https://launchpad.net/ubuntu/+archive/test-rebuild-20191220-focal/+build/18348607 RUN: /usr/share/launchpad-buildd/bin/builder-prep Kernel version: Linux bos02-s390x-007 4.4.0-170-generic #199-Ubuntu SMP Thu Nov 14 01:44:14 UTC 2019 s390x Buildd toolchain package versions: launchpad-buildd_183 python-lpbuildd_183 sbuild_0.67.0-2ubuntu7.1 bzr-builder_0.7.3+bzr174~ppa13~ubuntu14.10.1 bzr_2.7.0-2ubuntu3.1 git-build-recipe_0.3.6~git201906051340.ff11471~ubuntu16.04.1 git_1:2.7.4-0ubuntu1.7 dpkg-dev_1.18.4ubuntu1.6 python-debian_0.1.27ubuntu2. Syncing the system clock with the buildd NTP service... 5 Jan 10:42:47 ntpdate[1840]: adjust time server 10.211.37.1 offset 0.000761 sec RUN: /usr/share/launchpad-buildd/bin/in-target unpack-chroot --backend=chroot --series=focal --arch=s390x PACKAGEBUILD-18348607 --image-type chroot /home/buildd/filecache-default/1ac0229cc48d8f596a1790116aa52d00551197b1 Creating target for build PACKAGEBUILD-18348607 RUN: /usr/share/launchpad-buildd/bin/in-target mount-chroot --backend=chroot --series=focal --arch=s390x PACKAGEBUILD-18348607 Starting target for build PACKAGEBUILD-18348607 RUN: /usr/share/launchpad-buildd/bin/in-target override-sources-list --backend=chroot --series=focal --arch=s390x PACKAGEBUILD-18348607 'deb http://ftpmaster.internal/ubuntu focal main restricted universe multiverse' Overriding sources.list in build-PACKAGEBUILD-18348607 RUN: /usr/share/launchpad-buildd/bin/in-target update-debian-chroot --backend=chroot --series=focal --arch=s390x PACKAGEBUILD-18348607 Updating target for build PACKAGEBUILD-18348607 Get:1 http://ftpmaster.internal/ubuntu focal InRelease [255 kB] Get:2 http://ftpmaster.internal/ubuntu focal/main s390x Packages [916 kB] Get:3 http://ftpmaster.internal/ubuntu focal/main Translation-en [499 kB] Get:4 http://ftpmaster.internal/ubuntu focal/restricted s390x Packages [1288 B] Get:5 http://ftpmaster.internal/ubuntu focal/restricted Translation-en [5768 B] Get:6 http://ftpmaster.internal/ubuntu focal/universe s390x Packages [8337 kB] Get:7 http://ftpmaster.internal/ubuntu focal/universe Translation-en [5195 kB] Get:8 http://ftpmaster.internal/ubuntu focal/multiverse s390x Packages [119 kB] Get:9 http://ftpmaster.internal/ubuntu focal/multiverse Translation-en [110 kB] Fetched 15.4 MB in 3s (4713 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: libhogweed4 libisl21 libnettle6 libperl5.28 perl-modules-5.28 Use 'sudo apt autoremove' to remove them. The following NEW packages will be installed: libhogweed5 libisl22 libnettle7 libperl5.30 perl-modules-5.30 The following packages will be upgraded: apt base-files base-passwd bash binutils binutils-common binutils-s390x-linux-gnu bsdutils bzip2 cpp-9 debianutils fdisk g++-9 gcc-9 gcc-9-base gpg gpg-agent gpgconf gpgv gzip hostname libacl1 libapparmor1 libapt-pkg5.90 libasan5 libatomic1 libattr1 libaudit-common libaudit1 libbinutils libblkid1 libbz2-1.0 libc-bin libc-dev-bin libc6 libc6-dev libcap-ng0 libcap2 libcc1-0 libcryptsetup12 libdebconfclient0 libdevmapper1.02.1 libfdisk1 libgcc-9-dev libgcc1 libgcrypt20 libgnutls30 libgomp1 libitm1 libjson-c4 libkmod2 liblockfile-bin liblockfile1 liblz4-1 libmount1 libncurses6 libncursesw6 libp11-kit0 libpam-modules libpam-modules-bin libpam-runtime libpam0g libpcre2-8-0 libseccomp2 libselinux1 libsemanage-common libsemanage1 libsepol1 libsmartcols1 libsqlite3-0 libstdc++-9-dev libstdc++6 libsystemd0 libtasn1-6 libtinfo6 libubsan1 libudev1 libuuid1 libzstd1 linux-libc-dev lsb-base mount ncurses-base ncurses-bin perl