-1ubuntu1), xz-utils (= 5.2.4-1ubuntu1), zlib1g (= 1:1.2.11.dfsg-2ubuntu4), zlib1g-dev (= 1:1.2.11.dfsg-2ubuntu4) Environment: DEB_BUILD_OPTIONS="parallel=4" LANG="C.UTF-8" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1605418281" +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ libpbbam-dev_1.6.0+dfsg-2_amd64.deb ----------------------------------- new Debian package, version 2.0. size 75520 bytes: control archive=4328 bytes. 1137 bytes, 25 lines control 9232 bytes, 132 lines md5sums Package: libpbbam-dev Source: pbbam Version: 1.6.0+dfsg-2 Architecture: amd64 Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 592 Depends: libpbbam1.6.0 (= 1.6.0+dfsg-2), libhts-dev, libssl-dev Breaks: libpbbam (<< 0.18) Replaces: libpbbam (<< 0.18) Section: libdevel Priority: optional Homepage: http://pbbam.readthedocs.org/en/latest/index.html Description: Pacific Biosciences binary alignment/map (BAM) library (headers) The BAM format is a binary, compressed, record-oriented container format for raw or aligned sequence reads. The associated SAM format is a text representation of the same data. The specifications for BAM/SAM are maintained by the SAM/BAM Format Specification Working Group. . PacBio-produced BAM files are fully compatible with the BAM specification, but makes use of the extensibility mechanisms of the BAM specification to encode PacBio-specific information. The pbbam library provides tools to work with these files . This package contains the library header files. drwxr-xr-x root/root 0 2020-11-15 05:31 ./ drwxr-xr-x root/root 0 2020-11-15 05:31 ./usr/ drwxr-xr-x root/root 0 2020-11-15 05:31 ./usr/include/ drwxr-xr-x root/root 0 2020-11-15 05:31 ./usr/include/pbbam/ -rw-r--r-- root/root 274 2020-09-23 05:10 ./usr/include/pbbam/Accuracy.h -rw-r--r-- root/root 1567 2020-09-23 05:10 ./usr/include/pbbam/AlignmentPrinter.h -rw-r--r-- root/root 1468 2020-09-23 05:10 ./usr/include/pbbam/BaiIndexCache.h -rw-r--r-- root/root 3597 2020-09-23 05:10 ./usr/include/pbbam/BaiIndexedBamReader.h -rw-r--r-- root/root 5033 2020-09-23 05:10 ./usr/include/pbbam/BamFile.h -rw-r--r-- root/root 2701 2020-09-23 05:10 ./usr/include/pbbam/BamFileMerger.h -rw-r--r-- root/root 11306 2020-09-23 05:10 ./usr/include/pbbam/BamHeader.h -rw-r--r-- root/root 3894 2020-09-23 05:10 ./usr/include/pbbam/BamReader.h -rw-r--r-- root/root 49077 2020-09-23 05:10 ./usr/include/pbbam/BamRecord.h -rw-r--r-- root/root 21440 2020-09-23 05:10 ./usr/include/pbbam/BamRecordImpl.h -rw-r--r-- root/root 980 2020-09-23 05:10 ./usr/include/pbbam/BamRecordTag.h -rw-r--r-- root/root 4587 2020-09-23 05:10 ./usr/include/pbbam/BamRecordView.h -rw-r--r-- root/root 2623 2020-09-23 05:10 ./usr/include/pbbam/BamTagCodec.h -rw-r--r-- root/root 7695 2020-09-23 05:10 ./usr/include/pbbam/BamWriter.h -rw-r--r-- root/root 767 2020-09-23 05:10 ./usr/include/pbbam/BgzipFastaWriter.h -rw-r--r-- root/root 893 2020-09-23 05:10 ./usr/include/pbbam/BgzipFastqWriter.h -rw-r--r-- root/root 1965 2020-09-23 05:10 ./usr/include/pbbam/BgzipWriter.h -rw-r--r-- root/root 381 2020-09-23 