https://launchpad.net/ubuntu/+source/reapr/1.0.18+dfsg-5build1/+build/18888505 RUN: /usr/share/launchpad-buildd/bin/builder-prep Kernel version: Linux bos02-arm64-064 4.4.0-176-generic #206-Ubuntu SMP Fri Feb 28 05:03:00 UTC 2020 aarch64 Buildd toolchain package versions: launchpad-buildd_186 python-lpbuildd_186 sbuild_0.67.0-2ubuntu7.1 bzr-builder_0.7.3+bzr174~ppa13~ubuntu14.10.1 bzr_2.7.0-2ubuntu3.1 git-build-recipe_0.3.6~git201906051340.ff11471~ubuntu16.04.1 git_1:2.7.4-0ubuntu1.7 dpkg-dev_1.18.4ubuntu1.6 python-debian_0.1.27ubuntu2. Syncing the system clock with the buildd NTP service... 24 Mar 19:04:36 ntpdate[1872]: adjust time server 10.211.37.1 offset 0.017666 sec RUN: /usr/share/launchpad-buildd/bin/in-target unpack-chroot --backend=chroot --series=focal --arch=arm64 PACKAGEBUILD-18888505 --image-type chroot /home/buildd/filecache-default/9d93b4075e16ce7cfbdf01f21507152b0a173b17 Creating target for build PACKAGEBUILD-18888505 RUN: /usr/share/launchpad-buildd/bin/in-target mount-chroot --backend=chroot --series=focal --arch=arm64 PACKAGEBUILD-18888505 Starting target for build PACKAGEBUILD-18888505 RUN: /usr/share/launchpad-buildd/bin/in-target override-sources-list --backend=chroot --series=focal --arch=arm64 PACKAGEBUILD-18888505 'deb http://ftpmaster.internal/ubuntu focal main universe' 'deb http://ftpmaster.internal/ubuntu focal-security main universe' 'deb http://ftpmaster.internal/ubuntu focal-updates main universe' 'deb http://ftpmaster.internal/ubuntu focal-proposed main universe' Overriding sources.list in build-PACKAGEBUILD-18888505 RUN: /usr/share/launchpad-buildd/bin/in-target update-debian-chroot --backend=chroot --series=focal --arch=arm64 PACKAGEBUILD-18888505 Updating target for build PACKAGEBUILD-18888505 Get:1 http://ftpmaster.internal/ubuntu focal InRelease [255 kB] Get:2 http://ftpmaster.internal/ubuntu focal-security InRelease [79.7 kB] Get:3 http://ftpmaster.internal/ubuntu focal-updates InRelease [79.7 kB] Get:4 http://ftpmaster.internal/ubuntu focal-proposed InRelease [255 kB] Get:5 http://ftpmaster.internal/ubuntu focal/main arm64 Packages [942 kB] Get:6 http://ftpmaster.internal/ubuntu focal/main Translation-en [502 kB] Get:7 http://ftpmaster.internal/ubuntu focal/universe arm64 Packages [8425 kB] Get:8 http://ftpmaster.internal/ubuntu focal/universe Translation-en [5146 kB] Get:9 http://ftpmaster.internal/ubuntu focal-proposed/main arm64 Packages [38.2 kB] Get:10 http://ftpmaster.internal/ubuntu focal-proposed/main Translation-en [21.9 kB] Get:11 http://ftpmaster.internal/ubuntu focal-proposed/universe arm64 Packages [293 kB] Get:12 http://ftpmaster.internal/ubuntu focal-proposed/universe Translation-en [220 kB] Fetched 16.3 MB in 6s (2690 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: libffi6 libhogweed4 libisl21 libnettle6 libperl5.28 perl-modules-5.28 Use 'sudo apt autoremove' to remove them. The following NEW packages will be installed: gcc-10-base libapt-pkg6.0 libcrypt-dev libcrypt1 libctf-nobfd0 libctf0 libffi7 libgcc-s1 libhogweed5 libisl22 libnettle7 libperl5.30 libprocps8 perl-modules-5.30 The following packages will be upgraded: advancecomp apt base-files base-passwd bash binutils binutils-aarch64-linux-gnu binutils-common bsdutils bzip2 cpp cpp-9 debianutils dpkg dpkg-dev e2fsprogs fdisk findutils g++ g++-9 gcc gcc-9 gcc-9-base gpg gpg-agent gpgconf gpgv grep gzip hostname libacl1 libapparmor1 libapt-pkg5.90 libasan5 libassuan0 libatomic1 libattr1 libaudit-common libaudit1 libbinutils libblkid1 libbz2-1.0 libc-bin libc-dev-bin libc6 libc6-dev libcap-ng0 libcap2 libcc1-0 libcom-err2 libcryptsetup12 libdb5.3 libdebconfclient0 libdevmapper1.02.1 libdpkg-perl libext2fs2 libfdisk1 libgcc-9-dev libgcc1 libgcrypt20 libgmp10 libgnutls30 libgomp1 libgpg-error0 libip4tc2 libitm1 libjson-c4 libkmod2 liblockfile-bin liblockfile1 liblsan0 liblz4-1 libmount1 libncurses6 libncursesw6 libp11-kit0 libpam-modules libpam-modules-bin libpam-runtime libpam0g libpcre2-8-0 libpcre3 libpng16-16 libreadline8 libseccomp2 libselinux1 libsemanage-common libsemanage1 libsepol1 libsmartcols1 libsqlite3-0 libss2 libssl1.1 libstdc++-9-dev libstdc++6 libsystemd0 libtasn1-6 libtinfo6 libtsan0 libubsan1 libudev1 libuuid1 libzstd1 linux-libc-dev login logsave lsb-base mawk mount ncurses-base ncurses-bin openssl passwd perl perl-base pinentry-curses procps readline-common sensible-utils systemd systemd-sysv sysvinit-utils tar tzdata ubuntu-keyring util-linux zlib1g 127 upgraded, 14 newly installed, 0 to remove and 0 not upgraded. Need to get 64.6 MB of archives. After this operation, 45.2 MB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu focal/main arm64 gcc-10-base arm64 10-20200321-1ubuntu1 [18.7 kB] Get:2 http://ftpmaster.internal/ubuntu focal/main arm64 libgmp10 arm64 2:6.2.0+dfsg-4 [218 kB] Get:3 http://ftpmaster.internal/ubuntu focal/main arm64 libisl22 arm64 0.22.1-1 [537 kB] Get:4 http://ftpmaster.internal/ubuntu focal/main arm64 libcc1-0 arm64 10-20200321-1ubuntu1 [37.1 kB] Get:5 http://ftpmaster.internal/ubuntu focal/main arm64 libctf-nobfd0 arm64 2.34-5ubuntu1 [43.5 kB] Get:6 http://ftpmaster.internal/ubuntu focal/main arm64 libctf0 arm64 2.34-5ubuntu1 [43.1 kB] Get:7 http://ftpmaster.internal/ubuntu focal/main arm64 binutils-aarch64-linux-gnu arm64 2.34-5ubuntu1 [1985 kB] Get:8 http://ftpmaster.internal/ubuntu focal/main arm64 libbinutils arm64 2.34-5ubuntu1 [477 kB] Get:9 http://ftpmaster.internal/ubuntu focal/main arm64 binutils-common arm64 2.34-5ubuntu1 [207 kB] Get:10 http://ftpmaster.internal/ubuntu focal/main arm64 gcc-9-base arm64 9.3.0-7ubuntu1 [19.2 kB] Get:11 http://ftpmaster.internal/ubuntu focal/main arm64 libgcc-s1 arm64 10-20200321-1ubuntu1 [34.8 kB] Get:12 http://ftpmaster.internal/ubuntu focal/universe arm64 libgcc1 arm64 1:10-20200321-1ubuntu1 [34.7 kB] Get:13 http://ftpmaster.internal/ubuntu focal/main arm64 libgomp1 arm64 10-20200321-1ubuntu1 [92.0 kB] Get:14 http://ftpmaster.internal/ubuntu focal/main arm64 libitm1 arm64 10-20200321-1ubuntu1 [23.8 kB] Get:15 http://ftpmaster.internal/ubuntu focal/main arm64 libatomic1 arm64 10-20200321-1ubuntu1 [9176 B] Get:16 http://ftpmaster.internal/ubuntu focal/main arm64 libasan5 arm64 9.3.0-7ubuntu1 [365 kB] Get:17 http://ftpmaster.internal/ubuntu focal/main arm64 liblsan0 arm64 10-20200321-1ubuntu1 [130 kB] Get:18 http://ftpmaster.internal/ubuntu focal/main arm64 libtsan0 arm64 10-20200321-1ubuntu1 [302 kB] Get:19 http://ftpmaster.internal/ubuntu focal/main arm64 libubsan1 arm64 10-20200321-1ubuntu1 [126 kB] Get:20 http://ftpmaster.internal/ubuntu focal/main arm64 libgcc-9-dev arm64 9.3.0-7ubuntu1 [899 kB] Get:21 http://ftpmaster.internal/ubuntu focal/main arm64 libcrypt1 arm64 1:4.4.10-10ubuntu4 [82.5 kB] Get:22 http://ftpmaster.internal/ubuntu focal/main arm64 libc6 arm64 2.31-0ubuntu6 [2266 kB] Get:23 http://ftpmaster.internal/ubuntu focal/main arm64 libc-dev-bin arm64 2.31-0ubuntu6 [64.1 kB] Get:24 http://ftpmaster.internal/ubuntu focal/main arm64 libc-bin arm64 2.31-0ubuntu6 [501 kB] Get:25 http://ftpmaster.internal/ubuntu focal/main arm64 libc6-dev arm64 2.31-0ubuntu6 [2059 kB] Get:26 http://ftpmaster.internal/ubuntu focal/main arm64 libcrypt-dev arm64 1:4.4.10-10ubuntu4 [111 kB] Get:27 http://ftpmaster.internal/ubuntu focal/main arm64 binutils arm64 2.34-5ubuntu1 [3352 B] Get:28 http://ftpmaster.internal/ubuntu focal/main arm64 libstdc++-9-dev arm64 9.3.0-7ubuntu1 [1676 kB] Get:29 http://ftpmaster.internal/ubuntu focal/main arm64 g++-9 arm64 9.3.0-7ubuntu1 [6814 kB] Get:30 http://ftpmaster.internal/ubuntu focal/main arm64 gcc-9 arm64 9.3.0-7ubuntu1 [6682 kB] Get:31 http://ftpmaster.internal/ubuntu focal/main arm64 cpp-9 arm64 9.3.0-7ubuntu1 [5963 kB] Get:32 http://ftpmaster.internal/ubuntu focal/main arm64 libstdc++6 arm64 10-20200321-1ubuntu1 [462 kB] Get:33 http://ftpmaster.internal/ubuntu focal/main arm64 zlib1g arm64 1:1.2.11.dfsg-2ubuntu1 [51.1 kB] Get:34 http://ftpmaster.internal/ubuntu focal/main arm64 linux-libc-dev arm64 5.4.0-18.22 [1136 kB] Get:35 http://ftpmaster.internal/ubuntu focal/main arm64 base-files arm64 11ubuntu4 [60.0 kB] Get:36 http://ftpmaster.internal/ubuntu focal/main arm64 debianutils arm64 4.9.1 [85.6 kB] Get:37 http://ftpmaster.internal/ubuntu focal/main arm64 bash arm64 5.0-6ubuntu1 [604 kB] Get:38 http://ftpmaster.internal/ubuntu focal/main arm64 bsdutils arm64 1:2.34-0.1ubuntu8 [60.4 kB] Get:39 http://ftpmaster.internal/ubuntu focal-proposed/main arm64 tar arm64 1.30+dfsg-7 [227 kB] Get:40 http://ftpmaster.internal/ubuntu focal-proposed/main arm64 dpkg arm64 1.19.7ubuntu3 [1114 kB] Get:41 http://ftpmaster.internal/ubuntu focal/main arm64 findutils arm64 4.7.0-1ubuntu1 [320 kB] Get:42 http://ftpmaster.internal/ubuntu focal/main arm64 grep arm64 3.4-1 [143 kB] Get:43 http://ftpmaster.internal/ubuntu focal/main arm64 gzip arm64 1.10-0ubuntu4 [93.0 kB] Get:44 http://ftpmaster.internal/ubuntu focal/main arm64 hostname arm64 3.23 [11.1 kB] Get:45 http://ftpmaster.internal/ubuntu focal/main arm64 login arm64 1:4.8.1-1ubuntu3 [219 kB] Get:46 http://ftpmaster.internal/ubuntu focal/main arm64 libncurses6 arm64 6.2-0ubuntu2 [91.9 kB] Get:47 http://ftpmaster.internal/ubuntu focal/main arm64 libtinfo6 arm64 6.2-0ubuntu2 [81.1 kB] Get:48 http://ftpmaster.internal/ubuntu focal/main arm64 ncurses-bin arm64 6.2-0ubuntu2 [167 kB] Get:49 http://ftpmaster.internal/ubuntu focal/main arm64 libncursesw6 arm64 6.2-0ubuntu2 [120 kB] Get:50 http://ftpmaster.internal/ubuntu focal/main arm64 perl-modules-5.30 all 5.30.0-9build1 [2737 kB] Get:51 http://ftpmaster.internal/ubuntu focal/main arm64 libperl5.30 arm64 5.30.0-9build1 [3760 kB] Get:52 http://ftpmaster.internal/ubuntu focal/main arm64 perl arm64 5.30.0-9build1 [224 kB] Get:53 http://ftpmaster.internal/ubuntu focal/main arm64 perl-base arm64 5.30.0-9build1 [1389 kB] Get:54 http://ftpmaster.internal/ubuntu focal/main arm64 bzip2 arm64 1.0.8-2 [33.0 kB] Get:55 http://ftpmaster.internal/ubuntu focal/main arm64 libbz2-1.0 arm64 1.0.8-2 [32.9 kB] Get:56 http://ftpmaster.internal/ubuntu focal/main arm64 libdb5.3 arm64 5.3.28+dfsg1-0.6ubuntu2 [620 kB] Get:57 http://ftpmaster.internal/ubuntu focal/main arm64 libblkid1 arm64 2.34-0.1ubuntu8 [129 kB] Get:58 http://ftpmaster.internal/ubuntu focal/main arm64 libuuid1 arm64 2.34-0.1ubuntu8 [19.5 kB] Get:59 http://ftpmaster.internal/ubuntu focal/main arm64 libfdisk1 arm64 2.34-0.1ubuntu8 [160 kB] Get:60 http://ftpmaster.internal/ubuntu focal/main arm64 libpcre2-8-0 arm64 10.34-7 [170 kB] Get:61 http://ftpmaster.internal/ubuntu focal/main arm64 libselinux1 arm64 3.0-1build2 [65.0 kB] Get:62 http://ftpmaster.internal/ubuntu focal/main arm64 libmount1 arm64 2.34-0.1ubuntu8 [140 kB] Get:63 http://ftpmaster.internal/ubuntu focal/main arm64 libsmartcols1 arm64 2.34-0.1ubuntu8 [93.1 kB] Get:64 http://ftpmaster.internal/ubuntu focal/main arm64 fdisk arm64 2.34-0.1ubuntu8 [114 kB] Get:65 http://ftpmaster.internal/ubuntu focal/main arm64 util-linux arm64 2.34-0.1ubuntu8 [984 kB] Get:66 http://ftpmaster.internal/ubuntu focal/main arm64 libdebconfclient0 arm64 0.251ubuntu1 [6076 B] Get:67 http://ftpmaster.internal/ubuntu focal/main arm64 base-passwd arm64 3.5.47 [47.0 kB] Get:68 http://ftpmaster.internal/ubuntu focal/main arm64 ncurses-base all 6.2-0ubuntu2 [18.7 kB] Get:69 http://ftpmaster.internal/ubuntu focal/main arm64 lsb-base all 11.1.0ubuntu2 [12.1 kB] Get:70 http://ftpmaster.internal/ubuntu focal/main arm64 sysvinit-utils arm64 2.96-2.1ubuntu1 [20.4 kB] Get:71 http://ftpmaster.internal/ubuntu focal/main arm64 libgpg-error0 arm64 1.37-1 [55.1 kB] Get:72 http://ftpmaster.internal/ubuntu focal/main arm64 libgcrypt20 arm64 1.8.5-5ubuntu1 [350 kB] Get:73 http://ftpmaster.internal/ubuntu focal/main arm64 liblz4-1 arm64 1.9.2-2 [52.7 kB] Get:74 http://ftpmaster.internal/ubuntu focal-proposed/main arm64 systemd-sysv arm64 245.2-1ubuntu1 [9524 B] Get:75 http://ftpmaster.internal/ubuntu focal/main arm64 libacl1 arm64 2.2.53-6 [17.8 kB] Get:76 