https://launchpad.net/ubuntu/+source/blasr/5.3.5+dfsg-6build1/+build/26678012 RUN: /usr/share/launchpad-buildd/bin/builder-prep Kernel version: Linux lcy02-amd64-005 5.4.0-156-generic #173-Ubuntu SMP Tue Jul 11 07:25:22 UTC 2023 x86_64 Buildd toolchain package versions: launchpad-buildd_234~642~ubuntu20.04.1 python3-lpbuildd_234~642~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... 3 Sep 16:13:38 ntpdate[1818]: adjust time server 10.131.248.1 offset -0.300054 sec RUN: /usr/share/launchpad-buildd/bin/in-target unpack-chroot --backend=chroot --series=mantic --arch=amd64 PACKAGEBUILD-26678012 --image-type chroot /home/buildd/filecache-default/1fc1752c0976ad9eb0e621fd063fde252dab04e3 Creating target for build PACKAGEBUILD-26678012 RUN: /usr/share/launchpad-buildd/bin/in-target mount-chroot --backend=chroot --series=mantic --arch=amd64 PACKAGEBUILD-26678012 Starting target for build PACKAGEBUILD-26678012 RUN: /usr/share/launchpad-buildd/bin/in-target override-sources-list --backend=chroot --series=mantic --arch=amd64 PACKAGEBUILD-26678012 'deb http://ftpmaster.internal/ubuntu mantic main universe' 'deb http://ftpmaster.internal/ubuntu mantic-security main universe' 'deb http://ftpmaster.internal/ubuntu mantic-updates main universe' 'deb http://ftpmaster.internal/ubuntu mantic-proposed main universe' Overriding sources.list in build-PACKAGEBUILD-26678012 RUN: /usr/share/launchpad-buildd/bin/in-target update-debian-chroot --backend=chroot --series=mantic --arch=amd64 PACKAGEBUILD-26678012 Updating target for build PACKAGEBUILD-26678012 Get:1 http://ftpmaster.internal/ubuntu mantic InRelease [255 kB] Get:2 http://ftpmaster.internal/ubuntu mantic-security InRelease [90.7 kB] Get:3 http://ftpmaster.internal/ubuntu mantic-updates InRelease [90.7 kB] Get:4 http://ftpmaster.internal/ubuntu mantic-proposed InRelease [118 kB] Get:5 http://ftpmaster.internal/ubuntu mantic/main amd64 Packages [1408 kB] Get:6 http://ftpmaster.internal/ubuntu mantic/main Translation-en [516 kB] Get:7 http://ftpmaster.internal/ubuntu mantic/universe amd64 Packages [15.2 MB] Get:8 http://ftpmaster.internal/ubuntu mantic/universe Translation-en [5960 kB] Get:9 http://ftpmaster.internal/ubuntu mantic-proposed/main amd64 Packages [113 kB] Get:10 http://ftpmaster.internal/ubuntu mantic-proposed/main Translation-en [29.3 kB] Get:11 http://ftpmaster.internal/ubuntu mantic-proposed/universe amd64 Packages [139 kB] Get:12 http://ftpmaster.internal/ubuntu mantic-proposed/universe Translation-en [57.6 kB] Fetched 24.0 MB in 2s (10.4 MB/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: g++-12 libstdc++-12-dev Use 'sudo apt autoremove' to remove them. The following NEW packages will be installed: cpp-13 g++-13 gcc-13 gcc-13-base libgcc-13-dev libhwasan0 libproc2-0 libsframe1 libstdc++-13-dev systemd-dev The following packages will be upgraded: adduser advancecomp apt base-files bash binutils binutils-common binutils-x86-64-linux-gnu bsdutils build-essential ca-certificates coreutils cpp cpp-12 dash debconf debianutils diffutils dpkg dpkg-dev e2fsprogs fakeroot findutils g++ g++-12 gcc gcc-12 gcc-12-base gpg gpg-agent gpgconf gpgv grep hostname init init-system-helpers libacl1 libapparmor1 libapt-pkg6.0 libargon2-1 libasan8 libassuan0 libatomic1 libattr1 libaudit-common libaudit1 libbinutils libblkid1 libc-bin libc-dev-bin libc6 libc6-dev libcap-ng0 libcap2 libcc1-0 libcom-err2 libcrypt-dev libcrypt1 libcryptsetup12 libctf-nobfd0 libctf0 libdb5.3 libdebconfclient0 libdevmapper1.02.1 libdpkg-perl libext2fs2 libfakeroot libfdisk1 libgcc-12-dev libgcc-s1 libgcrypt20 libgmp10 libgnutls30 libgomp1 libgpg-error0 libgprofng0 libgssapi-krb5-2 libhogweed6 libidn2-0 libip4tc2 libisl23 libitm1 libjson-c5 libk5crypto3 libkmod2 libkrb5-3 libkrb5support0 liblsan0 liblzma5 libmd0 libmount1 libmpfr6 libncurses6 libncursesw6 libnettle8 libp11-kit0 libpam-modules libpam-modules-bin libpam-runtime libpam0g libpcre2-8-0 libperl5.36 libpng16-16 libquadmath0 libreadline8 libseccomp2 libselinux1 libsemanage-common libsemanage2 libsepol2 libsmartcols1 libsqlite3-0 libss2 libssl3 libstdc++-12-dev libstdc++6 libsystemd-shared libsystemd0 libtasn1-6 libtinfo6 libtsan2 libubsan1 libudev1 libuuid1 libzstd1 linux-libc-dev logsave lsb-base lto-disabled-list mawk mount ncurses-base ncurses-bin openssl perl perl-base perl-modules-5.36 pkgbinarymangler procps readline-common sed sensible-utils systemd systemd-sysv sysvinit-utils tar tzdata usrmerge util-linux util-linux-extra xz-utils zlib1g 152 upgraded, 10 newly installed, 0 to remove and 0 not upgraded. Need to get 164 MB of archives. After this operation, 174 MB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu mantic/main amd64 libcrypt-dev amd64 1:4.4.36-2 [112 kB] Get:2 http://ftpmaster.internal/ubuntu mantic/main amd64 libc6-dev amd64 2.38-1ubuntu4 [2116 kB] Get:3 http://ftpmaster.internal/ubuntu mantic/main amd64 libc-dev-bin amd64 2.38-1ubuntu4 [20.3 kB] Get:4 http://ftpmaster.internal/ubuntu mantic/main amd64 libcrypt1 amd64 1:4.4.36-2 [82.2 kB] Get:5 http://ftpmaster.internal/ubuntu mantic-proposed/main amd64 linux-libc-dev amd64 6.5.0-2.2 [1540 kB] Get:6 http://ftpmaster.internal/ubuntu mantic/main amd64 libc6 amd64 2.38-1ubuntu4 [3248 kB] Get:7 http://ftpmaster.internal/ubuntu mantic/main amd64 libc-bin amd64 2.38-1ubuntu4 [681 kB] Get:8 http://ftpmaster.internal/ubuntu mantic-proposed/main amd64 gcc-13-base amd64 13.2.0-3ubuntu1 [43.3 kB] Get:9 http://ftpmaster.internal/ubuntu mantic-proposed/main amd64 libgcc-s1 amd64 13.2.0-3ubuntu1 [62.4 kB] Get:10 http://ftpmaster.internal/ubuntu mantic/main amd64 base-files amd64 13ubuntu1 [74.0 kB] Get:11 http://ftpmaster.internal/ubuntu mantic/main amd64 debianutils amd64 5.8-1 [103 kB] Get:12 http://ftpmaster.internal/ubuntu mantic/main amd64 bash amd64 5.2.15-2ubuntu1 [795 kB] Get:13 http://ftpmaster.internal/ubuntu mantic/main amd64 bsdutils amd64 1:2.39.1-4ubuntu1 [93.0 kB] Get:14 http://ftpmaster.internal/ubuntu mantic/main amd64 coreutils amd64 9.1-1ubuntu2 [1407 kB] Get:15 http://ftpmaster.internal/ubuntu mantic/main amd64 liblzma5 amd64 5.4.1-0.2 [125 kB] Get:16 http://ftpmaster.internal/ubuntu mantic/main amd64 libzstd1 amd64 1.5.5+dfsg2-1ubuntu2 [295 kB] Get:17 http://ftpmaster.internal/ubuntu mantic-proposed/main amd64 libstdc++6 amd64 13.2.0-3ubuntu1 [772 kB] Get:18 http://ftpmaster.internal/ubuntu mantic/main amd64 libgpg-error0 amd64 1.47-2 [69.7 kB] Get:19 http://ftpmaster.internal/ubuntu mantic/main amd64 libgcrypt20 amd64 1.10.2-2ubuntu1 [531 kB] Get:20 http://ftpmaster.internal/ubuntu mantic/main amd64 libp11-kit0 amd64 0.25.0-4ubuntu1 [300 kB] Get:21 http://ftpmaster.internal/ubuntu mantic/main amd64 libacl1 amd64 2.3.1-3 [16.4 kB] Get:22 http://ftpmaster.internal/ubuntu mantic/main amd64 libapparmor1 amd64 4.0.0~alpha2-0ubuntu2 [46.9 kB] Get:23 http://ftpmaster.internal/ubuntu mantic/main amd64 libaudit-common all 1:3.1.1-1 [5426 B] Get:24 http://ftpmaster.internal/ubuntu mantic/main amd64 libcap-ng0 amd64 0.8.3-1build2 [15.3 kB] Get:25 http://ftpmaster.internal/ubuntu mantic/main amd64 libaudit1 amd64 1:3.1.1-1 [46.1 kB] Get:26 http://ftpmaster.internal/ubuntu mantic/main amd64 libblkid1 amd64 2.39.1-4ubuntu1 [121 kB] Get:27 http://ftpmaster.internal/ubuntu mantic/main amd64 libcap2 amd64 1:2.66-4ubuntu1 [29.4 kB] Get:28 http://ftpmaster.internal/ubuntu mantic/main amd64 libip4tc2 amd64 1.8.9-2ubuntu2 [22.2 kB] Get:29 http://ftpmaster.internal/ubuntu mantic/main amd64 libperl5.36 amd64 5.36.0-7ubuntu1 [4834 kB] Get:30 http://ftpmaster.internal/ubuntu mantic/main amd64 perl amd64 5.36.0-7ubuntu1 [235 kB] Get:31 http://ftpmaster.internal/ubuntu mantic/main amd64 perl-base amd64 5.36.0-7ubuntu1 [1784 kB] Get:32 http://ftpmaster.internal/ubuntu mantic/main amd64 perl-modules-5.36 all 5.36.0-7ubuntu1 [2984 kB] Get:33 http://ftpmaster.internal/ubuntu mantic/main amd64 libdb5.3 amd64 5.3.28+dfsg2-2 [736 kB] Get:34 http://ftpmaster.internal/ubuntu mantic/main amd64 zlib1g amd64 1:1.2.13.dfsg-1ubuntu5 [62.7 kB] Get:35 http://ftpmaster.internal/ubuntu mantic/main amd64 debconf all 1.5.82 [125 kB] Get:36 http://ftpmaster.internal/ubuntu mantic/main amd64 libssl3 amd64 3.0.10-1ubuntu2 [1929 kB] Get:37 http://ftpmaster.internal/ubuntu mantic/main amd64 libkmod2 amd64 30+20230519-1ubuntu3 [51.2 kB] Get:38 http://ftpmaster.internal/ubuntu mantic/main amd64 libpcre2-8-0 amd64 10.42-4 [228 kB] Get:39 http://ftpmaster.internal/ubuntu mantic/main amd64 libselinux1 amd64 3.5-1 [78.2 kB] Get:40 http://ftpmaster.internal/ubuntu mantic/main amd64 libmount1 amd64 2.39.1-4ubuntu1 [139 kB] Get:41 http://ftpmaster.internal/ubuntu mantic/main amd64 libpam0g amd64 1.5.2-6ubuntu1 [65.9 kB] Get:42 http://ftpmaster.internal/ubuntu mantic/main amd64 libseccomp2 amd64 2.5.4-1ubuntu3 [49.1 kB] Get:43 http://ftpmaster.internal/ubuntu mantic/main amd64 systemd-sysv amd64 253.5-1ubuntu4 [11.5 kB] Get:44 http://ftpmaster.internal/ubuntu mantic/main amd64 systemd amd64 253.5-1ubuntu4 [3072 kB] Get:45 http://ftpmaster.internal/ubuntu mantic/main amd64 libsystemd-shared amd64 253.5-1ubuntu4 [1871 kB] Get:46 http://ftpmaster.internal/ubuntu mantic/main amd64 systemd-dev all 253.5-1ubuntu4 [79.1 kB] Get:47 http://ftpmaster.internal/ubuntu mantic/main amd64 libargon2-1 amd64 0~20190702+dfsg-3 [20.3 kB] Get:48 http://ftpmaster.internal/ubuntu mantic/main amd64 libudev1 amd64 253.5-1ubuntu4 [160 kB] Get:49 http://ftpmaster.internal/ubuntu mantic/main amd64 libdevmapper1.02.1 amd64 2:1.02.185-2ubuntu1 [139 kB] Get:50 http://ftpmaster.internal/ubuntu mantic/main amd64 libjson-c5 amd64 0.17-1 [35.2 kB] Get:51 http://ftpmaster.internal/ubuntu mantic/main amd64 libuuid1 amd64 2.39.1-4ubuntu1 [33.4 kB] Get:52 http://ftpmaster.internal/ubuntu mantic/main amd64 libcryptsetup12 amd64 2:2.6.1-4ubuntu2 [242 kB] Get:53 http://ftpmaster.internal/ubuntu mantic/main amd64 libfdisk1 amd64 2.39.1-4ubuntu1 [145 kB] Get:54 http://ftpmaster.internal/ubuntu mantic/main amd64 mount amd64 2.39.1-4ubuntu1 [117 kB] Get:55 http://ftpmaster.internal/ubuntu mantic/main amd64 libsystemd0 amd64 253.5-1ubuntu4 [407 kB] Get:56 http://ftpmaster.internal/ubuntu mantic/main amd64 libapt-pkg6.0 amd64 2.7.3 [949 kB] Get:57 http://ftpmaster.internal/ubuntu mantic/main amd64 tar amd64 1.34+dfsg-1.2ubuntu1 [293 kB] Get:58 http://ftpmaster.internal/ubuntu mantic/main amd64 dpkg amd64 1.22.0ubuntu1 [1392 kB] Get:59 http://ftpmaster.internal/ubuntu mantic/main amd64 dash amd64 0.5.12-6ubuntu1 [90.0 kB] Get:60 http://ftpmaster.internal/ubuntu mantic/main amd64 diffutils amd64 1:3.8-4 [176 kB] Get:61 http://ftpmaster.internal/ubuntu mantic/main amd64 findutils amd64 4.9.0-5 [299 kB] Get:62 http://ftpmaster.internal/ubuntu mantic/main amd64 grep amd64 3.11-2 [161 kB] Get:63 http://ftpmaster.internal/ubuntu mantic/main amd64 hostname amd64 3.23+nmu1ubuntu1 [11.0 kB] Get:64 http://ftpmaster.internal/ubuntu mantic/main amd64 libncurses6 amd64 6.4+20230625-2 [112 kB] Get:65 http://ftpmaster.internal/ubuntu mantic/main amd64 libncursesw6 amd64 6.4+20230625-2 [149 kB] Get:66 http://ftpmaster.internal/ubuntu mantic/main amd64 libtinfo6 amd64 6.4+20230625-2 [108 kB] Get:67 http://ftpmaster.internal/ubuntu mantic/main amd64 ncurses-bin amd64 6.4+20230625-2 [185 kB] Get:68 http://ftpmaster.internal/ubuntu mantic/main amd64 sed amd64 4.9-1 [193 kB] Get:69 http://ftpmaster.internal/ubuntu mantic/main amd64 libsmartcols1 amd64 2.39.1-4ubuntu1 [62.7 kB] Get:70 http://ftpmaster.internal/ubuntu mantic/universe amd64 util-linux-extra amd64 2.39.1-4ubuntu1 [122 kB] Get:71 http://ftpmaster.internal/ubuntu mantic/main amd64 util-linux amd64 2.39.1-4ubuntu1 [1119 kB] Get:72 http://ftpmaster.internal/ubuntu mantic/main amd64 init-system-helpers all 1.65.2ubuntu1 [38.7 kB] Get:73 http://ftpmaster.internal/ubuntu mantic/main amd64 ncurses-base all 6.4+20230625-2 [24.5 kB] Get:74 http://ftpmaster.internal/ubuntu mantic/main amd64 sysvinit-utils amd64 3.07-1ubuntu1 [33.2 kB] Get:75 http://ftpmaster.internal/ubuntu mantic/main amd64 lsb-base all 11.6 [4606 B] Get:76 http://ftpmaster.internal/ubuntu mantic/main amd64 adduser all 3.137ubuntu1 [101 kB] Get:77 http://ftpmaster.internal/ubuntu mantic/main amd64 gpgv amd64 2.2.40-1.1ubuntu1 [140 kB] Get:78 http://ftpmaster.internal/ubuntu mantic/main amd64 libgmp10 amd64 2:6.3.0+dfsg-2ubuntu4 [256 kB] Get:79 http://ftpmaster.internal/ubuntu mantic/main amd64 libnettle8 amd64 3.9.1-2 [182 kB] Get:80 http://ftpmaster.internal/ubuntu mantic/main amd64 libhogweed6 amd64 3.9.1-2 [199 kB] Get:81 http://ftpmaster.internal/ubuntu mantic/main amd64 libidn2-0 amd64 2.3.4-1 [108 kB] Get:82 http://ftpmaster.internal/ubuntu mantic/main amd64 libtasn1-6 amd64 4.19.0-3 [44.5 kB] Get:83 http://ftpmaster.internal/ubuntu mantic/main amd64 libgnutls30 amd64 3.8.1-4ubuntu1 [989 kB] Get:84 http://ftpmaster.internal/ubuntu mantic/main amd64 apt amd64 2.7.3 [1375 kB] Get:85 http://ftpmaster.internal/ubuntu mantic/main amd64 libpam-modules-bin amd64 1.5.2-6ubuntu1 [47.3 kB] Get:86 http://ftpmaster.internal/ubuntu mantic/main amd64 libpam-modules amd64 1.5.2-6ubuntu1 [284 kB] Get:87 http://ftpmaster.internal/ubuntu mantic/main amd64 logsave amd64 1.47.0-2ubuntu1 [22.0 kB] Get:88 http://ftpmaster.internal/ubuntu mantic/main amd64 libext2fs2 amd64 1.47.0-2ubuntu1 [219 kB] Get:89 http://ftpmaster.internal/ubuntu mantic/main amd64 e2fsprogs amd64 1.47.0-2ubuntu1 [597 kB] Get:90 http://ftpmaster.internal/ubuntu mantic/main amd64 init amd64 1.65.2ubuntu1 [5508 B] Get:91 http://ftpmaster.internal/ubuntu mantic/main amd64 libattr1 amd64 1:2.5.1-4 [12.4 kB] Get:92 http://ftpmaster.internal/ubuntu mantic/main amd64 libdebconfclient0 amd64 0.270ubuntu1 [11.1 kB] Get:93 http://ftpmaster.internal/ubuntu mantic/main amd64 libmd0 amd64 1.1.0-1 [26.9 kB] Get:94 http://ftpmaster.internal/ubuntu mantic/main amd64 libpam-runtime all 1.5.2-6ubuntu1 [41.5 kB] Get:95 http://ftpmaster.internal/ubuntu mantic/main amd64 libsemanage-common all 3.5-1 [9890 B] Get:96 http://ftpmaster.internal/ubuntu mantic/main amd64 libsepol2 amd64 3.5-1 [301 kB] Get:97 http://ftpmaster.internal/ubuntu mantic/main amd64 libsemanage2 amd64 3.5-1 [93.3 kB] Get:98 http://ftpmaster.internal/ubuntu mantic/main amd64 usrmerge all 35ubuntu1 [58.2 kB] Get:99 http://ftpmaster.internal/ubuntu mantic/main amd64 libcom-err2 amd64 1.47.0-2ubuntu1 [22.2 kB] Get:100 http://ftpmaster.internal/ubuntu mantic/main amd64 libproc2-0 amd64 2:4.0.3-1ubuntu1 [55.9 kB] Get:101 http://ftpmaster.internal/ubuntu mantic/main amd64 libss2 amd64 1.47.0-2ubuntu1 [16.7 kB] Get:102 http://ftpmaster.internal/ubuntu mantic/main amd64 mawk amd64 1.3.4.20230730-1 [125 kB] Get:103 http://ftpmaster.internal/ubuntu mantic/main amd64 procps amd64 2:4.0.3-1ubuntu1 [609 kB] Get:104 http://ftpmaster.internal/ubuntu mantic/main amd64 sensible-utils all 0.0.20 [19.6 kB] Get:105 http://ftpmaster.internal/ubuntu mantic/main amd64 openssl amd64 3.0.10-1ubuntu2 [1187 kB] Get:106 http://ftpmaster.internal/ubuntu mantic/main amd64 ca-certificates all 20230311ubuntu1 [152 kB] Get:107 http://ftpmaster.internal/ubuntu mantic/main amd64 libgssapi-krb5-2 amd64 1.20.1-3ubuntu1 [142 kB] Get:108 http://ftpmaster.internal/ubuntu mantic/main amd64 libkrb5-3 amd64 1.20.1-3ubuntu1 [346 kB] Get:109 http://ftpmaster.internal/ubuntu mantic/main amd64 libk5crypto3 amd64 1.20.1-3ubuntu1 [81.3 kB] Get:110 http://ftpmaster.internal/ubuntu mantic/main amd64 libkrb5support0 amd64 1.20.1-3ubuntu1 [33.0 kB] Get:111 http://ftpmaster.internal/ubuntu mantic/main amd64 readline-common all 8.2-1.3 [55.7 kB] Get:112 http://ftpmaster.internal/ubuntu mantic/main amd64 libreadline8 amd64 8.2-1.3 [151 kB] Get:113 http://ftpmaster.internal/ubuntu mantic/main amd64 libsqlite3-0 amd64 3.42.0-1 [668 kB] Get:114 http://ftpmaster.internal/ubuntu mantic-proposed/main amd64 tzdata all 2023c-9ubuntu1 [270 kB] Get:115 http://ftpmaster.internal/ubuntu mantic/main amd64 libpng16-16 amd64 1.6.40-1 [186 kB] Get:116 http://ftpmaster.internal/ubuntu mantic/main amd64 xz-utils amd64 5.4.1-0.2 [270 kB] Get:117 http://ftpmaster.internal/ubuntu mantic/main amd64 advancecomp amd64 2.5-1 [180 kB] Get:118 http://ftpmaster.internal/ubuntu mantic/main amd64 libgprofng0 amd64 2.41-4ubuntu1 [847 kB] Get:119 http://ftpmaster.internal/ubuntu mantic/main amd64 libctf0 amd64 2.41-4ubuntu1 [94.1 kB] Get:120 http://ftpmaster.internal/ubuntu mantic/main amd64 libctf-nobfd0 amd64 2.41-4ubuntu1 [96.4 kB] Get:121 http://ftpmaster.internal/ubuntu mantic/main amd64 binutils-x86-64-linux-gnu amd64 2.41-4ubuntu1 [2469 kB] Get:122 http://ftpmaster.internal/ubuntu mantic/main amd64 libbinutils amd64 2.41-4ubuntu1 [561 kB] Get:123 http://ftpmaster.internal/ubuntu mantic/main amd64 binutils amd64 2.41-4ubuntu1 [18.0 kB] Get:124 http://ftpmaster.internal/ubuntu mantic/main amd64 binutils-common amd64 2.41-4ubuntu1 [248 kB] Get:125 http://ftpmaster.internal/ubuntu mantic/main amd64 libsframe1 amd64 2.41-4ubuntu1 [14.6 kB] Get:126 http://ftpmaster.internal/ubuntu mantic/main amd64 libisl23 amd64 0.26-3 [741 kB] Get:127 http://ftpmaster.internal/ubuntu mantic-proposed/main amd64 libmpfr6 amd64 4.2.1-1 [351 kB] Get:128 http://ftpmaster.internal/ubuntu mantic-proposed/main amd64 cpp-13 amd64 13.2.0-3ubuntu1 [10.7 MB] Get:129 http://ftpmaster.internal/ubuntu mantic/main amd64 g++ amd64 4:13.2.0-1ubuntu1 [1122 B] Get:130 http://ftpmaster.internal/ubuntu mantic/main amd64 gcc amd64 4:13.2.0-1ubuntu1 [5168 B] Get:131 http://ftpmaster.internal/ubuntu mantic/main amd64 cpp amd64 4:13.2.0-1ubuntu1 [28.9 kB] Get:132 http://ftpmaster.internal/ubuntu mantic-proposed/main amd64 libcc1-0 amd64 13.2.0-3ubuntu1 [48.1 kB] Get:133 http://ftpmaster.internal/ubuntu mantic-proposed/main amd64 libgomp1 amd64 13.2.0-3ubuntu1 [142 kB] Get:134 http://ftpmaster.internal/ubuntu mantic-proposed/main amd64 libitm1 amd64 13.2.0-3ubuntu1 [29.5 kB] Get:135 http://ftpmaster.internal/ubuntu mantic-proposed/main amd64 libatomic1 amd64 13.2.0-3ubuntu1 [10.4 kB] Get:136 http://ftpmaster.internal/ubuntu mantic-proposed/main amd64 libasan8 amd64 13.2.0-3ubuntu1 [2835 kB] Get:137 http://ftpmaster.internal/ubuntu mantic-proposed/main amd64 liblsan0 amd64 13.2.0-3ubuntu1 [1203 kB] Get:138 http://ftpmaster.internal/ubuntu mantic/universe amd64 g++-12 amd64 12.3.0-8ubuntu1 [12.1 MB] Get:139 http://ftpmaster.internal/ubuntu mantic/main amd64 gcc-12 amd64 12.3.0-8ubuntu1 [21.6 MB] Get:140 http://ftpmaster.internal/ubuntu mantic/main amd64 cpp-12 amd64 12.3.0-8ubuntu1 [10.7 MB] Get:141 http://ftpmaster.internal/ubuntu mantic-proposed/main amd64 libubsan1 amd64 13.2.0-3ubuntu1 [1105 kB] Get:142 http://ftpmaster.internal/ubuntu mantic/universe amd64 libstdc++-12-dev amd64 12.3.0-8ubuntu1 [2180 kB] Get:143 http://ftpmaster.internal/ubuntu mantic-proposed/main amd64 libquadmath0 amd64 13.2.0-3ubuntu1 [153 kB] Get:144 http://ftpmaster.internal/ubuntu mantic/main amd64 libgcc-12-dev amd64 12.3.0-8ubuntu1 [2574 kB] Get:145 http://ftpmaster.internal/ubuntu mantic-proposed/main amd64 libtsan2 amd64 13.2.0-3ubuntu1 [2606 kB] Get:146 http://ftpmaster.internal/ubuntu mantic/main amd64 gcc-12-base amd64 12.3.0-8ubuntu1 [43.4 kB] Get:147 http://ftpmaster.internal/ubuntu mantic-proposed/main amd64 libhwasan0 amd64 13.2.0-3ubuntu1 [1262 kB] Get:148 http://ftpmaster.internal/ubuntu mantic-proposed/main amd64 libgcc-13-dev amd64 13.2.0-3ubuntu1 [2686 kB] Get:149 http://ftpmaster.internal/ubuntu mantic-proposed/main amd64 gcc-13 amd64 13.2.0-3ubuntu1 [21.5 MB] Get:150 http://ftpmaster.internal/ubuntu mantic-proposed/main amd64 libstdc++-13-dev amd64 13.2.0-3ubuntu1 [2350 kB] Get:151 http://ftpmaster.internal/ubuntu mantic-proposed/main amd64 g++-13 amd64 13.2.0-3ubuntu1 [12.1 MB] Get:152 http://ftpmaster.internal/ubuntu mantic/main amd64 dpkg-dev all 1.22.0ubuntu1 [1137 kB] Get:153 http://ftpmaster.internal/ubuntu mantic/main amd64 libdpkg-perl all 1.22.0ubuntu1 [283 kB] Get:154 http://ftpmaster.internal/ubuntu mantic/main amd64 lto-disabled-list all 42 [12.4 kB] Get:155 http://ftpmaster.internal/ubuntu mantic/main amd64 build-essential amd64 12.10ubuntu1 [4928 B] Get:156 http://ftpmaster.internal/ubuntu mantic/main amd64 libfakeroot amd64 1.32.1-1 [31.9 kB] Get:157 http://ftpmaster.internal/ubuntu mantic/main amd64 fakeroot amd64 1.32.1-1 [60.1 kB] Get:158 http://ftpmaster.internal/ubuntu mantic/main amd64 libassuan0 amd64 2.5.6-1 [37.8 kB] Get:159 http://ftpmaster.internal/ubuntu mantic/main amd64 gpg amd64 2.2.40-1.1ubuntu1 [523 kB] Get:160 http://ftpmaster.internal/ubuntu mantic/main amd64 gpgconf amd64 2.2.40-1.1ubuntu1 [96.3 kB] Get:161 http://ftpmaster.internal/ubuntu mantic/main amd64 gpg-agent amd64 2.2.40-1.1ubuntu1 [216 kB] Get:162 http://ftpmaster.internal/ubuntu mantic/main amd64 pkgbinarymangler all 153 [16.3 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 164 MB in 1s (163 MB/s) (Reading database ... 13093 files and directories currently installed.) Preparing to unpack .../libcrypt-dev_1%3a4.4.36-2_amd64.deb ... Unpacking libcrypt-dev:amd64 (1:4.4.36-2) over (1:4.4.33-1) ... Preparing to unpack .../libc6-dev_2.38-1ubuntu4_amd64.deb ... Unpacking libc6-dev:amd64 (2.38-1ubuntu4) over (2.36-0ubuntu4) ... Replacing files in old package libc6:amd64 (2.36-0ubuntu4) ... Preparing to unpack .../libc-dev-bin_2.38-1ubuntu4_amd64.deb ... Unpacking libc-dev-bin (2.38-1ubuntu4) over (2.36-0ubuntu4) ... Preparing to unpack .../libcrypt1_1%3a4.4.36-2_amd64.deb ... Unpacking libcrypt1:amd64 (1:4.4.36-2) over (1:4.4.33-1) ... Setting up libcrypt1:amd64 (1:4.4.36-2) ... (Reading database ... 13099 files and directories currently installed.) Preparing to unpack .../linux-libc-dev_6.5.0-2.2_amd64.deb ... Unpacking linux-libc-dev:amd64 (6.5.0-2.2) over (5.19.0-21.21) ... Preparing to unpack .../libc6_2.38-1ubuntu4_amd64.deb ... Unpacking libc6:amd64 (2.38-1ubuntu4) over (2.36-0ubuntu4) ... Setting up libc6:amd64 (2.38-1ubuntu4) ... (Reading database ... 13107 files and directories currently installed.) Preparing to unpack .../libc-bin_2.38-1ubuntu4_amd64.deb ... Unpacking libc-bin (2.38-1ubuntu4) over (2.36-0ubuntu4) ... Setting up libc-bin (2.38-1ubuntu4) ... Selecting previously unselected package gcc-13-base:amd64. (Reading database ... 13109 files and directories currently installed.) Preparing to unpack .../gcc-13-base_13.2.0-3ubuntu1_amd64.deb ... Unpacking gcc-13-base:amd64 (13.2.0-3ubuntu1) ... Setting up gcc-13-base:amd64 (13.2.0-3ubuntu1) ... (Reading database ... 13114 files and directories currently installed.) Preparing to unpack .../libgcc-s1_13.2.0-3ubuntu1_amd64.deb ... Unpacking libgcc-s1:amd64 (13.2.0-3ubuntu1) over (12.2.0-10ubuntu1) ... Setting up libgcc-s1:amd64 (13.2.0-3ubuntu1) ... (Reading database ... 13114 files and directories currently installed.) Preparing to unpack .../base-files_13ubuntu1_amd64.deb ... Unpacking base-files (13ubuntu1) over (12.3ubuntu1) ... Setting up base-files (13ubuntu1) ... Installing new version of config file /etc/debian_version ... Installing new version of config file /etc/issue ... Installing new version of config file /etc/issue.net ... Installing new version of config file /etc/lsb-release ... (Reading database ... 13114 files and directories currently installed.) Preparing to unpack .../debianutils_5.8-1_amd64.deb ... Unpacking debianutils (5.8-1) over (5.7-0.4) ... Setting up debianutils (5.8-1) ... (Reading database ... 13114 files and directories currently installed.) Preparing to unpack .../bash_5.2.15-2ubuntu1_amd64.deb ... Unpacking bash (5.2.15-2ubuntu1) over (5.2-1ubuntu2) ... Setting up bash (5.2.15-2ubuntu1) ... update-alternatives: using /usr/share/man/man7/bash-builtins.7.gz to provide /usr/share/man/man7/builtins.7.gz (builtins.7.gz) in auto mode (Reading database ... 13114 files and directories currently installed.) Preparing to unpack .../bsdutils_1%3a2.39.1-4ubuntu1_amd64.deb ... Unpacking bsdutils (1:2.39.1-4ubuntu1) over (1:2.38.1-4ubuntu1) ... Setting up bsdutils (1:2.39.1-4ubuntu1) ... (Reading database ... 13114 files and directories currently installed.) Preparing to unpack .../coreutils_9.1-1ubuntu2_amd64.deb ... Unpacking coreutils (9.1-1ubuntu2) over (8.32-4.1ubuntu1) ... Setting up coreutils (9.1-1ubuntu2) ... (Reading database ... 