perl-base sensible-utils systemd systemd-sysv sysvinit-utils util-linux 91 upgraded, 5 newly installed, 0 to remove and 0 not upgraded. Need to get 58.1 MB of archives. After this operation, 49.1 MB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu focal/main s390x libc6-dev s390x 2.30-0ubuntu3 [2060 kB] Get:2 http://ftpmaster.internal/ubuntu focal/main s390x libc-dev-bin s390x 2.30-0ubuntu3 [63.9 kB] Get:3 http://ftpmaster.internal/ubuntu focal/main s390x linux-libc-dev s390x 5.3.0-24.26 [1094 kB] Get:4 http://ftpmaster.internal/ubuntu focal/main s390x libisl22 s390x 0.22-2 [546 kB] Get:5 http://ftpmaster.internal/ubuntu focal/main s390x libcc1-0 s390x 9.2.1-21ubuntu1 [46.5 kB] Get:6 http://ftpmaster.internal/ubuntu focal/main s390x binutils-s390x-linux-gnu s390x 2.33.1-6ubuntu3 [1468 kB] Get:7 http://ftpmaster.internal/ubuntu focal/main s390x libbinutils s390x 2.33.1-6ubuntu3 [301 kB] Get:8 http://ftpmaster.internal/ubuntu focal/main s390x binutils-common s390x 2.33.1-6ubuntu3 [203 kB] Get:9 http://ftpmaster.internal/ubuntu focal/main s390x binutils s390x 2.33.1-6ubuntu3 [3328 B] Get:10 http://ftpmaster.internal/ubuntu focal/main s390x gcc-9-base s390x 9.2.1-21ubuntu1 [19.1 kB] Get:11 http://ftpmaster.internal/ubuntu focal/main s390x libgcc1 s390x 1:9.2.1-21ubuntu1 [25.3 kB] Get:12 http://ftpmaster.internal/ubuntu focal/main s390x libgomp1 s390x 9.2.1-21ubuntu1 [83.3 kB] Get:13 http://ftpmaster.internal/ubuntu focal/main s390x libitm1 s390x 9.2.1-21ubuntu1 [27.1 kB] Get:14 http://ftpmaster.internal/ubuntu focal/main s390x libatomic1 s390x 9.2.1-21ubuntu1 [8264 B] Get:15 http://ftpmaster.internal/ubuntu focal/main s390x libasan5 s390x 9.2.1-21ubuntu1 [361 kB] Get:16 http://ftpmaster.internal/ubuntu focal/main s390x libubsan1 s390x 9.2.1-21ubuntu1 [125 kB] Get:17 http://ftpmaster.internal/ubuntu focal/main s390x g++-9 s390x 9.2.1-21ubuntu1 [8609 kB] Get:18 http://ftpmaster.internal/ubuntu focal/main s390x libstdc++-9-dev s390x 9.2.1-21ubuntu1 [1673 kB] Get:19 http://ftpmaster.internal/ubuntu focal/main s390x libgcc-9-dev s390x 9.2.1-21ubuntu1 [704 kB] Get:20 http://ftpmaster.internal/ubuntu focal/main s390x gcc-9 s390x 9.2.1-21ubuntu1 [8095 kB] Get:21 http://ftpmaster.internal/ubuntu focal/main s390x cpp-9 s390x 9.2.1-21ubuntu1 [7454 kB] Get:22 http://ftpmaster.internal/ubuntu focal/main s390x libstdc++6 s390x 9.2.1-21ubuntu1 [504 kB] Get:23 http://ftpmaster.internal/ubuntu focal/main s390x libc6 s390x 2.30-0ubuntu3 [2289 kB] Get:24 http://ftpmaster.internal/ubuntu focal/main s390x base-files s390x 11ubuntu2 [60.0 kB] Get:25 http://ftpmaster.internal/ubuntu focal/main s390x debianutils s390x 4.9.1 [85.7 kB] Get:26 http://ftpmaster.internal/ubuntu focal/main s390x bash s390x 5.0-5ubuntu1 [622 kB] Get:27 http://ftpmaster.internal/ubuntu focal/main s390x bsdutils s390x 1:2.34-0.1ubuntu4 [61.5 kB] Get:28 http://ftpmaster.internal/ubuntu focal/main s390x gzip s390x 1.10-0ubuntu4 [95.8 kB] Get:29 http://ftpmaster.internal/ubuntu focal/main s390x hostname s390x 3.23 [11.1 kB] Get:30 http://ftpmaster.internal/ubuntu focal/main s390x ncurses-bin s390x 6.1+20191019-1ubuntu1 [169 kB] Get:31 http://ftpmaster.internal/ubuntu focal/main s390x perl-modules-5.30 all 5.30.0-9 [2739 kB] Get:32 http://ftpmaster.internal/ubuntu focal/main s390x libperl5.30 s390x 5.30.0-9 [3782 kB] Get:33 http://ftpmaster.internal/ubuntu focal/main s390x perl s390x 5.30.0-9 [224 kB] Get:34 http://ftpmaster.internal/ubuntu focal/main s390x perl-base s390x 5.30.0-9 [1423 kB] Get:35 http://ftpmaster.internal/ubuntu