http://ftpmaster.internal/ubuntu focal/main arm64 libapparmor1 arm64 2.13.3-7ubuntu2 [33.0 kB] Get:77 http://ftpmaster.internal/ubuntu focal/main arm64 libaudit-common all 1:2.8.5-2ubuntu6 [3936 B] Get:78 http://ftpmaster.internal/ubuntu focal/main arm64 libcap-ng0 arm64 0.7.9-2.1build1 [10.5 kB] Get:79 http://ftpmaster.internal/ubuntu focal/main arm64 libaudit1 arm64 1:2.8.5-2ubuntu6 [38.2 kB] Get:80 http://ftpmaster.internal/ubuntu focal/main arm64 libcap2 arm64 1:2.32-1 [15.5 kB] Get:81 http://ftpmaster.internal/ubuntu focal-proposed/main arm64 libudev1 arm64 245.2-1ubuntu1 [71.6 kB] Get:82 http://ftpmaster.internal/ubuntu focal/main arm64 libdevmapper1.02.1 arm64 2:1.02.167-1ubuntu1 [110 kB] Get:83 http://ftpmaster.internal/ubuntu focal/main arm64 libjson-c4 arm64 0.13.1+dfsg-7 [28.0 kB] Get:84 http://ftpmaster.internal/ubuntu focal/main arm64 libssl1.1 arm64 1.1.1d-2ubuntu6 [1154 kB] Get:85 http://ftpmaster.internal/ubuntu focal/main arm64 libcryptsetup12 arm64 2:2.2.2-3ubuntu2 [166 kB] Get:86 http://ftpmaster.internal/ubuntu focal/main arm64 libnettle7 arm64 3.5.1+really3.5.1-2 [124 kB] Get:87 http://ftpmaster.internal/ubuntu focal/main arm64 libhogweed5 arm64 3.5.1+really3.5.1-2 [134 kB] Get:88 http://ftpmaster.internal/ubuntu focal-proposed/main arm64 libffi7 arm64 3.3-4 [17.1 kB] Get:89 http://ftpmaster.internal/ubuntu focal/main arm64 libp11-kit0 arm64 0.23.20-1build1 [178 kB] Get:90 http://ftpmaster.internal/ubuntu focal/main arm64 libtasn1-6 arm64 4.16.0-2 [36.5 kB] Get:91 http://ftpmaster.internal/ubuntu focal/main arm64 libgnutls30 arm64 3.6.11.1-2ubuntu2 [720 kB] Get:92 http://ftpmaster.internal/ubuntu focal/main arm64 libip4tc2 arm64 1.8.4-3ubuntu2 [18.4 kB] Get:93 http://ftpmaster.internal/ubuntu focal/main arm64 libkmod2 arm64 27-1ubuntu2 [40.9 kB] Get:94 http://ftpmaster.internal/ubuntu focal/main arm64 libpam0g arm64 1.3.1-5ubuntu4 [53.9 kB] Get:95 http://ftpmaster.internal/ubuntu focal/main arm64 libseccomp2 arm64 2.4.3-0ubuntu2 [38.7 kB] Get:96 http://ftpmaster.internal/ubuntu focal/main arm64 mount arm64 2.34-0.1ubuntu8 [112 kB] Get:97 http://ftpmaster.internal/ubuntu focal-proposed/main arm64 systemd arm64 245.2-1ubuntu1 [3497 kB] Get:98 http://ftpmaster.internal/ubuntu focal-proposed/main arm64 libsystemd0 arm64 245.2-1ubuntu1 [249 kB] Get:99 http://ftpmaster.internal/ubuntu focal/main arm64 libzstd1 arm64 1.4.4+dfsg-3 [216 kB] Get:100 http://ftpmaster.internal/ubuntu focal/main arm64 libapt-pkg6.0 arm64 2.0.0 [757 kB] Get:101 http://ftpmaster.internal/ubuntu focal/main arm64 libapt-pkg5.90 arm64 1.9.10 [778 kB] Get:102 http://ftpmaster.internal/ubuntu focal/main arm64 gpgv arm64 2.2.19-3ubuntu2 [183 kB] Get:103 http://ftpmaster.internal/ubuntu focal/main arm64 ubuntu-keyring all 2020.02.11.1 [22.3 kB] Get:104 http://ftpmaster.internal/ubuntu focal/main arm64 apt arm64 2.0.0 [1236 kB] Get:105 http://ftpmaster.internal/ubuntu focal/main arm64 libpam-modules-bin arm64 1.3.1-5ubuntu4 [35.8 kB] Get:106 http://ftpmaster.internal/ubuntu focal/main arm64 libpam-modules arm64 1.3.1-5ubuntu4 [242 kB] Get:107 http://ftpmaster.internal/ubuntu focal/main arm64 logsave arm64 1.45.5-2ubuntu1 [10.1 kB] Get:108 http://ftpmaster.internal/ubuntu focal/main arm64 libext2fs2 arm64 1.45.5-2ubuntu1 [177 kB] Get:109 http://ftpmaster.internal/ubuntu focal/main arm64 e2fsprogs arm64 1.45.5-2ubuntu1 [504 kB] Get:110 http://ftpmaster.internal/ubuntu focal/main arm64 libattr1 arm64 1:2.4.48-5 [12.5 kB] Get:111 http://ftpmaster.internal/ubuntu focal/main arm64 libpam-runtime all 1.3.1-5ubuntu4 [37.3 kB] Get:112 http://ftpmaster.internal/ubuntu focal-proposed/main arm64 libpcre3 arm64 2:8.39-12build1 [209 kB] Get:113 http://ftpmaster.internal/ubuntu focal/main arm64 libsepol1 arm64 3.0-1 [231 kB] Get:114 http://ftpmaster.internal/ubuntu focal/main arm64 libsemanage-common all 3.0-1build2 [9792 B] Get:115 http://ftpmaster.internal/ubuntu focal/main arm64 libsemanage1 arm64 3.0-1build2 [79.4 kB] Get:116 http://ftpmaster.internal/ubuntu focal/main arm64 passwd arm64 1:4.8.1-1ubuntu3 [771 kB] Get:117 http://ftpmaster.internal/ubuntu focal/main arm64 libcom-err2 arm64 1.45.5-2ubuntu1 [9228 B] Get:118 http://ftpmaster.internal/ubuntu focal/main arm64 libprocps8 arm64 2:3.3.16-1ubuntu2 [31.7 kB] Get:119 http://ftpmaster.internal/ubuntu focal/main arm64 libss2 arm64 1.45.5-2ubuntu1 [10.7 kB] Get:120 http://ftpmaster.internal/ubuntu focal/main arm64 mawk arm64 1.3.4.20200120-2 [89.7 kB] Get:121 http://ftpmaster.internal/ubuntu focal/main arm64 procps arm64 2:3.3.16-1ubuntu2 [229 kB] Get:122 http://ftpmaster.internal/ubuntu focal/main arm64 sensible-utils all 0.0.12+nmu1 [15.0 kB] Get:123 http://ftpmaster.internal/ubuntu focal/main arm64 readline-common all 8.0-4 [53.5 kB] Get:124 http://ftpmaster.internal/ubuntu focal/main arm64 libreadline8 arm64 8.0-4 [123 kB] Get:125 http://ftpmaster.internal/ubuntu focal/main arm64 libsqlite3-0 arm64 3.31.1-3 [505 kB] Get:126 http://ftpmaster.internal/ubuntu focal/main arm64 openssl arm64 1.1.1d-2ubuntu6 [599 kB] Get:127 http://ftpmaster.internal/ubuntu focal/main arm64 tzdata all 2019c-3ubuntu1 [294 kB] Get:128 http://ftpmaster.internal/ubuntu focal/main arm64 libpng16-16 arm64 1.6.37-2 [174 kB] Get:129 http://ftpmaster.internal/ubuntu focal/main arm64 advancecomp arm64 2.1-2.1build1 [175 kB] Get:130 http://ftpmaster.internal/ubuntu focal-proposed/main arm64 g++ arm64 4:9.3.0-1ubuntu2 [1592 B] Get:131 http://ftpmaster.internal/ubuntu focal-proposed/main arm64 gcc arm64 4:9.3.0-1ubuntu2 [5228 B] Get:132 http://ftpmaster.internal/ubuntu focal-proposed/main arm64 cpp arm64 4:9.3.0-1ubuntu2 [27.6 kB] Get:133 http://ftpmaster.internal/ubuntu focal-proposed/main arm64 dpkg-dev all 1.19.7ubuntu3 [679 kB] Get:134 http://ftpmaster.internal/ubuntu focal-proposed/main arm64 libdpkg-perl all 1.19.7ubuntu3 [230 kB] Get:135 http://ftpmaster.internal/ubuntu focal/main arm64 libassuan0 arm64 2.5.3-7ubuntu2 [33.1 kB] Get:136 http://ftpmaster.internal/ubuntu focal-proposed/main arm64 pinentry-curses arm64 1.1.0-3build1 [34.3 kB] Get:137 http://ftpmaster.internal/ubuntu focal/main arm64 gpg arm64 2.2.19-3ubuntu2 [442 kB] Get:138 http://ftpmaster.internal/ubuntu focal/main arm64 gpgconf arm64 2.2.19-3ubuntu2 [117 kB] Get:139 http://ftpmaster.internal/ubuntu focal/main arm64 gpg-agent arm64 2.2.19-3ubuntu2 [216 kB] Get:140 http://ftpmaster.internal/ubuntu focal/main arm64 liblockfile-bin arm64 1.16-1.1 [11.3 kB] Get:141 http://ftpmaster.internal/ubuntu focal/main arm64 liblockfile1 arm64 1.16-1.1 [6440 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 64.6 MB in 2s (31.6 MB/s) Selecting previously unselected package gcc-10-base:arm64. (Reading database ... 12731 files and directories currently installed.) Preparing to unpack .../gcc-10-base_10-20200321-1ubuntu1_arm64.deb ... Unpacking gcc-10-base:arm64 (10-20200321-1ubuntu1) ... Setting up gcc-10-base:arm64 (10-20200321-1ubuntu1) ... (Reading database ... 12737 files and directories currently installed.) Preparing to unpack .../libgmp10_2%3a6.2.0+dfsg-4_arm64.deb ... Unpacking libgmp10:arm64 (2:6.2.0+dfsg-4) over (2:6.1.2+dfsg-4) ... Setting up libgmp10:arm64 (2:6.2.0+dfsg-4) ... Selecting previously unselected package libisl22:arm64. (Reading database ... 12737 files and directories currently installed.) Preparing to unpack .../0-libisl22_0.22.1-1_arm64.deb ... Unpacking libisl22:arm64 (0.22.1-1) ... Preparing to unpack .../1-libcc1-0_10-20200321-1ubuntu1_arm64.deb ... Unpacking libcc1-0:arm64 (10-20200321-1ubuntu1) over (9.2.1-9ubuntu2) ... Selecting previously unselected package libctf-nobfd0:arm64. 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Setting up cpp-9 (9.3.0-7ubuntu1) ... Setting up libc6-dev:arm64 (2.31-0ubuntu6) ... Setting up libcryptsetup12:arm64 (2:2.2.2-3ubuntu2) ... Setting up gpg (2.2.19-3ubuntu2) ... Setting up gcc-9 (9.3.0-7ubuntu1) ... Setting up gpg-agent (2.2.19-3ubuntu2) ... Installing new version of config file /etc/logcheck/ignore.d.server/gpg-agent ... Created symlink /etc/systemd/user/sockets.target.wants/gpg-agent-browser.socket -> /usr/lib/systemd/user/gpg-agent-browser.socket. Created symlink /etc/systemd/user/sockets.target.wants/gpg-agent-extra.socket -> /usr/lib/systemd/user/gpg-agent-extra.socket. Created symlink /etc/systemd/user/sockets.target.wants/gpg-agent-ssh.socket -> /usr/lib/systemd/user/gpg-agent-ssh.socket. Created symlink /etc/systemd/user/sockets.target.wants/gpg-agent.socket -> /usr/lib/systemd/user/gpg-agent.socket. Setting up libstdc++-9-dev:arm64 (9.3.0-7ubuntu1) ... Setting up systemd (245.2-1ubuntu1) ... Installing new version of config file /etc/dhcp/dhclient-enter-hooks.d/resolved ... Installing new version of config file /etc/systemd/networkd.conf ... Installing new version of config file /etc/systemd/system.conf ... Installing new version of config file /etc/systemd/user.conf ... Initializing machine ID from KVM UUID. Setting up dpkg-dev (1.19.7ubuntu3) ... Setting up g++-9 (9.3.0-7ubuntu1) ... Setting up cpp (4:9.3.0-1ubuntu2) ... Setting up systemd-sysv (245.2-1ubuntu1) ... Setting up gcc (4:9.3.0-1ubuntu2) ... Setting up g++ (4:9.3.0-1ubuntu2) ... Processing triggers for libc-bin (2.31-0ubuntu6) ... RUN: /usr/share/launchpad-buildd/bin/sbuild-package PACKAGEBUILD-18888505 arm64 focal-proposed -c chroot:build-PACKAGEBUILD-18888505 --arch=arm64 --dist=focal-proposed --nolog reapr_1.0.18+dfsg-5build1.dsc Initiating build PACKAGEBUILD-18888505 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 4.4.0-176-generic #206-Ubuntu SMP Fri Feb 28 05:03:00 UTC 2020 aarch64 sbuild (Debian sbuild) 0.67.0 (26 Dec 2015) on bos02-arm64-064.buildd +==============================================================================+ | reapr 1.0.18+dfsg-5build1 (arm64) 24 Mar 2020 19:05 | +==============================================================================+ Package: reapr Version: 1.0.18+dfsg-5build1 Source Version: 1.0.18+dfsg-5build1 Distribution: focal-proposed Machine Architecture: arm64 Host Architecture: arm64 Build Architecture: arm64 I: NOTICE: Log filtering will replace 'build/reapr-IPzjNQ/reapr-1.0.18+dfsg' with '<>' I: NOTICE: Log filtering will replace 'build/reapr-IPzjNQ' with '<>' I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-18888505/chroot-autobuild' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- reapr_1.0.18+dfsg-5build1.dsc exists in .; copying to chroot Check architectures ------------------- Check dependencies ------------------ Merged Build-Depends: build-essential, fakeroot Filtered Build-Depends: build-essential, fakeroot dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/<>/resolver-jXreLq/apt_archive/sbuild-build-depends-core-dummy.deb'. Ign:1 copy:/<>/resolver-jXreLq/apt_archive ./ InRelease Get:2 copy:/<>/resolver-jXreLq/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-jXreLq/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-jXreLq/apt_archive ./ Sources [214 B] Get:5 copy:/<>/resolver-jXreLq/apt_archive ./ Packages [526 B] Fetched 2859 B in 0s (89.9 kB/s) Reading package lists... Reading package lists... +------------------------------------------------------------------------------+ | Install core build dependencies (apt-based resolver) | +------------------------------------------------------------------------------+ Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following packages were automatically installed and are no longer required: libffi6 libhogweed4 libisl21 libnettle6 libperl5.28 perl-modules-5.28 Use 'apt autoremove' to remove them. The following NEW packages will be installed: sbuild-build-depends-core-dummy 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 852 B of archives. After this operation, 0 B of additional disk space will be used. Get:1 copy:/<>/resolver-jXreLq/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [852 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 852 B in 0s (68.5 kB/s) Selecting previously unselected package sbuild-build-depends-core-dummy. (Reading database ... 