13114 files and directories currently installed.) Preparing to unpack .../liblzma5_5.4.1-0.2_amd64.deb ... Unpacking liblzma5:amd64 (5.4.1-0.2) over (5.2.9-0.0) ... Setting up liblzma5:amd64 (5.4.1-0.2) ... (Reading database ... 13114 files and directories currently installed.) Preparing to unpack .../libzstd1_1.5.5+dfsg2-1ubuntu2_amd64.deb ... Unpacking libzstd1:amd64 (1.5.5+dfsg2-1ubuntu2) over (1.5.2+dfsg-1) ... Setting up libzstd1:amd64 (1.5.5+dfsg2-1ubuntu2) ... (Reading database ... 13114 files and directories currently installed.) Preparing to unpack .../libstdc++6_13.2.0-3ubuntu1_amd64.deb ... Unpacking libstdc++6:amd64 (13.2.0-3ubuntu1) over (12.2.0-10ubuntu1) ... Setting up libstdc++6:amd64 (13.2.0-3ubuntu1) ... (Reading database ... 13114 files and directories currently installed.) Preparing to unpack .../libgpg-error0_1.47-2_amd64.deb ... Unpacking libgpg-error0:amd64 (1.47-2) over (1.46-1) ... Setting up libgpg-error0:amd64 (1.47-2) ... (Reading database ... 13114 files and directories currently installed.) Preparing to unpack .../libgcrypt20_1.10.2-2ubuntu1_amd64.deb ... Unpacking libgcrypt20:amd64 (1.10.2-2ubuntu1) over (1.10.1-2ubuntu1) ... Setting up libgcrypt20:amd64 (1.10.2-2ubuntu1) ... (Reading database ... 13114 files and directories currently installed.) Preparing to unpack .../libp11-kit0_0.25.0-4ubuntu1_amd64.deb ... Unpacking libp11-kit0:amd64 (0.25.0-4ubuntu1) over (0.24.1-1ubuntu2) ... Setting up libp11-kit0:amd64 (0.25.0-4ubuntu1) ... (Reading database ... 13114 files and directories currently installed.) Preparing to unpack .../libacl1_2.3.1-3_amd64.deb ... Unpacking libacl1:amd64 (2.3.1-3) over (2.3.1-2) ... Setting up libacl1:amd64 (2.3.1-3) ... (Reading database ... 13114 files and directories currently installed.) Preparing to unpack .../libapparmor1_4.0.0~alpha2-0ubuntu2_amd64.deb ... Unpacking libapparmor1:amd64 (4.0.0~alpha2-0ubuntu2) over (3.0.8-1ubuntu1) ... Preparing to unpack .../libaudit-common_1%3a3.1.1-1_all.deb ... Unpacking libaudit-common (1:3.1.1-1) over (1:3.0.7-1ubuntu3) ... Setting up libaudit-common (1:3.1.1-1) ... (Reading database ... 13114 files and directories currently installed.) Preparing to unpack .../libcap-ng0_0.8.3-1build2_amd64.deb ... Unpacking libcap-ng0:amd64 (0.8.3-1build2) over (0.8.3-1build1) ... Setting up libcap-ng0:amd64 (0.8.3-1build2) ... (Reading database ... 13114 files and directories currently installed.) Preparing to unpack .../libaudit1_1%3a3.1.1-1_amd64.deb ... Unpacking libaudit1:amd64 (1:3.1.1-1) over (1:3.0.7-1ubuntu3) ... Setting up libaudit1:amd64 (1:3.1.1-1) ... (Reading database ... 13114 files and directories currently installed.) Preparing to unpack .../libblkid1_2.39.1-4ubuntu1_amd64.deb ... Unpacking libblkid1:amd64 (2.39.1-4ubuntu1) over (2.38.1-4ubuntu1) ... Setting up libblkid1:amd64 (2.39.1-4ubuntu1) ... (Reading database ... 13114 files and directories currently installed.) Preparing to unpack .../libcap2_1%3a2.66-4ubuntu1_amd64.deb ... Unpacking libcap2:amd64 (1:2.66-4ubuntu1) over (1:2.44-1build3) ... Setting up libcap2:amd64 (1:2.66-4ubuntu1) ... (Reading database ... 13116 files and directories currently installed.) Preparing to unpack .../libip4tc2_1.8.9-2ubuntu2_amd64.deb ... Unpacking libip4tc2:amd64 (1.8.9-2ubuntu2) over (1.8.7-1ubuntu7) ... Preparing to unpack .../libperl5.36_5.36.0-7ubuntu1_amd64.deb ... Unpacking libperl5.36:amd64 (5.36.0-7ubuntu1) over (5.36.0-4ubuntu2) ... Preparing to unpack .../perl_5.36.0-7ubuntu1_amd64.deb ... Unpacking perl (5.36.0-7ubuntu1) over (5.36.0-4ubuntu2) ... Preparing to unpack .../perl-base_5.36.0-7ubuntu1_amd64.deb ... Unpacking perl-base (5.36.0-7ubuntu1) over (5.36.0-4ubuntu2) ... Setting up perl-base (5.36.0-7ubuntu1) ... (Reading database ... 13116 files and directories currently installed.) Preparing to unpack .../perl-modules-5.36_5.36.0-7ubuntu1_all.deb ... Unpacking perl-modules-5.36 (5.36.0-7ubuntu1) over (5.36.0-4ubuntu2) ... Preparing to unpack .../libdb5.3_5.3.28+dfsg2-2_amd64.deb ... Unpacking libdb5.3:amd64 (5.3.28+dfsg2-2) over (5.3.28+dfsg1-0.10) ... Setting up libdb5.3:amd64 (5.3.28+dfsg2-2) ... (Reading database ... 13116 files and directories currently installed.) Preparing to unpack .../zlib1g_1%3a1.2.13.dfsg-1ubuntu5_amd64.deb ... Unpacking zlib1g:amd64 (1:1.2.13.dfsg-1ubuntu5) over (1:1.2.11.dfsg-4.1ubuntu1) ... Setting up zlib1g:amd64 (1:1.2.13.dfsg-1ubuntu5) ... (Reading database ... 13116 files and directories currently installed.) Preparing to unpack .../debconf_1.5.82_all.deb ... Unpacking debconf (1.5.82) over (1.5.79ubuntu1) ... Setting up debconf (1.5.82) ... (Reading database ... 13116 files and directories currently installed.) Preparing to unpack .../libssl3_3.0.10-1ubuntu2_amd64.deb ... Unpacking libssl3:amd64 (3.0.10-1ubuntu2) over (3.0.5-2ubuntu2) ... Preparing to unpack .../libkmod2_30+20230519-1ubuntu3_amd64.deb ... Unpacking libkmod2:amd64 (30+20230519-1ubuntu3) over (30+20220905-1ubuntu1) ... Preparing to unpack .../libpcre2-8-0_10.42-4_amd64.deb ... Unpacking libpcre2-8-0:amd64 (10.42-4) over (10.40-1ubuntu1) ... Setting up libpcre2-8-0:amd64 (10.42-4) ... (Reading database ... 13116 files and directories currently installed.) Preparing to unpack .../libselinux1_3.5-1_amd64.deb ... Unpacking libselinux1:amd64 (3.5-1) over (3.4-1build1) ... Setting up libselinux1:amd64 (3.5-1) ... (Reading database ... 13116 files and directories currently installed.) Preparing to unpack .../libmount1_2.39.1-4ubuntu1_amd64.deb ... Unpacking libmount1:amd64 (2.39.1-4ubuntu1) over (2.38.1-4ubuntu1) ... Setting up libmount1:amd64 (2.39.1-4ubuntu1) ... (Reading database ... 13116 files and directories currently installed.) Preparing to unpack .../libpam0g_1.5.2-6ubuntu1_amd64.deb ... Unpacking libpam0g:amd64 (1.5.2-6ubuntu1) over (1.5.2-5ubuntu1) ... Setting up libpam0g:amd64 (1.5.2-6ubuntu1) ... (Reading database ... 13116 files and directories currently installed.) Preparing to unpack .../libseccomp2_2.5.4-1ubuntu3_amd64.deb ... Unpacking libseccomp2:amd64 (2.5.4-1ubuntu3) over (2.5.4-1ubuntu2) ... Setting up libseccomp2:amd64 (2.5.4-1ubuntu3) ... (Reading database ... 13116 files and directories currently installed.) Preparing to unpack .../systemd-sysv_253.5-1ubuntu4_amd64.deb ... Unpacking systemd-sysv (253.5-1ubuntu4) over (251.4-1ubuntu7) ... Setting up libssl3:amd64 (3.0.10-1ubuntu2) ... (Reading database ... 13117 files and directories currently installed.) Preparing to unpack .../systemd_253.5-1ubuntu4_amd64.deb ... Unpacking systemd (253.5-1ubuntu4) over (251.4-1ubuntu7) ... Preparing to unpack .../libsystemd-shared_253.5-1ubuntu4_amd64.deb ... Unpacking libsystemd-shared:amd64 (253.5-1ubuntu4) over (251.4-1ubuntu7) ... Selecting previously unselected package systemd-dev. Preparing to unpack .../systemd-dev_253.5-1ubuntu4_all.deb ... Unpacking systemd-dev (253.5-1ubuntu4) ... Preparing to unpack .../libargon2-1_0~20190702+dfsg-3_amd64.deb ... Unpacking libargon2-1:amd64 (0~20190702+dfsg-3) over (0~20171227-0.3) ... Preparing to unpack .../libudev1_253.5-1ubuntu4_amd64.deb ... Unpacking libudev1:amd64 (253.5-1ubuntu4) over (251.4-1ubuntu7) ... Setting up libudev1:amd64 (253.5-1ubuntu4) ... (Reading database ... 13172 files and directories currently installed.) Preparing to unpack .../libdevmapper1.02.1_2%3a1.02.185-2ubuntu1_amd64.deb ... Unpacking libdevmapper1.02.1:amd64 (2:1.02.185-2ubuntu1) over (2:1.02.185-1ubuntu1) ... Preparing to unpack .../libjson-c5_0.17-1_amd64.deb ... Unpacking libjson-c5:amd64 (0.17-1) over (0.16-2) ... Preparing to unpack .../libuuid1_2.39.1-4ubuntu1_amd64.deb ... Unpacking libuuid1:amd64 (2.39.1-4ubuntu1) over (2.38.1-4ubuntu1) ... Setting up libuuid1:amd64 (2.39.1-4ubuntu1) ... (Reading database ... 13172 files and directories currently installed.) Preparing to unpack .../libcryptsetup12_2%3a2.6.1-4ubuntu2_amd64.deb ... Unpacking libcryptsetup12:amd64 (2:2.6.1-4ubuntu2) over (2:2.5.0-6ubuntu3) ... Preparing to unpack .../libfdisk1_2.39.1-4ubuntu1_amd64.deb ... Unpacking libfdisk1:amd64 (2.39.1-4ubuntu1) over (2.38.1-4ubuntu1) ... Preparing to unpack .../mount_2.39.1-4ubuntu1_amd64.deb ... Unpacking mount (2.39.1-4ubuntu1) over (2.38.1-4ubuntu1) ... Preparing to unpack .../libsystemd0_253.5-1ubuntu4_amd64.deb ... Unpacking libsystemd0:amd64 (253.5-1ubuntu4) over (251.4-1ubuntu7) ... Setting up libsystemd0:amd64 (253.5-1ubuntu4) ... (Reading database ... 13173 files and directories currently installed.) Preparing to unpack .../libapt-pkg6.0_2.7.3_amd64.deb ... Unpacking libapt-pkg6.0:amd64 (2.7.3) over (2.5.4) ... Setting up libapt-pkg6.0:amd64 (2.7.3) ... (Reading database ... 13173 files and directories currently installed.) Preparing to unpack .../tar_1.34+dfsg-1.2ubuntu1_amd64.deb ... Unpacking tar (1.34+dfsg-1.2ubuntu1) over (1.34+dfsg-1.1) ... Setting up tar (1.34+dfsg-1.2ubuntu1) ... (Reading database ... 13173 files and directories currently installed.) Preparing to unpack .../dpkg_1.22.0ubuntu1_amd64.deb ... Unpacking dpkg (1.22.0ubuntu1) over (1.21.11ubuntu2) ... Setting up dpkg (1.22.0ubuntu1) ... (Reading database ... 13173 files and directories currently installed.) Preparing to unpack .../dash_0.5.12-6ubuntu1_amd64.deb ... Unpacking dash (0.5.12-6ubuntu1) over (0.5.11+git20210903+057cd650a4ed-9ubuntu1) ... Setting up dash (0.5.12-6ubuntu1) ... Removing 'diversion of /bin/sh to /bin/sh.distrib by dash' Removing 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by dash' (Reading database ... 13171 files and directories currently installed.) Preparing to unpack .../diffutils_1%3a3.8-4_amd64.deb ... Unpacking diffutils (1:3.8-4) over (1:3.8-1) ... Setting up diffutils (1:3.8-4) ... (Reading database ... 13171 files and directories currently installed.) Preparing to unpack .../findutils_4.9.0-5_amd64.deb ... Unpacking findutils (4.9.0-5) over (4.9.0-3ubuntu1) ... Setting up findutils (4.9.0-5) ... (Reading database ... 13171 files and directories currently installed.) Preparing to unpack .../archives/grep_3.11-2_amd64.deb ... Unpacking grep (3.11-2) over (3.8-3) ... Setting up grep (3.11-2) ... (Reading database ... 13171 files and directories currently installed.) Preparing to unpack .../hostname_3.23+nmu1ubuntu1_amd64.deb ... Unpacking hostname (3.23+nmu1ubuntu1) over (3.23ubuntu2) ... Setting up hostname (3.23+nmu1ubuntu1) ... (Reading database ... 13171 files and directories currently installed.) Preparing to unpack .../libncurses6_6.4+20230625-2_amd64.deb ... Unpacking libncurses6:amd64 (6.4+20230625-2) over (6.3+20220423-2) ... Preparing to unpack .../libncursesw6_6.4+20230625-2_amd64.deb ... Unpacking libncursesw6:amd64 (6.4+20230625-2) over (6.3+20220423-2) ... Preparing to unpack .../libtinfo6_6.4+20230625-2_amd64.deb ... Unpacking libtinfo6:amd64 (6.4+20230625-2) over (6.3+20220423-2) ... Setting up libtinfo6:amd64 (6.4+20230625-2) ... (Reading database ... 13171 files and directories currently installed.) Preparing to unpack .../ncurses-bin_6.4+20230625-2_amd64.deb ... Unpacking ncurses-bin (6.4+20230625-2) over (6.3+20220423-2) ... Setting up ncurses-bin (6.4+20230625-2) ... (Reading database ... 13171 files and directories currently installed.) Preparing to unpack .../archives/sed_4.9-1_amd64.deb ... Unpacking sed (4.9-1) over (4.8-1ubuntu2) ... Setting up sed (4.9-1) ... (Reading database ... 13171 files and directories currently installed.) Preparing to unpack .../libsmartcols1_2.39.1-4ubuntu1_amd64.deb ... Unpacking libsmartcols1:amd64 (2.39.1-4ubuntu1) over (2.38.1-4ubuntu1) ... Setting up libsmartcols1:amd64 (2.39.1-4ubuntu1) ... (Reading database ... 13171 files and directories currently installed.) Preparing to unpack .../util-linux-extra_2.39.1-4ubuntu1_amd64.deb ... Unpacking util-linux-extra (2.39.1-4ubuntu1) over (2.38.1-4ubuntu1) ... Setting up util-linux-extra (2.39.1-4ubuntu1) ... (Reading database ... 13182 files and directories currently installed.) Preparing to unpack .../util-linux_2.39.1-4ubuntu1_amd64.deb ... Unpacking util-linux (2.39.1-4ubuntu1) over (2.38.1-4ubuntu1) ... Setting up util-linux (2.39.1-4ubuntu1) ... (Reading database ... 13183 files and directories currently installed.) Preparing to unpack .../init-system-helpers_1.65.2ubuntu1_all.deb ... Unpacking init-system-helpers (1.65.2ubuntu1) over (1.65.2) ... Setting up init-system-helpers (1.65.2ubuntu1) ... (Reading database ... 13183 files and directories currently installed.) Preparing to unpack .../ncurses-base_6.4+20230625-2_all.deb ... Unpacking ncurses-base (6.4+20230625-2) over (6.3+20220423-2) ... Setting up ncurses-base (6.4+20230625-2) ... (Reading database ... 13181 files and directories currently installed.) Preparing to unpack .../archives/lsb-base_11.6_all.deb ... Unpacking lsb-base (11.6) over (11.2ubuntu1) ... Preparing to unpack .../sysvinit-utils_3.07-1ubuntu1_amd64.deb ... Unpacking sysvinit-utils (3.07-1ubuntu1) over (3.04-1ubuntu1) ... Setting up sysvinit-utils (3.07-1ubuntu1) ... (Reading database ... 13181 files and directories currently installed.) Preparing to unpack .../adduser_3.137ubuntu1_all.deb ... moving unchanged adduser.conf to adduser.conf.update-old. New dpkg-conffile will come from the package. Unpacking adduser (3.137ubuntu1) over (3.121ubuntu1) ... Setting up adduser (3.137ubuntu1) ... Installing new version of config file /etc/deluser.conf ... (Reading database ... 13145 files and directories currently installed.) Preparing to unpack .../gpgv_2.2.40-1.1ubuntu1_amd64.deb ... Unpacking gpgv (2.2.40-1.1ubuntu1) over (2.2.40-1ubuntu1) ... Setting up gpgv (2.2.40-1.1ubuntu1) ... (Reading database ... 13145 files and directories currently installed.) Preparing to unpack .../libgmp10_2%3a6.3.0+dfsg-2ubuntu4_amd64.deb ... Unpacking libgmp10:amd64 (2:6.3.0+dfsg-2ubuntu4) over (2:6.2.1+dfsg1-1.1ubuntu1) ... Setting up libgmp10:amd64 (2:6.3.0+dfsg-2ubuntu4) ... (Reading database ... 13145 files and directories currently installed.) Preparing to unpack .../libnettle8_3.9.1-2_amd64.deb ... Unpacking libnettle8:amd64 (3.9.1-2) over (3.8.1-2) ... Setting up libnettle8:amd64 (3.9.1-2) ... (Reading database ... 13145 files and directories currently installed.) Preparing to unpack .../libhogweed6_3.9.1-2_amd64.deb ... Unpacking libhogweed6:amd64 (3.9.1-2) over (3.8.1-2) ... Setting up libhogweed6:amd64 (3.9.1-2) ... (Reading database ... 13145 files and directories currently installed.) Preparing to unpack .../libidn2-0_2.3.4-1_amd64.deb ... Unpacking libidn2-0:amd64 (2.3.4-1) over (2.3.3-1build1) ... Setting up libidn2-0:amd64 (2.3.4-1) ... (Reading database ... 13145 files and directories currently installed.) Preparing to unpack .../libtasn1-6_4.19.0-3_amd64.deb ... Unpacking libtasn1-6:amd64 (4.19.0-3) over (4.19.0-2) ... Setting up libtasn1-6:amd64 (4.19.0-3) ... (Reading database ... 13145 files and directories currently installed.) Preparing to unpack .../libgnutls30_3.8.1-4ubuntu1_amd64.deb ... Unpacking libgnutls30:amd64 (3.8.1-4ubuntu1) over (3.7.7-2ubuntu2) ... Setting up libgnutls30:amd64 (3.8.1-4ubuntu1) ... (Reading database ... 13145 files and directories currently installed.) Preparing to unpack .../archives/apt_2.7.3_amd64.deb ... Unpacking apt (2.7.3) over (2.5.4) ... Setting up apt (2.7.3) ... Installing new version of config file /etc/apt/apt.conf.d/01autoremove ... (Reading database ... 13142 files and directories currently installed.) Preparing to unpack .../libpam-modules-bin_1.5.2-6ubuntu1_amd64.deb ... Unpacking libpam-modules-bin (1.5.2-6ubuntu1) over (1.5.2-5ubuntu1) ... Setting up libpam-modules-bin (1.5.2-6ubuntu1) ... (Reading database ... 13142 files and directories currently installed.) Preparing to unpack .../libpam-modules_1.5.2-6ubuntu1_amd64.deb ... Unpacking libpam-modules:amd64 (1.5.2-6ubuntu1) over (1.5.2-5ubuntu1) ... Setting up libpam-modules:amd64 (1.5.2-6ubuntu1) ... (Reading database ... 13142 files and directories currently installed.) Preparing to unpack .../logsave_1.47.0-2ubuntu1_amd64.deb ... Unpacking logsave (1.47.0-2ubuntu1) over (1.46.6~rc1-1ubuntu1) ... Preparing to unpack .../libext2fs2_1.47.0-2ubuntu1_amd64.deb ... Unpacking libext2fs2:amd64 (1.47.0-2ubuntu1) over (1.46.6~rc1-1ubuntu1) ... Setting up libext2fs2:amd64 (1.47.0-2ubuntu1) ... (Reading database ... 13142 files and directories currently installed.) Preparing to unpack .../e2fsprogs_1.47.0-2ubuntu1_amd64.deb ... Unpacking e2fsprogs (1.47.0-2ubuntu1) over (1.46.6~rc1-1ubuntu1) ... Setting up libargon2-1:amd64 (0~20190702+dfsg-3) ... Setting up libdevmapper1.02.1:amd64 (2:1.02.185-2ubuntu1) ... Setting up libjson-c5:amd64 (0.17-1) ... Setting up libcryptsetup12:amd64 (2:2.6.1-4ubuntu2) ... Setting up libfdisk1:amd64 (2.39.1-4ubuntu1) ... Setting up libkmod2:amd64 (30+20230519-1ubuntu3) ... Setting up libapparmor1:amd64 (4.0.0~alpha2-0ubuntu2) ... Setting up libip4tc2:amd64 (1.8.9-2ubuntu2) ... Setting up libsystemd-shared:amd64 (253.5-1ubuntu4) ... Setting up systemd-dev (253.5-1ubuntu4) ... Setting up mount (2.39.1-4ubuntu1) ... Setting up systemd (253.5-1ubuntu4) ... Installing new version of config file /etc/systemd/journald.conf ... Installing new version of config file /etc/systemd/logind.conf ... Installing new version of config file /etc/systemd/sleep.conf ... Installing new version of config file /etc/systemd/system.conf ... Installing new version of config file /etc/systemd/user.conf ... Initializing machine ID from random generator. Setting up systemd-sysv (253.5-1ubuntu4) ... (Reading database ... 13142 files and directories currently installed.) Preparing to unpack .../init_1.65.2ubuntu1_amd64.deb ... Unpacking init (1.65.2ubuntu1) over (1.65.2) ... Preparing to unpack .../libattr1_1%3a2.5.1-4_amd64.deb ... Unpacking libattr1:amd64 (1:2.5.1-4) over (1:2.5.1-3) ... Setting up libattr1:amd64 (1:2.5.1-4) ... (Reading database ... 13142 files and directories currently installed.) Preparing to unpack .../libdebconfclient0_0.270ubuntu1_amd64.deb ... Unpacking libdebconfclient0:amd64 (0.270ubuntu1) over (0.264ubuntu1) ... Setting up libdebconfclient0:amd64 (0.270ubuntu1) ... (Reading database ... 13142 files and directories currently installed.) Preparing to unpack .../libmd0_1.1.0-1_amd64.deb ... Unpacking libmd0:amd64 (1.1.0-1) over (1.0.4-2) ... Setting up libmd0:amd64 (1.1.0-1) ... (Reading database ... 13142 files and directories currently installed.) Preparing to unpack .../libpam-runtime_1.5.2-6ubuntu1_all.deb ... Unpacking libpam-runtime (1.5.2-6ubuntu1) over (1.5.2-5ubuntu1) ... Setting up libpam-runtime (1.5.2-6ubuntu1) ... (Reading database ... 13142 files and directories currently installed.) Preparing to unpack .../libsemanage-common_3.5-1_all.deb ... Unpacking libsemanage-common (3.5-1) over (3.4-1build1) ... Setting up libsemanage-common (3.5-1) ... (Reading database ... 13142 files and directories currently installed.) Preparing to unpack .../libsepol2_3.5-1_amd64.deb ... Unpacking libsepol2:amd64 (3.5-1) over (3.4-2) ... Setting up libsepol2:amd64 (3.5-1) ... (Reading database ... 13142 files and directories currently installed.) Preparing to unpack .../libsemanage2_3.5-1_amd64.deb ... Unpacking libsemanage2:amd64 (3.5-1) over (3.4-1build1) ... Setting up libsemanage2:amd64 (3.5-1) ... (Reading database ... 13142 files and directories currently installed.) Preparing to unpack .../usrmerge_35ubuntu1_all.deb ... Unpacking usrmerge (35ubuntu1) over (33ubuntu1) ... Setting up usrmerge (35ubuntu1) ... (Reading database ... 13142 files and directories currently installed.) Preparing to unpack .../00-libcom-err2_1.47.0-2ubuntu1_amd64.deb ... Unpacking libcom-err2:amd64 (1.47.0-2ubuntu1) over (1.46.6~rc1-1ubuntu1) ... Selecting previously unselected package libproc2-0:amd64. Preparing to unpack .../01-libproc2-0_2%3a4.0.3-1ubuntu1_amd64.deb ... Unpacking libproc2-0:amd64 (2:4.0.3-1ubuntu1) ... Preparing to unpack .../02-libss2_1.47.0-2ubuntu1_amd64.deb ... Unpacking libss2:amd64 (1.47.0-2ubuntu1) over (1.46.6~rc1-1ubuntu1) ... Preparing to unpack .../03-mawk_1.3.4.20230730-1_amd64.deb ... Unpacking mawk (1.3.4.20230730-1) over (1.3.4.20200120-3.1) ... Preparing to unpack .../04-procps_2%3a4.0.3-1ubuntu1_amd64.deb ... Unpacking procps (2:4.0.3-1ubuntu1) over (2:3.3.17-7ubuntu1) ... Preparing to unpack .../05-sensible-utils_0.0.20_all.deb ... Unpacking sensible-utils (0.0.20) over (0.0.17) ... Preparing to unpack .../06-openssl_3.0.10-1ubuntu2_amd64.deb ... Unpacking openssl (3.0.10-1ubuntu2) over (3.0.5-2ubuntu2) ... Preparing to unpack .../07-ca-certificates_20230311ubuntu1_all.deb ... Unpacking ca-certificates (20230311ubuntu1) over (20211016ubuntu1) ... Preparing to unpack .../08-libgssapi-krb5-2_1.20.1-3ubuntu1_amd64.deb ... Unpacking libgssapi-krb5-2:amd64 (1.20.1-3ubuntu1) over (1.20.1-1build1) ... Preparing to unpack .../09-libkrb5-3_1.20.1-3ubuntu1_amd64.deb ... Unpacking libkrb5-3:amd64 (1.20.1-3ubuntu1) over (1.20.1-1build1) ... Preparing to unpack .../10-libk5crypto3_1.20.1-3ubuntu1_amd64.deb ... Unpacking libk5crypto3:amd64 (1.20.1-3ubuntu1) over (1.20.1-1build1) ... Preparing to unpack .../11-libkrb5support0_1.20.1-3ubuntu1_amd64.deb ... Unpacking libkrb5support0:amd64 (1.20.1-3ubuntu1) over (1.20.1-1build1) ... Preparing to unpack .../12-readline-common_8.2-1.3_all.deb ... Unpacking readline-common (8.2-1.3) over (8.2-1.2) ... Preparing to unpack .../13-libreadline8_8.2-1.3_amd64.deb ... Unpacking libreadline8:amd64 (8.2-1.3) over (8.2-1.2) ... Preparing to unpack .../14-libsqlite3-0_3.42.0-1_amd64.deb ... Unpacking libsqlite3-0:amd64 (3.42.0-1) over (3.40.0-1) ... Preparing to unpack .../15-tzdata_2023c-9ubuntu1_all.deb ... Unpacking tzdata (2023c-9ubuntu1) over (2022g-1ubuntu1) ... Preparing to unpack .../16-libpng16-16_1.6.40-1_amd64.deb ... Unpacking libpng16-16:amd64 (1.6.40-1) over (1.6.39-2) ... Preparing to unpack .../17-xz-utils_5.4.1-0.2_amd64.deb ... Unpacking xz-utils (5.4.1-0.2) over (5.2.9-0.0) ... Preparing to unpack .../18-advancecomp_2.5-1_amd64.deb ... Unpacking advancecomp (2.5-1) over (2.4-1) ... Preparing to unpack .../19-libgprofng0_2.41-4ubuntu1_amd64.deb ... Unpacking libgprofng0:amd64 (2.41-4ubuntu1) over (2.39.50.20221224-1ubuntu1) ... Preparing to unpack .../20-libctf0_2.41-4ubuntu1_amd64.deb ... Unpacking libctf0:amd64 (2.41-4ubuntu1) over (2.39.50.20221224-1ubuntu1) ... Preparing to unpack .../21-libctf-nobfd0_2.41-4ubuntu1_amd64.deb ... Unpacking libctf-nobfd0:amd64 (2.41-4ubuntu1) over (2.39.50.20221224-1ubuntu1) ... Preparing to unpack .../22-binutils-x86-64-linux-gnu_2.41-4ubuntu1_amd64.deb ... Unpacking binutils-x86-64-linux-gnu (2.41-4ubuntu1) over (2.39.50.20221224-1ubuntu1) ... Preparing to unpack .../23-libbinutils_2.41-4ubuntu1_amd64.deb ... Unpacking libbinutils:amd64 (2.41-4ubuntu1) over (2.39.50.20221224-1ubuntu1) ... Preparing to unpack .../24-binutils_2.41-4ubuntu1_amd64.deb ... Unpacking binutils (2.41-4ubuntu1) over (2.39.50.20221224-1ubuntu1) ... Preparing to unpack .../25-binutils-common_2.41-4ubuntu1_amd64.deb ... Unpacking binutils-common:amd64 (2.41-4ubuntu1) over (2.39.50.20221224-1ubuntu1) ... Selecting previously unselected package libsframe1:amd64. Preparing to unpack .../26-libsframe1_2.41-4ubuntu1_amd64.deb ... Unpacking libsframe1:amd64 (2.41-4ubuntu1) ... Preparing to unpack .../27-libisl23_0.26-3_amd64.deb ... Unpacking libisl23:amd64 (0.26-3) over (0.25-1) ... Preparing to unpack .../28-libmpfr6_4.2.1-1_amd64.deb ... Unpacking libmpfr6:amd64 (4.2.1-1) over (4.1.0-3build3) ... Selecting previously unselected package cpp-13. Preparing to unpack .../29-cpp-13_13.2.0-3ubuntu1_amd64.deb ... Unpacking cpp-13 (13.2.0-3ubuntu1) ... Preparing to unpack .../30-g++_4%3a13.2.0-1ubuntu1_amd64.deb ... Unpacking g++ (4:13.2.0-1ubuntu1) over (4:12.2.0-1ubuntu1) ... Preparing to unpack .../31-gcc_4%3a13.2.0-1ubuntu1_amd64.deb ... Unpacking gcc (4:13.2.0-1ubuntu1) over (4:12.2.0-1ubuntu1) ... Preparing to unpack .../32-cpp_4%3a13.2.0-1ubuntu1_amd64.deb ... Unpacking cpp (4:13.2.0-1ubuntu1) over (4:12.2.0-1ubuntu1) ... Preparing to unpack .../33-libcc1-0_13.2.0-3ubuntu1_amd64.deb ... Unpacking libcc1-0:amd64 (13.2.0-3ubuntu1) over (12.2.0-10ubuntu1) ... Preparing to unpack .../34-libgomp1_13.2.0-3ubuntu1_amd64.deb ... Unpacking libgomp1:amd64 (13.2.0-3ubuntu1) over (12.2.0-10ubuntu1) ... Preparing to unpack .../35-libitm1_13.2.0-3ubuntu1_amd64.deb ... Unpacking libitm1:amd64 (13.2.0-3ubuntu1) over (12.2.0-10ubuntu1) ... Preparing to unpack .../36-libatomic1_13.2.0-3ubuntu1_amd64.deb ... Unpacking libatomic1:amd64 (13.2.0-3ubuntu1) over (12.2.0-10ubuntu1) ... Preparing to unpack .../37-libasan8_13.2.0-3ubuntu1_amd64.deb ... Unpacking libasan8:amd64 (13.2.0-3ubuntu1) over (12.2.0-10ubuntu1) ... Preparing to unpack .../38-liblsan0_13.2.0-3ubuntu1_amd64.deb ... Unpacking liblsan0:amd64 (13.2.0-3ubuntu1) over (12.2.0-10ubuntu1) ... Preparing to unpack .../39-g++-12_12.3.0-8ubuntu1_amd64.deb ... Unpacking g++-12 (12.3.0-8ubuntu1) over (12.2.0-10ubuntu1) ... Preparing to unpack .../40-gcc-12_12.3.0-8ubuntu1_amd64.deb ... Unpacking gcc-12 (12.3.0-8ubuntu1) over (12.2.0-10ubuntu1) ... Preparing to unpack .../41-cpp-12_12.3.0-8ubuntu1_amd64.deb ... Unpacking cpp-12 (12.3.0-8ubuntu1) over (12.2.0-10ubuntu1) ... Preparing to unpack .../42-libubsan1_13.2.0-3ubuntu1_amd64.deb ... Unpacking libubsan1:amd64 (13.2.0-3ubuntu1) over (12.2.0-10ubuntu1) ... Preparing to unpack .../43-libstdc++-12-dev_12.3.0-8ubuntu1_amd64.deb ... Unpacking libstdc++-12-dev:amd64 (12.3.0-8ubuntu1) over (12.2.0-10ubuntu1) ... Preparing to unpack .../44-libquadmath0_13.2.0-3ubuntu1_amd64.deb ... Unpacking libquadmath0:amd64 (13.2.0-3ubuntu1) over (12.2.0-10ubuntu1) ... Preparing to unpack .../45-libgcc-12-dev_12.3.0-8ubuntu1_amd64.deb ... Unpacking libgcc-12-dev:amd64 (12.3.0-8ubuntu1) over (12.2.0-10ubuntu1) ... Preparing to unpack .../46-libtsan2_13.2.0-3ubuntu1_amd64.deb ... Unpacking libtsan2:amd64 (13.2.0-3ubuntu1) over (12.2.0-10ubuntu1) ... Preparing to unpack .../47-gcc-12-base_12.3.0-8ubuntu1_amd64.deb ... Unpacking gcc-12-base:amd64 (12.3.0-8ubuntu1) over (12.2.0-10ubuntu1) ... Selecting previously unselected package libhwasan0:amd64. Preparing to unpack .../48-libhwasan0_13.2.0-3ubuntu1_amd64.deb ... Unpacking libhwasan0:amd64 (13.2.0-3ubuntu1) ... Selecting previously unselected package libgcc-13-dev:amd64. Preparing to unpack .../49-libgcc-13-dev_13.2.0-3ubuntu1_amd64.deb ... Unpacking libgcc-13-dev:amd64 (13.2.0-3ubuntu1) ... Selecting previously unselected package gcc-13. Preparing to unpack .../50-gcc-13_13.2.0-3ubuntu1_amd64.deb ... Unpacking gcc-13 (13.2.0-3ubuntu1) ... Selecting previously unselected package libstdc++-13-dev:amd64. Preparing to unpack .../51-libstdc++-13-dev_13.2.0-3ubuntu1_amd64.deb ... Unpacking libstdc++-13-dev:amd64 (13.2.0-3ubuntu1) ... Selecting previously unselected package g++-13. Preparing to unpack .../52-g++-13_13.2.0-3ubuntu1_amd64.deb ... Unpacking g++-13 (13.2.0-3ubuntu1) ... Preparing to unpack .../53-dpkg-dev_1.22.0ubuntu1_all.deb ... Unpacking dpkg-dev (1.22.0ubuntu1) over (1.21.11ubuntu2) ... Preparing to unpack .../54-libdpkg-perl_1.22.0ubuntu1_all.deb ... Unpacking libdpkg-perl (1.22.0ubuntu1) over (1.21.11ubuntu2) ... Preparing to unpack .../55-lto-disabled-list_42_all.deb ... Unpacking lto-disabled-list (42) over (37) ... Preparing to unpack .../56-build-essential_12.10ubuntu1_amd64.deb ... Unpacking build-essential (12.10ubuntu1) over (12.9ubuntu3) ... Preparing to unpack .../57-libfakeroot_1.32.1-1_amd64.deb ... Unpacking libfakeroot:amd64 (1.32.1-1) over (1.30.1-1ubuntu1) ... Preparing to unpack .../58-fakeroot_1.32.1-1_amd64.deb ... Unpacking fakeroot (1.32.1-1) over (1.30.1-1ubuntu1) ... Preparing to unpack .../59-libassuan0_2.5.6-1_amd64.deb ... Unpacking libassuan0:amd64 (2.5.6-1) over (2.5.5-5) ... Preparing to unpack .../60-gpg_2.2.40-1.1ubuntu1_amd64.deb ... Unpacking gpg (2.2.40-1.1ubuntu1) over (2.2.40-1ubuntu1) ... Preparing to unpack .../61-gpgconf_2.2.40-1.1ubuntu1_amd64.deb ... Unpacking gpgconf (2.2.40-1.1ubuntu1) over (2.2.40-1ubuntu1) ... Preparing to unpack .../62-gpg-agent_2.2.40-1.1ubuntu1_amd64.deb ... Unpacking gpg-agent (2.2.40-1.1ubuntu1) over (2.2.40-1ubuntu1) ... Preparing to unpack .../63-pkgbinarymangler_153_all.deb ... Unpacking pkgbinarymangler (153) over (149) ... Setting up lsb-base (11.6) ... Setting up lto-disabled-list (42) ... Setting up init (1.65.2ubuntu1) ... Setting up libsqlite3-0:amd64 (3.42.0-1) ... Setting up binutils-common:amd64 (2.41-4ubuntu1) ... Installing new version of config file /etc/gprofng.rc ... Setting up linux-libc-dev:amd64 (6.5.0-2.2) ... Setting up libctf-nobfd0:amd64 (2.41-4ubuntu1) ... Setting up libcom-err2:amd64 (1.47.0-2ubuntu1) ... Setting up libassuan0:amd64 (2.5.6-1) ... Setting up libgomp1:amd64 (13.2.0-3ubuntu1) ... Setting up libsframe1:amd64 (2.41-4ubuntu1) ... Setting up libfakeroot:amd64 (1.32.1-1) ... Setting up libkrb5support0:amd64 (1.20.1-3ubuntu1) ... Setting up gcc-12-base:amd64 (12.3.0-8ubuntu1) ... Setting up tzdata (2023c-9ubuntu1) ... Current default time zone: 'Etc/UTC' Local time is now: Sun Sep 3 16:14:03 UTC 2023. Universal Time is now: Sun Sep 3 16:14:03 UTC 2023. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up fakeroot (1.32.1-1) ... Setting up perl-modules-5.36 (5.36.0-7ubuntu1) ... Setting up libmpfr6:amd64 (4.2.1-1) ... Setting up libncurses6:amd64 (6.4+20230625-2) ... Setting up xz-utils (5.4.1-0.2) ... Setting up libquadmath0:amd64 (13.2.0-3ubuntu1) ... Setting up libproc2-0:amd64 (2:4.0.3-1ubuntu1) ... Setting up libpng16-16:amd64 (1.6.40-1) ... Setting up libatomic1:amd64 (13.2.0-3ubuntu1) ... Setting up libss2:amd64 (1.47.0-2ubuntu1) ... Setting up libncursesw6:amd64 (6.4+20230625-2) ... Setting up libk5crypto3:amd64 (1.20.1-3ubuntu1) ... Setting up logsave (1.47.0-2ubuntu1) ... Setting up libubsan1:amd64 (13.2.0-3ubuntu1) ... Setting up advancecomp (2.5-1) ... Setting up sensible-utils (0.0.20) ... Setting up libhwasan0:amd64 (13.2.0-3ubuntu1) ... Setting up libcrypt-dev:amd64 (1:4.4.36-2) ... Setting up libasan8:amd64 (13.2.0-3ubuntu1) ... Setting up procps (2:4.0.3-1ubuntu1) ... Setting up mawk (1.3.4.20230730-1) ... Setting up libkrb5-3:amd64 (1.20.1-3ubuntu1) ... Setting up libtsan2:amd64 (13.2.0-3ubuntu1) ... Setting up libbinutils:amd64 (2.41-4ubuntu1) ... Setting up libisl23:amd64 (0.26-3) ... Setting up libc-dev-bin (2.38-1ubuntu4) ... Setting up openssl (3.0.10-1ubuntu2) ... Installing new version of config file /etc/ssl/openssl.cnf ... Setting up readline-common (8.2-1.3) ... Setting up libcc1-0:amd64 (13.2.0-3ubuntu1) ... Setting up libperl5.36:amd64 (5.36.0-7ubuntu1) ... Setting up liblsan0:amd64 (13.2.0-3ubuntu1) ... Setting up libitm1:amd64 (13.2.0-3ubuntu1) ... Setting up libctf0:amd64 (2.41-4ubuntu1) ... Setting up cpp-12 (12.3.0-8ubuntu1) ... Setting up pkgbinarymangler (153) ... Setting up cpp-13 (13.2.0-3ubuntu1) ... Setting up libreadline8:amd64 (8.2-1.3) ... Setting up e2fsprogs (1.47.0-2ubuntu1) ... Setting up ca-certificates (20230311ubuntu1) ... Updating certificates in /etc/ssl/certs... rehash: warning: skipping ca-certificates.crt,it does not contain exactly one certificate or CRL 19 added, 6 removed; done. Setting up perl (5.36.0-7ubuntu1) ... Setting up libgprofng0:amd64 (2.41-4ubuntu1) ... Setting up libgcc-12-dev:amd64 (12.3.0-8ubuntu1) ... Setting up libgssapi-krb5-2:amd64 (1.20.1-3ubuntu1) ... Setting up libdpkg-perl (1.22.0ubuntu1) ... Setting up libgcc-13-dev:amd64 (13.2.0-3ubuntu1) ... Setting up cpp (4:13.2.0-1ubuntu1) ... Setting up gpgconf (2.2.40-1.1ubuntu1) ... Setting up libc6-dev:amd64 (2.38-1ubuntu4) ... Setting up gpg (2.2.40-1.1ubuntu1) ... Setting up libstdc++-13-dev:amd64 (13.2.0-3ubuntu1) ... Setting up binutils-x86-64-linux-gnu (2.41-4ubuntu1) ... Setting up gpg-agent (2.2.40-1.1ubuntu1) ... Setting up libstdc++-12-dev:amd64 (12.3.0-8ubuntu1) ... Setting up binutils (2.41-4ubuntu1) ... Setting up dpkg-dev (1.22.0ubuntu1) ... Setting up gcc-12 (12.3.0-8ubuntu1) ... Setting up gcc-13 (13.2.0-3ubuntu1) ... Setting up g++-12 (12.3.0-8ubuntu1) ... Setting up g++-13 (13.2.0-3ubuntu1) ... Setting up gcc (4:13.2.0-1ubuntu1) ... Setting up g++ (4:13.2.0-1ubuntu1) ... Setting up build-essential (12.10ubuntu1) ... Processing triggers for libc-bin (2.38-1ubuntu4) ... Processing triggers for debianutils (5.8-1) ... Processing triggers for ca-certificates (20230311ubuntu1) ... 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-26678012 amd64 mantic-proposed -c chroot:build-PACKAGEBUILD-26678012 --arch=amd64 --dist=mantic-proposed --nolog -A blasr_5.3.5+dfsg-6build1.dsc Initiating build PACKAGEBUILD-26678012 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 5.4.0-156-generic #173-Ubuntu SMP Tue Jul 11 07:25:22 UTC 2023 x86_64 sbuild (Debian sbuild) 0.79.0 (05 February 2020) on lcy02-amd64-005.buildd +==============================================================================+ | blasr 5.3.5+dfsg-6build1 (amd64) Sun, 03 Sep 2023 16:14:06 +0000 | +==============================================================================+ Package: blasr Version: 5.3.5+dfsg-6build1 Source Version: 5.3.5+dfsg-6build1 Distribution: mantic-proposed Machine Architecture: amd64 Host Architecture: amd64 Build Architecture: amd64 Build Type: binary I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-26678012/chroot-autobuild' with '<>' I: NOTICE: Log filtering will replace 'build/blasr-JmWzfk/resolver-KVhwUA' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- blasr_5.3.5+dfsg-6build1.dsc exists in .; copying to chroot I: NOTICE: Log filtering will replace 'build/blasr-JmWzfk/blasr-5.3.5+dfsg' with '<>' I: NOTICE: Log filtering will replace 'build/blasr-JmWzfk' with '<>' +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper-compat (= 13), python3:any, meson, cmake, pkg-config, libboost-dev, libhdf5-dev, zlib1g-dev, libpbseq-dev, libpbbam-dev, libpbdata-dev, libpbcopper-dev, libgtest-dev, libblasr-dev (>= 5.3.4+dfsg-4~), build-essential, fakeroot Filtered Build-Depends: debhelper-compat (= 13), python3:any, meson, cmake, pkg-config, libboost-dev, libhdf5-dev, zlib1g-dev, libpbseq-dev, libpbbam-dev, libpbdata-dev, libpbcopper-dev, libgtest-dev, libblasr-dev (>= 5.3.4+dfsg-4~), 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 [458 B] Get:5 copy:/<>/apt_archive ./ Packages [543 B] Fetched 1958 B in 0s (187 kB/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: g++-12 libstdc++-12-dev Use 'apt autoremove' to remove them. The following additional packages will be installed: autoconf automake autopoint autotools-dev bsdextrautils cmake cmake-data debhelper debugedit dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base googletest groff-base hdf5-helpers intltool-debian libaec-dev libaec0 libarchive-zip-perl libarchive13 libblasr-dev libblasr5.3.5 libboost-dev libboost1.74-dev libbrotli1 libcurl3-gnutls libcurl4 libcurl4-gnutls-dev libdebhelper-perl libdeflate-dev libdeflate0 libdw1 libelf1 libexpat1 libfile-stripnondeterminism-perl libgfortran5 libgtest-dev libhdf5-103-1 libhdf5-cpp-103-1 libhdf5-dev libhdf5-fortran-102 libhdf5-hl-100 libhdf5-hl-cpp-100 libhdf5-hl-fortran-100 libhts-dev libhts3 libhtscodecs2 libicu72 libjpeg-dev libjpeg-turbo8 libjpeg-turbo8-dev libjpeg8 libjpeg8-dev libjsoncpp25 libldap2 liblzma-dev libmagic-mgc libmagic1 libnghttp2-14 libpbbam-dev libpbbam2.3.0 libpbcopper-dev libpbcopper2.2.0 libpbdata-dev libpbihdf-dev libpbseq-dev libpipeline1 libpkgconf3 libpsl5 libpython3-stdlib libpython3.11-minimal libpython3.11-stdlib librhash0 librtmp1 libsasl2-2 libsasl2-modules-db libssh-4 libssl-dev libsub-override-perl libsz2 libtool libuchardet0 libuv1 libxml2 m4 man-db media-types meson ninja-build pkg-config pkgconf pkgconf-bin po-debconf python3 python3-distutils python3-lib2to3 python3-minimal python3-pkg-resources python3-setuptools python3.11 python3.11-minimal 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 libboost1.74-doc libboost-atomic1.74-dev libboost-chrono1.74-dev libboost-container1.74-dev libboost-context1.74-dev libboost-contract1.74-dev libboost-coroutine1.74-dev libboost-date-time1.74-dev libboost-exception1.74-dev libboost-fiber1.74-dev libboost-filesystem1.74-dev libboost-graph1.74-dev libboost-graph-parallel1.74-dev libboost-iostreams1.74-dev libboost-locale1.74-dev libboost-log1.74-dev libboost-math1.74-dev libboost-mpi1.74-dev libboost-mpi-python1.74-dev libboost-numpy1.74-dev libboost-program-options1.74-dev libboost-python1.74-dev libboost-random1.74-dev libboost-regex1.74-dev libboost-serialization1.74-dev libboost-stacktrace1.74-dev libboost-system1.74-dev libboost-test1.74-dev libboost-thread1.74-dev libboost-timer1.74-dev libboost-type-erasure1.74-dev libboost-wave1.74-dev libboost1.74-tools-dev libmpfrc++-dev libntl-dev libboost-nowide1.74-dev libcurl4-doc libgnutls28-dev libidn-dev libkrb5-dev libldap2-dev librtmp-dev libssh2-1-dev libhdf5-doc 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 python3.11-venv python3.11-doc binfmt-support 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 bsdextrautils cmake cmake-data debhelper debugedit dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base googletest groff-base hdf5-helpers intltool-debian libaec-dev libaec0 libarchive-zip-perl libarchive13 libblasr-dev libblasr5.3.5 libboost-dev libboost1.74-dev libbrotli1 libcurl3-gnutls libcurl4 libcurl4-gnutls-dev libdebhelper-perl libdeflate-dev libdeflate0 libdw1 libelf1 libexpat1 libfile-stripnondeterminism-perl libgfortran5 libgtest-dev libhdf5-103-1 libhdf5-cpp-103-1 libhdf5-dev libhdf5-fortran-102 libhdf5-hl-100 libhdf5-hl-cpp-100 libhdf5-hl-fortran-100 libhts-dev libhts3 libhtscodecs2 libicu72 libjpeg-dev libjpeg-turbo8 libjpeg-turbo8-dev libjpeg8 libjpeg8-dev libjsoncpp25 libldap2 liblzma-dev libmagic-mgc libmagic1 libnghttp2-14 libpbbam-dev libpbbam2.3.0 libpbcopper-dev libpbcopper2.2.0 libpbdata-dev libpbihdf-dev libpbseq-dev libpipeline1 libpkgconf3 libpsl5 libpython3-stdlib libpython3.11-minimal libpython3.11-stdlib librhash0 librtmp1 libsasl2-2 libsasl2-modules-db libssh-4 libssl-dev libsub-override-perl libsz2 libtool libuchardet0 libuv1 libxml2 m4 man-db media-types meson ninja-build pkg-config pkgconf pkgconf-bin po-debconf python3 python3-distutils python3-lib2to3 python3-minimal python3-pkg-resources python3-setuptools python3.11 python3.11-minimal sbuild-build-depends-main-dummy zlib1g-dev 0 upgraded, 106 newly installed, 0 to remove and 0 not upgraded. Need to get 74.4 MB of archives. After this operation, 385 MB of additional disk space will be used. Get:1 copy:/<>/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [760 B] Get:2 http://ftpmaster.internal/ubuntu mantic/main amd64 libpython3.11-minimal amd64 3.11.5-3 [838 kB] Get:3 http://ftpmaster.internal/ubuntu mantic/main amd64 libexpat1 amd64 2.5.0-2 [85.2 kB] Get:4 http://ftpmaster.internal/ubuntu mantic/main amd64 python3.11-minimal amd64 3.11.5-3 [2198 kB] Get:5 http://ftpmaster.internal/ubuntu mantic/main amd64 python3-minimal amd64 3.11.4-5 [26.8 kB] Get:6 http://ftpmaster.internal/ubuntu mantic/main amd64 media-types all 10.1.0 [27.5 kB] Get:7 http://ftpmaster.internal/ubuntu mantic/main amd64 libpython3.11-stdlib amd64 3.11.5-3 [1909 kB] Get:8 http://ftpmaster.internal/ubuntu mantic/main amd64 python3.11 amd64 3.11.5-3 [575 kB] Get:9 http://ftpmaster.internal/ubuntu mantic/main amd64 libpython3-stdlib amd64 3.11.4-5 [9502 B] Get:10 http://ftpmaster.internal/ubuntu mantic/main amd64 python3 amd64 3.11.4-5 [22.9 kB] Get:11 http://ftpmaster.internal/ubuntu mantic/main amd64 libelf1 amd64 0.189-4 [56.3 kB] Get:12 http://ftpmaster.internal/ubuntu mantic/main amd64 libicu72 amd64 72.1-3ubuntu2 [10.8 MB] Get:13 http://ftpmaster.internal/ubuntu mantic/main amd64 libxml2 amd64 2.9.14+dfsg-1.3 [764 kB] Get:14 http://ftpmaster.internal/ubuntu mantic/main amd64 python3-pkg-resources all 68.1.2-1 [167 kB] Get:15 http://ftpmaster.internal/ubuntu mantic/main amd64 bsdextrautils amd64 2.39.1-4ubuntu1 [73.6 kB] Get:16 http://ftpmaster.internal/ubuntu mantic/main amd64 libmagic-mgc amd64 1:5.44-3 [293 kB] Get:17 http://ftpmaster.internal/ubuntu mantic/main amd64 libmagic1 amd64 1:5.44-3 [85.6 kB] Get:18 http://ftpmaster.internal/ubuntu mantic/main amd64 file amd64 1:5.44-3 [21.8 kB] Get:19 http://ftpmaster.internal/ubuntu mantic/main amd64 gettext-base amd64 0.21-13 [38.1 kB] Get:20 http://ftpmaster.internal/ubuntu mantic/main amd64 libuchardet0 amd64 0.0.7-1build2 [76.9 kB] Get:21 http://ftpmaster.internal/ubuntu mantic/main amd64 groff-base amd64 1.23.0-2 [1023 kB] Get:22 http://ftpmaster.internal/ubuntu mantic/main amd64 libnghttp2-14 amd64 1.55.1-1 [72.8 kB] Get:23 http://ftpmaster.internal/ubuntu mantic/main amd64 libpipeline1 amd64 1.5.7-1 [23.3 kB] Get:24 http://ftpmaster.internal/ubuntu mantic/main amd64 libpsl5 amd64 0.21.2-1 [59.0 kB] Get:25 http://ftpmaster.internal/ubuntu mantic/main amd64 libuv1 amd64 1.44.2-1 [91.0 kB] Get:26 http://ftpmaster.internal/ubuntu mantic/main amd64 man-db amd64 2.11.2-3 [1220 kB] Get:27 http://ftpmaster.internal/ubuntu mantic/main amd64 m4 amd64 1.4.19-3 [243 kB] Get:28 http://ftpmaster.internal/ubuntu mantic/main amd64 autoconf all 2.71-3 [339 kB] Get:29 http://ftpmaster.internal/ubuntu mantic/main amd64 autotools-dev all 20220109.1 [44.9 kB] Get:30 http://ftpmaster.internal/ubuntu mantic/main amd64 automake all 1:1.16.5-1.3 [558 kB] Get:31 http://ftpmaster.internal/ubuntu mantic/main amd64 autopoint all 0.21-13 [422 kB] Get:32 http://ftpmaster.internal/ubuntu mantic/main amd64 libarchive13 amd64 3.6.2-1ubuntu1 [380 kB] Get:33 http://ftpmaster.internal/ubuntu mantic/main amd64 libbrotli1 amd64 1.0.9-2build8 [309 kB] Get:34 http://ftpmaster.internal/ubuntu mantic/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-3 [20.2 kB] Get:35 http://ftpmaster.internal/ubuntu mantic/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-3 [53.4 kB] Get:36 http://ftpmaster.internal/ubuntu mantic/main amd64 libldap2 amd64 2.6.6+dfsg-1~exp1ubuntu1 [193 kB] Get:37 http://ftpmaster.internal/ubuntu mantic/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2build4 [58.2 kB] Get:38 http://ftpmaster.internal/ubuntu mantic/main amd64 libssh-4 amd64 0.10.5-3ubuntu1 [187 kB] Get:39 http://ftpmaster.internal/ubuntu mantic/main amd64 libcurl4 amd64 8.2.1-1ubuntu2 [319 kB] Get:40 http://ftpmaster.internal/ubuntu mantic/main amd64 libjsoncpp25 amd64 1.9.5-6 [82.3 kB] Get:41 http://ftpmaster.internal/ubuntu mantic/main amd64 librhash0 amd64 1.4.3-3 [128 kB] Get:42 http://ftpmaster.internal/ubuntu mantic/main amd64 cmake-data all 3.27.4-1 [2128 kB] Get:43 http://ftpmaster.internal/ubuntu mantic/main amd64 cmake amd64 3.27.4-1 [11.1 MB] Get:44 http://ftpmaster.internal/ubuntu mantic/main amd64 libdebhelper-perl all 13.11.6ubuntu1 [85.4 kB] Get:45 http://ftpmaster.internal/ubuntu mantic/main amd64 libtool all 2.4.7-7 [166 kB] Get:46 http://ftpmaster.internal/ubuntu mantic/main amd64 dh-autoreconf all 20 [16.1 kB] Get:47 http://ftpmaster.internal/ubuntu mantic/main amd64 libarchive-zip-perl all 1.68-1 [90.2 kB] Get:48 http://ftpmaster.internal/ubuntu mantic/main amd64 libsub-override-perl all 0.09-4 [8706 B] Get:49 http://ftpmaster.internal/ubuntu mantic/main amd64 libfile-stripnondeterminism-perl all 1.13.1-1 [18.1 kB] Get:50 http://ftpmaster.internal/ubuntu mantic/main amd64 dh-strip-nondeterminism all 1.13.1-1 [5362 B] Get:51 http://ftpmaster.internal/ubuntu mantic/main amd64 libdw1 amd64 0.189-4 [257 kB] Get:52 http://ftpmaster.internal/ubuntu mantic/main amd64 debugedit amd64 1:5.0-5 [46.1 kB] Get:53 http://ftpmaster.internal/ubuntu mantic/main amd64 dwz amd64 0.15-1 [112 kB] Get:54 http://ftpmaster.internal/ubuntu mantic/main amd64 gettext amd64 0.21-13 [866 kB] Get:55 http://ftpmaster.internal/ubuntu mantic/main amd64 intltool-debian all 0.35.0+20060710.6 [23.2 kB] Get:56 http://ftpmaster.internal/ubuntu mantic/main amd64 po-debconf all 1.0.21+nmu1 [233 kB] Get:57 http://ftpmaster.internal/ubuntu mantic/main amd64 debhelper all 13.11.6ubuntu1 [935 kB] Get:58 http://ftpmaster.internal/ubuntu mantic/universe amd64 googletest all 1.13.0-5 [518 kB] Get:59 http://ftpmaster.internal/ubuntu mantic/universe amd64 hdf5-helpers amd64 1.10.8+repack1-1ubuntu1 [13.9 kB] Get:60 http://ftpmaster.internal/ubuntu mantic/universe amd64 libaec0 amd64 1.0.6-1 [20.1 kB] Get:61 http://ftpmaster.internal/ubuntu mantic/universe amd64 libsz2 amd64 1.0.6-1 [5354 B] Get:62 http://ftpmaster.internal/ubuntu mantic/universe amd64 libhdf5-103-1 amd64 1.10.8+repack1-1ubuntu1 [1301 kB] Get:63 http://ftpmaster.internal/ubuntu mantic/universe amd64 libhdf5-cpp-103-1 amd64 1.10.8+repack1-1ubuntu1 [122 kB] Get:64 http://ftpmaster.internal/ubuntu mantic/main amd64 libcurl3-gnutls amd64 8.2.1-1ubuntu2 [312 kB] Get:65 http://ftpmaster.internal/ubuntu mantic/main amd64 libdeflate0 amd64 1.18-1 [43.1 kB] Get:66 http://ftpmaster.internal/ubuntu mantic/universe amd64 libhtscodecs2 amd64 1.5.1-1 [96.7 kB] Get:67 http://ftpmaster.internal/ubuntu mantic/universe amd64 libhts3 amd64 1.17+ds-1 [429 kB] Get:68 http://ftpmaster.internal/ubuntu mantic/universe amd64 libpbcopper2.2.0 amd64 2.2.0+dfsg-1 [572 kB] Get:69 http://ftpmaster.internal/ubuntu mantic/universe amd64 libpbbam2.3.0 amd64 2.3.0+dfsg-1 [669 kB] Get:70 http://ftpmaster.internal/ubuntu mantic-proposed/universe amd64 libblasr5.3.5 amd64 5.3.5+dfsg-6 [1235 kB] Get:71 http://ftpmaster.internal/ubuntu mantic/universe amd64 libpbcopper-dev amd64 2.2.0+dfsg-1 [1166 kB] Get:72 http://ftpmaster.internal/ubuntu mantic-proposed/universe amd64 libpbdata-dev amd64 5.3.5+dfsg-6 [41.0 kB] Get:73 http://ftpmaster.internal/ubuntu mantic-proposed/main amd64 libgfortran5 amd64 13.2.0-3ubuntu1 [891 kB] Get:74 http://ftpmaster.internal/ubuntu mantic/universe amd64 libhdf5-fortran-102 amd64 1.10.8+repack1-1ubuntu1 [85.4 kB] Get:75 http://ftpmaster.internal/ubuntu mantic/universe amd64 libhdf5-hl-100 amd64 1.10.8+repack1-1ubuntu1 [56.0 kB] Get:76 http://ftpmaster.internal/ubuntu mantic/universe amd64 libhdf5-hl-fortran-100 amd64 1.10.8+repack1-1ubuntu1 [32.0 kB] Get:77 http://ftpmaster.internal/ubuntu mantic/universe amd64 libhdf5-hl-cpp-100 amd64 1.10.8+repack1-1ubuntu1 [10.8 kB] Get:78 http://ftpmaster.internal/ubuntu mantic/main amd64 zlib1g-dev amd64 1:1.2.13.dfsg-1ubuntu5 [895 kB] Get:79 http://ftpmaster.internal/ubuntu mantic/main amd64 libjpeg-turbo8 amd64 2.1.5-2ubuntu1 [147 kB] Get:80 http://ftpmaster.internal/ubuntu mantic/main amd64 libjpeg-turbo8-dev amd64 2.1.5-2ubuntu1 [294 kB] Get:81 http://ftpmaster.internal/ubuntu mantic/main amd64 libjpeg8 amd64 8c-2ubuntu11 [2148 B] Get:82 http://ftpmaster.internal/ubuntu mantic/main amd64 libjpeg8-dev amd64 8c-2ubuntu11 [1484 B] Get:83 http://ftpmaster.internal/ubuntu mantic/main amd64 libjpeg-dev amd64 8c-2ubuntu11 [1482 B] Get:84 http://ftpmaster.internal/ubuntu mantic/universe amd64 libaec-dev amd64 1.0.6-1 [17.9 kB] Get:85 http://ftpmaster.internal/ubuntu mantic/main amd64 libcurl4-gnutls-dev amd64 8.2.1-1ubuntu2 [420 kB] Get:86 http://ftpmaster.internal/ubuntu mantic/main amd64 libssl-dev amd64 3.0.10-1ubuntu2 [2403 kB] Get:87 http://ftpmaster.internal/ubuntu mantic/universe amd64 libhdf5-dev amd64 1.10.8+repack1-1ubuntu1 [2801 kB] Get:88 http://ftpmaster.internal/ubuntu mantic/main amd64 libdeflate-dev amd64 1.18-1 [49.8 kB] Get:89 http://ftpmaster.internal/ubuntu mantic/main amd64 liblzma-dev amd64 5.4.1-0.2 [177 kB] Get:90 http://ftpmaster.internal/ubuntu mantic/universe amd64 libhts-dev amd64 1.17+ds-1 [5756 kB] Get:91 http://ftpmaster.internal/ubuntu mantic/universe amd64 libpbbam-dev amd64 2.3.0+dfsg-1 [76.3 kB] Get:92 http://ftpmaster.internal/ubuntu mantic-proposed/universe amd64 libblasr-dev amd64 5.3.5+dfsg-6 [2432 kB] Get:93 http://ftpmaster.internal/ubuntu mantic/main amd64 libboost1.74-dev amd64 1.74.0+ds1-22ubuntu1 [9586 kB] Get:94 http://ftpmaster.internal/ubuntu mantic/main amd64 libboost-dev amd64 1.74.0.3ubuntu7 [3490 B] Get:95 http://ftpmaster.internal/ubuntu mantic/universe amd64 libgtest-dev amd64 1.13.0-5 [260 kB] Get:96 http://ftpmaster.internal/ubuntu mantic-proposed/universe amd64 libpbihdf-dev amd64 5.3.5+dfsg-6 [47.6 kB] Get:97 http://ftpmaster.internal/ubuntu mantic-proposed/universe amd64 libpbseq-dev amd64 5.3.5+dfsg-6 [3088 B] Get:98 http://ftpmaster.internal/ubuntu mantic/main amd64 libpkgconf3 amd64 1.8.1-2 [31.1 kB] Get:99 http://ftpmaster.internal/ubuntu mantic/universe amd64 ninja-build amd64 1.11.1-1 [127 kB] Get:100 http://ftpmaster.internal/ubuntu mantic/main amd64 python3-lib2to3 all 3.11.5-1 [79.0 kB] Get:101 http://ftpmaster.internal/ubuntu mantic/main amd64 python3-distutils all 3.11.5-1 [131 kB] Get:102 http://ftpmaster.internal/ubuntu mantic/main amd64 python3-setuptools all 68.1.2-1 [396 kB] Get:103 http://ftpmaster.internal/ubuntu mantic/universe amd64 meson all 1.2.1-3 [591 kB] Get:104 http://ftpmaster.internal/ubuntu mantic/main amd64 pkgconf-bin amd64 1.8.1-2 [20.7 kB] Get:105 http://ftpmaster.internal/ubuntu mantic/main amd64 pkgconf amd64 1.8.1-2 [16.8 kB] Get:106 http://ftpmaster.internal/ubuntu mantic/main amd64 pkg-config amd64 1.8.1-2 [7170 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 74.4 MB in 1s (125 MB/s) Selecting previously unselected package libpython3.11-minimal:amd64. (Reading database ... 