https://launchpad.net/ubuntu/+source/freebayes/1.3.7-1/+build/26676744 RUN: /usr/share/launchpad-buildd/bin/builder-prep Kernel version: Linux bos01-arm64-009 5.4.0-156-generic #173-Ubuntu SMP Tue Jul 11 07:25:14 UTC 2023 aarch64 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... 2 Sep 14:54:52 ntpdate[1940]: adjust time server 10.211.37.1 offset -0.005455 sec RUN: /usr/share/launchpad-buildd/bin/in-target unpack-chroot --backend=chroot --series=mantic --arch=arm64 PACKAGEBUILD-26676744 --image-type chroot /home/buildd/filecache-default/f16216f5497f1f0724e8a3a0f3bd4b5063e2189b Creating target for build PACKAGEBUILD-26676744 RUN: /usr/share/launchpad-buildd/bin/in-target mount-chroot --backend=chroot --series=mantic --arch=arm64 PACKAGEBUILD-26676744 Starting target for build PACKAGEBUILD-26676744 RUN: /usr/share/launchpad-buildd/bin/in-target override-sources-list --backend=chroot --series=mantic --arch=arm64 PACKAGEBUILD-26676744 '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-26676744 RUN: /usr/share/launchpad-buildd/bin/in-target update-debian-chroot --backend=chroot --series=mantic --arch=arm64 PACKAGEBUILD-26676744 Updating target for build PACKAGEBUILD-26676744 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 arm64 Packages [1382 kB] Get:6 http://ftpmaster.internal/ubuntu mantic/main Translation-en [516 kB] Get:7 http://ftpmaster.internal/ubuntu mantic/universe arm64 Packages [14.5 MB] Get:8 http://ftpmaster.internal/ubuntu mantic/universe Translation-en [5959 kB] Get:9 http://ftpmaster.internal/ubuntu mantic-proposed/main arm64 Packages [105 kB] Get:10 http://ftpmaster.internal/ubuntu mantic-proposed/main Translation-en [26.7 kB] Get:11 http://ftpmaster.internal/ubuntu mantic-proposed/universe arm64 Packages [121 kB] Get:12 http://ftpmaster.internal/ubuntu mantic-proposed/universe Translation-en [55.9 kB] Fetched 23.2 MB in 5s (4240 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages were automatically installed and are no longer required: 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 libproc2-0 libsframe1 libstdc++-13-dev systemd-dev The following packages will be upgraded: adduser advancecomp apt base-files bash binutils binutils-aarch64-linux-gnu binutils-common 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 libhwasan0 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 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, 9 newly installed, 0 to remove and 0 not upgraded. Need to get 151 MB of archives. After this operation, 160 MB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu mantic/main arm64 libcrypt-dev arm64 1:4.4.36-2 [118 kB] Get:2 http://ftpmaster.internal/ubuntu mantic-proposed/main arm64 libc6-dev arm64 2.38-1ubuntu4 [1571 kB] Get:3 http://ftpmaster.internal/ubuntu mantic-proposed/main arm64 libc-dev-bin arm64 2.38-1ubuntu4 [19.4 kB] Get:4 http://ftpmaster.internal/ubuntu mantic/main arm64 libcrypt1 arm64 1:4.4.36-2 [85.4 kB] Get:5 http://ftpmaster.internal/ubuntu mantic-proposed/main arm64 linux-libc-dev arm64 6.5.0-2.2 [1515 kB] Get:6 http://ftpmaster.internal/ubuntu mantic-proposed/main arm64 libc6 arm64 2.38-1ubuntu4 [2734 kB] Get:7 http://ftpmaster.internal/ubuntu mantic-proposed/main arm64 libc-bin arm64 2.38-1ubuntu4 [589 kB] Get:8 http://ftpmaster.internal/ubuntu mantic/main arm64 gcc-13-base arm64 13.2.0-2ubuntu1 [42.9 kB] Get:9 http://ftpmaster.internal/ubuntu mantic/main arm64 libgcc-s1 arm64 13.2.0-2ubuntu1 [46.7 kB] Get:10 http://ftpmaster.internal/ubuntu mantic/main arm64 base-files arm64 13ubuntu1 [74.1 kB] Get:11 http://ftpmaster.internal/ubuntu mantic/main arm64 debianutils arm64 5.8-1 [103 kB] Get:12 http://ftpmaster.internal/ubuntu mantic/main arm64 bash arm64 5.2.15-2ubuntu1 [780 kB] Get:13 http://ftpmaster.internal/ubuntu mantic/main arm64 bsdutils arm64 1:2.39.1-4ubuntu1 [95.9 kB] Get:14 http://ftpmaster.internal/ubuntu mantic/main arm64 coreutils arm64 9.1-1ubuntu2 [1347 kB] Get:15 http://ftpmaster.internal/ubuntu mantic/main arm64 liblzma5 arm64 5.4.1-0.2 [122 kB] Get:16 http://ftpmaster.internal/ubuntu mantic/main arm64 libzstd1 arm64 1.5.5+dfsg2-1ubuntu2 [270 kB] Get:17 http://ftpmaster.internal/ubuntu mantic/main arm64 libstdc++6 arm64 13.2.0-2ubuntu1 [731 kB] Get:18 http://ftpmaster.internal/ubuntu mantic/main arm64 libgpg-error0 arm64 1.47-2 [69.0 kB] Get:19 http://ftpmaster.internal/ubuntu mantic/main arm64 libgcrypt20 arm64 1.10.2-2ubuntu1 [470 kB] Get:20 http://ftpmaster.internal/ubuntu mantic/main arm64 libp11-kit0 arm64 0.25.0-4ubuntu1 [273 kB] Get:21 http://ftpmaster.internal/ubuntu mantic/main arm64 libacl1 arm64 2.3.1-3 [16.3 kB] Get:22 http://ftpmaster.internal/ubuntu mantic/main arm64 libapparmor1 arm64 4.0.0~alpha2-0ubuntu2 [47.3 kB] Get:23 http://ftpmaster.internal/ubuntu mantic/main arm64 libaudit-common all 1:3.1.1-1 [5426 B] Get:24 http://ftpmaster.internal/ubuntu mantic/main arm64 libcap-ng0 arm64 0.8.3-1build2 [14.6 kB] Get:25 http://ftpmaster.internal/ubuntu mantic/main arm64 libaudit1 arm64 1:3.1.1-1 [46.4 kB] Get:26 http://ftpmaster.internal/ubuntu mantic/main arm64 libblkid1 arm64 2.39.1-4ubuntu1 [120 kB] Get:27 http://ftpmaster.internal/ubuntu mantic/main arm64 libcap2 arm64 1:2.66-4ubuntu1 [29.1 kB] Get:28 http://ftpmaster.internal/ubuntu mantic/main arm64 libip4tc2 arm64 1.8.9-2ubuntu2 [22.3 kB] Get:29 http://ftpmaster.internal/ubuntu mantic/main arm64 libperl5.36 arm64 5.36.0-7ubuntu1 [4674 kB] Get:30 http://ftpmaster.internal/ubuntu mantic/main arm64 perl arm64 5.36.0-7ubuntu1 [235 kB] Get:31 http://ftpmaster.internal/ubuntu mantic/main arm64 perl-base arm64 5.36.0-7ubuntu1 [1730 kB] Get:32 http://ftpmaster.internal/ubuntu mantic/main arm64 perl-modules-5.36 all 5.36.0-7ubuntu1 [2984 kB] Get:33 http://ftpmaster.internal/ubuntu mantic/main arm64 libdb5.3 arm64 5.3.28+dfsg2-2 [731 kB] Get:34 http://ftpmaster.internal/ubuntu mantic/main arm64 zlib1g arm64 1:1.2.13.dfsg-1ubuntu5 [60.6 kB] Get:35 http://ftpmaster.internal/ubuntu mantic/main arm64 debconf all 1.5.82 [125 kB] Get:36 http://ftpmaster.internal/ubuntu mantic/main arm64 libssl3 arm64 3.0.10-1ubuntu2 [1763 kB] Get:37 http://ftpmaster.internal/ubuntu mantic/main arm64 libkmod2 arm64 30+20230519-1ubuntu3 [49.4 kB] Get:38 http://ftpmaster.internal/ubuntu mantic/main arm64 libpcre2-8-0 arm64 10.42-4 [210 kB] Get:39 http://ftpmaster.internal/ubuntu mantic/main arm64 libselinux1 arm64 3.5-1 [77.5 kB] Get:40 http://ftpmaster.internal/ubuntu mantic/main arm64 libmount1 arm64 2.39.1-4ubuntu1 [137 kB] Get:41 http://ftpmaster.internal/ubuntu mantic/main arm64 libpam0g arm64 1.5.2-6ubuntu1 [65.8 kB] Get:42 http://ftpmaster.internal/ubuntu mantic/main arm64 libseccomp2 arm64 2.5.4-1ubuntu3 [49.3 kB] Get:43 http://ftpmaster.internal/ubuntu mantic/main arm64 systemd-sysv arm64 253.5-1ubuntu4 [11.5 kB] Get:44 http://ftpmaster.internal/ubuntu mantic/main arm64 systemd arm64 253.5-1ubuntu4 [2976 kB] Get:45 http://ftpmaster.internal/ubuntu mantic/main arm64 libsystemd-shared arm64 253.5-1ubuntu4 [1786 kB] Get:46 http://ftpmaster.internal/ubuntu mantic/main arm64 systemd-dev all 253.5-1ubuntu4 [79.1 kB] Get:47 http://ftpmaster.internal/ubuntu mantic/main arm64 libargon2-1 arm64 0~20190702+dfsg-3 [18.9 kB] Get:48 http://ftpmaster.internal/ubuntu mantic/main arm64 libudev1 arm64 253.5-1ubuntu4 [157 kB] Get:49 http://ftpmaster.internal/ubuntu mantic/main arm64 libdevmapper1.02.1 arm64 2:1.02.185-2ubuntu1 [128 kB] Get:50 http://ftpmaster.internal/ubuntu mantic/main arm64 libjson-c5 arm64 0.17-1 [35.5 kB] Get:51 http://ftpmaster.internal/ubuntu mantic/main arm64 libuuid1 arm64 2.39.1-4ubuntu1 [33.2 kB] Get:52 http://ftpmaster.internal/ubuntu mantic/main arm64 libcryptsetup12 arm64 2:2.6.1-4ubuntu2 [238 kB] Get:53 http://ftpmaster.internal/ubuntu mantic/main arm64 libfdisk1 arm64 2.39.1-4ubuntu1 [141 kB] Get:54 http://ftpmaster.internal/ubuntu mantic/main arm64 mount arm64 2.39.1-4ubuntu1 [115 kB] Get:55 http://ftpmaster.internal/ubuntu mantic/main arm64 libsystemd0 arm64 253.5-1ubuntu4 [395 kB] Get:56 http://ftpmaster.internal/ubuntu mantic/main arm64 libapt-pkg6.0 arm64 2.7.3 [898 kB] Get:57 http://ftpmaster.internal/ubuntu mantic/main arm64 tar arm64 1.34+dfsg-1.2ubuntu1 [283 kB] Get:58 http://ftpmaster.internal/ubuntu mantic/main arm64 dpkg arm64 1.22.0ubuntu1 [1391 kB] Get:59 http://ftpmaster.internal/ubuntu mantic/main arm64 dash arm64 0.5.12-6ubuntu1 [89.9 kB] Get:60 http://ftpmaster.internal/ubuntu mantic/main arm64 diffutils arm64 1:3.8-4 [172 kB] Get:61 http://ftpmaster.internal/ubuntu mantic/main arm64 findutils arm64 4.9.0-5 [300 kB] Get:62 http://ftpmaster.internal/ubuntu mantic/main arm64 grep arm64 3.11-2 [158 kB] Get:63 http://ftpmaster.internal/ubuntu mantic/main arm64 hostname arm64 3.23+nmu1ubuntu1 [10.7 kB] Get:64 http://ftpmaster.internal/ubuntu mantic/main arm64 libncurses6 arm64 6.4+20230625-2 [109 kB] Get:65 http://ftpmaster.internal/ubuntu mantic/main arm64 libncursesw6 arm64 6.4+20230625-2 [142 kB] Get:66 http://ftpmaster.internal/ubuntu mantic/main arm64 libtinfo6 arm64 6.4+20230625-2 [104 kB] Get:67 http://ftpmaster.internal/ubuntu mantic/main arm64 ncurses-bin arm64 6.4+20230625-2 [184 kB] Get:68 http://ftpmaster.internal/ubuntu mantic/main arm64 sed arm64 4.9-1 [191 kB] Get:69 http://ftpmaster.internal/ubuntu mantic/main arm64 libsmartcols1 arm64 2.39.1-4ubuntu1 [61.9 kB] Get:70 http://ftpmaster.internal/ubuntu mantic/universe arm64 util-linux-extra arm64 2.39.1-4ubuntu1 [123 kB] Get:71 http://ftpmaster.internal/ubuntu mantic/main arm64 util-linux arm64 2.39.1-4ubuntu1 [1110 kB] Get:72 http://ftpmaster.internal/ubuntu mantic/main arm64 init-system-helpers all 1.65.2ubuntu1 [38.7 kB] Get:73 http://ftpmaster.internal/ubuntu mantic/main arm64 ncurses-base all 6.4+20230625-2 [24.5 kB] Get:74 http://ftpmaster.internal/ubuntu mantic/main arm64 sysvinit-utils arm64 3.07-1ubuntu1 [32.7 kB] Get:75 http://ftpmaster.internal/ubuntu mantic/main arm64 lsb-base all 11.6 [4606 B] Get:76 http://ftpmaster.internal/ubuntu mantic/main arm64 adduser all 3.137ubuntu1 [101 kB] Get:77 http://ftpmaster.internal/ubuntu mantic/main arm64 gpgv arm64 2.2.40-1.1ubuntu1 [135 kB] Get:78 http://ftpmaster.internal/ubuntu mantic/main arm64 libgmp10 arm64 2:6.3.0+dfsg-2ubuntu4 [241 kB] Get:79 http://ftpmaster.internal/ubuntu mantic/main arm64 libnettle8 arm64 3.9.1-2 [190 kB] Get:80 http://ftpmaster.internal/ubuntu mantic/main arm64 libhogweed6 arm64 3.9.1-2 [198 kB] Get:81 http://ftpmaster.internal/ubuntu mantic/main arm64 libidn2-0 arm64 2.3.4-1 [108 kB] Get:82 http://ftpmaster.internal/ubuntu mantic/main arm64 libtasn1-6 arm64 4.19.0-3 [42.8 kB] Get:83 http://ftpmaster.internal/ubuntu mantic/main arm64 libgnutls30 arm64 3.8.1-4ubuntu1 [937 kB] Get:84 http://ftpmaster.internal/ubuntu mantic/main arm64 apt arm64 2.7.3 [1327 kB] Get:85 http://ftpmaster.internal/ubuntu mantic/main arm64 libpam-modules-bin arm64 1.5.2-6ubuntu1 [46.1 kB] Get:86 http://ftpmaster.internal/ubuntu mantic/main arm64 libpam-modules arm64 1.5.2-6ubuntu1 [283 kB] Get:87 http://ftpmaster.internal/ubuntu mantic/main arm64 logsave arm64 1.47.0-2ubuntu1 [21.6 kB] Get:88 http://ftpmaster.internal/ubuntu mantic/main arm64 libext2fs2 arm64 1.47.0-2ubuntu1 [221 kB] Get:89 http://ftpmaster.internal/ubuntu mantic/main arm64 e2fsprogs arm64 1.47.0-2ubuntu1 [590 kB] Get:90 http://ftpmaster.internal/ubuntu mantic/main arm64 init arm64 1.65.2ubuntu1 [5508 B] Get:91 http://ftpmaster.internal/ubuntu mantic/main arm64 libattr1 arm64 1:2.5.1-4 [12.2 kB] Get:92 http://ftpmaster.internal/ubuntu mantic/main arm64 libdebconfclient0 arm64 0.270ubuntu1 [11.0 kB] Get:93 http://ftpmaster.internal/ubuntu mantic/main arm64 libmd0 arm64 1.1.0-1 [24.4 kB] Get:94 http://ftpmaster.internal/ubuntu mantic/main arm64 libpam-runtime all 1.5.2-6ubuntu1 [41.5 kB] Get:95 http://ftpmaster.internal/ubuntu mantic/main arm64 libsemanage-common all 3.5-1 [9890 B] Get:96 http://ftpmaster.internal/ubuntu mantic/main arm64 libsepol2 arm64 3.5-1 [289 kB] Get:97 http://ftpmaster.internal/ubuntu mantic/main arm64 libsemanage2 arm64 3.5-1 [89.3 kB] Get:98 http://ftpmaster.internal/ubuntu mantic/main arm64 usrmerge all 35ubuntu1 [58.2 kB] Get:99 http://ftpmaster.internal/ubuntu mantic/main arm64 libcom-err2 arm64 1.47.0-2ubuntu1 [21.6 kB] Get:100 http://ftpmaster.internal/ubuntu mantic/main arm64 libproc2-0 arm64 2:4.0.3-1ubuntu1 [53.1 kB] Get:101 http://ftpmaster.internal/ubuntu mantic/main arm64 libss2 arm64 1.47.0-2ubuntu1 [16.1 kB] Get:102 http://ftpmaster.internal/ubuntu mantic/main arm64 mawk arm64 1.3.4.20230730-1 [122 kB] Get:103 http://ftpmaster.internal/ubuntu mantic/main arm64 procps arm64 