https://launchpad.net/ubuntu/+source/pbbam/2.4.0+dfsg-1build1/+build/27789649 RUN: /usr/share/launchpad-buildd/bin/builder-prep Kernel version: Linux lcy02-amd64-083 5.4.0-171-generic #189-Ubuntu SMP Fri Jan 5 14:23:02 UTC 2024 x86_64 Buildd toolchain package versions: launchpad-buildd_235~645~ubuntu20.04.1 python3-lpbuildd_235~645~ubuntu20.04.1 sbuild_0.79.0-1ubuntu1 git-build-recipe_0.3.6 git_1:2.25.1-1ubuntu3.11 dpkg-dev_1.19.7ubuntu3.2 python3-debian_0.1.36ubuntu1.1. Syncing the system clock with the buildd NTP service... 18 Feb 18:23:43 ntpdate[1930]: adjust time server 10.131.248.1 offset 0.007129 sec RUN: /usr/share/launchpad-buildd/bin/in-target unpack-chroot --backend=chroot --series=noble --arch=amd64 PACKAGEBUILD-27789649 --image-type chroot /home/buildd/filecache-default/1fe94ca8758119221c8de2550665a1bb335bd6a9 Creating target for build PACKAGEBUILD-27789649 RUN: /usr/share/launchpad-buildd/bin/in-target mount-chroot --backend=chroot --series=noble --arch=amd64 PACKAGEBUILD-27789649 Starting target for build PACKAGEBUILD-27789649 RUN: /usr/share/launchpad-buildd/bin/in-target override-sources-list --backend=chroot --series=noble --arch=amd64 PACKAGEBUILD-27789649 'deb http://ftpmaster.internal/ubuntu noble main universe' 'deb http://ftpmaster.internal/ubuntu noble-security main universe' 'deb http://ftpmaster.internal/ubuntu noble-updates main universe' 'deb http://ftpmaster.internal/ubuntu noble-proposed main universe' Overriding sources.list in build-PACKAGEBUILD-27789649 RUN: /usr/share/launchpad-buildd/bin/in-target update-debian-chroot --backend=chroot --series=noble --arch=amd64 PACKAGEBUILD-27789649 Updating target for build PACKAGEBUILD-27789649 Get:1 http://ftpmaster.internal/ubuntu noble InRelease [255 kB] Get:2 http://ftpmaster.internal/ubuntu noble-security InRelease [90.7 kB] Get:3 http://ftpmaster.internal/ubuntu noble-updates InRelease [90.7 kB] Get:4 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] Get:5 http://ftpmaster.internal/ubuntu noble/main amd64 Packages [1435 kB] Get:6 http://ftpmaster.internal/ubuntu noble/main Translation-en [519 kB] Get:7 http://ftpmaster.internal/ubuntu noble/universe amd64 Packages [15.1 MB] Get:8 http://ftpmaster.internal/ubuntu noble/universe Translation-en [6029 kB] Get:9 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 Packages [229 kB] Get:10 http://ftpmaster.internal/ubuntu noble-proposed/main Translation-en [69.3 kB] Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe amd64 Packages [981 kB] Get:12 http://ftpmaster.internal/ubuntu noble-proposed/universe Translation-en [391 kB] Fetched 25.3 MB in 3s (9592 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: libperl5.36 libunistring2 perl-modules-5.36 Use 'sudo apt autoremove' to remove them. The following NEW packages will be installed: cpp-13-x86-64-linux-gnu cpp-x86-64-linux-gnu g++-13-x86-64-linux-gnu g++-x86-64-linux-gnu gcc-13-x86-64-linux-gnu gcc-14-base gcc-x86-64-linux-gnu libperl5.38 libunistring5 perl-modules-5.38 The following packages will be upgraded: apt apt-utils base-files base-passwd bash bash-completion binutils binutils-common binutils-x86-64-linux-gnu bsdextrautils bsdutils ca-certificates coreutils cpp cpp-13 debconf debconf-i18n debianutils diffutils dpkg dpkg-dev fakeroot g++ g++-13 gcc gcc-13 gcc-13-base gpg gpg-agent gpgconf gpgv grep init init-system-helpers krb5-locales libacl1 libapparmor1 libapt-pkg6.0 libargon2-1 libasan8 libatomic1 libattr1 libaudit-common libaudit1 libbinutils libblkid1 libc-bin libc-dev-bin libc6 libc6-dev libcap-ng0 libcc1-0 libcrypt-dev libcrypt1 libcryptsetup12 libctf-nobfd0 libctf0 libdb5.3 libdebconfclient0 libdpkg-perl libfakeroot libfdisk1 libffi8 libgcc-13-dev libgcc-s1 libgcrypt20 libgdbm-compat4 libgdbm6 libgnutls30 libgomp1 libgpg-error-l10n libgpg-error0 libgprofng0 libgssapi-krb5-2 libhwasan0 libidn2-0 libip4tc2 libitm1 libk5crypto3 libkeyutils1 libkmod2 libkrb5-3 libkrb5support0 liblocale-gettext-perl liblsan0 liblzma5 libmd0 libmount1 libncursesw6 libnsl-dev libnsl2 libp11-kit0 libpam-modules libpam-modules-bin libpam-runtime libpam0g libpcre2-8-0 libperl5.36 libpng16-16 libproc2-0 libquadmath0 libreadline8 libseccomp2 libselinux1 libsemanage-common libsemanage2 libsepol2 libsframe1 libsmartcols1 libsqlite3-0 libssl3 libstdc++-13-dev libstdc++6 libsystemd-shared libsystemd0 libtext-charwidth-perl libtext-iconv-perl libtinfo6 libtirpc-common libtirpc-dev libtirpc3 libtsan2 libubsan1 libudev1 libuuid1 libxxhash0 libzstd1 linux-libc-dev login lto-disabled-list mawk mount ncurses-base ncurses-bin openssl optipng passwd perl perl-base perl-modules-5.36 pinentry-curses procps psmisc readline-common sed sensible-utils systemd systemd-dev systemd-sysv sysvinit-utils tar tzdata ubuntu-keyring util-linux uuid-runtime xz-utils zlib1g 157 upgraded, 10 newly installed, 0 to remove and 0 not upgraded. Need to get 125 MB of archives. After this operation, 78.0 MB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu noble/main amd64 libnsl-dev amd64 1.3.0-3 [71.2 kB] Get:2 http://ftpmaster.internal/ubuntu noble/main amd64 libcrypt-dev amd64 1:4.4.36-4 [128 kB] Get:3 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libc6-dev amd64 2.39-0ubuntu1 [2126 kB] Get:4 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libc-dev-bin amd64 2.39-0ubuntu1 [20.4 kB] Get:5 http://ftpmaster.internal/ubuntu noble/main amd64 libtirpc-common all 1.3.4+ds-1build1 [8566 B] Get:6 http://ftpmaster.internal/ubuntu noble/main amd64 libtirpc-dev amd64 1.3.4+ds-1build1 [222 kB] Get:7 http://ftpmaster.internal/ubuntu noble/main amd64 libgssapi-krb5-2 amd64 1.20.1-5build1 [142 kB] Get:8 http://ftpmaster.internal/ubuntu noble/main amd64 libkrb5-3 amd64 1.20.1-5build1 [346 kB] Get:9 http://ftpmaster.internal/ubuntu noble/main amd64 libk5crypto3 amd64 1.20.1-5build1 [81.3 kB] Get:10 http://ftpmaster.internal/ubuntu noble/main amd64 libkrb5support0 amd64 1.20.1-5build1 [33.2 kB] Get:11 http://ftpmaster.internal/ubuntu noble/main amd64 libkeyutils1 amd64 1.6.3-3 [9386 B] Get:12 http://ftpmaster.internal/ubuntu noble/main amd64 libssl3 amd64 3.0.10-1ubuntu4 [1909 kB] Get:13 http://ftpmaster.internal/ubuntu noble/main amd64 libtirpc3 amd64 1.3.4+ds-1build1 [95.7 kB] Get:14 http://ftpmaster.internal/ubuntu noble/main amd64 libnsl2 amd64 1.3.0-3 [41.3 kB] Get:15 http://ftpmaster.internal/ubuntu noble/main amd64 libcrypt1 amd64 1:4.4.36-4 [95.3 kB] Get:16 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 linux-libc-dev amd64 6.8.0-11.11 [1595 kB] Get:17 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libc6 amd64 2.39-0ubuntu1 [3261 kB] Get:18 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libc-bin amd64 2.39-0ubuntu1 [679 kB] Get:19 http://ftpmaster.internal/ubuntu noble/main amd64 gcc-14-base amd64 14-20240201-3ubuntu1 [46.4 kB] Get:20 http://ftpmaster.internal/ubuntu noble/main amd64 libgcc-s1 amd64 14-20240201-3ubuntu1 [77.5 kB] Get:21 http://ftpmaster.internal/ubuntu noble/main amd64 base-files amd64 13ubuntu6 [84.5 kB] Get:22 http://ftpmaster.internal/ubuntu noble/main amd64 debianutils amd64 5.16 [93.9 kB] Get:23 http://ftpmaster.internal/ubuntu noble/main amd64 bash amd64 5.2.21-2ubuntu1 [795 kB] Get:24 http://ftpmaster.internal/ubuntu noble/main amd64 bsdutils amd64 1:2.39.2-6ubuntu1 [93.9 kB] Get:25 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 coreutils amd64 9.4-2ubuntu3 [1412 kB] Get:26 http://ftpmaster.internal/ubuntu noble/main amd64 diffutils amd64 1:3.10-1 [176 kB] Get:27 http://ftpmaster.internal/ubuntu noble/main amd64 libgpg-error-l10n all 1.47-3build1 [8024 B] Get:28 http://ftpmaster.internal/ubuntu noble/main amd64 libgpg-error0 amd64 1.47-3build1 [70.0 kB] Get:29 http://ftpmaster.internal/ubuntu noble/main amd64 libgcrypt20 amd64 1.10.3-2 [532 kB] Get:30 http://ftpmaster.internal/ubuntu noble/main amd64 liblzma5 amd64 5.4.5-0.3 [141 kB] Get:31 http://ftpmaster.internal/ubuntu noble/main amd64 libstdc++6 amd64 14-20240201-3ubuntu1 [795 kB] Get:32 http://ftpmaster.internal/ubuntu noble/main amd64 libacl1 amd64 2.3.1-4ubuntu1 [18.6 kB] Get:33 http://ftpmaster.internal/ubuntu noble/main amd64 libapparmor1 amd64 4.0.0~alpha4-0ubuntu1 [49.0 kB] Get:34 http://ftpmaster.internal/ubuntu noble/main amd64 libaudit-common all 1:3.1.2-2 [5594 B] Get:35 http://ftpmaster.internal/ubuntu noble/main amd64 libcap-ng0 amd64 0.8.4-2 [15.0 kB] Get:36 http://ftpmaster.internal/ubuntu noble/main amd64 libaudit1 amd64 1:3.1.2-2 [46.7 kB] Get:37 http://ftpmaster.internal/ubuntu noble/main amd64 libblkid1 amd64 2.39.2-6ubuntu1 [122 kB] Get:38 http://ftpmaster.internal/ubuntu noble/main amd64 libzstd1 amd64 1.5.5+dfsg2-2 [297 kB] Get:39 http://ftpmaster.internal/ubuntu noble/main amd64 libkmod2 amd64 30+20230601-2ubuntu1 [51.4 kB] Get:40 http://ftpmaster.internal/ubuntu noble/main amd64 libpcre2-8-0 amd64 10.42-4ubuntu1 [228 kB] Get:41 http://ftpmaster.internal/ubuntu noble/main amd64 libselinux1 amd64 3.5-2build1 [79.2 kB] Get:42 http://ftpmaster.internal/ubuntu noble/main amd64 libmount1 amd64 2.39.2-6ubuntu1 [132 kB] Get:43 http://ftpmaster.internal/ubuntu noble/main amd64 perl-modules-5.38 all 5.38.2-3 [3110 kB] Get:44 http://ftpmaster.internal/ubuntu noble/main amd64 libperl5.38 amd64 5.38.2-3 [4871 kB] Get:45 http://ftpmaster.internal/ubuntu noble/main amd64 perl amd64 5.38.2-3 [231 kB] Get:46 http://ftpmaster.internal/ubuntu noble/main amd64 perl-base amd64 5.38.2-3 [1823 kB] Get:47 http://ftpmaster.internal/ubuntu noble/main amd64 liblocale-gettext-perl amd64 1.07-6build1 [15.5 kB] Get:48 http://ftpmaster.internal/ubuntu noble/main amd64 libtext-iconv-perl amd64 1.7-8build1 [13.4 kB] Get:49 http://ftpmaster.internal/ubuntu noble/main amd64 libtext-charwidth-perl amd64 0.04-11build1 [9266 B] Get:50 http://ftpmaster.internal/ubuntu noble/main amd64 perl-modules-5.36 all 5.36.0-10ubuntu1 [2984 kB] Get:51 http://ftpmaster.internal/ubuntu noble/main amd64 libperl5.36 amd64 5.36.0-10ubuntu1 [4782 kB] Get:52 http://ftpmaster.internal/ubuntu noble/main amd64 libdb5.3 amd64 5.3.28+dfsg2-4 [736 kB] Get:53 http://ftpmaster.internal/ubuntu noble/main amd64 libgdbm6 amd64 1.23-5 [33.3 kB] Get:54 http://ftpmaster.internal/ubuntu noble/main amd64 libgdbm-compat4 amd64 1.23-5 [6498 B] Get:55 http://ftpmaster.internal/ubuntu noble/main amd64 zlib1g amd64 1:1.3.dfsg-3ubuntu1 [63.3 kB] Get:56 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 debconf-i18n all 1.5.86 [205 kB] Get:57 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 debconf all 1.5.86 [124 kB] Get:58 http://ftpmaster.internal/ubuntu noble/main amd64 libpam0g amd64 1.5.2-9.1ubuntu2 [65.7 kB] Get:59 http://ftpmaster.internal/ubuntu noble/main amd64 libseccomp2 amd64 2.5.5-1ubuntu1 [50.3 kB] Get:60 http://ftpmaster.internal/ubuntu noble/main amd64 systemd-sysv amd64 255.2-3ubuntu2 [11.9 kB] Get:61 http://ftpmaster.internal/ubuntu noble/main amd64 systemd-dev all 255.2-3ubuntu2 [101 kB] Get:62 http://ftpmaster.internal/ubuntu noble/main amd64 systemd amd64 255.2-3ubuntu2 [3466 kB] Get:63 http://ftpmaster.internal/ubuntu noble/main amd64 libsystemd-shared amd64 255.2-3ubuntu2 [2064 kB] Get:64 http://ftpmaster.internal/ubuntu noble/main amd64 libargon2-1 amd64 0~20190702+dfsg-4 [21.4 kB] Get:65 http://ftpmaster.internal/ubuntu noble/main amd64 libuuid1 amd64 2.39.2-6ubuntu1 [34.1 kB] Get:66 http://ftpmaster.internal/ubuntu noble/main amd64 libcryptsetup12 amd64 2:2.6.1-6ubuntu1 [242 kB] Get:67 http://ftpmaster.internal/ubuntu noble/main amd64 libfdisk1 amd64 2.39.2-6ubuntu1 [145 kB] Get:68 http://ftpmaster.internal/ubuntu noble/main amd64 mount amd64 2.39.2-6ubuntu1 [118 kB] Get:69 http://ftpmaster.internal/ubuntu noble/main amd64 libsystemd0 amd64 255.2-3ubuntu2 [426 kB] Get:70 http://ftpmaster.internal/ubuntu noble/main amd64 libudev1 amd64 255.2-3ubuntu2 [172 kB] Get:71 http://ftpmaster.internal/ubuntu noble/main amd64 libxxhash0 amd64 0.8.2-2 [25.5 kB] Get:72 http://ftpmaster.internal/ubuntu noble/main amd64 libapt-pkg6.0 amd64 2.7.11 [981 kB] Get:73 http://ftpmaster.internal/ubuntu noble/main amd64 tar amd64 1.35+dfsg-3 [253 kB] Get:74 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 dpkg amd64 1.22.4ubuntu3 [1285 kB] Get:75 http://ftpmaster.internal/ubuntu noble/main amd64 grep amd64 3.11-4 [176 kB] Get:76 http://ftpmaster.internal/ubuntu noble/main amd64 login amd64 1:4.13+dfsg1-3ubuntu1 [201 kB] Get:77 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 ncurses-bin amd64 6.4+20240113-1ubuntu1 [188 kB] Get:78 http://ftpmaster.internal/ubuntu noble/main amd64 sed amd64 4.9-2 [204 kB] Get:79 http://ftpmaster.internal/ubuntu noble/main amd64 util-linux amd64 2.39.2-6ubuntu1 [1120 kB] Get:80 http://ftpmaster.internal/ubuntu noble/main amd64 libdebconfclient0 amd64 0.271ubuntu1 [11.3 kB] Get:81 http://ftpmaster.internal/ubuntu noble/main amd64 base-passwd amd64 3.6.3 [51.2 kB] Get:82 http://ftpmaster.internal/ubuntu noble/main amd64 init-system-helpers all 1.66ubuntu1 [39.4 kB] Get:83 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 ncurses-base all 6.4+20240113-1ubuntu1 [25.4 kB] Get:84 http://ftpmaster.internal/ubuntu noble/main amd64 sysvinit-utils amd64 3.08-3ubuntu1 [33.7 kB] Get:85 http://ftpmaster.internal/ubuntu noble/main amd64 apt amd64 2.7.11 [1372 kB] Get:86 http://ftpmaster.internal/ubuntu noble/main amd64 apt-utils amd64 2.7.11 [217 kB] Get:87 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 gpgv amd64 2.4.4-2ubuntu3 [156 kB] Get:88 http://ftpmaster.internal/ubuntu noble/main amd64 ubuntu-keyring all 2023.11.28.1 [11.1 kB] Get:89 http://ftpmaster.internal/ubuntu noble/main amd64 libffi8 amd64 3.4.4-2 [24.4 kB] Get:90 http://ftpmaster.internal/ubuntu noble/main amd64 libp11-kit0 amd64 0.25.3-4ubuntu1 [299 kB] Get:91 http://ftpmaster.internal/ubuntu noble/main amd64 libunistring5 amd64 1.1-2 [537 kB] Get:92 http://ftpmaster.internal/ubuntu noble/main amd64 libidn2-0 amd64 2.3.7-2 [66.0 kB] Get:93 http://ftpmaster.internal/ubuntu noble/main amd64 libgnutls30 amd64 3.8.3-1ubuntu1 [996 kB] Get:94 http://ftpmaster.internal/ubuntu noble/main amd64 libpam-modules-bin amd64 1.5.2-9.1ubuntu2 [48.3 kB] Get:95 http://ftpmaster.internal/ubuntu noble/main amd64 libpam-modules amd64 1.5.2-9.1ubuntu2 [285 kB] Get:96 http://ftpmaster.internal/ubuntu noble/main amd64 init amd64 1.66ubuntu1 [6186 B] Get:97 http://ftpmaster.internal/ubuntu noble/main amd64 libsmartcols1 amd64 2.39.2-6ubuntu1 [63.3 kB] Get:98 http://ftpmaster.internal/ubuntu noble/main amd64 uuid-runtime amd64 2.39.2-6ubuntu1 [32.9 kB] Get:99 http://ftpmaster.internal/ubuntu noble/main amd64 libattr1 amd64 1:2.5.2-1 [11.4 kB] Get:100 http://ftpmaster.internal/ubuntu noble/main amd64 libmd0 amd64 1.1.0-2 [27.1 kB] Get:101 http://ftpmaster.internal/ubuntu noble/main amd64 libpam-runtime all 1.5.2-9.1ubuntu2 [40.6 kB] Get:102 http://ftpmaster.internal/ubuntu noble/main amd64 libsemanage-common all 3.5-1build2 [10.0 kB] Get:103 http://ftpmaster.internal/ubuntu noble/main amd64 libsepol2 amd64 3.5-2 [300 kB] Get:104 http://ftpmaster.internal/ubuntu noble/main amd64 libsemanage2 amd64 3.5-1build2 [92.9 kB] Get:105 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libncursesw6 amd64 6.4+20240113-1ubuntu1 [148 kB] Get:106 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libtinfo6 amd64 6.4+20240113-1ubuntu1 [108 kB] Get:107 http://ftpmaster.internal/ubuntu noble/main amd64 passwd amd64 1:4.13+dfsg1-3ubuntu1 [844 kB] Get:108 http://ftpmaster.internal/ubuntu noble/main amd64 g++-13 amd64 13.2.0-13ubuntu1 [14.0 kB] Get:109 http://ftpmaster.internal/ubuntu noble/main amd64 gcc-13 amd64 13.2.0-13ubuntu1 [473 kB] Get:110 http://ftpmaster.internal/ubuntu noble/main amd64 cpp-13 amd64 13.2.0-13ubuntu1 [1032 B] Get:111 http://ftpmaster.internal/ubuntu noble/main amd64 cpp-13-x86-64-linux-gnu amd64 13.2.0-13ubuntu1 [11.2 MB] Get:112 http://ftpmaster.internal/ubuntu noble/main amd64 libcc1-0 amd64 14-20240201-3ubuntu1 [47.5 kB] Get:113 http://ftpmaster.internal/ubuntu noble/main amd64 libgprofng0 amd64 2.42-2ubuntu1 [851 kB] Get:114 http://ftpmaster.internal/ubuntu noble/main amd64 libctf0 amd64 2.42-2ubuntu1 [94.6 kB] Get:115 http://ftpmaster.internal/ubuntu noble/main amd64 libctf-nobfd0 amd64 2.42-2ubuntu1 [96.8 kB] Get:116 http://ftpmaster.internal/ubuntu noble/main amd64 libsframe1 amd64 2.42-2ubuntu1 [14.5 kB] Get:117 http://ftpmaster.internal/ubuntu noble/main amd64 binutils-x86-64-linux-gnu amd64 2.42-2ubuntu1 [2467 kB] Get:118 http://ftpmaster.internal/ubuntu noble/main amd64 libbinutils amd64 2.42-2ubuntu1 [571 kB] Get:119 http://ftpmaster.internal/ubuntu noble/main amd64 binutils amd64 2.42-2ubuntu1 [18.1 kB] Get:120 http://ftpmaster.internal/ubuntu noble/main amd64 binutils-common amd64 2.42-2ubuntu1 [239 kB] Get:121 http://ftpmaster.internal/ubuntu noble/main amd64 libstdc++-13-dev amd64 13.2.0-13ubuntu1 [2337 kB] Get:122 http://ftpmaster.internal/ubuntu noble/main amd64 libgomp1 amd64 14-20240201-3ubuntu1 [147 kB] Get:123 http://ftpmaster.internal/ubuntu noble/main amd64 libitm1 amd64 14-20240201-3ubuntu1 [29.1 kB] Get:124 http://ftpmaster.internal/ubuntu noble/main amd64 libatomic1 amd64 14-20240201-3ubuntu1 [10.5 kB] Get:125 http://ftpmaster.internal/ubuntu noble/main amd64 libasan8 amd64 14-20240201-3ubuntu1 [3026 kB] Get:126 http://ftpmaster.internal/ubuntu noble/main amd64 liblsan0 amd64 14-20240201-3ubuntu1 [1309 kB] Get:127 http://ftpmaster.internal/ubuntu noble/main amd64 libgcc-13-dev amd64 13.2.0-13ubuntu1 [2687 kB] Get:128 http://ftpmaster.internal/ubuntu noble/main amd64 libtsan2 amd64 14-20240201-3ubuntu1 [2731 kB] Get:129 http://ftpmaster.internal/ubuntu noble/main amd64 libubsan1 amd64 