https://launchpad.net/ubuntu/+archive/test-rebuild-20201216-hirsute-gcc11/+build/20675635 RUN: /usr/share/launchpad-buildd/bin/builder-prep Kernel version: Linux bos02-s390x-009 4.15.0-134-generic #138-Ubuntu SMP Fri Jan 15 10:53:04 UTC 2021 s390x Buildd toolchain package versions: launchpad-buildd_194~476~ubuntu18.04.1 python3-lpbuildd_194~476~ubuntu18.04.1 sbuild_0.75.0-1ubuntu1 bzr-builder_0.7.3+bzr174~ppa13~ubuntu16.04.1 bzr_2.7.0+bzr6622-10 git-build-recipe_0.3.6~git201906051340.ff11471~ubuntu18.04.1 git_1:2.17.1-1ubuntu0.7 dpkg-dev_1.19.0.5ubuntu2.3 python-debian_0.1.32 python3-debian_0.1.32. Syncing the system clock with the buildd NTP service... 26 Jan 13:40:52 ntpdate[1705]: adjust time server 10.211.37.1 offset 0.008962 sec RUN: /usr/share/launchpad-buildd/bin/in-target unpack-chroot --backend=chroot --series=hirsute --arch=s390x PACKAGEBUILD-20675635 --image-type chroot /home/buildd/filecache-default/9aaab3d1c3367126bc5b66d2474faf9141147628 Creating target for build PACKAGEBUILD-20675635 RUN: /usr/share/launchpad-buildd/bin/in-target mount-chroot --backend=chroot --series=hirsute --arch=s390x PACKAGEBUILD-20675635 Starting target for build PACKAGEBUILD-20675635 RUN: /usr/share/launchpad-buildd/bin/in-target override-sources-list --backend=chroot --series=hirsute --arch=s390x PACKAGEBUILD-20675635 'deb http://ppa.launchpad.net/ubuntu-toolchain-r/ppa/ubuntu hirsute main' 'deb http://ppa.launchpad.net/ubuntu-toolchain-r/test/ubuntu hirsute main' 'deb http://ppa.launchpad.net/ubuntu-toolchain-r/volatile/ubuntu hirsute main' 'deb http://ftpmaster.internal/ubuntu hirsute main universe' Overriding sources.list in build-PACKAGEBUILD-20675635 RUN: /usr/share/launchpad-buildd/bin/in-target add-trusted-keys --backend=chroot --series=hirsute --arch=s390x PACKAGEBUILD-20675635 Adding trusted keys to build-PACKAGEBUILD-20675635 Warning: apt-key is deprecated. Manage keyring files in trusted.gpg.d instead (see apt-key(8)). OK Warning: apt-key is deprecated. Manage keyring files in trusted.gpg.d instead (see apt-key(8)). /etc/apt/trusted.gpg -------------------- pub rsa1024 2009-10-22 [SC] 60C3 1780 3A41 BA51 845E 371A 1E93 77A2 BA9E F27F uid [ unknown] Launchpad Toolchain builds /etc/apt/trusted.gpg.d/ubuntu-keyring-2012-cdimage.gpg ------------------------------------------------------ pub rsa4096 2012-05-11 [SC] 8439 38DF 228D 22F7 B374 2BC0 D94A A3F0 EFE2 1092 uid [ unknown] Ubuntu CD Image Automatic Signing Key (2012) /etc/apt/trusted.gpg.d/ubuntu-keyring-2018-archive.gpg ------------------------------------------------------ pub rsa4096 2018-09-17 [SC] F6EC B376 2474 EDA9 D21B 7022 8719 20D1 991B C93C uid [ unknown] Ubuntu Archive Automatic Signing Key (2018) RUN: /usr/share/launchpad-buildd/bin/in-target update-debian-chroot --backend=chroot --series=hirsute --arch=s390x PACKAGEBUILD-20675635 Updating target for build PACKAGEBUILD-20675635 Get:1 http://ftpmaster.internal/ubuntu hirsute InRelease [269 kB] Get:2 http://ppa.launchpad.net/ubuntu-toolchain-r/ppa/ubuntu hirsute InRelease [23.8 kB] Get:3 http://ppa.launchpad.net/ubuntu-toolchain-r/test/ubuntu hirsute InRelease [17.6 kB] Get:4 http://ftpmaster.internal/ubuntu hirsute/main s390x Packages [1330 kB] Get:5 http://ppa.launchpad.net/ubuntu-toolchain-r/volatile/ubuntu hirsute InRelease [17.6 kB] Get:6 http://ppa.launchpad.net/ubuntu-toolchain-r/ppa/ubuntu hirsute/main s390x Packages [16.8 kB] Get:7 http://ftpmaster.internal/ubuntu hirsute/main Translation-en [513 kB] Get:8 http://ppa.launchpad.net/ubuntu-toolchain-r/ppa/ubuntu hirsute/main Translation-en [10.0 kB] Get:9 http://ftpmaster.internal/ubuntu hirsute/universe s390x Packages [12.3 MB] Get:10 http://ppa.launchpad.net/ubuntu-toolchain-r/test/ubuntu hirsute/main s390x Packages [12.3 kB] Get:11 http://ftpmaster.internal/ubuntu hirsute/universe Translation-en [5419 kB] Get:12 http://ppa.launchpad.net/ubuntu-toolchain-r/test/ubuntu hirsute/main Translation-en [6856 B] Get:13 http://ppa.launchpad.net/ubuntu-toolchain-r/volatile/ubuntu hirsute/main s390x Packages [15.6 kB] Get:14 http://ppa.launchpad.net/ubuntu-toolchain-r/volatile/ubuntu hirsute/main Translation-en [11.0 kB] Fetched 20.0 MB in 3s (5765 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: libisl22 libperl5.30 perl-modules-5.30 Use 'sudo apt autoremove' to remove them. The following NEW packages will be installed: gcc-11-base libisl23 libperl5.32 libxxhash0 perl-modules-5.32 The following packages have been kept back: cpp g++ gcc The following packages will be upgraded: adduser apt base-files base-passwd bash binutils binutils-common binutils-s390x-linux-gnu bsdutils coreutils cpp-10 dash dpkg dpkg-dev fakeroot g++-10 gcc-10 gcc-10-base gpg gpg-agent gpgconf gpgv grep gzip init init-system-helpers libacl1 libapparmor1 libapt-pkg6.0 libasan6 libatomic1 libattr1 libaudit-common libaudit1 libbinutils libblkid1 libc-bin libc-dev-bin libc6 libc6-dev libcap-ng0 libcap2 libcc1-0 libcrypt-dev libcrypt1 libcryptsetup12 libctf-nobfd0 libctf0 libdebconfclient0 libdevmapper1.02.1 libdpkg-perl libfakeroot libgcc-10-dev libgcc-s1 libgcrypt20 libgdbm-compat4 libgdbm6 libgnutls30 libgomp1 libgssapi-krb5-2 libidn2-0 libip4tc2 libitm1 libk5crypto3 libkrb5-3 libkrb5support0 liblz4-1 libmount1 libmpc3 libncurses6 libncursesw6 libnpth0 libp11-kit0 libpcre2-8-0 libreadline8 libseccomp2 libselinux1 libsemanage-common libsemanage1 libsmartcols1 libsqlite3-0 libssl1.1 libstdc++-10-dev libstdc++6 libsystemd0 libtinfo6 libtirpc-common libtirpc-dev libtirpc3 libubsan1 libudev1 libuuid1 libzstd1 linux-libc-dev login mount ncurses-base ncurses-bin openssl passwd patch perl perl-base readline-common sensible-utils systemd systemd-sysv systemd-timesyncd sysvinit-utils tar tzdata util-linux 112 upgraded, 5 newly installed, 0 to remove and 3 not upgraded. Need to get 78.6 MB of archives. After this operation, 38.4 MB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu hirsute/main s390x libcrypt-dev s390x 1:4.4.17-1ubuntu1 [111 kB] Get:2 http://ppa.launchpad.net/ubuntu-toolchain-r/test/ubuntu hirsute/main s390x gcc-11-base s390x 11-20210123-1ubuntu1 [19.1 kB] Get:3 http://ppa.launchpad.net/ubuntu-toolchain-r/test/ubuntu hirsute/main s390x libgcc-s1 s390x 11-20210123-1ubuntu1 [25.6 kB] Get:4 http://ppa.launchpad.net/ubuntu-toolchain-r/test/ubuntu hirsute/main s390x libstdc++6 s390x 11-20210123-1ubuntu1 [584 kB] Get:5 http://ftpmaster.internal/ubuntu hirsute/main s390x libc6-dev s390x 2.32-0ubuntu6 [1745 kB] Get:6 http://ppa.launchpad.net/ubuntu-toolchain-r/test/ubuntu hirsute/main s390x libgomp1 s390x 11-20210123-1ubuntu1 [99.3 kB] Get:7 http://ppa.launchpad.net/ubuntu-toolchain-r/test/ubuntu hirsute/main s390x libitm1 s390x 11-20210123-1ubuntu1 [25.7 kB] Get:8 http://ppa.launchpad.net/ubuntu-toolchain-r/test/ubuntu hirsute/main s390x libatomic1 s390x 11-20210123-1ubuntu1 [8392 B] Get:9 http://ppa.launchpad.net/ubuntu-toolchain-r/test/ubuntu hirsute/main s390x libasan6 s390x 11-20210123-1ubuntu1 [1930 kB] Get:10 http://ftpmaster.internal/ubuntu hirsute/main s390x libc-dev-bin s390x 2.32-0ubuntu6 [29.8 kB] Get:11 http://ftpmaster.internal/ubuntu hirsute/main s390x libcrypt1 s390x 1:4.4.17-1ubuntu1 [84.3 kB] Get:12 http://ftpmaster.internal/ubuntu hirsute/main s390x linux-libc-dev s390x 5.8.0-36.40+21.04.1 [1138 kB] Get:13 http://ppa.launchpad.net/ubuntu-toolchain-r/test/ubuntu hirsute/main s390x libubsan1 s390x 11-20210123-1ubuntu1 [810 kB] Get:14 http://ftpmaster.internal/ubuntu hirsute/main s390x libtirpc-common all 1.3.1-1 [7452 B] Get:15 http://ftpmaster.internal/ubuntu hirsute/main s390x libk5crypto3 s390x 1.17-10ubuntu1 [78.5 kB] Get:16 http://ftpmaster.internal/ubuntu hirsute/main s390x libgssapi-krb5-2 s390x 1.17-10ubuntu1 [115 kB] Get:17 http://ppa.launchpad.net/ubuntu-toolchain-r/test/ubuntu hirsute/main s390x libcc1-0 s390x 11-20210123-1ubuntu1 [46.3 kB] Get:18 http://ftpmaster.internal/ubuntu hirsute/main s390x libkrb5-3 s390x 1.17-10ubuntu1 [374 kB] Get:19 http://ftpmaster.internal/ubuntu hirsute/main s390x libkrb5support0 s390x 1.17-10ubuntu1 [31.4 kB] Get:20 http://ftpmaster.internal/ubuntu hirsute/main s390x libssl1.1 s390x 1.1.1f-1ubuntu5 [1044 kB] Get:21 http://ftpmaster.internal/ubuntu hirsute/main s390x libtirpc-dev s390x 1.3.1-1 [190 kB] Get:22 http://ftpmaster.internal/ubuntu hirsute/main s390x libtirpc3 s390x 1.3.1-1 [75.1 kB] Get:23 http://ftpmaster.internal/ubuntu hirsute/main s390x libc6 s390x 2.32-0ubuntu6 [2332 kB] Get:24 http://ftpmaster.internal/ubuntu hirsute/main s390x base-files s390x 11ubuntu16 [60.4 kB] Get:25 http://ftpmaster.internal/ubuntu hirsute/main s390x bash s390x 5.1-1ubuntu1 [751 kB] Get:26 http://ftpmaster.internal/ubuntu hirsute/main s390x bsdutils s390x 1:2.36.1-1ubuntu2 [85.9 kB] Get:27 http://ftpmaster.internal/ubuntu hirsute/main s390x coreutils s390x 8.32-4ubuntu2 [1459 kB] Get:28 