focal/main s390x bzip2 s390x 1.0.8-2 [33.3 kB] Get:36 http://ftpmaster.internal/ubuntu focal/main s390x libbz2-1.0 s390x 1.0.8-2 [32.6 kB] Get:37 http://ftpmaster.internal/ubuntu focal/main s390x libblkid1 s390x 2.34-0.1ubuntu4 [128 kB] Get:38 http://ftpmaster.internal/ubuntu focal/main s390x libuuid1 s390x 2.34-0.1ubuntu4 [20.5 kB] Get:39 http://ftpmaster.internal/ubuntu focal/main s390x libfdisk1 s390x 2.34-0.1ubuntu4 [160 kB] Get:40 http://ftpmaster.internal/ubuntu focal/main s390x libpcre2-8-0 s390x 10.34-7 [109 kB] Get:41 http://ftpmaster.internal/ubuntu focal/main s390x libselinux1 s390x 3.0-1 [65.6 kB] Get:42 http://ftpmaster.internal/ubuntu focal/main s390x libmount1 s390x 2.34-0.1ubuntu4 [137 kB] Get:43 http://ftpmaster.internal/ubuntu focal/main s390x libncurses6 s390x 6.1+20191019-1ubuntu1 [94.7 kB] Get:44 http://ftpmaster.internal/ubuntu focal/main s390x libtinfo6 s390x 6.1+20191019-1ubuntu1 [83.6 kB] Get:45 http://ftpmaster.internal/ubuntu focal/main s390x libncursesw6 s390x 6.1+20191019-1ubuntu1 [122 kB] Get:46 http://ftpmaster.internal/ubuntu focal/main s390x libsmartcols1 s390x 2.34-0.1ubuntu4 [93.6 kB] Get:47 http://ftpmaster.internal/ubuntu focal/main s390x fdisk s390x 2.34-0.1ubuntu4 [113 kB] Get:48 http://ftpmaster.internal/ubuntu focal/main s390x util-linux s390x 2.34-0.1ubuntu4 [981 kB] Get:49 http://ftpmaster.internal/ubuntu focal/main s390x libdebconfclient0 s390x 0.250ubuntu2 [6152 B] Get:50 http://ftpmaster.internal/ubuntu focal/main s390x base-passwd s390x 3.5.47 [46.7 kB] Get:51 http://ftpmaster.internal/ubuntu focal/main s390x libc-bin s390x 2.30-0ubuntu3 [547 kB] Get:52 http://ftpmaster.internal/ubuntu focal/main s390x ncurses-base all 6.1+20191019-1ubuntu1 [17.9 kB] Get:53 http://ftpmaster.internal/ubuntu focal/main s390x lsb-base all 11.1.0ubuntu2 [12.1 kB] Get:54 http://ftpmaster.internal/ubuntu focal/main s390x sysvinit-utils s390x 2.96-1ubuntu1 [20.6 kB] Get:55 http://ftpmaster.internal/ubuntu focal/main s390x liblz4-1 s390x 1.9.2-2 [53.8 kB] Get:56 http://ftpmaster.internal/ubuntu focal/main s390x systemd-sysv s390x 244-3ubuntu1 [9364 B] Get:57 http://ftpmaster.internal/ubuntu focal/main s390x libacl1 s390x 2.2.53-5ubuntu1 [18.3 kB] Get:58 http://ftpmaster.internal/ubuntu focal/main s390x libapparmor1 s390x 2.13.3-7ubuntu1 [33.0 kB] Get:59 http://ftpmaster.internal/ubuntu focal/main s390x libaudit-common all 1:2.8.5-2ubuntu5 [4076 B] Get:60 http://ftpmaster.internal/ubuntu focal/main s390x libcap-ng0 s390x 0.7.9-2.1 [10.8 kB] Get:61 http://ftpmaster.internal/ubuntu focal/main s390x libaudit1 s390x 1:2.8.5-2ubuntu5 [37.3 kB] Get:62 http://ftpmaster.internal/ubuntu focal/main s390x libcap2 s390x 1:2.27-1 [14.2 kB] Get:63 http://ftpmaster.internal/ubuntu focal/main s390x libudev1 s390x 244-3ubuntu1 [71.8 kB] Get:64 http://ftpmaster.internal/ubuntu focal/main s390x libdevmapper1.02.1 s390x 2:1.02.155-2ubuntu7 [122 kB] Get:65 http://ftpmaster.internal/ubuntu focal/main s390x libjson-c4 s390x 0.13.1+dfsg-6 [27.9 kB] Get:66 http://ftpmaster.internal/ubuntu focal/main s390x libcryptsetup12 s390x 2:2.2.2-1ubuntu1 [160 kB] Get:67 http://ftpmaster.internal/ubuntu focal/main s390x libnettle7 s390x 3.5.1+really3.5.1-2 [124 kB] Get:68 http://ftpmaster.internal/ubuntu focal/main s390x libhogweed5 s390x 3.5.1+really3.5.1-2 [136 kB] Get:69 http://ftpmaster.internal/ubuntu focal/main s390x libp11-kit0 s390x 0.23.18.1-2 [172 kB] Get:70 http://ftpmaster.internal/ubuntu focal/main s390x libtasn1-6 s390x 4.15.0-2 [36.9 kB] Get:71 