14763 files and directories currently installed.) Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_arm64.deb ... Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ... Setting up sbuild-build-depends-core-dummy (0.invalid.0) ... Merged Build-Depends: debhelper-compat (= 12), libbamtools-dev, libtabixpp-dev, libhts-dev (>= 1.3), zlib1g-dev, asciidoctor, samtools (>= 1.3), bamtools, smalt, r-base, snpomatic, tabix, libfile-copy-link-perl Filtered Build-Depends: debhelper-compat (= 12), libbamtools-dev, libtabixpp-dev, libhts-dev (>= 1.3), zlib1g-dev, asciidoctor, samtools (>= 1.3), bamtools, smalt, r-base, snpomatic, tabix, libfile-copy-link-perl dpkg-deb: building package 'sbuild-build-depends-reapr-dummy' in '/<>/resolver-_Us0RI/apt_archive/sbuild-build-depends-reapr-dummy.deb'. Ign:1 copy:/<>/resolver-_Us0RI/apt_archive ./ InRelease Get:2 copy:/<>/resolver-_Us0RI/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-_Us0RI/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-_Us0RI/apt_archive ./ Sources [293 B] Get:5 copy:/<>/resolver-_Us0RI/apt_archive ./ Packages [615 B] Fetched 3027 B in 0s (82.5 kB/s) Reading package lists... Reading package lists... +------------------------------------------------------------------------------+ | Install reapr 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: libffi6 libhogweed4 libisl21 libnettle6 libperl5.28 perl-modules-5.28 Use 'apt autoremove' to remove them. The following additional packages will be installed: asciidoctor autoconf automake autopoint autotools-dev bamtools bsdmainutils debhelper dh-autoreconf dh-strip-nondeterminism dwz file fontconfig fontconfig-config fonts-dejavu-core gettext gettext-base groff-base intltool-debian libarchive-zip-perl libasn1-8-heimdal libbambamc0 libbamtools-dev libbamtools2.5.1 libblas3 libbrotli1 libbsd0 libcairo2 libcroco3 libcurl3-gnutls libcurl4 libdatrie1 libdebhelper-perl libdeflate0 libelf1 libexpat1 libfile-copy-link-perl libfile-stripnondeterminism-perl libfontconfig1 libfreetype6 libfribidi0 libgfortran5 libglib2.0-0 libgraphite2-3 libgssapi-krb5-2 libgssapi3-heimdal libharfbuzz0b libhcrypto4-heimdal libheimbase1-heimdal libheimntlm0-heimdal libhts-dev libhts3 libhx509-5-heimdal libice6 libicu66 libjbig0 libjpeg-turbo8 libjpeg8 libjsoncpp1 libk5crypto3 libkeyutils1 libkrb5-26-heimdal libkrb5-3 libkrb5support0 liblapack3 libldap-2.4-2 libldap-common 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 libpsl5 libroken18-heimdal librtmp1 libruby2.7 libsasl2-2 libsasl2-modules-db libsigsegv2 libsm6 libssh-4 libsub-override-perl libtabixpp-dev libtabixpp0 libtcl8.6 libthai-data libthai0 libtiff5 libtk8.6 libtool libuchardet0 libwebp6 libwind0-heimdal libx11-6 libx11-data libxau6 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxft2 libxml2 libxrender1 libxss1 libxt6 libyaml-0-2 m4 man-db po-debconf r-base r-base-core r-cran-boot r-cran-class r-cran-cluster r-cran-codetools r-cran-foreign r-cran-kernsmooth r-cran-lattice r-cran-mass r-cran-matrix r-cran-mgcv r-cran-nlme r-cran-nnet r-cran-rpart r-cran-spatial r-cran-survival r-recommended rake ruby ruby-asciidoctor ruby-did-you-mean ruby-minitest ruby-net-telnet ruby-power-assert ruby-test-unit ruby-xmlrpc ruby2.7 rubygems-integration samtools smalt snpomatic tabix ucf unzip x11-common xdg-utils zip zlib1g-dev Suggested packages: autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois vacation dh-make gettext-doc libasprintf-dev libgettextpo-dev groff libbamtools-doc krb5-doc krb5-user liblzma-doc tcl8.6 tk8.6 libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc apparmor less www-browser libmail-box-perl elpa-ess r-doc-info | r-doc-pdf r-mathlib r-base-html ri ruby-dev bundler Recommended packages: curl | wget | lynx libarchive-cpio-perl libglib2.0-data shared-mime-info xdg-user-dirs krb5-locales publicsuffix libsasl2-modules libltdl-dev libmail-sendmail-perl r-base-html r-doc-html r-base-dev fonts-lato libjs-jquery python3 cwltool libfile-mimeinfo-perl libnet-dbus-perl libx11-protocol-perl x11-utils x11-xserver-utils The following NEW packages will be installed: asciidoctor autoconf automake autopoint autotools-dev bamtools bsdmainutils debhelper dh-autoreconf dh-strip-nondeterminism dwz file fontconfig fontconfig-config fonts-dejavu-core gettext gettext-base groff-base intltool-debian libarchive-zip-perl libasn1-8-heimdal libbambamc0 libbamtools-dev libbamtools2.5.1 libblas3 libbrotli1 libbsd0 libcairo2 libcroco3 libcurl3-gnutls libcurl4 libdatrie1 libdebhelper-perl libdeflate0 libelf1 libexpat1 libfile-copy-link-perl libfile-stripnondeterminism-perl libfontconfig1 libfreetype6 libfribidi0 libgfortran5 libglib2.0-0 libgraphite2-3 libgssapi-krb5-2 libgssapi3-heimdal libharfbuzz0b libhcrypto4-heimdal libheimbase1-heimdal libheimntlm0-heimdal libhts-dev libhts3 libhx509-5-heimdal libice6 libicu66 libjbig0 libjpeg-turbo8 libjpeg8 libjsoncpp1 libk5crypto3 libkeyutils1 libkrb5-26-heimdal libkrb5-3 libkrb5support0 liblapack3 libldap-2.4-2 libldap-common 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 libpsl5 libroken18-heimdal librtmp1 libruby2.7 libsasl2-2 libsasl2-modules-db libsigsegv2 libsm6 libssh-4 libsub-override-perl libtabixpp-dev libtabixpp0 libtcl8.6 libthai-data libthai0 libtiff5 libtk8.6 libtool libuchardet0 libwebp6 libwind0-heimdal libx11-6 libx11-data libxau6 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxft2 libxml2 libxrender1 libxss1 libxt6 libyaml-0-2 m4 man-db po-debconf r-base r-base-core r-cran-boot r-cran-class r-cran-cluster r-cran-codetools r-cran-foreign r-cran-kernsmooth r-cran-lattice r-cran-mass r-cran-matrix r-cran-mgcv r-cran-nlme r-cran-nnet r-cran-rpart r-cran-spatial r-cran-survival r-recommended rake ruby ruby-asciidoctor ruby-did-you-mean ruby-minitest ruby-net-telnet ruby-power-assert ruby-test-unit ruby-xmlrpc ruby2.7 rubygems-integration samtools sbuild-build-depends-reapr-dummy smalt snpomatic tabix ucf unzip x11-common xdg-utils zip zlib1g-dev 0 upgraded, 156 newly installed, 0 to remove and 0 not upgraded. Need to get 78.8 MB of archives. After this operation, 198 MB of additional disk space will be used. Get:1 copy:/<>/resolver-_Us0RI/apt_archive ./ sbuild-build-depends-reapr-dummy 0.invalid.0 [948 B] Get:2 http://ftpmaster.internal/ubuntu focal/main arm64 libbsd0 arm64 0.10.0-1 [43.7 kB] Get:3 http://ftpmaster.internal/ubuntu focal/main arm64 bsdmainutils arm64 11.1.2ubuntu2 [175 kB] Get:4 http://ftpmaster.internal/ubuntu focal-proposed/main arm64 libuchardet0 arm64 0.0.6-3build1 [65.0 kB] Get:5 http://ftpmaster.internal/ubuntu focal-proposed/main arm64 groff-base arm64 1.22.4-4build1 [796 kB] Get:6 http://ftpmaster.internal/ubuntu focal/main arm64 libpipeline1 arm64 1.5.2-2build1 [26.1 kB] Get:7 http://ftpmaster.internal/ubuntu focal/main arm64 man-db arm64 2.9.1-1 [1095 kB] Get:8 http://ftpmaster.internal/ubuntu focal/main arm64 libmagic-mgc arm64 1:5.38-4 [218 kB] Get:9 http://ftpmaster.internal/ubuntu focal/main arm64 libmagic1 arm64 1:5.38-4 [71.7 kB] Get:10 http://ftpmaster.internal/ubuntu focal/main arm64 file arm64 1:5.38-4 [23.3 kB] Get:11 http://ftpmaster.internal/ubuntu focal/main arm64 libelf1 arm64 0.176-1.1build1 [44.2 kB] Get:12 http://ftpmaster.internal/ubuntu focal/main arm64 libexpat1 arm64 2.2.9-1build1 [61.3 kB] Get:13 http://ftpmaster.internal/ubuntu focal/main arm64 libfribidi0 arm64 1.0.8-2 [23.7 kB] Get:14 http://ftpmaster.internal/ubuntu focal/main arm64 libglib2.0-0 arm64 2.64.1-1 [1197 kB] Get:15 http://ftpmaster.internal/ubuntu focal/main arm64 libicu66 arm64 66.1-2ubuntu2 [8357 kB] Get:16 http://ftpmaster.internal/ubuntu focal/main arm64 libxml2 arm64 2.9.10+dfsg-4build1 [569 kB] Get:17 http://ftpmaster.internal/ubuntu focal/main arm64 libyaml-0-2 arm64 0.2.2-1 [44.4 kB] Get:18 http://ftpmaster.internal/ubuntu focal/main arm64 ucf all 3.0038+nmu1 [51.6 kB] Get:19 http://ftpmaster.internal/ubuntu focal-proposed/main arm64 gettext-base arm64 0.19.8.1-10build1 [48.2 kB] Get:20 http://ftpmaster.internal/ubuntu focal/main arm64 libkrb5support0 arm64 1.17-6ubuntu4 [30.4 kB] Get:21 http://ftpmaster.internal/ubuntu focal/main arm64 libk5crypto3 arm64 1.17-6ubuntu4 [80.5 kB] Get:22 http://ftpmaster.internal/ubuntu focal/main arm64 libkeyutils1 arm64 1.6-6ubuntu1 [10.1 kB] Get:23 http://ftpmaster.internal/ubuntu focal/main arm64 libkrb5-3 arm64 1.17-6ubuntu4 [312 kB] Get:24 http://ftpmaster.internal/ubuntu focal/main arm64 libgssapi-krb5-2 arm64 1.17-6ubuntu4 [113 kB] Get:25 http://ftpmaster.internal/ubuntu focal/main arm64 libpsl5 arm64 0.20.2-2 [49.9 kB] Get:26 http://ftpmaster.internal/ubuntu focal/main arm64 libxau6 arm64 1:1.0.9-0ubuntu1 [7356 B] Get:27 http://ftpmaster.internal/ubuntu focal/main arm64 libxdmcp6 arm64 1:1.1.3-0ubuntu1 [10.3 kB] Get:28 http://ftpmaster.internal/ubuntu focal/main arm64 libxcb1 arm64 1.13.1-5build1 [43.0 kB] Get:29 http://ftpmaster.internal/ubuntu focal/main arm64 libx11-data all 2:1.6.9-2ubuntu1 [113 kB] Get:30 http://ftpmaster.internal/ubuntu focal/main arm64 libx11-6 arm64 2:1.6.9-2ubuntu1 [553 kB] Get:31 http://ftpmaster.internal/ubuntu focal/main arm64 libxext6 arm64 2:1.3.4-0ubuntu1 [27.7 kB] Get:32 http://ftpmaster.internal/ubuntu focal/main arm64 rubygems-integration all 1.16 [5092 B] Get:33 http://ftpmaster.internal/ubuntu focal/main arm64 rake all 13.0.1-2 [45.2 kB] Get:34 http://ftpmaster.internal/ubuntu focal/main arm64 ruby-did-you-mean all 1.2.1-1 [9828 B] Get:35 http://ftpmaster.internal/ubuntu focal/main arm64 ruby-minitest all 5.13.0-1 [40.9 kB] Get:36 http://ftpmaster.internal/ubuntu focal/main arm64 ruby-net-telnet all 0.1.1-2 [12.6 kB] Get:37 http://ftpmaster.internal/ubuntu focal/main arm64 ruby-power-assert all 1.1.5-1 [11.3 kB] Get:38 http://ftpmaster.internal/ubuntu focal/main arm64 ruby-test-unit all 3.3.4-1 [73.1 kB] Get:39 http://ftpmaster.internal/ubuntu focal/main arm64 ruby-xmlrpc all 0.3.0-2 [23.8 kB] Get:40 http://ftpmaster.internal/ubuntu focal/main arm64 libruby2.7 arm64 2.7.0-4 [3360 kB] Get:41 http://ftpmaster.internal/ubuntu focal/main arm64 ruby2.7 arm64 2.7.0-4 [95.6 kB] Get:42 http://ftpmaster.internal/ubuntu focal/main arm64 ruby arm64 1:2.7~0 [5504 B] Get:43 http://ftpmaster.internal/ubuntu focal/universe arm64 ruby-asciidoctor all 2.0.10-2 [166 kB] Get:44 http://ftpmaster.internal/ubuntu focal/universe arm64 asciidoctor all 2.0.10-2 [40.3 kB] Get:45 http://ftpmaster.internal/ubuntu focal/main arm64 libsigsegv2 arm64 2.12-2 [13.3 kB] Get:46 http://ftpmaster.internal/ubuntu focal/main arm64 m4 arm64 1.4.18-4 [194 kB] Get:47 http://ftpmaster.internal/ubuntu focal/main arm64 autoconf all 2.69-11.1 [321 kB] Get:48 http://ftpmaster.internal/ubuntu focal/main arm64 autotools-dev all 20180224.1 [39.6 kB] Get:49 http://ftpmaster.internal/ubuntu focal/main arm64 automake all 1:1.16.1-4ubuntu6 [522 kB] Get:50 http://ftpmaster.internal/ubuntu focal-proposed/main arm64 autopoint all 0.19.8.1-10build1 [412 kB] Get:51 http://ftpmaster.internal/ubuntu focal-proposed/universe arm64 libbamtools2.5.1 arm64 2.5.1+dfsg-5build1 [140 kB] Get:52 http://ftpmaster.internal/ubuntu focal/main arm64 libjsoncpp1 arm64 1.7.4-3.1ubuntu2 [69.8 kB] Get:53 http://ftpmaster.internal/ubuntu focal-proposed/universe arm64 bamtools arm64 2.5.1+dfsg-5build1 [154 kB] Get:54 http://ftpmaster.internal/ubuntu focal/main arm64 libtool all 2.4.6-13 [161 kB] Get:55 http://ftpmaster.internal/ubuntu focal/main arm64 dh-autoreconf all 19 [16.1 kB] Get:56 http://ftpmaster.internal/ubuntu focal/main arm64 libdebhelper-perl all 12.9ubuntu1 [62.0 kB] Get:57 http://ftpmaster.internal/ubuntu focal/main arm64 libarchive-zip-perl all 1.67-2 [90.5 kB] Get:58 http://ftpmaster.internal/ubuntu focal/main arm64 libsub-override-perl all 0.09-2 [9532 B] Get:59 http://ftpmaster.internal/ubuntu focal/main arm64 libfile-stripnondeterminism-perl all 1.6.3-2 [16.0 kB] Get:60 http://ftpmaster.internal/ubuntu focal/main arm64 dh-strip-nondeterminism