http://ftpmaster.internal/ubuntu hirsute/main s390x tar s390x 1.32+dfsg-1 [307 kB] Get:29 http://ftpmaster.internal/ubuntu hirsute/main s390x dpkg s390x 1.20.7.1ubuntu1 [1263 kB] Get:30 http://ftpmaster.internal/ubuntu hirsute/main s390x dash s390x 0.5.11+git20200708+dd9ef66+really0.5.11+git20200708+dd9ef66-5ubuntu1 [112 kB] Get:31 http://ftpmaster.internal/ubuntu hirsute/main s390x grep s390x 3.6-1 [161 kB] Get:32 http://ftpmaster.internal/ubuntu hirsute/main s390x gzip s390x 1.10-2ubuntu2 [101 kB] Get:33 http://ftpmaster.internal/ubuntu hirsute/main s390x login s390x 1:4.8.1-1ubuntu8 [219 kB] Get:34 http://ftpmaster.internal/ubuntu hirsute/main s390x libncurses6 s390x 6.2+20201114-2 [106 kB] Get:35 http://ftpmaster.internal/ubuntu hirsute/main s390x libncursesw6 s390x 6.2+20201114-2 [136 kB] Get:36 http://ftpmaster.internal/ubuntu hirsute/main s390x libtinfo6 s390x 6.2+20201114-2 [92.4 kB] Get:37 http://ftpmaster.internal/ubuntu hirsute/main s390x ncurses-bin s390x 6.2+20201114-2 [176 kB] Get:38 http://ftpmaster.internal/ubuntu hirsute/main s390x perl-modules-5.32 all 5.32.0-6 [2754 kB] Get:39 http://ftpmaster.internal/ubuntu hirsute/main s390x libperl5.32 s390x 5.32.0-6 [3947 kB] Get:40 http://ftpmaster.internal/ubuntu hirsute/main s390x perl s390x 5.32.0-6 [225 kB] Get:41 http://ftpmaster.internal/ubuntu hirsute/main s390x perl-base s390x 5.32.0-6 [1574 kB] Get:42 http://ftpmaster.internal/ubuntu hirsute/main s390x libgdbm6 s390x 1.19-2 [28.1 kB] Get:43 http://ftpmaster.internal/ubuntu hirsute/main s390x libgdbm-compat4 s390x 1.19-2 [6320 B] Get:44 http://ftpmaster.internal/ubuntu hirsute/main s390x util-linux s390x 2.36.1-1ubuntu2 [1072 kB] Get:45 http://ftpmaster.internal/ubuntu hirsute/main s390x libdebconfclient0 s390x 0.256ubuntu1 [6076 B] Get:46 http://ftpmaster.internal/ubuntu hirsute/main s390x base-passwd s390x 3.5.48 [48.5 kB] Get:47 http://ftpmaster.internal/ubuntu hirsute/main s390x init-system-helpers all 1.59 [38.2 kB] Get:48 http://ftpmaster.internal/ubuntu hirsute/main s390x libc-bin s390x 2.32-0ubuntu6 [599 kB] Get:49 http://ftpmaster.internal/ubuntu hirsute/main s390x ncurses-base all 6.2+20201114-2 [18.4 kB] Get:50 http://ftpmaster.internal/ubuntu hirsute/main s390x sysvinit-utils s390x 2.96-5ubuntu1 [20.6 kB] Get:51 http://ftpmaster.internal/ubuntu hirsute/main s390x libxxhash0 s390x 0.8.0-2 [18.3 kB] Get:52 http://ftpmaster.internal/ubuntu hirsute/main s390x libgcrypt20 s390x 1.8.7-2ubuntu1 [393 kB] Get:53 http://ftpmaster.internal/ubuntu hirsute/main s390x liblz4-1 s390x 1.9.3-0ubuntu1 [57.8 kB] Get:54 http://ftpmaster.internal/ubuntu hirsute/main s390x systemd-sysv s390x 247.1-4ubuntu1 [10.3 kB] Get:55 http://ftpmaster.internal/ubuntu hirsute/main s390x libaudit-common all 1:2.8.5-3ubuntu3 [4048 B] Get:56 http://ftpmaster.internal/ubuntu hirsute/main s390x libcap-ng0 s390x 0.7.9-2.2build1 [11.0 kB] Get:57 http://ftpmaster.internal/ubuntu hirsute/main s390x libaudit1 s390x 1:2.8.5-3ubuntu3 [38.1 kB] Get:58 http://ftpmaster.internal/ubuntu hirsute/main s390x libpcre2-8-0 s390x 10.35-2ubuntu1 [110 kB] Get:59 http://ftpmaster.internal/ubuntu hirsute/main s390x libselinux1 s390x 3.1-2build2 [74.9 kB] Get:60 http://ftpmaster.internal/ubuntu hirsute/main s390x libsemanage-common all 3.1-1build2 [10.0 kB] Get:61 http://ftpmaster.internal/ubuntu hirsute/main s390x libsemanage1 s390x 3.1-1build2 [88.5 kB] Get:62 http://ftpmaster.internal/ubuntu hirsute/main s390x passwd s390x 1:4.8.1-1ubuntu8 [794 kB] Get:63 http://ftpmaster.internal/ubuntu hirsute/main s390x adduser all 3.118ubuntu5 [156 kB] Get:64 http://ftpmaster.internal/ubuntu hirsute/main s390x systemd-timesyncd s390x 247.1-4ubuntu1 [27.1 kB] Get:65 http://ftpmaster.internal/ubuntu hirsute/main s390x libapparmor1 s390x 3.0.0-0ubuntu5 [35.9 kB] Get:66 http://ftpmaster.internal/ubuntu hirsute/main s390x libblkid1 s390x 2.36.1-1ubuntu2 [128 kB] Get:67 http://ftpmaster.internal/ubuntu hirsute/main s390x libudev1 s390x 247.1-4ubuntu1 [75.0 kB] Get:68 http://ftpmaster.internal/ubuntu hirsute/main s390x libdevmapper1.02.1 s390x 2:1.02.167-1ubuntu4 [122 kB] Get:69 http://ftpmaster.internal/ubuntu hirsute/main s390x libuuid1 s390x 2.36.1-1ubuntu2 [21.6 kB] Get:70 http://ftpmaster.internal/ubuntu hirsute/main s390x libcryptsetup12 s390x 2:2.3.4-1ubuntu1 [184 kB] Get:71 http://ftpmaster.internal/ubuntu hirsute/main s390x libidn2-0 s390x 2.3.0-5 [51.2 kB] Get:72 http://ftpmaster.internal/ubuntu hirsute/main s390x libp11-kit0 s390x 0.23.22-1 [210 kB] Get:73 http://ftpmaster.internal/ubuntu hirsute/main s390x libgnutls30 s390x 3.7.0-5ubuntu1 [826 kB] Get:74 http://ftpmaster.internal/ubuntu hirsute/main s390x libip4tc2 s390x 1.8.5-3ubuntu4 [20.0 kB] Get:75 http://ftpmaster.internal/ubuntu hirsute/main s390x libseccomp2 s390x 2.4.3-1ubuntu6 [55.9 kB] Get:76 http://ftpmaster.internal/ubuntu hirsute/main s390x mount s390x 2.36.1-1ubuntu2 [119 kB] Get:77 http://ftpmaster.internal/ubuntu hirsute/main s390x systemd s390x 247.1-4ubuntu1 [4015 kB] Get:78 http://ftpmaster.internal/ubuntu hirsute/main s390x libsystemd0 s390x 247.1-4ubuntu1 [296 kB] Get:79 http://ftpmaster.internal/ubuntu hirsute/main s390x libzstd1 s390x 1.4.8+dfsg-1 [312 kB] Get:80 http://ftpmaster.internal/ubuntu hirsute/main s390x libapt-pkg6.0 s390x 2.1.18 [897 kB] Get:81 http://ftpmaster.internal/ubuntu hirsute/main s390x gpgv s390x 2.2.20-1ubuntu2 [218 kB] Get:82 http://ftpmaster.internal/ubuntu hirsute/main s390x apt s390x 2.1.18 [1306 kB] Get:83 http://ftpmaster.internal/ubuntu hirsute/main s390x init s390x 1.59 [6164 B] Get:84 http://ftpmaster.internal/ubuntu hirsute/main s390x libacl1 s390x 2.2.53-9 [17.6 kB] Get:85 http://ftpmaster.internal/ubuntu hirsute/main s390x libattr1 s390x 1:2.4.48-6 [12.8 kB] Get:86 http://ftpmaster.internal/ubuntu hirsute/main s390x libmount1 s390x 2.36.1-1ubuntu2 [142 kB] Get:87 http://ftpmaster.internal/ubuntu hirsute/main s390x libsmartcols1 s390x 2.36.1-1ubuntu2 [94.2 kB] Get:88 http://ftpmaster.internal/ubuntu hirsute/main s390x g++-10 s390x 10.2.1-6ubuntu1 [8825 kB] Get:89 http://ftpmaster.internal/ubuntu hirsute/main s390x gcc-10 s390x 10.2.1-6ubuntu1 [15.1 MB] Get:90 http://ftpmaster.internal/ubuntu hirsute/main s390x libstdc++-10-dev s390x 10.2.1-6ubuntu1 [1738 kB] Get:91 http://ftpmaster.internal/ubuntu hirsute/main s390x libgcc-10-dev s390x 10.2.1-6ubuntu1 [776 kB] Get:92 http://ftpmaster.internal/ubuntu hirsute/main s390x libisl23 s390x 0.23-1 [689 kB] Get:93 http://ftpmaster.internal/ubuntu hirsute/main s390x libmpc3 s390x 1.2.0-1 [43.6 kB] Get:94 http://ftpmaster.internal/ubuntu hirsute/main s390x libctf0 s390x 2.35.50.20210106-1ubuntu2 [108 kB] Get:95 http://ftpmaster.internal/ubuntu hirsute/main s390x libctf-nobfd0 s390x 2.35.50.20210106-1ubuntu2 [110 kB] Get:96 http://ftpmaster.internal/ubuntu hirsute/main s390x binutils-s390x-linux-gnu s390x 2.35.50.20210106-1ubuntu2 [1776 kB] Get:97 http://ftpmaster.internal/ubuntu hirsute/main s390x libbinutils s390x 2.35.50.20210106-1ubuntu2 [443 kB] Get:98 http://ftpmaster.internal/ubuntu hirsute/main s390x binutils s390x 2.35.50.20210106-1ubuntu2 [3360 B] Get:99 http://ftpmaster.internal/ubuntu hirsute/main s390x binutils-common s390x 2.35.50.20210106-1ubuntu2 [216 kB] Get:100 http://ftpmaster.internal/ubuntu hirsute/main s390x cpp-10 s390x 10.2.1-6ubuntu1 [7447 kB] Get:101 http://ftpmaster.internal/ubuntu hirsute/main s390x gcc-10-base s390x 10.2.1-6ubuntu1 [19.7 kB] Get:102 http://ftpmaster.internal/ubuntu hirsute/main s390x sensible-utils all 0.0.14 [13.5 kB] Get:103 http://ftpmaster.internal/ubuntu hirsute/main s390x libcap2 s390x 1:2.44-1 [18.3 kB] Get:104 http://ftpmaster.internal/ubuntu hirsute/main s390x readline-common all 8.1-1 [54.1 kB] Get:105 http://ftpmaster.internal/ubuntu hirsute/main s390x libreadline8 s390x 8.1-1 [143 kB] Get:106 http://ftpmaster.internal/ubuntu hirsute/main s390x libsqlite3-0 s390x 3.34.0-1 [650 kB] Get:107 http://ftpmaster.internal/ubuntu hirsute/main s390x openssl s390x 1.1.1f-1ubuntu5 [615 kB] Get:108 http://ftpmaster.internal/ubuntu hirsute/main s390x tzdata all 2020f-1ubuntu2 [294 kB] Get:109 http://ftpmaster.internal/ubuntu hirsute/main s390x dpkg-dev all 1.20.7.1ubuntu1 [934 kB] Get:110 http://ftpmaster.internal/ubuntu hirsute/main s390x libdpkg-perl all 1.20.7.1ubuntu1 [232 kB] Get:111 http://ftpmaster.internal/ubuntu hirsute/main s390x patch s390x 2.7.6-7 [114 kB] Get:112 http://ftpmaster.internal/ubuntu hirsute/main s390x libfakeroot s390x 1.25.3-1.1 [27.5 kB] Get:113 http://ftpmaster.internal/ubuntu hirsute/main s390x fakeroot s390x 1.25.3-1.1 [62.7 kB] Get:114 http://ftpmaster.internal/ubuntu hirsute/main s390x libnpth0 s390x 1.6-3 [8048 B] Get:115 http://ftpmaster.internal/ubuntu hirsute/main s390x gpg s390x 2.2.20-1ubuntu2 [511 kB] Get:116 http://ftpmaster.internal/ubuntu hirsute/main s390x gpgconf s390x 2.2.20-1ubuntu2 [138 kB] Get:117 http://ftpmaster.internal/ubuntu hirsute/main s390x gpg-agent s390x 2.2.20-1ubuntu2 [256 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 78.6 MB in 1s (59.5 MB/s) (Reading database ... 