14-20240201-3ubuntu1 [1171 kB] Get:130 http://ftpmaster.internal/ubuntu noble/main amd64 libhwasan0 amd64 14-20240201-3ubuntu1 [1629 kB] Get:131 http://ftpmaster.internal/ubuntu noble/main amd64 libquadmath0 amd64 14-20240201-3ubuntu1 [155 kB] Get:132 http://ftpmaster.internal/ubuntu noble/main amd64 gcc-13-x86-64-linux-gnu amd64 13.2.0-13ubuntu1 [21.8 MB] Get:133 http://ftpmaster.internal/ubuntu noble/main amd64 g++-13-x86-64-linux-gnu amd64 13.2.0-13ubuntu1 [12.5 MB] Get:134 http://ftpmaster.internal/ubuntu noble/main amd64 gcc-13-base amd64 13.2.0-13ubuntu1 [46.6 kB] Get:135 http://ftpmaster.internal/ubuntu noble/main amd64 libproc2-0 amd64 2:4.0.4-2ubuntu1 [59.0 kB] Get:136 http://ftpmaster.internal/ubuntu noble/main amd64 mawk amd64 1.3.4.20240123-1 [127 kB] Get:137 http://ftpmaster.internal/ubuntu noble/main amd64 procps amd64 2:4.0.4-2ubuntu1 [708 kB] Get:138 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 sensible-utils all 0.0.22 [22.5 kB] Get:139 http://ftpmaster.internal/ubuntu noble/main amd64 openssl amd64 3.0.10-1ubuntu4 [1002 kB] Get:140 http://ftpmaster.internal/ubuntu noble/main amd64 ca-certificates all 20240203 [159 kB] Get:141 http://ftpmaster.internal/ubuntu noble/main amd64 krb5-locales all 1.20.1-5build1 [13.7 kB] Get:142 http://ftpmaster.internal/ubuntu noble/main amd64 libip4tc2 amd64 1.8.10-3ubuntu1 [23.3 kB] Get:143 http://ftpmaster.internal/ubuntu noble/main amd64 readline-common all 8.2-3 [56.2 kB] Get:144 http://ftpmaster.internal/ubuntu noble/main amd64 libreadline8 amd64 8.2-3 [152 kB] Get:145 http://ftpmaster.internal/ubuntu noble/main amd64 libsqlite3-0 amd64 3.45.1-1 [701 kB] Get:146 http://ftpmaster.internal/ubuntu noble/main amd64 tzdata all 2024a-1ubuntu1 [273 kB] Get:147 http://ftpmaster.internal/ubuntu noble/main amd64 bash-completion all 1:2.11-8 [180 kB] Get:148 http://ftpmaster.internal/ubuntu noble/main amd64 bsdextrautils amd64 2.39.2-6ubuntu1 [73.5 kB] Get:149 http://ftpmaster.internal/ubuntu noble/main amd64 libpng16-16 amd64 1.6.42-1 [186 kB] Get:150 http://ftpmaster.internal/ubuntu noble/main amd64 psmisc amd64 23.6-2 [178 kB] Get:151 http://ftpmaster.internal/ubuntu noble/main amd64 xz-utils amd64 5.4.5-0.3 [276 kB] Get:152 http://ftpmaster.internal/ubuntu noble/main amd64 g++ amd64 4:13.2.0-7ubuntu1 [1100 B] Get:153 http://ftpmaster.internal/ubuntu noble/main amd64 gcc amd64 4:13.2.0-7ubuntu1 [5018 B] Get:154 http://ftpmaster.internal/ubuntu noble/main amd64 cpp amd64 4:13.2.0-7ubuntu1 [22.4 kB] Get:155 http://ftpmaster.internal/ubuntu noble/main amd64 cpp-x86-64-linux-gnu amd64 4:13.2.0-7ubuntu1 [5326 B] Get:156 http://ftpmaster.internal/ubuntu noble/main amd64 gcc-x86-64-linux-gnu amd64 4:13.2.0-7ubuntu1 [1212 B] Get:157 http://ftpmaster.internal/ubuntu noble/main amd64 g++-x86-64-linux-gnu amd64 4:13.2.0-7ubuntu1 [964 B] Get:158 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 dpkg-dev all 1.22.4ubuntu3 [1078 kB] Get:159 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libdpkg-perl all 1.22.4ubuntu3 [268 kB] Get:160 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Current default time zone: 'Etc/UTC' Local time is now: Sun Feb 18 18:24:05 UTC 2024. Universal Time is now: Sun Feb 18 18:24:05 UTC 2024. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up fakeroot (1.33-1) ... Setting up perl-modules-5.36 (5.36.0-10ubuntu1) ... Setting up gcc-13-base:amd64 (13.2.0-13ubuntu1) ... Setting up bash-completion (1:2.11-8) ... Setting up xz-utils (5.4.5-0.3) ... Setting up perl-modules-5.38 (5.38.2-3) ... Setting up libquadmath0:amd64 (14-20240201-3ubuntu1) ... Setting up libproc2-0:amd64 (2:4.0.4-2ubuntu1) ... Setting up libpng16-16:amd64 (1.6.42-1) ... Setting up libatomic1:amd64 (14-20240201-3ubuntu1) ... Setting up libncursesw6:amd64 (6.4+20240113-1ubuntu1) ... Setting up libk5crypto3:amd64 (1.20.1-5build1) ... Setting up libubsan1:amd64 (14-20240201-3ubuntu1) ... Setting up sensible-utils (0.0.22) ... Setting up uuid-runtime (2.39.2-6ubuntu1) ... Running in chroot, ignoring request. invoke-rc.d: policy-rc.d denied execution of restart. 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Setting up cpp-13-x86-64-linux-gnu (13.2.0-13ubuntu1) ... Setting up libreadline8:amd64 (8.2-3) ... Setting up debconf-i18n (1.5.86) ... Setting up ca-certificates (20240203) ... Updating certificates in /etc/ssl/certs... rehash: warning: skipping ca-certificates.crt,it does not contain exactly one certificate or CRL 14 added, 5 removed; done. Setting up libgprofng0:amd64 (2.42-2ubuntu1) ... Setting up optipng (0.7.8+ds-1) ... Setting up libgssapi-krb5-2:amd64 (1.20.1-5build1) ... Setting up libgdbm-compat4:amd64 (1.23-5) ... Setting up libgcc-13-dev:amd64 (13.2.0-13ubuntu1) ... Setting up gpgconf (2.4.4-2ubuntu3) ... Setting up libperl5.36:amd64 (5.36.0-10ubuntu1) ... Setting up gpg (2.4.4-2ubuntu3) ... Setting up binutils-x86-64-linux-gnu (2.42-2ubuntu1) ... Setting up cpp-x86-64-linux-gnu (4:13.2.0-7ubuntu1) ... Setting up libtirpc3:amd64 (1.3.4+ds-1build1) ... Setting up gpg-agent (2.4.4-2ubuntu3) ... Setting up cpp-13 (13.2.0-13ubuntu1) ... 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Processing triggers for ca-certificates (20240203) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. RUN: /usr/share/launchpad-buildd/bin/sbuild-package PACKAGEBUILD-27789649 amd64 noble-proposed -c chroot:build-PACKAGEBUILD-27789649 --arch=amd64 --dist=noble-proposed --nolog -A pbbam_2.4.0+dfsg-1build1.dsc Initiating build PACKAGEBUILD-27789649 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 5.4.0-171-generic #189-Ubuntu SMP Fri Jan 5 14:23:02 UTC 2024 x86_64 sbuild (Debian sbuild) 0.79.0 (05 February 2020) on lcy02-amd64-083.buildd +==============================================================================+ | pbbam 2.4.0+dfsg-1build1 (amd64) Sun, 18 Feb 2024 18:24:09 +0000 | +==============================================================================+ Package: pbbam Version: 2.4.0+dfsg-1build1 Source Version: 2.4.0+dfsg-1build1 Distribution: noble-proposed Machine Architecture: amd64 Host Architecture: amd64 Build Architecture: amd64 Build Type: binary I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-27789649/chroot-autobuild' with '<>' I: NOTICE: Log filtering will replace 'build/pbbam-FScOBr/resolver-Tr3EoR' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- pbbam_2.4.0+dfsg-1build1.dsc exists in .; copying to chroot I: NOTICE: Log filtering will replace 'build/pbbam-FScOBr/pbbam-2.4.0+dfsg' with '<>' I: NOTICE: Log filtering will replace 'build/pbbam-FScOBr' with '<>' +------------------------------------------------------------------------------+ | 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 (>> 2.2.0), python3-cram, libgtest-dev, samtools, build-essential, fakeroot Filtered Build-Depends: debhelper-compat (= 13), dh-exec, d-shlibs, meson, pkg-config, cmake, libboost-dev, zlib1g-dev, libssl-dev, libhts-dev, libpbcopper-dev (>> 2.2.0), python3-cram, libgtest-dev, samtools, build-essential, fakeroot dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/<>/apt_archive/sbuild-build-depends-main-dummy.deb'. Ign:1 copy:/<>/apt_archive ./ InRelease Get:2 copy:/<>/apt_archive ./ Release [957 B] Ign:3 copy:/<>/apt_archive ./ Release.gpg Get:4 copy:/<>/apt_archive ./ Sources [470 B] Get:5 copy:/<>/apt_archive ./ Packages [537 B] Fetched 1964 B in 0s (0 B/s) Reading package lists... Reading package lists... Install main 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: apt-utils bash-completion ca-certificates debconf-i18n krb5-locales libgpg-error-l10n libgpm2 libip4tc2 liblocale-gettext-perl libnss-nis libnss-nisplus libperl5.36 libtext-charwidth-perl libtext-iconv-perl libtext-wrapi18n-perl libunistring2 openssl perl-modules-5.36 psmisc uuid-runtime Use 'apt autoremove' to remove them. The following additional packages will be installed: autoconf automake autopoint autotools-dev cmake cmake-data d-shlibs debhelper debugedit dh-autoreconf dh-exec dh-strip-nondeterminism dwz file gettext gettext-base googletest groff-base intltool-debian libarchive-zip-perl libarchive13 libboost-dev libboost1.83-dev libbrotli1 libcurl3-gnutls libcurl4 libcurl4-gnutls-dev libdebhelper-perl libdeflate-dev libdeflate0 libdw1 libelf1 libexpat1 libfile-stripnondeterminism-perl libgtest-dev libhts-dev libhts3 libhtscodecs2 libicu74 libjsoncpp25 libldap2 liblzma-dev libmagic-mgc libmagic1 libncurses6 libnghttp2-14 libpbcopper-dev libpbcopper2.3.0 libpipeline1 libpkgconf3 libpsl5 libpython3-stdlib libpython3.12-minimal libpython3.12-stdlib librhash0 librtmp1 libsasl2-2 libsasl2-modules-db libssh-4 libssl-dev libsub-override-perl libtool libuchardet0 libuv1 libxml2 m4 man-db media-types meson netbase ninja-build pkg-config pkgconf pkgconf-bin po-debconf python3 python3-cram python3-distutils python3-lib2to3 python3-minimal python3-pkg-resources python3-setuptools python3.12 python3.12-minimal samtools zlib1g-dev Suggested packages: autoconf-archive gnu-standards autoconf-doc cmake-doc cmake-format elpa-cmake-mode dh-make gettext-doc libasprintf-dev libgettextpo-dev groff lrzip libboost-doc libboost1.83-doc libboost-atomic1.83-dev libboost-chrono1.83-dev libboost-container1.83-dev libboost-context1.83-dev libboost-contract1.83-dev libboost-coroutine1.83-dev libboost-date-time1.83-dev libboost-exception1.83-dev libboost-fiber1.83-dev libboost-filesystem1.83-dev libboost-graph-parallel1.83-dev libboost-graph1.83-dev libboost-iostreams1.83-dev libboost-json1.83-dev libboost-locale1.83-dev libboost-log1.83-dev libboost-math1.83-dev libboost-mpi-python1.83-dev libboost-mpi1.83-dev libboost-nowide1.83-dev libboost-numpy1.83-dev libboost-program-options1.83-dev libboost-python1.83-dev libboost-random1.83-dev libboost-regex1.83-dev libboost-serialization1.83-dev libboost-stacktrace1.83-dev libboost-system1.83-dev libboost-test1.83-dev libboost-thread1.83-dev libboost-timer1.83-dev libboost-type-erasure1.83-dev libboost-url1.83-dev libboost-wave1.83-dev libboost1.83-tools-dev libmpfrc++-dev libntl-dev libcurl4-doc libgnutls28-dev libidn-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 python-setuptools-doc python3.12-venv python3.12-doc binfmt-support cwltool Recommended packages: curl | wget | lynx libarchive-cpio-perl libldap-common publicsuffix libsasl2-modules libltdl-dev libmail-sendmail-perl The following NEW packages will be installed: autoconf automake autopoint autotools-dev cmake cmake-data d-shlibs debhelper debugedit dh-autoreconf dh-exec dh-strip-nondeterminism dwz file gettext gettext-base googletest groff-base intltool-debian libarchive-zip-perl libarchive13 libboost-dev libboost1.83-dev libbrotli1 libcurl3-gnutls libcurl4 libcurl4-gnutls-dev libdebhelper-perl libdeflate-dev libdeflate0 libdw1 libelf1 libexpat1 libfile-stripnondeterminism-perl libgtest-dev libhts-dev libhts3 libhtscodecs2 libicu74 libjsoncpp25 libldap2 liblzma-dev libmagic-mgc libmagic1 libncurses6 libnghttp2-14 libpbcopper-dev libpbcopper2.3.0 libpipeline1 libpkgconf3 libpsl5 libpython3-stdlib libpython3.12-minimal libpython3.12-stdlib librhash0 librtmp1 libsasl2-2 libsasl2-modules-db libssh-4 libssl-dev libsub-override-perl libtool libuchardet0 libuv1 libxml2 m4 man-db media-types meson netbase ninja-build pkg-config pkgconf pkgconf-bin po-debconf python3 python3-cram python3-distutils python3-lib2to3 python3-minimal python3-pkg-resources python3-setuptools python3.12 python3.12-minimal samtools sbuild-build-depends-main-dummy zlib1g-dev 0 upgraded, 87 newly installed, 0 to remove and 0 not upgraded. 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Fetched 71.3 MB in 1s (117 MB/s) Selecting previously unselected package libpython3.12-minimal:amd64. (Reading database ... 15816 files and directories currently installed.) Preparing to unpack .../libpython3.12-minimal_3.12.2-1_amd64.deb ... Unpacking libpython3.12-minimal:amd64 (3.12.2-1) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../libexpat1_2.6.0-1_amd64.deb ... Unpacking libexpat1:amd64 (2.6.0-1) ... Selecting previously unselected package python3.12-minimal. Preparing to unpack .../python3.12-minimal_3.12.2-1_amd64.deb ... Unpacking python3.12-minimal (3.12.2-1) ... Setting up libpython3.12-minimal:amd64 (3.12.2-1) ... Setting up libexpat1:amd64 (2.6.0-1) ... Setting up python3.12-minimal (3.12.2-1) ... Selecting previously unselected package python3-minimal. (Reading database ... 16134 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.12.1-0ubuntu1_amd64.deb ... 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Processing triggers for libc-bin (2.39-0ubuntu1) ... +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (amd64 included in any) +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 5.4.0-171-generic #189-Ubuntu SMP Fri Jan 5 14:23:02 UTC 2024 amd64 (x86_64) Toolchain package versions: binutils_2.42-2ubuntu1 dpkg-dev_1.22.4ubuntu3 g++-13_13.2.0-13ubuntu1 gcc-13_13.2.0-13ubuntu1 libc6-dev_2.39-0ubuntu1 libstdc++-13-dev_13.2.0-13ubuntu1 libstdc++6_14-20240201-3ubuntu1 linux-libc-dev_6.8.0-11.11 Package versions: adduser_3.137ubuntu1 advancecomp_2.5-1 apt_2.7.11 apt-utils_2.7.11 autoconf_2.71-3 automake_1:1.16.5-1.3ubuntu1 autopoint_0.21-14ubuntu1 autotools-dev_20220109.1 base-files_13ubuntu6 base-passwd_3.6.3 bash_5.2.21-2ubuntu1 bash-completion_1:2.11-8 binutils_2.42-2ubuntu1 binutils-common_2.42-2ubuntu1 binutils-x86-64-linux-gnu_2.42-2ubuntu1 bsdextrautils_2.39.2-6ubuntu1 bsdutils_1:2.39.2-6ubuntu1 build-essential_12.10ubuntu1 bzip2_1.0.8-5build1 ca-certificates_20240203 cmake_3.28.3-1 cmake-data_3.28.3-1 coreutils_9.4-2ubuntu3 cpp_4:13.2.0-7ubuntu1 cpp-13_13.2.0-13ubuntu1 cpp-13-x86-64-linux-gnu_13.2.0-13ubuntu1 cpp-x86-64-linux-gnu_4:13.2.0-7ubuntu1 d-shlibs_0.106 dash_0.5.12-6ubuntu1 debconf_1.5.86 debconf-i18n_1.5.86 debhelper_13.13ubuntu1 debianutils_5.16 debugedit_1:5.0-5 dh-autoreconf_20 dh-exec_0.28 dh-strip-nondeterminism_1.13.1-1 diffutils_1:3.10-1 dpkg_1.22.4ubuntu3 dpkg-dev_1.22.4ubuntu3 dwz_0.15-1 e2fsprogs_1.47.0-2ubuntu1 fakeroot_1.33-1 file_1:5.45-2 findutils_4.9.0-5 g++_4:13.2.0-7ubuntu1 g++-13_13.2.0-13ubuntu1 g++-13-x86-64-linux-gnu_13.2.0-13ubuntu1 g++-x86-64-linux-gnu_4:13.2.0-7ubuntu1 gcc_4:13.2.0-7ubuntu1 gcc-13_13.2.0-13ubuntu1 gcc-13-base_13.2.0-13ubuntu1 gcc-13-x86-64-linux-gnu_13.2.0-13ubuntu1 gcc-14-base_14-20240201-3ubuntu1 gcc-x86-64-linux-gnu_4:13.2.0-7ubuntu1 gettext_0.21-14ubuntu1 gettext-base_0.21-14ubuntu1 googletest_1.14.0-1 gpg_2.4.4-2ubuntu3 gpg-agent_2.4.4-2ubuntu3 gpgconf_2.4.4-2ubuntu3 gpgv_2.4.4-2ubuntu3 grep_3.11-4 groff-base_1.23.0-3 gzip_1.12-1ubuntu1 hostname_3.23+nmu1ubuntu1 init_1.66ubuntu1 init-system-helpers_1.66ubuntu1 intltool-debian_0.35.0+20060710.6 krb5-locales_1.20.1-5build1 libacl1_2.3.1-4ubuntu1 libapparmor1_4.0.0~alpha4-0ubuntu1 libapt-pkg6.0_2.7.11 libarchive-zip-perl_1.68-1 libarchive13_3.7.2-1ubuntu2 libargon2-1_0~20190702+dfsg-4 libasan8_14-20240201-3ubuntu1 libassuan0_2.5.6-1 libatomic1_14-20240201-3ubuntu1 libattr1_1:2.5.2-1 libaudit-common_1:3.1.2-2 libaudit1_1:3.1.2-2 libbinutils_2.42-2ubuntu1 libblkid1_2.39.2-6ubuntu1 libboost-dev_1.83.0.1ubuntu2 libboost1.83-dev_1.83.0-2ubuntu1 libbrotli1_1.1.0-2 libbz2-1.0_1.0.8-5build1 libc-bin_2.39-0ubuntu1 libc-dev-bin_2.39-0ubuntu1 libc6_2.39-0ubuntu1 libc6-dev_2.39-0ubuntu1 libcap-ng0_0.8.4-2 libcap2_1:2.66-4ubuntu1 libcc1-0_14-20240201-3ubuntu1 libcom-err2_1.47.0-2ubuntu1 libcrypt-dev_1:4.4.36-4 libcrypt1_1:4.4.36-4 libcryptsetup12_2:2.6.1-6ubuntu1 libctf-nobfd0_2.42-2ubuntu1 libctf0_2.42-2ubuntu1 libcurl3-gnutls_8.5.0-2ubuntu2 libcurl4_8.5.0-2ubuntu2 libcurl4-gnutls-dev_8.5.0-2ubuntu2 libdb5.3_5.3.28+dfsg2-4 libdebconfclient0_0.271ubuntu1 libdebhelper-perl_13.13ubuntu1 libdeflate-dev_1.19-1 libdeflate0_1.19-1 libdevmapper1.02.1_2:1.02.185-2ubuntu1 libdpkg-perl_1.22.4ubuntu3 libdw1_0.190-1 libelf1_0.190-1 libexpat1_2.6.0-1 libext2fs2_1.47.0-2ubuntu1 libfakeroot_1.33-1 libfdisk1_2.39.2-6ubuntu1 libffi8_3.4.4-2 libfile-stripnondeterminism-perl_1.13.1-1 libgcc-13-dev_13.2.0-13ubuntu1 libgcc-s1_14-20240201-3ubuntu1 libgcrypt20_1.10.3-2 libgdbm-compat4_1.23-5 libgdbm6_1.23-5 libgmp10_2:6.3.0+dfsg-2ubuntu4 libgnutls30_3.8.3-1ubuntu1 libgomp1_14-20240201-3ubuntu1 libgpg-error-l10n_1.47-3build1 libgpg-error0_1.47-3build1 libgpm2_1.20.7-10build1 libgprofng0_2.42-2ubuntu1 libgssapi-krb5-2_1.20.1-5build1 libgtest-dev_1.14.0-1 libhogweed6_3.9.1-2 libhts-dev_1.19+ds-1 libhts3_1.19+ds-1 libhtscodecs2_1.6.0-1 libhwasan0_14-20240201-3ubuntu1 libicu74_74.2-1ubuntu1 libidn2-0_2.3.7-2 libip4tc2_1.8.10-3ubuntu1 libisl23_0.26-3 libitm1_14-20240201-3ubuntu1 libjansson4_2.14-2 libjson-c5_0.17-1 libjsoncpp25_1.9.5-6 libk5crypto3_1.20.1-5build1 libkeyutils1_1.6.3-3 libkmod2_30+20230601-2ubuntu1 libkrb5-3_1.20.1-5build1 libkrb5support0_1.20.1-5build1 libldap2_2.6.7+dfsg-1~exp1ubuntu1 liblocale-gettext-perl_1.07-6build1 liblockfile-bin_1.17-1build2 liblockfile1_1.17-1build2 liblsan0_14-20240201-3ubuntu1 liblz4-1_1.9.4-1 liblzma-dev_5.4.5-0.3 liblzma5_5.4.5-0.3 libmagic-mgc_1:5.45-2 libmagic1_1:5.45-2 libmd0_1.1.0-2 libmount1_2.39.2-6ubuntu1 libmpc3_1.3.1-1 libmpfr6_4.2.1-1 libncurses6_6.4+20240113-1ubuntu1 libncursesw6_6.4+20240113-1ubuntu1 libnettle8_3.9.1-2 libnghttp2-14_1.59.0-1 libnpth0_1.6-3build2 libnsl-dev_1.3.0-3 libnsl2_1.3.0-3 libnss-nis_3.1-0ubuntu6 libnss-nisplus_1.3-0ubuntu6 libp11-kit0_0.25.3-4ubuntu1 libpam-modules_1.5.2-9.1ubuntu2 libpam-modules-bin_1.5.2-9.1ubuntu2 libpam-runtime_1.5.2-9.1ubuntu2 libpam0g_1.5.2-9.1ubuntu2 libpbcopper-dev_2.3.0+dfsg-2 libpbcopper2.3.0_2.3.0+dfsg-2 libpcre2-8-0_10.42-4ubuntu1 libperl5.36_5.36.0-10ubuntu1 libperl5.38_5.38.2-3 libpipeline1_1.5.7-1 