all 1.6.3-2 [5228 B] Get:61 http://ftpmaster.internal/ubuntu focal/main arm64 dwz arm64 0.13-5 [134 kB] Get:62 http://ftpmaster.internal/ubuntu focal/main arm64 libcroco3 arm64 0.6.13-1 [77.1 kB] Get:63 http://ftpmaster.internal/ubuntu focal-proposed/main arm64 gettext arm64 0.19.8.1-10build1 [850 kB] Get:64 http://ftpmaster.internal/ubuntu focal/main arm64 intltool-debian all 0.35.0+20060710.5 [24.9 kB] Get:65 http://ftpmaster.internal/ubuntu focal/main arm64 po-debconf all 1.0.21 [233 kB] Get:66 http://ftpmaster.internal/ubuntu focal/main arm64 debhelper all 12.9ubuntu1 [869 kB] Get:67 http://ftpmaster.internal/ubuntu focal/main arm64 libfreetype6 arm64 2.10.1-2 [316 kB] Get:68 http://ftpmaster.internal/ubuntu focal/main arm64 fonts-dejavu-core all 2.37-1 [1041 kB] Get:69 http://ftpmaster.internal/ubuntu focal/main arm64 fontconfig-config all 2.13.1-2ubuntu2 [28.9 kB] Get:70 http://ftpmaster.internal/ubuntu focal/main arm64 libfontconfig1 arm64 2.13.1-2ubuntu2 [111 kB] Get:71 http://ftpmaster.internal/ubuntu focal/main arm64 fontconfig arm64 2.13.1-2ubuntu2 [171 kB] Get:72 http://ftpmaster.internal/ubuntu focal/main arm64 libroken18-heimdal arm64 7.7.0+dfsg-1 [39.3 kB] Get:73 http://ftpmaster.internal/ubuntu focal/main arm64 libasn1-8-heimdal arm64 7.7.0+dfsg-1 [150 kB] Get:74 http://ftpmaster.internal/ubuntu focal/universe arm64 libbambamc0 arm64 0.0.50-3 [30.2 kB] Get:75 http://ftpmaster.internal/ubuntu focal-proposed/universe arm64 libbamtools-dev arm64 2.5.1+dfsg-5build1 [19.8 kB] Get:76 http://ftpmaster.internal/ubuntu focal-proposed/main arm64 libblas3 arm64 3.9.0-1build1 [89.1 kB] Get:77 http://ftpmaster.internal/ubuntu focal/main arm64 libbrotli1 arm64 1.0.7-6build1 [261 kB] Get:78 http://ftpmaster.internal/ubuntu focal/main arm64 libpixman-1-0 arm64 0.38.4-0ubuntu1 [130 kB] Get:79 http://ftpmaster.internal/ubuntu focal/main arm64 libxcb-render0 arm64 1.13.1-5build1 [14.7 kB] Get:80 http://ftpmaster.internal/ubuntu focal/main arm64 libxcb-shm0 arm64 1.13.1-5build1 [5564 B] Get:81 http://ftpmaster.internal/ubuntu focal/main arm64 libxrender1 arm64 1:0.9.10-1 [16.1 kB] Get:82 http://ftpmaster.internal/ubuntu focal/main arm64 libcairo2 arm64 1.16.0-4ubuntu1 [538 kB] Get:83 http://ftpmaster.internal/ubuntu focal/main arm64 libheimbase1-heimdal arm64 7.7.0+dfsg-1 [27.9 kB] Get:84 http://ftpmaster.internal/ubuntu focal/main arm64 libhcrypto4-heimdal arm64 7.7.0+dfsg-1 [86.5 kB] Get:85 http://ftpmaster.internal/ubuntu focal/main arm64 libwind0-heimdal arm64 7.7.0+dfsg-1 [47.2 kB] Get:86 http://ftpmaster.internal/ubuntu focal/main arm64 libhx509-5-heimdal arm64 7.7.0+dfsg-1 [98.6 kB] Get:87 http://ftpmaster.internal/ubuntu focal/main arm64 libkrb5-26-heimdal arm64 7.7.0+dfsg-1 [192 kB] Get:88 http://ftpmaster.internal/ubuntu focal/main arm64 libheimntlm0-heimdal arm64 7.7.0+dfsg-1 [14.8 kB] Get:89 http://ftpmaster.internal/ubuntu focal/main arm64 libgssapi3-heimdal arm64 7.7.0+dfsg-1 [88.3 kB] Get:90 http://ftpmaster.internal/ubuntu focal/main arm64 libsasl2-modules-db arm64 2.1.27+dfsg-2 [15.1 kB] Get:91 http://ftpmaster.internal/ubuntu focal/main arm64 libsasl2-2 arm64 2.1.27+dfsg-2 [48.4 kB] Get:92 http://ftpmaster.internal/ubuntu focal/main arm64 libldap-common all 2.4.49+dfsg-2ubuntu1 [17.3 kB] Get:93 http://ftpmaster.internal/ubuntu focal/main arm64 libldap-2.4-2 arm64 2.4.49+dfsg-2ubuntu1 [146 kB] Get:94 http://ftpmaster.internal/ubuntu focal-proposed/main arm64 libnghttp2-14 arm64 1.40.0-1build1 [74.7 kB] Get:95 http://ftpmaster.internal/ubuntu focal/main arm64 librtmp1 arm64 2.4+20151223.gitfa8646d.1-2build1 [53.3 kB] Get:96 http://ftpmaster.internal/ubuntu focal/main arm64 libssh-4 arm64 0.9.3-2ubuntu1 [159 kB] Get:97 http://ftpmaster.internal/ubuntu focal/main arm64 libcurl3-gnutls arm64 7.68.0-1ubuntu1 [211 kB] Get:98 http://ftpmaster.internal/ubuntu focal/main arm64 libcurl4 arm64 7.68.0-1ubuntu1 [213 kB] Get:99 http://ftpmaster.internal/ubuntu focal/main arm64 libdatrie1 arm64 0.2.12-3 [17.9 kB] Get:100 http://ftpmaster.internal/ubuntu focal/universe arm64 libdeflate0 arm64 1.5-3 [51.2 kB] Get:101 http://ftpmaster.internal/ubuntu focal/universe arm64 libfile-copy-link-perl all 0.140-2 [15.2 kB] Get:102 http://ftpmaster.internal/ubuntu focal/main arm64 libgfortran5 arm64 10-20200321-1ubuntu1 [342 kB] Get:103 http://ftpmaster.internal/ubuntu focal-proposed/main arm64 libgraphite2-3 arm64 1.3.13-11build1 [67.7 kB] Get:104 http://ftpmaster.internal/ubuntu focal/main arm64 libharfbuzz0b arm64 2.6.4-1ubuntu3 [352 kB] Get:105 http://ftpmaster.internal/ubuntu focal/universe arm64 libhts3 arm64 1.10.2-3 [316 kB] Get:106 http://ftpmaster.internal/ubuntu focal/main arm64 liblzma-dev arm64 5.2.4-1 [144 kB] Get:107 http://ftpmaster.internal/ubuntu focal/main arm64 zlib1g-dev arm64 1:1.2.11.dfsg-2ubuntu1 [154 kB] Get:108 http://ftpmaster.internal/ubuntu focal/universe arm64 libhts-dev arm64 1.10.2-3 [92.1 kB] Get:109 http://ftpmaster.internal/ubuntu focal/main arm64 x11-common all 1:7.7+19ubuntu14 [22.3 kB] Get:110 http://ftpmaster.internal/ubuntu focal/main arm64 libice6 arm64 2:1.0.10-0ubuntu1 [37.7 kB] Get:111 http://ftpmaster.internal/ubuntu focal/main arm64 libjpeg-turbo8 arm64 2.0.3-0ubuntu1 [101 kB] Get:112 http://ftpmaster.internal/ubuntu focal/main arm64 libjpeg8 arm64 8c-2ubuntu8 [2198 B] Get:113 http://ftpmaster.internal/ubuntu focal-proposed/main arm64 liblapack3 arm64 3.9.0-1build1 [1529 kB] Get:114 http://ftpmaster.internal/ubuntu focal/main arm64 libthai-data all 0.1.28-3 [134 kB] Get:115 http://ftpmaster.internal/ubuntu focal/main arm64 libthai0 arm64 0.1.28-3 [16.8 kB] Get:116 http://ftpmaster.internal/ubuntu focal/main arm64 libpango-1.0-0 arm64 1.44.7-1ubuntu3 [153 kB] Get:117 http://ftpmaster.internal/ubuntu focal/main arm64 libpangoft2-1.0-0 arm64 1.44.7-1ubuntu3 [32.0 kB] Get:118 http://ftpmaster.internal/ubuntu focal/main arm64 libpangocairo-1.0-0 arm64 1.44.7-1ubuntu3 [22.5 kB] Get:119 http://ftpmaster.internal/ubuntu focal/main arm64 libpaper1 arm64 1.1.28 [12.7 kB] Get:120 http://ftpmaster.internal/ubuntu focal/main arm64 libpaper-utils arm64 1.1.28 [8328 B] Get:121 http://ftpmaster.internal/ubuntu focal/main arm64 libsm6 arm64 2:1.2.3-1 [15.1 kB] Get:122 http://ftpmaster.internal/ubuntu focal/universe arm64 libtabixpp0 arm64 1.1.0-3 [8456 B] Get:123 http://ftpmaster.internal/ubuntu focal/universe arm64 libtabixpp-dev arm64 1.1.0-3 [6920 B] Get:124 http://ftpmaster.internal/ubuntu focal/main arm64 libtcl8.6 arm64 8.6.10+dfsg-1 [849 kB] Get:125 http://ftpmaster.internal/ubuntu focal/main arm64 libjbig0 arm64 2.1-3.1build1 [24.0 kB] Get:126 http://ftpmaster.internal/ubuntu focal/main arm64 libwebp6 arm64 0.6.1-2 [155 kB] Get:127 http://ftpmaster.internal/ubuntu focal/main arm64 libtiff5 arm64 4.1.0+git191117-2build1 [151 kB] Get:128 http://ftpmaster.internal/ubuntu focal/main arm64 libxft2 arm64 2.3.3-0ubuntu1 [35.9 kB] Get:129 http://ftpmaster.internal/ubuntu focal/main arm64 libxss1 arm64 1:1.2.3-1 [8080 B] Get:130 http://ftpmaster.internal/ubuntu focal/main arm64 libtk8.6 arm64 8.6.10-1 [674 kB] Get:131 http://ftpmaster.internal/ubuntu focal/main arm64 libxt6 arm64 1:1.1.5-1 [128 kB] Get:132 http://ftpmaster.internal/ubuntu focal/main arm64 zip arm64 3.0-11build1 [146 kB] Get:133 http://ftpmaster.internal/ubuntu focal/main arm64 unzip arm64 6.0-25ubuntu1 [163 kB] Get:134 http://ftpmaster.internal/ubuntu focal/main arm64 xdg-utils all 1.1.3-1ubuntu2 [60.5 kB] Get:135 http://ftpmaster.internal/ubuntu focal/universe arm64 r-base-core arm64 3.6.2.20200221-1build1 [24.3 MB] Get:136 http://ftpmaster.internal/ubuntu focal/universe arm64 r-cran-boot all 1.3-24-2 [615 kB] Get:137 http://ftpmaster.internal/ubuntu focal/universe arm64 r-cran-cluster arm64 2.1.0-2 [520 kB] Get:138 http://ftpmaster.internal/ubuntu focal/universe arm64 r-cran-foreign arm64 0.8.75-1 [226 kB] Get:139 http://ftpmaster.internal/ubuntu focal/universe arm64 r-cran-mass arm64 7.3-51.5-2 [1112 kB] Get:140 http://ftpmaster.internal/ubuntu focal/universe arm64 r-cran-kernsmooth arm64 2.23-16-1+1 [89.7 kB] Get:141 http://ftpmaster.internal/ubuntu focal/universe arm64 r-cran-lattice arm64 0.20-40-1 [1124 kB] Get:142 http://ftpmaster.internal/ubuntu focal/universe arm64 r-cran-nlme arm64 3.1.144-1 [2219 kB] Get:143 http://ftpmaster.internal/ubuntu focal/universe arm64 r-cran-matrix arm64 1.2-18-1 [3404 kB] Get:144 http://ftpmaster.internal/ubuntu focal/universe arm64 r-cran-mgcv arm64 1.8-31-1 [2704 kB] Get:145 http://ftpmaster.internal/ubuntu focal/universe arm64 r-cran-survival arm64 3.1-8-1 [7373 kB] Get:146 http://ftpmaster.internal/ubuntu focal/universe arm64 r-cran-rpart arm64 4.1-15-2 [676 kB] Get:147 http://ftpmaster.internal/ubuntu focal/universe arm64 r-cran-class arm64 7.3-15-1 [86.2 kB] Get:148 http://ftpmaster.internal/ubuntu focal/universe arm64 r-cran-nnet arm64 7.3-13-1 [110 kB] Get:149 http://ftpmaster.internal/ubuntu focal/universe arm64 r-cran-spatial arm64 7.3-11-2build2 [125 kB] Get:150 http://ftpmaster.internal/ubuntu focal/universe arm64 r-cran-codetools all 0.2-16-1 [89.3 kB] Get:151 http://ftpmaster.internal/ubuntu focal/universe arm64 r-recommended all 3.6.2.20200221-1build1 [2832 B] Get:152 http://ftpmaster.internal/ubuntu focal/universe arm64 r-base all 3.6.2.20200221-1build1 [9320 B] Get:153 http://ftpmaster.internal/ubuntu focal/universe arm64 samtools arm64 1.10-3 [474 kB] Get:154 http://ftpmaster.internal/ubuntu focal/universe arm64 smalt arm64 0.7.6-9 [104 kB] Get:155 http://ftpmaster.internal/ubuntu focal/universe arm64 snpomatic arm64 1.0-4build1 [75.2 kB] Get:156 http://ftpmaster.internal/ubuntu focal/universe arm64 tabix arm64 1.10.2-3 [326 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 78.8 MB in 4s (21.2 MB/s) Selecting previously unselected package libbsd0:arm64. 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Setting up unzip (6.0-25ubuntu1) ... Setting up libdebhelper-perl (12.9ubuntu1) ... Setting up libbrotli1:arm64 (1.0.7-6build1) ... Setting up x11-common (1:7.7+19ubuntu14) ... update-rc.d: warning: start and stop actions are no longer supported; falling back to defaults Running in chroot, ignoring request. invoke-rc.d: policy-rc.d denied execution of start. Setting up libnghttp2-14:arm64 (1.40.0-1build1) ... Setting up libmagic1:arm64 (1:5.38-4) ... Setting up libdeflate0 (1.5-3) ... Setting up gettext-base (0.19.8.1-10build1) ... Setting up rubygems-integration (1.16) ... Setting up file (1:5.38-4) ... Setting up libldap-common (2.4.49+dfsg-2ubuntu1) ... Setting up libjbig0:arm64 (2.1-3.1build1) ... Setting up libkrb5support0:arm64 (1.17-6ubuntu4) ... Setting up libsasl2-modules-db:arm64 (2.1.27+dfsg-2) ... Setting up ruby-minitest (5.13.0-1) ... Setting up zip (3.0-11build1) ... Setting up autotools-dev (20180224.1) ... Setting up libblas3:arm64 (3.9.0-1build1) ... 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 libfreetype6:arm64 (2.10.1-2) ... Setting up ruby-test-unit (3.3.4-1) ... Setting up libx11-data (2:1.6.9-2ubuntu1) ... Setting up librtmp1:arm64 (2.4+20151223.gitfa8646d.1-2build1) ... Setting up ruby-net-telnet (0.1.1-2) ... Setting up libsigsegv2:arm64 (2.12-2) ... Setting up libfribidi0:arm64 (1.0.8-2) ... Setting up libbambamc0 (0.0.50-3) ... Setting up libbamtools2.5.1:arm64 (2.5.1+dfsg-5build1) ... Setting up libtcl8.6:arm64 (8.6.10+dfsg-1) ... Setting up autopoint (0.19.8.1-10build1) ... Setting up libwebp6:arm64 (0.6.1-2) ... Setting up fonts-dejavu-core (2.37-1) ... Setting up ucf (3.0038+nmu1) ... Setting up libk5crypto3:arm64 (1.17-6ubuntu4) ... Setting up libjpeg-turbo8:arm64 (2.0.3-0ubuntu1) ... Setting up libsasl2-2:arm64 (2.1.27+dfsg-2) ... Setting up libgfortran5:arm64 (10-20200321-1ubuntu1) ... Setting up libroken18-heimdal:arm64 (7.7.0+dfsg-1) ... Setting up liblzma-dev:arm64 (5.2.4-1) ... Setting up zlib1g-dev:arm64 (1:1.2.11.dfsg-2ubuntu1) ... Setting up snpomatic (1.0-4build1) ... Setting up libuchardet0:arm64 (0.0.6-3build1) ... Setting up libsub-override-perl (0.09-2) ... Setting up libharfbuzz0b:arm64 (2.6.4-1ubuntu3) ... Setting up libthai-data (0.1.28-3) ... Setting up libkrb5-3:arm64 (1.17-6ubuntu4) ... Setting up ruby-did-you-mean (1.2.1-1) ... Setting up libbsd0:arm64 (0.10.0-1) ... Setting up libelf1:arm64 (0.176-1.1build1) ... Setting up ruby-xmlrpc (0.3.0-2) ... Setting up libxml2:arm64 (2.9.10+dfsg-4build1) ... Setting up xdg-utils (1.1.3-1ubuntu2) ... Setting up libjsoncpp1:arm64 (1.7.4-3.1ubuntu2) ... Setting up libheimbase1-heimdal:arm64 (7.7.0+dfsg-1) ... Setting up libjpeg8:arm64 (8c-2ubuntu8) ... Setting up libfile-stripnondeterminism-perl (1.6.3-2) ... Setting up smalt (0.7.6-9) ... Setting up libpaper1:arm64 (1.1.28) ... Creating config file /etc/papersize with new version Setting up libice6:arm64 (2:1.0.10-0ubuntu1) ... Setting up libxdmcp6:arm64 (1:1.1.3-0ubuntu1) ... Setting up liblapack3:arm64 (3.9.0-1build1) ... 