05:10 ./usr/include/pbbam/Cigar.h -rw-r--r-- root/root 559 2020-09-23 05:10 ./usr/include/pbbam/CigarOperation.h -rw-r--r-- root/root 733 2020-09-23 05:10 ./usr/include/pbbam/ClipType.h -rw-r--r-- root/root 9065 2020-09-23 05:10 ./usr/include/pbbam/CollectionMetadata.h -rw-r--r-- root/root 14941 2020-09-23 05:10 ./usr/include/pbbam/Compare.h -rw-r--r-- root/root 9921 2020-09-23 05:10 ./usr/include/pbbam/CompositeBamReader.h -rw-r--r-- root/root 1276 2020-09-23 05:10 ./usr/include/pbbam/CompositeFastaReader.h -rw-r--r-- root/root 1107 2020-09-23 05:10 ./usr/include/pbbam/Config.h -rw-r--r-- root/root 25671 2020-09-23 05:10 ./usr/include/pbbam/DataSet.h -rw-r--r-- root/root 38577 2020-09-23 05:10 ./usr/include/pbbam/DataSetTypes.h -rw-r--r-- root/root 2564 2020-09-23 05:10 ./usr/include/pbbam/DataSetXsd.h -rw-r--r-- root/root 1519 2020-09-23 05:10 ./usr/include/pbbam/Deleters.h -rw-r--r-- root/root 1694 2020-09-23 05:10 ./usr/include/pbbam/EntireFileQuery.h -rw-r--r-- root/root 2250 2020-09-23 05:10 ./usr/include/pbbam/FaiIndex.h -rw-r--r-- root/root 2181 2020-09-23 05:10 ./usr/include/pbbam/FastaCache.h -rw-r--r-- root/root 1638 2020-09-23 05:10 ./usr/include/pbbam/FastaReader.h -rw-r--r-- root/root 1286 2020-09-23 05:10 ./usr/include/pbbam/FastaSequence.h -rw-r--r-- root/root 1003 2020-09-23 05:10 ./usr/include/pbbam/FastaSequenceQuery.h -rw-r--r-- root/root 664 2020-09-23 05:10 ./usr/include/pbbam/FastaWriter.h -rw-r--r-- root/root 1646 2020-09-23 05:10 ./usr/include/pbbam/FastqReader.h -rw-r--r-- root/root 1601 2020-09-23 05:10 ./usr/include/pbbam/FastqSequence.h -rw-r--r-- root/root 791 2020-09-23 05:10 ./usr/include/pbbam/FastqWriter.h -rw-r--r-- root/root 938 2020-09-23 05:10 ./usr/include/pbbam/FormatUtils.h -rw-r--r-- root/root 789 2020-09-23 05:10 ./usr/include/pbbam/FrameEncodingType.h -rw-r--r-- root/root 270 2020-09-23 05:10 ./usr/include/pbbam/Frames.h -rw-r--r-- root/root 316 2020-09-23 05:10 ./usr/include/pbbam/GenomicInterval.h -rw-r--r-- root/root 3009 2020-09-23 05:10 ./usr/include/pbbam/GenomicIntervalQuery.h -rw-r--r-- root/root 578 2020-09-23 05:10 ./usr/include/pbbam/IFastaWriter.h -rw-r--r-- root/root 763 2020-09-23 05:10 ./usr/include/pbbam/IFastqWriter.h -rw-r--r-- root/root 1238 2020-09-23 05:10 ./usr/include/pbbam/IRecordWriter.h -rw-r--r-- root/root 4860 2020-09-23 05:10 ./usr/include/pbbam/IndexedBamWriter.h -rw-r--r-- root/root 4159 2020-09-23 05:10 ./usr/include/pbbam/IndexedFastaReader.h -rw-r--r-- root/root 4084 2020-09-23 05:10 ./usr/include/pbbam/IndexedFastqReader.h -rw-r--r-- root/root 274 2020-09-23 05:10 ./usr/include/pbbam/Interval.h -rw-r--r-- root/root 655 2020-09-23 05:10 ./usr/include/pbbam/LibraryInfo.h -rw-r--r-- root/root 664 2020-09-23 05:10 ./usr/include/pbbam/LocalContextFlags.h -rw-r--r-- root/root 305 2020-09-23 05:10 ./usr/include/pbbam/MD5.h -rw-r--r-- root/root 1280 2020-09-23 05:10 ./usr/include/pbbam/MoveAppend.h -rw-r--r-- root/root 300 2020-09-23 05:10 ./usr/include/pbbam/Orientation.h -rw-r--r-- root/root 487 2020-09-23 05:10 ./usr/include/pbbam/PbbamVersion.h -rw-r--r-- root/root 2167 2020-09-23 05:10 ./usr/include/pbbam/PbiBasicTypes.h -rw-r--r-- root/root 6876 2020-09-23 05:10 ./usr/include/pbbam/PbiBuilder.h -rw-r--r-- root/root 2242 2020-09-23 05:10 ./usr/include/pbbam/PbiFile.h -rw-r--r-- root/root 7356 2020-09-23 05:10 ./usr/include/pbbam/PbiFilter.h -rw-r--r-- root/root 2182 2020-09-23 05:10 ./usr/include/pbbam/PbiFilterQuery.h -rw-r--r-- root/root 31026 2020-09-23 05:10 ./usr/include/pbbam/PbiFilterTypes.h -rw-r--r-- root/root 3595 2020-09-23 05:10 ./usr/include/pbbam/PbiIndexedBamReader.h -rw-r--r-- root/root 11553 2020-09-23 05:10 ./usr/include/pbbam/PbiRawData.h -rw-r--r-- root/root 689 2020-09-23 05:10 ./usr/include/pbbam/Position.h -rw-r--r-- root/root 4257 2020-09-23 05:10 ./usr/include/pbbam/ProgramInfo.h -rw-r--r-- root/root 455 2020-09-23 05:10 ./usr/include/pbbam/PulseBehavior.h -rw-r--r-- root/root 418 2020-09-23 05:10 ./usr/include/pbbam/PulseExclusionReason.h -rw-r--r-- root/root 306 2020-09-23 05:10 ./usr/include/pbbam/QualityValue.h -rw-r--r-- root/root 345 2020-09-23 05:10 ./usr/include/pbbam/QualityValues.h -rw-r--r-- root/root 23743 2020-11-15 05:31 ./usr/include/pbbam/ReadGroupInfo.h -rw-r--r-- root/root 1220 2020-09-23 05:10 ./usr/include/pbbam/RecordType.h -rw-r--r-- root/root 1374 2020-09-23 05:10 ./usr/include/pbbam/RunMetadata.h -rw-r--r-- root/root 320 2020-09-23 05:10 ./usr/include/pbbam/SNR.h -rw-r--r-- root/root 1558 2020-09-23 05:10 ./usr/include/pbbam/SamReader.h -rw-r--r-- root/root 1588 2020-09-23 05:10 ./usr/include/pbbam/SamTagCodec.h -rw-r--r-- root/root 2664 2020-09-23 05:10 ./usr/include/pbbam/SamWriter.h -rw-r--r-- root/root 4528 2020-09-23 05:10 ./usr/include/pbbam/SequenceInfo.h -rw-r--r-- root/root 270 2020-09-23 05:10 ./usr/include/pbbam/Strand.h -rw-r--r-- root/root 953 2020-09-23 05:10 ./usr/include/pbbam/StringUtilities.h -rw-r--r-- root/root 14239 2020-09-23 05:10 ./usr/include/pbbam/Tag.h -rw-r--r-- root/root 832 2020-09-23 05:10 ./usr/include/pbbam/TagCollection.h -rw-r--r-- root/root 1865 2020-09-23 05:10 ./usr/include/pbbam/TextFileReader.h -rw-r--r-- root/root 1171 2020-09-23 05:10 ./usr/include/pbbam/TextFileWriter.h -rw-r--r-- root/root 5512 2020-09-23 05:10 ./usr/include/pbbam/Validator.h -rw-r--r-- root/root 3449 2020-09-23 05:10 ./usr/include/pbbam/ZmwGroupQuery.h -rw-r--r-- root/root 1519 2020-09-23 05:10 ./usr/include/pbbam/ZmwQuery.h -rw-r--r-- root/root 364 2020-09-23 05:10 ./usr/include/pbbam/ZmwType.h -rw-r--r-- root/root 419 2020-09-23 05:10 ./usr/include/pbbam/ZmwTypeMap.h drwxr-xr-x root/root 0 2020-11-15 05:31 ./usr/include/pbbam/bed/ -rw-r--r-- root/root 1746 2020-09-23 05:10 ./usr/include/pbbam/bed/BedReader.h -rw-r--r-- root/root 589 2020-09-23 05:10 ./usr/include/pbbam/bed/BedWriter.h drwxr-xr-x root/root 0 2020-11-15 05:31 ./usr/include/pbbam/ccs/ -rw-r--r-- root/root 391 2020-09-23 05:10 ./usr/include/pbbam/ccs/CCSHeader.h -rw-r--r-- root/root 1253 2020-09-23 05:10 ./usr/include/pbbam/ccs/CCSPbiBuilder.h -rw-r--r-- root/root 918 2020-09-23 05:10 ./usr/include/pbbam/ccs/CCSRecord.h -rw-r--r-- root/root 669 2020-09-23 05:10 ./usr/include/pbbam/ccs/CCSRecordFormat.h -rw-r--r-- root/root 755 2020-09-23 05:10 ./usr/include/pbbam/ccs/CCSRecordReader.h -rw-r--r-- root/root 893 2020-09-23 05:10 ./usr/include/pbbam/ccs/CCSRecordWriter.h drwxr-xr-x root/root 0 2020-11-15 05:31 ./usr/include/pbbam/exception/ -rw-r--r-- root/root 1086 2020-09-23 05:10 ./usr/include/pbbam/exception/BundleChemistryMappingException.h -rw-r--r-- root/root 2040 2020-09-23 05:10 ./usr/include/pbbam/exception/InvalidSequencingChemistryException.h -rw-r--r-- root/root 1335 2020-09-23 05:10 ./usr/include/pbbam/exception/ValidationException.h drwxr-xr-x root/root 0 2020-11-15 05:31 ./usr/include/pbbam/internal/ -rw-r--r-- root/root 1130 2020-09-23 05:10 ./usr/include/pbbam/internal/Compare.inl -rw-r--r-- root/root 5591 2020-09-23 05:10 ./usr/include/pbbam/internal/CompositeBamReader.inl -rw-r--r-- root/root 5225 2020-09-23 05:10 ./usr/include/pbbam/internal/DataSetBaseTypes.h -rw-r--r-- root/root 5105 2020-09-23 05:10 ./usr/include/pbbam/internal/DataSetElement.h -rw-r--r-- root/root 11155 2020-09-23 05:10 ./usr/include/pbbam/internal/DataSetElement.inl -rw-r--r-- root/root 607 2020-09-23 05:10 ./usr/include/pbbam/internal/PbiBasicTypes.inl -rw-r--r-- root/root 5921 2020-09-23 05:10 ./usr/include/pbbam/internal/PbiFilter.inl -rw-r--r-- root/root 18413 2020-09-23 05:10 ./usr/include/pbbam/internal/PbiFilterTypes.inl -rw-r--r-- root/root 2495 2020-09-23 05:10 ./usr/include/pbbam/internal/QueryBase.h -rw-r--r-- root/root 2924 2020-09-23 05:10 ./usr/include/pbbam/internal/QueryBase.inl drwxr-xr-x root/root 0 2020-11-15 05:31 ./usr/include/pbbam/vcf/ -rw-r--r-- root/root 461 2020-09-23 05:10 ./usr/include/pbbam/vcf/VcfFile.h -rw-r--r-- root/root 2710 2020-09-23 05:10 ./usr/include/pbbam/vcf/VcfFormat.h -rw-r--r-- root/root 3283 2020-09-23 05:10 ./usr/include/pbbam/vcf/VcfHeader.h -rw-r--r-- root/root 3060 2020-09-23 05:10 ./usr/include/pbbam/vcf/VcfHeaderTypes.h -rw-r--r-- root/root 770 2020-09-23 05:10 ./usr/include/pbbam/vcf/VcfQuery.h -rw-r--r-- root/root 703 2020-09-23 05:10 ./usr/include/pbbam/vcf/VcfReader.h -rw-r--r-- root/root 552 2020-09-23 05:10 ./usr/include/pbbam/vcf/VcfSort.h -rw-r--r-- root/root 4174 2020-09-23 05:10 ./usr/include/pbbam/vcf/VcfVariant.h -rw-r--r-- root/root 631 2020-09-23 05:10 ./usr/include/pbbam/vcf/VcfWriter.h drwxr-xr-x root/root 0 2020-11-15 05:31 ./usr/include/pbbam/virtual/ -rw-r--r-- root/root 394 2020-09-23 05:10 ./usr/include/pbbam/virtual/VirtualPolymeraseBamRecord.h -rw-r--r-- root/root 406 2020-09-23 05:10 ./usr/include/pbbam/virtual/VirtualPolymeraseCompositeReader.h -rw-r--r-- root/root 370 2020-09-23 05:10 ./usr/include/pbbam/virtual/VirtualPolymeraseReader.h -rw-r--r-- root/root 1258 2020-09-23 05:10 ./usr/include/pbbam/virtual/VirtualRegion.h -rw-r--r-- root/root 622 2020-09-23 05:10 ./usr/include/pbbam/virtual/VirtualRegionType.h -rw-r--r-- root/root 507 2020-09-23 05:10 ./usr/include/pbbam/virtual/VirtualRegionTypeMap.h -rw-r--r-- root/root 2121 2020-09-23 05:10 ./usr/include/pbbam/virtual/VirtualZmwBamRecord.h -rw-r--r-- root/root 3202 2020-09-23 05:10 ./usr/include/pbbam/virtual/WhitelistedZmwReadStitcher.h -rw-r--r-- root/root 2116 2020-09-23 05:10 ./usr/include/pbbam/virtual/ZmwReadStitcher.h -rw-r--r-- root/root 411 2020-09-23 05:10 ./usr/include/pbbam/virtual/ZmwWhitelistVirtualReader.h drwxr-xr-x root/root 0 2020-11-15 05:31 ./usr/lib/ drwxr-xr-x root/root 0 2020-11-15 05:31 ./usr/lib/x86_64-linux-gnu/ lrwxrwxrwx root/root 0 2020-11-15 05:31 ./usr/lib/x86_64-linux-gnu/libpbbam.so -> libpbbam.so.1.6.0 drwxr-xr-x root/root 0 2020-11-15 05:31 ./usr/lib/x86_64-linux-gnu/pkgconfig/ -rw-r--r-- root/root 300 2020-11-15 05:31 ./usr/lib/x86_64-linux-gnu/pkgconfig/pbbam.pc drwxr-xr-x root/root 0 2020-11-15 05:31 ./usr/share/ drwxr-xr-x root/root 0 2020-11-15 05:31 ./usr/share/doc/ drwxr-xr-x root/root 0 2020-11-15 05:31 ./usr/share/doc/libpbbam-dev/ lrwxrwxrwx root/root 0 2020-11-15 05:31 ./usr/share/doc/libpbbam-dev/changelog.Debian.gz -> ../libpbbam1.6.0/changelog.Debian.gz -rw-r--r-- root/root 3463 2020-11-15 05:31 ./usr/share/doc/libpbbam-dev/copyright libpbbam1.6.0_1.6.0+dfsg-2_amd64.deb ------------------------------------ new Debian package, version 2.0. size 672660 bytes: control archive=1160 bytes. 1164 bytes, 24 lines control 231 bytes, 3 lines md5sums 45 bytes, 1 lines shlibs 74 bytes, 2 lines triggers Package: libpbbam1.6.0 Source: pbbam Version: 1.6.0+dfsg-2 Architecture: amd64 Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 2657 Depends: libc6 (>= 2.14), libgcc-s1 (>= 3.0), libhts3 (>= 1.10), libpbcopper1.8.0 (>= 1.8.0+dfsg), libstdc++6 (>= 9), zlib1g (>= 1:1.2.3.3) Breaks: libpbbam (<< 1.6.0+dfsg-2) Replaces: libpbbam Section: libs Priority: optional Multi-Arch: same Homepage: http://pbbam.readthedocs.org/en/latest/index.html Description: Pacific Biosciences binary alignment/map (BAM) library The BAM format is a binary, compressed, record-oriented container format for raw or aligned sequence reads. The associated SAM format is a text representation of the same data. The specifications for BAM/SAM are maintained by the SAM/BAM Format Specification Working Group. . PacBio-produced BAM files are fully compatible with the BAM specification, but makes use of the extensibility mechanisms of the BAM specification to encode PacBio-specific information. The pbbam library provides tools to work with these files drwxr-xr-x root/root 0 2020-11-15 05:31 ./ drwxr-xr-x root/root 0 2020-11-15 05:31 ./usr/ drwxr-xr-x root/root 0 2020-11-15 05:31 ./usr/lib/ drwxr-xr-x root/root 0 2020-11-15 05:31 ./usr/lib/x86_64-linux-gnu/ -rw-r--r-- root/root 2693312 2020-11-15 05:31 ./usr/lib/x86_64-linux-gnu/libpbbam.so.1.6.0 drwxr-xr-x root/root 0 2020-11-15 05:31 ./usr/share/ drwxr-xr-x root/root 0 2020-11-15 05:31 ./usr/share/doc/ drwxr-xr-x root/root 0 2020-11-15 05:31 ./usr/share/doc/libpbbam1.6.0/ -rw-r--r-- root/root 1370 2020-11-15 05:31 ./usr/share/doc/libpbbam1.6.0/changelog.Debian.gz -rw-r--r-- root/root 3463 2020-11-15 05:31 ./usr/share/doc/libpbbam1.6.0/copyright pbbamtools_1.6.0+dfsg-2_amd64.deb --------------------------------- new Debian package, version 2.0. size 82116 bytes: control archive=1168 bytes. 