2:4.0.3-1ubuntu1 [606 kB] Get:104 http://ftpmaster.internal/ubuntu mantic/main arm64 sensible-utils all 0.0.20 [19.6 kB] Get:105 http://ftpmaster.internal/ubuntu mantic/main arm64 openssl arm64 3.0.10-1ubuntu2 [1166 kB] Get:106 http://ftpmaster.internal/ubuntu mantic/main arm64 ca-certificates all 20230311ubuntu1 [152 kB] Get:107 http://ftpmaster.internal/ubuntu mantic/main arm64 libgssapi-krb5-2 arm64 1.20.1-3ubuntu1 [139 kB] Get:108 http://ftpmaster.internal/ubuntu mantic/main arm64 libkrb5-3 arm64 1.20.1-3ubuntu1 [345 kB] Get:109 http://ftpmaster.internal/ubuntu mantic/main arm64 libk5crypto3 arm64 1.20.1-3ubuntu1 [84.9 kB] Get:110 http://ftpmaster.internal/ubuntu mantic/main arm64 libkrb5support0 arm64 1.20.1-3ubuntu1 [32.9 kB] Get:111 http://ftpmaster.internal/ubuntu mantic/main arm64 readline-common all 8.2-1.3 [55.7 kB] Get:112 http://ftpmaster.internal/ubuntu mantic/main arm64 libreadline8 arm64 8.2-1.3 [150 kB] Get:113 http://ftpmaster.internal/ubuntu mantic/main arm64 libsqlite3-0 arm64 3.42.0-1 [662 kB] Get:114 http://ftpmaster.internal/ubuntu mantic-proposed/main arm64 tzdata all 2023c-9ubuntu1 [270 kB] Get:115 http://ftpmaster.internal/ubuntu mantic/main arm64 libpng16-16 arm64 1.6.40-1 [182 kB] Get:116 http://ftpmaster.internal/ubuntu mantic/main arm64 xz-utils arm64 5.4.1-0.2 [271 kB] Get:117 http://ftpmaster.internal/ubuntu mantic/main arm64 advancecomp arm64 2.5-1 [171 kB] Get:118 http://ftpmaster.internal/ubuntu mantic/main arm64 libgprofng0 arm64 2.41-4ubuntu1 [806 kB] Get:119 http://ftpmaster.internal/ubuntu mantic/main arm64 libctf0 arm64 2.41-4ubuntu1 [94.7 kB] Get:120 http://ftpmaster.internal/ubuntu mantic/main arm64 libctf-nobfd0 arm64 2.41-4ubuntu1 [98.9 kB] Get:121 http://ftpmaster.internal/ubuntu mantic/main arm64 binutils-aarch64-linux-gnu arm64 2.41-4ubuntu1 [3310 kB] Get:122 http://ftpmaster.internal/ubuntu mantic/main arm64 libbinutils arm64 2.41-4ubuntu1 [753 kB] Get:123 http://ftpmaster.internal/ubuntu mantic/main arm64 binutils arm64 2.41-4ubuntu1 [18.0 kB] Get:124 http://ftpmaster.internal/ubuntu mantic/main arm64 binutils-common arm64 2.41-4ubuntu1 [248 kB] Get:125 http://ftpmaster.internal/ubuntu mantic/main arm64 libsframe1 arm64 2.41-4ubuntu1 [14.1 kB] Get:126 http://ftpmaster.internal/ubuntu mantic/main arm64 libisl23 arm64 0.26-3 [713 kB] Get:127 http://ftpmaster.internal/ubuntu mantic-proposed/main arm64 libmpfr6 arm64 4.2.1-1 [327 kB] Get:128 http://ftpmaster.internal/ubuntu mantic/main arm64 cpp-13 arm64 13.2.0-2ubuntu1 [9533 kB] Get:129 http://ftpmaster.internal/ubuntu mantic/main arm64 g++ arm64 4:13.2.0-1ubuntu1 [1108 B] Get:130 http://ftpmaster.internal/ubuntu mantic/main arm64 gcc arm64 4:13.2.0-1ubuntu1 [5190 B] Get:131 http://ftpmaster.internal/ubuntu mantic/main arm64 cpp arm64 4:13.2.0-1ubuntu1 [28.9 kB] Get:132 http://ftpmaster.internal/ubuntu mantic/main arm64 libcc1-0 arm64 13.2.0-2ubuntu1 [49.6 kB] Get:133 http://ftpmaster.internal/ubuntu mantic/main arm64 libgomp1 arm64 13.2.0-2ubuntu1 [134 kB] Get:134 http://ftpmaster.internal/ubuntu mantic/main arm64 libitm1 arm64 13.2.0-2ubuntu1 [27.9 kB] Get:135 http://ftpmaster.internal/ubuntu mantic/main arm64 libatomic1 arm64 13.2.0-2ubuntu1 [11.7 kB] Get:136 http://ftpmaster.internal/ubuntu mantic/main arm64 libasan8 arm64 13.2.0-2ubuntu1 [2747 kB] Get:137 http://ftpmaster.internal/ubuntu mantic/main arm64 liblsan0 arm64 13.2.0-2ubuntu1 [1184 kB] Get:138 http://ftpmaster.internal/ubuntu mantic/universe arm64 g++-12 arm64 12.3.0-8ubuntu1 [10.9 MB] Get:139 http://ftpmaster.internal/ubuntu mantic/main arm64 gcc-12 arm64 12.3.0-8ubuntu1 [19.1 MB] Get:140 http://ftpmaster.internal/ubuntu mantic/main arm64 cpp-12 arm64 12.3.0-8ubuntu1 [9574 kB] Get:141 http://ftpmaster.internal/ubuntu mantic/main arm64 libubsan1 arm64 13.2.0-2ubuntu1 [1089 kB] Get:142 http://ftpmaster.internal/ubuntu mantic/universe arm64 libstdc++-12-dev arm64 12.3.0-8ubuntu1 [2168 kB] Get:143 http://ftpmaster.internal/ubuntu mantic/main arm64 libhwasan0 arm64 13.2.0-2ubuntu1 [1242 kB] Get:144 http://ftpmaster.internal/ubuntu mantic/main arm64 libgcc-12-dev arm64 12.3.0-8ubuntu1 [1157 kB] Get:145 http://ftpmaster.internal/ubuntu mantic/main arm64 libtsan2 arm64 13.2.0-2ubuntu1 [2626 kB] Get:146 http://ftpmaster.internal/ubuntu mantic/main arm64 gcc-12-base arm64 12.3.0-8ubuntu1 [43.4 kB] Get:147 http://ftpmaster.internal/ubuntu mantic/main arm64 libgcc-13-dev arm64 13.2.0-2ubuntu1 [2466 kB] Get:148 http://ftpmaster.internal/ubuntu mantic/main arm64 gcc-13 arm64 13.2.0-2ubuntu1 [19.1 MB] Get:149 http://ftpmaster.internal/ubuntu mantic/main arm64 libstdc++-13-dev arm64 13.2.0-2ubuntu1 [2344 kB] Get:150 http://ftpmaster.internal/ubuntu mantic/main arm64 g++-13 arm64 13.2.0-2ubuntu1 [10.9 MB] Get:151 http://ftpmaster.internal/ubuntu mantic/main arm64 dpkg-dev all 1.22.0ubuntu1 [1137 kB] Get:152 http://ftpmaster.internal/ubuntu mantic/main arm64 libdpkg-perl all 1.22.0ubuntu1 [283 kB] Get:153 http://ftpmaster.internal/ubuntu mantic/main arm64 lto-disabled-list all 42 [12.4 kB] Get:154 http://ftpmaster.internal/ubuntu mantic/main arm64 build-essential arm64 12.10ubuntu1 [4932 B] Get:155 http://ftpmaster.internal/ubuntu mantic/main arm64 libfakeroot arm64 1.32.1-1 [31.8 kB] Get:156 http://ftpmaster.internal/ubuntu mantic/main arm64 fakeroot arm64 1.32.1-1 [59.7 kB] Get:157 http://ftpmaster.internal/ubuntu mantic/main arm64 libassuan0 arm64 2.5.6-1 [35.8 kB] Get:158 http://ftpmaster.internal/ubuntu mantic/main arm64 gpg arm64 2.2.40-1.1ubuntu1 [509 kB] Get:159 http://ftpmaster.internal/ubuntu mantic/main arm64 gpgconf arm64 2.2.40-1.1ubuntu1 [95.3 kB] Get:160 http://ftpmaster.internal/ubuntu mantic/main arm64 gpg-agent arm64 2.2.40-1.1ubuntu1 [211 kB] Get:161 http://ftpmaster.internal/ubuntu mantic/main arm64 pkgbinarymangler all 153 [16.3 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 151 MB in 7s (20.6 MB/s) (Reading database ... 13115 files and directories currently installed.) 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Setting up libreadline8:arm64 (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:arm64 (2.41-4ubuntu1) ... Setting up libgcc-12-dev:arm64 (12.3.0-8ubuntu1) ... Setting up libgssapi-krb5-2:arm64 (1.20.1-3ubuntu1) ... Setting up libdpkg-perl (1.22.0ubuntu1) ... Setting up libgcc-13-dev:arm64 (13.2.0-2ubuntu1) ... Setting up cpp (4:13.2.0-1ubuntu1) ... Setting up gpgconf (2.2.40-1.1ubuntu1) ... Setting up libc6-dev:arm64 (2.38-1ubuntu4) ... Setting up gpg (2.2.40-1.1ubuntu1) ... Setting up libstdc++-13-dev:arm64 (13.2.0-2ubuntu1) ... Setting up gpg-agent (2.2.40-1.1ubuntu1) ... Setting up libstdc++-12-dev:arm64 (12.3.0-8ubuntu1) ... Setting up binutils-aarch64-linux-gnu (2.41-4ubuntu1) ... 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 (13.2.0-2ubuntu1) ... Setting up g++-12 (12.3.0-8ubuntu1) ... Setting up g++-13 (13.2.0-2ubuntu1) ... 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-26676744 arm64 mantic-proposed -c chroot:build-PACKAGEBUILD-26676744 --arch=arm64 --dist=mantic-proposed --nolog freebayes_1.3.7-1.dsc Initiating build PACKAGEBUILD-26676744 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 5.4.0-156-generic #173-Ubuntu SMP Tue Jul 11 07:25:14 UTC 2023 aarch64 sbuild (Debian sbuild) 0.79.0 (05 February 2020) on bos01-arm64-009.buildd +==============================================================================+ | freebayes 1.3.7-1 (arm64) Sat, 02 Sep 2023 14:55:41 +0000 | +==============================================================================+ Package: freebayes Version: 1.3.7-1 Source Version: 1.3.7-1 Distribution: mantic-proposed Machine Architecture: arm64 Host Architecture: arm64 Build Architecture: arm64 Build Type: any I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-26676744/chroot-autobuild' with '<>' I: NOTICE: Log filtering will replace 'build/freebayes-NtDBaE/resolver-Y2QbFG' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- freebayes_1.3.7-1.dsc exists in .; copying to chroot I: NOTICE: Log filtering will replace 'build/freebayes-NtDBaE/freebayes-1.3.7' with '<>' I: NOTICE: Log filtering will replace 'build/freebayes-NtDBaE' with '<>' +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper-compat (= 13), meson, ninja-build, pkg-config, zlib1g-dev, libbamtools-dev, libvcflib-dev (>= 1.0.9+dfsg-1~), libtabixpp-dev, libseqlib-dev, bc, samtools, parallel, libvcflib-tools, debhelper, build-essential, fakeroot Filtered Build-Depends: debhelper-compat (= 13), meson, ninja-build, pkg-config, zlib1g-dev, libbamtools-dev, libvcflib-dev (>= 1.0.9+dfsg-1~), libtabixpp-dev, libseqlib-dev, bc, samtools, parallel, libvcflib-tools, debhelper, 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 [474 B] Get:5 copy:/<>/apt_archive ./ Packages [546 B] Fetched 1977 B in 0s (116 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 bc bsdextrautils debhelper debugedit dh-autoreconf dh-strip-nondeterminism dwz file fontconfig fontconfig-config fonts-noto-core fonts-noto-mono gettext gettext-base groff-base intltool-debian libarchive-zip-perl libbamtools-dev libbamtools2.5.2 libblas3 libbrotli1 libbsd0 libbwa-dev libcairo2 libcurl3-gnutls libcurl4 libcurl4-gnutls-dev libdatrie1 libdebhelper-perl libdeflate-dev libdeflate0 libdisorder-dev libdisorder0 libdw1 libelf1 libexpat1 libfastahack-dev libfastahack0 libfile-stripnondeterminism-perl libfml-dev libfml0 libfontconfig1 libfreetype6 libfribidi0 libgfortran5 libglib2.0-0 libgraphite2-3 libharfbuzz0b libhts-dev libhts3 libhtscodecs2 libice6 libicu72 libjbig0 libjpeg-turbo8 libjpeg8 libjsoncpp-dev libjsoncpp25 liblapack3 libldap2 liblerc4 liblzma-dev libmagic-mgc libmagic1 libnghttp2-14 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper1 libpipeline1 libpixman-1-0 libpkgconf3 libpsl5 libpython3-stdlib libpython3.11-minimal libpython3.11-stdlib librtmp1 libsasl2-2 libsasl2-modules-db libsensors-config libsensors5 libseqlib-dev libseqlib2 libsm6 libsmithwaterman-dev libsmithwaterman0 libssh-4 libssw-dev libssw0 libsub-override-perl libtabixpp-dev libtabixpp0 libtcl8.6 libthai-data libthai0 libtiff6 libtk8.6 libtool libuchardet0 libvcflib-dev libvcflib-tools libvcflib2 libwebp7 libwfa2-0 libwfa2-dev libx11-6 libx11-data libxau6 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxft2 libxml2 libxrender1 libxss1 libxt6 littler m4 man-db media-types meson ninja-build parallel pkg-config pkgconf pkgconf-bin po-debconf python3 python3-distutils python3-lib2to3 python3-minimal python3-pkg-resources python3-setuptools python3.11 python3.11-minimal r-base-core r-cran-cli r-cran-colorspace r-cran-fansi r-cran-farver r-cran-ggplot2 r-cran-glue r-cran-gridbase r-cran-gtable r-cran-isoband r-cran-labeling r-cran-lattice r-cran-lifecycle r-cran-littler r-cran-magrittr r-cran-mass r-cran-matrix r-cran-mgcv r-cran-munsell r-cran-nlme r-cran-pillar r-cran-pkgconfig r-cran-pkgkitten r-cran-plyr r-cran-r6 r-cran-rcolorbrewer r-cran-rcpp r-cran-rlang r-cran-scales r-cran-tibble r-cran-utf8 r-cran-vctrs r-cran-viridislite r-cran-withr samtools sysstat ucf unzip x11-common xdg-utils zip zlib1g-dev Suggested packages: autoconf-archive gnu-standards autoconf-doc dh-make gettext-doc libasprintf-dev libgettextpo-dev groff libbamtools-doc libcurl4-doc libgnutls28-dev libidn-dev libkrb5-dev libldap2-dev librtmp-dev libssh2-1-dev low-memory-monitor liblzma-doc lm-sensors tcl8.6 tk8.6 libtool-doc gfortran | fortran95-compiler gcj-jdk r-cran-pracma m4-doc apparmor less www-browser csh fish ksh tcsh zsh libmail-box-perl python3-doc python3-tk python3-venv python-setuptools-doc python3.11-venv python3.11-doc binfmt-support elpa-ess r-doc-info | r-doc-pdf r-mathlib r-base-html r-cran-callr r-cran-covr r-cran-crayon r-cran-digest r-cran-htmltools r-cran-htmlwidgets r-cran-knitr r-cran-processx r-cran-ps r-cran-rmarkdown r-cran-rprojroot r-cran-rstudioapi r-cran-whoami r-cran-kernsmooth r-cran-kernlab r-cran-mvtnorm r-cran-vcd r-cran-shiny r-cran-shinyjs r-cran-dplyr r-cran-png r-cran-jpeg r-cran-viridis r-cran-unitizer r-cran-profvis r-cran-rgeos r-cran-dbi r-cran-forcats r-cran-r.utils r-cran-rsqlite r-cran-stringr r-cran-waldo r-cran-magick r-cran-sf r-cran-lintr r-cran-tidyverse r-cran-getopt r-cran-bit64 r-cran-formattable r-cran-nanotime r-cran-palmerpenguins r-cran-stringi r-cran-survival r-cran-units r-cran-vdiffr r-cran-testthat r-cran-doparallel r-cran-foreach r-cran-iterators r-cran-itertools r-cran-inline r-cran-fs r-cran-usethis r-cran-dichromat r-cran-bench r-cran-blob r-cran-brio r-cran-evaluate r-cran-here r-cran-hms r-cran-pkgbuild r-cran-pkgload r-cran-purrr r-cran-tidyr r-cran-pkgdown r-cran-zeallot