12766 files and directories currently installed.) 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Preparing to unpack .../21-libcap2_1%3a2.44-1_s390x.deb ... Unpacking libcap2:s390x (1:2.44-1) over (1:2.43-1) ... Preparing to unpack .../22-readline-common_8.1-1_all.deb ... Unpacking readline-common (8.1-1) over (8.0-4) ... Preparing to unpack .../23-libreadline8_8.1-1_s390x.deb ... Unpacking libreadline8:s390x (8.1-1) over (8.0-4) ... Preparing to unpack .../24-libsqlite3-0_3.34.0-1_s390x.deb ... Unpacking libsqlite3-0:s390x (3.34.0-1) over (3.33.0-1) ... Preparing to unpack .../25-openssl_1.1.1f-1ubuntu5_s390x.deb ... Unpacking openssl (1.1.1f-1ubuntu5) over (1.1.1f-1ubuntu4) ... Preparing to unpack .../26-tzdata_2020f-1ubuntu2_all.deb ... Unpacking tzdata (2020f-1ubuntu2) over (2020b-1ubuntu1) ... Preparing to unpack .../27-dpkg-dev_1.20.7.1ubuntu1_all.deb ... Unpacking dpkg-dev (1.20.7.1ubuntu1) over (1.20.5ubuntu2) ... Preparing to unpack .../28-libdpkg-perl_1.20.7.1ubuntu1_all.deb ... Unpacking libdpkg-perl (1.20.7.1ubuntu1) over (1.20.5ubuntu2) ... Preparing to unpack .../29-patch_2.7.6-7_s390x.deb ... Unpacking patch (2.7.6-7) over (2.7.6-6) ... Preparing to unpack .../30-libfakeroot_1.25.3-1.1_s390x.deb ... Unpacking libfakeroot:s390x (1.25.3-1.1) over (1.25.2-1) ... Preparing to unpack .../31-fakeroot_1.25.3-1.1_s390x.deb ... Unpacking fakeroot (1.25.3-1.1) over (1.25.2-1) ... Preparing to unpack .../32-libnpth0_1.6-3_s390x.deb ... Unpacking libnpth0:s390x (1.6-3) over (1.6-2) ... Preparing to unpack .../33-gpg_2.2.20-1ubuntu2_s390x.deb ... Unpacking gpg (2.2.20-1ubuntu2) over (2.2.20-1ubuntu1) ... Preparing to unpack .../34-gpgconf_2.2.20-1ubuntu2_s390x.deb ... Unpacking gpgconf (2.2.20-1ubuntu2) over (2.2.20-1ubuntu1) ... Preparing to unpack .../35-gpg-agent_2.2.20-1ubuntu2_s390x.deb ... Unpacking gpg-agent (2.2.20-1ubuntu2) over (2.2.20-1ubuntu1) ... Setting up init (1.59) ... Setting up libtirpc-common (1.3.1-1) ... Setting up perl-modules-5.32 (5.32.0-6) ... Setting up libsqlite3-0:s390x (3.34.0-1) ... Setting up binutils-common:s390x (2.35.50.20210106-1ubuntu2) ... Setting up linux-libc-dev:s390x (5.8.0-36.40+21.04.1) ... Setting up libctf-nobfd0:s390x (2.35.50.20210106-1ubuntu2) ... Setting up libnpth0:s390x (1.6-3) ... Setting up libgomp1:s390x (11-20210123-1ubuntu1) ... Setting up libcap2:s390x (1:2.44-1) ... Setting up libfakeroot:s390x (1.25.3-1.1) ... Setting up libasan6:s390x (11-20210123-1ubuntu1) ... Setting up libkrb5support0:s390x (1.17-10ubuntu1) ... Setting up tzdata (2020f-1ubuntu2) ... Current default time zone: 'Etc/UTC' Local time is now: Tue Jan 26 13:41:16 UTC 2021. Universal Time is now: Tue Jan 26 13:41:16 UTC 2021. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up fakeroot (1.25.3-1.1) ... Setting up gcc-10-base:s390x (10.2.1-6ubuntu1) ... Setting up libncurses6:s390x (6.2+20201114-2) ... Setting up libmpc3:s390x (1.2.0-1) ... Setting up libatomic1:s390x (11-20210123-1ubuntu1) ... Setting up patch (2.7.6-7) ... Setting up libncursesw6:s390x (6.2+20201114-2) ... Setting up libk5crypto3:s390x (1.17-10ubuntu1) ... Setting up libubsan1:s390x (11-20210123-1ubuntu1) ... Setting up sensible-utils (0.0.14) ... Setting up libcrypt-dev:s390x (1:4.4.17-1ubuntu1) ... Setting up libkrb5-3:s390x (1.17-10ubuntu1) ... Setting up libbinutils:s390x (2.35.50.20210106-1ubuntu2) ... Setting up libisl23:s390x (0.23-1) ... Setting up libc-dev-bin (2.32-0ubuntu6) ... Setting up openssl (1.1.1f-1ubuntu5) ... Setting up readline-common (8.1-1) ... Setting up libcc1-0:s390x (11-20210123-1ubuntu1) ... Setting up cpp-10 (10.2.1-6ubuntu1) ... Setting up libitm1:s390x (11-20210123-1ubuntu1) ... Setting up libgdbm6:s390x (1.19-2) ... Setting up libctf0:s390x (2.35.50.20210106-1ubuntu2) ... Setting up binutils-s390x-linux-gnu (2.35.50.20210106-1ubuntu2) ... Setting up libgcc-10-dev:s390x (10.2.1-6ubuntu1) ... Setting up libreadline8:s390x (8.1-1) ... Setting up binutils (2.35.50.20210106-1ubuntu2) ... Setting up libgssapi-krb5-2:s390x (1.17-10ubuntu1) ... Setting up libgdbm-compat4:s390x (1.19-2) ... Setting up libperl5.32:s390x (5.32.0-6) ... Setting up gcc-10 (10.2.1-6ubuntu1) ... Setting up gpgconf (2.2.20-1ubuntu2) ... Setting up gpg (2.2.20-1ubuntu2) ... Setting up libtirpc3:s390x (1.3.1-1) ... Setting up gpg-agent (2.2.20-1ubuntu2) ... Setting up perl (5.32.0-6) ... Setting up libtirpc-dev:s390x (1.3.1-1) ... Setting up libdpkg-perl (1.20.7.1ubuntu1) ... Setting up libc6-dev:s390x (2.32-0ubuntu6) ... Setting up libstdc++-10-dev:s390x (10.2.1-6ubuntu1) ... Setting up g++-10 (10.2.1-6ubuntu1) ... Setting up dpkg-dev (1.20.7.1ubuntu1) ... Processing triggers for libc-bin (2.32-0ubuntu6) ... RUN: /usr/share/launchpad-buildd/bin/sbuild-package PACKAGEBUILD-20675635 s390x hirsute -c chroot:build-PACKAGEBUILD-20675635 --arch=s390x --dist=hirsute --nolog reapr_1.0.18+dfsg-5build1.dsc Initiating build PACKAGEBUILD-20675635 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 4.15.0-134-generic #138-Ubuntu SMP Fri Jan 15 10:53:04 UTC 2021 s390x sbuild (Debian sbuild) 0.75.0 (21 Mar 2018) on bos02-s390x-009.buildd +==============================================================================+ | reapr 1.0.18+dfsg-5build1 (s390x) Tue, 26 Jan 2021 13:41:17 +0000 | +==============================================================================+ Package: reapr Version: 1.0.18+dfsg-5build1 Source Version: 1.0.18+dfsg-5build1 Distribution: hirsute Machine Architecture: s390x Host Architecture: s390x Build Architecture: s390x Build Type: any I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-20675635/chroot-autobuild' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- reapr_1.0.18+dfsg-5build1.dsc exists in .; copying to chroot I: NOTICE: Log filtering will replace 'build/reapr-365eAB/reapr-1.0.18+dfsg' with '<>' I: NOTICE: Log filtering will replace 'build/reapr-365eAB' with '<>' +------------------------------------------------------------------------------+ | Install build-essential | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: build-essential, fakeroot Filtered Build-Depends: build-essential, fakeroot dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/<>/resolver-JkCQ0i/apt_archive/sbuild-build-depends-core-dummy.deb'. dpkg-scanpackages: warning: Packages in archive but missing from override file: dpkg-scanpackages: warning: sbuild-build-depends-core-dummy dpkg-scanpackages: info: Wrote 1 entries to output Packages file. Ign:1 copy:/<>/resolver-JkCQ0i/apt_archive ./ InRelease Get:2 copy:/<>/resolver-JkCQ0i/apt_archive ./ Release [957 B] Ign:3 copy:/<>/resolver-JkCQ0i/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-JkCQ0i/apt_archive ./ Sources [349 B] Get:5 copy:/<>/resolver-JkCQ0i/apt_archive ./ Packages [433 B] Fetched 1739 B in 0s (0 B/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: libisl22 libperl5.30 perl-modules-5.30 Use 'apt autoremove' to remove them. The following NEW packages will be installed: sbuild-build-depends-core-dummy 0 upgraded, 1 newly installed, 0 to remove and 3 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-JkCQ0i/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 (0 B/s) Selecting previously unselected package sbuild-build-depends-core-dummy. (Reading database ... 14767 files and directories currently installed.) Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_s390x.deb ... Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ... Setting up sbuild-build-depends-core-dummy (0.invalid.0) ... +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (s390x included in any) +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- 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-JkCQ0i/apt_archive/sbuild-build-depends-reapr-dummy.deb'. dpkg-scanpackages: warning: Packages in archive but missing from override file: dpkg-scanpackages: warning: sbuild-build-depends-core-dummy sbuild-build-depends-reapr-dummy dpkg-scanpackages: info: Wrote 2 entries to output Packages file. Ign:1 copy:/<>/resolver-JkCQ0i/apt_archive ./ InRelease Get:2 copy:/<>/resolver-JkCQ0i/apt_archive ./ Release [963 B] Ign:3 copy:/<>/resolver-JkCQ0i/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-JkCQ0i/apt_archive ./ Sources [575 B] Get:5 copy:/<>/resolver-JkCQ0i/apt_archive ./ Packages [658 B] Fetched 2196 B in 0s (0 B/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: libisl22 libperl5.30 perl-modules-5.30 Use 'apt autoremove' to remove them. The following additional packages will be installed: asciidoctor autoconf automake autopoint autotools-dev bamtools bsdextrautils 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 libcurl3-gnutls libcurl4 libcurl4-gnutls-dev libdatrie1 libdebhelper-perl libdeflate-dev libdeflate0 libelf1 libexpat1 libfile-copy-link-perl libfile-stripnondeterminism-perl libfontconfig1 libfreetype6 libfribidi0 libgfortran5 libglib2.0-0 libgraphite2-3 libgssapi3-heimdal libharfbuzz0b libhcrypto4-heimdal libheimbase1-heimdal libheimntlm0-heimdal libhts-dev libhts3 libhx509-5-heimdal libice6 libicu67 libjbig0 libjpeg-turbo8 libjpeg8 libjsoncpp24 libkrb5-26-heimdal liblapack3 libldap-2.4-2 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-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 dh-make gettext-doc libasprintf-dev libgettextpo-dev groff libbamtools-doc libcurl4-doc libgnutls28-dev libidn11-dev libkrb5-dev libldap2-dev librtmp-dev libssh2-1-dev pkg-config 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 cwltool Recommended packages: curl | wget | lynx libarchive-cpio-perl libglib2.0-data shared-mime-info xdg-user-dirs libldap-common publicsuffix libsasl2-modules libltdl-dev libmail-sendmail-perl r-base-html r-doc-html r-base-dev fonts-lato libjs-jquery 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 bsdextrautils 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 libcurl3-gnutls libcurl4 libcurl4-gnutls-dev libdatrie1 libdebhelper-perl libdeflate-dev libdeflate0 libelf1 libexpat1 libfile-copy-link-perl libfile-stripnondeterminism-perl libfontconfig1 libfreetype6 libfribidi0 libgfortran5 libglib2.0-0 libgraphite2-3 libgssapi3-heimdal libharfbuzz0b libhcrypto4-heimdal libheimbase1-heimdal libheimntlm0-heimdal libhts-dev libhts3 libhx509-5-heimdal libice6 libicu67 libjbig0 libjpeg-turbo8 libjpeg8 libjsoncpp24 libkrb5-26-heimdal liblapack3 libldap-2.4-2 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-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, 150 newly installed, 0 to remove and 3 not upgraded. Need to get 85.6 MB of archives. After this operation, 217 MB of additional disk space will be used. Get:1 copy:/<>/resolver-JkCQ0i/apt_archive ./ sbuild-build-depends-reapr-dummy 0.invalid.0 [948 B] Get:2 http://ftpmaster.internal/ubuntu hirsute/main s390x bsdextrautils s390x 2.36.1-1ubuntu2 [77.5 kB] Get:3 http://ppa.launchpad.net/ubuntu-toolchain-r/test/ubuntu hirsute/main s390x libgfortran5 s390x 11-20210123-1ubuntu1 [388 kB] Get:4 http://ftpmaster.internal/ubuntu hirsute/main s390x libuchardet0 s390x 0.0.7-1 [67.5 kB] Get:5 http://ftpmaster.internal/ubuntu hirsute/main s390x groff-base s390x 1.22.4-5 [812 kB] Get:6 http://ftpmaster.internal/ubuntu hirsute/main s390x libpipeline1 s390x 1.5.3-1 [28.7 kB] Get:7 http://ftpmaster.internal/ubuntu hirsute/main s390x man-db s390x 2.9.3-2 [1106 kB] Get:8 http://ftpmaster.internal/ubuntu hirsute/main s390x libmagic-mgc s390x 1:5.39-3 [229 kB] Get:9 http://ftpmaster.internal/ubuntu hirsute/main s390x libmagic1 s390x 1:5.39-3 [83.6 kB] Get:10 http://ftpmaster.internal/ubuntu hirsute/main s390x file s390x 1:5.39-3 [24.0 kB] Get:11 http://ftpmaster.internal/ubuntu hirsute/main s390x libbsd0 s390x 0.10.0-1 [43.7 kB] Get:12 http://ftpmaster.internal/ubuntu hirsute/main s390x libelf1 s390x 0.182-3 [48.4 kB] Get:13 http://ftpmaster.internal/ubuntu hirsute/main s390x libexpat1 s390x 2.2.10-1 [86.5 kB] Get:14 http://ftpmaster.internal/ubuntu hirsute/main s390x libfribidi0 s390x 1.0.8-2 [24.6 kB] Get:15 http://ftpmaster.internal/ubuntu hirsute/main s390x libglib2.0-0 s390x 2.66.4-1 [1322 kB] Get:16 http://ftpmaster.internal/ubuntu hirsute/main s390x libicu67 s390x 67.1-5 [8472 kB] Get:17 http://ftpmaster.internal/ubuntu hirsute/main s390x libxml2 s390x 2.9.10+dfsg-6.3build1 [645 kB] Get:18 http://ftpmaster.internal/ubuntu hirsute/main s390x libyaml-0-2 s390x 0.2.2-1 [42.3 kB] Get:19 http://ftpmaster.internal/ubuntu hirsute/main s390x ucf all 3.0043 [56.1 kB] Get:20 http://ftpmaster.internal/ubuntu hirsute/main s390x gettext-base s390x 0.21-3ubuntu2 [41.0 kB] Get:21 http://ftpmaster.internal/ubuntu hirsute/main s390x libpsl5 s390x 0.21.0-1.1ubuntu1 [52.5 kB] Get:22 http://ftpmaster.internal/ubuntu hirsute/main s390x libxau6 s390x 1:1.0.9-0ubuntu1 [7212 B] Get:23 http://ftpmaster.internal/ubuntu hirsute/main s390x libxdmcp6 s390x 1:1.1.3-0ubuntu1 [10.4 kB] Get:24 http://ftpmaster.internal/ubuntu hirsute/main s390x libxcb1 s390x 1.14-2.1 [45.0 kB] Get:25 http://ftpmaster.internal/ubuntu hirsute/main s390x libx11-data all 2:1.7.0-2 [112 kB] Get:26 http://ftpmaster.internal/ubuntu hirsute/main s390x libx11-6 s390x 2:1.7.0-2 [571 kB] Get:27 http://ftpmaster.internal/ubuntu hirsute/main s390x libxext6 s390x 2:1.3.4-0ubuntu1 [27.0 kB] Get:28 http://ftpmaster.internal/ubuntu hirsute/main s390x rubygems-integration all 1.17.3 [5208 B] Get:29 http://ftpmaster.internal/ubuntu hirsute/main s390x rake all 13.0.1-4 [61.6 kB] Get:30 http://ftpmaster.internal/ubuntu hirsute/main s390x ruby-minitest all 5.13.0-1 [40.9 kB] Get:31 http://ftpmaster.internal/ubuntu hirsute/main s390x ruby-net-telnet all 0.1.1-2 [12.6 kB] Get:32 http://ftpmaster.internal/ubuntu hirsute/main s390x ruby-power-assert all 1.1.7-1 [11.4 kB] Get:33 http://ftpmaster.internal/ubuntu hirsute/main s390x ruby-test-unit all 3.3.9-1 [73.6 kB] Get:34 http://ftpmaster.internal/ubuntu hirsute/main s390x ruby-xmlrpc all 0.3.0-2 [23.8 kB] Get:35 http://ftpmaster.internal/ubuntu hirsute/main s390x libruby2.7 s390x 2.7.2-3 [3629 kB] Get:36 http://ftpmaster.internal/ubuntu hirsute/main s390x ruby2.7 s390x 2.7.2-3 [95.4 kB] Get:37 http://ftpmaster.internal/ubuntu hirsute/main s390x ruby s390x 1:2.7+1 [5412 B] Get:38 http://ftpmaster.internal/ubuntu hirsute/universe s390x ruby-asciidoctor all 2.0.12-2 [168 kB] Get:39 http://ftpmaster.internal/ubuntu hirsute/universe s390x asciidoctor all 2.0.12-2 [43.7 kB] Get:40 http://ftpmaster.internal/ubuntu hirsute/main s390x libsigsegv2 s390x 2.12-3 [14.0 kB] Get:41 http://ftpmaster.internal/ubuntu hirsute/main s390x m4 s390x 1.4.18-5 [209 kB] Get:42 http://ftpmaster.internal/ubuntu hirsute/main s390x autoconf all 2.69-14 [293 kB] Get:43 http://ftpmaster.internal/ubuntu hirsute/main s390x autotools-dev all 20180224.1+nmu1 [39.4 kB] Get:44 http://ftpmaster.internal/ubuntu hirsute/main s390x automake all 1:1.16.3-2ubuntu1 [552 kB] Get:45 http://ftpmaster.internal/ubuntu hirsute/main s390x autopoint all 0.21-3ubuntu2 [422 kB] Get:46 http://ftpmaster.internal/ubuntu hirsute/universe s390x libbamtools2.5.1 s390x 2.5.1+dfsg-7build1 [155 kB] Get:47 http://ftpmaster.internal/ubuntu hirsute/main s390x libjsoncpp24 s390x 1.9.4-4 [72.6 kB] Get:48 http://ftpmaster.internal/ubuntu hirsute/universe s390x bamtools s390x 2.5.1+dfsg-7build1 [173 kB] Get:49 http://ftpmaster.internal/ubuntu hirsute/main s390x libtool all 2.4.6-15 [161 kB] Get:50 http://ftpmaster.internal/ubuntu hirsute/main s390x dh-autoreconf all 19 [16.1 kB] Get:51 http://ftpmaster.internal/ubuntu hirsute/main s390x libdebhelper-perl all 13.3.1ubuntu1 [62.2 kB] Get:52 http://ftpmaster.internal/ubuntu hirsute/main s390x libarchive-zip-perl all 1.68-1 [90.2 kB] Get:53 http://ftpmaster.internal/ubuntu hirsute/main s390x libsub-override-perl all 0.09-2 [9532 B] Get:54 http://ftpmaster.internal/ubuntu hirsute/main s390x libfile-stripnondeterminism-perl all 1.10.0-1 [17.0 kB] Get:55 http://ftpmaster.internal/ubuntu hirsute/main s390x dh-strip-nondeterminism all 1.10.0-1 [5228 B] Get:56 http://ftpmaster.internal/ubuntu hirsute/main s390x dwz s390x 0.13+20210118-1 [168 kB] Get:57 http://ftpmaster.internal/ubuntu hirsute/main s390x gettext s390x 0.21-3ubuntu2 [869 kB] Get:58 http://ftpmaster.internal/ubuntu hirsute/main s390x intltool-debian all 0.35.0+20060710.5 [24.9 kB] Get:59 http://ftpmaster.internal/ubuntu hirsute/main s390x po-debconf all 1.0.21+nmu1 [233 kB] Get:60 http://ftpmaster.internal/ubuntu hirsute/main s390x debhelper all 13.3.1ubuntu1 [882 kB] Get:61 http://ftpmaster.internal/ubuntu hirsute/main s390x libbrotli1 s390x 1.0.9-2build2 [271 kB] Get:62 http://ftpmaster.internal/ubuntu hirsute/main s390x libfreetype6 s390x 2.10.4+dfsg-1 [383 kB] Get:63 http://ftpmaster.internal/ubuntu hirsute/main s390x fonts-dejavu-core all 2.37-2 [1041 kB] Get:64 http://ftpmaster.internal/ubuntu hirsute/main s390x fontconfig-config all 2.13.1-4.2ubuntu2 [28.6 kB] Get:65 http://ftpmaster.internal/ubuntu hirsute/main s390x libfontconfig1 s390x 2.13.1-4.2ubuntu2 [152 kB] Get:66 http://ftpmaster.internal/ubuntu hirsute/main s390x fontconfig s390x 2.13.1-4.2ubuntu2 [182 kB] Get:67 http://ftpmaster.internal/ubuntu hirsute/main s390x libroken18-heimdal s390x 7.7.0+dfsg-2 [40.0 kB] Get:68 http://ftpmaster.internal/ubuntu hirsute/main s390x libasn1-8-heimdal s390x 7.7.0+dfsg-2 [148 kB] Get:69 http://ftpmaster.internal/ubuntu hirsute/universe s390x libbambamc0 s390x 0.0.50-4 [36.2 kB] Get:70 http://ftpmaster.internal/ubuntu hirsute/universe s390x libbamtools-dev s390x 