http://ftpmaster.internal/ubuntu focal/main s390x libgnutls30 s390x 3.6.11.1-2 [684 kB] Get:72 http://ftpmaster.internal/ubuntu focal/main s390x libkmod2 s390x 26-3ubuntu1 [40.0 kB] Get:73 http://ftpmaster.internal/ubuntu focal/main s390x libpam0g s390x 1.3.1-5ubuntu4 [52.9 kB] Get:74 http://ftpmaster.internal/ubuntu focal/main s390x libseccomp2 s390x 2.4.2-2ubuntu1 [38.6 kB] Get:75 http://ftpmaster.internal/ubuntu focal/main s390x mount s390x 2.34-0.1ubuntu4 [110 kB] Get:76 http://ftpmaster.internal/ubuntu focal/main s390x systemd s390x 244-3ubuntu1 [3325 kB] Get:77 http://ftpmaster.internal/ubuntu focal/main s390x libsystemd0 s390x 244-3ubuntu1 [239 kB] Get:78 http://ftpmaster.internal/ubuntu focal/main s390x libzstd1 s390x 1.4.4+dfsg-1 [217 kB] Get:79 http://ftpmaster.internal/ubuntu focal/main s390x libapt-pkg5.90 s390x 1.9.5 [789 kB] Get:80 http://ftpmaster.internal/ubuntu focal/main s390x libgcrypt20 s390x 1.8.5-3ubuntu1 [349 kB] Get:81 http://ftpmaster.internal/ubuntu focal/main s390x gpgv s390x 2.2.17-3ubuntu1 [186 kB] Get:82 http://ftpmaster.internal/ubuntu focal/main s390x apt s390x 1.9.5 [1242 kB] Get:83 http://ftpmaster.internal/ubuntu focal/main s390x libpam-modules-bin s390x 1.3.1-5ubuntu4 [36.5 kB] Get:84 http://ftpmaster.internal/ubuntu focal/main s390x libpam-modules s390x 1.3.1-5ubuntu4 [242 kB] Get:85 http://ftpmaster.internal/ubuntu focal/main s390x libattr1 s390x 1:2.4.48-5 [12.4 kB] Get:86 http://ftpmaster.internal/ubuntu focal/main s390x libpam-runtime all 1.3.1-5ubuntu4 [37.3 kB] Get:87 http://ftpmaster.internal/ubuntu focal/main s390x libsepol1 s390x 3.0-1 [227 kB] Get:88 http://ftpmaster.internal/ubuntu focal/main s390x libsemanage-common all 3.0-1 [9880 B] Get:89 http://ftpmaster.internal/ubuntu focal/main s390x libsemanage1 s390x 3.0-1 [80.3 kB] Get:90 http://ftpmaster.internal/ubuntu focal/main s390x sensible-utils all 0.0.12+nmu1 [15.0 kB] Get:91 http://ftpmaster.internal/ubuntu focal/main s390x libsqlite3-0 s390x 3.30.1-1ubuntu1 [504 kB] Get:92 http://ftpmaster.internal/ubuntu focal/main s390x gpg s390x 2.2.17-3ubuntu1 [442 kB] Get:93 http://ftpmaster.internal/ubuntu focal/main s390x gpgconf s390x 2.2.17-3ubuntu1 [119 kB] Get:94 http://ftpmaster.internal/ubuntu focal/main s390x gpg-agent s390x 2.2.17-3ubuntu1 [217 kB] Get:95 http://ftpmaster.internal/ubuntu focal/main s390x liblockfile-bin s390x 1.16-1.1 [11.4 kB] Get:96 http://ftpmaster.internal/ubuntu focal/main s390x liblockfile1 s390x 1.16-1.1 [6476 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 58.1 MB in 1s (81.8 MB/s) (Reading database ... 12530 files and directories currently installed.) Preparing to unpack .../0-libc6-dev_2.30-0ubuntu3_s390x.deb ... Unpacking libc6-dev:s390x (2.30-0ubuntu3) over (2.30-0ubuntu2) ... Preparing to unpack .../1-libc-dev-bin_2.30-0ubuntu3_s390x.deb ... Unpacking libc-dev-bin (2.30-0ubuntu3) over (2.30-0ubuntu2) ... Preparing to unpack .../2-linux-libc-dev_5.3.0-24.26_s390x.deb ... Unpacking linux-libc-dev:s390x (5.3.0-24.26) over (5.3.0-18.19) ... Selecting previously unselected package libisl22:s390x. Preparing to unpack .../3-libisl22_0.22-2_s390x.deb ... Unpacking libisl22:s390x (0.22-2) ... Preparing to unpack .../4-libcc1-0_9.2.1-21ubuntu1_s390x.deb ... Unpacking libcc1-0:s390x (9.2.1-21ubuntu1) over (9.2.1-9ubuntu2) ... Preparing to unpack .../5-binutils-s390x-linux-gnu_2.33.1-6ubuntu3_s390x.deb ... Unpacking binutils-s390x-linux-gnu (2.33.1-6ubuntu3) over (2.33-2ubuntu1) ... Preparing to unpack .../6-libbinutils_2.33.1-6ubuntu3_s390x.deb ... Unpacking libbinutils:s390x (2.33.1-6ubuntu3) over (2.33-2ubuntu1) ... 