cwltool isag Recommended packages: curl | wget | lynx libarchive-cpio-perl libglib2.0-data shared-mime-info xdg-user-dirs libldap-common publicsuffix libsasl2-modules libltdl-dev libmail-sendmail-perl r-recommended r-base-dev r-doc-html r-cran-testthat r-cran-mockery r-cran-covr r-cran-ragg r-cran-dplyr r-cran-hexbin r-cran-hmisc r-cran-interp r-cran-knitr r-cran-mapproj r-cran-maps r-cran-maptools r-cran-multcomp r-cran-quantreg r-cran-rmarkdown r-cran-rpart r-cran-sf r-cran-svglite r-cran-vdiffr r-cran-xml2 r-cran-crayon r-cran-lubridate r-cran-domc r-cran-abind r-cran-bit64 r-cran-hms r-cran-stringi r-cran-data.table r-cran-rsqlite r-cran-mockr r-cran-formattable r-cran-generics r-cran-waldo r-cran-dbi libfile-mimeinfo-perl libnet-dbus-perl libx11-protocol-perl x11-utils x11-xserver-utils The following NEW packages will be installed: autoconf automake autopoint autotools-dev bc bsdextrautils debhelper debugedit dh-autoreconf dh-strip-nondeterminism dwz file fontconfig fontconfig-config fonts-noto-core fonts-noto-mono gettext gettext-base groff-base intltool-debian libarchive-zip-perl libbamtools-dev libbamtools2.5.2 libblas3 libbrotli1 libbsd0 libbwa-dev libcairo2 libcurl3-gnutls libcurl4 libcurl4-gnutls-dev libdatrie1 libdebhelper-perl libdeflate-dev libdeflate0 libdisorder-dev libdisorder0 libdw1 libelf1 libexpat1 libfastahack-dev libfastahack0 libfile-stripnondeterminism-perl libfml-dev libfml0 libfontconfig1 libfreetype6 libfribidi0 libgfortran5 libglib2.0-0 libgraphite2-3 libharfbuzz0b libhts-dev libhts3 libhtscodecs2 libice6 libicu72 libjbig0 libjpeg-turbo8 libjpeg8 libjsoncpp-dev libjsoncpp25 liblapack3 libldap2 liblerc4 liblzma-dev libmagic-mgc libmagic1 libnghttp2-14 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper1 libpipeline1 libpixman-1-0 libpkgconf3 libpsl5 libpython3-stdlib libpython3.11-minimal libpython3.11-stdlib librtmp1 libsasl2-2 libsasl2-modules-db libsensors-config libsensors5 libseqlib-dev libseqlib2 libsm6 libsmithwaterman-dev libsmithwaterman0 libssh-4 libssw-dev libssw0 libsub-override-perl libtabixpp-dev libtabixpp0 libtcl8.6 libthai-data libthai0 libtiff6 libtk8.6 libtool libuchardet0 libvcflib-dev libvcflib-tools libvcflib2 libwebp7 libwfa2-0 libwfa2-dev libx11-6 libx11-data libxau6 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxft2 libxml2 libxrender1 libxss1 libxt6 littler m4 man-db media-types meson ninja-build parallel pkg-config pkgconf pkgconf-bin po-debconf python3 python3-distutils python3-lib2to3 python3-minimal python3-pkg-resources python3-setuptools python3.11 python3.11-minimal r-base-core r-cran-cli r-cran-colorspace r-cran-fansi r-cran-farver r-cran-ggplot2 r-cran-glue r-cran-gridbase r-cran-gtable r-cran-isoband r-cran-labeling r-cran-lattice r-cran-lifecycle r-cran-littler r-cran-magrittr r-cran-mass r-cran-matrix r-cran-mgcv r-cran-munsell r-cran-nlme r-cran-pillar r-cran-pkgconfig r-cran-pkgkitten r-cran-plyr r-cran-r6 r-cran-rcolorbrewer r-cran-rcpp r-cran-rlang r-cran-scales r-cran-tibble r-cran-utf8 r-cran-vctrs r-cran-viridislite r-cran-withr samtools sbuild-build-depends-main-dummy sysstat ucf unzip x11-common xdg-utils zip zlib1g-dev 0 upgraded, 185 newly installed, 0 to remove and 0 not upgraded. Need to get 123 MB of archives. After this operation, 325 MB of additional disk space will be used. Get:1 copy:/<>/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [766 B] Get:2 http://ftpmaster.internal/ubuntu mantic/main arm64 libpython3.11-minimal arm64 3.11.5-3 [834 kB] Get:3 http://ftpmaster.internal/ubuntu mantic/main arm64 libexpat1 arm64 2.5.0-2 [72.2 kB] Get:4 http://ftpmaster.internal/ubuntu mantic/main arm64 python3.11-minimal arm64 3.11.5-3 [2143 kB] Get:5 http://ftpmaster.internal/ubuntu mantic/main arm64 python3-minimal arm64 3.11.4-5 [26.8 kB] Get:6 http://ftpmaster.internal/ubuntu mantic/main arm64 media-types all 10.1.0 [27.5 kB] Get:7 http://ftpmaster.internal/ubuntu mantic/main arm64 libpython3.11-stdlib arm64 3.11.5-3 [1886 kB] Get:8 http://ftpmaster.internal/ubuntu mantic/main arm64 python3.11 arm64 3.11.5-3 [575 kB] Get:9 http://ftpmaster.internal/ubuntu mantic/main arm64 libpython3-stdlib arm64 3.11.4-5 [9504 B] Get:10 http://ftpmaster.internal/ubuntu mantic/main arm64 python3 arm64 3.11.4-5 [22.9 kB] Get:11 http://ftpmaster.internal/ubuntu mantic/main arm64 libbsd0 arm64 0.11.7-4 [40.8 kB] Get:12 http://ftpmaster.internal/ubuntu mantic/main arm64 libelf1 arm64 0.189-4 [56.2 kB] Get:13 http://ftpmaster.internal/ubuntu mantic/main arm64 libfribidi0 arm64 1.0.13-3 [26.5 kB] Get:14 http://ftpmaster.internal/ubuntu mantic/main arm64 libglib2.0-0 arm64 2.77.2-1 [1491 kB] Get:15 http://ftpmaster.internal/ubuntu mantic/main arm64 libicu72 arm64 72.1-3ubuntu2 [10.7 MB] Get:16 http://ftpmaster.internal/ubuntu mantic/main arm64 libxml2 arm64 2.9.14+dfsg-1.3 [722 kB] Get:17 http://ftpmaster.internal/ubuntu mantic/main arm64 python3-pkg-resources all 68.1.2-1 [167 kB] Get:18 http://ftpmaster.internal/ubuntu mantic/main arm64 ucf all 3.0043+nmu1 [56.5 kB] Get:19 http://ftpmaster.internal/ubuntu mantic/main arm64 bsdextrautils arm64 2.39.1-4ubuntu1 [71.2 kB] Get:20 http://ftpmaster.internal/ubuntu mantic/main arm64 libmagic-mgc arm64 1:5.44-3 [293 kB] Get:21 http://ftpmaster.internal/ubuntu mantic/main arm64 libmagic1 arm64 1:5.44-3 [84.3 kB] Get:22 http://ftpmaster.internal/ubuntu mantic/main arm64 file arm64 1:5.44-3 [21.8 kB] Get:23 http://ftpmaster.internal/ubuntu mantic/main arm64 gettext-base arm64 0.21-13 [37.1 kB] Get:24 http://ftpmaster.internal/ubuntu mantic/main arm64 libuchardet0 arm64 0.0.7-1build2 [77.3 kB] Get:25 http://ftpmaster.internal/ubuntu mantic/main arm64 groff-base arm64 1.23.0-2 [986 kB] Get:26 http://ftpmaster.internal/ubuntu mantic/main arm64 libnghttp2-14 arm64 1.55.1-1 [72.0 kB] Get:27 http://ftpmaster.internal/ubuntu mantic/main arm64 libpipeline1 arm64 1.5.7-1 [23.3 kB] Get:28 http://ftpmaster.internal/ubuntu mantic/main arm64 libpsl5 arm64 0.21.2-1 [59.0 kB] Get:29 http://ftpmaster.internal/ubuntu mantic/main arm64 libxau6 arm64 1:1.0.9-1build5 [7624 B] Get:30 http://ftpmaster.internal/ubuntu mantic/main arm64 libxdmcp6 arm64 1:1.1.3-0ubuntu5 [10.8 kB] Get:31 http://ftpmaster.internal/ubuntu mantic/main arm64 libxcb1 arm64 1.15-1 [47.6 kB] Get:32 http://ftpmaster.internal/ubuntu mantic/main arm64 libx11-data all 2:1.8.6-1 [115 kB] Get:33 http://ftpmaster.internal/ubuntu mantic/main arm64 libx11-6 arm64 2:1.8.6-1 [643 kB] Get:34 http://ftpmaster.internal/ubuntu mantic/main arm64 libxext6 arm64 2:1.3.4-1build1 [31.1 kB] Get:35 http://ftpmaster.internal/ubuntu mantic/main arm64 man-db arm64 2.11.2-3 [1214 kB] Get:36 http://ftpmaster.internal/ubuntu mantic/main arm64 m4 arm64 1.4.19-3 [239 kB] Get:37 http://ftpmaster.internal/ubuntu mantic/main arm64 autoconf all 2.71-3 [339 kB] Get:38 http://ftpmaster.internal/ubuntu mantic/main arm64 autotools-dev all 20220109.1 [44.9 kB] Get:39 http://ftpmaster.internal/ubuntu mantic/main arm64 automake all 1:1.16.5-1.3 [558 kB] Get:40 http://ftpmaster.internal/ubuntu mantic/main arm64 autopoint all 0.21-13 [422 kB] Get:41 http://ftpmaster.internal/ubuntu mantic/main arm64 bc arm64 1.07.1-3build1 [85.6 kB] Get:42 http://ftpmaster.internal/ubuntu mantic/main arm64 libdebhelper-perl all 13.11.6ubuntu1 [85.4 kB] Get:43 http://ftpmaster.internal/ubuntu mantic/main arm64 libtool all 2.4.7-7 [166 kB] Get:44 http://ftpmaster.internal/ubuntu mantic/main arm64 dh-autoreconf all 20 [16.1 kB] Get:45 http://ftpmaster.internal/ubuntu mantic/main arm64 libarchive-zip-perl all 1.68-1 [90.2 kB] Get:46 http://ftpmaster.internal/ubuntu mantic/main arm64 libsub-override-perl all 0.09-4 [8706 B] Get:47 http://ftpmaster.internal/ubuntu mantic/main arm64 libfile-stripnondeterminism-perl all 1.13.1-1 [18.1 kB] Get:48 http://ftpmaster.internal/ubuntu mantic/main arm64 dh-strip-nondeterminism all 1.13.1-1 [5362 B] Get:49 http://ftpmaster.internal/ubuntu mantic/main arm64 libdw1 arm64 0.189-4 [253 kB] Get:50 http://ftpmaster.internal/ubuntu mantic/main arm64 debugedit arm64 1:5.0-5 [45.9 kB] Get:51 http://ftpmaster.internal/ubuntu mantic/main arm64 dwz arm64 0.15-1 [110 kB] Get:52 http://ftpmaster.internal/ubuntu mantic/main arm64 gettext arm64 0.21-13 [841 kB] Get:53 http://ftpmaster.internal/ubuntu mantic/main arm64 intltool-debian all 0.35.0+20060710.6 [23.2 kB] Get:54 http://ftpmaster.internal/ubuntu mantic/main arm64 po-debconf all 1.0.21+nmu1 [233 kB] Get:55 http://ftpmaster.internal/ubuntu mantic/main arm64 debhelper all 13.11.6ubuntu1 [935 kB] Get:56 http://ftpmaster.internal/ubuntu mantic/main arm64 libbrotli1 arm64 1.0.9-2build8 [312 kB] Get:57 http://ftpmaster.internal/ubuntu mantic/main arm64 libfreetype6 arm64 2.13.1+dfsg-1 [389 kB] Get:58 http://ftpmaster.internal/ubuntu mantic/main arm64 fonts-noto-mono all 20201225-2 [435 kB] Get:59 http://ftpmaster.internal/ubuntu mantic/main arm64 fonts-noto-core all 20201225-2 [13.3 MB] Get:60 http://ftpmaster.internal/ubuntu mantic/main arm64 fontconfig-config arm64 2.14.2-4ubuntu1 [35.8 kB] Get:61 http://ftpmaster.internal/ubuntu mantic/main arm64 libfontconfig1 arm64 2.14.2-4ubuntu1 [139 kB] Get:62 http://ftpmaster.internal/ubuntu mantic/main arm64 fontconfig arm64 2.14.2-4ubuntu1 [190 kB] Get:63 http://ftpmaster.internal/ubuntu mantic/universe arm64 libbamtools2.5.2 arm64 2.5.2+dfsg-4 [134 kB] Get:64 http://ftpmaster.internal/ubuntu mantic/main arm64 zlib1g-dev arm64 1:1.2.13.dfsg-1ubuntu5 [893 kB] Get:65 http://ftpmaster.internal/ubuntu mantic/universe arm64 libbamtools-dev arm64 2.5.2+dfsg-4 [233 kB] Get:66 http://ftpmaster.internal/ubuntu mantic/main arm64 libblas3 arm64 3.11.0-2 [141 kB] Get:67 http://ftpmaster.internal/ubuntu mantic/universe arm64 libbwa-dev arm64 0.7.17-7 [148 kB] Get:68 http://ftpmaster.internal/ubuntu mantic/main arm64 libpixman-1-0 arm64 0.42.2-1 [193 kB] Get:69 http://ftpmaster.internal/ubuntu mantic/main arm64 libxcb-render0 arm64 1.15-1 [16.1 kB] Get:70 http://ftpmaster.internal/ubuntu mantic/main arm64 libxcb-shm0 arm64 1.15-1 [5780 B] Get:71 http://ftpmaster.internal/ubuntu mantic/main arm64 libxrender1 arm64 1:0.9.10-1.1 [19.1 kB] Get:72 http://ftpmaster.internal/ubuntu mantic/main arm64 libcairo2 arm64 1.17.8-2 [538 kB] Get:73 http://ftpmaster.internal/ubuntu mantic/main arm64 libsasl2-modules-db arm64 2.1.28+dfsg1-3 [21.0 kB] Get:74 http://ftpmaster.internal/ubuntu mantic/main arm64 libsasl2-2 arm64 2.1.28+dfsg1-3 [54.0 kB] Get:75 http://ftpmaster.internal/ubuntu mantic/main arm64 libldap2 arm64 2.6.6+dfsg-1~exp1ubuntu1 [191 kB] Get:76 http://ftpmaster.internal/ubuntu mantic/main arm64 librtmp1 arm64 2.4+20151223.gitfa8646d.1-2build4 [59.2 kB] Get:77 http://ftpmaster.internal/ubuntu mantic/main arm64 libssh-4 arm64 0.10.5-3ubuntu1 [185 kB] Get:78 http://ftpmaster.internal/ubuntu mantic/main arm64 libcurl3-gnutls arm64 8.2.1-1ubuntu2 [305 kB] Get:79 http://ftpmaster.internal/ubuntu mantic/main arm64 libcurl4 arm64 8.2.1-1ubuntu2 [311 kB] Get:80 http://ftpmaster.internal/ubuntu mantic/main arm64 libcurl4-gnutls-dev arm64 8.2.1-1ubuntu2 [424 kB] Get:81 http://ftpmaster.internal/ubuntu mantic/main arm64 libdatrie1 arm64 0.2.13-2 [19.8 kB] Get:82 http://ftpmaster.internal/ubuntu mantic/main arm64 libdeflate0 arm64 1.18-1 [42.6 kB] Get:83 http://ftpmaster.internal/ubuntu mantic/main arm64 libdeflate-dev arm64 1.18-1 [50.0 kB] Get:84 http://ftpmaster.internal/ubuntu mantic/universe arm64 libdisorder0 arm64 0.0.2+git20130809.8062ee1-4 [4578 B] Get:85 http://ftpmaster.internal/ubuntu mantic/universe arm64 libdisorder-dev arm64 0.0.2+git20130809.8062ee1-4 [3724 B] Get:86 http://ftpmaster.internal/ubuntu mantic/universe arm64 libfastahack0 arm64 1.0.0+dfsg-10 [25.6 kB] Get:87 http://ftpmaster.internal/ubuntu mantic/universe arm64 libfastahack-dev arm64 1.0.0+dfsg-10 [27.2 kB] Get:88 http://ftpmaster.internal/ubuntu mantic/universe arm64 libfml0 arm64 0.1+git20190320.b499514-1 [64.7 kB] Get:89 http://ftpmaster.internal/ubuntu mantic/universe arm64 libfml-dev arm64 0.1+git20190320.b499514-1 [77.8 kB] Get:90 http://ftpmaster.internal/ubuntu mantic/main arm64 libgfortran5 arm64 13.2.0-2ubuntu1 [423 kB] Get:91 http://ftpmaster.internal/ubuntu mantic/main arm64 libgraphite2-3 arm64 1.3.14-1build2 [68.9 kB] Get:92 http://ftpmaster.internal/ubuntu mantic/main arm64 libharfbuzz0b arm64 8.0.1-1 [451 kB] Get:93 http://ftpmaster.internal/ubuntu mantic/universe arm64 libhtscodecs2 arm64 1.5.1-1 [80.6 kB] Get:94 http://ftpmaster.internal/ubuntu mantic/universe arm64 libhts3 arm64 1.17+ds-1 [417 kB] Get:95 http://ftpmaster.internal/ubuntu mantic/main arm64 liblzma-dev arm64 5.4.1-0.2 [176 