2.5.1+dfsg-7build1 [221 kB] Get:71 http://ftpmaster.internal/ubuntu hirsute/main s390x libblas3 s390x 3.9.0-3ubuntu1 [131 kB] Get:72 http://ftpmaster.internal/ubuntu hirsute/main s390x libpixman-1-0 s390x 0.40.0-1 [154 kB] Get:73 http://ftpmaster.internal/ubuntu hirsute/main s390x libxcb-render0 s390x 1.14-2.1 [14.7 kB] Get:74 http://ftpmaster.internal/ubuntu hirsute/main s390x libxcb-shm0 s390x 1.14-2.1 [5436 B] Get:75 http://ftpmaster.internal/ubuntu hirsute/main s390x libxrender1 s390x 1:0.9.10-1 [17.8 kB] Get:76 http://ftpmaster.internal/ubuntu hirsute/main s390x libcairo2 s390x 1.16.0-5 [655 kB] Get:77 http://ftpmaster.internal/ubuntu hirsute/main s390x libheimbase1-heimdal s390x 7.7.0+dfsg-2 [27.7 kB] Get:78 http://ftpmaster.internal/ubuntu hirsute/main s390x libhcrypto4-heimdal s390x 7.7.0+dfsg-2 [83.1 kB] Get:79 http://ftpmaster.internal/ubuntu hirsute/main s390x libwind0-heimdal s390x 7.7.0+dfsg-2 [47.7 kB] Get:80 http://ftpmaster.internal/ubuntu hirsute/main s390x libhx509-5-heimdal s390x 7.7.0+dfsg-2 [97.9 kB] Get:81 http://ftpmaster.internal/ubuntu hirsute/main s390x libkrb5-26-heimdal s390x 7.7.0+dfsg-2 [191 kB] Get:82 http://ftpmaster.internal/ubuntu hirsute/main s390x libheimntlm0-heimdal s390x 7.7.0+dfsg-2 [14.4 kB] Get:83 http://ftpmaster.internal/ubuntu hirsute/main s390x libgssapi3-heimdal s390x 7.7.0+dfsg-2 [87.2 kB] Get:84 http://ftpmaster.internal/ubuntu hirsute/main s390x libsasl2-modules-db s390x 2.1.27+dfsg-2ubuntu1 [14.5 kB] Get:85 http://ftpmaster.internal/ubuntu hirsute/main s390x libsasl2-2 s390x 2.1.27+dfsg-2ubuntu1 [48.8 kB] Get:86 http://ftpmaster.internal/ubuntu hirsute/main s390x libldap-2.4-2 s390x 2.4.56+dfsg-1ubuntu1 [158 kB] Get:87 http://ftpmaster.internal/ubuntu hirsute/main s390x libnghttp2-14 s390x 1.42.0-1 [77.5 kB] Get:88 http://ftpmaster.internal/ubuntu hirsute/main s390x librtmp1 s390x 2.4+20151223.gitfa8646d.1-2build2 [50.7 kB] Get:89 http://ftpmaster.internal/ubuntu hirsute/main s390x libssh-4 s390x 0.9.5-1 [174 kB] Get:90 http://ftpmaster.internal/ubuntu hirsute/main s390x libcurl3-gnutls s390x 7.72.0-1ubuntu1 [239 kB] Get:91 http://ftpmaster.internal/ubuntu hirsute/main s390x libcurl4 s390x 7.72.0-1ubuntu1 [238 kB] Get:92 http://ftpmaster.internal/ubuntu hirsute/main s390x libcurl4-gnutls-dev s390x 7.72.0-1ubuntu1 [342 kB] Get:93 http://ftpmaster.internal/ubuntu hirsute/main s390x libdatrie1 s390x 0.2.12-3 [18.1 kB] Get:94 http://ftpmaster.internal/ubuntu hirsute/universe s390x libdeflate0 s390x 1.7-1 [63.8 kB] Get:95 http://ftpmaster.internal/ubuntu hirsute/universe s390x libdeflate-dev s390x 1.7-1 [45.0 kB] Get:96 http://ftpmaster.internal/ubuntu hirsute/universe s390x libfile-copy-link-perl all 0.140-2.1 [15.3 kB] Get:97 http://ftpmaster.internal/ubuntu hirsute/main s390x libgraphite2-3 s390x 1.3.14-1 [67.9 kB] Get:98 http://ftpmaster.internal/ubuntu hirsute/main s390x libharfbuzz0b s390x 2.6.7-1ubuntu1 [334 kB] Get:99 http://ftpmaster.internal/ubuntu hirsute/universe s390x libhts3 s390x 1.11-4 [355 kB] Get:100 http://ftpmaster.internal/ubuntu hirsute/main s390x liblzma-dev s390x 5.2.4-1ubuntu1 [146 kB] Get:101 http://ftpmaster.internal/ubuntu hirsute/main s390x zlib1g-dev s390x 1:1.2.11.dfsg-2ubuntu4 [166 kB] Get:102 http://ftpmaster.internal/ubuntu hirsute/universe s390x libhts-dev s390x 1.11-4 [3937 kB] Get:103 http://ftpmaster.internal/ubuntu hirsute/main s390x x11-common all 1:7.7+19ubuntu15 [22.2 kB] Get:104 http://ftpmaster.internal/ubuntu hirsute/main s390x libice6 s390x 2:1.0.10-1 [39.5 kB] Get:105 http://ftpmaster.internal/ubuntu hirsute/main s390x libjpeg-turbo8 s390x 2.0.3-0ubuntu2 [102 kB] Get:106 http://ftpmaster.internal/ubuntu hirsute/main s390x libjpeg8 s390x 8c-2ubuntu8 [2142 B] Get:107 http://ftpmaster.internal/ubuntu hirsute/main s390x liblapack3 s390x 3.9.0-3ubuntu1 [1731 kB] Get:108 http://ftpmaster.internal/ubuntu hirsute/main s390x libthai-data all 0.1.28-3 [134 kB] Get:109 http://ftpmaster.internal/ubuntu hirsute/main s390x libthai0 s390x 0.1.28-3 [18.1 kB] Get:110 http://ftpmaster.internal/ubuntu hirsute/main s390x libpango-1.0-0 s390x 1.46.2-3 [174 kB] Get:111 http://ftpmaster.internal/ubuntu hirsute/main s390x libpangoft2-1.0-0 s390x 1.46.2-3 [35.3 kB] Get:112 http://ftpmaster.internal/ubuntu hirsute/main s390x libpangocairo-1.0-0 s390x 1.46.2-3 [25.1 kB] Get:113 http://ftpmaster.internal/ubuntu hirsute/main s390x libpaper1 s390x 1.1.28 [12.7 kB] Get:114 http://ftpmaster.internal/ubuntu hirsute/main s390x libpaper-utils s390x 1.1.28 [8184 B] Get:115 http://ftpmaster.internal/ubuntu hirsute/main s390x libsm6 s390x 2:1.2.3-1 [15.2 kB] Get:116 http://ftpmaster.internal/ubuntu hirsute/universe s390x libtabixpp0 s390x 1.1.0-3 [8648 B] Get:117 http://ftpmaster.internal/ubuntu hirsute/universe s390x libtabixpp-dev s390x 1.1.0-3 [6964 B] Get:118 http://ftpmaster.internal/ubuntu hirsute/main s390x libtcl8.6 s390x 8.6.11+dfsg-1 [955 kB] Get:119 http://ftpmaster.internal/ubuntu hirsute/main s390x libjbig0 s390x 2.1-3.1build1 [26.3 kB] Get:120 http://ftpmaster.internal/ubuntu hirsute/main s390x libwebp6 s390x 0.6.1-2 [149 kB] Get:121 http://ftpmaster.internal/ubuntu hirsute/main s390x libtiff5 s390x 4.1.0+git201212-1ubuntu1 [167 kB] Get:122 http://ftpmaster.internal/ubuntu hirsute/main s390x libxft2 s390x 2.3.3-0ubuntu1 [36.8 kB] Get:123 http://ftpmaster.internal/ubuntu hirsute/main s390x libxss1 s390x 1:1.2.3-1 [7972 B] Get:124 http://ftpmaster.internal/ubuntu hirsute/main s390x libtk8.6 s390x 8.6.11-1 [792 kB] Get:125 http://ftpmaster.internal/ubuntu hirsute/main s390x libxt6 s390x 1:1.2.0-1 [169 kB] Get:126 http://ftpmaster.internal/ubuntu hirsute/main s390x zip s390x 3.0-11build1 [157 kB] Get:127 http://ftpmaster.internal/ubuntu hirsute/main s390x unzip s390x 6.0-25ubuntu1 [157 kB] Get:128 http://ftpmaster.internal/ubuntu hirsute/main s390x xdg-utils all 1.1.3-2ubuntu2 [61.5 kB] Get:129 http://ftpmaster.internal/ubuntu hirsute/universe s390x r-base-core s390x 4.0.3-1 [25.0 MB] Get:130 http://ftpmaster.internal/ubuntu hirsute/universe s390x r-cran-boot all 1.3-26-1 [610 kB] Get:131 http://ftpmaster.internal/ubuntu hirsute/universe s390x r-cran-cluster s390x 2.1.0-2build1 [521 kB] Get:132 http://ftpmaster.internal/ubuntu hirsute/universe s390x r-cran-foreign s390x 0.8.81-1 [237 kB] Get:133 http://ftpmaster.internal/ubuntu hirsute/universe s390x r-cran-mass s390x 7.3-53-1 [1108 kB] Get:134 http://ftpmaster.internal/ubuntu hirsute/universe s390x r-cran-kernsmooth s390x 2.23-18-1 [88.9 kB] Get:135 http://ftpmaster.internal/ubuntu hirsute/universe s390x r-cran-lattice s390x 0.20-41-1build1 [1119 kB] Get:136 http://ftpmaster.internal/ubuntu hirsute/universe s390x r-cran-nlme s390x 3.1.151-1 [2229 kB] Get:137 http://ftpmaster.internal/ubuntu hirsute/universe s390x r-cran-matrix s390x 1.2-18-1build1 [3432 kB] Get:138 http://ftpmaster.internal/ubuntu hirsute/universe s390x r-cran-mgcv s390x 1.8-33-1 [2927 kB] Get:139 http://ftpmaster.internal/ubuntu hirsute/universe s390x r-cran-survival s390x 3.2-7-1 [7601 kB] Get:140 http://ftpmaster.internal/ubuntu hirsute/universe s390x r-cran-rpart s390x 4.1-15-2build1 [676 kB] Get:141 http://ftpmaster.internal/ubuntu hirsute/universe s390x r-cran-class s390x 7.3-18-1 [87.4 kB] Get:142 http://ftpmaster.internal/ubuntu hirsute/universe s390x r-cran-nnet s390x 7.3-15-1 [111 kB] Get:143 http://ftpmaster.internal/ubuntu hirsute/universe s390x r-cran-spatial s390x 7.3-13-1 [128 kB] Get:144 http://ftpmaster.internal/ubuntu hirsute/universe s390x r-cran-codetools all 0.2-18-1 [90.8 kB] Get:145 http://ftpmaster.internal/ubuntu hirsute/universe s390x r-recommended all 4.0.3-1 [2812 B] Get:146 http://ftpmaster.internal/ubuntu hirsute/universe s390x r-base all 4.0.3-1 [9308 B] Get:147 http://ftpmaster.internal/ubuntu hirsute/universe s390x samtools s390x 1.11-1 [523 kB] Get:148 http://ftpmaster.internal/ubuntu hirsute/universe s390x smalt s390x 0.7.6-9 [107 kB] Get:149 http://ftpmaster.internal/ubuntu hirsute/universe s390x snpomatic s390x 1.0-5 [79.2 kB] Get:150 http://ftpmaster.internal/ubuntu hirsute/universe s390x tabix s390x 1.11-4 [323 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 85.6 MB in 3s (27.9 MB/s) Selecting previously unselected package bsdextrautils. (Reading database ... 