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Installing new version of config file /etc/issue.net ... Installing new version of config file /etc/lsb-release ... Installing new version of config file /etc/update-motd.d/50-motd-news ... Updating /root/.profile to current default. (Reading database ... 12536 files and directories currently installed.) Preparing to unpack .../debianutils_4.9.1_s390x.deb ... Unpacking debianutils (4.9.1) over (4.8.6.3) ... Setting up debianutils (4.9.1) ... (Reading database ... 12536 files and directories currently installed.) Preparing to unpack .../bash_5.0-5ubuntu1_s390x.deb ... Unpacking bash (5.0-5ubuntu1) over (5.0-4ubuntu1) ... Setting up bash (5.0-5ubuntu1) ... update-alternatives: using /usr/share/man/man7/bash-builtins.7.gz to provide /usr/share/man/man7/builtins.7.gz (builtins.7.gz) in auto mode (Reading database ... 12536 files and directories currently installed.) Preparing to unpack .../bsdutils_1%3a2.34-0.1ubuntu4_s390x.deb ... 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Setting up libperl5.30:s390x (5.30.0-9) ... Setting up libisl22:s390x (0.22-2) ... Setting up liblockfile1:s390x (1.16-1.1) ... Setting up libjson-c4:s390x (0.13.1+dfsg-6) ... Setting up libbinutils:s390x (2.33.1-6ubuntu3) ... Setting up libc-dev-bin (2.30-0ubuntu3) ... Setting up libcc1-0:s390x (9.2.1-21ubuntu1) ... Setting up gpg (2.2.17-3ubuntu1) ... Setting up libitm1:s390x (9.2.1-21ubuntu1) ... Setting up libkmod2:s390x (26-3ubuntu1) ... Setting up binutils-s390x-linux-gnu (2.33.1-6ubuntu3) ... Setting up gpg-agent (2.2.17-3ubuntu1) ... Installing new version of config file /etc/logcheck/ignore.d.server/gpg-agent ... Created symlink /etc/systemd/user/sockets.target.wants/gpg-agent-browser.socket -> /usr/lib/systemd/user/gpg-agent-browser.socket. Created symlink /etc/systemd/user/sockets.target.wants/gpg-agent-extra.socket -> /usr/lib/systemd/user/gpg-agent-extra.socket. Created symlink /etc/systemd/user/sockets.target.wants/gpg-agent-ssh.socket -> /usr/lib/systemd/user/gpg-agent-ssh.socket. Created symlink /etc/systemd/user/sockets.target.wants/gpg-agent.socket -> /usr/lib/systemd/user/gpg-agent.socket. Setting up binutils (2.33.1-6ubuntu3) ... Setting up libgcc-9-dev:s390x (9.2.1-21ubuntu1) ... Setting up perl (5.30.0-9) ... Setting up cpp-9 (9.2.1-21ubuntu1) ... Setting up libc6-dev:s390x (2.30-0ubuntu3) ... Setting up libcryptsetup12:s390x (2:2.2.2-1ubuntu1) ... Setting up gcc-9 (9.2.1-21ubuntu1) ... Setting up libstdc++-9-dev:s390x (9.2.1-21ubuntu1) ... Setting up systemd (244-3ubuntu1) ... Installing new version of config file /etc/dhcp/dhclient-enter-hooks.d/resolved ... Installing new version of config file /etc/systemd/networkd.conf ... Installing new version of config file /etc/systemd/system.conf ... Installing new version of config file /etc/systemd/user.conf ... Initializing machine ID from random generator. Setting up g++-9 (9.2.1-21ubuntu1) ... Setting up systemd-sysv (244-3ubuntu1) ... Processing triggers for libc-bin (2.30-0ubuntu3) ... RUN: /usr/share/launchpad-buildd/bin/sbuild-package PACKAGEBUILD-18348607 s390x focal -c chroot:build-PACKAGEBUILD-18348607 --arch=s390x --dist=focal --nolog reapr_1.0.18+dfsg-4.dsc Initiating build PACKAGEBUILD-18348607 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 4.4.0-170-generic #199-Ubuntu SMP Thu Nov 14 01:44:14 UTC 2019 s390x sbuild (Debian sbuild) 0.67.0 (26 Dec 2015) on bos02-s390x-007.buildd +==============================================================================+ | reapr 1.0.18+dfsg-4 (s390x) 05 Jan 2020 10:43 | +==============================================================================+ Package: reapr Version: 1.0.18+dfsg-4 Source Version: 1.0.18+dfsg-4 Distribution: focal Machine Architecture: s390x Host Architecture: s390x Build Architecture: s390x I: NOTICE: Log filtering will replace 'build/reapr-kAl4As/reapr-1.0.18+dfsg' with '<>' I: NOTICE: Log filtering will replace 'build/reapr-kAl4As' with '<>' I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-18348607/chroot-autobuild' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- reapr_1.0.18+dfsg-4.dsc exists in .; copying to chroot Check architectures ------------------- Check dependencies ------------------ Merged Build-Depends: build-essential, fakeroot Filtered Build-Depends: build-essential, fakeroot dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/<>/resolver-oLEoLo/apt_archive/sbuild-build-depends-core-dummy.deb'. Ign:1 copy:/<>/resolver-oLEoLo/apt_archive ./ InRelease Get:2 copy:/<>/resolver-oLEoLo/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-oLEoLo/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-oLEoLo/apt_archive ./ Sources [214 B] Get:5 copy:/<>/resolver-oLEoLo/apt_archive ./ Packages [527 B] Fetched 2860 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: libhogweed4 libisl21 libnettle6 libperl5.28 perl-modules-5.28 Use 'apt autoremove' to remove them. The following NEW packages will be installed: sbuild-build-depends-core-dummy 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 852 B of archives. After this operation, 0 B of additional disk space will be used. Get:1 copy:/<>/resolver-oLEoLo/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 ... 14440 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) ... Merged Build-Depends: debhelper (>= 11~), 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 (>= 11~), 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-QSogz_/apt_archive/sbuild-build-depends-reapr-dummy.deb'. Ign:1 copy:/<>/resolver-QSogz_/apt_archive ./ InRelease Get:2 copy:/<>/resolver-QSogz_/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-QSogz_/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-QSogz_/apt_archive ./ Sources [290 B] Get:5 copy:/<>/resolver-QSogz_/apt_archive ./ Packages [610 B] Fetched 3019 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: libhogweed4 libisl21 libnettle6 libperl5.28 perl-modules-5.28 Use 'apt autoremove' to remove them. The following additional packages will be installed: asciidoctor autoconf automake autopoint autotools-dev bamtools bsdmainutils debhelper dh-autoreconf dh-strip-nondeterminism dwz file fontconfig fontconfig-config fonts-dejavu-core gettext gettext-base groff-base intltool-debian libarchive-zip-perl libasn1-8-heimdal libbambamc0 libbamtools-dev libbamtools2.5.1 libblas3 libbrotli1 libbsd0 libcairo2 libcroco3 libcurl3-gnutls libcurl4 libdatrie1 libdebhelper-perl libdeflate0 libelf1 libexpat1 libfile-copy-link-perl libfile-stripnondeterminism-perl libfontconfig1 libfreetype6 libfribidi0 libgfortran5 libglib2.0-0 libgraphite2-3 libgssapi-krb5-2 libgssapi3-heimdal libharfbuzz0b libhcrypto4-heimdal libheimbase1-heimdal libheimntlm0-heimdal libhts-dev libhts2 libhx509-5-heimdal libice6 libicu63 libjbig0 libjpeg-turbo8 libjpeg8 libjsoncpp1 libk5crypto3 libkeyutils1 libkrb5-26-heimdal libkrb5-3 libkrb5support0 liblapack3 libldap-2.4-2 libldap-common liblzma-dev libmagic-mgc libmagic1 