kB] Get:96 http://ftpmaster.internal/ubuntu mantic/universe arm64 libhts-dev arm64 1.17+ds-1 [5711 kB] Get:97 http://ftpmaster.internal/ubuntu mantic/main arm64 x11-common all 1:7.7+23ubuntu2 [23.4 kB] Get:98 http://ftpmaster.internal/ubuntu mantic/main arm64 libice6 arm64 2:1.0.10-1build2 [41.7 kB] Get:99 http://ftpmaster.internal/ubuntu mantic/main arm64 libjpeg-turbo8 arm64 2.1.5-2ubuntu1 [160 kB] Get:100 http://ftpmaster.internal/ubuntu mantic/main arm64 libjpeg8 arm64 8c-2ubuntu11 [2148 B] Get:101 http://ftpmaster.internal/ubuntu mantic/main arm64 libjsoncpp25 arm64 1.9.5-6 [76.0 kB] Get:102 http://ftpmaster.internal/ubuntu mantic/main arm64 liblapack3 arm64 3.11.0-2 [2136 kB] Get:103 http://ftpmaster.internal/ubuntu mantic/main arm64 liblerc4 arm64 4.0.0+ds-2ubuntu2 [150 kB] Get:104 http://ftpmaster.internal/ubuntu mantic/main arm64 libthai-data all 0.1.29-1build1 [162 kB] Get:105 http://ftpmaster.internal/ubuntu mantic/main arm64 libthai0 arm64 0.1.29-1build1 [18.4 kB] Get:106 http://ftpmaster.internal/ubuntu mantic/main arm64 libpango-1.0-0 arm64 1.51.0+ds-2 [223 kB] Get:107 http://ftpmaster.internal/ubuntu mantic/main arm64 libpangoft2-1.0-0 arm64 1.51.0+ds-2 [40.6 kB] Get:108 http://ftpmaster.internal/ubuntu mantic/main arm64 libpangocairo-1.0-0 arm64 1.51.0+ds-2 [27.3 kB] Get:109 http://ftpmaster.internal/ubuntu mantic/main arm64 libpaper1 arm64 1.1.29 [13.1 kB] Get:110 http://ftpmaster.internal/ubuntu mantic/main arm64 libpaper-utils arm64 1.1.29 [8480 B] Get:111 http://ftpmaster.internal/ubuntu mantic/main arm64 libpkgconf3 arm64 1.8.1-2 [31.2 kB] Get:112 http://ftpmaster.internal/ubuntu mantic/main arm64 libsensors-config all 1:3.6.0-7ubuntu1 [5274 B] Get:113 http://ftpmaster.internal/ubuntu mantic/main arm64 libsensors5 arm64 1:3.6.0-7ubuntu1 [26.1 kB] Get:114 http://ftpmaster.internal/ubuntu mantic/universe arm64 libssw0 arm64 1.1-14 [21.1 kB] Get:115 http://ftpmaster.internal/ubuntu mantic/universe arm64 libseqlib2 arm64 1.2.0+dfsg-10 [163 kB] Get:116 http://ftpmaster.internal/ubuntu mantic/main arm64 libjsoncpp-dev arm64 1.9.5-6 [23.0 kB] Get:117 http://ftpmaster.internal/ubuntu mantic/universe arm64 libssw-dev arm64 1.1-14 [22.9 kB] Get:118 http://ftpmaster.internal/ubuntu mantic/universe arm64 libseqlib-dev arm64 1.2.0+dfsg-10 [232 kB] Get:119 http://ftpmaster.internal/ubuntu mantic/main arm64 libsm6 arm64 2:1.2.3-1build2 [16.1 kB] Get:120 http://ftpmaster.internal/ubuntu mantic/universe arm64 libsmithwaterman0 arm64 0.0+git20160702.2610e25-12 [35.9 kB] Get:121 http://ftpmaster.internal/ubuntu mantic/universe arm64 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http://ftpmaster.internal/ubuntu mantic/main arm64 pkgconf arm64 1.8.1-2 [16.7 kB] Get:182 http://ftpmaster.internal/ubuntu mantic/main arm64 pkg-config arm64 1.8.1-2 [7170 B] Get:183 http://ftpmaster.internal/ubuntu mantic/universe arm64 samtools arm64 1.17-1 [570 kB] Get:184 http://ftpmaster.internal/ubuntu mantic/main arm64 sysstat arm64 12.6.1-1ubuntu1 [480 kB] Get:185 http://ftpmaster.internal/ubuntu mantic/universe arm64 parallel all 20221122+ds-2 [1871 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 123 MB in 6s (21.5 MB/s) Selecting previously unselected package libpython3.11-minimal:arm64. 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Setting up libpipeline1:arm64 (1.5.7-1) ... Setting up libgraphite2-3:arm64 (1.3.14-1build2) ... Setting up libdisorder0:arm64 (0.0.2+git20130809.8062ee1-4) ... Setting up libpixman-1-0:arm64 (0.42.2-1) ... Setting up libwfa2-0:arm64 (2.3.3-2) ... Setting up libxau6:arm64 (1:1.0.9-1build5) ... Setting up libpsl5:arm64 (0.21.2-1) ... Setting up libicu72:arm64 (72.1-3ubuntu2) ... Setting up liblerc4:arm64 (4.0.0+ds-2ubuntu2) ... Setting up fonts-noto-mono (20201225-2) ... Setting up bsdextrautils (2.39.1-4ubuntu1) ... Setting up libdatrie1:arm64 (0.2.13-2) ... Setting up libmagic-mgc (1:5.44-3) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libglib2.0-0:arm64 (2.77.2-1) ... No schema files found: doing nothing. Setting up unzip (6.0-28ubuntu1) ... Setting up libpython3.11-stdlib:arm64 (3.11.5-3) ... Setting up libdebhelper-perl (13.11.6ubuntu1) ... Setting up libbrotli1:arm64 (1.0.9-2build8) ... Setting up x11-common (1:7.7+23ubuntu2) ... Running in chroot, ignoring request. invoke-rc.d: policy-rc.d denied execution of start. Setting up libsensors-config (1:3.6.0-7ubuntu1) ... Setting up libsmithwaterman0:arm64 (0.0+git20160702.2610e25-12) ... Setting up libnghttp2-14:arm64 (1.55.1-1) ... Setting up libmagic1:arm64 (1:5.44-3) ... Setting up libdeflate0:arm64 (1.18-1) ... Setting up bc (1.07.1-3build1) ... Setting up gettext-base (0.21-13) ... Setting up m4 (1.4.19-3) ... Setting up libwfa2-dev (2.3.3-2) ... Setting up file (1:5.44-3) ... Setting up libfml0:arm64 (0.1+git20190320.b499514-1) ... Setting up libfastahack0:arm64 (1.0.0+dfsg-10) ... Setting up libjbig0:arm64 (2.1-6.1ubuntu1) ... Setting up ninja-build (1.11.1-1) ... Setting up libsasl2-modules-db:arm64 (2.1.28+dfsg1-3) ... Setting up libfastahack-dev:arm64 (1.0.0+dfsg-10) ... Setting up zip (3.0-13) ... Setting up autotools-dev (20220109.1) ... Setting up libblas3:arm64 (3.11.0-2) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/aarch64-linux-gnu/libblas.so.3 (libblas.so.3-aarch64-linux-gnu) in auto mode Setting up libpkgconf3:arm64 (1.8.1-2) ... Setting up libfreetype6:arm64 (2.13.1+dfsg-1) ... Setting up libx11-data (2:1.8.6-1) ... Setting up librtmp1:arm64 (2.4+20151223.gitfa8646d.1-2build4) ... Setting up libfribidi0:arm64 (1.0.13-3) ... Setting up libtcl8.6:arm64 (8.6.13+dfsg-2) ... Setting up autopoint (0.21-13) ... Setting up libjsoncpp25:arm64 (1.9.5-6) ... Setting up ucf (3.0043+nmu1) ... Setting up pkgconf-bin (1.8.1-2) ... Setting up libsensors5:arm64 (1:3.6.0-7ubuntu1) ... Setting up libdisorder-dev:arm64 (0.0.2+git20130809.8062ee1-4) ... Setting up libjpeg-turbo8:arm64 (2.1.5-2ubuntu1) ... Setting up libbamtools2.5.2:arm64 (2.5.2+dfsg-4) ... Setting up libsasl2-2:arm64 (2.1.28+dfsg1-3) ... Setting up libssh-4:arm64 (0.10.5-3ubuntu1) ... Setting up libgfortran5:arm64 (13.2.0-2ubuntu1) ... Setting up autoconf (2.71-3) ... Setting up libbwa-dev (0.7.17-7) ... Setting up libwebp7:arm64 (1.2.4-0.2) ... Setting up liblzma-dev:arm64 (5.4.1-0.2) ... Setting up zlib1g-dev:arm64 (1:1.2.13.dfsg-1ubuntu5) ... Setting up libuchardet0:arm64 (0.0.7-1build2) ... Setting up libsub-override-perl (0.09-4) ... Setting up libharfbuzz0b:arm64 (8.0.1-1) ... Setting up libthai-data (0.1.29-1build1) ... Setting up libbsd0:arm64 (0.11.7-4) ... Setting up libdeflate-dev:arm64 (1.18-1) ... Setting up libelf1:arm64 (0.189-4) ... Setting up libssw0:arm64 (1.1-14) ... Setting up libxml2:arm64 (2.9.14+dfsg-1.3) ... Setting up sysstat (12.6.1-1ubuntu1) ... Creating config file /etc/default/sysstat with new version update-alternatives: using /usr/bin/sar.sysstat to provide /usr/bin/sar (sar) in auto mode Created symlink /etc/systemd/system/sysstat.service.wants/sysstat-collect.timer → /lib/systemd/system/sysstat-collect.timer. Created symlink /etc/systemd/system/sysstat.service.wants/sysstat-summary.timer → /lib/systemd/system/sysstat-summary.timer. Created symlink /etc/systemd/system/multi-user.target.wants/sysstat.service → /lib/systemd/system/sysstat.service. Setting up fonts-noto-core (20201225-2) ... Setting up xdg-utils (1.1.3-4.1ubuntu3) ... update-alternatives: using /usr/bin/xdg-open to provide /usr/bin/open (open) in auto mode Setting up libldap2:arm64 (2.6.6+dfsg-1~exp1ubuntu1) ... Setting up libpython3-stdlib:arm64 (3.11.4-5) ... Setting up libjpeg8:arm64 (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 libpaper1:arm64 (1.1.29) ... Creating config file /etc/papersize with new version Setting up python3.11 (3.11.5-3) ... Setting up libice6:arm64 (2:1.0.10-1build2) ... Setting up libjsoncpp-dev:arm64 (1.9.5-6) ... Setting up libdw1:arm64 (0.189-4) ... Setting up libxdmcp6:arm64 (1:1.1.3-0ubuntu5) ... Setting up liblapack3:arm64 (3.11.0-2) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/aarch64-linux-gnu/liblapack.so.3 (liblapack.so.3-aarch64-linux-gnu) in auto mode Setting up libxcb1:arm64 (1.15-1) ... Setting up gettext (0.21-13) ... Setting up libfml-dev:arm64 (0.1+git20190320.b499514-1) ... Setting up libssw-dev:arm64 (1.1-14) ... Setting up libtool (2.4.7-7) ... Setting up libxcb-render0:arm64 (1.15-1) ... Setting up fontconfig-config (2.14.2-4ubuntu1) ... Setting up libcurl3-gnutls:arm64 (8.2.1-1ubuntu2) ... Setting up python3 (3.11.4-5) ... Setting up libxcb-shm0:arm64 (1.15-1) ... Setting up libpaper-utils (1.1.29) ... Setting up libcurl4-gnutls-dev:arm64 (8.2.1-1ubuntu2) ... Setting up pkgconf:arm64 (1.8.1-2) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up libthai0:arm64 (0.1.29-1build1) ... Setting up libbamtools-dev:arm64 (2.5.2+dfsg-4) ... Setting up pkg-config:arm64 (1.8.1-2) ... Setting up libsmithwaterman-dev:arm64 (0.0+git20160702.2610e25-12) ... Setting up parallel (20221122+ds-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 libtiff6:arm64 (4.5.1+git230720-1ubuntu1) ... Setting up debugedit (1:5.0-5) ... Setting up libcurl4:arm64 (8.2.1-1ubuntu2) ... Setting up libx11-6:arm64 (2:1.8.6-1) ... Setting up libfontconfig1:arm64 (2.14.2-4ubuntu1) ... Setting up python3-lib2to3 (3.11.5-1) ... Setting up libsm6:arm64 (2:1.2.3-1build2) ... Setting up python3-pkg-resources (68.1.2-1) ... Setting up python3-distutils (3.11.5-1) ... Setting up fontconfig (2.14.2-4ubuntu1) ... Regenerating fonts cache... done. Setting up libhts3:arm64 (1.17+ds-1) ... Setting up python3-setuptools (68.1.2-1) ... Setting up libxrender1:arm64 (1:0.9.10-1.1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libpango-1.0-0:arm64 (1.51.0+ds-2) ... Setting up libxext6:arm64 (2:1.3.4-1build1) ... Setting up libhts-dev:arm64 (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 libcairo2:arm64 (1.17.8-2) ... Setting up samtools (1.17-1) ... Setting up libxt6:arm64 (1:1.2.1-1.1) ... Setting up libtabixpp0:arm64 (1.1.2-1) ... Setting up libxss1:arm64 (1:1.2.3-1build2) ... Setting up libpangoft2-1.0-0:arm64 (1.51.0+ds-2) ... Setting up libseqlib2:arm64 (1.2.0+dfsg-10) ... Setting up libpangocairo-1.0-0:arm64 (1.51.0+ds-2) ... Setting up libxft2:arm64 (2.3.6-1) ... Setting up libtk8.6:arm64 (8.6.13-2) ... Setting up libseqlib-dev:arm64 (1.2.0+dfsg-10) ... Setting up debhelper (13.11.6ubuntu1) ... Setting up libvcflib2:arm64 (1.0.9+dfsg1-2) ... Setting up r-base-core (4.3.1-4) ... Creating config file /etc/R/Renviron with new version Setting up r-cran-labeling (0.4.2-1) ... Setting up r-cran-lattice (0.21-8-2) ... Setting up r-cran-nlme (3.1.163-1) ... Setting up r-cran-farver (2.1.1-1) ... Setting up r-cran-viridislite (0.4.2-2) ... Setting up libtabixpp-dev:arm64 (1.1.2-1) ... Setting up r-cran-r6 (2.5.1-1) ... Setting up r-cran-pkgkitten (0.2.3-1) ... Setting up r-cran-magrittr (2.0.3-1) ... Setting up r-cran-littler (0.3.18-2) ... Setting up libvcflib-dev:arm64 (1.0.9+dfsg1-2) ... Setting up r-cran-rcpp (1.0.11-1) ... Setting up r-cran-rlang (1.1.1-1) ... Setting up r-cran-gridbase (0.4-7-5build1) ... Setting up littler (0.3.18-2) ... Setting up r-cran-withr (2.5.0-1) ... Setting up r-cran-fansi (1.0.4-1) ... Setting up r-cran-mass (7.3-60-2) ... Setting up r-cran-glue (1.6.2-1) ... Setting up r-cran-cli (3.6.1-1) ... Setting up r-cran-lifecycle (1.0.3+dfsg-1) ... Setting up r-cran-pkgconfig (2.0.3-2build1) ... Setting up r-cran-utf8 (1.2.3-1) ... Setting up r-cran-colorspace (2.1-0+dfsg-1) ... Setting up r-cran-plyr (1.8.8-1) ... Setting up r-cran-rcolorbrewer (1.1-3-1build1) ... Setting up r-cran-isoband (0.2.7-1) ... Setting up r-cran-gtable (0.3.3+dfsg-1) ... Setting up r-cran-matrix (1.6-1-1) ... Setting up r-cran-mgcv (1.9-0-1) ... Setting up r-cran-vctrs (0.6.3-1) ... Setting up r-cran-pillar (1.9.0+dfsg-1) ... Setting up r-cran-munsell (0.5.0-2build1) ... Setting up r-cran-tibble (3.2.1+dfsg-2) ... Setting up r-cran-scales (1.2.1-1) ... Setting up r-cran-ggplot2 (3.4.2+dfsg-2) ... Setting up libvcflib-tools (1.0.9+dfsg1-2) ... 