13700 files and directories currently installed.) Preparing to unpack .../libpython3.11-minimal_3.11.5-3_amd64.deb ... Unpacking libpython3.11-minimal:amd64 (3.11.5-3) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../libexpat1_2.5.0-2_amd64.deb ... Unpacking libexpat1:amd64 (2.5.0-2) ... Selecting previously unselected package python3.11-minimal. Preparing to unpack .../python3.11-minimal_3.11.5-3_amd64.deb ... Unpacking python3.11-minimal (3.11.5-3) ... Setting up libpython3.11-minimal:amd64 (3.11.5-3) ... Setting up libexpat1:amd64 (2.5.0-2) ... Setting up python3.11-minimal (3.11.5-3) ... Selecting previously unselected package python3-minimal. (Reading database ... 14014 files and directories currently installed.) Preparing to unpack .../python3-minimal_3.11.4-5_amd64.deb ... Unpacking python3-minimal (3.11.4-5) ... Selecting previously unselected package media-types. Preparing to unpack .../media-types_10.1.0_all.deb ... Unpacking media-types (10.1.0) ... Selecting previously unselected package libpython3.11-stdlib:amd64. Preparing to unpack .../libpython3.11-stdlib_3.11.5-3_amd64.deb ... Unpacking libpython3.11-stdlib:amd64 (3.11.5-3) ... Selecting previously unselected package python3.11. Preparing to unpack .../python3.11_3.11.5-3_amd64.deb ... Unpacking python3.11 (3.11.5-3) ... Selecting previously unselected package libpython3-stdlib:amd64. Preparing to unpack .../libpython3-stdlib_3.11.4-5_amd64.deb ... Unpacking libpython3-stdlib:amd64 (3.11.4-5) ... Setting up python3-minimal (3.11.4-5) ... Selecting previously unselected package python3. (Reading database ... 14422 files and directories currently installed.) Preparing to unpack .../00-python3_3.11.4-5_amd64.deb ... Unpacking python3 (3.11.4-5) ... Selecting previously unselected package libelf1:amd64. Preparing to unpack .../01-libelf1_0.189-4_amd64.deb ... Unpacking libelf1:amd64 (0.189-4) ... Selecting previously unselected package libicu72:amd64. Preparing to unpack .../02-libicu72_72.1-3ubuntu2_amd64.deb ... Unpacking libicu72:amd64 (72.1-3ubuntu2) ... Selecting previously unselected package libxml2:amd64. Preparing to unpack .../03-libxml2_2.9.14+dfsg-1.3_amd64.deb ... Unpacking libxml2:amd64 (2.9.14+dfsg-1.3) ... Selecting previously unselected package python3-pkg-resources. Preparing to unpack .../04-python3-pkg-resources_68.1.2-1_all.deb ... Unpacking python3-pkg-resources (68.1.2-1) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../05-bsdextrautils_2.39.1-4ubuntu1_amd64.deb ... Unpacking bsdextrautils (2.39.1-4ubuntu1) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../06-libmagic-mgc_1%3a5.44-3_amd64.deb ... Unpacking libmagic-mgc (1:5.44-3) ... Selecting previously unselected package libmagic1:amd64. Preparing to unpack .../07-libmagic1_1%3a5.44-3_amd64.deb ... Unpacking libmagic1:amd64 (1:5.44-3) ... Selecting previously unselected package file. Preparing to unpack .../08-file_1%3a5.44-3_amd64.deb ... Unpacking file (1:5.44-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../09-gettext-base_0.21-13_amd64.deb ... Unpacking gettext-base (0.21-13) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../10-libuchardet0_0.0.7-1build2_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.7-1build2) ... Selecting previously unselected package groff-base. Preparing to unpack .../11-groff-base_1.23.0-2_amd64.deb ... Unpacking groff-base (1.23.0-2) ... Selecting previously unselected package libnghttp2-14:amd64. Preparing to unpack .../12-libnghttp2-14_1.55.1-1_amd64.deb ... Unpacking libnghttp2-14:amd64 (1.55.1-1) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../13-libpipeline1_1.5.7-1_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.7-1) ... Selecting previously unselected package libpsl5:amd64. Preparing to unpack .../14-libpsl5_0.21.2-1_amd64.deb ... Unpacking libpsl5:amd64 (0.21.2-1) ... Selecting previously unselected package libuv1:amd64. Preparing to unpack .../15-libuv1_1.44.2-1_amd64.deb ... Unpacking libuv1:amd64 (1.44.2-1) ... Selecting previously unselected package man-db. Preparing to unpack .../16-man-db_2.11.2-3_amd64.deb ... Unpacking man-db (2.11.2-3) ... Selecting previously unselected package m4. Preparing to unpack .../17-m4_1.4.19-3_amd64.deb ... Unpacking m4 (1.4.19-3) ... Selecting previously unselected package autoconf. Preparing to unpack .../18-autoconf_2.71-3_all.deb ... Unpacking autoconf (2.71-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../19-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../20-automake_1%3a1.16.5-1.3_all.deb ... Unpacking automake (1:1.16.5-1.3) ... Selecting previously unselected package autopoint. Preparing to unpack .../21-autopoint_0.21-13_all.deb ... Unpacking autopoint (0.21-13) ... Selecting previously unselected package libarchive13:amd64. Preparing to unpack .../22-libarchive13_3.6.2-1ubuntu1_amd64.deb ... Unpacking libarchive13:amd64 (3.6.2-1ubuntu1) ... Selecting previously unselected package libbrotli1:amd64. Preparing to unpack .../23-libbrotli1_1.0.9-2build8_amd64.deb ... Unpacking libbrotli1:amd64 (1.0.9-2build8) ... Selecting previously unselected package libsasl2-modules-db:amd64. Preparing to unpack .../24-libsasl2-modules-db_2.1.28+dfsg1-3_amd64.deb ... Unpacking libsasl2-modules-db:amd64 (2.1.28+dfsg1-3) ... Selecting previously unselected package libsasl2-2:amd64. Preparing to unpack .../25-libsasl2-2_2.1.28+dfsg1-3_amd64.deb ... Unpacking libsasl2-2:amd64 (2.1.28+dfsg1-3) ... Selecting previously unselected package libldap2:amd64. Preparing to unpack .../26-libldap2_2.6.6+dfsg-1~exp1ubuntu1_amd64.deb ... Unpacking libldap2:amd64 (2.6.6+dfsg-1~exp1ubuntu1) ... Selecting previously unselected package librtmp1:amd64. Preparing to unpack .../27-librtmp1_2.4+20151223.gitfa8646d.1-2build4_amd64.deb ... Unpacking librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2build4) ... Selecting previously unselected package libssh-4:amd64. Preparing to unpack .../28-libssh-4_0.10.5-3ubuntu1_amd64.deb ... Unpacking libssh-4:amd64 (0.10.5-3ubuntu1) ... Selecting previously unselected package libcurl4:amd64. Preparing to unpack .../29-libcurl4_8.2.1-1ubuntu2_amd64.deb ... Unpacking libcurl4:amd64 (8.2.1-1ubuntu2) ... Selecting previously unselected package libjsoncpp25:amd64. Preparing to unpack .../30-libjsoncpp25_1.9.5-6_amd64.deb ... Unpacking libjsoncpp25:amd64 (1.9.5-6) ... Selecting previously unselected package librhash0:amd64. Preparing to unpack .../31-librhash0_1.4.3-3_amd64.deb ... Unpacking librhash0:amd64 (1.4.3-3) ... Selecting previously unselected package cmake-data. Preparing to unpack .../32-cmake-data_3.27.4-1_all.deb ... Unpacking cmake-data (3.27.4-1) ... Selecting previously unselected package cmake. Preparing to unpack .../33-cmake_3.27.4-1_amd64.deb ... Unpacking cmake (3.27.4-1) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../34-libdebhelper-perl_13.11.6ubuntu1_all.deb ... Unpacking libdebhelper-perl (13.11.6ubuntu1) ... Selecting previously unselected package libtool. Preparing to unpack .../35-libtool_2.4.7-7_all.deb ... Unpacking libtool (2.4.7-7) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../36-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../37-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libsub-override-perl. Preparing to unpack .../38-libsub-override-perl_0.09-4_all.deb ... Unpacking libsub-override-perl (0.09-4) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../39-libfile-stripnondeterminism-perl_1.13.1-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.13.1-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../40-dh-strip-nondeterminism_1.13.1-1_all.deb ... Unpacking dh-strip-nondeterminism (1.13.1-1) ... Selecting previously unselected package libdw1:amd64. Preparing to unpack .../41-libdw1_0.189-4_amd64.deb ... Unpacking libdw1:amd64 (0.189-4) ... Selecting previously unselected package debugedit. Preparing to unpack .../42-debugedit_1%3a5.0-5_amd64.deb ... Unpacking debugedit (1:5.0-5) ... Selecting previously unselected package dwz. Preparing to unpack .../43-dwz_0.15-1_amd64.deb ... Unpacking dwz (0.15-1) ... Selecting previously unselected package gettext. Preparing to unpack .../44-gettext_0.21-13_amd64.deb ... Unpacking gettext (0.21-13) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../45-intltool-debian_0.35.0+20060710.6_all.deb ... Unpacking intltool-debian (0.35.0+20060710.6) ... Selecting previously unselected package po-debconf. Preparing to unpack .../46-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../47-debhelper_13.11.6ubuntu1_all.deb ... Unpacking debhelper (13.11.6ubuntu1) ... Selecting previously unselected package googletest. Preparing to unpack .../48-googletest_1.13.0-5_all.deb ... Unpacking googletest (1.13.0-5) ... Selecting previously unselected package hdf5-helpers. Preparing to unpack .../49-hdf5-helpers_1.10.8+repack1-1ubuntu1_amd64.deb ... Unpacking hdf5-helpers (1.10.8+repack1-1ubuntu1) ... Selecting previously unselected package libaec0:amd64. Preparing to unpack .../50-libaec0_1.0.6-1_amd64.deb ... Unpacking libaec0:amd64 (1.0.6-1) ... Selecting previously unselected package libsz2:amd64. Preparing to unpack .../51-libsz2_1.0.6-1_amd64.deb ... Unpacking libsz2:amd64 (1.0.6-1) ... Selecting previously unselected package libhdf5-103-1:amd64. Preparing to unpack .../52-libhdf5-103-1_1.10.8+repack1-1ubuntu1_amd64.deb ... Unpacking libhdf5-103-1:amd64 (1.10.8+repack1-1ubuntu1) ... Selecting previously unselected package libhdf5-cpp-103-1:amd64. Preparing to unpack .../53-libhdf5-cpp-103-1_1.10.8+repack1-1ubuntu1_amd64.deb ... Unpacking libhdf5-cpp-103-1:amd64 (1.10.8+repack1-1ubuntu1) ... Selecting previously unselected package libcurl3-gnutls:amd64. Preparing to unpack .../54-libcurl3-gnutls_8.2.1-1ubuntu2_amd64.deb ... Unpacking libcurl3-gnutls:amd64 (8.2.1-1ubuntu2) ... Selecting previously unselected package libdeflate0:amd64. Preparing to unpack .../55-libdeflate0_1.18-1_amd64.deb ... Unpacking libdeflate0:amd64 (1.18-1) ... Selecting previously unselected package libhtscodecs2:amd64. Preparing to unpack .../56-libhtscodecs2_1.5.1-1_amd64.deb ... Unpacking libhtscodecs2:amd64 (1.5.1-1) ... Selecting previously unselected package libhts3:amd64. Preparing to unpack .../57-libhts3_1.17+ds-1_amd64.deb ... Unpacking libhts3:amd64 (1.17+ds-1) ... Selecting previously unselected package libpbcopper2.2.0:amd64. Preparing to unpack .../58-libpbcopper2.2.0_2.2.0+dfsg-1_amd64.deb ... Unpacking libpbcopper2.2.0:amd64 (2.2.0+dfsg-1) ... Selecting previously unselected package libpbbam2.3.0:amd64. Preparing to unpack .../59-libpbbam2.3.0_2.3.0+dfsg-1_amd64.deb ... Unpacking libpbbam2.3.0:amd64 (2.3.0+dfsg-1) ... Selecting previously unselected package libblasr5.3.5:amd64. Preparing to unpack .../60-libblasr5.3.5_5.3.5+dfsg-6_amd64.deb ... Unpacking libblasr5.3.5:amd64 (5.3.5+dfsg-6) ... Selecting previously unselected package libpbcopper-dev:amd64. Preparing to unpack .../61-libpbcopper-dev_2.2.0+dfsg-1_amd64.deb ... Unpacking libpbcopper-dev:amd64 (2.2.0+dfsg-1) ... Selecting previously unselected package libpbdata-dev:amd64. Preparing to unpack .../62-libpbdata-dev_5.3.5+dfsg-6_amd64.deb ... Unpacking libpbdata-dev:amd64 (5.3.5+dfsg-6) ... Selecting previously unselected package libgfortran5:amd64. Preparing to unpack .../63-libgfortran5_13.2.0-3ubuntu1_amd64.deb ... Unpacking libgfortran5:amd64 (13.2.0-3ubuntu1) ... Selecting previously unselected package libhdf5-fortran-102:amd64. Preparing to unpack .../64-libhdf5-fortran-102_1.10.8+repack1-1ubuntu1_amd64.deb ... Unpacking libhdf5-fortran-102:amd64 (1.10.8+repack1-1ubuntu1) ... Selecting previously unselected package libhdf5-hl-100:amd64. Preparing to unpack .../65-libhdf5-hl-100_1.10.8+repack1-1ubuntu1_amd64.deb ... Unpacking libhdf5-hl-100:amd64 (1.10.8+repack1-1ubuntu1) ... Selecting previously unselected package libhdf5-hl-fortran-100:amd64. Preparing to unpack .../66-libhdf5-hl-fortran-100_1.10.8+repack1-1ubuntu1_amd64.deb ... Unpacking libhdf5-hl-fortran-100:amd64 (1.10.8+repack1-1ubuntu1) ... Selecting previously unselected package libhdf5-hl-cpp-100:amd64. Preparing to unpack .../67-libhdf5-hl-cpp-100_1.10.8+repack1-1ubuntu1_amd64.deb ... Unpacking libhdf5-hl-cpp-100:amd64 (1.10.8+repack1-1ubuntu1) ... Selecting previously unselected package zlib1g-dev:amd64. Preparing to unpack .../68-zlib1g-dev_1%3a1.2.13.dfsg-1ubuntu5_amd64.deb ... Unpacking zlib1g-dev:amd64 (1:1.2.13.dfsg-1ubuntu5) ... Selecting previously unselected package libjpeg-turbo8:amd64. Preparing to unpack .../69-libjpeg-turbo8_2.1.5-2ubuntu1_amd64.deb ... Unpacking libjpeg-turbo8:amd64 (2.1.5-2ubuntu1) ... Selecting previously unselected package libjpeg-turbo8-dev:amd64. Preparing to unpack .../70-libjpeg-turbo8-dev_2.1.5-2ubuntu1_amd64.deb ... Unpacking libjpeg-turbo8-dev:amd64 (2.1.5-2ubuntu1) ... Selecting previously unselected package libjpeg8:amd64. Preparing to unpack .../71-libjpeg8_8c-2ubuntu11_amd64.deb ... Unpacking libjpeg8:amd64 (8c-2ubuntu11) ... Selecting previously unselected package libjpeg8-dev:amd64. Preparing to unpack .../72-libjpeg8-dev_8c-2ubuntu11_amd64.deb ... Unpacking libjpeg8-dev:amd64 (8c-2ubuntu11) ... Selecting previously unselected package libjpeg-dev:amd64. Preparing to unpack .../73-libjpeg-dev_8c-2ubuntu11_amd64.deb ... Unpacking libjpeg-dev:amd64 (8c-2ubuntu11) ... Selecting previously unselected package libaec-dev:amd64. Preparing to unpack .../74-libaec-dev_1.0.6-1_amd64.deb ... Unpacking libaec-dev:amd64 (1.0.6-1) ... Selecting previously unselected package libcurl4-gnutls-dev:amd64. Preparing to unpack .../75-libcurl4-gnutls-dev_8.2.1-1ubuntu2_amd64.deb ... Unpacking libcurl4-gnutls-dev:amd64 (8.2.1-1ubuntu2) ... Selecting previously unselected package libssl-dev:amd64. Preparing to unpack .../76-libssl-dev_3.0.10-1ubuntu2_amd64.deb ... Unpacking libssl-dev:amd64 (3.0.10-1ubuntu2) ... Selecting previously unselected package libhdf5-dev. Preparing to unpack .../77-libhdf5-dev_1.10.8+repack1-1ubuntu1_amd64.deb ... Unpacking libhdf5-dev (1.10.8+repack1-1ubuntu1) ... Selecting previously unselected package libdeflate-dev:amd64. Preparing to unpack .../78-libdeflate-dev_1.18-1_amd64.deb ... Unpacking libdeflate-dev:amd64 (1.18-1) ... Selecting previously unselected package liblzma-dev:amd64. Preparing to unpack .../79-liblzma-dev_5.4.1-0.2_amd64.deb ... Unpacking liblzma-dev:amd64 (5.4.1-0.2) ... Selecting previously unselected package libhts-dev:amd64. Preparing to unpack .../80-libhts-dev_1.17+ds-1_amd64.deb ... Unpacking libhts-dev:amd64 (1.17+ds-1) ... Selecting previously unselected package libpbbam-dev:amd64. Preparing to unpack .../81-libpbbam-dev_2.3.0+dfsg-1_amd64.deb ... Unpacking libpbbam-dev:amd64 (2.3.0+dfsg-1) ... Selecting previously unselected package libblasr-dev:amd64. Preparing to unpack .../82-libblasr-dev_5.3.5+dfsg-6_amd64.deb ... Unpacking libblasr-dev:amd64 (5.3.5+dfsg-6) ... Selecting previously unselected package libboost1.74-dev:amd64. Preparing to unpack .../83-libboost1.74-dev_1.74.0+ds1-22ubuntu1_amd64.deb ... Unpacking libboost1.74-dev:amd64 (1.74.0+ds1-22ubuntu1) ... Selecting previously unselected package libboost-dev:amd64. Preparing to unpack .../84-libboost-dev_1.74.0.3ubuntu7_amd64.deb ... Unpacking libboost-dev:amd64 (1.74.0.3ubuntu7) ... Selecting previously unselected package libgtest-dev:amd64. Preparing to unpack .../85-libgtest-dev_1.13.0-5_amd64.deb ... Unpacking libgtest-dev:amd64 (1.13.0-5) ... Selecting previously unselected package libpbihdf-dev:amd64. Preparing to unpack .../86-libpbihdf-dev_5.3.5+dfsg-6_amd64.deb ... Unpacking libpbihdf-dev:amd64 (5.3.5+dfsg-6) ... Selecting previously unselected package libpbseq-dev:amd64. Preparing to unpack .../87-libpbseq-dev_5.3.5+dfsg-6_amd64.deb ... Unpacking libpbseq-dev:amd64 (5.3.5+dfsg-6) ... Selecting previously unselected package libpkgconf3:amd64. Preparing to unpack .../88-libpkgconf3_1.8.1-2_amd64.deb ... Unpacking libpkgconf3:amd64 (1.8.1-2) ... Selecting previously unselected package ninja-build. Preparing to unpack .../89-ninja-build_1.11.1-1_amd64.deb ... Unpacking ninja-build (1.11.1-1) ... Selecting previously unselected package python3-lib2to3. Preparing to unpack .../90-python3-lib2to3_3.11.5-1_all.deb ... Unpacking python3-lib2to3 (3.11.5-1) ... Selecting previously unselected package python3-distutils. Preparing to unpack .../91-python3-distutils_3.11.5-1_all.deb ... Unpacking python3-distutils (3.11.5-1) ... Selecting previously unselected package python3-setuptools. Preparing to unpack .../92-python3-setuptools_68.1.2-1_all.deb ... Unpacking python3-setuptools (68.1.2-1) ... Selecting previously unselected package meson. Preparing to unpack .../93-meson_1.2.1-3_all.deb ... Unpacking meson (1.2.1-3) ... Selecting previously unselected package pkgconf-bin. Preparing to unpack .../94-pkgconf-bin_1.8.1-2_amd64.deb ... Unpacking pkgconf-bin (1.8.1-2) ... Selecting previously unselected package pkgconf:amd64. Preparing to unpack .../95-pkgconf_1.8.1-2_amd64.deb ... Unpacking pkgconf:amd64 (1.8.1-2) ... Selecting previously unselected package pkg-config:amd64. Preparing to unpack .../96-pkg-config_1.8.1-2_amd64.deb ... Unpacking pkg-config:amd64 (1.8.1-2) ... Selecting previously unselected package sbuild-build-depends-main-dummy. Preparing to unpack .../97-sbuild-build-depends-main-dummy_0.invalid.0_amd64.deb ... Unpacking sbuild-build-depends-main-dummy (0.invalid.0) ... Setting up libhtscodecs2:amd64 (1.5.1-1) ... Setting up media-types (10.1.0) ... Setting up libpipeline1:amd64 (1.5.7-1) ... Setting up libpsl5:amd64 (0.21.2-1) ... Setting up libboost1.74-dev:amd64 (1.74.0+ds1-22ubuntu1) ... Setting up libicu72:amd64 (72.1-3ubuntu2) ... Setting up bsdextrautils (2.39.1-4ubuntu1) ... Setting up hdf5-helpers (1.10.8+repack1-1ubuntu1) ... Setting up libmagic-mgc (1:5.44-3) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libpython3.11-stdlib:amd64 (3.11.5-3) ... Setting up libdebhelper-perl (13.11.6ubuntu1) ... Setting up libbrotli1:amd64 (1.0.9-2build8) ... Setting up libnghttp2-14:amd64 (1.55.1-1) ... Setting up libmagic1:amd64 (1:5.44-3) ... Setting up libdeflate0:amd64 (1.18-1) ... Setting up gettext-base (0.21-13) ... Setting up m4 (1.4.19-3) ... Setting up file (1:5.44-3) ... Setting up googletest (1.13.0-5) ... Setting up libpbcopper2.2.0:amd64 (2.2.0+dfsg-1) ... Setting up libaec0:amd64 (1.0.6-1) ... Setting up ninja-build (1.11.1-1) ... Setting up libsasl2-modules-db:amd64 (2.1.28+dfsg1-3) ... Setting up autotools-dev (20220109.1) ... Setting up libpkgconf3:amd64 (1.8.1-2) ... Setting up libuv1:amd64 (1.44.2-1) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2build4) ... Setting up libssl-dev:amd64 (3.0.10-1ubuntu2) ... Setting up autopoint (0.21-13) ... Setting up libjsoncpp25:amd64 (1.9.5-6) ... Setting up pkgconf-bin (1.8.1-2) ... Setting up libpbcopper-dev:amd64 (2.2.0+dfsg-1) ... Setting up libjpeg-turbo8:amd64 (2.1.5-2ubuntu1) ... Setting up libsasl2-2:amd64 (2.1.28+dfsg1-3) ... Setting up libssh-4:amd64 (0.10.5-3ubuntu1) ... Setting up libgfortran5:amd64 (13.2.0-3ubuntu1) ... Setting up autoconf (2.71-3) ... Setting up liblzma-dev:amd64 (5.4.1-0.2) ... Setting up zlib1g-dev:amd64 (1:1.2.13.dfsg-1ubuntu5) ... Setting up librhash0:amd64 (1.4.3-3) ... Setting up libuchardet0:amd64 (0.0.7-1build2) ... Setting up libsub-override-perl (0.09-4) ... Setting up cmake-data (3.27.4-1) ... Setting up libboost-dev:amd64 (1.74.0.3ubuntu7) ... Setting up libdeflate-dev:amd64 (1.18-1) ... Setting up libelf1:amd64 (0.189-4) ... Setting up libxml2:amd64 (2.9.14+dfsg-1.3) ... Setting up libldap2:amd64 (2.6.6+dfsg-1~exp1ubuntu1) ... Setting up libsz2:amd64 (1.0.6-1) ... Setting up libpython3-stdlib:amd64 (3.11.4-5) ... Setting up libjpeg8:amd64 (8c-2ubuntu11) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.13.1-1) ... Setting up python3.11 (3.11.5-3) ... Setting up libdw1:amd64 (0.189-4) ... Setting up libjpeg-turbo8-dev:amd64 (2.1.5-2ubuntu1) ... Setting up gettext (0.21-13) ... Setting up libgtest-dev:amd64 (1.13.0-5) ... Setting up libtool (2.4.7-7) ... Setting up libarchive13:amd64 (3.6.2-1ubuntu1) ... Setting up libaec-dev:amd64 (1.0.6-1) ... Setting up libpbdata-dev:amd64 (5.3.5+dfsg-6) ... Setting up libcurl3-gnutls:amd64 (8.2.1-1ubuntu2) ... Setting up python3 (3.11.4-5) ... Setting up libcurl4-gnutls-dev:amd64 (8.2.1-1ubuntu2) ... Setting up pkgconf:amd64 (1.8.1-2) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up pkg-config:amd64 (1.8.1-2) ... Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up dwz (0.15-1) ... Setting up groff-base (1.23.0-2) ... Setting up debugedit (1:5.0-5) ... Setting up libcurl4:amd64 (8.2.1-1ubuntu2) ... Setting up libjpeg8-dev:amd64 (8c-2ubuntu11) ... Setting up python3-lib2to3 (3.11.5-1) ... Setting up python3-pkg-resources (68.1.2-1) ... Setting up python3-distutils (3.11.5-1) ... Setting up libhts3:amd64 (1.17+ds-1) ... Setting up python3-setuptools (68.1.2-1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libjpeg-dev:amd64 (8c-2ubuntu11) ... Setting up libhts-dev:amd64 (1.17+ds-1) ... Setting up meson (1.2.1-3) ... Setting up man-db (2.11.2-3) ... Not building database; man-db/auto-update is not 'true'. Created symlink /etc/systemd/system/timers.target.wants/man-db.timer → /lib/systemd/system/man-db.timer. Setting up libpbbam2.3.0:amd64 (2.3.0+dfsg-1) ... Setting up libhdf5-103-1:amd64 (1.10.8+repack1-1ubuntu1) ... Setting up libhdf5-cpp-103-1:amd64 (1.10.8+repack1-1ubuntu1) ... Setting up cmake (3.27.4-1) ... Setting up libpbbam-dev:amd64 (2.3.0+dfsg-1) ... Setting up libhdf5-hl-100:amd64 (1.10.8+repack1-1ubuntu1) ... Setting up debhelper (13.11.6ubuntu1) ... Setting up libblasr5.3.5:amd64 (5.3.5+dfsg-6) ... Setting up libhdf5-hl-cpp-100:amd64 (1.10.8+repack1-1ubuntu1) ... Setting up libhdf5-fortran-102:amd64 (1.10.8+repack1-1ubuntu1) ... Setting up libhdf5-hl-fortran-100:amd64 (1.10.8+repack1-1ubuntu1) ... Setting up libhdf5-dev (1.10.8+repack1-1ubuntu1) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/pkgconfig/hdf5-serial.pc to provide /usr/lib/x86_64-linux-gnu/pkgconfig/hdf5.pc (hdf5.pc) in auto mode Setting up libpbihdf-dev:amd64 (5.3.5+dfsg-6) ... Setting up libblasr-dev:amd64 (5.3.5+dfsg-6) ... Setting up libpbseq-dev:amd64 (5.3.5+dfsg-6) ... Setting up sbuild-build-depends-main-dummy (0.invalid.0) ... Processing triggers for systemd (253.5-1ubuntu4) ... Processing triggers for libc-bin (2.38-1ubuntu4) ... +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (amd64 included in any) +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 5.4.0-156-generic #173-Ubuntu SMP Tue Jul 11 07:25:22 UTC 2023 amd64 (x86_64) Toolchain package versions: binutils_2.41-4ubuntu1 dpkg-dev_1.22.0ubuntu1 g++-12_12.3.0-8ubuntu1 g++-13_13.2.0-3ubuntu1 gcc-12_12.3.0-8ubuntu1 gcc-13_13.2.0-3ubuntu1 libc6-dev_2.38-1ubuntu4 libstdc++-12-dev_12.3.0-8ubuntu1 libstdc++-13-dev_13.2.0-3ubuntu1 libstdc++6_13.2.0-3ubuntu1 linux-libc-dev_6.5.0-2.2 Package versions: adduser_3.137ubuntu1 advancecomp_2.5-1 apt_2.7.3 autoconf_2.71-3 automake_1:1.16.5-1.3 autopoint_0.21-13 autotools-dev_20220109.1 base-files_13ubuntu1 base-passwd_3.6.1 bash_5.2.15-2ubuntu1 binutils_2.41-4ubuntu1 binutils-common_2.41-4ubuntu1 binutils-x86-64-linux-gnu_2.41-4ubuntu1 bsdextrautils_2.39.1-4ubuntu1 bsdutils_1:2.39.1-4ubuntu1 build-essential_12.10ubuntu1 bzip2_1.0.8-5build1 ca-certificates_20230311ubuntu1 cmake_3.27.4-1 cmake-data_3.27.4-1 coreutils_9.1-1ubuntu2 cpp_4:13.2.0-1ubuntu1 cpp-12_12.3.0-8ubuntu1 cpp-13_13.2.0-3ubuntu1 dash_0.5.12-6ubuntu1 debconf_1.5.82 debhelper_13.11.6ubuntu1 debianutils_5.8-1 debugedit_1:5.0-5 dh-autoreconf_20 dh-strip-nondeterminism_1.13.1-1 diffutils_1:3.8-4 dpkg_1.22.0ubuntu1 dpkg-dev_1.22.0ubuntu1 dwz_0.15-1 e2fsprogs_1.47.0-2ubuntu1 fakeroot_1.32.1-1 file_1:5.44-3 findutils_4.9.0-5 g++_4:13.2.0-1ubuntu1 g++-12_12.3.0-8ubuntu1 g++-13_13.2.0-3ubuntu1 gcc_4:13.2.0-1ubuntu1 gcc-12_12.3.0-8ubuntu1 gcc-12-base_12.3.0-8ubuntu1 gcc-13_13.2.0-3ubuntu1 gcc-13-base_13.2.0-3ubuntu1 gettext_0.21-13 gettext-base_0.21-13 googletest_1.13.0-5 gpg_2.2.40-1.1ubuntu1 gpg-agent_2.2.40-1.1ubuntu1 gpgconf_2.2.40-1.1ubuntu1 gpgv_2.2.40-1.1ubuntu1 grep_3.11-2 groff-base_1.23.0-2 gzip_1.12-1ubuntu1 hdf5-helpers_1.10.8+repack1-1ubuntu1 hostname_3.23+nmu1ubuntu1 init_1.65.2ubuntu1 init-system-helpers_1.65.2ubuntu1 intltool-debian_0.35.0+20060710.6 libacl1_2.3.1-3 libaec-dev_1.0.6-1 libaec0_1.0.6-1 libapparmor1_4.0.0~alpha2-0ubuntu2 libapt-pkg6.0_2.7.3 libarchive-zip-perl_1.68-1 libarchive13_3.6.2-1ubuntu1 libargon2-1_0~20190702+dfsg-3 libasan8_13.2.0-3ubuntu1 libassuan0_2.5.6-1 libatomic1_13.2.0-3ubuntu1 libattr1_1:2.5.1-4 libaudit-common_1:3.1.1-1 libaudit1_1:3.1.1-1 libbinutils_2.41-4ubuntu1 libblasr-dev_5.3.5+dfsg-6 libblasr5.3.5_5.3.5+dfsg-6 libblkid1_2.39.1-4ubuntu1 libboost-dev_1.74.0.3ubuntu7 libboost1.74-dev_1.74.0+ds1-22ubuntu1 libbrotli1_1.0.9-2build8 libbz2-1.0_1.0.8-5build1 libc-bin_2.38-1ubuntu4 libc-dev-bin_2.38-1ubuntu4 libc6_2.38-1ubuntu4 libc6-dev_2.38-1ubuntu4 libcap-ng0_0.8.3-1build2 libcap2_1:2.66-4ubuntu1 libcc1-0_13.2.0-3ubuntu1 libcom-err2_1.47.0-2ubuntu1 libcrypt-dev_1:4.4.36-2 libcrypt1_1:4.4.36-2 libcryptsetup12_2:2.6.1-4ubuntu2 libctf-nobfd0_2.41-4ubuntu1 libctf0_2.41-4ubuntu1 libcurl3-gnutls_8.2.1-1ubuntu2 libcurl4_8.2.1-1ubuntu2 libcurl4-gnutls-dev_8.2.1-1ubuntu2 libdb5.3_5.3.28+dfsg2-2 libdebconfclient0_0.270ubuntu1 libdebhelper-perl_13.11.6ubuntu1 libdeflate-dev_1.18-1 libdeflate0_1.18-1 libdevmapper1.02.1_2:1.02.185-2ubuntu1 libdpkg-perl_1.22.0ubuntu1 libdw1_0.189-4 libelf1_0.189-4 libexpat1_2.5.0-2 libext2fs2_1.47.0-2ubuntu1 libfakeroot_1.32.1-1 libfdisk1_2.39.1-4ubuntu1 libffi8_3.4.4-1 libfile-stripnondeterminism-perl_1.13.1-1 libgcc-12-dev_12.3.0-8ubuntu1 libgcc-13-dev_13.2.0-3ubuntu1 libgcc-s1_13.2.0-3ubuntu1 libgcrypt20_1.10.2-2ubuntu1 libgdbm-compat4_1.23-3 libgdbm6_1.23-3 libgfortran5_13.2.0-3ubuntu1 libgmp10_2:6.3.0+dfsg-2ubuntu4 libgnutls30_3.8.1-4ubuntu1 libgomp1_13.2.0-3ubuntu1 libgpg-error0_1.47-2 libgprofng0_2.41-4ubuntu1 libgssapi-krb5-2_1.20.1-3ubuntu1 libgtest-dev_1.13.0-5 libhdf5-103-1_1.10.8+repack1-1ubuntu1 libhdf5-cpp-103-1_1.10.8+repack1-1ubuntu1 libhdf5-dev_1.10.8+repack1-1ubuntu1 libhdf5-fortran-102_1.10.8+repack1-1ubuntu1 libhdf5-hl-100_1.10.8+repack1-1ubuntu1 libhdf5-hl-cpp-100_1.10.8+repack1-1ubuntu1 libhdf5-hl-fortran-100_1.10.8+repack1-1ubuntu1 libhogweed6_3.9.1-2 libhts-dev_1.17+ds-1 libhts3_1.17+ds-1 libhtscodecs2_1.5.1-1 libhwasan0_13.2.0-3ubuntu1 libicu72_72.1-3ubuntu2 libidn2-0_2.3.4-1 libip4tc2_1.8.9-2ubuntu2 libisl23_0.26-3 libitm1_13.2.0-3ubuntu1 libjansson4_2.14-2 libjpeg-dev_8c-2ubuntu11 libjpeg-turbo8_2.1.5-2ubuntu1 libjpeg-turbo8-dev_2.1.5-2ubuntu1 libjpeg8_8c-2ubuntu11 libjpeg8-dev_8c-2ubuntu11 libjson-c5_0.17-1 libjsoncpp25_1.9.5-6 libk5crypto3_1.20.1-3ubuntu1 libkeyutils1_1.6.3-2 libkmod2_30+20230519-1ubuntu3 libkrb5-3_1.20.1-3ubuntu1 libkrb5support0_1.20.1-3ubuntu1 libldap2_2.6.6+dfsg-1~exp1ubuntu1 liblockfile-bin_1.17-1build2 liblockfile1_1.17-1build2 liblsan0_13.2.0-3ubuntu1 liblz4-1_1.9.4-1 liblzma-dev_5.4.1-0.2 liblzma5_5.4.1-0.2 libmagic-mgc_1:5.44-3 libmagic1_1:5.44-3 libmd0_1.1.0-1 libmount1_2.39.1-4ubuntu1 libmpc3_1.3.1-1 libmpfr6_4.2.1-1 libncurses6_6.4+20230625-2 libncursesw6_6.4+20230625-2 libnettle8_3.9.1-2 libnghttp2-14_1.55.1-1 libnpth0_1.6-3build2 libnsl-dev_1.3.0-2build2 libnsl2_1.3.0-2build2 libp11-kit0_0.25.0-4ubuntu1 libpam-modules_1.5.2-6ubuntu1 libpam-modules-bin_1.5.2-6ubuntu1 libpam-runtime_1.5.2-6ubuntu1 libpam0g_1.5.2-6ubuntu1 libpbbam-dev_2.3.0+dfsg-1 libpbbam2.3.0_2.3.0+dfsg-1 libpbcopper-dev_2.2.0+dfsg-1 libpbcopper2.2.0_2.2.0+dfsg-1 libpbdata-dev_5.3.5+dfsg-6 libpbihdf-dev_5.3.5+dfsg-6 libpbseq-dev_5.3.5+dfsg-6 libpcre2-8-0_10.42-4 libperl5.36_5.36.0-7ubuntu1 libpipeline1_1.5.7-1 libpkgconf3_1.8.1-2 libpng16-16_1.6.40-1 libproc2-0_2:4.0.3-1ubuntu1 libprocps8_2:3.3.17-7ubuntu1 libpsl5_0.21.2-1 libpython3-stdlib_3.11.4-5 libpython3.11-minimal_3.11.5-3 libpython3.11-stdlib_3.11.5-3 libquadmath0_13.2.0-3ubuntu1 libreadline8_8.2-1.3 librhash0_1.4.3-3 librtmp1_2.4+20151223.gitfa8646d.1-2build4 libsasl2-2_2.1.28+dfsg1-3 libsasl2-modules-db_2.1.28+dfsg1-3 libseccomp2_2.5.4-1ubuntu3 libselinux1_3.5-1 libsemanage-common_3.5-1 libsemanage2_3.5-1 libsepol2_3.5-1 libsframe1_2.41-4ubuntu1 libsmartcols1_2.39.1-4ubuntu1 libsqlite3-0_3.42.0-1 libss2_1.47.0-2ubuntu1 libssh-4_0.10.5-3ubuntu1 libssl-dev_3.0.10-1ubuntu2 libssl3_3.0.10-1ubuntu2 libstdc++-12-dev_12.3.0-8ubuntu1 libstdc++-13-dev_13.2.0-3ubuntu1 libstdc++6_13.2.0-3ubuntu1 libsub-override-perl_0.09-4 libsystemd-shared_253.5-1ubuntu4 libsystemd0_253.5-1ubuntu4 libsz2_1.0.6-1 libtasn1-6_4.19.0-3 libtinfo6_6.4+20230625-2 libtirpc-common_1.3.3+ds-1 libtirpc-dev_1.3.3+ds-1 libtirpc3_1.3.3+ds-1 libtool_2.4.7-7 libtsan2_13.2.0-3ubuntu1 libubsan1_13.2.0-3ubuntu1 libuchardet0_0.0.7-1build2 libudev1_253.5-1ubuntu4 libunistring2_1.0-2 libuuid1_2.39.1-4ubuntu1 libuv1_1.44.2-1 libxml2_2.9.14+dfsg-1.3 libxxhash0_0.8.1-1 libzstd1_1.5.5+dfsg2-1ubuntu2 linux-libc-dev_6.5.0-2.2 lockfile-progs_0.1.19build1 login_1:4.13+dfsg1-1ubuntu1 logsave_1.47.0-2ubuntu1 lsb-base_11.6 lto-disabled-list_42 m4_1.4.19-3 make_4.3-4.1build1 man-db_2.11.2-3 mawk_1.3.4.20230730-1 media-types_10.1.0 meson_1.2.1-3 mount_2.39.1-4ubuntu1 ncurses-base_6.4+20230625-2 ncurses-bin_6.4+20230625-2 ninja-build_1.11.1-1 openssl_3.0.10-1ubuntu2 optipng_0.7.7-2build1 passwd_1:4.13+dfsg1-1ubuntu1 patch_2.7.6-7build2 perl_5.36.0-7ubuntu1 perl-base_5.36.0-7ubuntu1 perl-modules-5.36_5.36.0-7ubuntu1 pinentry-curses_1.2.1-1ubuntu1 pkg-config_1.8.1-2 pkgbinarymangler_153 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_2:4.0.3-1ubuntu1 python3_3.11.4-5 python3-distutils_3.11.5-1 python3-lib2to3_3.11.5-1 python3-minimal_3.11.4-5 python3-pkg-resources_68.1.2-1 python3-setuptools_68.1.2-1 python3.11_3.11.5-3 python3.11-minimal_3.11.5-3 readline-common_8.2-1.3 rpcsvc-proto_1.4.2-0ubuntu6 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.9-1 sensible-utils_0.0.20 systemd_253.5-1ubuntu4 systemd-dev_253.5-1ubuntu4 systemd-sysv_253.5-1ubuntu4 sysvinit-utils_3.07-1ubuntu1 tar_1.34+dfsg-1.2ubuntu1 tzdata_2023c-9ubuntu1 ubuntu-keyring_2021.03.26 usrmerge_35ubuntu1 util-linux_2.39.1-4ubuntu1 util-linux-extra_2.39.1-4ubuntu1 xz-utils_5.4.1-0.2 zlib1g_1:1.2.13.dfsg-1ubuntu5 zlib1g-dev_1:1.2.13.dfsg-1ubuntu5 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: blasr Binary: blasr Architecture: any Version: 5.3.5+dfsg-6build1 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille Homepage: https://github.com/PacificBiosciences/blasr Standards-Version: 4.6.1 Vcs-Browser: https://salsa.debian.org/med-team/blasr Vcs-Git: https://salsa.debian.org/med-team/blasr.git Testsuite: autopkgtest Build-Depends: debhelper-compat (= 13), python3:any, meson, cmake, pkg-config, libboost-dev, libhdf5-dev, zlib1g-dev, libpbseq-dev, libpbbam-dev, libpbdata-dev, libpbcopper-dev, libgtest-dev, libblasr-dev (>= 5.3.4+dfsg-4~) Package-List: blasr deb science optional arch=any Checksums-Sha1: 334132438305cfaf3d7ee6208bcb4cc4b493be5d 124460 blasr_5.3.5+dfsg.orig.tar.xz a64a02582e876a51fa34c103792f32baf972411d 11464 blasr_5.3.5+dfsg-6build1.debian.tar.xz Checksums-Sha256: 765ac47ae74f56e3bee17e2a3c81d404faf7419e42eb45bc9f2a71c7a5942205 124460 blasr_5.3.5+dfsg.orig.tar.xz d64626620f693cd4cd790076b3746ed4f056066cee2b04c5f5aed77174397347 11464 blasr_5.3.5+dfsg-6build1.debian.tar.xz Files: 46c888e8f9c606d840b0d9dcc8036b21 124460 blasr_5.3.5+dfsg.orig.tar.xz a217843947f27139fa9c1c632991ee72 11464 blasr_5.3.5+dfsg-6build1.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQIzBAEBCgAdFiEETQvhLw5HdtiqzpaW5mx3Wuv+bH0FAmT0mhcACgkQ5mx3Wuv+ bH1FtxAAhoohAkPa2UZADnin2hKDYqobfLVG9X2vjmIkyuKHdsuu5ZFG17QVmJdf NkdTh8J7S9Qj3CA8WXJc4lAZIm8S/mKXtekOFPjMfHNNNs0M/+oYyxqqrteXIoHI eLoLfbmMZdMDcntJdN/JIYbqTCEMKo0NHcj4C4r6kWL/ZsLSJd/gf2H5O27Eyqk2 URNLQvQh5BzqjkPtCVpvTs933HSWpGyRrEGkW+zvXGABOor5hbfh/Ul+9DFPACFE ujdtdEXI7IIg/Ku0HxLc1/ZiC04cIvI2XV6aUbD2/JstQVe2cp5JFldMbebcOXZu rR+WV9cea9K3jDYBnmyD7kJ9l336reOqoG8la7t5F8qZcHkwabpv1ClSq8ZpXRKA sEVqROmJ4Hx5/6Yiu8zxZHhl//jkxgm3m9lwQGqB5QpEUIljJhckHBFUNeFmwl6d J68wUaK2LqBaeXU7tGFyB9Tp9ZOKUqLKx64uvfksFD5s/BW3zvpp210gvbOYOuQs LBYD2l4uGT5wbAc72Lq2ng4WHMi6BVmD4QM61+jZAkw63BGGW7A3BEnrYrPf2s1D tuYbqWMejDs1eDilfCNs+6LxcfOuG/ZBBTSXSbXS0FIYrd/HApPRZF0ySVYhOXg0 Fi6MvM0iM4ZW/DbiFrGaGfTyfvk7ThD2JY9FZQtejm3Q4teeOfc= =j89y -----END PGP SIGNATURE----- gpgv: Signature made Sun Sep 3 14:37:11 2023 UTC gpgv: using RSA key 4D0BE12F0E4776D8AACE9696E66C775AEBFE6C7D gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./blasr_5.3.5+dfsg-6build1.dsc: no acceptable signature found dpkg-source: info: extracting blasr in /<> dpkg-source: info: unpacking blasr_5.3.5+dfsg.orig.tar.xz dpkg-source: info: unpacking blasr_5.3.5+dfsg-6build1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying use_debian_packaged_pblibs.patch dpkg-source: info: applying 2to3.patch Check disk space ---------------- Sufficient free space for build User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf DEB_BUILD_OPTIONS=parallel=4 HOME=/sbuild-nonexistent LANG=C.UTF-8 LC_ALL=C.UTF-8 LOGNAME=buildd PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games SCHROOT_ALIAS_NAME=build-PACKAGEBUILD-26678012 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-26678012 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-26678012 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 blasr dpkg-buildpackage: info: source version 5.3.5+dfsg-6build1 dpkg-buildpackage: info: source distribution mantic dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean --buildsystem=meson dh_auto_clean -O--buildsystem=meson 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 debian/rules override_dh_auto_configure make[1]: Entering directory '/<>' LDFLAGS="-L/usr/lib/x86_64-linux-gnu -L/usr/lib/x86_64-linux-gnu/hdf5/serial -lhdf5_cpp -lhdf5 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro" CPPFLAGS="-isystem /usr/include/hdf5/serial" dh_auto_configure -- -Dtests=false 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 -Dtests=false The Meson build system Version: 1.2.1 Source dir: /<> Build dir: /<>/obj-x86_64-linux-gnu Build type: native build Project name: blasr Project version: 5.3.5 C++ compiler for the host machine: c++ (gcc 13.2.0 "c++ (Ubuntu 13.2.0-3ubuntu1) 13.2.0") C++ linker for the host machine: c++ ld.bfd 2.41 Host machine cpu family: x86_64 Host machine cpu: x86_64 Compiler for C++ supports arguments -Wno-delete-non-virtual-dtor: YES Compiler for C++ supports arguments -Wno-non-virtual-dtor: YES Compiler for C++ supports arguments -Wno-unused-but-set-variable: YES Compiler for C++ supports arguments -Wno-unused-variable: YES Run-time dependency threads found: YES Found pkg-config: /usr/bin/pkg-config (1.8.1) Run-time dependency Boost found: YES 1.74.0 (/usr/include) Library pbbam found: YES Run-time dependency libblasr found: YES 5.3.5 Run-time dependency zlib found: YES 1.2.13 Run-time dependency htslib found: YES 1.17 Library pbcopper found: YES Configuring BlasrVersion.h using configuration Build targets in project: 5 blasr 5.3.5 User defined options buildtype : plain libdir : lib/x86_64-linux-gnu localstatedir : /var prefix : /usr sysconfdir : /etc wrap_mode : nodownload python.bytecompile: -1 tests : false Found ninja-1.11.1 at /usr/bin/ninja make[1]: Leaving directory '/<>' dh_auto_build -O--buildsystem=meson cd obj-x86_64-linux-gnu && LC_ALL=C.UTF-8 ninja -j4 -v [1/25] /usr/bin/meson --internal vcstagger ../BlasrGitHash.h.in BlasrGitHash.h 5.3.5 /<> @BLASR_GIT_SHA1@ '(.*)' git describe --always '--dirty=*' [2/25] c++ -Ilibblasr_impl.a.p -I. -I.. -I/usr/include/libblasr -I/usr/include/hdf5/serial -I/usr/include/pbseq -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -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/blasr-5.3.5+dfsg-6build1 -DHAVE_HDF5_1_10_1 -isystem /usr/include/hdf5/serial -fPIC -DBOOST_ALL_NO_LIB -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -MD -MQ libblasr_impl.a.p/extrautils_SAModify.cpp.o -MF libblasr_impl.a.p/extrautils_SAModify.cpp.o.d -o libblasr_impl.a.p/extrautils_SAModify.cpp.o -c ../extrautils/SAModify.cpp [3/25] c++ -Ilibblasr_impl.a.p -I. -I.. -I/usr/include/libblasr -I/usr/include/hdf5/serial -I/usr/include/pbseq -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -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/blasr-5.3.5+dfsg-6build1 -DHAVE_HDF5_1_10_1 -isystem /usr/include/hdf5/serial -fPIC -DBOOST_ALL_NO_LIB -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -MD -MQ libblasr_impl.a.p/extrautils_BwtToSuffixArray.cpp.o -MF libblasr_impl.a.p/extrautils_BwtToSuffixArray.cpp.o.d -o libblasr_impl.a.p/extrautils_BwtToSuffixArray.cpp.o -c ../extrautils/BwtToSuffixArray.cpp [4/25] c++ -Ilibblasr_impl.a.p -I. -I.. -I/usr/include/libblasr -I/usr/include/hdf5/serial -I/usr/include/pbseq -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -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/blasr-5.3.5+dfsg-6build1 -DHAVE_HDF5_1_10_1 -isystem /usr/include/hdf5/serial -fPIC -DBOOST_ALL_NO_LIB -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -MD -MQ libblasr_impl.a.p/extrautils_SuffixArrayToBWT.cpp.o -MF libblasr_impl.a.p/extrautils_SuffixArrayToBWT.cpp.o.d -o libblasr_impl.a.p/extrautils_SuffixArrayToBWT.cpp.o -c ../extrautils/SuffixArrayToBWT.cpp In file included from ../extrautils/SuffixArrayToBWT.cpp:4: /usr/include/pbseq/alignment/bwt/BWT.hpp: In member function ‘void Bwt::InitializeDNACharacterCount() [with T_BWT_Sequence = PackedDNASequence; T_DNASequence = FASTASequence]’: /usr/include/pbseq/alignment/bwt/BWT.hpp:192:21: warning: this statement may fall through [-Wimplicit-fallthrough=] 192 | charCount[0]++; | ^~~~~~~~~ /usr/include/pbseq/alignment/bwt/BWT.hpp:193:17: note: here 193 | case 0: //A | ^~~~ /usr/include/pbseq/alignment/bwt/BWT.hpp:194:21: warning: this statement may fall through [-Wimplicit-fallthrough=] 194 | charCount[1]++; | ^~~~~~~~~ /usr/include/pbseq/alignment/bwt/BWT.hpp:195:17: note: here 195 | case 1: //C | ^~~~ /usr/include/pbseq/alignment/bwt/BWT.hpp:196:21: warning: this statement may fall through [-Wimplicit-fallthrough=] 196 | charCount[2]++; | ^~~~~~~~~ /usr/include/pbseq/alignment/bwt/BWT.hpp:197:17: note: here 197 | case 2: //G | ^~~~ /usr/include/pbseq/alignment/bwt/BWT.hpp:198:21: warning: this statement may fall through [-Wimplicit-fallthrough=] 198 | charCount[3]++; | ^~~~~~~~~ /usr/include/pbseq/alignment/bwt/BWT.hpp:199:17: note: here 199 | case 3: //T | ^~~~ /usr/include/pbseq/alignment/bwt/BWT.hpp:200:21: warning: this statement may fall through [-Wimplicit-fallthrough=] 200 | charCount[4]++; | ^~~~~~~~~ /usr/include/pbseq/alignment/bwt/BWT.hpp:201:17: note: here 201 | case 4: //N | ^~~~ [5/25] c++ -Ilibblasr_impl.a.p -I. -I.. -I/usr/include/libblasr -I/usr/include/hdf5/serial -I/usr/include/pbseq -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -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/blasr-5.3.5+dfsg-6build1 -DHAVE_HDF5_1_10_1 -isystem /usr/include/hdf5/serial -fPIC -DBOOST_ALL_NO_LIB -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -MD -MQ libblasr_impl.a.p/extrautils_SWMatcher.cpp.o -MF libblasr_impl.a.p/extrautils_SWMatcher.cpp.o.d -o libblasr_impl.a.p/extrautils_SWMatcher.cpp.o -c ../extrautils/SWMatcher.cpp In file included from /usr/include/pbseq/alignment/algorithms/alignment/AlignmentUtils.hpp:7, from ../extrautils/SWMatcher.cpp:6: /usr/include/pbseq/alignment/datastructures/alignment/Alignment.hpp: In instantiation of ‘void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = blasr::CompSeqAlignment; _Args = {const blasr::CompSeqAlignment&}; _Tp = blasr::CompSeqAlignment]’: /usr/include/c++/13/bits/alloc_traits.h:537:17: required from ‘static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = blasr::CompSeqAlignment; _Args = {const blasr::CompSeqAlignment&}; _Tp = blasr::CompSeqAlignment; allocator_type = std::allocator]’ /usr/include/c++/13/bits/stl_vector.h:1283:30: required from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = blasr::CompSeqAlignment; _Alloc = std::allocator; value_type = blasr::CompSeqAlignment]’ /usr/include/pbseq/alignment/algorithms/alignment/AlignmentUtilsImpl.hpp:112:29: required from here /usr/include/pbseq/alignment/datastructures/alignment/Alignment.hpp:209:7: warning: implicitly-declared ‘blasr::Alignment::Alignment(const blasr::Alignment&)’ is deprecated [-Wdeprecated-copy] 209 | class CompSeqAlignment : public Alignment | ^~~~~~~~~~~~~~~~ /usr/include/pbseq/alignment/datastructures/alignment/Alignment.hpp:103:16: note: because ‘blasr::Alignment’ has user-provided ‘blasr::Alignment& blasr::Alignment::operator=(const blasr::Alignment&)’ 103 | Alignment &operator=(const Alignment &rhs); | ^~~~~~~~ /usr/include/pbseq/alignment/datastructures/alignment/Alignment.hpp:58:7: warning: implicitly-declared ‘constexpr blasr::AlignmentStats::AlignmentStats(const blasr::AlignmentStats&)’ is deprecated [-Wdeprecated-copy] 58 | class Alignment : public AlignmentStats | ^~~~~~~~~ In file included from /usr/include/pbseq/alignment/datastructures/alignment/Alignment.hpp:8: /usr/include/pbseq/alignment/datastructures/alignment/AlignmentStats.hpp:19:21: note: because ‘blasr::AlignmentStats’ has user-provided ‘blasr::AlignmentStats& blasr::AlignmentStats::operator=(const blasr::AlignmentStats&)’ 19 | AlignmentStats &operator=(const AlignmentStats &rhs); | ^~~~~~~~ /usr/include/pbseq/alignment/datastructures/alignment/Alignment.hpp:209:7: note: synthesized method ‘blasr::Alignment::Alignment(const blasr::Alignment&)’ first required here 209 | class CompSeqAlignment : public Alignment | ^~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/c++/13/bits/c++allocator.h:33, from /usr/include/c++/13/bits/allocator.h:46, from /usr/include/c++/13/string:43, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /usr/include/c++/13/iostream:41, from ../extrautils/SWMatcher.cpp:2: /usr/include/c++/13/bits/new_allocator.h:187:11: note: synthesized method ‘blasr::CompSeqAlignment::CompSeqAlignment(const blasr::CompSeqAlignment&)’ first required here 187 | { ::new((void *)__p) _Up(std::forward<_Args>(__args)...); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [6/25] c++ -Ilibblasr_impl.a.p -I. -I.. -I/usr/include/libblasr -I/usr/include/hdf5/serial -I/usr/include/pbseq -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -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/blasr-5.3.5+dfsg-6build1 -DHAVE_HDF5_1_10_1 -isystem /usr/include/hdf5/serial -fPIC -DBOOST_ALL_NO_LIB -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -MD -MQ libblasr_impl.a.p/extrautils_ExciseRepeats.cpp.o -MF libblasr_impl.a.p/extrautils_ExciseRepeats.cpp.o.d -o libblasr_impl.a.p/extrautils_ExciseRepeats.cpp.o -c ../extrautils/ExciseRepeats.cpp [7/25] c++ -Ilibblasr_impl.a.p -I. -I.. -I/usr/include/libblasr -I/usr/include/hdf5/serial -I/usr/include/pbseq -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -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/blasr-5.3.5+dfsg-6build1 -DHAVE_HDF5_1_10_1 -isystem /usr/include/hdf5/serial -fPIC -DBOOST_ALL_NO_LIB -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -MD -MQ libblasr_impl.a.p/extrautils_SALS.cpp.o -MF libblasr_impl.a.p/extrautils_SALS.cpp.o.d -o libblasr_impl.a.p/extrautils_SALS.cpp.o -c ../extrautils/SALS.cpp [8/25] c++ -Ilibblasr_impl.a.p -I. -I.. -I/usr/include/libblasr -I/usr/include/hdf5/serial -I/usr/include/pbseq -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -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/blasr-5.3.5+dfsg-6build1 -DHAVE_HDF5_1_10_1 -isystem /usr/include/hdf5/serial -fPIC -DBOOST_ALL_NO_LIB -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -MD -MQ libblasr_impl.a.p/extrautils_SimpleShredder.cpp.o -MF libblasr_impl.a.p/extrautils_SimpleShredder.cpp.o.d -o libblasr_impl.a.p/extrautils_SimpleShredder.cpp.o -c ../extrautils/SimpleShredder.cpp [9/25] c++ -Ilibblasr_impl.a.p -I. -I.. -I/usr/include/libblasr -I/usr/include/hdf5/serial -I/usr/include/pbseq -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -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/blasr-5.3.5+dfsg-6build1 -DHAVE_HDF5_1_10_1 -isystem /usr/include/hdf5/serial -fPIC -DBOOST_ALL_NO_LIB -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -MD -MQ libblasr_impl.a.p/extrautils_Evolve.cpp.o -MF libblasr_impl.a.p/extrautils_Evolve.cpp.o.d -o libblasr_impl.a.p/extrautils_Evolve.cpp.o -c ../extrautils/Evolve.cpp [10/25] c++ -Ilibblasr_impl.a.p -I. -I.. -I/usr/include/libblasr -I/usr/include/hdf5/serial -I/usr/include/pbseq -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -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/blasr-5.3.5+dfsg-6build1 -DHAVE_HDF5_1_10_1 -isystem /usr/include/hdf5/serial -fPIC -DBOOST_ALL_NO_LIB -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -MD -MQ libblasr_impl.a.p/extrautils_BuildSequenceDB.cpp.o -MF libblasr_impl.a.p/extrautils_BuildSequenceDB.cpp.o.d -o libblasr_impl.a.p/extrautils_BuildSequenceDB.cpp.o -c ../extrautils/BuildSequenceDB.cpp [11/25] c++ -Ilibblasr_impl.a.p -I. -I.. -I/usr/include/libblasr -I/usr/include/hdf5/serial -I/usr/include/pbseq -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -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/blasr-5.3.5+dfsg-6build1 -DHAVE_HDF5_1_10_1 -isystem /usr/include/hdf5/serial -fPIC -DBOOST_ALL_NO_LIB -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -MD -MQ libblasr_impl.a.p/extrautils_PrintTupleCountTable.cpp.o -MF libblasr_impl.a.p/extrautils_PrintTupleCountTable.cpp.o.d -o libblasr_impl.a.p/extrautils_PrintTupleCountTable.cpp.o -c ../extrautils/PrintTupleCountTable.cpp [12/25] c++ -Ilibblasr_impl.a.p -I. -I.. -I/usr/include/libblasr -I/usr/include/hdf5/serial -I/usr/include/pbseq -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -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/blasr-5.3.5+dfsg-6build1 -DHAVE_HDF5_1_10_1 -isystem /usr/include/hdf5/serial -fPIC -DBOOST_ALL_NO_LIB -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -MD -MQ libblasr_impl.a.p/extrautils_StoreQualityByContextFromCmpH5.cpp.o -MF libblasr_impl.a.p/extrautils_StoreQualityByContextFromCmpH5.cpp.o.d -o libblasr_impl.a.p/extrautils_StoreQualityByContextFromCmpH5.cpp.o -c ../extrautils/StoreQualityByContextFromCmpH5.cpp In file included from /usr/include/pbseq/hdf/DatasetCollection.hpp:9, from /usr/include/pbseq/hdf/HDFBasReader.hpp:11, from /usr/include/pbseq/alignment/files/ReaderAgglomerate.hpp:8, from ../extrautils/StoreQualityByContextFromCmpH5.cpp:2: /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:123:1: required from here /usr/include/pbseq/hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ In file included from /usr/include/pbseq/hdf/HDF2DArray.hpp:4, from /usr/include/pbseq/hdf/HDFBasReader.hpp:12: /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = int; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:124:1: required from here /usr/include/pbseq/hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = unsigned int; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:125:1: required