14767 files and directories currently installed.) Preparing to unpack .../000-bsdextrautils_2.36.1-1ubuntu2_s390x.deb ... Unpacking bsdextrautils (2.36.1-1ubuntu2) ... Selecting previously unselected package libuchardet0:s390x. Preparing to unpack .../001-libuchardet0_0.0.7-1_s390x.deb ... Unpacking libuchardet0:s390x (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../002-groff-base_1.22.4-5_s390x.deb ... Unpacking groff-base (1.22.4-5) ... Selecting previously unselected package libpipeline1:s390x. Preparing to unpack .../003-libpipeline1_1.5.3-1_s390x.deb ... Unpacking libpipeline1:s390x (1.5.3-1) ... Selecting previously unselected package man-db. Preparing to unpack .../004-man-db_2.9.3-2_s390x.deb ... Unpacking man-db (2.9.3-2) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../005-libmagic-mgc_1%3a5.39-3_s390x.deb ... Unpacking libmagic-mgc (1:5.39-3) ... Selecting previously unselected package libmagic1:s390x. Preparing to unpack .../006-libmagic1_1%3a5.39-3_s390x.deb ... Unpacking libmagic1:s390x (1:5.39-3) ... Selecting previously unselected package file. Preparing to unpack .../007-file_1%3a5.39-3_s390x.deb ... Unpacking file (1:5.39-3) ... Selecting previously unselected package libbsd0:s390x. Preparing to unpack .../008-libbsd0_0.10.0-1_s390x.deb ... Unpacking libbsd0:s390x (0.10.0-1) ... Selecting previously unselected package libelf1:s390x. Preparing to unpack .../009-libelf1_0.182-3_s390x.deb ... Unpacking libelf1:s390x (0.182-3) ... Selecting previously unselected package libexpat1:s390x. Preparing to unpack .../010-libexpat1_2.2.10-1_s390x.deb ... Unpacking libexpat1:s390x (2.2.10-1) ... Selecting previously unselected package libfribidi0:s390x. Preparing to unpack .../011-libfribidi0_1.0.8-2_s390x.deb ... Unpacking libfribidi0:s390x (1.0.8-2) ... Selecting previously unselected package libglib2.0-0:s390x. Preparing to unpack .../012-libglib2.0-0_2.66.4-1_s390x.deb ... Unpacking libglib2.0-0:s390x (2.66.4-1) ... Selecting previously unselected package libicu67:s390x. Preparing to unpack .../013-libicu67_67.1-5_s390x.deb ... Unpacking libicu67:s390x (67.1-5) ... Selecting previously unselected package libxml2:s390x. Preparing to unpack .../014-libxml2_2.9.10+dfsg-6.3build1_s390x.deb ... Unpacking libxml2:s390x (2.9.10+dfsg-6.3build1) ... Selecting previously unselected package libyaml-0-2:s390x. Preparing to unpack .../015-libyaml-0-2_0.2.2-1_s390x.deb ... Unpacking libyaml-0-2:s390x (0.2.2-1) ... Selecting previously unselected package ucf. Preparing to unpack .../016-ucf_3.0043_all.deb ... Moving old data out of the way Unpacking ucf (3.0043) ... Selecting previously unselected package gettext-base. Preparing to unpack .../017-gettext-base_0.21-3ubuntu2_s390x.deb ... Unpacking gettext-base (0.21-3ubuntu2) ... Selecting previously unselected package libpsl5:s390x. 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Unpacking samtools (1.11-1) ... Selecting previously unselected package smalt. Preparing to unpack .../146-smalt_0.7.6-9_s390x.deb ... Unpacking smalt (0.7.6-9) ... Selecting previously unselected package snpomatic. Preparing to unpack .../147-snpomatic_1.0-5_s390x.deb ... Unpacking snpomatic (1.0-5) ... Selecting previously unselected package tabix. Preparing to unpack .../148-tabix_1.11-4_s390x.deb ... Unpacking tabix (1.11-4) ... Selecting previously unselected package sbuild-build-depends-reapr-dummy. Preparing to unpack .../149-sbuild-build-depends-reapr-dummy_0.invalid.0_s390x.deb ... Unpacking sbuild-build-depends-reapr-dummy (0.invalid.0) ... Setting up libexpat1:s390x (2.2.10-1) ... Setting up libpipeline1:s390x (1.5.3-1) ... Setting up libgraphite2-3:s390x (1.3.14-1) ... Setting up libpixman-1-0:s390x (0.40.0-1) ... Setting up libxau6:s390x (1:1.0.9-0ubuntu1) ... Setting up libpsl5:s390x (0.21.0-1.1ubuntu1) ... Setting up libfile-copy-link-perl (0.140-2.1) ... Setting up bsdextrautils (2.36.1-1ubuntu2) ... update-alternatives: using /usr/bin/write.ul to provide /usr/bin/write (write) in auto mode Setting up libicu67:s390x (67.1-5) ... Setting up libdatrie1:s390x (0.2.12-3) ... Setting up ruby-power-assert (1.1.7-1) ... Setting up libmagic-mgc (1:5.39-3) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libyaml-0-2:s390x (0.2.2-1) ... Setting up libglib2.0-0:s390x (2.66.4-1) ... No schema files found: doing nothing. Setting up unzip (6.0-25ubuntu1) ... Setting up libdebhelper-perl (13.3.1ubuntu1) ... Setting up libbrotli1:s390x (1.0.9-2build2) ... Setting up x11-common (1:7.7+19ubuntu15) ... 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:s390x (1.42.0-1) ... Setting up libmagic1:s390x (1:5.39-3) ... Setting up libdeflate0:s390x (1.7-1) ... Setting up gettext-base (0.21-3ubuntu2) ... Setting up rubygems-integration (1.17.3) ... Setting up file (1:5.39-3) ... Setting up libjbig0:s390x (2.1-3.1build1) ... Setting up libsasl2-modules-db:s390x (2.1.27+dfsg-2ubuntu1) ... Setting up ruby-minitest (5.13.0-1) ... Setting up zip (3.0-11build1) ... Setting up autotools-dev (20180224.1+nmu1) ... Setting up libblas3:s390x (3.9.0-3ubuntu1) ... update-alternatives: using /usr/lib/s390x-linux-gnu/blas/libblas.so.3 to provide /usr/lib/s390x-linux-gnu/libblas.so.3 (libblas.so.3-s390x-linux-gnu) in auto mode Setting up libfreetype6:s390x (2.10.4+dfsg-1) ... Setting up ruby-test-unit (3.3.9-1) ... Setting up libx11-data (2:1.7.0-2) ... Setting up librtmp1:s390x (2.4+20151223.gitfa8646d.1-2build2) ... Setting up ruby-net-telnet (0.1.1-2) ... Setting up libsigsegv2:s390x (2.12-3) ... Setting up libfribidi0:s390x (1.0.8-2) ... Setting up libbambamc0 (0.0.50-4) ... Setting up libbamtools2.5.1:s390x (2.5.1+dfsg-7build1) ... Setting up libtcl8.6:s390x (8.6.11+dfsg-1) ... Setting up autopoint (0.21-3ubuntu2) ... Setting up libwebp6:s390x (0.6.1-2) ... Setting up fonts-dejavu-core (2.37-2) ... Setting up ucf (3.0043) ... Setting up libjpeg-turbo8:s390x (2.0.3-0ubuntu2) ... Setting up libsasl2-2:s390x (2.1.27+dfsg-2ubuntu1) ... Setting up libssh-4:s390x (0.9.5-1) ... Setting up libgfortran5:s390x (11-20210123-1ubuntu1) ... Setting up libroken18-heimdal:s390x (7.7.0+dfsg-2) ... Setting up libjsoncpp24:s390x (1.9.4-4) ... Setting up liblzma-dev:s390x (5.2.4-1ubuntu1) ... Setting up zlib1g-dev:s390x (1:1.2.11.dfsg-2ubuntu4) ... Setting up bamtools (2.5.1+dfsg-7build1) ... Setting up snpomatic (1.0-5) ... Setting up libuchardet0:s390x (0.0.7-1) ... Setting up libsub-override-perl (0.09-2) ... Setting up libharfbuzz0b:s390x (2.6.7-1ubuntu1) ... Setting up libthai-data (0.1.28-3) ... Setting up libbsd0:s390x (0.10.0-1) ... Setting up libdeflate-dev:s390x (1.7-1) ... Setting up tabix (1.11-4) ... Setting up libelf1:s390x (0.182-3) ... Setting up ruby-xmlrpc (0.3.0-2) ... Setting up libxml2:s390x (2.9.10+dfsg-6.3build1) ... Setting up xdg-utils (1.1.3-2ubuntu2) ... Setting up libheimbase1-heimdal:s390x (7.7.0+dfsg-2) ... Setting up libjpeg8:s390x (8c-2ubuntu8) ... Setting up libfile-stripnondeterminism-perl (1.10.0-1) ... Setting up smalt (0.7.6-9) ... Setting up libpaper1:s390x (1.1.28) ... Creating config file /etc/papersize with new version Setting up libice6:s390x (2:1.0.10-1) ... Setting up libxdmcp6:s390x (1:1.1.3-0ubuntu1) ... Setting up liblapack3:s390x (3.9.0-3ubuntu1) ... update-alternatives: using /usr/lib/s390x-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/s390x-linux-gnu/liblapack.so.3 (liblapack.so.3-s390x-linux-gnu) in auto mode Setting up libxcb1:s390x (1.14-2.1) ... Setting up gettext (0.21-3ubuntu2) ... Setting up libtool (2.4.6-15) ... Setting up libxcb-render0:s390x (1.14-2.1) ... Setting up fontconfig-config (2.13.1-4.2ubuntu2) ... Setting up libasn1-8-heimdal:s390x (7.7.0+dfsg-2) ... Setting up m4 (1.4.18-5) ... Setting up libxcb-shm0:s390x (1.14-2.1) ... Setting up libpaper-utils (1.1.28) ... Setting up libhcrypto4-heimdal:s390x (7.7.0+dfsg-2) ... Setting up intltool-debian (0.35.0+20060710.5) ... Setting up libthai0:s390x (0.1.28-3) ... Setting up libwind0-heimdal:s390x (7.7.0+dfsg-2) ... Setting up libbamtools-dev:s390x (2.5.1+dfsg-7build1) ... Setting up autoconf (2.69-14) ... Setting up dh-strip-nondeterminism (1.10.0-1) ... Setting up dwz (0.13+20210118-1) ... Setting up groff-base (1.22.4-5) ... Setting up libx11-6:s390x (2:1.7.0-2) ... Setting up libtiff5:s390x (4.1.0+git201212-1ubuntu1) ... Setting up libfontconfig1:s390x (2.13.1-4.2ubuntu2) ... Setting up libsm6:s390x (2:1.2.3-1) ... Setting up automake (1:1.16.3-2ubuntu1) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up fontconfig (2.13.1-4.2ubuntu2) ... Regenerating fonts cache... done. Setting up libxrender1:s390x (1:0.9.10-1) ... Setting up libhx509-5-heimdal:s390x (7.7.0+dfsg-2) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libpango-1.0-0:s390x (1.46.2-3) ... Setting up libxext6:s390x (2:1.3.4-0ubuntu1) ... Setting up man-db (2.9.3-2) ... 