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 (1.13.1-5build1) ... Setting up libtool (2.4.6-13) ... Setting up libxcb-render0:arm64 (1.13.1-5build1) ... Setting up fontconfig-config (2.13.1-2ubuntu2) ... Setting up libasn1-8-heimdal:arm64 (7.7.0+dfsg-1) ... Setting up m4 (1.4.18-4) ... Setting up libxcb-shm0:arm64 (1.13.1-5build1) ... Setting up libpaper-utils (1.1.28) ... Setting up libhcrypto4-heimdal:arm64 (7.7.0+dfsg-1) ... Setting up libthai0:arm64 (0.1.28-3) ... Setting up libwind0-heimdal:arm64 (7.7.0+dfsg-1) ... Setting up libbamtools-dev:arm64 (2.5.1+dfsg-5build1) ... Setting up bsdmainutils (11.1.2ubuntu2) ... update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode Setting up libgssapi-krb5-2:arm64 (1.17-6ubuntu4) ... Setting up libcroco3:arm64 (0.6.13-1) ... Setting up libssh-4:arm64 (0.9.3-2ubuntu1) ... Setting up autoconf (2.69-11.1) ... Setting up dh-strip-nondeterminism (1.6.3-2) ... Setting up dwz (0.13-5) ... Setting up groff-base (1.22.4-4build1) ... Setting up bamtools (2.5.1+dfsg-5build1) ... Setting up libx11-6:arm64 (2:1.6.9-2ubuntu1) ... Setting up libtiff5:arm64 (4.1.0+git191117-2build1) ... Setting up libfontconfig1:arm64 (2.13.1-2ubuntu2) ... Setting up libsm6:arm64 (2:1.2.3-1) ... Setting up automake (1:1.16.1-4ubuntu6) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up fontconfig (2.13.1-2ubuntu2) ... Regenerating fonts cache... done. Setting up gettext (0.19.8.1-10build1) ... Setting up libxrender1:arm64 (1:0.9.10-1) ... Setting up libhx509-5-heimdal:arm64 (7.7.0+dfsg-1) ... Setting up libpango-1.0-0:arm64 (1.44.7-1ubuntu3) ... Setting up libxext6:arm64 (2:1.3.4-0ubuntu1) ... Setting up man-db (2.9.1-1) ... 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 (1.16.0-4ubuntu1) ... Setting up intltool-debian (0.35.0+20060710.5) ... Setting up libxt6:arm64 (1:1.1.5-1) ... Setting up libxss1:arm64 (1:1.2.3-1) ... Setting up libpangoft2-1.0-0:arm64 (1.44.7-1ubuntu3) ... Setting up libpangocairo-1.0-0:arm64 (1.44.7-1ubuntu3) ... Setting up libkrb5-26-heimdal:arm64 (7.7.0+dfsg-1) ... Setting up libxft2:arm64 (2.3.3-0ubuntu1) ... Setting up po-debconf (1.0.21) ... Setting up libtk8.6:arm64 (8.6.10-1) ... Setting up libheimntlm0-heimdal:arm64 (7.7.0+dfsg-1) ... Setting up libgssapi3-heimdal:arm64 (7.7.0+dfsg-1) ... Setting up libldap-2.4-2:arm64 (2.4.49+dfsg-2ubuntu1) ... Setting up libcurl3-gnutls:arm64 (7.68.0-1ubuntu1) ... Setting up libcurl4:arm64 (7.68.0-1ubuntu1) ... Setting up tabix (1.10.2-3) ... Setting up libhts3:arm64 (1.10.2-3) ... Setting up libhts-dev:arm64 (1.10.2-3) ... Setting up samtools (1.10-3) ... Setting up r-base-core (3.6.2.20200221-1build1) ... Creating config file /etc/R/Renviron with new version Setting up r-cran-lattice (0.20-40-1) ... Setting up r-cran-nlme (3.1.144-1) ... Setting up r-cran-cluster (2.1.0-2) ... Setting up libtabixpp0:arm64 (1.1.0-3) ... Setting up r-cran-nnet (7.3-13-1) ... Setting up r-cran-codetools (0.2-16-1) ... Setting up r-cran-boot (1.3-24-2) ... Setting up r-cran-spatial (7.3-11-2build2) ... Setting up r-cran-mass (7.3-51.5-2) ... Setting up r-cran-foreign (0.8.75-1) ... Setting up r-cran-matrix (1.2-18-1) ... Setting up r-cran-kernsmooth (2.23-16-1+1) ... Setting up r-cran-mgcv (1.8-31-1) ... Setting up libtabixpp-dev:arm64 (1.1.0-3) ... Setting up r-cran-class (7.3-15-1) ... Setting up r-cran-survival (3.1-8-1) ... Setting up r-cran-rpart (4.1-15-2) ... Setting up r-recommended (3.6.2.20200221-1build1) ... Setting up r-base (3.6.2.20200221-1build1) ... Setting up dh-autoreconf (19) ... Setting up rake (13.0.1-2) ... Setting up debhelper (12.9ubuntu1) ... Setting up libruby2.7:arm64 (2.7.0-4) ... Setting up ruby2.7 (2.7.0-4) ... Setting up ruby (1:2.7~0) ... Setting up ruby-asciidoctor (2.0.10-2) ... Setting up asciidoctor (2.0.10-2) ... Setting up sbuild-build-depends-reapr-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.31-0ubuntu6) ... Processing triggers for systemd (245.2-1ubuntu1) ... +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 4.4.0-176-generic arm64 (aarch64) Toolchain package versions: binutils_2.34-5ubuntu1 dpkg-dev_1.19.7ubuntu3 g++-9_9.3.0-7ubuntu1 gcc-9_9.3.0-7ubuntu1 libc6-dev_2.31-0ubuntu6 libstdc++-9-dev_9.3.0-7ubuntu1 libstdc++6_10-20200321-1ubuntu1 linux-libc-dev_5.4.0-18.22 Package versions: adduser_3.118ubuntu1 advancecomp_2.1-2.1build1 apt_2.0.0 asciidoctor_2.0.10-2 autoconf_2.69-11.1 automake_1:1.16.1-4ubuntu6 autopoint_0.19.8.1-10build1 autotools-dev_20180224.1 bamtools_2.5.1+dfsg-5build1 base-files_11ubuntu4 base-passwd_3.5.47 bash_5.0-6ubuntu1 binutils_2.34-5ubuntu1 binutils-aarch64-linux-gnu_2.34-5ubuntu1 binutils-common_2.34-5ubuntu1 bsdmainutils_11.1.2ubuntu2 bsdutils_1:2.34-0.1ubuntu8 build-essential_12.8ubuntu1 bzip2_1.0.8-2 ca-certificates_20190110 coreutils_8.30-3ubuntu2 cpp_4:9.3.0-1ubuntu2 cpp-9_9.3.0-7ubuntu1 dash_0.5.10.2-6 debconf_1.5.73 debhelper_12.9ubuntu1 debianutils_4.9.1 dh-autoreconf_19 dh-strip-nondeterminism_1.6.3-2 diffutils_1:3.7-3 dpkg_1.19.7ubuntu3 dpkg-dev_1.19.7ubuntu3 dwz_0.13-5 e2fsprogs_1.45.5-2ubuntu1 fakeroot_1.24-1 fdisk_2.34-0.1ubuntu8 file_1:5.38-4 findutils_4.7.0-1ubuntu1 fontconfig_2.13.1-2ubuntu2 fontconfig-config_2.13.1-2ubuntu2 fonts-dejavu-core_2.37-1 g++_4:9.3.0-1ubuntu2 g++-9_9.3.0-7ubuntu1 gcc_4:9.3.0-1ubuntu2 gcc-10-base_10-20200321-1ubuntu1 gcc-9_9.3.0-7ubuntu1 gcc-9-base_9.3.0-7ubuntu1 gettext_0.19.8.1-10build1 gettext-base_0.19.8.1-10build1 gpg_2.2.19-3ubuntu2 gpg-agent_2.2.19-3ubuntu2 gpgconf_2.2.19-3ubuntu2 gpgv_2.2.19-3ubuntu2 grep_3.4-1 groff-base_1.22.4-4build1 gzip_1.10-0ubuntu4 hostname_3.23 init_1.57 init-system-helpers_1.57 intltool-debian_0.35.0+20060710.5 libacl1_2.2.53-6 libapparmor1_2.13.3-7ubuntu2 libapt-pkg5.90_1.9.10 libapt-pkg6.0_2.0.0 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readline-common_8.0-4 ruby_1:2.7~0 ruby-asciidoctor_2.0.10-2 ruby-did-you-mean_1.2.1-1 ruby-minitest_5.13.0-1 ruby-net-telnet_0.1.1-2 ruby-power-assert_1.1.5-1 ruby-test-unit_3.3.4-1 ruby-xmlrpc_0.3.0-2 ruby2.7_2.7.0-4 rubygems-integration_1.16 samtools_1.10-3 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-reapr-dummy_0.invalid.0 sed_4.7-1 sensible-utils_0.0.12+nmu1 smalt_0.7.6-9 snpomatic_1.0-4build1 systemd_245.2-1ubuntu1 systemd-sysv_245.2-1ubuntu1 sysvinit-utils_2.96-2.1ubuntu1 tabix_1.10.2-3 tar_1.30+dfsg-7 tzdata_2019c-3ubuntu1 ubuntu-keyring_2020.02.11.1 ucf_3.0038+nmu1 unzip_6.0-25ubuntu1 util-linux_2.34-0.1ubuntu8 x11-common_1:7.7+19ubuntu14 xdg-utils_1.1.3-1ubuntu2 xz-utils_5.2.4-1 zip_3.0-11build1 zlib1g_1:1.2.11.dfsg-2ubuntu1 zlib1g-dev_1:1.2.11.dfsg-2ubuntu1 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- gpgv: Signature made Tue Mar 24 14:27:24 2020 UTC gpgv: using RSA key D56571B88A8BBAF140BF63D6BD7EAA60778FA6F5 gpgv: issuer "doko@ubuntu.com" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./reapr_1.0.18+dfsg-5build1.dsc dpkg-source: info: extracting reapr in reapr-1.0.18+dfsg dpkg-source: info: unpacking reapr_1.0.18+dfsg.orig.tar.gz dpkg-source: info: unpacking reapr_1.0.18+dfsg-5build1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying spelling dpkg-source: info: applying use_shared_libs dpkg-source: info: applying hardening dpkg-source: info: applying fix_sort_samtools13 dpkg-source: info: applying ld_as_needed Check disc space ---------------- Sufficient free space for build User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf DEB_BUILD_OPTIONS=parallel=4 HOME=/sbuild-nonexistent LANG=C.UTF-8 LC_ALL=C.UTF-8 LOGNAME=buildd PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games SCHROOT_ALIAS_NAME=build-PACKAGEBUILD-18888505 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-18888505 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-18888505 SCHROOT_UID=2001 SCHROOT_USER=buildd SHELL=/bin/sh TERM=unknown USER=buildd V=1 dpkg-buildpackage ----------------- dpkg-buildpackage: info: source package reapr dpkg-buildpackage: info: source version 1.0.18+dfsg-5build1 dpkg-buildpackage: info: source distribution focal dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 fakeroot debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/<>/reapr-1.0.18+dfsg' rm -rf /<>/reapr-1.0.18+dfsg/debian/man_src/*.html /<>/reapr-1.0.18+dfsg/debian/man_src/*.? rm -rf /<>/reapr-1.0.18+dfsg/debian/man rm -rf /<>/reapr-1.0.18+dfsg/debian/test dh_auto_clean -- make[1]: Leaving directory '/<>/reapr-1.0.18+dfsg' dh_clean debian/rules build-arch dh build-arch dh_update_autotools_config -a dh_autoreconf -a debian/rules override_dh_auto_build make[1]: Entering directory '/<>/reapr-1.0.18+dfsg' cd src && /usr/bin/make make[2]: Entering directory '/<>/reapr-1.0.18+dfsg/src' g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/reapr-1.0.18+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -I /usr/include/bamtools -I /usr/include -c errorWindow.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/reapr-1.0.18+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -I /usr/include/bamtools -I /usr/include -c utils.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/reapr-1.0.18+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -I /usr/include/bamtools -I /usr/include -c histogram.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/reapr-1.0.18+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -I /usr/include/bamtools -I /usr/include -c task_score.cpp task_score.cpp: In function ‘int main(int, char**)’: task_score.cpp:235:79: warning: variable ‘p’ set but not used [-Wunused-but-set-variable] 235 | map > >::iterator p = globalGaps.find(currentRefID); | ^ g++ -o task_score -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/reapr-1.0.18+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -I /usr/include/bamtools -I /usr/include task_score.o errorWindow.o utils.o histogram.o -lbamtools -ltabixpp -lhts -lz -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/reapr-1.0.18+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -I /usr/include/bamtools -I /usr/include -c trianglePlot.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/reapr-1.0.18+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -I /usr/include/bamtools -I /usr/include -c coveragePlot.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/reapr-1.0.18+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -I /usr/include/bamtools -I /usr/include -c fasta.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/reapr-1.0.18+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -I /usr/include/bamtools -I /usr/include -c task_stats.cpp task_stats.cpp: In function ‘int main(int, char**)’: task_stats.cpp:441:16: warning: ‘ti_perfect’ may be used uninitialized in this function [-Wmaybe-uninitialized] 441 | delete ti_perfect; | ^~~~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/reapr-1.0.18+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -I /usr/include/bamtools -I /usr/include task_stats.o trianglePlot.o coveragePlot.o fasta.o histogram.o utils.o -lbamtools -ltabixpp -lhts -lz -o task_stats -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/reapr-1.0.18+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -I /usr/include/bamtools -I /usr/include -c task_break.