from here /usr/include/pbseq/hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = unsigned char; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:126:1: required from here /usr/include/pbseq/hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = short unsigned int; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:127:1: required from here /usr/include/pbseq/hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = short int; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:128:1: required from here /usr/include/pbseq/hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = float; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:137:1: required from here /usr/include/pbseq/hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = char; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray >’: /usr/include/pbseq/hdf/HDF2DArray.hpp:7:7: required from ‘class HDF2DArray >’ /usr/include/pbseq/hdf/HDFCmpRootGroup.hpp:17:29: required from here /usr/include/pbseq/hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ In file included from /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:156: /usr/include/pbseq/hdf/BufferedHDF2DArrayImpl.hpp:70:5: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = std::__cxx11::basic_string; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 70 | int BufferedHDF2DArray::Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength, | ^~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/pbseq/alignment/algorithms/alignment/AlignmentUtils.hpp:7, from /usr/include/pbseq/alignment/format/StickAlignmentPrinter.hpp:8, from ../extrautils/StoreQualityByContextFromCmpH5.cpp:3: /usr/include/pbseq/alignment/datastructures/alignment/Alignment.hpp: In instantiation of ‘void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = blasr::CompSeqAlignment; _Args = {const blasr::CompSeqAlignment&}; _Tp = blasr::CompSeqAlignment]’: /usr/include/c++/13/bits/alloc_traits.h:537:17: required from ‘static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = blasr::CompSeqAlignment; _Args = {const blasr::CompSeqAlignment&}; _Tp = blasr::CompSeqAlignment; allocator_type = std::allocator]’ /usr/include/c++/13/bits/stl_vector.h:1283:30: required from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = blasr::CompSeqAlignment; _Alloc = std::allocator; value_type = blasr::CompSeqAlignment]’ /usr/include/pbseq/alignment/algorithms/alignment/AlignmentUtilsImpl.hpp:112:29: required from here /usr/include/pbseq/alignment/datastructures/alignment/Alignment.hpp:209:7: warning: implicitly-declared ‘blasr::Alignment::Alignment(const blasr::Alignment&)’ is deprecated [-Wdeprecated-copy] 209 | class CompSeqAlignment : public Alignment | ^~~~~~~~~~~~~~~~ /usr/include/pbseq/alignment/datastructures/alignment/Alignment.hpp:103:16: note: because ‘blasr::Alignment’ has user-provided ‘blasr::Alignment& blasr::Alignment::operator=(const blasr::Alignment&)’ 103 | Alignment &operator=(const Alignment &rhs); | ^~~~~~~~ /usr/include/pbseq/alignment/datastructures/alignment/Alignment.hpp:58:7: warning: implicitly-declared ‘constexpr blasr::AlignmentStats::AlignmentStats(const blasr::AlignmentStats&)’ is deprecated [-Wdeprecated-copy] 58 | class Alignment : public AlignmentStats | ^~~~~~~~~ In file included from /usr/include/pbseq/alignment/datastructures/alignment/Alignment.hpp:8: /usr/include/pbseq/alignment/datastructures/alignment/AlignmentStats.hpp:19:21: note: because ‘blasr::AlignmentStats’ has user-provided ‘blasr::AlignmentStats& blasr::AlignmentStats::operator=(const blasr::AlignmentStats&)’ 19 | AlignmentStats &operator=(const AlignmentStats &rhs); | ^~~~~~~~ /usr/include/pbseq/alignment/datastructures/alignment/Alignment.hpp:209:7: note: synthesized method ‘blasr::Alignment::Alignment(const blasr::Alignment&)’ first required here 209 | class CompSeqAlignment : public Alignment | ^~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/c++/13/bits/c++allocator.h:33, from /usr/include/c++/13/bits/allocator.h:46, from /usr/include/c++/13/vector:63, from /usr/include/pbseq/alignment/datastructures/alignment/CmpFile.hpp:4, from ../extrautils/StoreQualityByContextFromCmpH5.cpp:1: /usr/include/c++/13/bits/new_allocator.h:187:11: note: synthesized method ‘blasr::CompSeqAlignment::CompSeqAlignment(const blasr::CompSeqAlignment&)’ first required here 187 | { ::new((void *)__p) _Up(std::forward<_Args>(__args)...); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [13/25] c++ -Ilibblasr_impl.a.p -I. -I.. -I/usr/include/libblasr -I/usr/include/hdf5/serial -I/usr/include/pbseq -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -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/blasr-5.3.5+dfsg-6build1 -DHAVE_HDF5_1_10_1 -isystem /usr/include/hdf5/serial -fPIC -DBOOST_ALL_NO_LIB -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -MD -MQ libblasr_impl.a.p/utils_SamToM4.cpp.o -MF libblasr_impl.a.p/utils_SamToM4.cpp.o.d -o libblasr_impl.a.p/utils_SamToM4.cpp.o -c ../utils/SamToM4.cpp In file included from /usr/include/pbseq/alignment/algorithms/alignment/AlignmentUtils.hpp:7, from ../utils/SamToM4.cpp:21: /usr/include/pbseq/alignment/datastructures/alignment/Alignment.hpp: In instantiation of ‘void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = blasr::CompSeqAlignment; _Args = {const blasr::CompSeqAlignment&}; _Tp = blasr::CompSeqAlignment]’: /usr/include/c++/13/bits/alloc_traits.h:537:17: required from ‘static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = blasr::CompSeqAlignment; _Args = {const blasr::CompSeqAlignment&}; _Tp = blasr::CompSeqAlignment; allocator_type = std::allocator]’ /usr/include/c++/13/bits/stl_vector.h:1283:30: required from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = blasr::CompSeqAlignment; _Alloc = std::allocator; value_type = blasr::CompSeqAlignment]’ /usr/include/pbseq/alignment/algorithms/alignment/AlignmentUtilsImpl.hpp:112:29: required from here /usr/include/pbseq/alignment/datastructures/alignment/Alignment.hpp:209:7: warning: implicitly-declared ‘blasr::Alignment::Alignment(const blasr::Alignment&)’ is deprecated [-Wdeprecated-copy] 209 | class CompSeqAlignment : public Alignment | ^~~~~~~~~~~~~~~~ /usr/include/pbseq/alignment/datastructures/alignment/Alignment.hpp:103:16: note: because ‘blasr::Alignment’ has user-provided ‘blasr::Alignment& blasr::Alignment::operator=(const blasr::Alignment&)’ 103 | Alignment &operator=(const Alignment &rhs); | ^~~~~~~~ /usr/include/pbseq/alignment/datastructures/alignment/Alignment.hpp:58:7: warning: implicitly-declared ‘constexpr blasr::AlignmentStats::AlignmentStats(const blasr::AlignmentStats&)’ is deprecated [-Wdeprecated-copy] 58 | class Alignment : public AlignmentStats | ^~~~~~~~~ In file included from /usr/include/pbseq/alignment/datastructures/alignment/Alignment.hpp:8: /usr/include/pbseq/alignment/datastructures/alignment/AlignmentStats.hpp:19:21: note: because ‘blasr::AlignmentStats’ has user-provided ‘blasr::AlignmentStats& blasr::AlignmentStats::operator=(const blasr::AlignmentStats&)’ 19 | AlignmentStats &operator=(const AlignmentStats &rhs); | ^~~~~~~~ /usr/include/pbseq/alignment/datastructures/alignment/Alignment.hpp:209:7: note: synthesized method ‘blasr::Alignment::Alignment(const blasr::Alignment&)’ first required here 209 | class CompSeqAlignment : public Alignment | ^~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/c++/13/bits/c++allocator.h:33, from /usr/include/c++/13/bits/allocator.h:46, from /usr/include/c++/13/string:43, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /usr/include/c++/13/iostream:41, from ../utils/SamToM4.cpp:19: /usr/include/c++/13/bits/new_allocator.h:187:11: note: synthesized method ‘blasr::CompSeqAlignment::CompSeqAlignment(const blasr::CompSeqAlignment&)’ first required here 187 | { ::new((void *)__p) _Up(std::forward<_Args>(__args)...); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [14/25] c++ -Ilibblasr_impl.a.p -I. -I.. -I/usr/include/libblasr -I/usr/include/hdf5/serial -I/usr/include/pbseq -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -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/blasr-5.3.5+dfsg-6build1 -DHAVE_HDF5_1_10_1 -isystem /usr/include/hdf5/serial -fPIC -DBOOST_ALL_NO_LIB -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -MD -MQ libblasr_impl.a.p/utils_SDPMatcher.cpp.o -MF libblasr_impl.a.p/utils_SDPMatcher.cpp.o.d -o libblasr_impl.a.p/utils_SDPMatcher.cpp.o -c ../utils/SDPMatcher.cpp In file included from /usr/include/pbseq/alignment/algorithms/alignment/AlignmentUtils.hpp:7, from ../utils/SDPMatcher.cpp:8: /usr/include/pbseq/alignment/datastructures/alignment/Alignment.hpp: In instantiation of ‘void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = blasr::CompSeqAlignment; _Args = {const blasr::CompSeqAlignment&}; _Tp = blasr::CompSeqAlignment]’: /usr/include/c++/13/bits/alloc_traits.h:537:17: required from ‘static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = blasr::CompSeqAlignment; _Args = {const blasr::CompSeqAlignment&}; _Tp = blasr::CompSeqAlignment; allocator_type = std::allocator]’ /usr/include/c++/13/bits/stl_vector.h:1283:30: required from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = blasr::CompSeqAlignment; _Alloc = std::allocator; value_type = blasr::CompSeqAlignment]’ /usr/include/pbseq/alignment/algorithms/alignment/AlignmentUtilsImpl.hpp:112:29: required from here /usr/include/pbseq/alignment/datastructures/alignment/Alignment.hpp:209:7: warning: implicitly-declared ‘blasr::Alignment::Alignment(const blasr::Alignment&)’ is deprecated [-Wdeprecated-copy] 209 | class CompSeqAlignment : public Alignment | ^~~~~~~~~~~~~~~~ /usr/include/pbseq/alignment/datastructures/alignment/Alignment.hpp:103:16: note: because ‘blasr::Alignment’ has user-provided ‘blasr::Alignment& blasr::Alignment::operator=(const blasr::Alignment&)’ 103 | Alignment &operator=(const Alignment &rhs); | ^~~~~~~~ /usr/include/pbseq/alignment/datastructures/alignment/Alignment.hpp:58:7: warning: implicitly-declared ‘constexpr blasr::AlignmentStats::AlignmentStats(const blasr::AlignmentStats&)’ is deprecated [-Wdeprecated-copy] 58 | class Alignment : public AlignmentStats | ^~~~~~~~~ In file included from /usr/include/pbseq/alignment/datastructures/alignment/Alignment.hpp:8: /usr/include/pbseq/alignment/datastructures/alignment/AlignmentStats.hpp:19:21: note: because ‘blasr::AlignmentStats’ has user-provided ‘blasr::AlignmentStats& blasr::AlignmentStats::operator=(const blasr::AlignmentStats&)’ 19 | AlignmentStats &operator=(const AlignmentStats &rhs); | ^~~~~~~~ /usr/include/pbseq/alignment/datastructures/alignment/Alignment.hpp:209:7: note: synthesized method ‘blasr::Alignment::Alignment(const blasr::Alignment&)’ first required here 209 | class CompSeqAlignment : public Alignment | ^~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/c++/13/bits/c++allocator.h:33, from /usr/include/c++/13/bits/allocator.h:46, from /usr/include/c++/13/string:43, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /usr/include/c++/13/iostream:41, from ../utils/SDPMatcher.cpp:3: /usr/include/c++/13/bits/new_allocator.h:187:11: note: synthesized method ‘blasr::CompSeqAlignment::CompSeqAlignment(const blasr::CompSeqAlignment&)’ first required here 187 | { ::new((void *)__p) _Up(std::forward<_Args>(__args)...); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [15/25] c++ -Ilibblasr_impl.a.p -I. -I.. -I/usr/include/libblasr -I/usr/include/hdf5/serial -I/usr/include/pbseq -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -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/blasr-5.3.5+dfsg-6build1 -DHAVE_HDF5_1_10_1 -isystem /usr/include/hdf5/serial -fPIC -DBOOST_ALL_NO_LIB -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -MD -MQ libblasr_impl.a.p/utils_SamToCmpH5.cpp.o -MF libblasr_impl.a.p/utils_SamToCmpH5.cpp.o.d -o libblasr_impl.a.p/utils_SamToCmpH5.cpp.o -c ../utils/SamToCmpH5.cpp In file included from /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:12, from /usr/include/pbseq/hdf/HDF2DArray.hpp:4, from /usr/include/pbseq/hdf/HDFCmpFile.hpp:11, from /usr/include/pbseq/alignment/datastructures/alignmentset/AlignmentSetToCmpH5Adapter.hpp:7, from ../utils/SamToCmpH5.cpp:5: /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:123:1: required from here /usr/include/pbseq/hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = int; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:124:1: required from here /usr/include/pbseq/hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = unsigned int; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:125:1: required from here /usr/include/pbseq/hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = unsigned char; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:126:1: required from here /usr/include/pbseq/hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = short unsigned int; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:127:1: required from here /usr/include/pbseq/hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = short int; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:128:1: required from here /usr/include/pbseq/hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = float; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:137:1: required from here /usr/include/pbseq/hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = char; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray >’: /usr/include/pbseq/hdf/HDF2DArray.hpp:7:7: required from ‘class HDF2DArray >’ /usr/include/pbseq/hdf/HDFCmpRootGroup.hpp:17:29: required from here /usr/include/pbseq/hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ In file included from /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:156: /usr/include/pbseq/hdf/BufferedHDF2DArrayImpl.hpp:70:5: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = std::__cxx11::basic_string; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 70 | int BufferedHDF2DArray::Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength, | ^~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/pbseq/alignment/datastructures/alignment/AlignmentCandidate.hpp:6, from ../utils/SamToCmpH5.cpp:3: /usr/include/pbseq/alignment/datastructures/alignment/Alignment.hpp: In instantiation of ‘void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = blasr::CompSeqAlignment; _Args = {const blasr::CompSeqAlignment&}; _Tp = blasr::CompSeqAlignment]’: /usr/include/c++/13/bits/alloc_traits.h:537:17: required from ‘static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = blasr::CompSeqAlignment; _Args = {const blasr::CompSeqAlignment&}; _Tp = blasr::CompSeqAlignment; allocator_type = std::allocator]’ /usr/include/c++/13/bits/stl_vector.h:1283:30: required from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = blasr::CompSeqAlignment; _Alloc = std::allocator; value_type = blasr::CompSeqAlignment]’ /usr/include/pbseq/alignment/algorithms/alignment/AlignmentUtilsImpl.hpp:112:29: required from here /usr/include/pbseq/alignment/datastructures/alignment/Alignment.hpp:209:7: warning: implicitly-declared ‘blasr::Alignment::Alignment(const blasr::Alignment&)’ is deprecated [-Wdeprecated-copy] 209 | class CompSeqAlignment : public Alignment | ^~~~~~~~~~~~~~~~ /usr/include/pbseq/alignment/datastructures/alignment/Alignment.hpp:103:16: note: because ‘blasr::Alignment’ has user-provided ‘blasr::Alignment& blasr::Alignment::operator=(const blasr::Alignment&)’ 103 | Alignment &operator=(const Alignment &rhs); | ^~~~~~~~ /usr/include/pbseq/alignment/datastructures/alignment/Alignment.hpp:58:7: warning: implicitly-declared ‘constexpr blasr::AlignmentStats::AlignmentStats(const blasr::AlignmentStats&)’ is deprecated [-Wdeprecated-copy] 58 | class Alignment : public AlignmentStats | ^~~~~~~~~ In file included from /usr/include/pbseq/alignment/datastructures/alignment/Alignment.hpp:8: /usr/include/pbseq/alignment/datastructures/alignment/AlignmentStats.hpp:19:21: note: because ‘blasr::AlignmentStats’ has user-provided ‘blasr::AlignmentStats& blasr::AlignmentStats::operator=(const blasr::AlignmentStats&)’ 19 | AlignmentStats &operator=(const AlignmentStats &rhs); | ^~~~~~~~ /usr/include/pbseq/alignment/datastructures/alignment/Alignment.hpp:209:7: note: synthesized method ‘blasr::Alignment::Alignment(const blasr::Alignment&)’ first required here 209 | class CompSeqAlignment : public Alignment | ^~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/c++/13/bits/c++allocator.h:33, from /usr/include/c++/13/bits/allocator.h:46, from /usr/include/c++/13/string:43, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /usr/include/c++/13/iostream:41, from ../utils/SamToCmpH5.cpp:1: /usr/include/c++/13/bits/new_allocator.h:187:11: note: synthesized method ‘blasr::CompSeqAlignment::CompSeqAlignment(const blasr::CompSeqAlignment&)’ first required here 187 | { ::new((void *)__p) _Up(std::forward<_Args>(__args)...); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/pbseq/alignment/datastructures/alignmentset/AlignmentSetToCmpH5Adapter.hpp:79: /usr/include/pbseq/alignment/datastructures/alignmentset/AlignmentSetToCmpH5AdapterImpl.hpp: In instantiation of ‘unsigned int AlignmentSetToCmpH5Adapter::StoreRefGroup(std::string, T_CmpFile&) [with T_CmpFile = HDFCmpFile >; std::string = std::__cxx11::basic_string]’: /usr/include/pbseq/alignment/datastructures/alignmentset/AlignmentSetToCmpH5AdapterImpl.hpp:136:31: required from ‘void AlignmentSetToCmpH5Adapter::StoreAlignmentCandidate(AlignmentCandidate<>&, int, T_CmpFile&, int, bool) [with T_CmpFile = HDFCmpFile >]’ /usr/include/pbseq/alignment/datastructures/alignmentset/AlignmentSetToCmpH5AdapterImpl.hpp:246:32: required from ‘void AlignmentSetToCmpH5Adapter::StoreAlignmentCandidateList(std::vector >&, T_CmpFile&, int, bool) [with T_CmpFile = HDFCmpFile >]’ ../utils/SamToCmpH5.cpp:199:56: required from here /usr/include/pbseq/alignment/datastructures/alignmentset/AlignmentSetToCmpH5AdapterImpl.hpp:64:45: warning: implicitly-declared ‘RefGroupNameId& RefGroupNameId::operator=(const RefGroupNameId&)’ is deprecated [-Wdeprecated-copy] 64 | refNameToRefGroupNameandId[refName] = RefGroupNameId(refGroupName, refGroupId); /usr/include/pbseq/alignment/datastructures/alignmentset/AlignmentSetToCmpH5Adapter.hpp:28:5: note: because ‘RefGroupNameId’ has user-provided ‘RefGroupNameId::RefGroupNameId(const RefGroupNameId&)’ 28 | RefGroupNameId(const RefGroupNameId &rhs) | ^~~~~~~~~~~~~~ [16/25] c++ -Ilibblasr_impl.a.p -I. -I.. -I/usr/include/libblasr -I/usr/include/hdf5/serial -I/usr/include/pbseq -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -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/blasr-5.3.5+dfsg-6build1 -DHAVE_HDF5_1_10_1 -isystem /usr/include/hdf5/serial -fPIC -DBOOST_ALL_NO_LIB -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -MD -MQ libblasr_impl.a.p/utils_PulseToFasta.cpp.o -MF libblasr_impl.a.p/utils_PulseToFasta.cpp.o.d -o libblasr_impl.a.p/utils_PulseToFasta.cpp.o -c ../utils/PulseToFasta.cpp In file included from /usr/include/pbseq/hdf/DatasetCollection.hpp:9, from /usr/include/pbseq/hdf/HDFBasReader.hpp:11, from /usr/include/pbseq/alignment/files/ReaderAgglomerate.hpp:8, from ../utils/PulseToFasta.cpp:5: /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:123:1: required from here /usr/include/pbseq/hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ In file included from /usr/include/pbseq/hdf/HDF2DArray.hpp:4, from /usr/include/pbseq/hdf/HDFBasReader.hpp:12: /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = int; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:124:1: required from here /usr/include/pbseq/hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = unsigned int; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:125:1: required from here /usr/include/pbseq/hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = unsigned char; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:126:1: required from here /usr/include/pbseq/hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = short unsigned int; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:127:1: required from here /usr/include/pbseq/hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = short int; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:128:1: required from here /usr/include/pbseq/hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = float; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:137:1: required from here /usr/include/pbseq/hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = char; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ [17/25] c++ -Ilibblasr_impl.a.p -I. -I.. -I/usr/include/libblasr -I/usr/include/hdf5/serial -I/usr/include/pbseq -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -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/blasr-5.3.5+dfsg-6build1 -DHAVE_HDF5_1_10_1 -isystem /usr/include/hdf5/serial -fPIC -DBOOST_ALL_NO_LIB -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -MD -MQ libblasr_impl.a.p/utils_SamFilter.cpp.o -MF libblasr_impl.a.p/utils_SamFilter.cpp.o.d -o libblasr_impl.a.p/utils_SamFilter.cpp.o -c ../utils/SamFilter.cpp In file included from /usr/include/pbseq/alignment/algorithms/alignment/AlignmentUtils.hpp:7, from ../utils/SamFilter.cpp:32: /usr/include/pbseq/alignment/datastructures/alignment/Alignment.hpp: In instantiation of ‘void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = blasr::CompSeqAlignment; _Args = {const blasr::CompSeqAlignment&}; _Tp = blasr::CompSeqAlignment]’: /usr/include/c++/13/bits/alloc_traits.h:537:17: required from ‘static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = blasr::CompSeqAlignment; _Args = {const blasr::CompSeqAlignment&}; _Tp = blasr::CompSeqAlignment; allocator_type = std::allocator]’ /usr/include/c++/13/bits/stl_vector.h:1283:30: required from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = blasr::CompSeqAlignment; _Alloc = std::allocator; value_type = blasr::CompSeqAlignment]’ /usr/include/pbseq/alignment/algorithms/alignment/AlignmentUtilsImpl.hpp:112:29: required from here /usr/include/pbseq/alignment/datastructures/alignment/Alignment.hpp:209:7: warning: implicitly-declared ‘blasr::Alignment::Alignment(const blasr::Alignment&)’ is deprecated [-Wdeprecated-copy] 209 | class CompSeqAlignment : public Alignment | ^~~~~~~~~~~~~~~~ /usr/include/pbseq/alignment/datastructures/alignment/Alignment.hpp:103:16: note: because ‘blasr::Alignment’ has user-provided ‘blasr::Alignment& blasr::Alignment::operator=(const blasr::Alignment&)’ 103 | Alignment &operator=(const Alignment &rhs); | ^~~~~~~~ /usr/include/pbseq/alignment/datastructures/alignment/Alignment.hpp:58:7: warning: implicitly-declared ‘constexpr blasr::AlignmentStats::AlignmentStats(const blasr::AlignmentStats&)’ is deprecated [-Wdeprecated-copy] 58 | class Alignment : public AlignmentStats | ^~~~~~~~~ In file included from /usr/include/pbseq/alignment/datastructures/alignment/Alignment.hpp:8: /usr/include/pbseq/alignment/datastructures/alignment/AlignmentStats.hpp:19:21: note: because ‘blasr::AlignmentStats’ has user-provided ‘blasr::AlignmentStats& blasr::AlignmentStats::operator=(const blasr::AlignmentStats&)’ 19 | AlignmentStats &operator=(const AlignmentStats &rhs); | ^~~~~~~~ /usr/include/pbseq/alignment/datastructures/alignment/Alignment.hpp:209:7: note: synthesized method ‘blasr::Alignment::Alignment(const blasr::Alignment&)’ first required here 209 | class CompSeqAlignment : public Alignment | ^~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/c++/13/bits/c++allocator.h:33, from /usr/include/c++/13/bits/allocator.h:46, from /usr/include/c++/13/string:43, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /usr/include/c++/13/iostream:41, from ../utils/SamFilter.cpp:29: /usr/include/c++/13/bits/new_allocator.h:187:11: note: synthesized method ‘blasr::CompSeqAlignment::CompSeqAlignment(const blasr::CompSeqAlignment&)’ first required here 187 | { ::new((void *)__p) _Up(std::forward<_Args>(__args)...); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [18/25] c++ -Isawriter.p -I. -I.. -I/usr/include/libblasr -I/usr/include/hdf5/serial -I/usr/include/pbseq -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -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/blasr-5.3.5+dfsg-6build1 -DHAVE_HDF5_1_10_1 -isystem /usr/include/hdf5/serial -DBOOST_ALL_NO_LIB -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -DCMAKE_BUILD=1 -MD -MQ sawriter.p/utils_SAWriter.cpp.o -MF sawriter.p/utils_SAWriter.cpp.o.d -o sawriter.p/utils_SAWriter.cpp.o -c ../utils/SAWriter.cpp [19/25] c++ -Ilibblasr_impl.a.p -I. -I.. -I/usr/include/libblasr -I/usr/include/hdf5/serial -I/usr/include/pbseq -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -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/blasr-5.3.5+dfsg-6build1 -DHAVE_HDF5_1_10_1 -isystem /usr/include/hdf5/serial -fPIC -DBOOST_ALL_NO_LIB -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -MD -MQ libblasr_impl.a.p/utils_LoadPulses.cpp.o -MF libblasr_impl.a.p/utils_LoadPulses.cpp.o.d -o libblasr_impl.a.p/utils_LoadPulses.cpp.o -c ../utils/LoadPulses.cpp In file included from /usr/include/pbseq/hdf/DatasetCollection.hpp:9, from /usr/include/pbseq/hdf/HDFBasReader.hpp:11, from ../utils/LoadPulses.cpp:16: /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:123:1: required from here /usr/include/pbseq/hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ In file included from /usr/include/pbseq/hdf/HDF2DArray.hpp:4, from /usr/include/pbseq/hdf/HDFBasReader.hpp:12: /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = int; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:124:1: required from here /usr/include/pbseq/hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = unsigned int; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:125:1: required from here /usr/include/pbseq/hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = unsigned char; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:126:1: required from here /usr/include/pbseq/hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = short unsigned int; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:127:1: required from here /usr/include/pbseq/hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = short int; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:128:1: required from here /usr/include/pbseq/hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = float; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:137:1: required from here /usr/include/pbseq/hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = char; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray >’: /usr/include/pbseq/hdf/HDF2DArray.hpp:7:7: required from ‘class HDF2DArray >’ /usr/include/pbseq/hdf/HDFCmpRootGroup.hpp:17:29: required from here /usr/include/pbseq/hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ In file included from /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:156: /usr/include/pbseq/hdf/BufferedHDF2DArrayImpl.hpp:70:5: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = std::__cxx11::basic_string; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 70 | int BufferedHDF2DArray::Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength, | ^~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/pbseq/alignment/algorithms/alignment/AlignmentUtils.hpp:7, from /usr/include/pbseq/alignment/datastructures/alignment/ByteAlignment.h:6, from ../utils/LoadPulses.cpp:11: /usr/include/pbseq/alignment/datastructures/alignment/Alignment.hpp: In instantiation of ‘void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = blasr::CompSeqAlignment; _Args = {const blasr::CompSeqAlignment&}; _Tp = blasr::CompSeqAlignment]’: /usr/include/c++/13/bits/alloc_traits.h:537:17: required from ‘static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = blasr::CompSeqAlignment; _Args = {const blasr::CompSeqAlignment&}; _Tp = blasr::CompSeqAlignment; allocator_type = std::allocator]’ /usr/include/c++/13/bits/stl_vector.h:1283:30: required from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = blasr::CompSeqAlignment; _Alloc = std::allocator; value_type = blasr::CompSeqAlignment]’ /usr/include/pbseq/alignment/algorithms/alignment/AlignmentUtilsImpl.hpp:112:29: required from here /usr/include/pbseq/alignment/datastructures/alignment/Alignment.hpp:209:7: warning: implicitly-declared ‘blasr::Alignment::Alignment(const blasr::Alignment&)’ is deprecated [-Wdeprecated-copy] 209 | class CompSeqAlignment : public Alignment | ^~~~~~~~~~~~~~~~ /usr/include/pbseq/alignment/datastructures/alignment/Alignment.hpp:103:16: note: because ‘blasr::Alignment’ has user-provided ‘blasr::Alignment& blasr::Alignment::operator=(const blasr::Alignment&)’ 103 | Alignment &operator=(const Alignment &rhs); | ^~~~~~~~ /usr/include/pbseq/alignment/datastructures/alignment/Alignment.hpp:58:7: warning: implicitly-declared ‘constexpr blasr::AlignmentStats::AlignmentStats(const blasr::AlignmentStats&)’ is deprecated [-Wdeprecated-copy] 58 | class Alignment : public AlignmentStats | ^~~~~~~~~ In file included from /usr/include/pbseq/alignment/datastructures/alignment/Alignment.hpp:8: /usr/include/pbseq/alignment/datastructures/alignment/AlignmentStats.hpp:19:21: note: because ‘blasr::AlignmentStats’ has user-provided ‘blasr::AlignmentStats& blasr::AlignmentStats::operator=(const blasr::AlignmentStats&)’ 19 | AlignmentStats &operator=(const AlignmentStats &rhs); | ^~~~~~~~ /usr/include/pbseq/alignment/datastructures/alignment/Alignment.hpp:209:7: note: synthesized method ‘blasr::Alignment::Alignment(const blasr::Alignment&)’ first required here 209 | class CompSeqAlignment : public Alignment | ^~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/c++/13/bits/c++allocator.h:33, from /usr/include/c++/13/bits/allocator.h:46, from /usr/include/c++/13/bits/stl_tree.h:64, from /usr/include/c++/13/map:62, from ../utils/LoadPulses.cpp:6: /usr/include/c++/13/bits/new_allocator.h:187:11: note: synthesized method ‘blasr::CompSeqAlignment::CompSeqAlignment(const blasr::CompSeqAlignment&)’ first required here 187 | { ::new((void *)__p) _Up(std::forward<_Args>(__args)...); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [20/25] rm -f libblasr_impl.a && gcc-ar csrDT libblasr_impl.a libblasr_impl.a.p/extrautils_SuffixArrayToBWT.cpp.o libblasr_impl.a.p/extrautils_BwtToSuffixArray.cpp.o libblasr_impl.a.p/extrautils_SWMatcher.cpp.o libblasr_impl.a.p/extrautils_SAModify.cpp.o libblasr_impl.a.p/extrautils_ExciseRepeats.cpp.o libblasr_impl.a.p/extrautils_StoreQualityByContextFromCmpH5.cpp.o libblasr_impl.a.p/extrautils_SALS.cpp.o libblasr_impl.a.p/extrautils_SimpleShredder.cpp.o libblasr_impl.a.p/extrautils_Evolve.cpp.o libblasr_impl.a.p/extrautils_BuildSequenceDB.cpp.o libblasr_impl.a.p/extrautils_PrintTupleCountTable.cpp.o libblasr_impl.a.p/utils_SamToM4.cpp.o libblasr_impl.a.p/utils_SamToCmpH5.cpp.o libblasr_impl.a.p/utils_SDPMatcher.cpp.o libblasr_impl.a.p/utils_LoadPulses.cpp.o libblasr_impl.a.p/utils_PulseToFasta.cpp.o libblasr_impl.a.p/utils_SamFilter.cpp.o [21/25] c++ -ItoAfg.p -I. -I.. -I/usr/include/libblasr -I/usr/include/hdf5/serial -I/usr/include/pbseq -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -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/blasr-5.3.5+dfsg-6build1 -DHAVE_HDF5_1_10_1 -isystem /usr/include/hdf5/serial -DBOOST_ALL_NO_LIB -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -DCMAKE_BUILD=1 -MD -MQ toAfg.p/utils_ToAfg.cpp.o -MF toAfg.p/utils_ToAfg.cpp.o.d -o toAfg.p/utils_ToAfg.cpp.o -c ../utils/ToAfg.cpp In file included from /usr/include/pbseq/hdf/DatasetCollection.hpp:9, from /usr/include/pbseq/hdf/HDFBasReader.hpp:11, from /usr/include/pbseq/alignment/files/ReaderAgglomerate.hpp:8, from ../utils/ToAfg.cpp:6: /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:123:1: required from here /usr/include/pbseq/hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ In file included from /usr/include/pbseq/hdf/HDF2DArray.hpp:4, from /usr/include/pbseq/hdf/HDFBasReader.hpp:12: /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = int; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:124:1: required from here /usr/include/pbseq/hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = unsigned int; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:125:1: required from here /usr/include/pbseq/hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = unsigned char; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:126:1: required from here /usr/include/pbseq/hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = short unsigned int; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:127:1: required from here /usr/include/pbseq/hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = short int; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:128:1: required from here /usr/include/pbseq/hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = float; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:137:1: required from here /usr/include/pbseq/hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = char; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ [22/25] c++ -o sawriter sawriter.p/utils_SAWriter.cpp.o -L/usr/lib/x86_64-linux-gnu -L/usr/lib/x86_64-linux-gnu/hdf5/serial -I/usr/include/pbseq -Wl,--as-needed -Wl,--no-undefined -Wl,--start-group -lhdf5_cpp -lhdf5 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -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/blasr-5.3.5+dfsg-6build1 -DHAVE_HDF5_1_10_1 -isystem /usr/include/hdf5/serial libblasr_impl.a -pthread -lpbbam /usr/lib/x86_64-linux-gnu/libblasr.so /usr/lib/x86_64-linux-gnu/libpbbam.so /usr/lib/x86_64-linux-gnu/libpbcopper.so -lpbcopper /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libhts.so -lpbbam -lpbcopper -Wl,--end-group [23/25] c++ -o toAfg toAfg.p/utils_ToAfg.cpp.o -L/usr/lib/x86_64-linux-gnu -L/usr/lib/x86_64-linux-gnu/hdf5/serial -I/usr/include/pbseq -Wl,--as-needed -Wl,--no-undefined -Wl,--start-group -lhdf5_cpp -lhdf5 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -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/blasr-5.3.5+dfsg-6build1 -DHAVE_HDF5_1_10_1 -isystem /usr/include/hdf5/serial libblasr_impl.a -pthread -lpbbam /usr/lib/x86_64-linux-gnu/libblasr.so /usr/lib/x86_64-linux-gnu/libpbbam.so /usr/lib/x86_64-linux-gnu/libpbcopper.so -lpbcopper /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libhts.so -lpbbam -lpbcopper -Wl,--end-group [24/25] c++ -Iblasr.p -I. -I.. -I/usr/include/libblasr -I/usr/include/hdf5/serial -I/usr/include/pbseq -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -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/blasr-5.3.5+dfsg-6build1 -DHAVE_HDF5_1_10_1 -isystem /usr/include/hdf5/serial -DBOOST_ALL_NO_LIB -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -DCMAKE_BUILD=1 -MD -MQ blasr.p/Blasr.cpp.o -MF blasr.p/Blasr.cpp.o.d -o blasr.p/Blasr.cpp.o -c ../Blasr.cpp In file included from /usr/include/pbseq/hdf/DatasetCollection.hpp:9, from /usr/include/pbseq/hdf/HDFBasReader.hpp:11, from /usr/include/pbseq/alignment/files/ReaderAgglomerate.hpp:8, from ../iblasr/BlasrHeaders.h:59, from ../iblasr/BlasrAlign.hpp:4, from ../Blasr.cpp:3: /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:123:1: required from here /usr/include/pbseq/hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ In file included from /usr/include/pbseq/hdf/HDF2DArray.hpp:4, from /usr/include/pbseq/hdf/HDFBasReader.hpp:12: /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = int; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:124:1: required from here /usr/include/pbseq/hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = unsigned int; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:125:1: required from here /usr/include/pbseq/hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = unsigned char; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:126:1: required from here /usr/include/pbseq/hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = short unsigned int; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:127:1: required from here /usr/include/pbseq/hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = short int; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:128:1: required from here /usr/include/pbseq/hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = float; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp: In instantiation of ‘class BufferedHDF2DArray’: /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:137:1: required from here /usr/include/pbseq/hdf/HDFData.hpp:44:17: warning: ‘virtual int HDFData::Initialize(HDFGroup&, const std::string&)’ was hidden [-Woverloaded-virtual=] 44 | virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName); | ^~~~~~~~~~ /usr/include/pbseq/hdf/BufferedHDF2DArray.hpp:75:9: note: by ‘int BufferedHDF2DArray::Initialize(HDFGroup&, std::string, DSLength, int, bool) [with T = char; std::string = std::__cxx11::basic_string; DSLength = long unsigned int]’ 75 | int Initialize(HDFGroup &group, std::string datasetName, DSLength _rowLength = 0, | ^~~~~~~~~~ In file included from ../iblasr/BlasrMiscs.hpp:56, from ../iblasr/BlasrAlign.hpp:5: ../iblasr/BlasrMiscsImpl.hpp: In function ‘void MakeSubreadIntervals(std::vector&, std::vector&)’: ../iblasr/BlasrMiscsImpl.hpp:136:25: warning: implicitly-declared ‘SMRTSequence::SMRTSequence(const SMRTSequence&)’ is deprecated [-Wdeprecated-copy] 136 | for (auto subread : subreads) { | ^~~~~~~~ In file included from /usr/include/pbseq/pbdata/CCSSequence.hpp:5, from /usr/include/pbseq/alignment/files/CCSIterator.hpp:4, from ../iblasr/BlasrHeaders.h:57: /usr/include/pbseq/pbdata/SMRTSequence.hpp:171:19: note: because ‘SMRTSequence’ has user-provided ‘SMRTSequence& SMRTSequence::operator=(const SMRTSequence&)’ 171 | SMRTSequence &operator=(const SMRTSequence &rhs); | ^~~~~~~~ In file included from ../iblasr/MappingIPC.h:5, from ../iblasr/BlasrHeaders.h:99: ../iblasr/MappingParameters.h: In copy constructor ‘MappingParameters::MappingParameters(const MappingParameters&)’: ../iblasr/MappingParameters.h:19:7: warning: implicitly-declared ‘constexpr AnchorParameters::AnchorParameters(const AnchorParameters&)’ is deprecated [-Wdeprecated-copy] 19 | class MappingParameters | ^~~~~~~~~~~~~~~~~ In file included from /usr/include/pbseq/alignment/algorithms/anchoring/BWTSearch.hpp:7, from ../iblasr/BlasrHeaders.h:42: /usr/include/pbseq/alignment/datastructures/anchoring/AnchorParameters.hpp:33:23: note: because ‘AnchorParameters’ has user-provided ‘AnchorParameters& AnchorParameters::operator=(const AnchorParameters&)’ 33 | AnchorParameters &operator=(const AnchorParameters &rhs); | ^~~~~~~~ ../Blasr.cpp: In function ‘void MapReadsNonCCS(MappingData >, FASTASequence, DNATuple>*, MappingBuffers&, SMRTSequence&, SMRTSequence&, std::vector&, MappingParameters&, const int&, ReadAlignments&, std::ofstream&)’: ../Blasr.cpp:382:49: note: synthesized method ‘MappingParameters::MappingParameters(const MappingParameters&)’ first required here 382 | MappingParameters sensitiveParams = params; | ^~~~~~ ../Blasr.cpp: In function ‘int main(int, char**)’: ../Blasr.cpp:1407:32: warning: cast between incompatible function types from ‘void (*)(MappingData >, FASTASequence, DNATuple>*)’ to ‘void* (*)(void*)’ [-Wcast-function-type] 1407 | (void *(*)(void *))MapReads, &mapdb[procIndex]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/pbseq/alignment/format/BAMPrinter.hpp:29, from ../iblasr/BlasrHeaders.h:60: /usr/include/pbseq/alignment/format/BAMPrinterImpl.hpp: In instantiation of ‘void AlignmentToBamRecord(T_AlignmentCandidate&, T_Sequence&, T_Sequence&, PacBio::BAM::BamRecord&, AlignmentContext&, SupplementalQVList&, SAMOutput::Clipping, bool, bool) [with T_Sequence = SMRTSequence; T_AlignmentCandidate = AlignmentCandidate]’: /usr/include/pbseq/alignment/format/BAMPrinterImpl.hpp:170:25: required from ‘void BAMOutput::PrintAlignment(T_AlignmentCandidate&, T_Sequence&, T_Sequence&, PacBio::BAM::IRecordWriter&, AlignmentContext&, SupplementalQVList&, SAMOutput::Clipping, bool, bool) [with T_Sequence = SMRTSequence; T_AlignmentCandidate = AlignmentCandidate]’ ../iblasr/BlasrUtilsImpl.hpp:951:38: required from here /usr/include/pbseq/alignment/format/BAMPrinterImpl.hpp:30:45: warning: the compiler can assume that the address of ‘read’ will never be NULL [-Waddress] 30 | if (dynamic_cast(&read) == NULL) { | ^ /usr/include/pbseq/alignment/format/BAMPrinterImpl.hpp:19:72: note: ‘read’ declared here 19 | void AlignmentToBamRecord(T_AlignmentCandidate &alignment, T_Sequence &read, T_Sequence &subread, | ~~~~~~~~~~~~^~~~ In file included from /usr/include/pbseq/alignment/algorithms/alignment/AlignmentUtils.hpp:7, from /usr/include/pbseq/alignment/algorithms/alignment/GuidedAlign.hpp:11, from /usr/include/pbseq/alignment/algorithms/alignment/AffineGuidedAlign.hpp:4, from ../iblasr/BlasrHeaders.h:30: /usr/include/pbseq/alignment/datastructures/alignment/Alignment.hpp: In instantiation of ‘void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = blasr::CompSeqAlignment; _Args = {const blasr::CompSeqAlignment&}; _Tp = blasr::CompSeqAlignment]’: /usr/include/c++/13/bits/alloc_traits.h:537:17: required from ‘static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = blasr::CompSeqAlignment; _Args = {const blasr::CompSeqAlignment&}; _Tp = blasr::CompSeqAlignment; allocator_type = std::allocator]’ /usr/include/c++/13/bits/stl_vector.h:1283:30: required from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = blasr::CompSeqAlignment; _Alloc = std::allocator; value_type = blasr::CompSeqAlignment]’ /usr/include/pbseq/alignment/algorithms/alignment/AlignmentUtilsImpl.hpp:112:29: required from here /usr/include/pbseq/alignment/datastructures/alignment/Alignment.hpp:209:7: warning: implicitly-declared ‘blasr::Alignment::Alignment(const blasr::Alignment&)’ is deprecated [-Wdeprecated-copy] 209 | class CompSeqAlignment : public Alignment | ^~~~~~~~~~~~~~~~ /usr/include/pbseq/alignment/datastructures/alignment/Alignment.hpp:103:16: note: because ‘blasr::Alignment’ has user-provided ‘blasr::Alignment& blasr::Alignment::operator=(const blasr::Alignment&)’ 103 | Alignment &operator=(const Alignment &rhs); | ^~~~~~~~ /usr/include/pbseq/alignment/datastructures/alignment/Alignment.hpp:58:7: warning: implicitly-declared ‘constexpr blasr::AlignmentStats::AlignmentStats(const blasr::AlignmentStats&)’ is deprecated [-Wdeprecated-copy] 58 | class Alignment : public AlignmentStats | ^~~~~~~~~ In file included from /usr/include/pbseq/alignment/datastructures/alignment/Alignment.hpp:8: /usr/include/pbseq/alignment/datastructures/alignment/AlignmentStats.hpp:19:21: note: because ‘blasr::AlignmentStats’ has user-provided ‘blasr::AlignmentStats& blasr::AlignmentStats::operator=(const blasr::AlignmentStats&)’ 19 | AlignmentStats &operator=(const AlignmentStats &rhs); | ^~~~~~~~ /usr/include/pbseq/alignment/datastructures/alignment/Alignment.hpp:209:7: note: synthesized method ‘blasr::Alignment::Alignment(const blasr::Alignment&)’ first required here 209 | class CompSeqAlignment : public Alignment | ^~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/c++/13/bits/c++allocator.h:33, from /usr/include/c++/13/bits/allocator.h:46, from /usr/include/c++/13/string:43, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /usr/include/c++/13/iostream:41, from ../iblasr/BlasrHeaders.h:10: /usr/include/c++/13/bits/new_allocator.h:187:11: note: synthesized method ‘blasr::CompSeqAlignment::CompSeqAlignment(const blasr::CompSeqAlignment&)’ first required here 187 | { ::new((void *)__p) _Up(std::forward<_Args>(__args)...); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/cassert:44, from /usr/include/pbseq/alignment/algorithms/alignment/sdp/SparseDynamicProgrammingImpl.hpp:5, from /usr/include/pbseq/alignment/algorithms/alignment/sdp/SparseDynamicProgramming.hpp:35, from /usr/include/pbseq/alignment/algorithms/alignment/SDPAlignImpl.hpp:18, from /usr/include/pbseq/alignment/algorithms/alignment/SDPAlign.hpp:44, from /usr/include/pbseq/alignment/algorithms/alignment/GuidedAlign.hpp:13: /usr/include/pbseq/alignment/algorithms/alignment/GuidedAlign.hpp: In instantiation of ‘int GuidedAlign(QSequence&, TSequence&, blasr::Alignment&, T_ScoreFn&, int, blasr::Alignment&, std::vector&, std::vector&, std::vector&, std::vector&, std::vector&, std::vector&, std::vector&, std::vector&, AlignmentType, bool) [with QSequence = SMRTSequence; TSequence = DNASequence; T_ScoreFn = IDSScoreFunction]’: /usr/include/pbseq/alignment/algorithms/alignment/GuidedAlign.hpp:526:23: required from ‘int GuidedAlign(QSequence&, TSequence&, blasr::Alignment&, T_ScoreFn&, int, T_BufferCache&, blasr::Alignment&, AlignmentType, bool) [with QSequence = SMRTSequence; TSequence = DNASequence; T_ScoreFn = IDSScoreFunction; T_BufferCache = MappingBuffers]’ /usr/include/pbseq/alignment/algorithms/alignment/GuidedAlign.hpp:512:23: required from ‘int GuidedAlign(QSequence&, TSequence&, T_ScoreFn&, int, int, int, float, T_BufferCache&, blasr::Alignment&, AlignmentType, bool, int) [with QSequence = SMRTSequence; TSequence = DNASequence; T_ScoreFn = IDSScoreFunction; T_BufferCache = MappingBuffers]’ ../iblasr/BlasrAlignImpl.hpp:1449:20: required from here /usr/include/pbseq/alignment/algorithms/alignment/GuidedAlign.hpp:97:24: warning: comparison of unsigned expression in ‘>= 0’ is always true [-Wtype-limits] 97 | assert(matrixNElem >= 0); | ~~~~~~~~~~~~^~~~ In file included from /usr/include/c++/13/cassert:44, from /usr/include/pbseq/alignment/statistics/StatUtils.hpp:5, from /usr/include/pbseq/alignment/algorithms/alignment/KBandAlign.hpp:12, from /usr/include/pbseq/alignment/algorithms/alignment/AffineKBandAlign.hpp:9, from ../iblasr/BlasrHeaders.h:31: /usr/include/pbseq/alignment/algorithms/alignment/KBandAlign.hpp: In instantiation of ‘int KBandAlign(T_QuerySequence&, T_TargetSequence&, int (*)[5], int, int, DNALength, std::vector&, std::vector&, T_Alignment&, AlignmentType, T_ScoreFn&, bool) [with T_QuerySequence = SMRTSequence; T_TargetSequence = DNASequence; T_Alignment = AlignmentCandidate; T_ScoreFn = IDSScoreFunction; DNALength = unsigned int]’: /usr/include/pbseq/alignment/algorithms/alignment/KBandAlign.hpp:30:22: required from ‘int KBandAlign(T_QuerySequence&, T_TargetSequence&, int (*)[5], int, int, DNALength, std::vector&, std::vector&, T_Alignment&, T_ScoreFn&, AlignmentType, bool) [with T_QuerySequence = SMRTSequence; T_TargetSequence = DNASequence; T_Alignment = AlignmentCandidate; T_ScoreFn = IDSScoreFunction; DNALength = unsigned int]’ ../iblasr/BlasrUtilsImpl.hpp:639:19: required from ‘void RefineAlignment(std::vector&, T_RefSequence&, T_AlignmentCandidate&, MappingParameters&, MappingBuffers&) [with T_RefSequence = DNASequence; T_Sequence = SMRTSequence; T_AlignmentCandidate = AlignmentCandidate]’ ../iblasr/BlasrAlignImpl.hpp:1555:32: required from here /usr/include/pbseq/alignment/algorithms/alignment/KBandAlign.hpp:151:26: warning: comparison of unsigned expression in ‘>= 0’ is always true [-Wtype-limits] 151 | assert(t - 1 >= 0); | ~~~~~~^~~~ /usr/include/pbseq/alignment/algorithms/alignment/KBandAlign.hpp:152:26: warning: comparison of unsigned expression in ‘>= 0’ is always true [-Wtype-limits] 152 | assert(q - 1 >= 0); | ~~~~~~^~~~ /usr/include/pbseq/alignment/algorithms/alignment/GuidedAlign.hpp: In instantiation of ‘int GuidedAlign(QSequence&, TSequence&, blasr::Alignment&, T_ScoreFn&, int, blasr::Alignment&, std::vector&, std::vector&, std::vector&, std::vector&, std::vector&, std::vector&, std::vector&, std::vector&, AlignmentType, bool) [with QSequence = FASTQSequence; TSequence = DNASequence; T_ScoreFn = IDSScoreFunction]’: /usr/include/pbseq/alignment/algorithms/alignment/GuidedAlign.hpp:526:23: required from ‘int GuidedAlign(QSequence&, TSequence&, blasr::Alignment&, T_ScoreFn&, int, T_BufferCache&, blasr::Alignment&, AlignmentType, bool) [with QSequence = FASTQSequence; TSequence = DNASequence; T_ScoreFn = IDSScoreFunction; T_BufferCache = MappingBuffers]’ ../iblasr/BlasrUtilsImpl.hpp:689:32: required from ‘void RefineAlignment(std::vector&, T_RefSequence&, T_AlignmentCandidate&, MappingParameters&, MappingBuffers&) [with