libpkgconf3_1.8.1-2 libpng16-16_1.6.42-1 libproc2-0_2:4.0.4-2ubuntu1 libpsl5_0.21.2-1build1 libpython3-stdlib_3.12.1-0ubuntu1 libpython3.12-minimal_3.12.2-1 libpython3.12-stdlib_3.12.2-1 libquadmath0_14-20240201-3ubuntu1 libreadline8_8.2-3 librhash0_1.4.3-3 librtmp1_2.4+20151223.gitfa8646d.1-2build4 libsasl2-2_2.1.28+dfsg1-4 libsasl2-modules-db_2.1.28+dfsg1-4 libseccomp2_2.5.5-1ubuntu1 libselinux1_3.5-2build1 libsemanage-common_3.5-1build2 libsemanage2_3.5-1build2 libsepol2_3.5-2 libsframe1_2.42-2ubuntu1 libsmartcols1_2.39.2-6ubuntu1 libsqlite3-0_3.45.1-1 libss2_1.47.0-2ubuntu1 libssh-4_0.10.6-2 libssl-dev_3.0.10-1ubuntu4 libssl3_3.0.10-1ubuntu4 libstdc++-13-dev_13.2.0-13ubuntu1 libstdc++6_14-20240201-3ubuntu1 libsub-override-perl_0.10-1 libsystemd-shared_255.2-3ubuntu2 libsystemd0_255.2-3ubuntu2 libtasn1-6_4.19.0-3 libtext-charwidth-perl_0.04-11build1 libtext-iconv-perl_1.7-8build1 libtext-wrapi18n-perl_0.06-10 libtinfo6_6.4+20240113-1ubuntu1 libtirpc-common_1.3.4+ds-1build1 libtirpc-dev_1.3.4+ds-1build1 libtirpc3_1.3.4+ds-1build1 libtool_2.4.7-7 libtsan2_14-20240201-3ubuntu1 libubsan1_14-20240201-3ubuntu1 libuchardet0_0.0.8-1 libudev1_255.2-3ubuntu2 libunistring2_1.0-2 libunistring5_1.1-2 libuuid1_2.39.2-6ubuntu1 libuv1_1.46.0-3ubuntu1 libxml2_2.9.14+dfsg-1.3ubuntu1 libxxhash0_0.8.2-2 libzstd1_1.5.5+dfsg2-2 linux-libc-dev_6.8.0-11.11 lockfile-progs_0.1.19build1 login_1:4.13+dfsg1-3ubuntu1 logsave_1.47.0-2ubuntu1 lto-disabled-list_46 m4_1.4.19-4 make_4.3-4.1build1 man-db_2.12.0-3 mawk_1.3.4.20240123-1 media-types_10.1.0 meson_1.3.2-1 mount_2.39.2-6ubuntu1 ncurses-base_6.4+20240113-1ubuntu1 ncurses-bin_6.4+20240113-1ubuntu1 netbase_6.4 ninja-build_1.11.1-2 openssl_3.0.10-1ubuntu4 optipng_0.7.8+ds-1 passwd_1:4.13+dfsg1-3ubuntu1 patch_2.7.6-7build2 perl_5.38.2-3 perl-base_5.38.2-3 perl-modules-5.36_5.36.0-10ubuntu1 perl-modules-5.38_5.38.2-3 pinentry-curses_1.2.1-3ubuntu1 pkg-config_1.8.1-2 pkgbinarymangler_154 pkgconf_1.8.1-2 pkgconf-bin_1.8.1-2 po-debconf_1.0.21+nmu1 policyrcd-script-zg2_0.1-3.1 procps_2:4.0.4-2ubuntu1 psmisc_23.6-2 python3_3.12.1-0ubuntu1 python3-cram_0.7-5 python3-distutils_3.11.5-1 python3-lib2to3_3.11.5-1 python3-minimal_3.12.1-0ubuntu1 python3-pkg-resources_68.1.2-2 python3-setuptools_68.1.2-2 python3.12_3.12.2-1 python3.12-minimal_3.12.2-1 readline-common_8.2-3 rpcsvc-proto_1.4.2-0ubuntu6 samtools_1.19.2-1 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.9-2 sensible-utils_0.0.22 systemd_255.2-3ubuntu2 systemd-dev_255.2-3ubuntu2 systemd-sysv_255.2-3ubuntu2 sysvinit-utils_3.08-3ubuntu1 tar_1.35+dfsg-3 tzdata_2024a-1ubuntu1 ubuntu-keyring_2023.11.28.1 usrmerge_35ubuntu1 util-linux_2.39.2-6ubuntu1 uuid-runtime_2.39.2-6ubuntu1 xz-utils_5.4.5-0.3 zlib1g_1:1.3.dfsg-3ubuntu1 zlib1g-dev_1:1.3.dfsg-3ubuntu1 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: pbbam Binary: pbbamtools, libpbbam2.4.0, libpbbam-dev Architecture: any Version: 2.4.0+dfsg-1build1 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille Homepage: https://pbbam.readthedocs.org/en/latest/index.html Standards-Version: 4.6.2 Vcs-Browser: https://salsa.debian.org/med-team/pbbam Vcs-Git: https://salsa.debian.org/med-team/pbbam.git Testsuite: autopkgtest Testsuite-Triggers: @builddeps@ Build-Depends: debhelper-compat (= 13), dh-exec, d-shlibs, meson, pkg-config, cmake, libboost-dev, zlib1g-dev, libssl-dev, libhts-dev, libpbcopper-dev (>> 2.2.0), python3-cram, libgtest-dev , samtools Package-List: libpbbam-dev deb libdevel optional arch=any libpbbam2.4.0 deb libs optional arch=any pbbamtools deb science optional arch=any Checksums-Sha1: c18a5477be1369d03c515bf59103d3233785d583 7826464 pbbam_2.4.0+dfsg.orig.tar.xz e39e2fc09c574d8a6b2d9f065603d985020c7e80 9060 pbbam_2.4.0+dfsg-1build1.debian.tar.xz Checksums-Sha256: e991e5f5470976f2ad0cca93658a273989738ca48cce4f024fd074cc1e8cbe2b 7826464 pbbam_2.4.0+dfsg.orig.tar.xz 8696ed2b075f62fb6adb42772ff6e394a8507b9b1e6ef02ec52b94632d1a0919 9060 pbbam_2.4.0+dfsg-1build1.debian.tar.xz Files: 315039ff474e762e609442ca84988512 7826464 pbbam_2.4.0+dfsg.orig.tar.xz 6cf4657153b01d2a03ff5ca19099f544 9060 pbbam_2.4.0+dfsg-1build1.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQIzBAEBCgAdFiEETQvhLw5HdtiqzpaW5mx3Wuv+bH0FAmXSStIACgkQ5mx3Wuv+ bH2DBxAAhdGLtNJeJOB6tsT/y5J43qkqs7uEGsa8+oJBC3sIS9gFLIi7Ku3wPPj0 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info: unpacking pbbam_2.4.0+dfsg.orig.tar.xz dpkg-source: info: unpacking pbbam_2.4.0+dfsg-1build1.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 spelling 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-27789649 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-27789649 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-27789649 SCHROOT_UID=2001 SCHROOT_USER=buildd SHELL=/bin/sh TERM=unknown USER=buildd V=1 dpkg-buildpackage ----------------- Command: dpkg-buildpackage -us -uc -mLaunchpad Build Daemon -b -rfakeroot dpkg-buildpackage: info: source package pbbam dpkg-buildpackage: info: source version 2.4.0+dfsg-1build1 dpkg-buildpackage: info: source distribution noble 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 '/<>' dh_auto_clean find -name "*.deb.t" -delete rm -f -r /<>/gendata make[1]: Leaving directory '/<>' 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 && DEB_PYTHON_INSTALL_LAYOUT=deb LC_ALL=C.UTF-8 meson setup .. --wrap-mode=nodownload --buildtype=plain --prefix=/usr --sysconfdir=/etc --localstatedir=/var --libdir=lib/x86_64-linux-gnu -Dpython.bytecompile=-1 The Meson build system Version: 1.3.2 Source dir: /<> Build dir: /<>/obj-x86_64-linux-gnu Build type: native build Project name: PacBioBAM Project version: 2.4.0 C compiler for the host machine: cc (gcc 13.2.0 "cc (Ubuntu 13.2.0-13ubuntu1) 13.2.0") C linker for the host machine: cc ld.bfd 2.42 C++ compiler for the host machine: c++ (gcc 13.2.0 "c++ (Ubuntu 13.2.0-13ubuntu1) 13.2.0") C++ linker for the host machine: c++ ld.bfd 2.42 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: YES (/usr/bin/pkg-config) 1.8.1 Run-time dependency Boost found: YES 1.83.0 (/usr/include) Run-time dependency zlib found: YES 1.3 Run-time dependency htslib found: YES 1.19 Run-time dependency pbcopper found: YES 2.3.0 Configuring PbbamVersion.cpp using configuration Configuring LibraryVersion.h using configuration Program tools/check-formatting found: YES (/<>/tools/check-formatting) Program python3 found: YES (/usr/bin/python3) Program cram3 found: YES (/usr/bin/cram3) Run-time dependency GTest found: YES 1.14.0 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 PacBioBAM 2.4.0 User defined options buildtype : plain libdir : lib/x86_64-linux-gnu localstatedir : /var prefix : /usr sysconfdir : /etc wrap_mode : nodownload python.bytecompile: -1 Found ninja-1.11.1 at /usr/bin/ninja dh_auto_build -O--buildsystem=meson cd obj-x86_64-linux-gnu && LC_ALL=C.UTF-8 ninja -j4 -v [1/226] /usr/bin/meson --internal vcstagger ../src/LibraryGitHash.h.in src/LibraryGitHash.h 2.4.0 /<>/src @PBBAM_GIT_SHA1@ '(.*)' git describe --always '--dirty=*' [2/226] /usr/bin/meson --internal vcstagger ../src/PbbamGitHash.cpp.in src/PbbamGitHash.cpp 2.4.0 /<>/src @PBBAM_GIT_SHA1@ '(.*)' git describe --always '--dirty=*' [3/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -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.2.4.0.p/meson-generated_.._PbbamGitHash.cpp.o -MF src/libpbbam.so.2.4.0.p/meson-generated_.._PbbamGitHash.cpp.o.d -o src/libpbbam.so.2.4.0.p/meson-generated_.._PbbamGitHash.cpp.o -c src/PbbamGitHash.cpp [4/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -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.2.4.0.p/BaiIndexCache.cpp.o -MF src/libpbbam.so.2.4.0.p/BaiIndexCache.cpp.o.d -o src/libpbbam.so.2.4.0.p/BaiIndexCache.cpp.o -c ../src/BaiIndexCache.cpp [5/226] c++ 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src/libpbbam.so.2.4.0.p/Compare.cpp.o.d -o src/libpbbam.so.2.4.0.p/Compare.cpp.o -c ../src/Compare.cpp [24/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -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.2.4.0.p/CollectionMetadata.cpp.o -MF src/libpbbam.so.2.4.0.p/CollectionMetadata.cpp.o.d -o src/libpbbam.so.2.4.0.p/CollectionMetadata.cpp.o -c ../src/CollectionMetadata.cpp [25/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -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.2.4.0.p/Config.cpp.o -MF src/libpbbam.so.2.4.0.p/Config.cpp.o.d -o src/libpbbam.so.2.4.0.p/Config.cpp.o -c ../src/Config.cpp [26/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -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.2.4.0.p/CompositeFastaReader.cpp.o -MF src/libpbbam.so.2.4.0.p/CompositeFastaReader.cpp.o.d -o src/libpbbam.so.2.4.0.p/CompositeFastaReader.cpp.o -c ../src/CompositeFastaReader.cpp [27/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -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.2.4.0.p/CompositeBamReader.cpp.o -MF src/libpbbam.so.2.4.0.p/CompositeBamReader.cpp.o.d -o src/libpbbam.so.2.4.0.p/CompositeBamReader.cpp.o -c ../src/CompositeBamReader.cpp [28/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -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.2.4.0.p/DataSetElement.cpp.o -MF src/libpbbam.so.2.4.0.p/DataSetElement.cpp.o.d -o src/libpbbam.so.2.4.0.p/DataSetElement.cpp.o -c ../src/DataSetElement.cpp [29/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -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.2.4.0.p/DataSetIO.cpp.o -MF src/libpbbam.so.2.4.0.p/DataSetIO.cpp.o.d -o src/libpbbam.so.2.4.0.p/DataSetIO.cpp.o -c ../src/DataSetIO.cpp [30/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -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.2.4.0.p/DataSetBaseTypes.cpp.o -MF src/libpbbam.so.2.4.0.p/DataSetBaseTypes.cpp.o.d -o src/libpbbam.so.2.4.0.p/DataSetBaseTypes.cpp.o -c ../src/DataSetBaseTypes.cpp [31/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -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.2.4.0.p/DataSetXsd.cpp.o -MF src/libpbbam.so.2.4.0.p/DataSetXsd.cpp.o.d -o src/libpbbam.so.2.4.0.p/DataSetXsd.cpp.o -c ../src/DataSetXsd.cpp [32/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -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.2.4.0.p/DataSet.cpp.o -MF src/libpbbam.so.2.4.0.p/DataSet.cpp.o.d -o src/libpbbam.so.2.4.0.p/DataSet.cpp.o -c ../src/DataSet.cpp [33/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -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.2.4.0.p/ErrnoReason.cpp.o -MF src/libpbbam.so.2.4.0.p/ErrnoReason.cpp.o.d -o src/libpbbam.so.2.4.0.p/ErrnoReason.cpp.o -c ../src/ErrnoReason.cpp [34/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -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.2.4.0.p/FaiZmwChunker.cpp.o -MF src/libpbbam.so.2.4.0.p/FaiZmwChunker.cpp.o.d -o src/libpbbam.so.2.4.0.p/FaiZmwChunker.cpp.o -c ../src/FaiZmwChunker.cpp [35/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -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.2.4.0.p/FaiIndex.cpp.o -MF src/libpbbam.so.2.4.0.p/FaiIndex.cpp.o.d -o src/libpbbam.so.2.4.0.p/FaiIndex.cpp.o -c ../src/FaiIndex.cpp [36/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -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.2.4.0.p/EntireFileQuery.cpp.o -MF src/libpbbam.so.2.4.0.p/EntireFileQuery.cpp.o.d -o src/libpbbam.so.2.4.0.p/EntireFileQuery.cpp.o -c ../src/EntireFileQuery.cpp [37/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -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.2.4.0.p/DataSetTypes.cpp.o -MF src/libpbbam.so.2.4.0.p/DataSetTypes.cpp.o.d -o src/libpbbam.so.2.4.0.p/DataSetTypes.cpp.o -c ../src/DataSetTypes.cpp In file included from /usr/include/c++/13/map:62, from ../include/pbbam/ProgramInfo.h:6, from ../include/pbbam/BamHeader.h:6, from ../include/pbbam/BamFile.h:6, from ../include/pbbam/DataSetTypes.h:6, from ../src/DataSetTypes.cpp:3: In member function ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::_Reuse_or_alloc_node::_Reuse_or_alloc_node(std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >&)’, inlined from ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::operator=(std::_Rb_tree, std::_Select1st >, std::less, std::allocator > > const&)’ at /usr/include/c++/13/bits/stl_tree.h:1800:25, inlined from ‘std::map, std::allocator > >::operator=(std::map, std::allocator > > const&)’ at /usr/include/c++/13/bits/stl_map.h:331:7, inlined from ‘PacBio::BAM::NamespaceRegistry::operator=(PacBio::BAM::NamespaceRegistry const&)’ at ../include/pbbam/DataSetXsd.h:65:20, inlined from ‘PacBio::BAM::DataSetBase::DeepCopy() const’ at ../src/DataSetTypes.cpp:329:25: /usr/include/c++/13/bits/stl_tree.h:446:11: warning: array subscript 25 is outside array bounds of ‘void[184]’ [-Warray-bounds=] 446 | : _M_root(__t._M_root()), _M_nodes(__t._M_rightmost()), _M_t(__t) | ^~~~~~~~~~~~~~~~~~~~~~ ../src/DataSetTypes.cpp: In member function ‘PacBio::BAM::DataSetBase::DeepCopy() const’: ../src/DataSetTypes.cpp:327:49: note: at offset 200 into object of size 184 allocated by ‘operator new(unsigned long)’ 327 | auto* copyDataset = new DataSetElement(*this); | ^ In member function ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::_Reuse_or_alloc_node::_Reuse_or_alloc_node(std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >&)’, inlined from ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::operator=(std::_Rb_tree, std::_Select1st >, std::less, std::allocator > > const&)’ at /usr/include/c++/13/bits/stl_tree.h:1800:25, inlined from ‘std::map, std::allocator > >::operator=(std::map, std::allocator > > const&)’ at /usr/include/c++/13/bits/stl_map.h:331:7, inlined from ‘PacBio::BAM::NamespaceRegistry::operator=(PacBio::BAM::NamespaceRegistry const&)’ at ../include/pbbam/DataSetXsd.h:65:20, inlined from ‘PacBio::BAM::DataSetBase::DeepCopy() const’ at ../src/DataSetTypes.cpp:329:25: /usr/include/c++/13/bits/stl_tree.h:446:35: warning: array subscript 27 is outside array bounds of ‘void[184]’ [-Warray-bounds=] 446 | : _M_root(__t._M_root()), _M_nodes(__t._M_rightmost()), _M_t(__t) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../src/DataSetTypes.cpp: In member function ‘PacBio::BAM::DataSetBase::DeepCopy() const’: ../src/DataSetTypes.cpp:327:49: note: at offset 216 into object of size 184 allocated by ‘operator new(unsigned long)’ 327 | auto* copyDataset = new DataSetElement(*this); | ^ In member function ‘std::_Rb_tree_header::_M_reset()’, inlined from ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::operator=(std::_Rb_tree, std::_Select1st >, std::less, std::allocator > > const&)’ at /usr/include/c++/13/bits/stl_tree.h:1801:20, inlined from ‘std::map, std::allocator > >::operator=(std::map, std::allocator > > const&)’ at /usr/include/c++/13/bits/stl_map.h:331:7, inlined from ‘PacBio::BAM::NamespaceRegistry::operator=(PacBio::BAM::NamespaceRegistry const&)’ at ../include/pbbam/DataSetXsd.h:65:20, inlined from ‘PacBio::BAM::DataSetBase::DeepCopy() const’ at ../src/DataSetTypes.cpp:329:25: /usr/include/c++/13/bits/stl_tree.h:208:27: warning: array subscript 4 is outside array bounds of ‘void[184]’ [-Warray-bounds=] 208 | _M_header._M_parent = 0; | ~~~~~~~~~~~~~~~~~~~~^~~ ../src/DataSetTypes.cpp: In member function ‘PacBio::BAM::DataSetBase::DeepCopy() const’: ../src/DataSetTypes.cpp:327:49: note: at offset 192 into object of size 184 allocated by ‘operator new(unsigned long)’ 327 | auto* copyDataset = new DataSetElement(*this); | ^ In member function ‘std::_Rb_tree_header::_M_reset()’, inlined from ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::operator=(std::_Rb_tree, std::_Select1st >, std::less, std::allocator > > const&)’ at /usr/include/c++/13/bits/stl_tree.h:1801:20, inlined from ‘std::map, std::allocator > >::operator=(std::map, std::allocator > > const&)’ at /usr/include/c++/13/bits/stl_map.h:331:7, inlined from ‘PacBio::BAM::NamespaceRegistry::operator=(PacBio::BAM::NamespaceRegistry const&)’ at ../include/pbbam/DataSetXsd.h:65:20, inlined from ‘PacBio::BAM::DataSetBase::DeepCopy() const’ at ../src/DataSetTypes.cpp:329:25: /usr/include/c++/13/bits/stl_tree.h:209:27: warning: array subscript 4 is outside array bounds of ‘void[184]’ [-Warray-bounds=] 209 | _M_header._M_left = &_M_header; | ^~~~~~~~~~ ../src/DataSetTypes.cpp: In member function ‘PacBio::BAM::DataSetBase::DeepCopy() const’: ../src/DataSetTypes.cpp:327:49: note: at offset 192 into object of size 184 allocated by ‘operator new(unsigned long)’ 327 | auto* copyDataset = new DataSetElement(*this); | ^ In member function ‘std::_Rb_tree_header::_M_reset()’, inlined from ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::operator=(std::_Rb_tree, std::_Select1st >, std::less, std::allocator > > const&)’ at /usr/include/c++/13/bits/stl_tree.h:1801:20, inlined from ‘std::map, std::allocator > >::operator=(std::map, std::allocator > > const&)’ at /usr/include/c++/13/bits/stl_map.h:331:7, inlined from ‘PacBio::BAM::NamespaceRegistry::operator=(PacBio::BAM::NamespaceRegistry const&)’ at ../include/pbbam/DataSetXsd.h:65:20, inlined from ‘PacBio::BAM::DataSetBase::DeepCopy() const’ at ../src/DataSetTypes.cpp:329:25: /usr/include/c++/13/bits/stl_tree.h:209:25: warning: array subscript 4 is outside array bounds of ‘void[184]’ [-Warray-bounds=] 209 | _M_header._M_left = &_M_header; | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ ../src/DataSetTypes.cpp: In member function ‘PacBio::BAM::DataSetBase::DeepCopy() const’: ../src/DataSetTypes.cpp:327:49: note: at offset 192 into object of size 184 allocated by ‘operator new(unsigned long)’ 327 | auto* copyDataset = new DataSetElement(*this); | ^ In member function ‘std::_Rb_tree_header::_M_reset()’, inlined from ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::operator=(std::_Rb_tree, std::_Select1st >, std::less, std::allocator > > const&)’ at /usr/include/c++/13/bits/stl_tree.h:1801:20, inlined from ‘std::map, std::allocator > >::operator=(std::map, std::allocator > > const&)’ at /usr/include/c++/13/bits/stl_map.h:331:7, inlined from ‘PacBio::BAM::NamespaceRegistry::operator=(PacBio::BAM::NamespaceRegistry const&)’ at ../include/pbbam/DataSetXsd.h:65:20, inlined from ‘PacBio::BAM::DataSetBase::DeepCopy() const’ at ../src/DataSetTypes.cpp:329:25: /usr/include/c++/13/bits/stl_tree.h:210:26: warning: array subscript 4 is outside array bounds of ‘void[184]’ [-Warray-bounds=] 210 | _M_header._M_right = &_M_header; | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ ../src/DataSetTypes.cpp: In member function ‘PacBio::BAM::DataSetBase::DeepCopy() const’: ../src/DataSetTypes.cpp:327:49: note: at offset 192 into object of size 184 allocated by ‘operator new(unsigned long)’ 327 | auto* copyDataset = new DataSetElement(*this); | ^ In member function ‘std::_Rb_tree_header::_M_reset()’, inlined from ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::operator=(std::_Rb_tree, std::_Select1st >, std::less, std::allocator > > const&)’ at /usr/include/c++/13/bits/stl_tree.h:1801:20, inlined from ‘std::map, std::allocator > >::operator=(std::map, std::allocator > > const&)’ at /usr/include/c++/13/bits/stl_map.h:331:7, inlined from ‘PacBio::BAM::NamespaceRegistry::operator=(PacBio::BAM::NamespaceRegistry const&)’ at ../include/pbbam/DataSetXsd.h:65:20, inlined from ‘PacBio::BAM::DataSetBase::DeepCopy() const’ at ../src/DataSetTypes.cpp:329:25: /usr/include/c++/13/bits/stl_tree.h:211:21: warning: array subscript 4 is outside array bounds of ‘void[184]’ [-Warray-bounds=] 211 | _M_node_count = 0; | ~~~~~~~~~~~~~~^~~ ../src/DataSetTypes.cpp: In member function ‘PacBio::BAM::DataSetBase::DeepCopy() const’: ../src/DataSetTypes.cpp:327:49: note: at offset 192 into object of size 184 allocated by ‘operator new(unsigned long)’ 327 | auto* copyDataset = new DataSetElement(*this); | ^ In member function ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::_M_copy, std::_Select1st >, std::less, std::allocator > >::_Reuse_or_alloc_node>(std::_Rb_tree, std::_Select1st >, std::less, std::allocator > > const&, std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::_Reuse_or_alloc_node&)std::_Rb_tree_node >*’, inlined from ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::operator=(std::_Rb_tree, std::_Select1st >, std::less, std::allocator > > const&)’ at /usr/include/c++/13/bits/stl_tree.h:1804:38, inlined from ‘std::map, std::allocator > >::operator=(std::map, std::allocator > > const&)’ at /usr/include/c++/13/bits/stl_map.h:331:7, inlined from ‘PacBio::BAM::NamespaceRegistry::operator=(PacBio::BAM::NamespaceRegistry const&)’ at ../include/pbbam/DataSetXsd.h:65:20, inlined from ‘PacBio::BAM::DataSetBase::DeepCopy() const’ at ../src/DataSetTypes.cpp:329:25: /usr/include/c++/13/bits/stl_tree.h:893:25: warning: array subscript 26 is outside array bounds of ‘void[184]’ [-Warray-bounds=] 893 | _M_leftmost() = _S_minimum(__root); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ ../src/DataSetTypes.cpp: In member function ‘PacBio::BAM::DataSetBase::DeepCopy() const’: ../src/DataSetTypes.cpp:327:49: note: at offset 208 into object of size 184 allocated by ‘operator new(unsigned long)’ 327 | auto* copyDataset = new DataSetElement(*this); | ^ In member function ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::_M_copy, std::_Select1st >, std::less, std::allocator > >::_Reuse_or_alloc_node>(std::_Rb_tree, std::_Select1st >, std::less, std::allocator > > const&, std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::_Reuse_or_alloc_node&)std::_Rb_tree_node >*’, inlined from ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::operator=(std::_Rb_tree, std::_Select1st >, std::less, std::allocator > > const&)’ at /usr/include/c++/13/bits/stl_tree.h:1804:38, inlined from ‘std::map, std::allocator > >::operator=(std::map, std::allocator > > const&)’ at /usr/include/c++/13/bits/stl_map.h:331:7, inlined from ‘PacBio::BAM::NamespaceRegistry::operator=(PacBio::BAM::NamespaceRegistry const&)’ at ../include/pbbam/DataSetXsd.h:65:20, inlined from ‘PacBio::BAM::DataSetBase::DeepCopy() const’ at ../src/DataSetTypes.cpp:329:25: /usr/include/c++/13/bits/stl_tree.h:894:26: warning: array subscript 27 is outside array bounds of ‘void[184]’ [-Warray-bounds=] 894 | _M_rightmost() = _S_maximum(__root); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ ../src/DataSetTypes.cpp: In member function ‘PacBio::BAM::DataSetBase::DeepCopy() const’: ../src/DataSetTypes.cpp:327:49: note: at offset 216 into object of size 184 allocated by ‘operator new(unsigned long)’ 327 | auto* copyDataset = new DataSetElement(*this); | ^ In member function ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::_M_copy, std::_Select1st >, std::less, std::allocator > >::_Reuse_or_alloc_node>(std::_Rb_tree, std::_Select1st >, std::less, std::allocator > > const&, std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::_Reuse_or_alloc_node&)std::_Rb_tree_node >*’, inlined from ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::operator=(std::_Rb_tree, std::_Select1st >, std::less, std::allocator > > const&)’ at /usr/include/c++/13/bits/stl_tree.h:1804:38, inlined from ‘std::map, std::allocator > >::operator=(std::map, std::allocator > > const&)’ at /usr/include/c++/13/bits/stl_map.h:331:7, inlined from ‘PacBio::BAM::NamespaceRegistry::operator=(PacBio::BAM::NamespaceRegistry const&)’ at ../include/pbbam/DataSetXsd.h:65:20, inlined from ‘PacBio::BAM::DataSetBase::DeepCopy() const’ at ../src/DataSetTypes.cpp:329:25: /usr/include/c++/13/bits/stl_tree.h:895:33: warning: array subscript 3 is outside array bounds of ‘void[184]’ [-Warray-bounds=] 895 | _M_impl._M_node_count = __x._M_impl._M_node_count; | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../src/DataSetTypes.cpp: In member function ‘PacBio::BAM::DataSetBase::DeepCopy() const’: ../src/DataSetTypes.cpp:327:49: note: at offset 184 into object of size 184 allocated by ‘operator new(unsigned long)’ 327 | auto* copyDataset = new DataSetElement(*this); | ^ In member function ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::operator=(std::_Rb_tree, std::_Select1st >, std::less, std::allocator > > const&)’, inlined from ‘std::map, std::allocator > >::operator=(std::map, std::allocator > > const&)’ at /usr/include/c++/13/bits/stl_map.h:331:7, inlined from ‘PacBio::BAM::NamespaceRegistry::operator=(PacBio::BAM::NamespaceRegistry const&)’ at ../include/pbbam/DataSetXsd.h:65:20, inlined from ‘PacBio::BAM::DataSetBase::DeepCopy() const’ at ../src/DataSetTypes.cpp:329:25: /usr/include/c++/13/bits/stl_tree.h:1804:23: warning: array subscript 25 is outside array bounds of ‘void[184]’ [-Warray-bounds=] 1804 | _M_root() = _M_copy<__as_lvalue>(__x, __roan); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../src/DataSetTypes.cpp: In member function ‘PacBio::BAM::DataSetBase::DeepCopy() const’: ../src/DataSetTypes.cpp:327:49: note: at offset 200 into object of size 184 allocated by ‘operator new(unsigned long)’ 327 | auto* copyDataset = new DataSetElement(*this); | ^ In file included from ../include/pbbam/internal/DataSetElement.h:6, from ../include/pbbam/internal/DataSetBaseTypes.h:6, from ../include/pbbam/CollectionMetadata.h:6, from ../include/pbbam/DataSetTypes.h:7: In member function ‘PacBio::BAM::NamespaceRegistry::operator=(PacBio::BAM::NamespaceRegistry const&)’, inlined from ‘PacBio::BAM::DataSetBase::DeepCopy() const’ at ../src/DataSetTypes.cpp:329:25: ../include/pbbam/DataSetXsd.h:65:20: warning: array subscript 3 is outside array bounds of ‘void[184]’ [-Warray-bounds=] 65 | class PBBAM_EXPORT NamespaceRegistry | ^~~~~~~~~~~~~~~~~ ../src/DataSetTypes.cpp: In member function ‘PacBio::BAM::DataSetBase::DeepCopy() const’: ../src/DataSetTypes.cpp:327:49: note: at offset 184 into object of size 184 allocated by ‘operator new(unsigned long)’ 327 | auto* copyDataset = new DataSetElement(*this); | ^ [38/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -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.2.4.0.p/FastaSequence.cpp.o -MF src/libpbbam.so.2.4.0.p/FastaSequence.cpp.o.d -o 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-DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -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.2.4.0.p/FastaReader.cpp.o -MF src/libpbbam.so.2.4.0.p/FastaReader.cpp.o.d -o src/libpbbam.so.2.4.0.p/FastaReader.cpp.o -c ../src/FastaReader.cpp [41/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -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.2.4.0.p/FastqSequence.cpp.o -MF src/libpbbam.so.2.4.0.p/FastqSequence.cpp.o.d -o src/libpbbam.so.2.4.0.p/FastqSequence.cpp.o -c ../src/FastqSequence.cpp [42/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -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.2.4.0.p/FastaWriter.cpp.o -MF src/libpbbam.so.2.4.0.p/FastaWriter.cpp.o.d -o src/libpbbam.so.2.4.0.p/FastaWriter.cpp.o -c ../src/FastaWriter.cpp [43/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -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.2.4.0.p/FastaSequenceQuery.cpp.o -MF src/libpbbam.so.2.4.0.p/FastaSequenceQuery.cpp.o.d -o src/libpbbam.so.2.4.0.p/FastaSequenceQuery.cpp.o -c ../src/FastaSequenceQuery.cpp [44/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -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.2.4.0.p/FileProducer.cpp.o -MF src/libpbbam.so.2.4.0.p/FileProducer.cpp.o.d -o src/libpbbam.so.2.4.0.p/FileProducer.cpp.o -c ../src/FileProducer.cpp [45/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -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.2.4.0.p/FastqWriter.cpp.o -MF src/libpbbam.so.2.4.0.p/FastqWriter.cpp.o.d -o src/libpbbam.so.2.4.0.p/FastqWriter.cpp.o -c ../src/FastqWriter.cpp [46/226] 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-g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -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.2.4.0.p/RecordType.cpp.o -MF src/libpbbam.so.2.4.0.p/RecordType.cpp.o.d -o src/libpbbam.so.2.4.0.p/RecordType.cpp.o -c ../src/RecordType.cpp [74/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat 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-Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.2.4.0.p/PbiRawData.cpp.o -MF src/libpbbam.so.2.4.0.p/PbiRawData.cpp.o.d -o src/libpbbam.so.2.4.0.p/PbiRawData.cpp.o -c ../src/PbiRawData.cpp [76/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -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.2.4.0.p/RunMetadataParser.cpp.o -MF src/libpbbam.so.2.4.0.p/RunMetadataParser.cpp.o.d -o src/libpbbam.so.2.4.0.p/RunMetadataParser.cpp.o -c ../src/RunMetadataParser.cpp [77/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -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.2.4.0.p/SamReader.cpp.o -MF src/libpbbam.so.2.4.0.p/SamReader.cpp.o.d -o src/libpbbam.so.2.4.0.p/SamReader.cpp.o -c ../src/SamReader.cpp [78/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -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.2.4.0.p/SamTagCodec.cpp.o -MF src/libpbbam.so.2.4.0.p/SamTagCodec.cpp.o.d -o src/libpbbam.so.2.4.0.p/SamTagCodec.cpp.o -c ../src/SamTagCodec.cpp ../src/SamTagCodec.cpp: In static member function ‘static PacBio::BAM::TagCollection PacBio::BAM::SamTagCodec::Decode(const std::string&)’: ../src/SamTagCodec.cpp:79:63: warning: ignoring return value of ‘constexpr std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::const_reference std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator[](size_type) const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator; const_reference = const char&; size_type = long unsigned int]’, declared with attribute ‘nodiscard’ [-Wunused-result] 79 | tags[name] = Tag{static_cast(remainder[0], TagModifier::ASCII_CHAR)}; | ^ In file included from /usr/include/c++/13/string:54, from ../include/pbbam/Tag.h:7, from ../include/pbbam/TagCollection.h:6, from ../include/pbbam/SamTagCodec.h:6, from ../src/SamTagCodec.cpp:3: /usr/include/c++/13/bits/basic_string.h:1236:7: note: declared here 1236 | operator[] (size_type __pos) const _GLIBCXX_NOEXCEPT | ^~~~~~~~ [79/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra 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-DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -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.2.4.0.p/TextFileWriter.cpp.o -MF src/libpbbam.so.2.4.0.p/TextFileWriter.cpp.o.d -o src/libpbbam.so.2.4.0.p/TextFileWriter.cpp.o -c ../src/TextFileWriter.cpp [86/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -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.2.4.0.p/ValidationErrors.cpp.o -MF src/libpbbam.so.2.4.0.p/ValidationErrors.cpp.o.d -o src/libpbbam.so.2.4.0.p/ValidationErrors.cpp.o -c ../src/ValidationErrors.cpp [87/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -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.2.4.0.p/TextFileReader.cpp.o -MF src/libpbbam.so.2.4.0.p/TextFileReader.cpp.o.d -o src/libpbbam.so.2.4.0.p/TextFileReader.cpp.o -c ../src/TextFileReader.cpp [88/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -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.2.4.0.p/ValidationException.cpp.o -MF src/libpbbam.so.2.4.0.p/ValidationException.cpp.o.d -o src/libpbbam.so.2.4.0.p/ValidationException.cpp.o -c ../src/ValidationException.cpp [89/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -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.2.4.0.p/Version.cpp.o -MF src/libpbbam.so.2.4.0.p/Version.cpp.o.d -o src/libpbbam.so.2.4.0.p/Version.cpp.o -c ../src/Version.cpp [90/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -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.2.4.0.p/Tag.cpp.o -MF src/libpbbam.so.2.4.0.p/Tag.cpp.o.d -o src/libpbbam.so.2.4.0.p/Tag.cpp.o -c ../src/Tag.cpp [91/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -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.2.4.0.p/Validator.cpp.o -MF src/libpbbam.so.2.4.0.p/Validator.cpp.o.d -o src/libpbbam.so.2.4.0.p/Validator.cpp.o -c ../src/Validator.cpp [92/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -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.2.4.0.p/VirtualRegion.cpp.o -MF src/libpbbam.so.2.4.0.p/VirtualRegion.cpp.o.d -o src/libpbbam.so.2.4.0.p/VirtualRegion.cpp.o -c ../src/VirtualRegion.cpp [93/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -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.2.4.0.p/VirtualRegionTypeMap.cpp.o -MF src/libpbbam.so.2.4.0.p/VirtualRegionTypeMap.cpp.o.d -o src/libpbbam.so.2.4.0.p/VirtualRegionTypeMap.cpp.o -c ../src/VirtualRegionTypeMap.cpp [94/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -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.2.4.0.p/VirtualZmwBamRecord.cpp.o -MF src/libpbbam.so.2.4.0.p/VirtualZmwBamRecord.cpp.o.d -o src/libpbbam.so.2.4.0.p/VirtualZmwBamRecord.cpp.o -c ../src/VirtualZmwBamRecord.cpp [95/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -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.2.4.0.p/VirtualZmwCompositeReader.cpp.o -MF src/libpbbam.so.2.4.0.p/VirtualZmwCompositeReader.cpp.o.d -o src/libpbbam.so.2.4.0.p/VirtualZmwCompositeReader.cpp.o -c ../src/VirtualZmwCompositeReader.cpp [96/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -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.2.4.0.p/VirtualZmwReader.cpp.o -MF src/libpbbam.so.2.4.0.p/VirtualZmwReader.cpp.o.d -o src/libpbbam.so.2.4.0.p/VirtualZmwReader.cpp.o -c ../src/VirtualZmwReader.cpp [97/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -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.2.4.0.p/XmlWriter.cpp.o -MF src/libpbbam.so.2.4.0.p/XmlWriter.cpp.o.d -o src/libpbbam.so.2.4.0.p/XmlWriter.cpp.o -c ../src/XmlWriter.cpp [98/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -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.2.4.0.p/XmlReader.cpp.o -MF src/libpbbam.so.2.4.0.p/XmlReader.cpp.o.d -o src/libpbbam.so.2.4.0.p/XmlReader.cpp.o -c ../src/XmlReader.cpp [99/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -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.2.4.0.p/ZmwChunkedFastaReader.cpp.o -MF src/libpbbam.so.2.4.0.p/ZmwChunkedFastaReader.cpp.o.d -o src/libpbbam.so.2.4.0.p/ZmwChunkedFastaReader.cpp.o -c ../src/ZmwChunkedFastaReader.cpp ../src/ZmwChunkedFastaReader.cpp: In constructor ‘PacBio::BAM::ZmwChunkedFastaReader::ZmwChunkedFastaReaderPrivate::ZmwChunkedFastaReaderPrivate(const std::string&, size_t)’: ../src/ZmwChunkedFastaReader.cpp:78:48: warning: redundant move in initialization [-Wredundant-move] 78 | : reader_{MakeFastaReaderImpl(std::move(fn), numChunks)} | ~~~~~~~~~^~~~ ../src/ZmwChunkedFastaReader.cpp:78:48: note: remove ‘std::move’ call [100/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -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.2.4.0.p/ZmwChunkedFastxBgzfReader.cpp.o -MF src/libpbbam.so.2.4.0.p/ZmwChunkedFastxBgzfReader.cpp.o.d -o src/libpbbam.so.2.4.0.p/ZmwChunkedFastxBgzfReader.cpp.o -c ../src/ZmwChunkedFastxBgzfReader.cpp [101/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -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.2.4.0.p/ZmwChunkedFastxReaderImpl.cpp.o -MF src/libpbbam.so.2.4.0.p/ZmwChunkedFastxReaderImpl.cpp.o.d -o src/libpbbam.so.2.4.0.p/ZmwChunkedFastxReaderImpl.cpp.o -c ../src/ZmwChunkedFastxReaderImpl.cpp [102/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -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.2.4.0.p/WhitelistedZmwReadStitcher.cpp.o -MF src/libpbbam.so.2.4.0.p/WhitelistedZmwReadStitcher.cpp.o.d -o src/libpbbam.so.2.4.0.p/WhitelistedZmwReadStitcher.cpp.o -c ../src/WhitelistedZmwReadStitcher.cpp [103/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -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.2.4.0.p/ZmwChunkedFastqReader.cpp.o -MF src/libpbbam.so.2.4.0.p/ZmwChunkedFastqReader.cpp.o.d -o src/libpbbam.so.2.4.0.p/ZmwChunkedFastqReader.cpp.o -c ../src/ZmwChunkedFastqReader.cpp ../src/ZmwChunkedFastqReader.cpp: In constructor ‘PacBio::BAM::ZmwChunkedFastqReader::ZmwChunkedFastqReaderPrivate::ZmwChunkedFastqReaderPrivate(const std::string&, size_t)’: ../src/ZmwChunkedFastqReader.cpp:78:48: warning: redundant move in initialization [-Wredundant-move] 78 | : reader_{MakeFastqReaderImpl(std::move(fn), numChunks)} | ~~~~~~~~~^~~~ ../src/ZmwChunkedFastqReader.cpp:78:48: note: remove ‘std::move’ call [104/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -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.2.4.0.p/ZmwChunkedFastxTextReader.cpp.o -MF src/libpbbam.so.2.4.0.p/ZmwChunkedFastxTextReader.cpp.o.d -o src/libpbbam.so.2.4.0.p/ZmwChunkedFastxTextReader.cpp.o -c ../src/ZmwChunkedFastxTextReader.cpp [105/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -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.2.4.0.p/ZmwTypeMap.cpp.o -MF src/libpbbam.so.2.4.0.p/ZmwTypeMap.cpp.o.d -o src/libpbbam.so.2.4.0.p/ZmwTypeMap.cpp.o -c ../src/ZmwTypeMap.cpp [106/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -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.2.4.0.p/bed_BedReader.cpp.o -MF src/libpbbam.so.2.4.0.p/bed_BedReader.cpp.o.d -o src/libpbbam.so.2.4.0.p/bed_BedReader.cpp.o -c ../src/bed/BedReader.cpp [107/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -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.2.4.0.p/ZmwQuery.cpp.o -MF src/libpbbam.so.2.4.0.p/ZmwQuery.cpp.o.d -o src/libpbbam.so.2.4.0.p/ZmwQuery.cpp.o -c ../src/ZmwQuery.cpp [108/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -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.2.4.0.p/ZmwReadStitcher.cpp.o -MF src/libpbbam.so.2.4.0.p/ZmwReadStitcher.cpp.o.d -o src/libpbbam.so.2.4.0.p/ZmwReadStitcher.cpp.o -c ../src/ZmwReadStitcher.cpp [109/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -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.2.4.0.p/ZmwGroupQuery.cpp.o -MF src/libpbbam.so.2.4.0.p/ZmwGroupQuery.cpp.o.d -o src/libpbbam.so.2.4.0.p/ZmwGroupQuery.cpp.o -c ../src/ZmwGroupQuery.cpp [110/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -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.2.4.0.p/bed_BedWriter.cpp.o -MF src/libpbbam.so.2.4.0.p/bed_BedWriter.cpp.o.d -o src/libpbbam.so.2.4.0.p/bed_BedWriter.cpp.o -c ../src/bed/BedWriter.cpp [111/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -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.2.4.0.p/vcf_VcfFile.cpp.o -MF src/libpbbam.so.2.4.0.p/vcf_VcfFile.cpp.o.d -o src/libpbbam.so.2.4.0.p/vcf_VcfFile.cpp.o -c ../src/vcf/VcfFile.cpp [112/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -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.2.4.0.p/csv_CsvWriter.cpp.o -MF src/libpbbam.so.2.4.0.p/csv_CsvWriter.cpp.o.d -o src/libpbbam.so.2.4.0.p/csv_CsvWriter.cpp.o -c ../src/csv/CsvWriter.cpp [113/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -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.2.4.0.p/vcf_VcfHeaderTypes.cpp.o -MF src/libpbbam.so.2.4.0.p/vcf_VcfHeaderTypes.cpp.o.d -o src/libpbbam.so.2.4.0.p/vcf_VcfHeaderTypes.cpp.o -c ../src/vcf/VcfHeaderTypes.cpp [114/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -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.2.4.0.p/vcf_VcfHeader.cpp.o -MF src/libpbbam.so.2.4.0.p/vcf_VcfHeader.cpp.o.d -o src/libpbbam.so.2.4.0.p/vcf_VcfHeader.cpp.o -c ../src/vcf/VcfHeader.cpp [115/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -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.2.4.0.p/csv_CsvReader.cpp.o -MF src/libpbbam.so.2.4.0.p/csv_CsvReader.cpp.o.d -o src/libpbbam.so.2.4.0.p/csv_CsvReader.cpp.o -c ../src/csv/CsvReader.cpp [116/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -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.2.4.0.p/vcf_VcfFormat.cpp.o -MF src/libpbbam.so.2.4.0.p/vcf_VcfFormat.cpp.o.d -o src/libpbbam.so.2.4.0.p/vcf_VcfFormat.cpp.o -c ../src/vcf/VcfFormat.cpp [117/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -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.2.4.0.p/vcf_VcfReader.cpp.o -MF src/libpbbam.so.2.4.0.p/vcf_VcfReader.cpp.o.d -o src/libpbbam.so.2.4.0.p/vcf_VcfReader.cpp.o -c ../src/vcf/VcfReader.cpp [118/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -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.2.4.0.p/vcf_VcfQuery.cpp.o -MF src/libpbbam.so.2.4.0.p/vcf_VcfQuery.cpp.o.d -o src/libpbbam.so.2.4.0.p/vcf_VcfQuery.cpp.o -c ../src/vcf/VcfQuery.cpp [119/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -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.2.4.0.p/vcf_VcfWriter.cpp.o -MF src/libpbbam.so.2.4.0.p/vcf_VcfWriter.cpp.o.d -o src/libpbbam.so.2.4.0.p/vcf_VcfWriter.cpp.o -c ../src/vcf/VcfWriter.cpp [120/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -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.2.4.0.p/meson-generated_.._PbbamVersion.cpp.o -MF src/libpbbam.so.2.4.0.p/meson-generated_.._PbbamVersion.cpp.o.d -o src/libpbbam.so.2.4.0.p/meson-generated_.._PbbamVersion.cpp.o -c src/PbbamVersion.cpp [121/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -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.2.4.0.p/vcf_VcfVariant.cpp.o -MF src/libpbbam.so.2.4.0.p/vcf_VcfVariant.cpp.o.d -o src/libpbbam.so.2.4.0.p/vcf_VcfVariant.cpp.o -c ../src/vcf/VcfVariant.cpp ../src/vcf/VcfVariant.cpp: In member function ‘PacBio::VCF::VcfVariant& PacBio::VCF::VcfVariant::RemoveInfoField(const std::string&)’: ../src/vcf/VcfVariant.cpp:250:35: warning: redundant move in initialization [-Wredundant-move] 250 | AddInfoField(std::move(field)); | ~~~~~~~~~^~~~~~~ ../src/vcf/VcfVariant.cpp:250:35: note: remove ‘std::move’ call [122/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -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.2.4.0.p/vcf_VcfSort.cpp.o -MF src/libpbbam.so.2.4.0.p/vcf_VcfSort.cpp.o.d -o src/libpbbam.so.2.4.0.p/vcf_VcfSort.cpp.o -c ../src/vcf/VcfSort.cpp [123/226] c++ -Itests/pbbam_test.p -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -DBOOST_ALL_NO_LIB -DGTEST_HAS_PTHREAD=1 -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tests/pbbam_test.p/src_test_BamReader.cpp.o -MF tests/pbbam_test.p/src_test_BamReader.cpp.o.d -o tests/pbbam_test.p/src_test_BamReader.cpp.o -c ../tests/src/test_BamReader.cpp [124/226] c++ -Isrc/libpbbam.so.2.4.0.p -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -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.2.4.0.p/pugixml_pugixml.cpp.o -MF src/libpbbam.so.2.4.0.p/pugixml_pugixml.cpp.o.d -o src/libpbbam.so.2.4.0.p/pugixml_pugixml.cpp.o -c ../src/pugixml/pugixml.cpp [125/226] c++ -Itests/pbbam_test.p -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -DBOOST_ALL_NO_LIB -DGTEST_HAS_PTHREAD=1 -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tests/pbbam_test.p/src_test_BamHeader.cpp.o -MF tests/pbbam_test.p/src_test_BamHeader.cpp.o.d -o tests/pbbam_test.p/src_test_BamHeader.cpp.o -c ../tests/src/test_BamHeader.cpp [126/226] c++ -Itests/pbbam_test.p -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -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 ../tests/src/test_BamRecordImplCore.cpp: In member function ‘virtual void BAM_BamRecordImplCore_can_be_move_constructed_Test::TestBody()’: ../tests/src/test_BamRecordImplCore.cpp:425:73: warning: moving a temporary object prevents copy elision [-Wpessimizing-move] 425 | BamRecordImpl bam(std::move(BamRecordImplCoreTests::CreateBamImpl())); | ^ ../tests/src/test_BamRecordImplCore.cpp:425:73: note: remove ‘std::move’ call [127/226] c++ -Itests/pbbam_test.p -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -DBOOST_ALL_NO_LIB -DGTEST_HAS_PTHREAD=1 -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tests/pbbam_test.p/src_test_BamRecordImplTags.cpp.o -MF tests/pbbam_test.p/src_test_BamRecordImplTags.cpp.o.d -o tests/pbbam_test.p/src_test_BamRecordImplTags.cpp.o -c ../tests/src/test_BamRecordImplTags.cpp [128/226] c++ -Itests/pbbam_test.p -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -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_BamRecord.cpp.o -MF tests/pbbam_test.p/src_test_BamRecord.cpp.o.d -o tests/pbbam_test.p/src_test_BamRecord.cpp.o -c ../tests/src/test_BamRecord.cpp ../tests/src/test_BamRecord.cpp: In member function ‘virtual void BAM_BamRecord_can_be_constructed_from_bamrecordimpl_Test::TestBody()’: ../tests/src/test_BamRecord.cpp:771:29: warning: moving a temporary object prevents copy elision [-Wpessimizing-move] 771 | BamRecord bam3(std::move(BamRecordTests::CreateBamImpl())); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../tests/src/test_BamRecord.cpp:771:29: note: remove ‘std::move’ call ../tests/src/test_BamRecord.cpp:797:21: warning: moving a temporary object prevents copy elision [-Wpessimizing-move] 797 | bam4 = std::move(BamRecordTests::CreateBamImpl()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../tests/src/test_BamRecord.cpp:797:21: note: remove ‘std::move’ call [129/226] c++ -o src/libpbbam.so.2.4.0 src/libpbbam.so.2.4.0.p/meson-generated_.._PbbamGitHash.cpp.o src/libpbbam.so.2.4.0.p/AlignmentPrinter.cpp.o src/libpbbam.so.2.4.0.p/BaiIndexCache.cpp.o src/libpbbam.so.2.4.0.p/BaiIndexedBamReader.cpp.o src/libpbbam.so.2.4.0.p/BamFile.cpp.o src/libpbbam.so.2.4.0.p/BamFileMerger.cpp.o src/libpbbam.so.2.4.0.p/BamHeader.cpp.o src/libpbbam.so.2.4.0.p/BamReader.cpp.o src/libpbbam.so.2.4.0.p/BamRecord.cpp.o src/libpbbam.so.2.4.0.p/BamRecordImpl.cpp.o src/libpbbam.so.2.4.0.p/BamRecordTags.cpp.o src/libpbbam.so.2.4.0.p/BamRecordView.cpp.o src/libpbbam.so.2.4.0.p/BamTagCodec.cpp.o src/libpbbam.so.2.4.0.p/BamWriter.cpp.o src/libpbbam.so.2.4.0.p/BgzipFastaWriter.cpp.o src/libpbbam.so.2.4.0.p/BgzipFastqWriter.cpp.o src/libpbbam.so.2.4.0.p/BgzipWriter.cpp.o src/libpbbam.so.2.4.0.p/ChemistryTable.cpp.o src/libpbbam.so.2.4.0.p/CollectionMetadata.cpp.o src/libpbbam.so.2.4.0.p/Compare.cpp.o src/libpbbam.so.2.4.0.p/CompositeBamReader.cpp.o src/libpbbam.so.2.4.0.p/CompositeFastaReader.cpp.o src/libpbbam.so.2.4.0.p/Config.cpp.o src/libpbbam.so.2.4.0.p/DataSet.cpp.o src/libpbbam.so.2.4.0.p/DataSetBaseTypes.cpp.o src/libpbbam.so.2.4.0.p/DataSetElement.cpp.o src/libpbbam.so.2.4.0.p/DataSetIO.cpp.o src/libpbbam.so.2.4.0.p/DataSetTypes.cpp.o src/libpbbam.so.2.4.0.p/DataSetXsd.cpp.o src/libpbbam.so.2.4.0.p/EntireFileQuery.cpp.o src/libpbbam.so.2.4.0.p/ErrnoReason.cpp.o src/libpbbam.so.2.4.0.p/FaiIndex.cpp.o src/libpbbam.so.2.4.0.p/FaiZmwChunker.cpp.o src/libpbbam.so.2.4.0.p/FastaCache.cpp.o src/libpbbam.so.2.4.0.p/FastaReader.cpp.o src/libpbbam.so.2.4.0.p/FastaSequence.cpp.o src/libpbbam.so.2.4.0.p/FastaSequenceQuery.cpp.o src/libpbbam.so.2.4.0.p/FastaWriter.cpp.o src/libpbbam.so.2.4.0.p/FastqReader.cpp.o src/libpbbam.so.2.4.0.p/FastqSequence.cpp.o src/libpbbam.so.2.4.0.p/FastqWriter.cpp.o src/libpbbam.so.2.4.0.p/FileProducer.cpp.o src/libpbbam.so.2.4.0.p/FileUtils.cpp.o src/libpbbam.so.2.4.0.p/FofnReader.cpp.o src/libpbbam.so.2.4.0.p/FormatUtils.cpp.o src/libpbbam.so.2.4.0.p/GenomicIntervalQuery.cpp.o src/libpbbam.so.2.4.0.p/IFastaWriter.cpp.o src/libpbbam.so.2.4.0.p/IFastqWriter.cpp.o src/libpbbam.so.2.4.0.p/IndexedBamWriter.cpp.o src/libpbbam.so.2.4.0.p/IndexedFastaReader.cpp.o src/libpbbam.so.2.4.0.p/IndexedFastqBgzfReader.cpp.o src/libpbbam.so.2.4.0.p/IndexedFastqReader.cpp.o src/libpbbam.so.2.4.0.p/IndexedFastqTextReader.cpp.o src/libpbbam.so.2.4.0.p/IndexedFastqReaderImpl.cpp.o src/libpbbam.so.2.4.0.p/IRecordWriter.cpp.o src/libpbbam.so.2.4.0.p/KSeqReader.cpp.o src/libpbbam.so.2.4.0.p/LibraryInfo.cpp.o src/libpbbam.so.2.4.0.p/MD5.cpp.o src/libpbbam.so.2.4.0.p/MemoryUtils.cpp.o src/libpbbam.so.2.4.0.p/PbiBuilder.cpp.o src/libpbbam.so.2.4.0.p/PbiBuilderBase.cpp.o src/libpbbam.so.2.4.0.p/PbiFile.cpp.o src/libpbbam.so.2.4.0.p/PbiFilter.cpp.o src/libpbbam.so.2.4.0.p/PbiFilterQuery.cpp.o src/libpbbam.so.2.4.0.p/PbiFilterTypes.cpp.o src/libpbbam.so.2.4.0.p/PbiIndexedBamReader.cpp.o src/libpbbam.so.2.4.0.p/PbiIndexIO.cpp.o src/libpbbam.so.2.4.0.p/PbiRawData.cpp.o src/libpbbam.so.2.4.0.p/ProgramInfo.cpp.o src/libpbbam.so.2.4.0.p/ReadGroupInfo.cpp.o src/libpbbam.so.2.4.0.p/RecordType.cpp.o src/libpbbam.so.2.4.0.p/RunMetadata.cpp.o src/libpbbam.so.2.4.0.p/RunMetadataParser.cpp.o src/libpbbam.so.2.4.0.p/SamReader.cpp.o src/libpbbam.so.2.4.0.p/SamTagCodec.cpp.o src/libpbbam.so.2.4.0.p/SamWriter.cpp.o src/libpbbam.so.2.4.0.p/SequenceInfo.cpp.o src/libpbbam.so.2.4.0.p/StringUtilities.cpp.o src/libpbbam.so.2.4.0.p/Tag.cpp.o src/libpbbam.so.2.4.0.p/TagCollection.cpp.o src/libpbbam.so.2.4.0.p/TextFileReader.cpp.o src/libpbbam.so.2.4.0.p/TextFileWriter.cpp.o src/libpbbam.so.2.4.0.p/TimeUtils.cpp.o src/libpbbam.so.2.4.0.p/Validator.cpp.o src/libpbbam.so.2.4.0.p/ValidationErrors.cpp.o src/libpbbam.so.2.4.0.p/ValidationException.cpp.o src/libpbbam.so.2.4.0.p/Version.cpp.o src/libpbbam.so.2.4.0.p/VirtualZmwBamRecord.cpp.o src/libpbbam.so.2.4.0.p/VirtualZmwCompositeReader.cpp.o src/libpbbam.so.2.4.0.p/VirtualZmwReader.cpp.o src/libpbbam.so.2.4.0.p/VirtualRegion.cpp.o src/libpbbam.so.2.4.0.p/VirtualRegionTypeMap.cpp.o src/libpbbam.so.2.4.0.p/XmlReader.cpp.o src/libpbbam.so.2.4.0.p/XmlWriter.cpp.o src/libpbbam.so.2.4.0.p/WhitelistedZmwReadStitcher.cpp.o src/libpbbam.so.2.4.0.p/ZmwChunkedFastaReader.cpp.o src/libpbbam.so.2.4.0.p/ZmwChunkedFastqReader.cpp.o src/libpbbam.so.2.4.0.p/ZmwChunkedFastxBgzfReader.cpp.o src/libpbbam.so.2.4.0.p/ZmwChunkedFastxReaderImpl.cpp.o src/libpbbam.so.2.4.0.p/ZmwChunkedFastxTextReader.cpp.o src/libpbbam.so.2.4.0.p/ZmwGroupQuery.cpp.o src/libpbbam.so.2.4.0.p/ZmwReadStitcher.cpp.o src/libpbbam.so.2.4.0.p/ZmwQuery.cpp.o src/libpbbam.so.2.4.0.p/ZmwTypeMap.cpp.o src/libpbbam.so.2.4.0.p/bed_BedReader.cpp.o src/libpbbam.so.2.4.0.p/bed_BedWriter.cpp.o src/libpbbam.so.2.4.0.p/csv_CsvReader.cpp.o src/libpbbam.so.2.4.0.p/csv_CsvWriter.cpp.o src/libpbbam.so.2.4.0.p/vcf_VcfFile.cpp.o src/libpbbam.so.2.4.0.p/vcf_VcfFormat.cpp.o src/libpbbam.so.2.4.0.p/vcf_VcfHeader.cpp.o src/libpbbam.so.2.4.0.p/vcf_VcfHeaderTypes.cpp.o src/libpbbam.so.2.4.0.p/vcf_VcfQuery.cpp.o src/libpbbam.so.2.4.0.p/vcf_VcfReader.cpp.o src/libpbbam.so.2.4.0.p/vcf_VcfSort.cpp.o src/libpbbam.so.2.4.0.p/vcf_VcfVariant.cpp.o src/libpbbam.so.2.4.0.p/vcf_VcfWriter.cpp.o src/libpbbam.so.2.4.0.p/pugixml_pugixml.cpp.o src/libpbbam.so.2.4.0.p/meson-generated_.._PbbamVersion.cpp.o -Wl,--as-needed -Wl,--no-undefined -shared -fPIC -Wl,--start-group -Wl,-soname,libpbbam.so.2.4.0 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -pthread /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libhts.so 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-fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -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_ReadGroupInfo.cpp.o -MF tests/pbbam_test.p/src_test_ReadGroupInfo.cpp.o.d -o tests/pbbam_test.p/src_test_ReadGroupInfo.cpp.o -c ../tests/src/test_ReadGroupInfo.cpp [170/226] c++ -Itests/pbbam_test.p -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -DBOOST_ALL_NO_LIB -DGTEST_HAS_PTHREAD=1 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-Wformat=1 -MD -MQ tests/pbbam_test.p/src_test_ReadGroupHashing.cpp.o -MF tests/pbbam_test.p/src_test_ReadGroupHashing.cpp.o.d -o tests/pbbam_test.p/src_test_ReadGroupHashing.cpp.o -c ../tests/src/test_ReadGroupHashing.cpp [172/226] c++ -Itests/pbbam_test.p -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -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_RunMetadata.cpp.o -MF tests/pbbam_test.p/src_test_RunMetadata.cpp.o.d -o tests/pbbam_test.p/src_test_RunMetadata.cpp.o -c ../tests/src/test_RunMetadata.cpp [173/226] c++ -Itests/pbbam_test.p -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -DBOOST_ALL_NO_LIB -DGTEST_HAS_PTHREAD=1 -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tests/pbbam_test.p/src_test_PbiFilter.cpp.o -MF tests/pbbam_test.p/src_test_PbiFilter.cpp.o.d -o tests/pbbam_test.p/src_test_PbiFilter.cpp.o -c ../tests/src/test_PbiFilter.cpp [174/226] c++ -Itests/pbbam_test.p -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -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_SamIO.cpp.o -MF tests/pbbam_test.p/src_test_SamIO.cpp.o.d -o tests/pbbam_test.p/src_test_SamIO.cpp.o -c ../tests/src/test_SamIO.cpp In file included from /usr/include/c++/13/ios:45, from /usr/include/c++/13/istream:40, from /usr/include/c++/13/sstream:40, from ../include/pbbam/exception/InvalidSequencingChemistryException.h:7, from ../include/pbbam/ReadGroupInfo.h:6, from ../include/pbbam/BamHeader.h:7, from ../include/pbbam/SamReader.h:6, from ../tests/src/test_SamIO.cpp:1: In member function ‘std::basic_streambuf >::egptr() const’, inlined from ‘std::basic_streambuf >::sbumpc()’ at /usr/include/c++/13/streambuf:326:49, inlined from ‘std::istreambuf_iterator >::operator++()’ at /usr/include/c++/13/bits/streambuf_iterator.h:173:17, inlined from ‘std::__cxx11::basic_string, std::allocator >::_M_construct > >(std::istreambuf_iterator >, std::istreambuf_iterator >, std::input_iterator_tag)void’ at /usr/include/c++/13/bits/basic_string.tcc:182:6, inlined from ‘std::__cxx11::basic_string, std::allocator >::basic_string >, void>(std::istreambuf_iterator >, std::istreambuf_iterator >, std::allocator const&)’ at /usr/include/c++/13/bits/basic_string.h:765:16, inlined from ‘BAM_SamWriter_can_roundtrip_header_Test::TestBody()’ at ../tests/src/test_SamIO.cpp:78:64: /usr/include/c++/13/streambuf:495:30: warning: potential null pointer dereference [-Wnull-dereference] 495 | egptr() const { return _M_in_end; } | ^~~~~~~~~ In member function ‘std::basic_streambuf >::gptr() const’, inlined from ‘std::basic_streambuf >::sbumpc()’ at /usr/include/c++/13/streambuf:326:33, inlined from ‘std::istreambuf_iterator >::operator++()’ at /usr/include/c++/13/bits/streambuf_iterator.h:173:17, inlined from ‘std::__cxx11::basic_string, std::allocator >::_M_construct > >(std::istreambuf_iterator >, std::istreambuf_iterator >, std::input_iterator_tag)void’ at /usr/include/c++/13/bits/basic_string.tcc:182:6, inlined from ‘std::__cxx11::basic_string, std::allocator >::basic_string >, void>(std::istreambuf_iterator >, std::istreambuf_iterator >, std::allocator const&)’ at /usr/include/c++/13/bits/basic_string.h:765:16, inlined from ‘BAM_SamWriter_can_roundtrip_header_Test::TestBody()’ at ../tests/src/test_SamIO.cpp:78:64: /usr/include/c++/13/streambuf:492:30: warning: potential null pointer dereference [-Wnull-dereference] 492 | gptr() const { return _M_in_cur; } | ^~~~~~~~~ In member function ‘std::basic_streambuf >::egptr() const’, inlined from ‘std::basic_streambuf >::sbumpc()’ at /usr/include/c++/13/streambuf:326:49, inlined from ‘std::istreambuf_iterator >::operator++()’ at /usr/include/c++/13/bits/streambuf_iterator.h:173:17, inlined from ‘std::__cxx11::basic_string, std::allocator >::_M_construct > >(std::istreambuf_iterator >, std::istreambuf_iterator >, std::input_iterator_tag)void’ at /usr/include/c++/13/bits/basic_string.tcc:209:6, inlined from ‘std::__cxx11::basic_string, std::allocator >::basic_string >, void>(std::istreambuf_iterator >, std::istreambuf_iterator >, std::allocator const&)’ at /usr/include/c++/13/bits/basic_string.h:765:16, inlined from ‘BAM_SamWriter_can_roundtrip_header_Test::TestBody()’ at ../tests/src/test_SamIO.cpp:78:64: /usr/include/c++/13/streambuf:495:30: warning: potential null pointer dereference [-Wnull-dereference] 495 | egptr() const { return _M_in_end; } | ^~~~~~~~~ In member function ‘std::basic_streambuf >::gptr() const’, inlined from ‘std::basic_streambuf >::sbumpc()’ at /usr/include/c++/13/streambuf:326:33, inlined from ‘std::istreambuf_iterator >::operator++()’ at /usr/include/c++/13/bits/streambuf_iterator.h:173:17, inlined from ‘std::__cxx11::basic_string, std::allocator >::_M_construct > >(std::istreambuf_iterator >, std::istreambuf_iterator >, std::input_iterator_tag)void’ at /usr/include/c++/13/bits/basic_string.tcc:209:6, inlined from ‘std::__cxx11::basic_string, std::allocator >::basic_string >, void>(std::istreambuf_iterator >, std::istreambuf_iterator >, std::allocator const&)’ at /usr/include/c++/13/bits/basic_string.h:765:16, inlined from ‘BAM_SamWriter_can_roundtrip_header_Test::TestBody()’ at ../tests/src/test_SamIO.cpp:78:64: /usr/include/c++/13/streambuf:492:30: warning: potential null pointer dereference [-Wnull-dereference] 492 | gptr() const { return _M_in_cur; } | ^~~~~~~~~ [175/226] c++ -Itests/pbbam_test.p -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -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_SequenceUtils.cpp.o -MF tests/pbbam_test.p/src_test_SequenceUtils.cpp.o.d -o tests/pbbam_test.p/src_test_SequenceUtils.cpp.o -c ../tests/src/test_SequenceUtils.cpp [176/226] c++ -Itests/pbbam_test.p -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -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_StringUtils.cpp.o -MF tests/pbbam_test.p/src_test_StringUtils.cpp.o.d -o tests/pbbam_test.p/src_test_StringUtils.cpp.o -c ../tests/src/test_StringUtils.cpp [177/226] c++ -Itests/pbbam_test.p -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -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_SegmentReads.cpp.o -MF tests/pbbam_test.p/src_test_SegmentReads.cpp.o.d -o tests/pbbam_test.p/src_test_SegmentReads.cpp.o -c ../tests/src/test_SegmentReads.cpp [178/226] c++ -Itests/pbbam_test.p -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -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_TextFileWriter.cpp.o -MF tests/pbbam_test.p/src_test_TextFileWriter.cpp.o.d -o tests/pbbam_test.p/src_test_TextFileWriter.cpp.o -c ../tests/src/test_TextFileWriter.cpp [179/226] c++ -Itests/pbbam_test.p -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -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_TextFileReader.cpp.o -MF tests/pbbam_test.p/src_test_TextFileReader.cpp.o.d -o tests/pbbam_test.p/src_test_TextFileReader.cpp.o -c ../tests/src/test_TextFileReader.cpp [180/226] c++ -Itests/pbbam_test.p -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -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_TimeUtils.cpp.o -MF tests/pbbam_test.p/src_test_TimeUtils.cpp.o.d -o tests/pbbam_test.p/src_test_TimeUtils.cpp.o -c ../tests/src/test_TimeUtils.cpp [181/226] c++ -Itests/pbbam_test.p -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -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_VcfFile.cpp.o -MF tests/pbbam_test.p/src_test_VcfFile.cpp.o.d -o tests/pbbam_test.p/src_test_VcfFile.cpp.o -c ../tests/src/test_VcfFile.cpp [182/226] c++ -Itests/pbbam_test.p -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -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 [183/226] c++ -Itests/pbbam_test.p -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -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_Validator.cpp.o -MF tests/pbbam_test.p/src_test_Validator.cpp.o.d -o tests/pbbam_test.p/src_test_Validator.cpp.o -c ../tests/src/test_Validator.cpp [184/226] c++ -Itests/pbbam_test.p -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -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 [185/226] c++ -Itests/pbbam_test.p -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -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 In file included from ../tests/src/test_Tags.cpp:14: In function ‘testing::internal::CmpHelperEQ(char const*, char const*, unsigned int const&, unsigned int const&)testing::AssertionResult’, inlined from ‘testing::internal::EqHelper::Compare(char const*, char const*, unsigned int const&, unsigned int const&)testing::AssertionResult’ at /usr/include/gtest/gtest.h:1398:64, inlined from ‘BAM_Tag_can_describe_uint32_tag_Test::TestBody()’ at ../tests/src/test_Tags.cpp:391:5: /usr/include/gtest/gtest.h:1379:3: warning: ‘v2’ may be used uninitialized [-Wmaybe-uninitialized] 1379 | if (lhs == rhs) { | ^~ ../tests/src/test_Tags.cpp: In member function ‘BAM_Tag_can_describe_uint32_tag_Test::TestBody()’: ../tests/src/test_Tags.cpp:375:14: note: ‘v2’ was declared here 375 | uint32_t v2; | ^~ In function ‘testing::internal::CmpHelperEQ(char const*, char const*, unsigned short const&, unsigned short const&)testing::AssertionResult’, inlined from ‘testing::internal::EqHelper::Compare(char const*, char const*, unsigned short const&, unsigned short const&)testing::AssertionResult’ at /usr/include/gtest/gtest.h:1398:64, inlined from ‘BAM_Tag_can_describe_uint16_tag_Test::TestBody()’ at ../tests/src/test_Tags.cpp:343:5: /usr/include/gtest/gtest.h:1379:3: warning: ‘v2’ may be used uninitialized [-Wmaybe-uninitialized] 1379 | if (lhs == rhs) { | ^~ ../tests/src/test_Tags.cpp: In member function ‘BAM_Tag_can_describe_uint16_tag_Test::TestBody()’: ../tests/src/test_Tags.cpp:327:14: note: ‘v2’ was declared here 327 | uint16_t v2; | ^~ [186/226] c++ -Itests/pbbam_test.p -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -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 [187/226] c++ -Itests/pbbam_test.p -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -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 [188/226] c++ -Itests/pbbam_test.p -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -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 [189/226] c++ -Itests/pbbam_test.p -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -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 [190/226] c++ -Itests/pbbam_test.p -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -DBOOST_ALL_NO_LIB -DGTEST_HAS_PTHREAD=1 -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tests/pbbam_test.p/src_test_VcfWriter.cpp.o -MF tests/pbbam_test.p/src_test_VcfWriter.cpp.o.d -o tests/pbbam_test.p/src_test_VcfWriter.cpp.o -c ../tests/src/test_VcfWriter.cpp [191/226] c++ -Itests/pbbam_test.p -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -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 [192/226] c++ -Itests/pbbam_test.p -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -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 [193/226] /usr/bin/python3 ../tests/scripts/generate_data.py /<>/tests/data /<>/obj-x86_64-linux-gnu/tests Generating test data in /<>/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. [194/226] c++ -Itests/pbbam_test.p -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -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 [195/226] c++ -Itools/bam2sam.p -Itools -I../tools -Iinclude -I../include -I../tools/bam2sam -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tools/bam2sam.p/bam2sam_src_main.cpp.o -MF tools/bam2sam.p/bam2sam_src_main.cpp.o.d -o tools/bam2sam.p/bam2sam_src_main.cpp.o -c ../tools/bam2sam/src/main.cpp [196/226] 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 -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -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 [197/226] 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 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 '-Wl,-rpath,$ORIGIN/../../src' -Wl,-rpath-link,/<>/obj-x86_64-linux-gnu/src -Wl,--start-group src/libpbbam.so.2.4.0 /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 [198/226] c++ -Itests/pbbam_test.p -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -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 [199/226] c++ -Itools/bam2sam.p -Itools -I../tools -Iinclude -I../include -I../tools/bam2sam -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -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 [200/226] c++ -Itools/bam2sam.p -Itools -I../tools -Iinclude -I../include -I../tools/bam2sam -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -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 [201/226] c++ -Itests/pbbam_test.p -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -DBOOST_ALL_NO_LIB -DGTEST_HAS_PTHREAD=1 -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tests/pbbam_test.p/src_test_ZmwReadStitcher.cpp.o -MF tests/pbbam_test.p/src_test_ZmwReadStitcher.cpp.o.d -o tests/pbbam_test.p/src_test_ZmwReadStitcher.cpp.o -c ../tests/src/test_ZmwReadStitcher.cpp [202/226] c++ -Itools/pbindex.p -Itools -I../tools -Iinclude -I../include -I../tools/pbindex -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -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 [203/226] 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 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -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 [204/226] c++ -Itools/pbindex.p -Itools -I../tools -Iinclude -I../include -I../tools/pbindex -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -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 [205/226] c++ -Itools/pbindex.p -Itools -I../tools -Iinclude -I../include -I../tools/pbindex -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -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 [206/226] 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 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 '-Wl,-rpath,$ORIGIN/../src' -Wl,-rpath-link,/<>/obj-x86_64-linux-gnu/src -Wl,--start-group src/libpbbam.so.2.4.0 /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 [207/226] c++ -Itools/pbindexdump.p -Itools -I../tools -Iinclude -I../include -I../tools/pbindexdump -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -DBOOST_ALL_NO_LIB -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tools/pbindexdump.p/pbindexdump_src_CppFormatter.cpp.o -MF tools/pbindexdump.p/pbindexdump_src_CppFormatter.cpp.o.d -o 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-Itools/pbindexdump.p -Itools -I../tools -Iinclude -I../include -I../tools/pbindexdump -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -DBOOST_ALL_NO_LIB -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tools/pbindexdump.p/pbindexdump_src_main.cpp.o -MF tools/pbindexdump.p/pbindexdump_src_main.cpp.o.d -o tools/pbindexdump.p/pbindexdump_src_main.cpp.o -c ../tools/pbindexdump/src/main.cpp [211/226] c++ -Itools/pbmerge.p -Itools -I../tools -Iinclude -I../include -I../tools/pbmerge -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -DBOOST_ALL_NO_LIB -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tools/pbmerge.p/pbmerge_src_main.cpp.o -MF tools/pbmerge.p/pbmerge_src_main.cpp.o.d -o tools/pbmerge.p/pbmerge_src_main.cpp.o -c ../tools/pbmerge/src/main.cpp [212/226] c++ -Itools/pbindexdump.p -Itools -I../tools -Iinclude -I../include -I../tools/pbindexdump -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects 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-fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -DBOOST_ALL_NO_LIB -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tools/pbmerge.p/pbmerge_src_PbMergeSettings.cpp.o -MF tools/pbmerge.p/pbmerge_src_PbMergeSettings.cpp.o.d -o tools/pbmerge.p/pbmerge_src_PbMergeSettings.cpp.o -c ../tools/pbmerge/src/PbMergeSettings.cpp [214/226] c++ -Itools/pbmerge.p -Itools -I../tools -Iinclude -I../include -I../tools/pbmerge -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -DBOOST_ALL_NO_LIB -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tools/pbmerge.p/pbmerge_src_PbMergeWorkflow.cpp.o -MF tools/pbmerge.p/pbmerge_src_PbMergeWorkflow.cpp.o.d -o tools/pbmerge.p/pbmerge_src_PbMergeWorkflow.cpp.o -c ../tools/pbmerge/src/PbMergeWorkflow.cpp [215/226] c++ -o tools/pbindexdump tools/pbindexdump.p/pbindexdump_src_CppFormatter.cpp.o tools/pbindexdump.p/pbindexdump_src_JsonFormatter.cpp.o tools/pbindexdump.p/pbindexdump_src_PbIndexDumpSettings.cpp.o tools/pbindexdump.p/pbindexdump_src_PbIndexDumpWorkflow.cpp.o tools/pbindexdump.p/pbindexdump_src_main.cpp.o -Wl,--as-needed -Wl,--no-undefined -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 '-Wl,-rpath,$ORIGIN/../src' -Wl,-rpath-link,/<>/obj-x86_64-linux-gnu/src -Wl,--start-group src/libpbbam.so.2.4.0 /usr/lib/x86_64-linux-gnu/libhts.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libpbcopper.so -Wl,--end-group [216/226] c++ -o tools/pbmerge tools/pbmerge.p/pbmerge_src_main.cpp.o tools/pbmerge.p/pbmerge_src_PbMergeSettings.cpp.o tools/pbmerge.p/pbmerge_src_PbMergeWorkflow.cpp.o -Wl,--as-needed -Wl,--no-undefined -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 '-Wl,-rpath,$ORIGIN/../src' -Wl,-rpath-link,/<>/obj-x86_64-linux-gnu/src -Wl,--start-group src/libpbbam.so.2.4.0 /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 [217/226] c++ -Itools/pbbamify.p -Itools -I../tools -Iinclude -I../include -I../tools/pbbamify -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -DBOOST_ALL_NO_LIB -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tools/pbbamify.p/pbbamify_src_main.cpp.o -MF tools/pbbamify.p/pbbamify_src_main.cpp.o.d -o tools/pbbamify.p/pbbamify_src_main.cpp.o -c ../tools/pbbamify/src/main.cpp [218/226] c++ -Itools/pbbamify.p -Itools -I../tools -Iinclude -I../include -I../tools/pbbamify -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -DBOOST_ALL_NO_LIB -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tools/pbbamify.p/pbbamify_src_PbBamifySettings.cpp.o -MF tools/pbbamify.p/pbbamify_src_PbBamifySettings.cpp.o.d -o tools/pbbamify.p/pbbamify_src_PbBamifySettings.cpp.o -c ../tools/pbbamify/src/PbBamifySettings.cpp [219/226] c++ -Itools/ccs-kinetics-bystrandify.p -Itools -I../tools -Iinclude -I../include -I../tools/ccs-kinetics-bystrandify -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -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 [220/226] c++ -Itools/pbbamify.p -Itools -I../tools -Iinclude -I../include -I../tools/pbbamify 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-fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -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 [222/226] c++ -Itools/ccs-kinetics-bystrandify.p -Itools -I../tools -Iinclude -I../include -I../tools/ccs-kinetics-bystrandify -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -DBOOST_ALL_NO_LIB -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ tools/ccs-kinetics-bystrandify.p/ccs-kinetics-bystrandify_src_CcsKineticsBystrandifySettings.cpp.o -MF tools/ccs-kinetics-bystrandify.p/ccs-kinetics-bystrandify_src_CcsKineticsBystrandifySettings.cpp.o.d -o tools/ccs-kinetics-bystrandify.p/ccs-kinetics-bystrandify_src_CcsKineticsBystrandifySettings.cpp.o -c ../tools/ccs-kinetics-bystrandify/src/CcsKineticsBystrandifySettings.cpp [223/226] 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 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 '-Wl,-rpath,$ORIGIN/../src' -Wl,-rpath-link,/<>/obj-x86_64-linux-gnu/src -Wl,--start-group src/libpbbam.so.2.4.0 /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 [224/226] c++ -Itools/ccs-kinetics-bystrandify.p -Itools -I../tools -Iinclude -I../include -I../tools/ccs-kinetics-bystrandify -fdiagnostics-color=always -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++20 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 -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 [225/226] 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 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 '-Wl,-rpath,$ORIGIN/../src' -Wl,-rpath-link,/<>/obj-x86_64-linux-gnu/src -Wl,--start-group src/libpbbam.so.2.4.0 /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 [226/226] c++ -o tests/pbbam_test tests/pbbam_test.p/src_test_AlignmentPrinter.cpp.o tests/pbbam_test.p/src_test_BamFile.cpp.o tests/pbbam_test.p/src_test_BamHeader.cpp.o tests/pbbam_test.p/src_test_BamReader.cpp.o tests/pbbam_test.p/src_test_BamRecord.cpp.o tests/pbbam_test.p/src_test_BamRecordClipping.cpp.o tests/pbbam_test.p/src_test_BamRecordImplCore.cpp.o tests/pbbam_test.p/src_test_BamRecordImplTags.cpp.o tests/pbbam_test.p/src_test_BamRecordImplVariableData.cpp.o tests/pbbam_test.p/src_test_BamRecordMapping.cpp.o tests/pbbam_test.p/src_test_BamWriter.cpp.o tests/pbbam_test.p/src_test_BedReader.cpp.o tests/pbbam_test.p/src_test_BedWriter.cpp.o tests/pbbam_test.p/src_test_BgzipFastaWriter.cpp.o tests/pbbam_test.p/src_test_BgzipFastqWriter.cpp.o tests/pbbam_test.p/src_test_BgzipWriter.cpp.o tests/pbbam_test.p/src_test_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_Csv.