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 (arm64 included in any) +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 5.4.0-156-generic #173-Ubuntu SMP Tue Jul 11 07:25:14 UTC 2023 arm64 (aarch64) Toolchain package versions: binutils_2.41-4ubuntu1 dpkg-dev_1.22.0ubuntu1 g++-12_12.3.0-8ubuntu1 g++-13_13.2.0-2ubuntu1 gcc-12_12.3.0-8ubuntu1 gcc-13_13.2.0-2ubuntu1 libc6-dev_2.38-1ubuntu4 libstdc++-12-dev_12.3.0-8ubuntu1 libstdc++-13-dev_13.2.0-2ubuntu1 libstdc++6_13.2.0-2ubuntu1 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 bc_1.07.1-3build1 binutils_2.41-4ubuntu1 binutils-aarch64-linux-gnu_2.41-4ubuntu1 binutils-common_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 coreutils_9.1-1ubuntu2 cpp_4:13.2.0-1ubuntu1 cpp-12_12.3.0-8ubuntu1 cpp-13_13.2.0-2ubuntu1 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 fontconfig_2.14.2-4ubuntu1 fontconfig-config_2.14.2-4ubuntu1 fonts-noto-core_20201225-2 fonts-noto-mono_20201225-2 g++_4:13.2.0-1ubuntu1 g++-12_12.3.0-8ubuntu1 g++-13_13.2.0-2ubuntu1 gcc_4:13.2.0-1ubuntu1 gcc-12_12.3.0-8ubuntu1 gcc-12-base_12.3.0-8ubuntu1 gcc-13_13.2.0-2ubuntu1 gcc-13-base_13.2.0-2ubuntu1 gettext_0.21-13 gettext-base_0.21-13 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 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 libapparmor1_4.0.0~alpha2-0ubuntu2 libapt-pkg6.0_2.7.3 libarchive-zip-perl_1.68-1 libargon2-1_0~20190702+dfsg-3 libasan8_13.2.0-2ubuntu1 libassuan0_2.5.6-1 libatomic1_13.2.0-2ubuntu1 libattr1_1:2.5.1-4 libaudit-common_1:3.1.1-1 libaudit1_1:3.1.1-1 libbamtools-dev_2.5.2+dfsg-4 libbamtools2.5.2_2.5.2+dfsg-4 libbinutils_2.41-4ubuntu1 libblas3_3.11.0-2 libblkid1_2.39.1-4ubuntu1 libbrotli1_1.0.9-2build8 libbsd0_0.11.7-4 libbwa-dev_0.7.17-7 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 libcairo2_1.17.8-2 libcap-ng0_0.8.3-1build2 libcap2_1:2.66-4ubuntu1 libcc1-0_13.2.0-2ubuntu1 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 libdatrie1_0.2.13-2 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 libdisorder-dev_0.0.2+git20130809.8062ee1-4 libdisorder0_0.0.2+git20130809.8062ee1-4 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 libfastahack-dev_1.0.0+dfsg-10 libfastahack0_1.0.0+dfsg-10 libfdisk1_2.39.1-4ubuntu1 libffi8_3.4.4-1 libfile-stripnondeterminism-perl_1.13.1-1 libfml-dev_0.1+git20190320.b499514-1 libfml0_0.1+git20190320.b499514-1 libfontconfig1_2.14.2-4ubuntu1 libfreetype6_2.13.1+dfsg-1 libfribidi0_1.0.13-3 libgcc-12-dev_12.3.0-8ubuntu1 libgcc-13-dev_13.2.0-2ubuntu1 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x11-common_1:7.7+23ubuntu2 xdg-utils_1.1.3-4.1ubuntu3 xz-utils_5.4.1-0.2 zip_3.0-13 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: freebayes Binary: freebayes Architecture: any Version: 1.3.7-1 Maintainer: Debian Med Packaging Team Uploaders: Brad Chapman , Andreas Tille Homepage: https://github.com/ekg/freebayes Standards-Version: 4.6.2 Vcs-Browser: https://salsa.debian.org/med-team/freebayes Vcs-Git: https://salsa.debian.org/med-team/freebayes.git Testsuite: autopkgtest Build-Depends: debhelper-compat (= 13), meson, ninja-build, pkg-config, zlib1g-dev, libbamtools-dev, libvcflib-dev (>= 1.0.9+dfsg-1~), libtabixpp-dev, libseqlib-dev, bc, samtools, parallel , libvcflib-tools , debhelper Package-List: freebayes deb science optional arch=any Checksums-Sha1: aa5e76b874f5daa90102152d542fa30f5bac701f 2901909 freebayes_1.3.7.orig.tar.gz a09e02c045aba29995c62fa6e4abf0ff78ea3766 11812 freebayes_1.3.7-1.debian.tar.xz Checksums-Sha256: 73de20987bfad317099e5bb2f651073351906b9fb1392d704332f401fbfbb5c6 2901909 freebayes_1.3.7.orig.tar.gz 952bcb0e3bb5f6583b3fea22a92c742b1b44e32669462d3b34bbaf819d6a5b56 11812 freebayes_1.3.7-1.debian.tar.xz Files: 83a9eaef72b98e3c03c287ec73c69687 2901909 freebayes_1.3.7.orig.tar.gz 3c6f7bea75fda1cf07ba01381993bde4 11812 freebayes_1.3.7-1.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQIzBAEBCgAdFiEEck1gkzcRPHEFUNdHPCZ2P2xn5uIFAmTjVdAACgkQPCZ2P2xn 5uIY3RAAzZaoII+50EQ5LZUGZSNAnPkI7I7TTjJvPcqXp4+Mq4ugFdt1b6vTqucx AhNG9ICJBgPdNYbkpR3XKif6396BlVJprztnuHi4xIwKN3qNZWGOeRz/wRnYl78X 8MVSi4bOHr+/wW9pdrVe5yWQ9Lc66TudfNh176T3CEWVjljQ1nH5lbboab4jp7FN y7peGqhnClyMgXTf8CE8ATph0s+ZdzsTEv2BK+Kqg5wD2R4l8gZoJKiXAH9qwOEr 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---------------- 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-26676744 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-26676744 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-26676744 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 freebayes dpkg-buildpackage: info: source version 1.3.7-1 dpkg-buildpackage: info: source distribution unstable dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 debian/rules clean dh clean --buildsystem=meson --builddir=build dh_auto_clean -O--buildsystem=meson -O--builddir=build dh_autoreconf_clean -O--buildsystem=meson -O--builddir=build dh_clean -O--buildsystem=meson -O--builddir=build debian/rules binary-arch dh binary-arch --buildsystem=meson --builddir=build dh_update_autotools_config -a -O--buildsystem=meson -O--builddir=build dh_autoreconf -a -O--buildsystem=meson -O--builddir=build dh_auto_configure -a -O--buildsystem=meson -O--builddir=build cd build && 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/aarch64-linux-gnu -Dpython.bytecompile=-1 The Meson build system Version: 1.2.1 Source dir: /<> Build dir: /<>/build Build type: native build Project name: freebayes Project version: 1.3.6 C compiler for the host machine: cc (gcc 13.2.0 "cc (Ubuntu 13.2.0-2ubuntu1) 13.2.0") C linker for the host machine: cc ld.bfd 2.41 C++ compiler for the host machine: c++ (gcc 13.2.0 "c++ (Ubuntu 13.2.0-2ubuntu1) 13.2.0") C++ linker for the host machine: c++ ld.bfd 2.41 Host machine cpu family: aarch64 Host machine cpu: aarch64 Found pkg-config: /usr/bin/pkg-config (1.8.1) Run-time dependency zlib found: YES 1.2.13 Run-time dependency liblzma found: YES 5.4.1 Run-time dependency threads found: YES Library tabixpp found: YES Run-time dependency htslib found: YES 1.17 Library tabixpp found: YES Run-time dependency libvcflib found: YES 1.0 Run-time dependency libseqlib found: YES 1.0 Compiler for C++ supports arguments -fpermissive: YES Compiler for C++ supports arguments -Wno-reorder: YES Compiler for C++ supports arguments -Wno-sign-compare: YES Compiler for C++ supports arguments -Wno-unused-variable: YES Compiler for C++ supports arguments -Wno-unused-but-set-variable: YES Program prove found: YES (/usr/bin/prove) Build targets in project: 3 freebayes 1.3.6 User defined options buildtype : plain libdir : lib/aarch64-linux-gnu localstatedir : /var prefix : /usr sysconfdir : /etc wrap_mode : nodownload python.bytecompile: -1 Found ninja-1.11.1 at /usr/bin/ninja dh_auto_build -a -O--buildsystem=meson -O--builddir=build cd build && LC_ALL=C.UTF-8 ninja -j4 -v [1/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../contrib/ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++17 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/freebayes-1.3.7-1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_Bias.cpp.o -MF libfreebayes_common.a.p/src_Bias.cpp.o.d -o libfreebayes_common.a.p/src_Bias.cpp.o -c ../src/Bias.cpp [2/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../contrib/ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++17 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/freebayes-1.3.7-1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_BedReader.cpp.o -MF libfreebayes_common.a.p/src_BedReader.cpp.o.d -o libfreebayes_common.a.p/src_BedReader.cpp.o -c ../src/BedReader.cpp [3/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../contrib/ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++17 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/freebayes-1.3.7-1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_CNV.cpp.o -MF libfreebayes_common.a.p/src_CNV.cpp.o.d -o libfreebayes_common.a.p/src_CNV.cpp.o -c ../src/CNV.cpp [4/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../contrib/ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++17 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/freebayes-1.3.7-1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_Contamination.cpp.o -MF libfreebayes_common.a.p/src_Contamination.cpp.o.d -o libfreebayes_common.a.p/src_Contamination.cpp.o -c ../src/Contamination.cpp [5/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../contrib/ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++17 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/freebayes-1.3.7-1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_Dirichlet.cpp.o -MF libfreebayes_common.a.p/src_Dirichlet.cpp.o.d -o libfreebayes_common.a.p/src_Dirichlet.cpp.o -c ../src/Dirichlet.cpp [6/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../contrib/ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++17 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/freebayes-1.3.7-1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_Ewens.cpp.o -MF libfreebayes_common.a.p/src_Ewens.cpp.o.d -o libfreebayes_common.a.p/src_Ewens.cpp.o -c ../src/Ewens.cpp [7/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../contrib/ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++17 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/freebayes-1.3.7-1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_Allele.cpp.o -MF libfreebayes_common.a.p/src_Allele.cpp.o.d -o libfreebayes_common.a.p/src_Allele.cpp.o -c ../src/Allele.cpp [8/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../contrib/ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++17 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/freebayes-1.3.7-1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_DataLikelihood.cpp.o -MF libfreebayes_common.a.p/src_DataLikelihood.cpp.o.d -o libfreebayes_common.a.p/src_DataLikelihood.cpp.o -c ../src/DataLikelihood.cpp In file included from ../src/AlleleParser.h:32, from ../src/DataLikelihood.h:20, from ../src/DataLikelihood.cpp:1: /usr/include/vcflib/Variant.h:650:28: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 650 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, 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 ../src/DataLikelihood.h:4: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /usr/include/vcflib/Variant.h:651:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 651 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [9/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../contrib/ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++17 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/freebayes-1.3.7-1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_IndelAllele.cpp.o -MF libfreebayes_common.a.p/src_IndelAllele.cpp.o.d -o libfreebayes_common.a.p/src_IndelAllele.cpp.o -c ../src/IndelAllele.cpp [10/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../contrib/ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++17 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/freebayes-1.3.7-1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_FBFasta.cpp.o -MF libfreebayes_common.a.p/src_FBFasta.cpp.o.d -o libfreebayes_common.a.p/src_FBFasta.cpp.o -c ../src/FBFasta.cpp ../src/FBFasta.cpp: In member function ‘FB::FastaReference::getRawSequence(std::__cxx11::basic_string, std::allocator >)’: ../src/FBFasta.cpp:273:20: warning: pointer ‘pbegin_35’ used after ‘free’ [-Wuse-after-free] 273 | s.resize((pend - pbegin)/sizeof(char)); | ~~~~~^~~~~~~~ ../src/FBFasta.cpp:272:9: note: call to ‘free’ here 272 | free(seq); | ~~~~^~~~~ ../src/FBFasta.cpp: In member function ‘FB::FastaReference::getRawSubSequence(std::__cxx11::basic_string, std::allocator >, int, int)’: ../src/FBFasta.cpp:316:20: warning: pointer ‘pbegin_59’ used after ‘free’ [-Wuse-after-free] 316 | s.resize((pend - pbegin)/sizeof(char)); | ~~~~~^~~~~~~~ ../src/FBFasta.cpp:315:9: note: call to ‘free’ here 315 | free(seq); | ~~~~^~~~~ [11/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../contrib/ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++17 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/freebayes-1.3.7-1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_LeftAlign.cpp.o -MF libfreebayes_common.a.p/src_LeftAlign.cpp.o.d -o libfreebayes_common.a.p/src_LeftAlign.cpp.o -c ../src/LeftAlign.cpp [12/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../contrib/ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++17 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/freebayes-1.3.7-1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_Multinomial.cpp.o -MF libfreebayes_common.a.p/src_Multinomial.cpp.o.d -o libfreebayes_common.a.p/src_Multinomial.cpp.o -c ../src/Multinomial.cpp [13/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../contrib/ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++17 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/freebayes-1.3.7-1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_Marginals.cpp.o -MF libfreebayes_common.a.p/src_Marginals.cpp.o.d -o libfreebayes_common.a.p/src_Marginals.cpp.o -c ../src/Marginals.cpp In file included from ../src/AlleleParser.h:32, from ../src/ResultData.h:10, from ../src/Marginals.h:7, from ../src/Marginals.cpp:1: /usr/include/vcflib/Variant.h:650:28: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 650 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from ../src/Marginals.h:4: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /usr/include/vcflib/Variant.h:651:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 651 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [14/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../contrib/ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++17 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/freebayes-1.3.7-1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_NonCall.cpp.o -MF libfreebayes_common.a.p/src_NonCall.cpp.o.d -o libfreebayes_common.a.p/src_NonCall.cpp.o -c ../src/NonCall.cpp [15/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../contrib/ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++17 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/freebayes-1.3.7-1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_Result.cpp.o -MF libfreebayes_common.a.p/src_Result.cpp.o.d -o libfreebayes_common.a.p/src_Result.cpp.o -c ../src/Result.cpp [16/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../contrib/ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++17 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/freebayes-1.3.7-1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_Genotype.cpp.o -MF libfreebayes_common.a.p/src_Genotype.cpp.o.d -o libfreebayes_common.a.p/src_Genotype.cpp.o -c ../src/Genotype.cpp [17/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../contrib/ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++17 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/freebayes-1.3.7-1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_Parameters.cpp.o -MF libfreebayes_common.a.p/src_Parameters.cpp.o.d -o libfreebayes_common.a.p/src_Parameters.cpp.o -c ../src/Parameters.cpp [18/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../contrib/ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++17 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/freebayes-1.3.7-1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_SegfaultHandler.cpp.o -MF libfreebayes_common.a.p/src_SegfaultHandler.cpp.o.d -o libfreebayes_common.a.p/src_SegfaultHandler.cpp.o -c ../src/SegfaultHandler.cpp [19/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../contrib/ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++17 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/freebayes-1.3.7-1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_AlleleParser.cpp.o -MF libfreebayes_common.a.p/src_AlleleParser.cpp.o.d -o libfreebayes_common.a.p/src_AlleleParser.cpp.o -c ../src/AlleleParser.cpp In file included from ../src/AlleleParser.h:32, from ../src/AlleleParser.cpp:1: /usr/include/vcflib/Variant.h:650:28: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 650 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, 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 ../src/AlleleParser.h:4: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /usr/include/vcflib/Variant.h:651:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 651 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [20/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../contrib/ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++17 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/freebayes-1.3.7-1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_Sample.cpp.o -MF libfreebayes_common.a.p/src_Sample.cpp.o.d -o libfreebayes_common.a.p/src_Sample.cpp.o -c ../src/Sample.cpp [21/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../contrib/ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++17 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/freebayes-1.3.7-1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_Utility.cpp.o -MF libfreebayes_common.a.p/src_Utility.cpp.o.d -o libfreebayes_common.a.p/src_Utility.cpp.o -c ../src/Utility.cpp In file included from ../contrib/ttmath/ttmathint.h:48, from ../contrib/ttmath/ttmathbig.h:46, from ../contrib/ttmath/ttmath.h:58, from ../src/Utility.h:18, from ../src/Utility.cpp:3: In member function ‘ttmath::UInt<2u>::operator=(ttmath::UInt<2u> const&)’, inlined from ‘ttmath::Big<8u, 2u>::operator=(ttmath::Big<8u, 2u> const&)’ at ../contrib/ttmath/ttmathbig.h:3648:12, inlined from ‘ttmath::Big<8u, 2u>::Big(ttmath::Big<8u, 2u> const&)’ at ../contrib/ttmath/ttmathbig.h:3660:12, inlined from ‘ttmath::Exp >(ttmath::Big<8u, 2u> const&, ttmath::ErrorCode*)ttmath::Big<8u, 2u>’ at ../contrib/ttmath/ttmath.h:326:10, inlined from ‘big_exp(long double)’ at ../src/Utility.cpp:363:25: ../contrib/ttmath/ttmathuint.h:2740:43: warning: ‘MEM[(const struct UInt &)&x + 32].table[0]’ may be used uninitialized [-Wmaybe-uninitialized] 2740 | table[i] = p.table[i]; | ~~~~~~~^ ../src/Utility.cpp: In function ‘big_exp(long double)’: ../src/Utility.cpp:361:14: note: ‘x’ declared here 361 | BigFloat x, result; | ^ In member function ‘ttmath::UInt<2u>::operator=(ttmath::UInt<2u> const&)’, inlined from ‘ttmath::Big<8u, 2u>::operator=(ttmath::Big<8u, 2u> const&)’ at ../contrib/ttmath/ttmathbig.h:3648:12, inlined from ‘ttmath::Big<8u, 2u>::Big(ttmath::Big<8u, 2u> const&)’ at ../contrib/ttmath/ttmathbig.h:3660:12, inlined from ‘ttmath::Exp >(ttmath::Big<8u, 2u> const&, ttmath::ErrorCode*)ttmath::Big<8u, 2u>’ at ../contrib/ttmath/ttmath.h:326:10, inlined from ‘big_exp(long double)’ at ../src/Utility.cpp:363:25: ../contrib/ttmath/ttmathuint.h:2740:43: warning: ‘MEM[(const struct UInt &)&x + 32].table[1]’ may be used uninitialized [-Wmaybe-uninitialized] 2740 | table[i] = p.table[i]; | ~~~~~~~^ ../src/Utility.cpp: In function ‘big_exp(long double)’: ../src/Utility.cpp:361:14: note: ‘x’ declared here 361 | BigFloat x, result; | ^ In member function ‘ttmath::UInt<2u>::operator=(ttmath::UInt<2u> const&)’, inlined from ‘ttmath::Big<8u, 2u>::operator=(ttmath::Big<8u, 2u> const&)’ at ../contrib/ttmath/ttmathbig.h:3648:12, inlined from ‘ttmath::Big<8u, 2u>::Big(ttmath::Big<8u, 2u> const&)’ at ../contrib/ttmath/ttmathbig.h:3660:12, inlined from ‘ttmath::Big<8u, 2u>::operator+(ttmath::Big<8u, 2u> const&) const’ at ../contrib/ttmath/ttmathbig.h:5570:15, inlined from ‘logsumexp_probs(std::vector > const&)’ at ../src/Utility.cpp:381:48: ../contrib/ttmath/ttmathuint.h:2740:43: warning: ‘MEM[(const struct UInt &)&maxNb + 32].table[0]’ may be used uninitialized [-Wmaybe-uninitialized] 2740 | table[i] = p.table[i]; | ~~~~~~~^ ../src/Utility.cpp: In function ‘logsumexp_probs(std::vector > const&)’: ../src/Utility.cpp:380:14: note: ‘maxNb’ declared here 380 | BigFloat maxNb; maxNb.FromDouble(maxN); | ^~~~~ In member function ‘ttmath::UInt<2u>::operator=(ttmath::UInt<2u> const&)’, inlined from ‘ttmath::Big<8u, 2u>::operator=(ttmath::Big<8u, 2u> const&)’ at ../contrib/ttmath/ttmathbig.h:3648:12, inlined from ‘ttmath::Big<8u, 2u>::Big(ttmath::Big<8u, 2u> const&)’ at ../contrib/ttmath/ttmathbig.h:3660:12, inlined from ‘ttmath::Big<8u, 2u>::operator+(ttmath::Big<8u, 2u> const&) const’ at ../contrib/ttmath/ttmathbig.h:5570:15, inlined from ‘logsumexp_probs(std::vector > const&)’ at ../src/Utility.cpp:381:48: ../contrib/ttmath/ttmathuint.h:2740:43: warning: ‘MEM[(const struct UInt &)&maxNb + 32].table[1]’ may be used uninitialized [-Wmaybe-uninitialized] 2740 | table[i] = p.table[i]; | ~~~~~~~^ ../src/Utility.cpp: In function ‘logsumexp_probs(std::vector > const&)’: ../src/Utility.cpp:380:14: note: ‘maxNb’ declared here 380 | BigFloat maxNb; maxNb.FromDouble(maxN); | ^~~~~ In member function ‘ttmath::UInt<2u>::operator=(ttmath::UInt<2u> const&)’, inlined from ‘ttmath::Big<8u, 2u>::operator=(ttmath::Big<8u, 2u> const&)’ at ../contrib/ttmath/ttmathbig.h:3648:12, inlined from ‘ttmath::Big<8u, 2u>::Big(ttmath::Big<8u, 2u> const&)’ at ../contrib/ttmath/ttmathbig.h:3660:12, inlined from ‘ttmath::Log >(ttmath::Big<8u, 2u> const&, ttmath::Big<8u, 2u> const&, ttmath::ErrorCode*)ttmath::Big<8u, 2u>’ at ../contrib/ttmath/ttmath.h:311:9, inlined from ‘big2phred(ttmath::Big<8u, 2u> const&)’ at ../src/Utility.cpp:58:44: ../contrib/ttmath/ttmathuint.h:2740:43: warning: ‘MEM[(const struct UInt &)&result + 32].table[0]’ may be used uninitialized [-Wmaybe-uninitialized] 2740 | table[i] = p.table[i]; | ~~~~~~~^ ../contrib/ttmath/ttmath.h: In function ‘big2phred(ttmath::Big<8u, 2u> const&)’: ../contrib/ttmath/ttmath.h:288:27: note: ‘result’ declared here 288 | ValueType result; | ^~~~~~ In member function ‘ttmath::UInt<2u>::operator=(ttmath::UInt<2u> const&)’, inlined from ‘ttmath::Big<8u, 2u>::operator=(ttmath::Big<8u, 2u> const&)’ at ../contrib/ttmath/ttmathbig.h:3648:12, inlined from ‘ttmath::Big<8u, 2u>::Big(ttmath::Big<8u, 2u> const&)’ at ../contrib/ttmath/ttmathbig.h:3660:12, inlined from ‘ttmath::Log >(ttmath::Big<8u, 2u> const&, ttmath::Big<8u, 2u> const&, ttmath::ErrorCode*)ttmath::Big<8u, 2u>’ at ../contrib/ttmath/ttmath.h:311:9, inlined from ‘big2phred(ttmath::Big<8u, 2u> const&)’ at ../src/Utility.cpp:58:44: ../contrib/ttmath/ttmathuint.h:2740:43: warning: ‘MEM[(const struct UInt &)&result + 32].table[1]’ may be used uninitialized [-Wmaybe-uninitialized] 2740 | table[i] = p.table[i]; | ~~~~~~~^ ../contrib/ttmath/ttmath.h: In function ‘big2phred(ttmath::Big<8u, 2u> const&)’: ../contrib/ttmath/ttmath.h:288:27: note: ‘result’ declared here 288 | ValueType result; | ^~~~~~ In member function ‘ttmath::UInt<2u>::operator=(ttmath::UInt<2u> const&)’, inlined from ‘ttmath::Big<8u, 2u>::operator=(ttmath::Big<8u, 2u> const&)’ at ../contrib/ttmath/ttmathbig.h:3648:12, inlined from ‘ttmath::Big<8u, 2u>::Big(ttmath::Big<8u, 2u> const&)’ at ../contrib/ttmath/ttmathbig.h:3660:12, inlined from ‘ttmath::Log >(ttmath::Big<8u, 2u> const&, ttmath::Big<8u, 2u> const&, ttmath::ErrorCode*)ttmath::Big<8u, 2u>’ at ../contrib/ttmath/ttmath.h:311:9, inlined from ‘big2phred(ttmath::Big<8u, 2u> const&)’ at ../src/Utility.cpp:58:44: ../contrib/ttmath/ttmathuint.h:2740:43: warning: ‘MEM[(const struct UInt &)&result + 32].table[0]’ may be used uninitialized [-Wmaybe-uninitialized] 2740 | table[i] = p.table[i]; | ~~~~~~~^ ../contrib/ttmath/ttmath.h: In function ‘big2phred(ttmath::Big<8u, 2u> const&)’: ../contrib/ttmath/ttmath.h:288:27: note: ‘result’ declared here 288 | ValueType result; | ^~~~~~ In member function ‘ttmath::UInt<2u>::operator=(ttmath::UInt<2u> const&)’, inlined from ‘ttmath::Big<8u, 2u>::operator=(ttmath::Big<8u, 2u> const&)’ at ../contrib/ttmath/ttmathbig.h:3648:12, inlined from ‘ttmath::Big<8u, 2u>::Big(ttmath::Big<8u, 2u> const&)’ at ../contrib/ttmath/ttmathbig.h:3660:12, inlined from ‘ttmath::Log >(ttmath::Big<8u, 2u> const&, ttmath::Big<8u, 2u> const&, ttmath::ErrorCode*)ttmath::Big<8u, 2u>’ at ../contrib/ttmath/ttmath.h:311:9, inlined from ‘big2phred(ttmath::Big<8u, 2u> const&)’ at ../src/Utility.cpp:58:44: ../contrib/ttmath/ttmathuint.h:2740:43: warning: ‘MEM[(const struct UInt &)&result + 32].table[1]’ may be used uninitialized [-Wmaybe-uninitialized] 2740 | table[i] = p.table[i]; | ~~~~~~~^ ../contrib/ttmath/ttmath.h: In function ‘big2phred(ttmath::Big<8u, 2u> const&)’: ../contrib/ttmath/ttmath.h:288:27: note: ‘result’ declared here 288 | ValueType result; | ^~~~~~ [22/27] c++ -Ibamleftalign.p -I. -I.. -I../src -I../contrib/ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++17 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/freebayes-1.3.7-1 -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ bamleftalign.p/src_bamleftalign.cpp.o -MF bamleftalign.p/src_bamleftalign.cpp.o.d -o bamleftalign.p/src_bamleftalign.cpp.o -c ../src/bamleftalign.cpp [23/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../contrib/ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++17 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/freebayes-1.3.7-1 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_ResultData.cpp.o -MF libfreebayes_common.a.p/src_ResultData.cpp.o.d -o libfreebayes_common.a.p/src_ResultData.cpp.o -c ../src/ResultData.cpp In file included from ../src/AlleleParser.h:32, from ../src/ResultData.h:10, from ../src/ResultData.cpp:1: /usr/include/vcflib/Variant.h:650:28: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 650 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from ../src/ResultData.h:4: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /usr/include/vcflib/Variant.h:651:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 651 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [24/27] rm -f libfreebayes_common.a && gcc-ar csrDT