T_RefSequence = DNASequence; T_Sequence = SMRTSequence; T_AlignmentCandidate = AlignmentCandidate]’ ../iblasr/BlasrAlignImpl.hpp:1555:32: required from here /usr/include/pbseq/alignment/algorithms/alignment/GuidedAlign.hpp:97:24: warning: comparison of unsigned expression in ‘>= 0’ is always true [-Wtype-limits] 97 | assert(matrixNElem >= 0); | ~~~~~~~~~~~~^~~~ /usr/include/pbseq/alignment/algorithms/alignment/GuidedAlign.hpp: In instantiation of ‘int GuidedAlign(QSequence&, TSequence&, blasr::Alignment&, T_ScoreFn&, int, blasr::Alignment&, std::vector&, std::vector&, std::vector&, std::vector&, std::vector&, std::vector&, std::vector&, std::vector&, AlignmentType, bool) [with QSequence = FASTQSequence; TSequence = DNASequence; T_ScoreFn = DistanceMatrixScoreFunction]’: /usr/include/pbseq/alignment/algorithms/alignment/GuidedAlign.hpp:526:23: required from ‘int GuidedAlign(QSequence&, TSequence&, blasr::Alignment&, T_ScoreFn&, int, T_BufferCache&, blasr::Alignment&, AlignmentType, bool) [with QSequence = FASTQSequence; TSequence = DNASequence; T_ScoreFn = DistanceMatrixScoreFunction; T_BufferCache = MappingBuffers]’ ../iblasr/BlasrUtilsImpl.hpp:698:32: required from ‘void RefineAlignment(std::vector&, T_RefSequence&, T_AlignmentCandidate&, MappingParameters&, MappingBuffers&) [with T_RefSequence = DNASequence; T_Sequence = SMRTSequence; T_AlignmentCandidate = AlignmentCandidate]’ ../iblasr/BlasrAlignImpl.hpp:1555:32: required from here /usr/include/pbseq/alignment/algorithms/alignment/GuidedAlign.hpp:97:24: warning: comparison of unsigned expression in ‘>= 0’ is always true [-Wtype-limits] /usr/include/pbseq/alignment/algorithms/alignment/OneGapAlignment.hpp: In instantiation of ‘int OneGapAlign(T_QuerySequence&, T_RefSequence&, T_ScoreFunction&, T_BufferList&, blasr::Alignment&) [with T_QuerySequence = FASTQSequence; T_RefSequence = DNASequence; T_ScoreFunction = DistanceMatrixScoreFunction; T_BufferList = MappingBuffers]’: ../iblasr/BlasrAlignImpl.hpp:918:40: required from ‘void AlignIntervals(T_TargetSequence&, T_QuerySequence&, T_QuerySequence&, WeightedIntervalSet&, int (*)[5], int, int, int, int, SequenceIndexDatabase&, std::vector*>&, MappingParameters&, MappingBuffers&, int) [with T_TargetSequence = FASTASequence; T_QuerySequence = SMRTSequence; TDBSequence = FASTQSequence]’ ../iblasr/BlasrAlignImpl.hpp:280:23: required from ‘void MapRead(T_Sequence&, T_Sequence&, T_RefSequence&, T_SuffixArray&, BWT&, SeqBoundaryFtr&, T_TupleCountTable&, SequenceIndexDatabase&, MappingParameters&, MappingMetrics&, std::vector*>&, MappingBuffers&, MappingIPC*, MappingSemaphores&) [with T_Sequence = SMRTSequence; T_RefSequence = FASTASequence; T_SuffixArray = SuffixArray >; T_TupleCountTable = TupleCountTable; BWT = Bwt; MappingIPC = MappingData >, FASTASequence, DNATuple>]’ ../Blasr.cpp:347:16: required from here /usr/include/pbseq/alignment/algorithms/alignment/OneGapAlignment.hpp:337:40: warning: comparison of unsigned expression in ‘>= 0’ is always true [-Wtype-limits] 337 | assert(distanceBetweenLeftAndRight >= 0); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /usr/include/pbseq/alignment/algorithms/alignment/KBandAlign.hpp: In instantiation of ‘int KBandAlign(T_QuerySequence&, T_TargetSequence&, int (*)[5], int, int, DNALength, std::vector&, std::vector&, T_Alignment&, AlignmentType, T_ScoreFn&, bool) [with T_QuerySequence = FASTQSequence; T_TargetSequence = DNASequence; T_Alignment = AlignmentCandidate; T_ScoreFn = IDSScoreFunction; DNALength = unsigned int]’: /usr/include/pbseq/alignment/algorithms/alignment/KBandAlign.hpp:30:22: required from ‘int KBandAlign(T_QuerySequence&, T_TargetSequence&, int (*)[5], int, int, DNALength, std::vector&, std::vector&, T_Alignment&, T_ScoreFn&, AlignmentType, bool) [with T_QuerySequence = FASTQSequence; T_TargetSequence = DNASequence; T_Alignment = AlignmentCandidate; T_ScoreFn = IDSScoreFunction; DNALength = unsigned int]’ ../iblasr/BlasrAlignImpl.hpp:1301:38: required from ‘void PairwiseLocalAlign(T_Sequence&, T_RefSequence&, int, MappingParameters&, T_AlignmentCandidate&, MappingBuffers&, AlignmentType) [with T_RefSequence = DNASequence; T_Sequence = FASTQSequence; T_AlignmentCandidate = AlignmentCandidate]’ ../iblasr/BlasrUtilsImpl.hpp:873:27: required from ‘void RefineAlignment(std::vector&, T_RefSequence&, T_AlignmentCandidate&, MappingParameters&, MappingBuffers&) [with T_RefSequence = DNASequence; T_Sequence = SMRTSequence; T_AlignmentCandidate = AlignmentCandidate]’ ../iblasr/BlasrAlignImpl.hpp:1555:32: required from here /usr/include/pbseq/alignment/algorithms/alignment/KBandAlign.hpp:151:26: warning: comparison of unsigned expression in ‘>= 0’ is always true [-Wtype-limits] 151 | assert(t - 1 >= 0); | ~~~~~~^~~~ /usr/include/pbseq/alignment/algorithms/alignment/KBandAlign.hpp:152:26: warning: comparison of unsigned expression in ‘>= 0’ is always true [-Wtype-limits] 152 | assert(q - 1 >= 0); | ~~~~~~^~~~ /usr/include/pbseq/alignment/algorithms/alignment/KBandAlign.hpp: In instantiation of ‘int KBandAlign(T_QuerySequence&, T_TargetSequence&, int (*)[5], int, int, DNALength, std::vector&, std::vector&, T_Alignment&, AlignmentType, T_ScoreFn&, bool) [with T_QuerySequence = FASTQSequence; T_TargetSequence = DNASequence; T_Alignment = AlignmentCandidate; T_ScoreFn = QualityValueScoreFunction; DNALength = unsigned int]’: /usr/include/pbseq/alignment/algorithms/alignment/KBandAlign.hpp:30:22: required from ‘int KBandAlign(T_QuerySequence&, T_TargetSequence&, int (*)[5], int, int, DNALength, std::vector&, std::vector&, T_Alignment&, T_ScoreFn&, AlignmentType, bool) [with T_QuerySequence = FASTQSequence; T_TargetSequence = DNASequence; T_Alignment = AlignmentCandidate; T_ScoreFn = QualityValueScoreFunction; DNALength = unsigned int]’ ../iblasr/BlasrAlignImpl.hpp:1310:38: required from ‘void PairwiseLocalAlign(T_Sequence&, T_RefSequence&, int, MappingParameters&, T_AlignmentCandidate&, MappingBuffers&, AlignmentType) [with T_RefSequence = DNASequence; T_Sequence = FASTQSequence; T_AlignmentCandidate = AlignmentCandidate]’ ../iblasr/BlasrUtilsImpl.hpp:873:27: required from ‘void RefineAlignment(std::vector&, T_RefSequence&, T_AlignmentCandidate&, MappingParameters&, MappingBuffers&) [with T_RefSequence = DNASequence; T_Sequence = SMRTSequence; T_AlignmentCandidate = AlignmentCandidate]’ ../iblasr/BlasrAlignImpl.hpp:1555:32: required from here /usr/include/pbseq/alignment/algorithms/alignment/KBandAlign.hpp:151:26: warning: comparison of unsigned expression in ‘>= 0’ is always true [-Wtype-limits] 151 | assert(t - 1 >= 0); | ~~~~~~^~~~ /usr/include/pbseq/alignment/algorithms/alignment/KBandAlign.hpp:152:26: warning: comparison of unsigned expression in ‘>= 0’ is always true [-Wtype-limits] 152 | assert(q - 1 >= 0); | ~~~~~~^~~~ /usr/include/pbseq/alignment/format/BAMPrinterImpl.hpp: In function ‘AlignmentToBamRecord(AlignmentCandidate&, SMRTSequence&, SMRTSequence&, PacBio::BAM::BamRecord&, AlignmentContext&, SupplementalQVList&, SAMOutput::Clipping, bool, bool)void’: /usr/include/pbseq/alignment/format/BAMPrinterImpl.hpp:30:5: warning: ‘nonnull’ argument ‘read’ compared to NULL [-Wnonnull-compare] 30 | if (dynamic_cast(&read) == NULL) { | ^~ [25/25] c++ -o blasr blasr.p/Blasr.cpp.o -L/usr/lib/x86_64-linux-gnu -L/usr/lib/x86_64-linux-gnu/hdf5/serial -I/usr/include/pbseq -Wl,--as-needed -Wl,--no-undefined -Wl,--start-group -lhdf5_cpp -lhdf5 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -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/blasr-5.3.5+dfsg-6build1 -DHAVE_HDF5_1_10_1 -isystem /usr/include/hdf5/serial libblasr_impl.a -pthread -lpbbam /usr/lib/x86_64-linux-gnu/libblasr.so /usr/lib/x86_64-linux-gnu/libpbbam.so /usr/lib/x86_64-linux-gnu/libpbcopper.so -lpbcopper /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libhts.so -lpbbam -lpbcopper -Wl,--end-group debian/rules override_dh_auto_test make[1]: Entering directory '/<>' echo Tests require data not available in the source distribution Tests require data not available in the source distribution make[1]: Leaving directory '/<>' create-stamp debian/debhelper-build-stamp dh_testroot -O--buildsystem=meson dh_prep -O--buildsystem=meson dh_auto_install --destdir=debian/blasr/ -O--buildsystem=meson cd obj-x86_64-linux-gnu && DESTDIR=/<>/blasr-5.3.5\+dfsg/debian/blasr LC_ALL=C.UTF-8 ninja install [1/4] Generating BlasrGitHash.h with a custom command [1/2] Installing files. Installing blasr to /<>/debian/blasr/usr/bin Installing sawriter to /<>/debian/blasr/usr/bin dh_install -O--buildsystem=meson dh_installdocs -O--buildsystem=meson dh_installchangelogs -O--buildsystem=meson dh_installexamples -O--buildsystem=meson dh_installman -O--buildsystem=meson dh_installsystemduser -O--buildsystem=meson dh_lintian -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/blasr/usr/bin/blasr: Unknown DWARF DW_FORM_0x1f20 7189c9a1431aa072df2cf4bafbfb01240972b2ec debugedit: debian/blasr/usr/bin/sawriter: Unknown DWARF DW_FORM_0x1f20 6d2bb67231f6beae82b36e92aa5600bcc0cb2dca 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 153 INFO: pkgstriptranslations version 153 pkgstriptranslations: processing blasr (in debian/blasr); do_strip: , oemstrip: pkgstriptranslations: processing blasr-dbgsym (in debian/.debhelper/blasr/dbgsym-root); do_strip: , oemstrip: pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/blasr/DEBIAN/control, package blasr, directory debian/blasr pkgstripfiles: Running PNG optimization (using 4 cpus) for package blasr ... pkgstripfiles: No PNG files. dpkg-deb: building package 'blasr' in '../blasr_5.3.5+dfsg-6build1_amd64.deb'. pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/.debhelper/blasr/dbgsym-root/DEBIAN/control, package blasr-dbgsym, directory debian/.debhelper/blasr/dbgsym-root dpkg-deb: building package 'blasr-dbgsym' in 'debian/.debhelper/scratch-space/build-blasr/blasr-dbgsym_5.3.5+dfsg-6build1_amd64.deb'. Renaming blasr-dbgsym_5.3.5+dfsg-6build1_amd64.deb to blasr-dbgsym_5.3.5+dfsg-6build1_amd64.ddeb dpkg-genbuildinfo --build=binary -O../blasr_5.3.5+dfsg-6build1_amd64.buildinfo dpkg-genchanges --build=binary -mLaunchpad Build Daemon -O../blasr_5.3.5+dfsg-6build1_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 2023-09-03T16:15:17Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ blasr_5.3.5+dfsg-6build1_amd64.changes: --------------------------------------- Format: 1.8 Date: Sun, 03 Sep 2023 10:36:47 -0400 Source: blasr Binary: blasr Built-For-Profiles: noudeb Architecture: amd64 Version: 5.3.5+dfsg-6build1 Distribution: mantic-proposed Urgency: medium Maintainer: Launchpad Build Daemon Changed-By: Jeremy Bícha Description: blasr - mapping single-molecule sequencing reads Changes: blasr (5.3.5+dfsg-6build1) mantic; urgency=medium . * Rebuild against latest pbbam & pbcopper Checksums-Sha1: d51ede5254cc7600879ed332099a8be60314aa5b 2775546 blasr-dbgsym_5.3.5+dfsg-6build1_amd64.ddeb 99398f32bc0189e9e70824e48a88c0da259dc19c 8593 blasr_5.3.5+dfsg-6build1_amd64.buildinfo 04f2d5a6c0a32cedc1c67791df5d95abc3f193f1 232786 blasr_5.3.5+dfsg-6build1_amd64.deb Checksums-Sha256: 3ce732e5717b17bb5d1fe2eb9250bfeafab4b2f78ea2de7eb8d94b974949860d 2775546 blasr-dbgsym_5.3.5+dfsg-6build1_amd64.ddeb 3e72b3cac8a809ee0436f1dbc260d65bb8d3fadb737784d873059a9a54df7f2e 8593 blasr_5.3.5+dfsg-6build1_amd64.buildinfo 4ea193402696dcad337c7e5a534625e3d4ef5dbc9545039f91926d117672d12c 232786 blasr_5.3.5+dfsg-6build1_amd64.deb Files: 4c073d811a91707fb6b28e7e168580f4 2775546 debug optional blasr-dbgsym_5.3.5+dfsg-6build1_amd64.ddeb b0a1cba9df3b1ede3f65e9bea1dd5ea3 8593 science optional blasr_5.3.5+dfsg-6build1_amd64.buildinfo 33391c55917c28acee4cfbc573a95537 232786 science optional blasr_5.3.5+dfsg-6build1_amd64.deb /<>/blasr_5.3.5+dfsg-6build1_amd64.changes.new could not be renamed to /<>/blasr_5.3.5+dfsg-6build1_amd64.changes: Illegal seek Distribution field may be wrong!!! +------------------------------------------------------------------------------+ | Buildinfo | +------------------------------------------------------------------------------+ Format: 1.0 Source: blasr Binary: blasr blasr-dbgsym Architecture: amd64 Version: 5.3.5+dfsg-6build1 Checksums-Md5: 4c073d811a91707fb6b28e7e168580f4 2775546 blasr-dbgsym_5.3.5+dfsg-6build1_amd64.ddeb 33391c55917c28acee4cfbc573a95537 232786 blasr_5.3.5+dfsg-6build1_amd64.deb Checksums-Sha1: d51ede5254cc7600879ed332099a8be60314aa5b 2775546 blasr-dbgsym_5.3.5+dfsg-6build1_amd64.ddeb 04f2d5a6c0a32cedc1c67791df5d95abc3f193f1 232786 blasr_5.3.5+dfsg-6build1_amd64.deb Checksums-Sha256: 3ce732e5717b17bb5d1fe2eb9250bfeafab4b2f78ea2de7eb8d94b974949860d 2775546 blasr-dbgsym_5.3.5+dfsg-6build1_amd64.ddeb 4ea193402696dcad337c7e5a534625e3d4ef5dbc9545039f91926d117672d12c 232786 blasr_5.3.5+dfsg-6build1_amd64.deb Build-Origin: Ubuntu Build-Architecture: amd64 Build-Date: Sun, 03 Sep 2023 16:15:17 +0000 Build-Path: /<> Build-Tainted-By: merged-usr-via-aliased-dirs usr-local-has-programs Installed-Build-Depends: autoconf (= 2.71-3), automake (= 1:1.16.5-1.3), autopoint (= 0.21-13), autotools-dev (= 20220109.1), base-files (= 13ubuntu1), base-passwd (= 3.6.1), bash (= 5.2.15-2ubuntu1), binutils (= 2.41-4ubuntu1), binutils-common (= 2.41-4ubuntu1), binutils-x86-64-linux-gnu (= 2.41-4ubuntu1), bsdextrautils (= 2.39.1-4ubuntu1), bsdutils (= 1:2.39.1-4ubuntu1), build-essential (= 12.10ubuntu1), bzip2 (= 1.0.8-5build1), cmake (= 3.27.4-1), cmake-data (= 3.27.4-1), coreutils (= 9.1-1ubuntu2), cpp (= 4:13.2.0-1ubuntu1), cpp-12 (= 12.3.0-8ubuntu1), cpp-13 (= 13.2.0-3ubuntu1), dash (= 0.5.12-6ubuntu1), debconf (= 1.5.82), debhelper (= 13.11.6ubuntu1), debianutils (= 5.8-1), debugedit (= 1:5.0-5), dh-autoreconf (= 20), dh-strip-nondeterminism (= 1.13.1-1), diffutils (= 1:3.8-4), dpkg (= 1.22.0ubuntu1), dpkg-dev (= 1.22.0ubuntu1), dwz (= 0.15-1), file (= 1:5.44-3), findutils (= 4.9.0-5), g++ (= 4:13.2.0-1ubuntu1), g++-13 (= 13.2.0-3ubuntu1), gcc (= 4:13.2.0-1ubuntu1), gcc-12 (= 12.3.0-8ubuntu1), gcc-12-base (= 12.3.0-8ubuntu1), gcc-13 (= 13.2.0-3ubuntu1), gcc-13-base (= 13.2.0-3ubuntu1), gettext (= 0.21-13), gettext-base (= 0.21-13), googletest (= 1.13.0-5), grep (= 3.11-2), groff-base (= 1.23.0-2), gzip (= 1.12-1ubuntu1), hdf5-helpers (= 1.10.8+repack1-1ubuntu1), hostname (= 3.23+nmu1ubuntu1), init-system-helpers (= 1.65.2ubuntu1), intltool-debian (= 0.35.0+20060710.6), libacl1 (= 2.3.1-3), libaec-dev (= 1.0.6-1), libaec0 (= 1.0.6-1), libarchive-zip-perl (= 1.68-1), libarchive13 (= 3.6.2-1ubuntu1), libasan8 (= 13.2.0-3ubuntu1), libatomic1 (= 13.2.0-3ubuntu1), libattr1 (= 1:2.5.1-4), libaudit-common (= 1:3.1.1-1), libaudit1 (= 1:3.1.1-1), libbinutils (= 2.41-4ubuntu1), libblasr-dev (= 5.3.5+dfsg-6), libblasr5.3.5 (= 5.3.5+dfsg-6), libblkid1 (= 2.39.1-4ubuntu1), libboost-dev (= 1.74.0.3ubuntu7), libboost1.74-dev (= 1.74.0+ds1-22ubuntu1), libbrotli1 (= 1.0.9-2build8), libbz2-1.0 (= 1.0.8-5build1), libc-bin (= 2.38-1ubuntu4), libc-dev-bin (= 2.38-1ubuntu4), libc6 (= 2.38-1ubuntu4), libc6-dev (= 2.38-1ubuntu4), libcap-ng0 (= 0.8.3-1build2), libcap2 (= 1:2.66-4ubuntu1), libcc1-0 (= 13.2.0-3ubuntu1), libcom-err2 (= 1.47.0-2ubuntu1), libcrypt-dev (= 1:4.4.36-2), libcrypt1 (= 1:4.4.36-2), libctf-nobfd0 (= 2.41-4ubuntu1), libctf0 (= 2.41-4ubuntu1), libcurl3-gnutls (= 8.2.1-1ubuntu2), libcurl4 (= 8.2.1-1ubuntu2), libcurl4-gnutls-dev (= 8.2.1-1ubuntu2), libdb5.3 (= 5.3.28+dfsg2-2), libdebconfclient0 (= 0.270ubuntu1), libdebhelper-perl (= 13.11.6ubuntu1), libdeflate-dev (= 1.18-1), libdeflate0 (= 1.18-1), libdpkg-perl (= 1.22.0ubuntu1), libdw1 (= 0.189-4), libelf1 (= 0.189-4), libexpat1 (= 2.5.0-2), libffi8 (= 3.4.4-1), libfile-stripnondeterminism-perl (= 1.13.1-1), libgcc-12-dev (= 12.3.0-8ubuntu1), libgcc-13-dev (= 13.2.0-3ubuntu1), libgcc-s1 (= 13.2.0-3ubuntu1), libgcrypt20 (= 1.10.2-2ubuntu1), libgdbm-compat4 (= 1.23-3), libgdbm6 (= 1.23-3), libgfortran5 (= 13.2.0-3ubuntu1), libgmp10 (= 2:6.3.0+dfsg-2ubuntu4), libgnutls30 (= 3.8.1-4ubuntu1), libgomp1 (= 13.2.0-3ubuntu1), libgpg-error0 (= 1.47-2), libgprofng0 (= 2.41-4ubuntu1), libgssapi-krb5-2 (= 1.20.1-3ubuntu1), libgtest-dev (= 1.13.0-5), libhdf5-103-1 (= 1.10.8+repack1-1ubuntu1), libhdf5-cpp-103-1 (= 1.10.8+repack1-1ubuntu1), libhdf5-dev (= 1.10.8+repack1-1ubuntu1), libhdf5-fortran-102 (= 1.10.8+repack1-1ubuntu1), libhdf5-hl-100 (= 1.10.8+repack1-1ubuntu1), libhdf5-hl-cpp-100 (= 1.10.8+repack1-1ubuntu1), libhdf5-hl-fortran-100 (= 1.10.8+repack1-1ubuntu1), libhogweed6 (= 3.9.1-2), libhts-dev (= 1.17+ds-1), libhts3 (= 1.17+ds-1), libhtscodecs2 (= 1.5.1-1), libhwasan0 (= 13.2.0-3ubuntu1), libicu72 (= 72.1-3ubuntu2), libidn2-0 (= 2.3.4-1), libisl23 (= 0.26-3), libitm1 (= 13.2.0-3ubuntu1), libjansson4 (= 2.14-2), libjpeg-dev (= 8c-2ubuntu11), libjpeg-turbo8 (= 2.1.5-2ubuntu1), libjpeg-turbo8-dev (= 2.1.5-2ubuntu1), libjpeg8 (= 8c-2ubuntu11), libjpeg8-dev (= 8c-2ubuntu11), libjsoncpp25 (= 1.9.5-6), libk5crypto3 (= 1.20.1-3ubuntu1), libkeyutils1 (= 1.6.3-2), libkrb5-3 (= 1.20.1-3ubuntu1), libkrb5support0 (= 1.20.1-3ubuntu1), libldap2 (= 2.6.6+dfsg-1~exp1ubuntu1), liblsan0 (= 13.2.0-3ubuntu1), liblz4-1 (= 1.9.4-1), liblzma-dev (= 5.4.1-0.2), liblzma5 (= 5.4.1-0.2), libmagic-mgc (= 1:5.44-3), libmagic1 (= 1:5.44-3), libmd0 (= 1.1.0-1), libmount1 (= 2.39.1-4ubuntu1), libmpc3 (= 1.3.1-1), libmpfr6 (= 4.2.1-1), libncursesw6 (= 6.4+20230625-2), libnettle8 (= 3.9.1-2), libnghttp2-14 (= 1.55.1-1), libnsl-dev (= 1.3.0-2build2), libnsl2 (= 1.3.0-2build2), libp11-kit0 (= 0.25.0-4ubuntu1), libpam-modules (= 1.5.2-6ubuntu1), libpam-modules-bin (= 1.5.2-6ubuntu1), libpam-runtime (= 1.5.2-6ubuntu1), libpam0g (= 1.5.2-6ubuntu1), libpbbam-dev (= 2.3.0+dfsg-1), libpbbam2.3.0 (= 2.3.0+dfsg-1), libpbcopper-dev (= 2.2.0+dfsg-1), libpbcopper2.2.0 (= 2.2.0+dfsg-1), libpbdata-dev (= 5.3.5+dfsg-6), libpbihdf-dev (= 5.3.5+dfsg-6), libpbseq-dev (= 5.3.5+dfsg-6), libpcre2-8-0 (= 10.42-4), libperl5.36 (= 5.36.0-7ubuntu1), libpipeline1 (= 1.5.7-1), libpkgconf3 (= 1.8.1-2), libproc2-0 (= 2:4.0.3-1ubuntu1), libpsl5 (= 0.21.2-1), libpython3-stdlib (= 3.11.4-5), libpython3.11-minimal (= 3.11.5-3), libpython3.11-stdlib (= 3.11.5-3), libquadmath0 (= 13.2.0-3ubuntu1), libreadline8 (= 8.2-1.3), librhash0 (= 1.4.3-3), librtmp1 (= 2.4+20151223.gitfa8646d.1-2build4), libsasl2-2 (= 2.1.28+dfsg1-3), libsasl2-modules-db (= 2.1.28+dfsg1-3), libseccomp2 (= 2.5.4-1ubuntu3), libselinux1 (= 3.5-1), libsframe1 (= 2.41-4ubuntu1), libsmartcols1 (= 2.39.1-4ubuntu1), libsqlite3-0 (= 3.42.0-1), libssh-4 (= 0.10.5-3ubuntu1), libssl-dev (= 3.0.10-1ubuntu2), libssl3 (= 3.0.10-1ubuntu2), libstdc++-13-dev (= 13.2.0-3ubuntu1), libstdc++6 (= 13.2.0-3ubuntu1), libsub-override-perl (= 0.09-4), libsystemd0 (= 253.5-1ubuntu4), libsz2 (= 1.0.6-1), libtasn1-6 (= 4.19.0-3), libtinfo6 (= 6.4+20230625-2), libtirpc-common (= 1.3.3+ds-1), libtirpc-dev (= 1.3.3+ds-1), libtirpc3 (= 1.3.3+ds-1), libtool (= 2.4.7-7), libtsan2 (= 13.2.0-3ubuntu1), libubsan1 (= 13.2.0-3ubuntu1), libuchardet0 (= 0.0.7-1build2), libudev1 (= 253.5-1ubuntu4), libunistring2 (= 1.0-2), libuuid1 (= 2.39.1-4ubuntu1), libuv1 (= 1.44.2-1), libxml2 (= 2.9.14+dfsg-1.3), libzstd1 (= 1.5.5+dfsg2-1ubuntu2), linux-libc-dev (= 6.5.0-2.2), login (= 1:4.13+dfsg1-1ubuntu1), lto-disabled-list (= 42), m4 (= 1.4.19-3), make (= 4.3-4.1build1), man-db (= 2.11.2-3), mawk (= 1.3.4.20230730-1), media-types (= 10.1.0), meson (= 1.2.1-3), ncurses-base (= 6.4+20230625-2), ncurses-bin (= 6.4+20230625-2), ninja-build (= 1.11.1-1), patch (= 2.7.6-7build2), perl (= 5.36.0-7ubuntu1), perl-base (= 5.36.0-7ubuntu1), perl-modules-5.36 (= 5.36.0-7ubuntu1), pkg-config (= 1.8.1-2), pkgconf (= 1.8.1-2), pkgconf-bin (= 1.8.1-2), po-debconf (= 1.0.21+nmu1), procps (= 2:4.0.3-1ubuntu1), python3 (= 3.11.4-5), python3-distutils (= 3.11.5-1), python3-lib2to3 (= 3.11.5-1), python3-minimal (= 3.11.4-5), python3-pkg-resources (= 68.1.2-1), python3-setuptools (= 68.1.2-1), python3.11 (= 3.11.5-3), python3.11-minimal (= 3.11.5-3), readline-common (= 8.2-1.3), rpcsvc-proto (= 1.4.2-0ubuntu6), sed (= 4.9-1), sensible-utils (= 0.0.20), sysvinit-utils (= 3.07-1ubuntu1), tar (= 1.34+dfsg-1.2ubuntu1), tzdata (= 2023c-9ubuntu1), util-linux (= 2.39.1-4ubuntu1), xz-utils (= 5.4.1-0.2), zlib1g (= 1:1.2.13.dfsg-1ubuntu5), zlib1g-dev (= 1:1.2.13.dfsg-1ubuntu5) Environment: DEB_BUILD_OPTIONS="parallel=4" DEB_BUILD_PROFILES="noudeb" LANG="C.UTF-8" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1693751807" +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ blasr_5.3.5+dfsg-6build1_amd64.deb ---------------------------------- new Debian package, version 2.0. size 232786 bytes: control archive=1142 bytes. 895 bytes, 15 lines control 982 bytes, 15 lines md5sums Package: blasr Version: 5.3.5+dfsg-6build1 Architecture: amd64 Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 629 Depends: libblasr5.3.5 (>= 5.3.5+dfsg), libc6 (>= 2.38), libgcc-s1 (>= 3.3.1), libhdf5-cpp-103-1 (>= 1.10.5), libpbbam2.3.0 (>= 2.3.0+dfsg), libpbcopper2.2.0 (>= 2.2.0+dfsg), libstdc++6 (>= 13.1), libpbseq (>= 5.3.5+dfsg-4~) Section: science Priority: optional Homepage: https://github.com/PacificBiosciences/blasr Description: mapping single-molecule sequencing reads Basic local alignment with successive refinement (BLASR) is a method for mapping single-molecule sequencing reads against a reference genome. Such reads are thousands of bases long, with divergence between them and the genome being dominated by insertion and deletion error. drwxr-xr-x root/root 0 2023-09-03 14:36 ./ drwxr-xr-x root/root 0 2023-09-03 14:36 ./usr/ drwxr-xr-x root/root 0 2023-09-03 14:36 ./usr/bin/ -rwxr-xr-x root/root 567800 2023-09-03 14:36 ./usr/bin/blasr -rwxr-xr-x root/root 43488 2023-09-03 14:36 ./usr/bin/sawriter drwxr-xr-x root/root 0 2023-09-03 14:36 ./usr/share/ drwxr-xr-x root/root 0 2023-09-03 14:36 ./usr/share/doc/ drwxr-xr-x root/root 0 2023-09-03 14:36 ./usr/share/doc/blasr/ -rw-r--r-- root/root 373 2022-12-05 19:49 ./usr/share/doc/blasr/NEWS.Debian.gz -rw-r--r-- root/root 1291 2021-02-18 10:03 ./usr/share/doc/blasr/README.md -rw-r--r-- root/root 208 2022-12-05 19:49 ./usr/share/doc/blasr/README.source -rw-r--r-- root/root 542 2022-12-05 19:49 ./usr/share/doc/blasr/README.test -rw-r--r-- root/root 41 2022-12-05 19:49 ./usr/share/doc/blasr/TODO.Debian -rw-r--r-- root/root 1498 2023-09-03 14:36 ./usr/share/doc/blasr/changelog.Debian.gz -rw-r--r-- root/root 2196 2022-12-05 19:49 ./usr/share/doc/blasr/copyright drwxr-xr-x root/root 0 2023-09-03 14:36 ./usr/share/doc/blasr/examples/ -rw-r--r-- root/root 65 2022-12-05 19:49 ./usr/share/doc/blasr/examples/query.fasta -rw-r--r-- root/root 72 2022-12-05 19:49 ./usr/share/doc/blasr/examples/ref.fa -rw-r--r-- root/root 1067 2022-12-05 19:49 ./usr/share/doc/blasr/run-unit-test drwxr-xr-x root/root 0 2023-09-03 14:36 ./usr/share/lintian/ drwxr-xr-x root/root 0 2023-09-03 14:36 ./usr/share/lintian/overrides/ -rw-r--r-- root/root 163 2022-12-05 19:49 ./usr/share/lintian/overrides/blasr drwxr-xr-x root/root 0 2023-09-03 14:36 ./usr/share/man/ drwxr-xr-x root/root 0 2023-09-03 14:36 ./usr/share/man/man1/ -rw-r--r-- root/root 1369 2023-09-03 14:36 ./usr/share/man/man1/blasr.1.gz -rw-r--r-- root/root 872 2023-09-03 14:36 ./usr/share/man/man1/sawriter.1.gz +------------------------------------------------------------------------------+ | Post Build | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not removing build depends: as requested +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: amd64 Build Type: binary Build-Space: 112028 Build-Time: 57 Distribution: mantic-proposed Host Architecture: amd64 Install-Time: 12 Job: blasr_5.3.5+dfsg-6build1.dsc Machine Architecture: amd64 Package: blasr Package-Time: 71 Source-Version: 5.3.5+dfsg-6build1 Space: 112028 Status: successful Version: 5.3.5+dfsg-6build1 -------------------------------------------------------------------------------- Finished at 2023-09-03T16:15:17Z Build needed 00:01:11, 112028k disk space RUN: /usr/share/launchpad-buildd/bin/in-target scan-for-processes --backend=chroot --series=mantic --arch=amd64 PACKAGEBUILD-26678012 Scanning for processes to kill in build PACKAGEBUILD-26678012