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/reapr-1.0.18+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -I /usr/include/bamtools -I /usr/include task_break.o -lbamtools fasta.o utils.o -lbamtools -ltabixpp -lhts -lz -o task_break -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/reapr-1.0.18+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -I /usr/include/bamtools -I /usr/include -c bam2fragCov.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/reapr-1.0.18+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -I /usr/include/bamtools -I /usr/include bam2fragCov.o -lbamtools coveragePlot.o utils.o -lbamtools -ltabixpp -lhts -lz -o bam2fragCov -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/reapr-1.0.18+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -I /usr/include/bamtools -I /usr/include -c bam2insert.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/reapr-1.0.18+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -I /usr/include/bamtools -I /usr/include bam2insert.o -lbamtools histogram.o utils.o -lbamtools -ltabixpp -lhts -lz -o bam2insert -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/reapr-1.0.18+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -I /usr/include/bamtools -I /usr/include -c bam2fcdEstimate.cpp bam2fcdEstimate.cpp: In function ‘int main(int, char**)’: bam2fcdEstimate.cpp:84:34: warning: comparison of integer expressions of different signedness: ‘int32_t’ {aka ‘int’} and ‘long unsigned int’ [-Wsign-compare] 84 | while (bamAlign.Position > triplot.centreCoord()) | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ bam2fcdEstimate.cpp: In function ‘void initialiseFCDHists(std::vector&, CmdLineOptions&)’: bam2fcdEstimate.cpp:210:33: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘long int’ [-Wsign-compare] 210 | for (unsigned long i = 0; i <= ops.maxInsert; i++) | ~~^~~~~~~~~~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/reapr-1.0.18+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -I /usr/include/bamtools -I /usr/include bam2fcdEstimate.o -lbamtools histogram.o utils.o trianglePlot.o -ltabixpp -lhts -lz -o bam2fcdEstimate -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/reapr-1.0.18+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -I /usr/include/bamtools -I /usr/include -c make_plots.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/reapr-1.0.18+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -I /usr/include/bamtools -I /usr/include make_plots.o -o make_plots -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/reapr-1.0.18+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -I /usr/include/bamtools -I /usr/include -c fa2gaps.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/reapr-1.0.18+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -I /usr/include/bamtools -I /usr/include fa2gaps.o fasta.o -o fa2gaps -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/reapr-1.0.18+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -I /usr/include/bamtools -I /usr/include -c fa2gc.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/reapr-1.0.18+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -I /usr/include/bamtools -I /usr/include fa2gc.o fasta.o -o fa2gc -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/reapr-1.0.18+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -I /usr/include/bamtools -I /usr/include -c scaff2contig.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/reapr-1.0.18+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -I /usr/include/bamtools -I /usr/include scaff2contig.o fasta.o -o scaff2contig -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/reapr-1.0.18+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -I /usr/include/bamtools -I /usr/include -c n50.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/reapr-1.0.18+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -I /usr/include/bamtools -I /usr/include n50.o fasta.o -o n50 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/reapr-1.0.18+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -I /usr/include/bamtools -I /usr/include -c task_gapresize.cpp task_gapresize.cpp: In function ‘int main(int, char**)’: task_gapresize.cpp:129:127: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘int64_t’ {aka ‘long int’} [-Wsign-compare] 129 | if (!bamAlign.IsReverseStrand() && pairOrientation == INNIE && bamAlign.InsertSize > 0 && gapIter->second < fragEnd && fragEnd <= gapIter->second + options.maxFragLength) | ~~~~~~~~~~~~~~~~^~~~~~~~~ task_gapresize.cpp:129:148: warning: comparison of integer expressions of different signedness: ‘int64_t’ {aka ‘long int’} and ‘long unsigned int’ [-Wsign-compare] 129 | if (!bamAlign.IsReverseStrand() && pairOrientation == INNIE && bamAlign.InsertSize > 0 && gapIter->second < fragEnd && fragEnd <= gapIter->second + options.maxFragLength) | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/reapr-1.0.18+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -I /usr/include/bamtools -I /usr/include task_gapresize.o -lbamtools utils.o trianglePlot.o fasta.o -ltabixpp -lhts -lz -o task_gapresize -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/reapr-1.0.18+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -I /usr/include/bamtools -I /usr/include -c task_fcdrate.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/reapr-1.0.18+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -I /usr/include/bamtools -I /usr/include task_fcdrate.o -ltabixpp -lhts -lz histogram.o utils.o -lbamtools -o task_fcdrate -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/reapr-1.0.18+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -I /usr/include/bamtools -I /usr/include -c bam2perfect.cpp bam2perfect.cpp: In function ‘void writeAlignments(std::multimap&, BamTools::BamWriter&, long unsigned int)’: bam2perfect.cpp:213:32: warning: comparison of integer expressions of different signedness: ‘int32_t’ {aka ‘int’} and ‘long unsigned int’ [-Wsign-compare] 213 | if (p->second.Position >= endPos) break; | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/reapr-1.0.18+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -I /usr/include/bamtools -I /usr/include bam2perfect.o -lbamtools utils.o -lbamtools -ltabixpp -lhts -lz -o bam2perfect -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now make[2]: Leaving directory '/<>/reapr-1.0.18+dfsg/src' make[1]: Leaving directory '/<>/reapr-1.0.18+dfsg' debian/rules override_dh_auto_test make[1]: Entering directory '/<>/reapr-1.0.18+dfsg' mkdir /<>/reapr-1.0.18+dfsg/debian/test ln -s /<>/reapr-1.0.18+dfsg/src/reapr.pl /<>/reapr-1.0.18+dfsg/debian/test/reapr PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/<>/reapr-1.0.18+dfsg/src:/<>/reapr-1.0.18+dfsg/debian/test /<>/reapr-1.0.18+dfsg/debian/tests/test-example [wgsim] seed = 42 [wgsim_core] calculating the total length of the reference sequence... [wgsim_core] 1 sequences, total length: 1000111 foo 1384 T K + foo 4961 T W + foo 5885 - T - foo 9598 A C - foo 10177 G R + foo 11305 G K + foo 11592 G R + foo 13931 T - - foo 15907 C A - foo 17264 G K + foo 17780 A - - foo 18711 A W + foo 19249 T W + foo 19522 C S + foo 23053 T K + foo 23681 A R + foo 23730 C S + foo 24075 G S + foo 24555 G C - foo 26775 G K + foo 26896 C M + foo 27253 G K + foo 28210 T Y + foo 28224 A W + foo 28377 - G + foo 29035 G K + foo 29898 C M + foo 30274 A R + foo 30542 G K + foo 31566 A C - foo 32252 - A - foo 33303 T K + foo 33390 - G + foo 34073 A R + foo 34171 G R + foo 34718 T Y + foo 34801 - C + foo 35204 T W + foo 35342 G S + foo 35489 G T - foo 36153 A M + foo 36273 C S + foo 37356 G T - foo 37596 C S + foo 39308 T - - foo 40333 C G - foo 42295 T K + foo 42372 T Y + foo 44433 C G - foo 44630 - AG + foo 44902 T C - foo 47156 C A - foo 48210 C M + foo 48390 A R + foo 49652 C M + foo 52739 T Y + foo 52858 A M + foo 54737 A G - foo 55306 C T - foo 55434 C T - foo 59204 A W + foo 59300 G C - foo 59335 T Y + foo 59444 T - - foo 59531 C S + foo 59766 C Y + foo 61950 C S + foo 62887 G S + foo 63390 A G - foo 64365 G K + foo 64703 C S + foo 64932 C Y + foo 68383 - CG + foo 68464 A W + foo 68727 A W + foo 69080 A M + foo 72071 T C - foo 72720 - G - foo 73354 C T - foo 73637 G T - foo 74741 A M + foo 75101 C T - foo 75207 T K + foo 76400 T Y + foo 76780 A C - foo 77172 A W + foo 78385 C Y + foo 80705 C M + foo 82440 A R + foo 83021 G K + foo 83116 A - - foo 83846 T K + foo 84633 G S + foo 85891 G S + foo 87759 A C - foo 87778 T W + foo 88581 T K + foo 88606 T Y + foo 88880 A G - foo 89945 G C - foo 90728 T K + foo 91798 G R + foo 95957 G C - foo 96173 T W + foo 96665 A M + foo 98019 - G + foo 98131 A M + foo 98669 A R + foo 98719 G T - foo 99062 A W + foo 99590 A T - foo 100532 - TC + foo 103015 A W + foo 103172 G S + foo 103609 G R + foo 106549 T Y + foo 108808 C Y + foo 109191 G C - foo 111686 C G - foo 113436 C A - foo 113763 A W + foo 115671 C T - foo 117460 - A - foo 118193 G - - foo 118585 T K + foo 121219 A M + foo 121876 T K + foo 122071 T A - foo 124918 C G - foo 125300 G S + foo 125967 C S + foo 127443 G S + foo 127565 C Y + foo 128700 C A - foo 129912 G A - foo 130847 T W + foo 131677 G S + foo 132189 T C - foo 135878 CGGC - - foo 136825 T K + foo 138881 TGT - - foo 139288 A W + foo 141054 A W + foo 141055 - T + foo 141101 C S + foo 141404 A R + foo 142698 T C - foo 143990 C A - foo 144167 T Y + foo 144814 C Y + foo 146381 T Y + foo 146393 C A - foo 146510 A C - foo 147182 A W + foo 148783 T C - foo 149068 G S + foo 150208 T K + foo 151554 T W + foo 151709 C G - foo 153072 G R + foo 153307 T Y + foo 154050 G S + foo 154415 C S + foo 154594 G R + foo 155839 G T - foo 156106 G A - foo 159356 T W + foo 159926 A W + foo 160303 T K + foo 161323 C Y + foo 161904 G S + foo 162533 - ACC - foo 164738 C G - foo 165413 A R + foo 166944 C M + foo 167464 T Y + foo 168420 T C - foo 168579 A M + foo 168787 T W + foo 168959 A T - foo 169884 G S + foo 170032 G T - foo 172058 G K + foo 174942 A R + foo 175014 G K + foo 178406 G A - foo 179028 - A + foo 182394 C M + foo 182735 T Y + foo 183384 T K + foo 183893 - AT - foo 185360 G A - foo 185538 - G - foo 187948 G S + foo 188120 T G - foo 188179 T W + foo 188316 T Y + foo 189963 - G + foo 190093 C Y + foo 192220 C M + foo 192368 A W + foo 192782 T K + foo 193307 A R + foo 193501 G K + foo 194276 G S + foo 194930 C S + foo 196728 A W + foo 197559 G C - foo 198467 T W + foo 199042 C Y + foo 199259 AA - - foo 199687 TT - - foo 200287 C A - foo 200678 A R + foo 201208 C T - foo 201882 A - - foo 204456 T K + foo 206327 G R + foo 207311 G T - foo 209184 G A - foo 209279 C Y + foo 211459 C Y + foo 213807 T Y + foo 213846 T Y + foo 214635 A G - foo 214884 C A - foo 216244 A M + foo 216652 A M + foo 216745 T - - foo 216909 A T - foo 217579 A G - foo 217895 C Y + foo 218870 G K + foo 223098 T A - foo 223283 - C + foo 223666 C A - foo 224011 - C + foo 225681 C S + foo 227345 T C - foo 228778 T G - foo 229926 C - - foo 230778 T K + foo 230939 CG - - foo 231988 CT - - foo 234593 T W + foo 235496 C S + foo 235705 G K + foo 235758 A G - foo 236852 T C - foo 238790 A M + foo 238865 T K + foo 239329 A M + foo 239576 - C + foo 243058 G S + foo 244147 T - - foo 244462 C G - foo 245443 - A + foo 246544 C Y + foo 246744 T W + foo 247473 C M + foo 248129 C T - foo 249060 A C - foo 249515 G T - foo 250138 G S + foo 250567 C A - foo 254381 G R + foo 257864 C M + foo 257879 C Y + foo 259859 A M + foo 260643 C S + foo 261681 C G - foo 262645 T Y + foo 263279 A R + foo 263575 A - - foo 264587 - TA + foo 264689 T K + foo 265758 G K + foo 266272 A M + foo 268550 C M + foo 269986 G S + foo 270321 AC - - foo 273346 C S + foo 275367 C A - foo 277334 C G - foo 277629 G T - foo 278431 C Y + foo 281456 T Y + foo 281556 T G - foo 281737 G K + foo 282290 AC - - foo 282851 - C - foo 284405 A C - foo 288751 A C - foo 290501 TAAA - - foo 291315 A W + foo 291368 C - - foo 292154 A C - foo 292385 C M + foo 292555 G K + foo 297709 G C - foo 298183 A W + foo 298228 T W + foo 299902 T G - foo 302575 A T - foo 304823 G R + foo 305308 T Y + foo 305487 G S + foo 305697 G T - foo 306098 C G - foo 306882 T Y + foo 308201 A M + foo 308833 A T - foo 312033 A - - foo 312895 C G - foo 313889 C - - foo 315109 A R + foo 316083 C - - foo 316466 A R + foo 318040 G C - foo 319446 T C - foo 320236 C S + foo 320652 A - - foo 320716 T K + foo 323644 A - - foo 325359 G T - foo 329476 - CA + foo 329706 T G - foo 330181 T Y + foo 330703 C Y + foo 331315 G S + foo 332351 C A - foo 333408 A R + foo 333468 C S + foo 336247 A G - foo 336586 A M + foo 337364 G K + foo 337686 A T - foo 338043 A - - foo 338292 C G - foo 338962 A C - foo 339353 G K + foo 340647 - A + foo 341705 G R + foo 344283 C M + foo 345898 - AG - foo 347959 T - - foo 349162 C M + foo 352072 T Y + foo 354614 C Y + foo 359304 T - - foo 359312 - G + foo 360972 C S + foo 363857 C Y + foo 366226 A C - foo 367259 C M + foo 372502 T Y + foo 372747 A M + foo 375140 C S + foo 376298 T W + foo 376313 C - - foo 376760 T W + foo 378494 A W + foo 381137 T G - foo 381186 A R + foo 381701 A G - foo 382614 A W + foo 382761 C T - foo 382854 T C - foo 383201 C T - foo 385104 G S + foo 385233 - A + foo 386138 C T - foo 386316 A W + foo 387072 A R + foo 387642 - A + foo 388232 T C - foo 388890 GGG - - foo 390508 C S + foo 390625 C M + foo 391921 C G - foo 395256 G T - foo 395542 G S + foo 397015 A - - foo 397516 C Y + foo 397528 GC - - foo 398152 C T - foo 399802 A W + foo 400972 T K + foo 401419 - T + foo 401477 T W + foo 402437 A M + foo 402722 G R + foo 403452 C M + foo 404234 - A + foo 405344 A W + foo 407040 G S + foo 408483 G R + foo 408586 A C - foo 408721 A R + foo 409494 A M + foo 410078 A G - foo 411170 C A - foo 415342 T Y + foo 416265 C G - foo 417740 C A - foo 418622 C S + foo 420232 A W + foo 420288 T Y + foo 420908 A W + foo 421109 T A - foo 421357 A R + foo 422799 G A - foo 424383 C S + foo 424871 - GCA + foo 427273 T A - foo 429822 C M + foo 429846 T W + foo 432015 A G - foo 432414 G K + foo 433606 C Y + foo 433831 T Y + foo 437721 - A - foo 438402 G - - foo 438799 A T - foo 439422 C M + foo 440734 C A - foo 441840 T G - foo 442021 - C + foo 445021 T A - foo 445591 G A - foo 446138 T W + foo 447757 A W + foo 449156 T - - foo 449161 G K + foo 450114 A W + foo 450688 A W + foo 454421 C G - foo 454718 T Y + foo 455675 TC - - foo 461721 G R + foo 462526 G S + foo 467296 G A - foo 467510 G K + foo 468267 T K + foo 469118 G R + foo 469830 C Y + foo 471073 G T - foo 472056 G A - foo 472773 - A + foo 473046 G R + foo 473188 G A - foo 473742 C - - foo 474789 T A - foo 477763 G R + foo 478246 T W + foo 478975 T G - foo 479038 A R + foo 480275 T Y + foo 480317 G A - foo 481512 T K + foo 482069 G S + foo 482534 A R + foo 483760 C Y + foo 485281 T W + foo 486255 T C - foo 487038 T K + foo 487225 T A - foo 488012 C Y + foo 488795 T C - foo 490241 A R + foo 492595 - CGG + foo 493224 C A - foo 494284 A T - foo 495990 - T - foo 497306 A R + foo 497403 T Y + foo 499569 C Y + foo 499651 T K + foo 503139 T C - foo 504660 A R + foo 508679 C - - foo 513643 G K + foo 515668 CC - - foo 515836 G R + foo 516488 C S + foo 517602 G R + foo 517962 G K + foo 517975 T K + foo 519144 A T - foo 520068 T K + foo 520926 A W + foo 521562 C S + foo 522076 CG - - foo 522838 T Y + foo 523513 - C + foo 523907 - TA + foo 526271 T A - foo 526533 AC - - foo 526767 C Y + foo 528217 C Y + foo 531924 G S + foo 532333 - TT + foo 533132 C M + foo 534689 A T - foo 534779 A W + foo 535594 C A - foo 535795 G R + foo 538368 A R + foo 540879 G K + foo 542530 A - - foo 543620 G R + foo 544733 - C - foo 546300 - TT + foo 548196 A T - foo 548878 C M + foo 548885 G R + foo 549459 T K + foo 550908 A G - foo 551170 A - - foo 553130 T Y + foo 555293 T G - foo 556198 G R + foo 556355 A T - foo 557688 G K + foo 558415 G C - foo 558461 - G + foo 559287 T Y + foo 559465 C M + foo 560184 T W + foo 560252 T W + foo 562579 A M + foo 562961 G A - foo 566986 C A - foo 568134 C A - foo 569698 T C - foo 570180 T K + foo 570451 TG - - foo 570832 - A - foo 571589 A W + foo 572208 C M + foo 572871 C S + foo 574334 G - - foo 575673 T Y + foo 576797 G S + foo 578486 - C - foo 578494 C S + foo 579257 G A - foo 580103 G T - foo 580872 A W + foo 580925 G S + foo 580950 G C - foo 581637 T Y + foo 581654 A G - foo 582538 A T - foo 582691 C M + foo 582938 A W + foo 583104 T K + foo 584763 T W + foo 585723 T W + foo 588253 T Y + foo 588972 T C - foo 589438 - C - foo 591131 C Y + foo 591950 G R + foo 592194 T G - foo 592310 G S + foo 593892 G A - foo 598556 A - - foo 601660 G S + foo 602112 G T - foo 602412 T Y + foo 607282 - C + foo 607394 A M + foo 608438 A T - foo 609255 A W + foo 609365 - T + foo 611161 G K + foo 612224 C G - foo 614493 G R + foo 614601 G A - foo 614607 C Y + foo 619507 C M + foo 619798 T C - foo 621872 C T - foo 622375 C Y + foo 623208 - G - foo 624366 C A - foo 625320 - ACA - foo 626664 - G + foo 627140 T C - foo 627353 G T - foo 628714 T Y + foo 628744 A - - foo 629152 A G - foo 630110 T G - foo 631744 G K + foo 632763 C S + foo 634419 G - - foo 634459 A G - foo 634571 G A - foo 635366 - A + foo 635604 G T - foo 637057 T C - foo 637525 A T - foo 638412 A R + foo 640547 A W + foo 641514 T K + foo 642219 A R + foo 642427 A G - foo 642612 A R + foo 643553 T W + foo 647316 - T + foo 647598 C - - foo 651093 G A - foo 651718 G R + foo 652235 A G - foo 652579 A C - foo 653355 A W + foo 655174 C M + foo 655487 A M + foo 656849 G S + foo 661081 T K + foo 661134 G C - foo 661935 A W + foo 662010 A M + foo 662040 G R + foo 663030 A W + foo 663268 - C + foo 664991 T - - foo 665489 T K + foo 665555 C M + foo 665965 C Y + foo 668725 A C - foo 668834 - G - foo 668873 C S + foo 669654 T W + foo 671041 G S + foo 671485 T W + foo 671690 C M + foo 673022 G R + foo 674137 - T + foo 674782 A C - foo 676373 G T - foo 676793 T C - foo 677409 G S + foo 677536 - AA - foo 677620 G K + foo 677686 C Y + foo 678327 G S + foo 678704 G S + foo 678771 A C - foo 678866 C T - foo 679960 A W + foo 680447 - C + foo 682102 C T - foo 685497 T A - foo 686884 G S + foo 687324 ACA - - foo 687684 - AC + foo 687823 T C - foo 688590 G K + foo 690802 C M + foo 691388 T C - foo 691403 T G - foo 691790 G A - foo 692973 C A - foo 694058 G S + foo 694550 G R + foo 694968 T W + foo 695898 A T - foo 696721 C S + foo 696787 C S + foo 696935 A M + foo 698024 - C + foo 699813 A - - foo 700179 G R + foo 701421 A M + foo 701989 T A - foo 702862 C A - foo 707020 G A - foo 708420 A - - foo 708669 C G - foo 710521 T W + foo 711801 G C - foo 711913 T G - foo 715830 C M + foo 717664 TC - - foo 718845 A W + foo 719069 T Y + foo 719565 A W + foo 721136 T K + foo 726116 T K + foo 727809 T K + foo 728864 G K + foo 728918 G A - foo 730296 - T + foo 731988 C Y + foo 734658 A M + foo 734715 A W + foo 736618 C G - foo 737257 T Y + foo 740864 C A - foo 741640 G - - foo 741859 - TA - foo 742011 T K + foo 742237 A R + foo 742960 G K + foo 743731 G R + foo 743971 A W + foo 744635 T K + foo 746430 C G - foo 746489 - GC - foo 746881 C M + foo 756997 TC - - foo 757776 A M + foo 759870 A T - foo 760224 G K + foo 760799 G C - foo 761692 T C - foo 762569 G S + foo 763140 A G - foo 763842 - T - foo 764192 A M + foo 764334 G A - foo 764889 - AAT + foo 766464 G S + foo 768226 G A - foo 770272 T G - foo 771145 C Y + foo 772209 T A - foo 773672 T K + foo 773932 G C - foo 774658 C S + foo 775969 A M + foo 776816 T G - foo 777591 C Y + foo 777891 A M + foo 778164 C M + foo 778219 T W + foo 779260 G T - foo 779465 A W + foo 779779 G S + foo 780033 G K + foo 783243 C M + foo 783860 A R + foo 788345 A M + foo 789554 G - - foo 790025 G K + foo 791454 T K + foo 792009 C A - foo 792872 C G - foo 794616 T W + foo 795031 G R + foo 796919 C M + foo 797020 G S + foo 797042 G C - foo 797149 G A - foo 797177 A C - foo 799076 G C - foo 799580 G S + foo 800356 A R + foo 802297 G T - foo 802309 T Y + foo 802343 - C + foo 802769 A W + foo 803104 C G - foo 805819 C Y + foo 805972 T Y + foo 807503 T K + foo 807950 C M + foo 807994 - A - foo 809167 A G - foo 809658 A W + foo 810152 A M + foo 811506 G R + foo 813494 A M + foo 814035 G T - foo 814476 A W + foo 819399 T K + foo 820171 T W + foo 820445 G C - foo 822178 C G - foo 822504 C T - foo 823378 C M + foo 823591 CG - - foo 824229 C M + foo 824579 C T - foo 824858 C M + foo 826101 T K + foo 827593 C G - foo 827794 T Y + foo 828228 A M + foo 828367 T K + foo 828788 C M + foo 829002 C Y + foo 830345 C M + foo 831018 C A - foo 831459 T K + foo 832413 A T - foo 832782 T Y + foo 832908 T Y + foo 833130 T - - foo 833142 G S + foo 833241 G A - foo 836727 A T - foo 836829 G S + foo 838452 T G - foo 838543 A T - foo 838605 C M + foo 838954 G C - foo 841829 G K + foo 842324 - TC + foo 842996 - C + foo 844390 C A - foo 844793 A C - foo 844925 C A - foo 845082 G C - foo 846202 G R + foo 846707 A G - foo 848713 G A - foo 849372 C S + foo 849742 G A - foo 850499 C - - foo 850927 GT - - foo 851084 - G + foo 852247 A R + foo 852972 C A - foo 854808 T W + foo 855956 G K + foo 856225 G A - foo 856582 T K + foo 857351 C M + foo 857504 AC - - foo 858324 A T - foo 858858 T C - foo 859488 T Y + foo 862441 T Y + foo 863827 C Y + foo 864165 C A - foo 865997 C M + foo 866370 G S + foo 867653 G S + foo 867722 C Y + foo 868696 C M + foo 869005 T W + foo 869791 T Y + foo 875339 C Y + foo 875347 C M + foo 875584 T G - foo 876780 C T - foo 878368 A C - foo 878916 - CAG + foo 879005 A R + foo 880112 G T - foo 881021 - T - foo 881175 T W + foo 882168 - GGG + foo 882223 - G - foo 883033 TG - - foo 883381 C G - foo 884378 C - - foo 885075 A M + foo 885190 A W + foo 885568 A W + foo 885827 T Y + foo 887610 TG - - foo 889139 G R + foo 890978 T - - foo 891500 C Y + foo 892257 G C - foo 892642 G R + foo 892644 T W + foo 892757 C A - foo 893222 T - - foo 893348 T W + foo 894161 - C - foo 894447 A G - foo 894614 A W + foo 897817 T W + foo 899408 C S + foo 902450 A T - foo 902970 AT - - foo 905836 G K + foo 906524 GA - - foo 907484 A W + foo 907537 C M + foo 908515 G R + foo 908642 C T - foo 911145 T C - foo 912220 T Y + foo 912682 C Y + foo 914260 C S + foo 914757 T Y + foo 916413 G C - foo 916783 T G - foo 917033 G C - foo 917218 A - - foo 918225 G - - foo 918459 A - - foo 918732 A M + foo 919640 TC - - foo 920824 T W + foo 920836 G C - foo 924560 G R + foo 924659 GA - - foo 925868 T A - foo 928254 T G - foo 928369 - A - foo 928641 - AG + foo 929857 C M + foo 930211 T W + foo 930935 C T - foo 931986 A M + foo 932852 G T - foo 933965 T A - foo 935564 A W + foo 936034 T Y + foo 936221 AC - - foo 936670 C S + foo 936704 T A - foo 936786 T W + foo 939218 C S + foo 939312 A W + foo 939467 A W + foo 939934 C S + foo 941603 C Y + foo 942910 A W + foo 944654 T Y + foo 945301 A C - foo 945770 C T - foo 946078 G S + foo 948833 G K + foo 948999 A W + foo 949193 A R + foo 950276 C M + foo 950414 A W + foo 951285 G C - foo 953158 G R + foo 953287 A W + foo 954150 C G - foo 954258 G - - foo 955396 CC - - foo 956490 - AC + foo 958129 A R + foo 959027 T A - foo 959964 A W + foo 962042 A G - foo 962742 C G - foo 963306 T W + foo 963422 G K + foo 964082 G S + foo 965561 C S + foo 966531 T K + foo 967324 T W + foo 968419 - C - foo 969054 G - - foo 969158 G S + foo 972658 C M + foo 974266 T W + foo 974629 G K + foo 975034 A R + foo 975636 T W + foo 977078 - A - foo 978321 G T - foo 978595 C G - foo 979090 C M + foo 983855 TA - - foo 985725 T A - foo 988497 C Y + foo 990171 C M + foo 990804 - CA - foo 990941 T W + foo 991797 A W + foo 992469 A M + foo 994610 C Y + foo 998107 - T + foo 999725 G R + [REAPR smaltmap] Running: smalt index -k 13 -s 2 out.bam.tmp.6339.smaltmap.smalt_index foo1.fasta # Command line: smalt index -k 13 -s 2 out.bam.tmp.6339.smaltmap.smalt_index foo1.fasta # Reading sequences ... # Writing sequence set ... # Setting up hash index with collisions ... # word length = 13 