libfreebayes_common.a libfreebayes_common.a.p/src_Allele.cpp.o libfreebayes_common.a.p/src_AlleleParser.cpp.o libfreebayes_common.a.p/src_BedReader.cpp.o libfreebayes_common.a.p/src_Bias.cpp.o libfreebayes_common.a.p/src_CNV.cpp.o libfreebayes_common.a.p/src_Contamination.cpp.o libfreebayes_common.a.p/src_DataLikelihood.cpp.o libfreebayes_common.a.p/src_Dirichlet.cpp.o libfreebayes_common.a.p/src_Ewens.cpp.o libfreebayes_common.a.p/src_FBFasta.cpp.o libfreebayes_common.a.p/src_Genotype.cpp.o libfreebayes_common.a.p/src_IndelAllele.cpp.o libfreebayes_common.a.p/src_LeftAlign.cpp.o libfreebayes_common.a.p/src_Marginals.cpp.o libfreebayes_common.a.p/src_Multinomial.cpp.o libfreebayes_common.a.p/src_NonCall.cpp.o libfreebayes_common.a.p/src_Parameters.cpp.o libfreebayes_common.a.p/src_Result.cpp.o libfreebayes_common.a.p/src_ResultData.cpp.o libfreebayes_common.a.p/src_Sample.cpp.o libfreebayes_common.a.p/src_SegfaultHandler.cpp.o libfreebayes_common.a.p/src_Utility.cpp.o [25/27] c++ -Ifreebayes.p -I. -I.. -I../src -I../contrib/ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++17 -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/freebayes-1.3.7-1 -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ freebayes.p/src_freebayes.cpp.o -MF freebayes.p/src_freebayes.cpp.o.d -o freebayes.p/src_freebayes.cpp.o -c ../src/freebayes.cpp In file included from ../src/AlleleParser.h:32, from ../src/freebayes.cpp:29: /usr/include/vcflib/Variant.h:650:28: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 650 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, 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 ../src/freebayes.cpp:9: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /usr/include/vcflib/Variant.h:651:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 651 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [26/27] c++ -o bamleftalign bamleftalign.p/src_bamleftalign.cpp.o -Wl,--as-needed -Wl,--no-undefined -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/freebayes-1.3.7-1 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,--start-group libfreebayes_common.a /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/liblzma.so -pthread /usr/lib/aarch64-linux-gnu/libhts.so /usr/lib/gcc/aarch64-linux-gnu/13/../../../aarch64-linux-gnu/libvcflib.so /usr/lib/gcc/aarch64-linux-gnu/13/../../../aarch64-linux-gnu/libsmithwaterman.so /usr/lib/gcc/aarch64-linux-gnu/13/../../../aarch64-linux-gnu/libdisorder.so /usr/lib/gcc/aarch64-linux-gnu/13/../../../aarch64-linux-gnu/libfastahack.so /usr/lib/aarch64-linux-gnu/libseqlib.so /usr/lib/libbwa.a /usr/lib/gcc/aarch64-linux-gnu/13/../../../aarch64-linux-gnu/libtabixpp.so -Wl,--end-group [27/27] c++ -o freebayes freebayes.p/src_freebayes.cpp.o -Wl,--as-needed -Wl,--no-undefined -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/freebayes-1.3.7-1 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,--start-group libfreebayes_common.a /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/liblzma.so -pthread /usr/lib/aarch64-linux-gnu/libhts.so /usr/lib/gcc/aarch64-linux-gnu/13/../../../aarch64-linux-gnu/libtabixpp.so /usr/lib/gcc/aarch64-linux-gnu/13/../../../aarch64-linux-gnu/libvcflib.so /usr/lib/gcc/aarch64-linux-gnu/13/../../../aarch64-linux-gnu/libsmithwaterman.so /usr/lib/gcc/aarch64-linux-gnu/13/../../../aarch64-linux-gnu/libdisorder.so /usr/lib/gcc/aarch64-linux-gnu/13/../../../aarch64-linux-gnu/libfastahack.so /usr/lib/aarch64-linux-gnu/libseqlib.so /usr/lib/libbwa.a -Wl,--end-group debian/rules override_dh_auto_test make[1]: Entering directory '/<>' mkdir -p test/bash-tap/ ln -s -t test/bash-tap /<>/debian/bash-tap/* mkdir -p test/test-simple-bash ln -s -t test/test-simple-bash /<>/debian/test-simple-bash/* dh_auto_test -- -v --timeout-multiplier 100 cd build && DEB_PYTHON_INSTALL_LAYOUT=deb LC_ALL=C.UTF-8 MESON_TESTTHREADS=4 meson test -v --timeout-multiplier 100 ninja: Entering directory `/<>/build' ninja: no work to do. 1/5 T00 RUNNING >>> MALLOC_PERTURB_=114 /usr/bin/prove -e bash -v t/00_region_and_target_handling.t 2/5 T01 RUNNING >>> MALLOC_PERTURB_=75 /usr/bin/prove -e bash -v t/01_call_variants.t 3/5 T01b RUNNING >>> MALLOC_PERTURB_=151 /usr/bin/prove -e bash -v t/01b_call_variants.t 4/5 T02 RUNNING >>> MALLOC_PERTURB_=30 /usr/bin/prove -e bash -v t/02_multi_bam.t 1/5 T00 OK 0.45s ――――――――――――――――――――――――――――――――――――― ✀ ――――――――――――――――――――――――――――――――――――― t/00_region_and_target_handling.t .. 1..12 ok 1 - ref:4-5 ref:6-7 are empty ok 2 - ref:4 ref:6 are empty ok 3 - ref:5-6 ref:7-8 ok 4 - ref:5 ref:7 ok 5 - ref:5- ok 6 - full output ok 7 - --targets t/../00_region_and_target_handling.t.bed ok 8 - --region ref ok 9 - ref:1,0- ok 10 - ref:1,0-1,1 ok 11 - ref:0-1 ok 12 - region outside of bounds error ok All tests successful. Files=1, Tests=12, 0 wallclock secs ( 0.04 usr 0.01 sys + 0.12 cusr 0.09 csys = 0.26 CPU) Result: PASS ―――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――― 5/5 T03 RUNNING >>> MALLOC_PERTURB_=107 /usr/bin/prove -e bash -v t/03_reference_bases.t 4/5 T02 OK 0.49s ――――――――――――――――――――――――――――――――――――― ✀ ――――――――――――――――――――――――――――――――――――― t/02_multi_bam.t .. 1..7 ok 1 - freebayes calls from two identical BAMs ok 2 - freebayes calls from two BAMs with different samples for different read groups ok 3 - freebayes calls from two BAMs with different technologies for different read groups ok 4 - freebayes rejects two BAMs with different samples for same read groups ok 5 - freebayes rejects two BAMs with different technologies for same read groups ok 6 - freebayes calls multiple alts from two different BAMs ok 7 - freebayes rejects two BAMs with the same name ok All tests successful. Files=1, Tests=7, 0 wallclock secs ( 0.04 usr 0.01 sys + 0.13 cusr 0.08 csys = 0.26 CPU) Result: PASS ―――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――― 5/5 T03 OK 0.23s ――――――――――――――――――――――――――――――――――――― ✀ ――――――――――――――――――――――――――――――――――――― t/03_reference_bases.t .. 1..3 ok 1 - freebayes rejects invalid reference ok 2 - freebayes does not put uppercase IUPAC bases in VCFs ok 3 - freebayes does not put lowercase IUPAC bases in VCFs ok All tests successful. Files=1, Tests=3, 1 wallclock secs ( 0.03 usr 0.00 sys + 0.04 cusr 0.03 csys = 0.10 CPU) Result: PASS ―――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――― 3/5 T01b OK 6.51s ――――――――――――――――――――――――――――――――――――― ✀ ――――――――――――――――――――――――――――――――――――― t/01b_call_variants.t .. 1..10 ok 1 - running in parallel makes no difference ok 2 - freebayes handles spaces in file names ok 3 - freebayes handles region and variant input even with : in contig names ok 4 - freebayes can handle spliced reads ok 5 - freebayes produces the expected number of lines of gVCF output ok 6 - freebayes produces the expected number of lines of gVCF output ok 7 - freebayes produces the expected number of lines of gVCF output ok 8 - the CNV map may be used to specify per-sample copy numbers ok 9 - freebayes makes the expected number of calls when capping coverage ok 10 - freebayes correctly uses CNV map with multiple entries ok All tests successful. Files=1, Tests=10, 6 wallclock secs ( 0.03 usr 0.01 sys + 6.69 cusr 0.68 csys = 7.41 CPU) Result: PASS ―――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――― 2/5 T01 OK 16.65s ――――――――――――――――――――――――――――――――――――― ✀ ――――――――――――――――――――――――――――――――――――― stdout: t/01_call_variants.t .. 1..16 ok 1 - variant calling recovers most of the GiAB variants in a test region ok 2 - freebayes produces the same number of calls if targeted per site or called without targets ok 3 - a targets bed file can be used with the same effect as running by region ok 4 - reading from stdin or not makes no difference ok 5 - freebayes processes all alignments in BAM input ok 6 - freebayes processes all alignments in CRAM input ok 7 - freebayes correctly handles variant input ok 8 - freebayes puts required variants in output ok 9 - freebayes limits calls to input variants correctly ok 10 - freebayes reports all input variants even when there is no input data ok 11 - freebayes handles region and variant input ok 12 - freebayes limits to variant input correctly when region is given ok 13 - freebayes handles variant input and reading from stdin ok 14 - freebayes limits to variant input when reading from stdin ok 15 - freebayes handles region, stdin, and variant input ok 16 - ! ok All tests successful. Files=1, Tests=16, 17 wallclock secs ( 0.05 usr 0.00 sys + 12.34 cusr 9.66 csys = 22.05 CPU) Result: PASS stderr: [E::idx_find_and_load] Could not retrieve index file for '-' Random access with SetRegion not available for STDIN reading (no index file) ERROR(freebayes): Could not SetRegion to q:1..10000 t/01_call_variants.t: line 107: 12398 Aborted (core dumped) freebayes -f tiny/q.fa.gz -@ tiny/q_spiked.vcf.gz -r q:1-10000 -l - < tiny/NA12878.chr22.tiny.bam > /dev/null 2> /dev/null ―――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――― Ok: 5 Expected Fail: 0 Fail: 0 Unexpected Pass: 0 Skipped: 0 Timeout: 0 Full log written to /<>/build/meson-logs/testlog.txt find . -name core -delete rm -Rf test/bash-tap rm -Rf test/test-simple-bash make[1]: Leaving directory '/<>' create-stamp debian/debhelper-build-stamp dh_testroot -a -O--buildsystem=meson -O--builddir=build dh_prep -a -O--buildsystem=meson -O--builddir=build dh_auto_install --destdir=debian/freebayes/ -a -O--buildsystem=meson -O--builddir=build cd build && DESTDIR=/<>/debian/freebayes LC_ALL=C.UTF-8 ninja install [0/1] Installing files. Installing freebayes to /<>/debian/freebayes/usr/bin Installing bamleftalign to /<>/debian/freebayes/usr/bin dh_install -a -O--buildsystem=meson -O--builddir=build dh_installdocs -a -O--buildsystem=meson -O--builddir=build dh_installchangelogs -a -O--buildsystem=meson -O--builddir=build dh_installexamples -a -O--buildsystem=meson -O--builddir=build dh_installsystemduser -a -O--buildsystem=meson -O--builddir=build dh_perl -a -O--buildsystem=meson -O--builddir=build dh_link -a -O--buildsystem=meson -O--builddir=build dh_strip_nondeterminism -a -O--buildsystem=meson -O--builddir=build dh_compress -a -O--buildsystem=meson -O--builddir=build dh_fixperms -a -O--buildsystem=meson -O--builddir=build dh_missing -a -O--buildsystem=meson -O--builddir=build dh_dwz -a -O--buildsystem=meson -O--builddir=build dh_strip -a -O--buildsystem=meson -O--builddir=build debugedit: debian/freebayes/usr/bin/bamleftalign: Unknown DWARF DW_FORM_0x1f20 cdee6195158beb9b7e595219210d1fa6816de9f0 debugedit: debian/freebayes/usr/bin/freebayes: Unknown DWARF DW_FORM_0x1f20 0e1acaf2cf5532bb538577311daa5c2dcbcbe15e dh_makeshlibs -a -O--buildsystem=meson -O--builddir=build dh_shlibdeps -a -O--buildsystem=meson -O--builddir=build dh_installdeb -a -O--buildsystem=meson -O--builddir=build dh_gencontrol -a -O--buildsystem=meson -O--builddir=build dpkg-gencontrol: warning: package freebayes: substitution variable ${perl:Depends} unused, but is defined dpkg-gencontrol: warning: package freebayes: substitution variable ${perl:Depends} unused, but is defined dh_md5sums -a -O--buildsystem=meson -O--builddir=build dh_builddeb -a -O--buildsystem=meson -O--builddir=build INFO: pkgstriptranslations version 153 INFO: pkgstriptranslations version 153 pkgstriptranslations: processing freebayes (in debian/freebayes); do_strip: , oemstrip: pkgstriptranslations: processing freebayes-dbgsym (in debian/.debhelper/freebayes/dbgsym-root); do_strip: , oemstrip: pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/freebayes/DEBIAN/control, package freebayes, directory debian/freebayes pkgstripfiles: processing control file: debian/.debhelper/freebayes/dbgsym-root/DEBIAN/control, package freebayes-dbgsym, directory debian/.debhelper/freebayes/dbgsym-root pkgstripfiles: Running PNG optimization (using 4 cpus) for package freebayes ... dpkg-deb: building package 'freebayes-dbgsym' in 'debian/.debhelper/scratch-space/build-freebayes/freebayes-dbgsym_1.3.7-1_arm64.deb'. pkgstripfiles: No PNG files. dpkg-deb: building package 'freebayes' in '../freebayes_1.3.7-1_arm64.deb'. Renaming freebayes-dbgsym_1.3.7-1_arm64.deb to freebayes-dbgsym_1.3.7-1_arm64.ddeb dpkg-genbuildinfo --build=any -O../freebayes_1.3.7-1_arm64.buildinfo dpkg-genchanges --build=any -mLaunchpad Build Daemon -O../freebayes_1.3.7-1_arm64.changes dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) -------------------------------------------------------------------------------- Build finished at 2023-09-02T14:58:03Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ freebayes_1.3.7-1_arm64.changes: -------------------------------- Format: 1.8 