libnghttp2-14 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper1 libpipeline1 libpixman-1-0 libpsl5 libroken18-heimdal librtmp1 libruby2.5 libsasl2-2 libsasl2-modules-db libsigsegv2 libsm6 libssh-4 libsub-override-perl libtabixpp-dev libtabixpp0 libtcl8.6 libthai-data libthai0 libtiff5 libtk8.6 libtool libuchardet0 libwebp6 libwind0-heimdal libx11-6 libx11-data libxau6 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxft2 libxml2 libxrender1 libxss1 libxt6 libyaml-0-2 m4 man-db po-debconf r-base r-base-core r-cran-boot r-cran-class r-cran-cluster r-cran-codetools r-cran-foreign r-cran-kernsmooth r-cran-lattice r-cran-mass r-cran-matrix r-cran-mgcv r-cran-nlme r-cran-nnet r-cran-rpart r-cran-spatial r-cran-survival r-recommended rake ruby ruby-asciidoctor ruby-did-you-mean ruby-minitest ruby-net-telnet ruby-power-assert ruby-test-unit ruby-xmlrpc ruby2.5 rubygems-integration samtools smalt snpomatic tabix ucf unzip x11-common xdg-utils zip zlib1g-dev Suggested packages: autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois vacation dh-make gettext-doc libasprintf-dev libgettextpo-dev groff libbamtools-doc krb5-doc krb5-user liblzma-doc tcl8.6 tk8.6 libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc apparmor less www-browser libmail-box-perl elpa-ess r-doc-info | r-doc-pdf r-mathlib r-base-html ri ruby-dev bundler Recommended packages: curl | wget | lynx libarchive-cpio-perl libglib2.0-data shared-mime-info xdg-user-dirs krb5-locales publicsuffix libsasl2-modules libltdl-dev libmail-sendmail-perl r-base-html r-doc-html r-base-dev fonts-lato libjs-jquery python3 cwltool libfile-mimeinfo-perl libnet-dbus-perl libx11-protocol-perl x11-utils x11-xserver-utils The following NEW packages will be installed: asciidoctor autoconf automake autopoint autotools-dev bamtools bsdmainutils debhelper dh-autoreconf dh-strip-nondeterminism dwz file fontconfig fontconfig-config fonts-dejavu-core gettext gettext-base groff-base intltool-debian libarchive-zip-perl libasn1-8-heimdal libbambamc0 libbamtools-dev libbamtools2.5.1 libblas3 libbrotli1 libbsd0 libcairo2 libcroco3 libcurl3-gnutls libcurl4 libdatrie1 libdebhelper-perl libdeflate0 libelf1 libexpat1 libfile-copy-link-perl libfile-stripnondeterminism-perl libfontconfig1 libfreetype6 libfribidi0 libgfortran5 libglib2.0-0 libgraphite2-3 libgssapi-krb5-2 libgssapi3-heimdal libharfbuzz0b libhcrypto4-heimdal libheimbase1-heimdal libheimntlm0-heimdal libhts-dev libhts2 libhx509-5-heimdal libice6 libicu63 libjbig0 libjpeg-turbo8 libjpeg8 libjsoncpp1 libk5crypto3 libkeyutils1 libkrb5-26-heimdal libkrb5-3 libkrb5support0 liblapack3 libldap-2.4-2 libldap-common liblzma-dev libmagic-mgc libmagic1 libnghttp2-14 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper1 libpipeline1 libpixman-1-0 libpsl5 libroken18-heimdal librtmp1 libruby2.5 libsasl2-2 libsasl2-modules-db libsigsegv2 libsm6 libssh-4 libsub-override-perl libtabixpp-dev libtabixpp0 libtcl8.6 libthai-data libthai0 libtiff5 libtk8.6 libtool libuchardet0 libwebp6 libwind0-heimdal libx11-6 libx11-data libxau6 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxft2 libxml2 libxrender1 libxss1 libxt6 libyaml-0-2 m4 man-db po-debconf r-base r-base-core r-cran-boot r-cran-class r-cran-cluster r-cran-codetools r-cran-foreign r-cran-kernsmooth r-cran-lattice r-cran-mass r-cran-matrix r-cran-mgcv r-cran-nlme r-cran-nnet r-cran-rpart r-cran-spatial r-cran-survival r-recommended rake ruby ruby-asciidoctor ruby-did-you-mean ruby-minitest ruby-net-telnet ruby-power-assert