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:s390x (1.16.0-5) ... Setting up libxt6:s390x (1:1.2.0-1) ... Setting up libxss1:s390x (1:1.2.3-1) ... Setting up libpangoft2-1.0-0:s390x (1.46.2-3) ... Setting up libpangocairo-1.0-0:s390x (1.46.2-3) ... Setting up libkrb5-26-heimdal:s390x (7.7.0+dfsg-2) ... Setting up libxft2:s390x (2.3.3-0ubuntu1) ... Setting up libtk8.6:s390x (8.6.11-1) ... Setting up libheimntlm0-heimdal:s390x (7.7.0+dfsg-2) ... Setting up libgssapi3-heimdal:s390x (7.7.0+dfsg-2) ... Setting up libldap-2.4-2:s390x (2.4.56+dfsg-1ubuntu1) ... Setting up libcurl3-gnutls:s390x (7.72.0-1ubuntu1) ... Setting up libcurl4-gnutls-dev:s390x (7.72.0-1ubuntu1) ... Setting up libcurl4:s390x (7.72.0-1ubuntu1) ... Setting up libhts3:s390x (1.11-4) ... Setting up libhts-dev:s390x (1.11-4) ... Setting up samtools (1.11-1) ... Setting up r-base-core (4.0.3-1) ... Creating config file /etc/R/Renviron with new version Setting up r-cran-lattice (0.20-41-1build1) ... Setting up r-cran-nlme (3.1.151-1) ... Setting up r-cran-cluster (2.1.0-2build1) ... Setting up libtabixpp0:s390x (1.1.0-3) ... Setting up r-cran-nnet (7.3-15-1) ... Setting up r-cran-codetools (0.2-18-1) ... Setting up r-cran-boot (1.3-26-1) ... Setting up r-cran-spatial (7.3-13-1) ... Setting up r-cran-mass (7.3-53-1) ... Setting up r-cran-foreign (0.8.81-1) ... Setting up r-cran-matrix (1.2-18-1build1) ... Setting up r-cran-kernsmooth (2.23-18-1) ... Setting up r-cran-mgcv (1.8-33-1) ... Setting up libtabixpp-dev:s390x (1.1.0-3) ... Setting up r-cran-class (7.3-18-1) ... Setting up r-cran-survival (3.2-7-1) ... Setting up r-cran-rpart (4.1-15-2build1) ... Setting up r-recommended (4.0.3-1) ... Setting up r-base (4.0.3-1) ... Setting up dh-autoreconf (19) ... Setting up rake (13.0.1-4) ... Setting up debhelper (13.3.1ubuntu1) ... Setting up libruby2.7:s390x (2.7.2-3) ... Setting up ruby2.7 (2.7.2-3) ... Setting up ruby (1:2.7+1) ... Setting up ruby-asciidoctor (2.0.12-2) ... Setting up asciidoctor (2.0.12-2) ... Setting up sbuild-build-depends-reapr-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.32-0ubuntu6) ... +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 4.15.0-134-generic s390x (s390x) Toolchain package versions: binutils_2.35.50.20210106-1ubuntu2 dpkg-dev_1.20.7.1ubuntu1 g++-10_10.2.1-6ubuntu1 gcc-10_10.2.1-6ubuntu1 libc6-dev_2.32-0ubuntu6 libstdc++-10-dev_10.2.1-6ubuntu1 libstdc++6_11-20210123-1ubuntu1 linux-libc-dev_5.8.0-36.40+21.04.1 Package versions: adduser_3.118ubuntu5 advancecomp_2.1-2.1build1 apt_2.1.18 asciidoctor_2.0.12-2 autoconf_2.69-14 automake_1:1.16.3-2ubuntu1 autopoint_0.21-3ubuntu2 autotools-dev_20180224.1+nmu1 bamtools_2.5.1+dfsg-7build1 base-files_11ubuntu16 base-passwd_3.5.48 bash_5.1-1ubuntu1 binutils_2.35.50.20210106-1ubuntu2 binutils-common_2.35.50.20210106-1ubuntu2 binutils-s390x-linux-gnu_2.35.50.20210106-1ubuntu2 bsdextrautils_2.36.1-1ubuntu2 bsdutils_1:2.36.1-1ubuntu2 build-essential_12.8ubuntu3 bzip2_1.0.8-4ubuntu2 ca-certificates_20200601 coreutils_8.32-4ubuntu2 cpp_4:10.2.0-1ubuntu1 cpp-10_10.2.1-6ubuntu1 dash_0.5.11+git20200708+dd9ef66+really0.5.11+git20200708+dd9ef66-5ubuntu1 debconf_1.5.74 debhelper_13.3.1ubuntu1 debianutils_4.11.2 dh-autoreconf_19 dh-strip-nondeterminism_1.10.0-1 diffutils_1:3.7-3ubuntu1 dpkg_1.20.7.1ubuntu1 dpkg-dev_1.20.7.1ubuntu1 dwz_0.13+20210118-1 e2fsprogs_1.45.6-1ubuntu1 fakeroot_1.25.3-1.1 file_1:5.39-3 findutils_4.7.0-1ubuntu2 fontconfig_2.13.1-4.2ubuntu2 fontconfig-config_2.13.1-4.2ubuntu2 fonts-dejavu-core_2.37-2 g++_4:10.2.0-1ubuntu1 g++-10_10.2.1-6ubuntu1 gcc_4:10.2.0-1ubuntu1 gcc-10_10.2.1-6ubuntu1 gcc-10-base_10.2.1-6ubuntu1 gcc-11-base_11-20210123-1ubuntu1 gettext_0.21-3ubuntu2 gettext-base_0.21-3ubuntu2 gpg_2.2.20-1ubuntu2 gpg-agent_2.2.20-1ubuntu2 gpgconf_2.2.20-1ubuntu2 gpgv_2.2.20-1ubuntu2 grep_3.6-1 groff-base_1.22.4-5 gzip_1.10-2ubuntu2 hostname_3.23 init_1.59 init-system-helpers_1.59 intltool-debian_0.35.0+20060710.5 libacl1_2.2.53-9 libapparmor1_3.0.0-0ubuntu5 libapt-pkg6.0_2.1.18 libarchive-zip-perl_1.68-1 libargon2-1_0~20171227-0.2build20.10.0 libasan6_11-20210123-1ubuntu1 libasn1-8-heimdal_7.7.0+dfsg-2 libassuan0_2.5.3-7.1 libatomic1_11-20210123-1ubuntu1 libattr1_1:2.4.48-6 libaudit-common_1:2.8.5-3ubuntu3 libaudit1_1:2.8.5-3ubuntu3 libbambamc0_0.0.50-4 libbamtools-dev_2.5.1+dfsg-7build1 libbamtools2.5.1_2.5.1+dfsg-7build1 libbinutils_2.35.50.20210106-1ubuntu2 libblas3_3.9.0-3ubuntu1 libblkid1_2.36.1-1ubuntu2 libbrotli1_1.0.9-2build2 libbsd0_0.10.0-1 libbz2-1.0_1.0.8-4ubuntu2 libc-bin_2.32-0ubuntu6 libc-dev-bin_2.32-0ubuntu6 libc6_2.32-0ubuntu6 libc6-dev_2.32-0ubuntu6 libcairo2_1.16.0-5 libcap-ng0_0.7.9-2.2build1 libcap2_1:2.44-1 libcc1-0_11-20210123-1ubuntu1 libcom-err2_1.45.6-1ubuntu1 libcrypt-dev_1:4.4.17-1ubuntu1 libcrypt1_1:4.4.17-1ubuntu1 libcryptsetup12_2:2.3.4-1ubuntu1 libctf-nobfd0_2.35.50.20210106-1ubuntu2 libctf0_2.35.50.20210106-1ubuntu2 libcurl3-gnutls_7.72.0-1ubuntu1 libcurl4_7.72.0-1ubuntu1 libcurl4-gnutls-dev_7.72.0-1ubuntu1 libdatrie1_0.2.12-3 libdb5.3_5.3.28+dfsg1-0.6ubuntu3 libdebconfclient0_0.256ubuntu1 libdebhelper-perl_13.3.1ubuntu1 libdeflate-dev_1.7-1 libdeflate0_1.7-1 libdevmapper1.02.1_2:1.02.167-1ubuntu4 libdpkg-perl_1.20.7.1ubuntu1 libelf1_0.182-3 libexpat1_2.2.10-1 libext2fs2_1.45.6-1ubuntu1 libfakeroot_1.25.3-1.1 libffi8ubuntu1_3.4~20200819gead65ca871-0ubuntu3 libfile-copy-link-perl_0.140-2.1 libfile-stripnondeterminism-perl_1.10.0-1 libfontconfig1_2.13.1-4.2ubuntu2 libfreetype6_2.10.4+dfsg-1 libfribidi0_1.0.8-2 libgcc-10-dev_10.2.1-6ubuntu1 libgcc-s1_11-20210123-1ubuntu1 libgcrypt20_1.8.7-2ubuntu1 libgdbm-compat4_1.19-2 libgdbm6_1.19-2 libgfortran5_11-20210123-1ubuntu1 libglib2.0-0_2.66.4-1 libgmp10_2:6.2.0+dfsg-6ubuntu1 libgnutls30_3.7.0-5ubuntu1 libgomp1_11-20210123-1ubuntu1 libgpg-error0_1.38-2 libgraphite2-3_1.3.14-1 libgssapi-krb5-2_1.17-10ubuntu1 libgssapi3-heimdal_7.7.0+dfsg-2 libharfbuzz0b_2.6.7-1ubuntu1 libhcrypto4-heimdal_7.7.0+dfsg-2 libheimbase1-heimdal_7.7.0+dfsg-2 libheimntlm0-heimdal_7.7.0+dfsg-2 libhogweed6_3.6-2 libhts-dev_1.11-4 libhts3_1.11-4 libhx509-5-heimdal_7.7.0+dfsg-2 libice6_2:1.0.10-1 libicu67_67.1-5 libidn2-0_2.3.0-5 libip4tc2_1.8.5-3ubuntu4 libisl22_0.22.1-1 libisl23_0.23-1 libitm1_11-20210123-1ubuntu1 libjbig0_2.1-3.1build1 libjpeg-turbo8_2.0.3-0ubuntu2 libjpeg8_8c-2ubuntu8 libjson-c5_0.15-1 libjsoncpp24_1.9.4-4 libk5crypto3_1.17-10ubuntu1 libkeyutils1_1.6.1-2ubuntu1 libkmod2_27+20200310-2ubuntu1 libkrb5-26-heimdal_7.7.0+dfsg-2 libkrb5-3_1.17-10ubuntu1 libkrb5support0_1.17-10ubuntu1 liblapack3_3.9.0-3ubuntu1 libldap-2.4-2_2.4.56+dfsg-1ubuntu1 liblockfile-bin_1.16-1.1 liblockfile1_1.16-1.1 liblz4-1_1.9.3-0ubuntu1 liblzma-dev_5.2.4-1ubuntu1 liblzma5_5.2.4-1ubuntu1 libmagic-mgc_1:5.39-3 libmagic1_1:5.39-3 libmount1_2.36.1-1ubuntu2 libmpc3_1.2.0-1 libmpfr6_4.1.0-3 libncurses6_6.2+20201114-2 libncursesw6_6.2+20201114-2 libnettle8_3.6-2 libnghttp2-14_1.42.0-1 libnpth0_1.6-3 libnsl-dev_1.3.0-0ubuntu3 libnsl2_1.3.0-0ubuntu3 libnss-nis_3.1-0ubuntu4 libnss-nisplus_1.3-0ubuntu4 libp11-kit0_0.23.22-1 libpam-modules_1.3.1-5ubuntu6 libpam-modules-bin_1.3.1-5ubuntu6 libpam-runtime_1.3.1-5ubuntu6 libpam0g_1.3.1-5ubuntu6 libpango-1.0-0_1.46.2-3 libpangocairo-1.0-0_1.46.2-3 libpangoft2-1.0-0_1.46.2-3 libpaper-utils_1.1.28 libpaper1_1.1.28 libpcre2-8-0_10.35-2ubuntu1 libpcre3_2:8.39-13 libperl5.30_5.30.3-4 libperl5.32_5.32.0-6 libpipeline1_1.5.3-1 libpixman-1-0_0.40.0-1 libpng16-16_1.6.37-3 libprocps8_2:3.3.16-5ubuntu2 libpsl5_0.21.0-1.1ubuntu1 libreadline8_8.1-1 libroken18-heimdal_7.7.0+dfsg-2 librtmp1_2.4+20151223.gitfa8646d.1-2build2 libruby2.7_2.7.2-3 libsasl2-2_2.1.27+dfsg-2ubuntu1 libsasl2-modules-db_2.1.27+dfsg-2ubuntu1 libseccomp2_2.4.3-1ubuntu6 libselinux1_3.1-2build2 libsemanage-common_3.1-1build2 libsemanage1_3.1-1build2 libsepol1_3.1-1 libsigsegv2_2.12-3 libsm6_2:1.2.3-1 libsmartcols1_2.36.1-1ubuntu2 libsqlite3-0_3.34.0-1 libss2_1.45.6-1ubuntu1 libssh-4_0.9.5-1 libssl1.1_1.1.1f-1ubuntu5 libstdc++-10-dev_10.2.1-6ubuntu1 libstdc++6_11-20210123-1ubuntu1 libsub-override-perl_0.09-2 libsystemd0_247.1-4ubuntu1 libtabixpp-dev_1.1.0-3 libtabixpp0_1.1.0-3 libtasn1-6_4.16.0-2 libtcl8.6_8.6.11+dfsg-1 libthai-data_0.1.28-3 libthai0_0.1.28-3 libtiff5_4.1.0+git201212-1ubuntu1 libtinfo6_6.2+20201114-2 libtirpc-common_1.3.1-1 libtirpc-dev_1.3.1-1 libtirpc3_1.3.1-1 libtk8.6_8.6.11-1 libtool_2.4.6-15 libubsan1_11-20210123-1ubuntu1 libuchardet0_0.0.7-1 libudev1_247.1-4ubuntu1 libunistring2_0.9.10-4 libuuid1_2.36.1-1ubuntu2 libwebp6_0.6.1-2 libwind0-heimdal_7.7.0+dfsg-2 libx11-6_2:1.7.0-2 libx11-data_2:1.7.0-2 libxau6_1:1.0.9-0ubuntu1 libxcb-render0_1.14-2.1 libxcb-shm0_1.14-2.1 libxcb1_1.14-2.1 libxdmcp6_1:1.1.3-0ubuntu1 libxext6_2:1.3.4-0ubuntu1 libxft2_2.3.3-0ubuntu1 libxml2_2.9.10+dfsg-6.3build1 libxrender1_1:0.9.10-1 libxss1_1:1.2.3-1 libxt6_1:1.2.0-1 libxxhash0_0.8.0-2 libyaml-0-2_0.2.2-1 libzstd1_1.4.8+dfsg-1 linux-libc-dev_5.8.0-36.40+21.04.1 lockfile-progs_0.1.18 login_1:4.8.1-1ubuntu8 logsave_1.45.6-1ubuntu1 lsb-base_11.1.0ubuntu2 m4_1.4.18-5 make_4.3-4ubuntu1 man-db_2.9.3-2 mawk_1.3.4.20200120-2 mount_2.36.1-1ubuntu2 ncurses-base_6.2+20201114-2 ncurses-bin_6.2+20201114-2 openssl_1.1.1f-1ubuntu5 optipng_0.7.7-1 passwd_1:4.8.1-1ubuntu8 patch_2.7.6-7 perl_5.32.0-6 perl-base_5.32.0-6 perl-modules-5.30_5.30.3-4 perl-modules-5.32_5.32.0-6 pinentry-curses_1.1.0-4build1 pkgbinarymangler_146 po-debconf_1.0.21+nmu1 policyrcd-script-zg2_0.1-3 procps_2:3.3.16-5ubuntu2 