Date: Mon, 21 Aug 2023 13:22:14 +0200 Source: freebayes Binary: freebayes Built-For-Profiles: noudeb Architecture: arm64 Version: 1.3.7-1 Distribution: mantic-proposed Urgency: medium Maintainer: Launchpad Build Daemon Changed-By: Michael R. Crusoe Description: freebayes - Bayesian haplotype-based polymorphism discovery and genotyping Changes: freebayes (1.3.7-1) unstable; urgency=medium . * Team Upload. . [ Andreas Tille ] * Bump versioned Build-Depends: libvcflib-dev (>= 1.0.9+dfsg-1~) * Do not build on i386 on Salsa CI . [ Michael R. Crusoe ] * d/control: applied fix for :unnecessary greater-than versioned dependency * d/copyright: update path for ttmath * Set upstream metadata fields: Bug-Database, Bug-Submit, Repository, Repository-Browse. * d/rules: delete any by-products from testing Checksums-Sha1: 501bf017ac8911de9064445d0908d502b44ef188 4623498 freebayes-dbgsym_1.3.7-1_arm64.ddeb ff01febaeeefca615fcd2350312b337946aca392 10962 freebayes_1.3.7-1_arm64.buildinfo 93c347222fe14aebc861871040a00829e700bbf9 1466226 freebayes_1.3.7-1_arm64.deb Checksums-Sha256: 03ede4e6623cfdafa2d61c36222a88735bb8907dc66e28329b88918a8a4de99e 4623498 freebayes-dbgsym_1.3.7-1_arm64.ddeb f2815c3780564d17231196ce40fbc8fb207c49dc0d800cd1ea13c9db88f4985e 10962 freebayes_1.3.7-1_arm64.buildinfo 370e5132c59ca49776a1a57e7e896cc0dc9e6a4d5d5acb058aeaef3de9d924c7 1466226 freebayes_1.3.7-1_arm64.deb Files: a7c58d3ce1141f5c70c77627ae1f886f 4623498 debug optional freebayes-dbgsym_1.3.7-1_arm64.ddeb 1b4da6737be73915651285f635972f41 10962 science optional freebayes_1.3.7-1_arm64.buildinfo 06c8bcd9c07d8d46c8bd3543ce778053 1466226 science optional freebayes_1.3.7-1_arm64.deb /<>/freebayes_1.3.7-1_arm64.changes.new could not be renamed to /<>/freebayes_1.3.7-1_arm64.changes: Illegal seek Distribution field may be wrong!!! +------------------------------------------------------------------------------+ | Buildinfo | +------------------------------------------------------------------------------+ Format: 1.0 Source: freebayes Binary: freebayes freebayes-dbgsym Architecture: arm64 Version: 1.3.7-1 Checksums-Md5: a7c58d3ce1141f5c70c77627ae1f886f 4623498 freebayes-dbgsym_1.3.7-1_arm64.ddeb 06c8bcd9c07d8d46c8bd3543ce778053 1466226 freebayes_1.3.7-1_arm64.deb Checksums-Sha1: 501bf017ac8911de9064445d0908d502b44ef188 4623498 freebayes-dbgsym_1.3.7-1_arm64.ddeb 93c347222fe14aebc861871040a00829e700bbf9 1466226 freebayes_1.3.7-1_arm64.deb Checksums-Sha256: 03ede4e6623cfdafa2d61c36222a88735bb8907dc66e28329b88918a8a4de99e 4623498 freebayes-dbgsym_1.3.7-1_arm64.ddeb 370e5132c59ca49776a1a57e7e896cc0dc9e6a4d5d5acb058aeaef3de9d924c7 1466226 freebayes_1.3.7-1_arm64.deb Build-Origin: Ubuntu Build-Architecture: arm64 Build-Date: Sat, 02 Sep 2023 14:58:02 +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), bc (= 1.07.1-3build1), binutils (= 2.41-4ubuntu1), binutils-aarch64-linux-gnu (= 2.41-4ubuntu1), binutils-common (= 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), coreutils (= 9.1-1ubuntu2), cpp (= 4:13.2.0-1ubuntu1), cpp-12 (= 12.3.0-8ubuntu1), cpp-13 (= 13.2.0-2ubuntu1), 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), fontconfig (= 2.14.2-4ubuntu1), fontconfig-config (= 2.14.2-4ubuntu1), fonts-noto-core (= 20201225-2), fonts-noto-mono (= 20201225-2), g++ (= 4:13.2.0-1ubuntu1), g++-13 (= 13.2.0-2ubuntu1), gcc (= 4:13.2.0-1ubuntu1), gcc-12 (= 12.3.0-8ubuntu1), gcc-12-base (= 12.3.0-8ubuntu1), gcc-13 (= 13.2.0-2ubuntu1), gcc-13-base (= 13.2.0-2ubuntu1), gettext (= 0.21-13), gettext-base (= 0.21-13), grep (= 3.11-2), groff-base (= 1.23.0-2), gzip (= 1.12-1ubuntu1), hostname (= 3.23+nmu1ubuntu1), init-system-helpers (= 1.65.2ubuntu1), intltool-debian (= 0.35.0+20060710.6), libacl1 (= 2.3.1-3), libarchive-zip-perl (= 1.68-1), libasan8 (= 13.2.0-2ubuntu1), libatomic1 (= 13.2.0-2ubuntu1), libattr1 (= 1:2.5.1-4), libaudit-common (= 1:3.1.1-1), libaudit1 (= 1:3.1.1-1), libbamtools-dev (= 2.5.2+dfsg-4), libbamtools2.5.2 (= 2.5.2+dfsg-4), libbinutils (= 2.41-4ubuntu1), libblas3 (= 3.11.0-2), libblkid1 (= 2.39.1-4ubuntu1), libbrotli1 (= 1.0.9-2build8), libbsd0 (= 0.11.7-4), libbwa-dev (= 0.7.17-7), 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), libcairo2 (= 1.17.8-2), libcap-ng0 (= 0.8.3-1build2), libcap2 (= 1:2.66-4ubuntu1), libcc1-0 (= 13.2.0-2ubuntu1), 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), libdatrie1 (= 0.2.13-2), libdb5.3 (= 5.3.28+dfsg2-2), libdebconfclient0 (= 0.270ubuntu1), libdebhelper-perl (= 13.11.6ubuntu1), libdeflate-dev (= 1.18-1), libdeflate0 (= 1.18-1), libdisorder-dev (= 0.0.2+git20130809.8062ee1-4), libdisorder0 (= 0.0.2+git20130809.8062ee1-4), libdpkg-perl (= 1.22.0ubuntu1), libdw1 (= 0.189-4), libelf1 (= 0.189-4), libexpat1 (= 2.5.0-2), libfastahack-dev (= 1.0.0+dfsg-10), libfastahack0 (= 1.0.0+dfsg-10), libffi8 (= 3.4.4-1), libfile-stripnondeterminism-perl (= 1.13.1-1), libfml-dev (= 0.1+git20190320.b499514-1), libfml0 (= 0.1+git20190320.b499514-1), libfontconfig1 (= 2.14.2-4ubuntu1), libfreetype6 (= 2.13.1+dfsg-1), libfribidi0 (= 1.0.13-3), libgcc-12-dev (= 12.3.0-8ubuntu1), libgcc-13-dev (= 13.2.0-2ubuntu1), libgcc-s1 (= 13.2.0-2ubuntu1), libgcrypt20 (= 1.10.2-2ubuntu1), libgdbm-compat4 (= 1.23-3), libgdbm6 (= 1.23-3), libgfortran5 (= 13.2.0-2ubuntu1), libglib2.0-0 (= 2.77.2-1), libgmp10 (= 2:6.3.0+dfsg-2ubuntu4), libgnutls30 (= 3.8.1-4ubuntu1), libgomp1 (= 13.2.0-2ubuntu1), libgpg-error0 (= 1.47-2), libgprofng0 (= 2.41-4ubuntu1), libgraphite2-3 (= 1.3.14-1build2), libgssapi-krb5-2 (= 1.20.1-3ubuntu1), libharfbuzz0b (= 8.0.1-1), libhogweed6 (= 3.9.1-2), libhts-dev (= 1.17+ds-1), libhts3 (= 1.17+ds-1), libhtscodecs2 (= 1.5.1-1), libhwasan0 (= 13.2.0-2ubuntu1), libice6 (= 2:1.0.10-1build2), libicu72 (= 72.1-3ubuntu2), libidn2-0 (= 2.3.4-1), libisl23 (= 0.26-3), libitm1 (= 13.2.0-2ubuntu1), libjansson4 (= 2.14-2), libjbig0 (= 2.1-6.1ubuntu1), libjpeg-turbo8 (= 2.1.5-2ubuntu1), libjpeg8 (= 8c-2ubuntu11), libjsoncpp-dev (= 1.9.5-6), 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), liblapack3 (= 3.11.0-2), libldap2 (= 2.6.6+dfsg-1~exp1ubuntu1), liblerc4 (= 4.0.0+ds-2ubuntu2), liblsan0 (= 13.2.0-2ubuntu1), 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), 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), libpango-1.0-0 (= 1.51.0+ds-2), libpangocairo-1.0-0 (= 1.51.0+ds-2), libpangoft2-1.0-0 (= 1.51.0+ds-2), libpaper-utils (= 1.1.29), libpaper1 (= 1.1.29), libpcre2-8-0 (= 10.42-4), libperl5.36 (= 5.36.0-7ubuntu1), libpipeline1 (= 1.5.7-1), libpixman-1-0 (= 0.42.2-1), libpkgconf3 (= 1.8.1-2), libpng16-16 (= 1.6.40-1), 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), libreadline8 (= 8.2-1.3), 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), libsensors-config (= 1:3.6.0-7ubuntu1), libsensors5 (= 1:3.6.0-7ubuntu1), libseqlib-dev (= 1.2.0+dfsg-10), libseqlib2 (= 1.2.0+dfsg-10), libsframe1 (= 2.41-4ubuntu1), libsm6 (= 2:1.2.3-1build2), libsmartcols1 (= 2.39.1-4ubuntu1), libsmithwaterman-dev (= 0.0+git20160702.2610e25-12), libsmithwaterman0 (= 0.0+git20160702.2610e25-12), libsqlite3-0 (= 3.42.0-1), libssh-4 (= 0.10.5-3ubuntu1), libssl3 (= 3.0.10-1ubuntu2), libssw-dev (= 1.1-14), libssw0 (= 1.1-14), libstdc++-13-dev (= 13.2.0-2ubuntu1), libstdc++6 (= 13.2.0-2ubuntu1), libsub-override-perl (= 0.09-4), libsystemd0 (= 253.5-1ubuntu4), libtabixpp-dev (= 1.1.2-1), libtabixpp0 (= 1.1.2-1), libtasn1-6 (= 4.19.0-3), libtcl8.6 (= 8.6.13+dfsg-2), libthai-data (= 0.1.29-1build1), libthai0 (= 0.1.29-1build1), libtiff6 (= 4.5.1+git230720-1ubuntu1), 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), libtk8.6 (= 8.6.13-2), libtool (= 2.4.7-7), libtsan2 (= 13.2.0-2ubuntu1), libubsan1 (= 13.2.0-2ubuntu1), libuchardet0 (= 0.0.7-1build2), libudev1 (= 253.5-1ubuntu4), libunistring2 (= 1.0-2), libuuid1 (= 2.39.1-4ubuntu1), libvcflib-dev (= 1.0.9+dfsg1-2), libvcflib-tools (= 1.0.9+dfsg1-2), libvcflib2 (= 1.0.9+dfsg1-2), libwebp7 (= 1.2.4-0.2), libwfa2-0 (= 2.3.3-2), libwfa2-dev (= 2.3.3-2), libx11-6 (= 2:1.8.6-1), libx11-data (= 2:1.8.6-1), libxau6 (= 1:1.0.9-1build5), libxcb-render0 (= 1.15-1), libxcb-shm0 (= 1.15-1), libxcb1 (= 1.15-1), libxdmcp6 (= 1:1.1.3-0ubuntu5), libxext6 (= 2:1.3.4-1build1), libxft2 (= 2.3.6-1), libxml2 (= 2.9.14+dfsg-1.3), libxrender1 (= 1:0.9.10-1.1), libxss1 (= 1:1.2.3-1build2), libxt6 (= 1:1.2.1-1.1), libzstd1 (= 1.5.5+dfsg2-1ubuntu2), linux-libc-dev (= 6.5.0-2.2), littler (= 0.3.18-2), login (= 1:4.13+dfsg1-1ubuntu1), 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), ncurses-base (= 6.4+20230625-2), ncurses-bin (= 6.4+20230625-2), ninja-build (= 1.11.1-1), openssl (= 3.0.10-1ubuntu2), parallel (= 20221122+ds-2), 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), r-base-core (= 4.3.1-4), r-cran-cli (= 3.6.1-1), r-cran-colorspace (= 2.1-0+dfsg-1), r-cran-fansi (= 1.0.4-1), r-cran-farver (= 2.1.1-1), r-cran-ggplot2 (= 3.4.2+dfsg-2), r-cran-glue (= 1.6.2-1), r-cran-gridbase (= 0.4-7-5build1), r-cran-gtable (= 0.3.3+dfsg-1), r-cran-isoband (= 0.2.7-1), r-cran-labeling (= 0.4.2-1), r-cran-lattice (= 0.21-8-2), r-cran-lifecycle (= 1.0.3+dfsg-1), r-cran-littler (= 0.3.18-2), r-cran-magrittr (= 2.0.3-1), r-cran-mass (= 7.3-60-2), r-cran-matrix (= 1.6-1-1), r-cran-mgcv (= 1.9-0-1), r-cran-munsell (= 0.5.0-2build1), r-cran-nlme (= 3.1.163-1), r-cran-pillar (= 1.9.0+dfsg-1), r-cran-pkgconfig (= 2.0.3-2build1), r-cran-pkgkitten (= 0.2.3-1), r-cran-plyr (= 1.8.8-1), r-cran-r6 (= 2.5.1-1), r-cran-rcolorbrewer (= 1.1-3-1build1), r-cran-rcpp (= 1.0.11-1), r-cran-rlang (= 1.1.1-1), r-cran-scales (= 1.2.1-1), r-cran-tibble (= 3.2.1+dfsg-2), r-cran-utf8 (= 1.2.3-1), r-cran-vctrs (= 0.6.3-1), r-cran-viridislite (= 0.4.2-2), r-cran-withr (= 2.5.0-1), readline-common (= 8.2-1.3), rpcsvc-proto (= 1.4.2-0ubuntu6), samtools (= 1.17-1), sed (= 4.9-1), sensible-utils (= 0.0.20), sysstat (= 12.6.1-1ubuntu1), sysvinit-utils (= 3.07-1ubuntu1), tar (= 1.34+dfsg-1.2ubuntu1), tzdata (= 2023c-9ubuntu1), ucf (= 3.0043+nmu1), unzip (= 6.0-28ubuntu1), util-linux (= 2.39.1-4ubuntu1), x11-common (= 1:7.7+23ubuntu2), xdg-utils (= 1.1.3-4.1ubuntu3), xz-utils (= 5.4.1-0.2), zip (= 3.0-13), 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="1692616934" +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ freebayes_1.3.7-1_arm64.deb --------------------------- new Debian package, version 2.0. size 1466226 bytes: control archive=2640 bytes. 942 bytes, 18 lines control 6305 bytes, 75 lines md5sums Package: freebayes Version: 1.3.7-1 Architecture: arm64 Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 2869 Depends: libc6 (>= 2.38), libgcc-s1 (>= 4.5), libseqlib2 (>= 1.2.0+dfsg), libstdc++6 (>= 13.1), libtabixpp0 (>= 1.0.0), libvcflib2 (>= 1.0.9+dfsg1), zlib1g (>= 1:1.1.4), python3 Recommends: parallel Section: science Priority: optional Homepage: https://github.com/ekg/freebayes Description: Bayesian haplotype-based polymorphism discovery and genotyping FreeBayes is a Bayesian genetic variant detector designed to find small polymorphisms, specifically SNPs (single-nucleotide polymorphisms), indels (insertions and deletions), MNPs (multi-nucleotide polymorphisms), and complex events (composite insertion and substitution events) smaller than the length of a short-read sequencing alignment. drwxr-xr-x root/root 0 2023-08-21 11:22 ./ drwxr-xr-x root/root 0 2023-08-21 11:22 ./usr/ drwxr-xr-x root/root 0 2023-08-21 11:22 ./usr/bin/ -rwxr-xr-x root/root 330392 2023-08-21 11:22 ./usr/bin/bamleftalign -rwxr-xr-x root/root 1575440 2023-08-21 11:22 ./usr/bin/freebayes drwxr-xr-x root/root 0 2023-08-21 11:22 ./usr/share/ drwxr-xr-x root/root 0 2023-08-21 11:22 ./usr/share/doc/ drwxr-xr-x root/root 0 2023-08-21 11:22 ./usr/share/doc/freebayes/ -rw-r--r-- root/root 10293 2023-02-12 03:55 ./usr/share/doc/freebayes/README.md.gz -rw-r--r-- root/root 278 2021-01-28 10:06 ./usr/share/doc/freebayes/README.test -rw-r--r-- root/root 83 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+------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: arm64 Build Type: any Build-Space: 133304 Build-Time: 108 Distribution: mantic-proposed Host Architecture: arm64 Install-Time: 32 Job: freebayes_1.3.7-1.dsc Machine Architecture: arm64 Package: freebayes Package-Time: 142 Source-Version: 1.3.7-1 Space: 133304 Status: successful Version: 1.3.7-1 -------------------------------------------------------------------------------- Finished at 2023-09-02T14:58:03Z Build needed 00:02:22, 133304k disk space RUN: /usr/share/launchpad-buildd/bin/in-target scan-for-processes --backend=chroot --series=mantic --arch=arm64 PACKAGEBUILD-26676744 Scanning for processes to kill in build PACKAGEBUILD-26676744