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_Pulse2BaseCache.cpp.o tests/pbbam_test.p/src_test_ReadGroupHashing.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_SegmentReads.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 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/pbbam-2.4.0+dfsg-1build1 -Wdate-time -D_FORTIFY_SOURCE=3 '-Wl,-rpath,$ORIGIN/../src' -Wl,-rpath-link,/<>/obj-x86_64-linux-gnu/src -Wl,--start-group src/libpbbam.so.2.4.0 /usr/lib/x86_64-linux-gnu/libgtest_main.a /usr/lib/x86_64-linux-gnu/libgtest.a /usr/lib/x86_64-linux-gnu/libhts.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libpbcopper.so -Wl,--end-group debian/rules override_dh_auto_test make[1]: Entering directory '/<>' sed \ -e 's/$BAM2SAM/samtools view/g' \ -e 's/\-\-header\-only/-H/g' \ -e 's/\-\-no\-header//g' \ -e 's|@PacBioBAM_BinDir@/||g' \ -e 's|$TOOLS_BIN/||g' \ -e 's|@PacBioBAM_TestsDir@|/<>/tests|g' \ -e 's|@PacBioBAM_VERSION@|2.4.0+dfsg|g' \ -e 's|@GeneratedTestDataDir@|/<>/gendata|g' \ -e '/@PG/s|+dfsg||g' \ -e 's/$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@|/<>/tests|g' \ -e 's|@PacBioBAM_VERSION@|2.4.0+dfsg|g' \ -e 's|@GeneratedTestDataDir@|/<>/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|$TOOLS_BIN/||g' \ -e 's|@PacBioBAM_TestsDir@|/<>/tests|g' \ -e 's|@PacBioBAM_VERSION@|2.4.0+dfsg|g' \ -e 's|@GeneratedTestDataDir@|/<>/gendata|g' \ -e '/@PG/s|+dfsg||g' \ -e 's/$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@|/<>/tests|g' \ -e 's|@PacBioBAM_VERSION@|2.4.0+dfsg|g' \ -e 's|@GeneratedTestDataDir@|/<>/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|$TOOLS_BIN/||g' \ -e 's|@PacBioBAM_TestsDir@|/<>/tests|g' \ -e 's|@PacBioBAM_VERSION@|2.4.0+dfsg|g' \ -e 's|@GeneratedTestDataDir@|/<>/gendata|g' \ -e '/@PG/s|+dfsg||g' \ -e 's/$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@|/<>/tests|g' \ -e 's|@PacBioBAM_VERSION@|2.4.0+dfsg|g' \ -e 's|@GeneratedTestDataDir@|/<>/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|$TOOLS_BIN/||g' \ -e 's|@PacBioBAM_TestsDir@|/<>/tests|g' \ -e 's|@PacBioBAM_VERSION@|2.4.0+dfsg|g' \ -e 's|@GeneratedTestDataDir@|/<>/gendata|g' \ -e '/@PG/s|+dfsg||g' \ -e 's/$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@|/<>/tests|g' \ -e 's|@PacBioBAM_VERSION@|2.4.0+dfsg|g' \ -e 's|@GeneratedTestDataDir@|/<>/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 && DEB_PYTHON_INSTALL_LAYOUT=deb LC_ALL=C.UTF-8 meson setup .. --wrap-mode=nodownload --buildtype=plain --prefix=/usr --sysconfdir=/etc --localstatedir=/var --libdir=lib/x86_64-linux-gnu -Dpython.bytecompile=-1 Directory already configured. Just run your build command (e.g. ninja) and Meson will regenerate as necessary. Run "meson setup --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. mkdir -p /<>/gendata python3 tests/scripts/generate_data.py /<>/tests/data /<>/gendata Generating test data in /<>/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 '/<>' 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-2.4.0\+dfsg/debian/tmp LC_ALL=C.UTF-8 ninja install [0/1] Regenerating build files. Cleaning... 0 files. The Meson build system Version: 1.3.2 Source dir: /<> Build dir: /<>/obj-x86_64-linux-gnu Build type: native build Project name: PacBioBAM Project version: 2.4.0 C compiler for the host machine: cc (gcc 13.2.0 "cc (Ubuntu 13.2.0-13ubuntu1) 13.2.0") C linker for the host machine: cc ld.bfd 2.42 C++ compiler for the host machine: c++ (gcc 13.2.0 "c++ (Ubuntu 13.2.0-13ubuntu1) 13.2.0") C++ linker for the host machine: c++ ld.bfd 2.42 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 1.83.0 (cached) Dependency zlib found: YES 1.3 (cached) Dependency htslib found: YES 1.19 (cached) Dependency pbcopper found: YES 2.3.0 (cached) Configuring PbbamVersion.cpp using configuration Configuring LibraryVersion.h using configuration Program tools/check-formatting found: YES (/<>/tools/check-formatting) Program python3 found: YES (/usr/bin/python3) Program cram3 found: YES (/usr/bin/cram3) Dependency gtest found: YES 1.14.0 (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 Found pkg-config: YES (/usr/bin/pkg-config) 1.8.1 Build targets in project: 12 PacBioBAM 2.4.0 User defined options buildtype : plain libdir : lib/x86_64-linux-gnu localstatedir : /var prefix : /usr sysconfdir : /etc wrap_mode : nodownload python.bytecompile: -1 Found ninja-1.11.1 at /usr/bin/ninja [1/15] Generating tests/pbbam_generate_data with a custom command [2/15] Generating src/LibraryGitHash.h with a custom command [3/14] Generating src/PbbamGitHash.cpp with a custom command [3/4] Installing files. Installing src/libpbbam.so.2.4.0 to /<>/debian/tmp/usr/lib/x86_64-linux-gnu Installing tools/bam2sam to /<>/debian/tmp/usr/bin Installing tools/pbindex to /<>/debian/tmp/usr/bin Installing tools/pbindexdump to /<>/debian/tmp/usr/bin Installing tools/pbmerge to /<>/debian/tmp/usr/bin Installing tools/pbbamify to /<>/debian/tmp/usr/bin Installing tools/ccs-kinetics-bystrandify to /<>/debian/tmp/usr/bin Installing /<>/include/pbbam/AlignmentPrinter.h to /<>/debian/tmp/usr/include/pbbam Installing /<>/include/pbbam/BaiIndexCache.h to /<>/debian/tmp/usr/include/pbbam Installing /<>/include/pbbam/BaiIndexedBamReader.h to /<>/debian/tmp/usr/include/pbbam Installing /<>/include/pbbam/BamFile.h to /<>/debian/tmp/usr/include/pbbam Installing /<>/include/pbbam/BamFileMerger.h to /<>/debian/tmp/usr/include/pbbam Installing /<>/include/pbbam/BamHeader.h to /<>/debian/tmp/usr/include/pbbam Installing /<>/include/pbbam/BamReader.h to /<>/debian/tmp/usr/include/pbbam Installing /<>/include/pbbam/BamRecord.h to /<>/debian/tmp/usr/include/pbbam Installing /<>/include/pbbam/BamRecordImpl.h to /<>/debian/tmp/usr/include/pbbam Installing /<>/include/pbbam/BamRecordTag.h to /<>/debian/tmp/usr/include/pbbam Installing /<>/include/pbbam/BamRecordView.h to /<>/debian/tmp/usr/include/pbbam Installing /<>/include/pbbam/BamTagCodec.h to /<>/debian/tmp/usr/include/pbbam Installing /<>/include/pbbam/BamWriter.h to /<>/debian/tmp/usr/include/pbbam Installing /<>/include/pbbam/BgzipFastaWriter.h to /<>/debian/tmp/usr/include/pbbam Installing /<>/include/pbbam/BgzipFastqWriter.h to /<>/debian/tmp/usr/include/pbbam Installing /<>/include/pbbam/BgzipWriter.h to /<>/debian/tmp/usr/include/pbbam Installing /<>/include/pbbam/ClipType.h to /<>/debian/tmp/usr/include/pbbam Installing /<>/include/pbbam/CollectionMetadata.h to /<>/debian/tmp/usr/include/pbbam Installing /<>/include/pbbam/Compare.h to /<>/debian/tmp/usr/include/pbbam Installing /<>/include/pbbam/CompositeBamReader.h to /<>/debian/tmp/usr/include/pbbam Installing /<>/include/pbbam/CompositeFastaReader.h to /<>/debian/tmp/usr/include/pbbam Installing /<>/include/pbbam/Config.h to /<>/debian/tmp/usr/include/pbbam Installing /<>/include/pbbam/DataSet.h to /<>/debian/tmp/usr/include/pbbam Installing /<>/include/pbbam/DataSetTypes.h to /<>/debian/tmp/usr/include/pbbam Installing /<>/include/pbbam/DataSetXsd.h to /<>/debian/tmp/usr/include/pbbam Installing /<>/include/pbbam/Deleters.h to /<>/debian/tmp/usr/include/pbbam Installing /<>/include/pbbam/EntireFileQuery.h to /<>/debian/tmp/usr/include/pbbam Installing /<>/include/pbbam/FaiIndex.h to /<>/debian/tmp/usr/include/pbbam Installing /<>/include/pbbam/FastaCache.h to /<>/debian/tmp/usr/include/pbbam Installing /<>/include/pbbam/FastaReader.h to /<>/debian/tmp/usr/include/pbbam Installing /<>/include/pbbam/FastaSequence.h to /<>/debian/tmp/usr/include/pbbam Installing /<>/include/pbbam/FastaSequenceQuery.h to /<>/debian/tmp/usr/include/pbbam Installing /<>/include/pbbam/FastaWriter.h to /<>/debian/tmp/usr/include/pbbam Installing /<>/include/pbbam/FastqReader.h to /<>/debian/tmp/usr/include/pbbam Installing /<>/include/pbbam/FastqSequence.h to /<>/debian/tmp/usr/include/pbbam Installing /<>/include/pbbam/FastqWriter.h to /<>/debian/tmp/usr/include/pbbam Installing /<>/include/pbbam/FormatUtils.h to /<>/debian/tmp/usr/include/pbbam Installing /<>/include/pbbam/FrameEncodingType.h to /<>/debian/tmp/usr/include/pbbam Installing /<>/include/pbbam/GenomicIntervalQuery.h to /<>/debian/tmp/usr/include/pbbam Installing /<>/include/pbbam/IFastaWriter.h to /<>/debian/tmp/usr/include/pbbam Installing /<>/include/pbbam/IFastqWriter.h to /<>/debian/tmp/usr/include/pbbam Installing /<>/include/pbbam/IndexedBamWriter.h to /<>/debian/tmp/usr/include/pbbam Installing /<>/include/pbbam/IndexedFastaReader.h to /<>/debian/tmp/usr/include/pbbam Installing /<>/include/pbbam/IndexedFastqReader.h to /<>/debian/tmp/usr/include/pbbam Installing /<>/include/pbbam/IRecordWriter.h to /<>/debian/tmp/usr/include/pbbam Installing /<>/include/pbbam/LibraryInfo.h to /<>/debian/tmp/usr/include/pbbam Installing /<>/include/pbbam/MD5.h to /<>/debian/tmp/usr/include/pbbam Installing /<>/include/pbbam/MoveAppend.h to /<>/debian/tmp/usr/include/pbbam Installing /<>/include/pbbam/PbbamVersion.h to /<>/debian/tmp/usr/include/pbbam Installing /<>/include/pbbam/PbiBasicTypes.h to /<>/debian/tmp/usr/include/pbbam Installing /<>/include/pbbam/PbiBuilder.h to /<>/debian/tmp/usr/include/pbbam Installing /<>/include/pbbam/PbiFile.h to /<>/debian/tmp/usr/include/pbbam Installing /<>/include/pbbam/PbiFilter.h to /<>/debian/tmp/usr/include/pbbam Installing /<>/include/pbbam/PbiFilterQuery.h to /<>/debian/tmp/usr/include/pbbam Installing /<>/include/pbbam/PbiFilterTypes.h to /<>/debian/tmp/usr/include/pbbam Installing /<>/include/pbbam/PbiIndexedBamReader.h to /<>/debian/tmp/usr/include/pbbam Installing /<>/include/pbbam/PbiRawData.h to /<>/debian/tmp/usr/include/pbbam Installing /<>/include/pbbam/ProgramInfo.h to /<>/debian/tmp/usr/include/pbbam Installing /<>/include/pbbam/PulseBehavior.h to /<>/debian/tmp/usr/include/pbbam Installing /<>/include/pbbam/PulseExclusionReason.h to /<>/debian/tmp/usr/include/pbbam Installing /<>/include/pbbam/ReadGroupInfo.h to /<>/debian/tmp/usr/include/pbbam Installing /<>/include/pbbam/RecordType.h to /<>/debian/tmp/usr/include/pbbam Installing /<>/include/pbbam/RunMetadata.h to /<>/debian/tmp/usr/include/pbbam Installing /<>/include/pbbam/SamReader.h to /<>/debian/tmp/usr/include/pbbam Installing /<>/include/pbbam/SamTagCodec.h to /<>/debian/tmp/usr/include/pbbam Installing /<>/include/pbbam/SamWriter.h to /<>/debian/tmp/usr/include/pbbam Installing /<>/include/pbbam/SequenceInfo.h to /<>/debian/tmp/usr/include/pbbam Installing /<>/include/pbbam/StringUtilities.h to /<>/debian/tmp/usr/include/pbbam Installing /<>/include/pbbam/Tag.h to /<>/debian/tmp/usr/include/pbbam Installing /<>/include/pbbam/TagCollection.h to /<>/debian/tmp/usr/include/pbbam Installing /<>/include/pbbam/TextFileReader.h to /<>/debian/tmp/usr/include/pbbam Installing /<>/include/pbbam/TextFileWriter.h to /<>/debian/tmp/usr/include/pbbam Installing /<>/include/pbbam/Validator.h to /<>/debian/tmp/usr/include/pbbam Installing /<>/include/pbbam/ZmwGroupQuery.h to /<>/debian/tmp/usr/include/pbbam Installing /<>/include/pbbam/ZmwQuery.h to /<>/debian/tmp/usr/include/pbbam Installing /<>/include/pbbam/ZmwType.h to /<>/debian/tmp/usr/include/pbbam Installing /<>/include/pbbam/ZmwTypeMap.h to /<>/debian/tmp/usr/include/pbbam Installing /<>/include/pbbam/bed/BedReader.h to /<>/debian/tmp/usr/include/pbbam/bed Installing /<>/include/pbbam/bed/BedWriter.h to /<>/debian/tmp/usr/include/pbbam/bed Installing /<>/include/pbbam/csv/CsvReader.h to /<>/debian/tmp/usr/include/pbbam/csv Installing /<>/include/pbbam/csv/CsvTypes.h to /<>/debian/tmp/usr/include/pbbam/csv Installing /<>/include/pbbam/csv/CsvWriter.h to /<>/debian/tmp/usr/include/pbbam/csv Installing /<>/include/pbbam/exception/BundleChemistryMappingException.h to /<>/debian/tmp/usr/include/pbbam/exception Installing /<>/include/pbbam/exception/InvalidSequencingChemistryException.h to /<>/debian/tmp/usr/include/pbbam/exception Installing /<>/include/pbbam/exception/ValidationException.h to /<>/debian/tmp/usr/include/pbbam/exception Installing /<>/include/pbbam/internal/Compare.inl to /<>/debian/tmp/usr/include/pbbam/internal Installing /<>/include/pbbam/internal/CompositeBamReader.inl to /<>/debian/tmp/usr/include/pbbam/internal Installing /<>/include/pbbam/internal/DataSetBaseTypes.h to /<>/debian/tmp/usr/include/pbbam/internal Installing /<>/include/pbbam/internal/DataSetElement.h to /<>/debian/tmp/usr/include/pbbam/internal Installing /<>/include/pbbam/internal/DataSetElement.inl to /<>/debian/tmp/usr/include/pbbam/internal Installing /<>/include/pbbam/internal/PbiBasicTypes.inl to /<>/debian/tmp/usr/include/pbbam/internal Installing /<>/include/pbbam/internal/PbiFilter.inl to /<>/debian/tmp/usr/include/pbbam/internal Installing /<>/include/pbbam/internal/PbiFilterTypes.inl to /<>/debian/tmp/usr/include/pbbam/internal Installing /<>/include/pbbam/internal/QueryBase.h to /<>/debian/tmp/usr/include/pbbam/internal Installing /<>/include/pbbam/internal/QueryBase.inl to /<>/debian/tmp/usr/include/pbbam/internal Installing /<>/include/pbbam/vcf/VcfVariant.h to /<>/debian/tmp/usr/include/pbbam/vcf Installing /<>/include/pbbam/vcf/VcfFile.h to /<>/debian/tmp/usr/include/pbbam/vcf Installing /<>/include/pbbam/vcf/VcfFormat.h to /<>/debian/tmp/usr/include/pbbam/vcf Installing /<>/include/pbbam/vcf/VcfHeader.h to /<>/debian/tmp/usr/include/pbbam/vcf Installing /<>/include/pbbam/vcf/VcfHeaderTypes.h to /<>/debian/tmp/usr/include/pbbam/vcf Installing /<>/include/pbbam/vcf/VcfReader.h to /<>/debian/tmp/usr/include/pbbam/vcf Installing /<>/include/pbbam/vcf/VcfSort.h to /<>/debian/tmp/usr/include/pbbam/vcf Installing /<>/include/pbbam/vcf/VcfQuery.h to /<>/debian/tmp/usr/include/pbbam/vcf Installing /<>/include/pbbam/vcf/VcfWriter.h to /<>/debian/tmp/usr/include/pbbam/vcf Installing /<>/include/pbbam/virtual/VirtualPolymeraseBamRecord.h to /<>/debian/tmp/usr/include/pbbam/virtual Installing /<>/include/pbbam/virtual/VirtualPolymeraseCompositeReader.h to /<>/debian/tmp/usr/include/pbbam/virtual Installing /<>/include/pbbam/virtual/VirtualPolymeraseReader.h to /<>/debian/tmp/usr/include/pbbam/virtual Installing /<>/include/pbbam/virtual/VirtualRegion.h to /<>/debian/tmp/usr/include/pbbam/virtual Installing /<>/include/pbbam/virtual/VirtualRegionType.h to /<>/debian/tmp/usr/include/pbbam/virtual Installing /<>/include/pbbam/virtual/VirtualRegionTypeMap.h to /<>/debian/tmp/usr/include/pbbam/virtual Installing /<>/include/pbbam/virtual/VirtualZmwBamRecord.h to /<>/debian/tmp/usr/include/pbbam/virtual Installing /<>/include/pbbam/virtual/WhitelistedZmwReadStitcher.h to /<>/debian/tmp/usr/include/pbbam/virtual Installing /<>/include/pbbam/virtual/ZmwReadStitcher.h to /<>/debian/tmp/usr/include/pbbam/virtual Installing /<>/include/pbbam/virtual/ZmwWhitelistVirtualReader.h to /<>/debian/tmp/usr/include/pbbam/virtual Installing /<>/obj-x86_64-linux-gnu/meson-private/pbbam.pc to /<>/debian/tmp/usr/lib/x86_64-linux-gnu/pkgconfig Installing symlink pointing to libpbbam.so.2.4.0 to /<>/debian/tmp/usr/lib/x86_64-linux-gnu/libpbbam.so debian/rules override_dh_install make[1]: Entering directory '/<>' 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/libpbbam2.4.0/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 /<>/debian/tmp/usr/lib/x86_64-linux-gnu/libpbbam.so.2.4.0 debian/libpbbam2.4.0/usr/lib/x86_64-linux-gnu PKGDEV=libpbbam-dev PKGSHL=libpbbam2.4.0 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 '/<>' dh_installdocs -O--buildsystem=meson debian/rules override_dh_installchangelogs make[1]: Entering directory '/<>' dh_installchangelogs CHANGELOG.md make[1]: Leaving directory '/<>' 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 debugedit: debian/pbbamtools/usr/bin/ccs-kinetics-bystrandify: Unknown DWARF DW_FORM_0x1f20 a228ae87a059367965711194c4ebf5beed9e85bf debugedit: debian/pbbamtools/usr/bin/pbindexdump: Unknown DWARF DW_FORM_0x1f20 8bdfed7f04a70b6add34f8fa97142140bd3dc48c debugedit: debian/pbbamtools/usr/bin/pbbamify: Unknown DWARF DW_FORM_0x1f21 dc605710a35bf9774e6ca057fc909f0c0ed9f566 debugedit: debian/pbbamtools/usr/bin/bam2sam: Unknown DWARF DW_FORM_0x1f21 c09b50ce8ea2e1085fe949973a7ab81c4ae12272 debugedit: debian/pbbamtools/usr/bin/pbmerge: Unknown DWARF DW_FORM_0x1f20 6b109b68d74bb7da1afa09f9626c0c57b74fd63a debugedit: debian/pbbamtools/usr/bin/pbindex: Unknown DWARF DW_FORM_0x1f20 906d1c1fa174017e6db25c736d0307fc0f84ba8a 7aded037bbbf6416441e4b0a623a82ce4a000bfc dh_makeshlibs -a -O--buildsystem=meson dh_shlibdeps -a -O--buildsystem=meson dh_installdeb -O--buildsystem=meson dh_gencontrol -O--buildsystem=meson dh_md5sums -O--buildsystem=meson dh_builddeb -O--buildsystem=meson INFO: pkgstriptranslations version 154 INFO: pkgstriptranslations version 154 INFO: pkgstriptranslations version 154 pkgstriptranslations: processing pbbamtools (in debian/pbbamtools); do_strip: , oemstrip: pkgstriptranslations: processing libpbbam2.4.0 (in debian/libpbbam2.4.0); do_strip: , oemstrip: pkgstriptranslations: processing libpbbam-dev (in debian/libpbbam-dev); 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 libpbbam2.4.0... symlinking changelog.Debian.gz in pbbamtools to file in libpbbam2.4.0 pkgstripfiles: Running PNG optimization (using 4 cpus) for package pbbamtools ... pkgstripfiles: processing control file: debian/libpbbam2.4.0/DEBIAN/control, package libpbbam2.4.0, directory debian/libpbbam2.4.0 pkgstripfiles: No PNG files. .. removing usr/share/doc/libpbbam2.4.0/changelog.gz dpkg-deb: building package 'pbbamtools' in '../pbbamtools_2.4.0+dfsg-1build1_amd64.deb'. pkgstripfiles: Running PNG optimization (using 4 cpus) for package libpbbam2.4.0 ... pkgstripfiles: No PNG files. pkgstripfiles: processing control file: debian/libpbbam-dev/DEBIAN/control, package libpbbam-dev, directory debian/libpbbam-dev dpkg-deb: building package 'libpbbam2.4.0' in '../libpbbam2.4.0_2.4.0+dfsg-1build1_amd64.deb'. .. removing usr/share/doc/libpbbam-dev/changelog.gz Searching for duplicated docs in dependency libpbbam2.4.0... symlinking changelog.Debian.gz in libpbbam-dev to file in libpbbam2.4.0 pkgstripfiles: Running PNG optimization (using 4 cpus) for package libpbbam-dev ... pkgstripfiles: No PNG files. dpkg-deb: building package 'libpbbam-dev' in '../libpbbam-dev_2.4.0+dfsg-1build1_amd64.deb'. INFO: pkgstriptranslations version 154 pkgstriptranslations: processing pbbamtools-dbgsym (in debian/.debhelper/pbbamtools/dbgsym-root); do_strip: , oemstrip: pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " 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_2.4.0+dfsg-1build1_amd64.deb'. INFO: pkgstriptranslations version 154 pkgstriptranslations: processing libpbbam2.4.0-dbgsym (in debian/.debhelper/libpbbam2.4.0/dbgsym-root); do_strip: , oemstrip: pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " Renaming pbbamtools-dbgsym_2.4.0+dfsg-1build1_amd64.deb to pbbamtools-dbgsym_2.4.0+dfsg-1build1_amd64.ddeb pkgstripfiles: processing control file: debian/.debhelper/libpbbam2.4.0/dbgsym-root/DEBIAN/control, package libpbbam2.4.0-dbgsym, directory debian/.debhelper/libpbbam2.4.0/dbgsym-root dpkg-deb: building package 'libpbbam2.4.0-dbgsym' in 'debian/.debhelper/scratch-space/build-libpbbam2.4.0/libpbbam2.4.0-dbgsym_2.4.0+dfsg-1build1_amd64.deb'. Renaming libpbbam2.4.0-dbgsym_2.4.0+dfsg-1build1_amd64.deb to libpbbam2.4.0-dbgsym_2.4.0+dfsg-1build1_amd64.ddeb dpkg-genbuildinfo --build=binary -O../pbbam_2.4.0+dfsg-1build1_amd64.buildinfo dpkg-genchanges --build=binary -mLaunchpad Build Daemon -O../pbbam_2.4.0+dfsg-1build1_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 2024-02-18T18:29:48Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ pbbam_2.4.0+dfsg-1build1_amd64.changes: --------------------------------------- Format: 1.8 Date: Sun, 18 Feb 2024 13:22:04 -0500 Source: pbbam Binary: libpbbam-dev libpbbam2.4.0 pbbamtools Built-For-Profiles: noudeb Architecture: amd64 Version: 2.4.0+dfsg-1build1 Distribution: noble-proposed Urgency: medium Maintainer: Launchpad Build Daemon Changed-By: Jeremy Bícha Description: libpbbam-dev - Pacific Biosciences binary alignment/map (BAM) library (headers) libpbbam2.4.0 - Pacific Biosciences binary alignment/map (BAM) library pbbamtools - processing Pacific Biosciences binary alignment/map files Changes: pbbam (2.4.0+dfsg-1build1) noble; urgency=medium . * Rebuild against latest pbcopper Checksums-Sha1: ceccc1fa265e8903a5549d708844f49bdef3b9bc 77394 libpbbam-dev_2.4.0+dfsg-1build1_amd64.deb ef6be4bc1f04e1a7aa2cec8fec9c0f1ec495996c 13633402 libpbbam2.4.0-dbgsym_2.4.0+dfsg-1build1_amd64.ddeb eba7deee85dc304720e0dd7b16628b3cdd67361e 679606 libpbbam2.4.0_2.4.0+dfsg-1build1_amd64.deb b1d9adf2761ad91d8139978ff83ce0aa9df6f23a 9480 pbbam_2.4.0+dfsg-1build1_amd64.buildinfo 6a32de0664ba64b93aaeb4819bac377e1e9a9c1e 2584118 pbbamtools-dbgsym_2.4.0+dfsg-1build1_amd64.ddeb 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libpam-modules-bin (= 1.5.2-9.1ubuntu2), libpam-runtime (= 1.5.2-9.1ubuntu2), libpam0g (= 1.5.2-9.1ubuntu2), libpbcopper-dev (= 2.3.0+dfsg-2), libpbcopper2.3.0 (= 2.3.0+dfsg-2), libpcre2-8-0 (= 10.42-4ubuntu1), libperl5.38 (= 5.38.2-3), libpipeline1 (= 1.5.7-1), libpkgconf3 (= 1.8.1-2), libproc2-0 (= 2:4.0.4-2ubuntu1), libpsl5 (= 0.21.2-1build1), libpython3-stdlib (= 3.12.1-0ubuntu1), libpython3.12-minimal (= 3.12.2-1), libpython3.12-stdlib (= 3.12.2-1), libquadmath0 (= 14-20240201-3ubuntu1), libreadline8 (= 8.2-3), librhash0 (= 1.4.3-3), librtmp1 (= 2.4+20151223.gitfa8646d.1-2build4), libsasl2-2 (= 2.1.28+dfsg1-4), libsasl2-modules-db (= 2.1.28+dfsg1-4), libseccomp2 (= 2.5.5-1ubuntu1), libselinux1 (= 3.5-2build1), libsemanage-common (= 3.5-1build2), libsemanage2 (= 3.5-1build2), libsepol2 (= 3.5-2), libsframe1 (= 2.42-2ubuntu1), libsmartcols1 (= 2.39.2-6ubuntu1), libsqlite3-0 (= 3.45.1-1), libssh-4 (= 0.10.6-2), libssl-dev (= 3.0.10-1ubuntu4), libssl3 (= 3.0.10-1ubuntu4), libstdc++-13-dev (= 13.2.0-13ubuntu1), libstdc++6 (= 14-20240201-3ubuntu1), libsub-override-perl (= 0.10-1), libsystemd0 (= 255.2-3ubuntu2), libtasn1-6 (= 4.19.0-3), libtinfo6 (= 6.4+20240113-1ubuntu1), libtirpc-common (= 1.3.4+ds-1build1), libtirpc-dev (= 1.3.4+ds-1build1), libtirpc3 (= 1.3.4+ds-1build1), libtool (= 2.4.7-7), libtsan2 (= 14-20240201-3ubuntu1), libubsan1 (= 14-20240201-3ubuntu1), libuchardet0 (= 0.0.8-1), libudev1 (= 255.2-3ubuntu2), libunistring5 (= 1.1-2), libuuid1 (= 2.39.2-6ubuntu1), libuv1 (= 1.46.0-3ubuntu1), libxml2 (= 2.9.14+dfsg-1.3ubuntu1), libxxhash0 (= 0.8.2-2), libzstd1 (= 1.5.5+dfsg2-2), linux-libc-dev (= 6.8.0-11.11), login (= 1:4.13+dfsg1-3ubuntu1), lto-disabled-list (= 46), m4 (= 1.4.19-4), make (= 4.3-4.1build1), man-db (= 2.12.0-3), mawk (= 1.3.4.20240123-1), media-types (= 10.1.0), meson (= 1.3.2-1), ncurses-base (= 6.4+20240113-1ubuntu1), ncurses-bin (= 6.4+20240113-1ubuntu1), netbase (= 6.4), ninja-build (= 1.11.1-2), passwd (= 1:4.13+dfsg1-3ubuntu1), patch (= 2.7.6-7build2), perl (= 5.38.2-3), perl-base (= 5.38.2-3), perl-modules-5.38 (= 5.38.2-3), pkg-config (= 1.8.1-2), pkgconf (= 1.8.1-2), pkgconf-bin (= 1.8.1-2), po-debconf (= 1.0.21+nmu1), procps (= 2:4.0.4-2ubuntu1), python3 (= 3.12.1-0ubuntu1), python3-cram (= 0.7-5), python3-distutils (= 3.11.5-1), python3-lib2to3 (= 3.11.5-1), python3-minimal (= 3.12.1-0ubuntu1), python3-pkg-resources (= 68.1.2-2), python3-setuptools (= 68.1.2-2), python3.12 (= 3.12.2-1), python3.12-minimal (= 3.12.2-1), readline-common (= 8.2-3), rpcsvc-proto (= 1.4.2-0ubuntu6), samtools (= 1.19.2-1), sed (= 4.9-2), sensible-utils (= 0.0.22), sysvinit-utils (= 3.08-3ubuntu1), tar (= 1.35+dfsg-3), tzdata (= 2024a-1ubuntu1), ubuntu-keyring (= 2023.11.28.1), util-linux (= 2.39.2-6ubuntu1), xz-utils (= 5.4.5-0.3), zlib1g (= 1:1.3.dfsg-3ubuntu1), zlib1g-dev (= 1:1.3.dfsg-3ubuntu1) Environment: DEB_BUILD_OPTIONS="parallel=4" DEB_BUILD_PROFILES="noudeb" LANG="C.UTF-8" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1708280524" +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ libpbbam-dev_2.4.0+dfsg-1build1_amd64.deb ----------------------------------------- new Debian package, version 2.0. size 77394 bytes: control archive=3931 bytes. 1140 bytes, 24 lines control 8164 bytes, 116 lines md5sums Package: libpbbam-dev Source: pbbam Version: 2.4.0+dfsg-1build1 Architecture: amd64 Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 602 Depends: libpbbam2.4.0 (= 2.4.0+dfsg-1build1), libhts-dev, libpbcopper-dev, zlib1g-dev, libssl-dev Section: libdevel Priority: optional Multi-Arch: same Homepage: https://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 2024-02-18 18:22 ./ drwxr-xr-x root/root 0 2024-02-18 18:22 ./usr/ drwxr-xr-x root/root 0 2024-02-18 18:22 ./usr/include/ drwxr-xr-x root/root 0 2024-02-18 18:22 ./usr/include/pbbam/ -rw-r--r-- root/root 1561 2023-04-24 06:41 ./usr/include/pbbam/AlignmentPrinter.h -rw-r--r-- root/root 1532 2023-04-24 06:41 ./usr/include/pbbam/BaiIndexCache.h -rw-r--r-- root/root 3642 2023-04-24 06:41 ./usr/include/pbbam/BaiIndexedBamReader.h -rw-r--r-- root/root 5021 2023-04-24 06:41 ./usr/include/pbbam/BamFile.h -rw-r--r-- root/root 2701 2023-04-24 06:41 ./usr/include/pbbam/BamFileMerger.h -rw-r--r-- root/root 11288 2023-04-24 06:41 ./usr/include/pbbam/BamHeader.h -rw-r--r-- root/root 3989 2023-04-24 06:41 ./usr/include/pbbam/BamReader.h -rw-r--r-- root/root 58173 2023-04-24 06:41 ./usr/include/pbbam/BamRecord.h -rw-r--r-- root/root 22178 2023-04-24 06:41 ./usr/include/pbbam/BamRecordImpl.h -rw-r--r-- root/root 1178 2023-04-24 06:41 ./usr/include/pbbam/BamRecordTag.h -rw-r--r-- root/root 4551 2023-04-24 06:41 ./usr/include/pbbam/BamRecordView.h -rw-r--r-- root/root 2623 2023-04-24 06:41 ./usr/include/pbbam/BamTagCodec.h -rw-r--r-- root/root 7671 2023-04-24 06:41 ./usr/include/pbbam/BamWriter.h -rw-r--r-- root/root 767 2023-04-24 06:41 ./usr/include/pbbam/BgzipFastaWriter.h -rw-r--r-- root/root 893 2023-04-24 06:41 ./usr/include/pbbam/BgzipFastqWriter.h -rw-r--r-- root/root 1965 2023-04-24 06:41 ./usr/include/pbbam/BgzipWriter.h -rw-r--r-- root/root 733 2023-04-24 06:41 ./usr/include/pbbam/ClipType.h -rw-r--r-- root/root 9038 2023-04-24 06:41 ./usr/include/pbbam/CollectionMetadata.h -rw-r--r-- root/root 14835 2023-04-24 06:41 ./usr/include/pbbam/Compare.h -rw-r--r-- root/root 10166 2023-04-24 06:41 ./usr/include/pbbam/CompositeBamReader.h -rw-r--r-- root/root 1276 2023-04-24 06:41 ./usr/include/pbbam/CompositeFastaReader.h -rw-r--r-- root/root 945 2023-04-24 06:41 ./usr/include/pbbam/Config.h -rw-r--r-- root/root 26716 2023-04-24 06:41 ./usr/include/pbbam/DataSet.h -rw-r--r-- root/root 40796 2023-04-24 06:41 ./usr/include/pbbam/DataSetTypes.h -rw-r--r-- root/root 2564 2023-04-24 06:41 ./usr/include/pbbam/DataSetXsd.h -rw-r--r-- root/root 1567 2023-04-24 06:41 ./usr/include/pbbam/Deleters.h -rw-r--r-- root/root 1804 2023-04-24 06:41 ./usr/include/pbbam/EntireFileQuery.h -rw-r--r-- root/root 2244 2023-04-24 06:41 ./usr/include/pbbam/FaiIndex.h -rw-r--r-- root/root 2181 2023-04-24 06:41 ./usr/include/pbbam/FastaCache.h -rw-r--r-- root/root 1638 2023-04-24 06:41 ./usr/include/pbbam/FastaReader.h -rw-r--r-- root/root 1286 2023-04-24 06:41 ./usr/include/pbbam/FastaSequence.h -rw-r--r-- root/root 1125 2023-04-24 06:41 ./usr/include/pbbam/FastaSequenceQuery.h -rw-r--r-- root/root 664 2023-04-24 06:41 ./usr/include/pbbam/FastaWriter.h -rw-r--r-- root/root 1646 2023-04-24 06:41 ./usr/include/pbbam/FastqReader.h -rw-r--r-- root/root 1610 2023-04-24 06:41 ./usr/include/pbbam/FastqSequence.h -rw-r--r-- root/root 791 2023-04-24 06:41 ./usr/include/pbbam/FastqWriter.h -rw-r--r-- root/root 938 2023-04-24 06:41 ./usr/include/pbbam/FormatUtils.h -rw-r--r-- root/root 789 2023-04-24 06:41 ./usr/include/pbbam/FrameEncodingType.h -rw-r--r-- root/root 3138 2023-04-24 06:41 ./usr/include/pbbam/GenomicIntervalQuery.h -rw-r--r-- root/root 578 2023-04-24 06:41 ./usr/include/pbbam/IFastaWriter.h -rw-r--r-- root/root 763 2023-04-24 06:41 ./usr/include/pbbam/IFastqWriter.h -rw-r--r-- root/root 1238 2023-04-24 06:41 ./usr/include/pbbam/IRecordWriter.h -rw-r--r-- root/root 4811 2023-04-24 06:41 ./usr/include/pbbam/IndexedBamWriter.h -rw-r--r-- root/root 4200 2023-04-24 06:41 ./usr/include/pbbam/IndexedFastaReader.h -rw-r--r-- root/root 4076 2023-04-24 06:41 ./usr/include/pbbam/IndexedFastqReader.h -rw-r--r-- root/root 655 2023-04-24 06:41 ./usr/include/pbbam/LibraryInfo.h -rw-r--r-- root/root 305 2023-04-24 06:41 ./usr/include/pbbam/MD5.h -rw-r--r-- root/root 1280 2023-04-24 06:41 ./usr/include/pbbam/MoveAppend.h -rw-r--r-- root/root 487 2023-04-24 06:41 ./usr/include/pbbam/PbbamVersion.h -rw-r--r-- root/root 2167 2023-04-24 06:41 ./usr/include/pbbam/PbiBasicTypes.h -rw-r--r-- root/root 6902 2023-04-24 06:41 ./usr/include/pbbam/PbiBuilder.h -rw-r--r-- root/root 2316 2023-04-24 06:41 ./usr/include/pbbam/PbiFile.h -rw-r--r-- root/root 7344 2023-04-24 06:41 ./usr/include/pbbam/PbiFilter.h -rw-r--r-- root/root 2287 2023-04-24 06:41 ./usr/include/pbbam/PbiFilterQuery.h -rw-r--r-- root/root 30722 2023-04-24 06:41 ./usr/include/pbbam/PbiFilterTypes.h -rw-r--r-- root/root 3720 2023-04-24 06:41 ./usr/include/pbbam/PbiIndexedBamReader.h -rw-r--r-- root/root 11650 2023-04-24 06:41 ./usr/include/pbbam/PbiRawData.h -rw-r--r-- root/root 4257 2023-04-24 06:41 ./usr/include/pbbam/ProgramInfo.h -rw-r--r-- root/root 455 2023-04-24 06:41 ./usr/include/pbbam/PulseBehavior.h -rw-r--r-- root/root 418 2023-04-24 06:41 ./usr/include/pbbam/PulseExclusionReason.h -rw-r--r-- root/root 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drwxr-xr-x root/root 0 2024-02-18 18:22 ./usr/lib/x86_64-linux-gnu/ lrwxrwxrwx root/root 0 2024-02-18 18:22 ./usr/lib/x86_64-linux-gnu/libpbbam.so -> libpbbam.so.2.4.0 drwxr-xr-x root/root 0 2024-02-18 18:22 ./usr/lib/x86_64-linux-gnu/pkgconfig/ -rw-r--r-- root/root 300 2024-02-18 18:22 ./usr/lib/x86_64-linux-gnu/pkgconfig/pbbam.pc drwxr-xr-x root/root 0 2024-02-18 18:22 ./usr/share/ drwxr-xr-x root/root 0 2024-02-18 18:22 ./usr/share/doc/ drwxr-xr-x root/root 0 2024-02-18 18:22 ./usr/share/doc/libpbbam-dev/ lrwxrwxrwx root/root 0 2024-02-18 18:22 ./usr/share/doc/libpbbam-dev/changelog.Debian.gz -> ../libpbbam2.4.0/changelog.Debian.gz -rw-r--r-- root/root 3463 2023-11-08 16:24 ./usr/share/doc/libpbbam-dev/copyright libpbbam2.4.0_2.4.0+dfsg-1build1_amd64.deb ------------------------------------------ new Debian package, version 2.0. size 679606 bytes: control archive=1040 bytes. 1163 bytes, 23 lines control 231 bytes, 3 lines md5sums 45 bytes, 1 lines shlibs 73 bytes, 2 lines triggers Package: libpbbam2.4.0 Source: pbbam Version: 2.4.0+dfsg-1build1 Architecture: amd64 Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 2156 Depends: libc6 (>= 2.38), libgcc-s1 (>= 3.3.1), libhts3 (>= 1.17), libpbcopper2.3.0 (>= 2.3.0+dfsg), libstdc++6 (>= 13.1), zlib1g (>= 1:1.2.3.3) Breaks: libpbbam (<< 2.4.0+dfsg-1build1) Section: libs Priority: optional Multi-Arch: same Homepage: https://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 2024-02-18 18:22 ./ drwxr-xr-x root/root 0 2024-02-18 18:22 ./usr/ drwxr-xr-x root/root 0 2024-02-18 18:22 ./usr/lib/ drwxr-xr-x root/root 0 2024-02-18 18:22 ./usr/lib/x86_64-linux-gnu/ -rw-r--r-- root/root 2180688 2024-02-18 18:22 ./usr/lib/x86_64-linux-gnu/libpbbam.so.2.4.0 drwxr-xr-x root/root 0 2024-02-18 18:22 ./usr/share/ drwxr-xr-x root/root 0 2024-02-18 18:22 ./usr/share/doc/ drwxr-xr-x root/root 0 2024-02-18 18:22 ./usr/share/doc/libpbbam2.4.0/ -rw-r--r-- root/root 1692 2024-02-18 18:22 ./usr/share/doc/libpbbam2.4.0/changelog.Debian.gz -rw-r--r-- root/root 3463 2023-11-08 16:24 ./usr/share/doc/libpbbam2.4.0/copyright pbbamtools_2.4.0+dfsg-1build1_amd64.deb --------------------------------------- new Debian package, version 2.0. size 111338 bytes: control archive=1059 bytes. 1169 bytes, 24 lines control 462 bytes, 8 lines md5sums Package: pbbamtools Source: pbbam Version: 2.4.0+dfsg-1build1 Architecture: amd64 Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 410 Depends: libc6 (>= 2.34), libgcc-s1 (>= 3.3.1), libhts3 (>= 1.17), libpbbam2.4.0 (= 2.4.0+dfsg-1build1), libpbcopper2.3.0 (>= 2.3.0+dfsg), libstdc++6 (>= 13.1) Recommends: samtools Section: science Priority: optional Homepage: https://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 2024-02-18 18:22 ./ drwxr-xr-x root/root 0 2024-02-18 18:22 ./usr/ drwxr-xr-x root/root 0 2024-02-18 18:22 ./usr/bin/ -rwxr-xr-x root/root 27168 2024-02-18 18:22 ./usr/bin/bam2sam -rwxr-xr-x root/root 113216 2024-02-18 18:22 ./usr/bin/ccs-kinetics-bystrandify -rwxr-xr-x root/root 92736 2024-02-18 18:22 ./usr/bin/pbbamify -rwxr-xr-x root/root 23072 2024-02-18 18:22 ./usr/bin/pbindex -rwxr-xr-x root/root 104992 2024-02-18 18:22 ./usr/bin/pbindexdump -rwxr-xr-x root/root 31296 2024-02-18 18:22 ./usr/bin/pbmerge drwxr-xr-x root/root 0 2024-02-18 18:22 ./usr/share/ drwxr-xr-x root/root 0 2024-02-18 18:22 ./usr/share/doc/ drwxr-xr-x root/root 0 2024-02-18 18:22 ./usr/share/doc/pbbamtools/ -rw-r--r-- root/root 97 2023-11-08 16:24 ./usr/share/doc/pbbamtools/TODO.Debian lrwxrwxrwx root/root 0 2024-02-18 18:22 ./usr/share/doc/pbbamtools/changelog.Debian.gz -> ../libpbbam2.4.0/changelog.Debian.gz -rw-r--r-- root/root 3463 2023-11-08 16:24 ./usr/share/doc/pbbamtools/copyright +------------------------------------------------------------------------------+ | Post Build | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not removing build depends: as requested +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: amd64 Build Type: binary Build-Space: 1042728 Build-Time: 327 Distribution: noble-proposed Host Architecture: amd64 Install-Time: 11 Job: pbbam_2.4.0+dfsg-1build1.dsc Machine Architecture: amd64 Package: pbbam Package-Time: 339 Source-Version: 2.4.0+dfsg-1build1 Space: 1042728 Status: successful Version: 2.4.0+dfsg-1build1 -------------------------------------------------------------------------------- Finished at 2024-02-18T18:29:48Z Build needed 00:05:39, 1042728k disk space RUN: /usr/share/launchpad-buildd/bin/in-target scan-for-processes --backend=chroot --series=noble --arch=amd64 PACKAGEBUILD-27789649 Scanning for processes to kill in build PACKAGEBUILD-27789649