r-base_4.0.3-1 r-base-core_4.0.3-1 r-cran-boot_1.3-26-1 r-cran-class_7.3-18-1 r-cran-cluster_2.1.0-2build1 r-cran-codetools_0.2-18-1 r-cran-foreign_0.8.81-1 r-cran-kernsmooth_2.23-18-1 r-cran-lattice_0.20-41-1build1 r-cran-mass_7.3-53-1 r-cran-matrix_1.2-18-1build1 r-cran-mgcv_1.8-33-1 r-cran-nlme_3.1.151-1 r-cran-nnet_7.3-15-1 r-cran-rpart_4.1-15-2build1 r-cran-spatial_7.3-13-1 r-cran-survival_3.2-7-1 r-recommended_4.0.3-1 rake_13.0.1-4 readline-common_8.1-1 rpcsvc-proto_1.4.2-0ubuntu4 ruby_1:2.7+1 ruby-asciidoctor_2.0.12-2 ruby-minitest_5.13.0-1 ruby-net-telnet_0.1.1-2 ruby-power-assert_1.1.7-1 ruby-test-unit_3.3.9-1 ruby-xmlrpc_0.3.0-2 ruby2.7_2.7.2-3 rubygems-integration_1.17.3 samtools_1.11-1 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-reapr-dummy_0.invalid.0 sed_4.7-1ubuntu1 sensible-utils_0.0.14 smalt_0.7.6-9 snpomatic_1.0-5 systemd_247.1-4ubuntu1 systemd-sysv_247.1-4ubuntu1 systemd-timesyncd_247.1-4ubuntu1 sysvinit-utils_2.96-5ubuntu1 tabix_1.11-4 tar_1.32+dfsg-1 tzdata_2020f-1ubuntu2 ubuntu-keyring_2020.06.17.1 ucf_3.0043 unzip_6.0-25ubuntu1 util-linux_2.36.1-1ubuntu2 x11-common_1:7.7+19ubuntu15 xdg-utils_1.1.3-2ubuntu2 xz-utils_5.2.4-1ubuntu1 zip_3.0-11build1 zlib1g_1:1.2.11.dfsg-2ubuntu4 zlib1g-dev_1:1.2.11.dfsg-2ubuntu4 +------------------------------------------------------------------------------+ | 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 disk space ---------------- Sufficient free space for build User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf DEB_BUILD_OPTIONS=noautodbgsym 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-20675635 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-20675635 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-20675635 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 s390x 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 -ffile-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 -ffile-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 -ffile-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 histogram.cpp: In member function ‘void Histogram::plot(std::string, std::string, std::string, std::string)’: histogram.cpp:333:50: warning: ‘stddev’ may be used uninitialized in this function [-Wmaybe-uninitialized] 333 | if (plotTrim_ && xval < mean - plotTrim_ * stddev) | ~~~~~~~~~~^~~~~~~~ histogram.cpp:321:17: warning: ‘mean’ may be used uninitialized in this function [-Wmaybe-uninitialized] 321 | mean = mean ? mean : 1; | ~~~~~^~~~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-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 -ffile-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 -ffile-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 -ffile-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 -ffile-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 -ffile-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 -ffile-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 -ffile-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 -ffile-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 -ffile-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 -ffile-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 -ffile-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 -ffile-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 -ffile-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 -ffile-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 -ffile-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 -ffile-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 -ffile-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 -ffile-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 -ffile-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 -ffile-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 -ffile-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 -ffile-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 -ffile-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 -ffile-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 -ffile-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 -ffile-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 -ffile-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 -ffile-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 -ffile-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 -ffile-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.6078.smaltmap.smalt_index foo1.fasta # Command line: smalt index -k 13 -s 2 out.bam.tmp.6078.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.6078.smaltmap.smalt_sample out.bam.tmp.6078.smaltmap.smalt_index foofq.1.fastq foofq.2.fastq # Command line: smalt sample -u 1000 -o out.bam.tmp.6078.smaltmap.smalt_sample out.bam.tmp.6078.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:4 seconds # smalt: Total elapsed wall clock time: 4 seconds [REAPR smaltmap] Running: smalt map -r 0 -x -y 0.5 -g out.bam.tmp.6078.smaltmap.smalt_sample -f samsoft out.bam.tmp.6078.smaltmap.smalt_index foofq.1.fastq foofq.2.fastq | awk '$1!~/^#/' | samtools view -S -T foo1.fasta -b - > out.bam.tmp.6078.smaltmap.raw.bam # Command line: smalt map -r 0 -x -y 0.5 -g out.bam.tmp.6078.smaltmap.smalt_sample -f samsoft out.bam.tmp.6078.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:15 seconds # smalt: Total elapsed wall clock time: 15 seconds [REAPR smaltmap] Running: samtools sort out.bam.tmp.6078.smaltmap.raw.bam -O bam -o out.bam.tmp.6078.smaltmap.raw.bam.sort.bam [REAPR smaltmap] Running: samtools rmdup out.bam.tmp.6078.smaltmap.raw.bam.sort.bam out.bam.tmp.6078.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.6078.smaltmap.header [REAPR smaltmap] Running: samtools view -H out.bam.tmp.6078.smaltmap.rmdup.bam >> out.bam.tmp.6078.smaltmap.header [REAPR smaltmap] Running: samtools reheader out.bam.tmp.6078.smaltmap.header out.bam.tmp.6078.smaltmap.rmdup.bam > out.bam [REAPR smaltmap] Running: samtools index out.bam [REAPR smaltmap] Running: rm out.bam.tmp.6078.smaltmap.* Running reapr version 1.0.18 pipeline: reapr foo1.fasta out.bam result [REAPR pipeline] Running facheck [REAPR pipeline] Running preprocess terminate called after throwing an instance of 'std::bad_alloc' what(): std::bad_alloc Aborted (core dumped) [REAPR preprocess] sampling region foo:1169-3476. Already sampled 0 bases [REAPR preprocess] No coverage in foo:1169-3476. Skipping [REAPR preprocess] sampling region foo:3492-5726. Already sampled 0 bases [REAPR preprocess] No coverage in foo:3492-5726. Skipping [REAPR preprocess] sampling region foo:5756-12551. Already sampled 0 bases [REAPR preprocess] No coverage in foo:5756-12551. Skipping [REAPR preprocess] sampling region foo:12591-998105. Already sampled 0 bases [REAPR preprocess] No coverage in foo:12591-998105. Skipping [REAPR preprocess] Error sampling from files '00.Sample/fragCov.gz', '00.assembly.fa.gc.gz' Most likely causes are: 1. A character in the assembly sequence names that broke tabix, such as :,| or -. You can check for this by running reapr facheck 2. A mismatch of names in the input BAM and assembly fasta files. A common cause is trailing whitespace in the fasta file, or everything after the first whitesace character in a name being removed by the mapper, so the name is different in the BAM file. 3. There is not enough fragment coverage because the assembly is too fragmented. You may want to compare your mean contig length with the insert size of the reads. Also have a look at this plot of the insert size distribution: 00.Sample/insert.in.pdf make[1]: *** [debian/rules:41: override_dh_auto_test] Error 1 make[1]: Leaving directory '/<>/reapr-1.0.18+dfsg' make: *** [debian/rules:4: build-arch] Error 2 dpkg-buildpackage: error: debian/rules build-arch subprocess returned exit status 2 -------------------------------------------------------------------------------- Build finished at 2021-01-26T13:42:35Z Finished -------- +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not removing build depends: as requested E: Build failure (dpkg-buildpackage died) +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: s390x Build Type: any Build-Space: n/a Build-Time: 59 Distribution: hirsute Fail-Stage: build Host Architecture: s390x Install-Time: 18 Job: reapr_1.0.18+dfsg-5build1.dsc Machine Architecture: s390x Package: reapr Package-Time: 78 Source-Version: 1.0.18+dfsg-5build1 Space: n/a Status: attempted Version: 1.0.18+dfsg-5build1 -------------------------------------------------------------------------------- Finished at 2021-01-26T13:42:35Z Build needed 00:01:18, no disk space E: Build failure (dpkg-buildpackage died) RUN: /usr/share/launchpad-buildd/bin/in-target scan-for-processes --backend=chroot --series=hirsute --arch=s390x PACKAGEBUILD-20675635 Scanning for processes to kill in build PACKAGEBUILD-20675635