1153 bytes, 24 lines control 462 bytes, 8 lines md5sums Package: pbbamtools Source: pbbam Version: 1.6.0+dfsg-2 Architecture: amd64 Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 370 Depends: libc6 (>= 2.14), libgcc-s1 (>= 3.0), libhts3 (>= 1.10), libpbbam1.6.0 (= 1.6.0+dfsg-2), libpbcopper1.8.0 (>= 1.8.0+dfsg), libstdc++6 (>= 5.2) Recommends: samtools Section: science Priority: optional Homepage: http://pbbam.readthedocs.org/en/latest/index.html Description: processing Pacific Biosciences binary alignment/map files The BAM format is a binary, compressed, record-oriented container format for raw or aligned sequence reads. The associated SAM format is a text representation of the same data. The specifications for BAM/SAM are maintained by the SAM/BAM Format Specification Working Group. . PacBio-produced BAM files are fully compatible with the BAM specification, but makes use of the extensibility mechanisms of the BAM specification to encode PacBio-specific information. . This package provides command-line utilities for working with PacBio BAM files. drwxr-xr-x root/root 0 2020-11-15 05:31 ./ drwxr-xr-x root/root 0 2020-11-15 05:31 ./usr/ drwxr-xr-x root/root 0 2020-11-15 05:31 ./usr/bin/ -rwxr-xr-x root/root 27112 2020-11-15 05:31 ./usr/bin/bam2sam -rwxr-xr-x root/root 63976 2020-11-15 05:31 ./usr/bin/ccs-kinetics-bystrandify -rwxr-xr-x root/root 84456 2020-11-15 05:31 ./usr/bin/pbbamify -rwxr-xr-x root/root 23016 2020-11-15 05:31 ./usr/bin/pbindex -rwxr-xr-x root/root 117224 2020-11-15 05:31 ./usr/bin/pbindexdump -rwxr-xr-x root/root 35304 2020-11-15 05:31 ./usr/bin/pbmerge drwxr-xr-x root/root 0 2020-11-15 05:31 ./usr/share/ drwxr-xr-x root/root 0 2020-11-15 05:31 ./usr/share/doc/ drwxr-xr-x root/root 0 2020-11-15 05:31 ./usr/share/doc/pbbamtools/ -rw-r--r-- root/root 97 2020-11-15 05:31 ./usr/share/doc/pbbamtools/TODO.Debian lrwxrwxrwx root/root 0 2020-11-15 05:31 ./usr/share/doc/pbbamtools/changelog.Debian.gz -> ../libpbbam1.6.0/changelog.Debian.gz -rw-r--r-- root/root 3463 2020-11-15 05:31 ./usr/share/doc/pbbamtools/copyright +------------------------------------------------------------------------------+ | Post Build | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not removing build depends: as requested +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: amd64 Build Type: binary Build-Space: n/a Build-Time: 956 Distribution: hirsute-proposed Host Architecture: amd64 Install-Time: 36 Job: pbbam_1.6.0+dfsg-2.dsc Machine Architecture: amd64 Package: pbbam Package-Time: 994 Source-Version: 1.6.0+dfsg-2 Space: n/a Status: successful Version: 1.6.0+dfsg-2 -------------------------------------------------------------------------------- Finished at 2020-11-19T11:51:16Z Build needed 00:16:34, no disk space RUN: /usr/share/launchpad-buildd/bin/in-target scan-for-processes --backend=chroot --series=hirsute --arch=amd64 PACKAGEBUILD-20314170 Scanning for processes to kill in build PACKAGEBUILD-20314170