bases, skip step = 2 bases ... # number of bits for key = 18 with 0 perfect bits # Counting keys ... # Counting k-tuples ... # Allocating k-tuple arrays ... # Counting k-tuple occurrences ... # Setting the k-tuple positions in index ... # Hash table is set up. # =-=-=-=-= Hash Index Stats =-=-=-=-= # Hash index with collisions. # Word length: 13 bases # Skip step: 2 bases # Number of hash keys: 262144 # Number of word positions: 499970 # Number of different words: 498076 # Maximum number of words per key: 11 # Number of keys without words: 39377 # =-=-= End of Hash Index Stats =-=-= # Writing table to file ... # smalt: Total elapsed wall clock time: 0 seconds [REAPR smaltmap] Running: smalt sample -u 1000 -o out.bam.tmp.6339.smaltmap.smalt_sample out.bam.tmp.6339.smaltmap.smalt_index foofq.1.fastq foofq.2.fastq # Command line: smalt sample -u 1000 -o out.bam.tmp.6339.smaltmap.smalt_sample out.bam.tmp.6339.smaltmap.smalt_index foofq.1.fastq foofq.2.fastq # Opening read files ... # Reading reference sequences ... # Reading hash table ... # =-=-=-=-= Hash Index Stats =-=-=-=-= # Hash index with collisions. # Word length: 13 bases # Skip step: 2 bases # Number of hash keys: 262144 # Number of word positions: 499970 # Number of different words: 498076 # Maximum number of words per key: 11 # Number of keys without words: 39377 # =-=-= End of Hash Index Stats =-=-= # Check of read pairs ok ... # Mate names match ... # Sampling insert size distribution ... # Processed 9999 read pairs. # smalt: Time spent setting up hash index:0 seconds # smalt: Time spent mapping reads:7 seconds # smalt: Total elapsed wall clock time: 7 seconds [REAPR smaltmap] Running: smalt map -r 0 -x -y 0.5 -g out.bam.tmp.6339.smaltmap.smalt_sample -f samsoft out.bam.tmp.6339.smaltmap.smalt_index foofq.1.fastq foofq.2.fastq | awk '$1!~/^#/' | samtools view -S -T foo1.fasta -b - > out.bam.tmp.6339.smaltmap.raw.bam # Command line: smalt map -r 0 -x -y 0.5 -g out.bam.tmp.6339.smaltmap.smalt_sample -f samsoft out.bam.tmp.6339.smaltmap.smalt_index foofq.1.fastq foofq.2.fastq # Reading distribution of insert sizes from file ... # Sampled histogram # Smoothed histogram # Opening read files ... # Reading reference sequences ... # Reading hash table ... # =-=-=-=-= Hash Index Stats =-=-=-=-= # Hash index with collisions. # Word length: 13 bases # Skip step: 2 bases # Number of hash keys: 262144 # Number of word positions: 499970 # Number of different words: 498076 # Maximum number of words per key: 11 # Number of keys without words: 39377 # =-=-= End of Hash Index Stats =-=-= # Processing query reads ... # Processed 10000 read pairs. # smalt: Time spent setting up hash index:0 seconds # smalt: Time spent mapping reads:31 seconds # smalt: Total elapsed wall clock time: 31 seconds [REAPR smaltmap] Running: samtools sort out.bam.tmp.6339.smaltmap.raw.bam -O bam -o out.bam.tmp.6339.smaltmap.raw.bam.sort.bam [REAPR smaltmap] Running: samtools rmdup out.bam.tmp.6339.smaltmap.raw.bam.sort.bam out.bam.tmp.6339.smaltmap.rmdup.bam [bam_rmdup_core] processing reference foo... [bam_rmdup_core] 1 / 10000 = 0.0001 in library ' ' [REAPR smaltmap] Running: echo "@HD VN:1.0 SO:coordinate" | awk '{OFS="\t"; $1=$1; print}' > out.bam.tmp.6339.smaltmap.header [REAPR smaltmap] Running: samtools view -H out.bam.tmp.6339.smaltmap.rmdup.bam >> out.bam.tmp.6339.smaltmap.header [REAPR smaltmap] Running: samtools reheader out.bam.tmp.6339.smaltmap.header out.bam.tmp.6339.smaltmap.rmdup.bam > out.bam [REAPR smaltmap] Running: samtools index out.bam [REAPR smaltmap] Running: rm out.bam.tmp.6339.smaltmap.* Running reapr version 1.0.18 pipeline: reapr foo1.fasta out.bam result [REAPR pipeline] Running facheck [REAPR pipeline] Running preprocess [REAPR preprocess] sampling region foo:1169-3476. Already sampled 0 bases [REAPR preprocess] sampling region foo:3492-5726. Already sampled 2308 bases [REAPR preprocess] sampling region foo:5756-12551. Already sampled 4543 bases [REAPR preprocess] sampling region foo:12591-998105. Already sampled 11339 bases [REAPR preprocess] Sampled 996854 bases for GC/coverage estimation [REAPR pipeline] Running stats [REAPR pipeline] Running fcdrate [REAPR pipeline] Running score [REAPR pipeline] Running break [REAPR pipeline] Running summary rm -rf /<>/reapr-1.0.18+dfsg/debian/test make[1]: Leaving directory '/<>/reapr-1.0.18+dfsg' create-stamp debian/debhelper-build-stamp fakeroot debian/rules binary-arch dh binary-arch dh_testroot -a dh_prep -a debian/rules override_dh_auto_install make[1]: Entering directory '/<>/reapr-1.0.18+dfsg' mkdir -p debian/reapr/usr/lib/reapr install src/reapr.pl debian/reapr/usr/lib/reapr/reapr.pl chmod -x src/*.cpp find src -executable -exec install {} debian/reapr/usr/lib/reapr \; install: omitting directory 'src' dh_auto_install -- make[1]: Leaving directory '/<>/reapr-1.0.18+dfsg' debian/rules override_dh_install make[1]: Entering directory '/<>/reapr-1.0.18+dfsg' for pl in `grep -Rl '#!/usr/bin/env' debian/*/usr/*` ; do \ sed -i '1s?^#!/usr/bin/env[[:space:]]\+perl?#!/usr/bin/perl?' ${pl} ; \ done make[1]: Leaving directory '/<>/reapr-1.0.18+dfsg' dh_installdocs -a dh_installchangelogs -a debian/rules override_dh_installman make[1]: Entering directory '/<>/reapr-1.0.18+dfsg' mkdir -p /<>/reapr-1.0.18+dfsg/debian/man asciidoctor -a docdate='' -b manpage /<>/reapr-1.0.18+dfsg/debian/man_src/*.adoc cp /<>/reapr-1.0.18+dfsg/debian/man_src/*.? /<>/reapr-1.0.18+dfsg/debian/man dh_installman -- make[1]: Leaving directory '/<>/reapr-1.0.18+dfsg' dh_perl -a dh_link -a dh_strip_nondeterminism -a dh_compress -a dh_fixperms -a dh_missing -a dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dh_installdeb -a dh_gencontrol -a dpkg-gencontrol: warning: package reapr: substitution variable ${perl:Depends} unused, but is defined dpkg-gencontrol: warning: package reapr: substitution variable ${perl:Depends} unused, but is defined dh_md5sums -a dh_builddeb -a INFO: pkgstriptranslations version 144 INFO: pkgstriptranslations version 144 pkgstriptranslations: processing reapr (in debian/reapr); do_strip: , oemstrip: pkgstriptranslations: processing reapr-dbgsym (in debian/.debhelper/reapr/dbgsym-root); do_strip: , oemstrip: pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/reapr/DEBIAN/control, package reapr, directory debian/reapr pkgstripfiles: Running PNG optimization (using 4 cpus) for package reapr ... pkgstripfiles: No PNG files. dpkg-deb: building package 'reapr' in '../reapr_1.0.18+dfsg-5build1_arm64.deb'. pkgstripfiles: processing control file: debian/.debhelper/reapr/dbgsym-root/DEBIAN/control, package reapr-dbgsym, directory debian/.debhelper/reapr/dbgsym-root dpkg-deb: building package 'reapr-dbgsym' in 'debian/.debhelper/scratch-space/build-reapr/reapr-dbgsym_1.0.18+dfsg-5build1_arm64.deb'. Renaming reapr-dbgsym_1.0.18+dfsg-5build1_arm64.deb to reapr-dbgsym_1.0.18+dfsg-5build1_arm64.ddeb dpkg-genbuildinfo --build=any dpkg-genchanges --build=any -mLaunchpad Build Daemon >../reapr_1.0.18+dfsg-5build1_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 20200324-1911 Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Post Build Chroot | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ reapr_1.0.18+dfsg-5build1_arm64.changes: ---------------------------------------- Format: 1.8 Date: Tue, 24 Mar 2020 15:15:24 +0100 Source: reapr Binary: reapr Architecture: arm64 Version: 1.0.18+dfsg-5build1 Distribution: focal-proposed Urgency: medium Maintainer: Launchpad Build Daemon Changed-By: Matthias Klose Description: reapr - universal tool for genome assembly evaluation Changes: reapr (1.0.18+dfsg-5build1) focal; urgency=medium . * No-change rebuild for libgcc-s1 package name change. Checksums-Sha1: fa9261f451d5c1f29e41a6ebadeeece6d02aa6d0 3466256 reapr-dbgsym_1.0.18+dfsg-5build1_arm64.ddeb ae57bd82b6d2220528533a3e8603001c08f75602 9538 reapr_1.0.18+dfsg-5build1_arm64.buildinfo dee3ba46fca6c169ea670b9cd8e8b1798f55f597 174640 reapr_1.0.18+dfsg-5build1_arm64.deb Checksums-Sha256: 413fff711e99d510b4b54b64bb8cbe1a9f301fc6e34491468af5d61c133bcd10 3466256 reapr-dbgsym_1.0.18+dfsg-5build1_arm64.ddeb fad17da370bbc64cf8db527e5af637347d403131aed3508e49ff1f0b0efc21af 9538 reapr_1.0.18+dfsg-5build1_arm64.buildinfo 2933c800cffc8c21f89480c55582d0e713a0095a8d93c113491b3acd145a0d73 174640 reapr_1.0.18+dfsg-5build1_arm64.deb Files: 1c1c36ffed83d6e261ba8c08a2ceb3dd 3466256 debug optional reapr-dbgsym_1.0.18+dfsg-5build1_arm64.ddeb a1fdd3e7c9fe95bcf4ad6a093e229338 9538 science optional reapr_1.0.18+dfsg-5build1_arm64.buildinfo 67948f47ba0e9d78ac13c9e72b44f977 174640 science optional reapr_1.0.18+dfsg-5build1_arm64.deb +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ reapr_1.0.18+dfsg-5build1_arm64.deb ----------------------------------- new debian package, version 2.0. size 174640 bytes: control archive=2164 bytes. 1519 bytes, 25 lines control 2623 bytes, 40 lines md5sums Package: reapr Version: 1.0.18+dfsg-5build1 Architecture: arm64 Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 905 Depends: libbamtools2.5.1 (>= 2.5.1+dfsg), libc6 (>= 2.17), libgcc-s1 (>= 3.0), libstdc++6 (>= 9), libtabixpp0 (>= 1.0.0), samtools (>= 1.3), bamtools, smalt, r-base, snpomatic, tabix, libfile-copy-link-perl Section: science Priority: optional Homepage: https://www.sanger.ac.uk/science/tools/reapr Description: universal tool for genome assembly evaluation REAPR is a tool that evaluates the accuracy of a genome assembly using mapped paired end reads, without the use of a reference genome for comparison. It can be used in any stage of an assembly pipeline to automatically break incorrect scaffolds and flag other errors in an assembly for manual inspection. It reports mis-assemblies and other warnings, and produces a new broken assembly based on the error calls. . The software requires as input an assembly in FASTA format and paired reads mapped to the assembly in a BAM file. Mapping information such as the fragment coverage and insert size distribution is analysed to locate mis-assemblies. REAPR works best using mapped read pairs from a large insert library (at least 1000bp). Additionally, if a short insert Illumina library is also available, REAPR can combine this with the large insert library in order to score each base of the assembly. drwxr-xr-x root/root 0 2020-03-24 14:15 ./ drwxr-xr-x root/root 0 2020-03-24 14:15 ./usr/ drwxr-xr-x root/root 0 2020-03-24 14:15 ./usr/bin/ lrwxrwxrwx root/root 0 2020-03-24 14:15 ./usr/bin/reapr -> ../lib/reapr/reapr.pl drwxr-xr-x root/root 0 2020-03-24 14:15 ./usr/lib/ drwxr-xr-x root/root 0 2020-03-24 14:15 ./usr/lib/reapr/ -rwxr-xr-x root/root 80040 2020-03-24 14:15 ./usr/lib/reapr/bam2fcdEstimate -rwxr-xr-x root/root 51368 2020-03-24 14:15 ./usr/lib/reapr/bam2fragCov -rwxr-xr-x root/root 67752 2020-03-24 14:15 ./usr/lib/reapr/bam2insert -rwxr-xr-x root/root 55464 2020-03-24 14:15 ./usr/lib/reapr/bam2perfect -rwxr-xr-x root/root 18600 2020-03-24 14:15 ./usr/lib/reapr/fa2gaps -rwxr-xr-x root/root 22696 2020-03-24 14:15 ./usr/lib/reapr/fa2gc -rwxr-xr-x root/root 26792 2020-03-24 14:15 ./usr/lib/reapr/make_plots 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+------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not removing build depends: as requested +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: arm64 Build-Space: 59892 Build-Time: 292 Distribution: focal-proposed Host Architecture: arm64 Install-Time: 40 Job: reapr_1.0.18+dfsg-5build1.dsc Machine Architecture: arm64 Package: reapr Package-Time: 334 Source-Version: 1.0.18+dfsg-5build1 Space: 59892 Status: successful Version: 1.0.18+dfsg-5build1 -------------------------------------------------------------------------------- Finished at 20200324-1911 Build needed 00:05:34, 59892k disc space RUN: /usr/share/launchpad-buildd/bin/in-target scan-for-processes --backend=chroot --series=focal --arch=arm64 PACKAGEBUILD-18888505 Scanning for processes to kill in build PACKAGEBUILD-18888505