ruby-test-unit ruby-xmlrpc ruby2.5 rubygems-integration samtools sbuild-build-depends-reapr-dummy smalt snpomatic tabix ucf unzip x11-common xdg-utils zip zlib1g-dev 0 upgraded, 156 newly installed, 0 to remove and 0 not upgraded. Need to get 78.4 MB of archives. After this operation, 201 MB of additional disk space will be used. Get:1 copy:/<>/resolver-QSogz_/apt_archive ./ sbuild-build-depends-reapr-dummy 0.invalid.0 [944 B] Get:2 http://ftpmaster.internal/ubuntu focal/main s390x libbsd0 s390x 0.10.0-1 [43.7 kB] Get:3 http://ftpmaster.internal/ubuntu focal/main s390x bsdmainutils s390x 11.1.2ubuntu2 [181 kB] Get:4 http://ftpmaster.internal/ubuntu focal/main s390x libuchardet0 s390x 0.0.6-3 [64.5 kB] Get:5 http://ftpmaster.internal/ubuntu focal/main s390x groff-base s390x 1.22.4-4 [824 kB] Get:6 http://ftpmaster.internal/ubuntu focal/main s390x libpipeline1 s390x 1.5.1-3 [26.2 kB] Get:7 http://ftpmaster.internal/ubuntu focal/main s390x man-db s390x 2.9.0-2 [1103 kB] Get:8 http://ftpmaster.internal/ubuntu focal/main s390x libmagic-mgc s390x 1:5.37-6 [210 kB] Get:9 http://ftpmaster.internal/ubuntu focal/main s390x libmagic1 s390x 1:5.37-6 [72.3 kB] Get:10 http://ftpmaster.internal/ubuntu focal/main s390x file s390x 1:5.37-6 [23.0 kB] Get:11 http://ftpmaster.internal/ubuntu focal/main s390x libelf1 s390x 0.176-1.1 [41.4 kB] Get:12 http://ftpmaster.internal/ubuntu focal/main s390x libexpat1 s390x 2.2.9-1 [69.8 kB] Get:13 http://ftpmaster.internal/ubuntu focal/main s390x libfribidi0 s390x 1.0.7-1.1 [24.5 kB] Get:14 http://ftpmaster.internal/ubuntu focal/main s390x libglib2.0-0 s390x 2.63.3-1 [1176 kB] Get:15 http://ftpmaster.internal/ubuntu focal/main s390x libicu63 s390x 63.2-2 [8044 kB] Get:16 http://ftpmaster.internal/ubuntu focal/main s390x libxml2 s390x 2.9.4+dfsg1-8ubuntu1 [664 kB] Get:17 http://ftpmaster.internal/ubuntu focal/main s390x libyaml-0-2 s390x 0.2.2-1 [42.3 kB] Get:18 http://ftpmaster.internal/ubuntu focal/main s390x ucf all 3.0038+nmu1 [51.6 kB] Get:19 http://ftpmaster.internal/ubuntu focal/main s390x gettext-base s390x 0.19.8.1-10 [49.1 kB] Get:20 http://ftpmaster.internal/ubuntu focal/main s390x libkrb5support0 s390x 1.17-6 [30.4 kB] Get:21 http://ftpmaster.internal/ubuntu focal/main s390x libk5crypto3 s390x 1.17-6 [77.9 kB] Get:22 http://ftpmaster.internal/ubuntu focal/main s390x libkeyutils1 s390x 1.6-6ubuntu1 [9848 B] Get:23 http://ftpmaster.internal/ubuntu focal/main s390x libkrb5-3 s390x 1.17-6 [308 kB] Get:24 http://ftpmaster.internal/ubuntu focal/main s390x libgssapi-krb5-2 s390x 1.17-6 [110 kB] Get:25 http://ftpmaster.internal/ubuntu focal/main s390x libpsl5 s390x 0.20.2-2 [49.8 kB] Get:26 http://ftpmaster.internal/ubuntu focal/main s390x libxau6 s390x 1:1.0.9-0ubuntu1 [7212 B] Get:27 http://ftpmaster.internal/ubuntu focal/main s390x libxdmcp6 s390x 1:1.1.3-0ubuntu1 [10.4 kB] Get:28 http://ftpmaster.internal/ubuntu focal/main s390x libxcb1 s390x 1.13.1-2 [43.0 kB] Get:29 http://ftpmaster.internal/ubuntu focal/main s390x libx11-data all 2:1.6.8-1 [113 kB] Get:30 http://ftpmaster.internal/ubuntu focal/main s390x libx11-6 s390x 2:1.6.8-1 [542 kB] Get:31 http://ftpmaster.internal/ubuntu focal/main s390x libxext6 s390x 2:1.3.4-0ubuntu1 [27.0 kB] Get:32 http://ftpmaster.internal/ubuntu focal/main s390x rubygems-integration all 1.14 [5044 B] Get:33 http://ftpmaster.internal/ubuntu focal/main s390x rake all 12.3.3-1 [45.1 kB] Get:34 http://ftpmaster.internal/ubuntu focal/main s390x ruby-did-you-mean all 1.2.1-1 [9828 B] Get:35 http://ftpmaster.internal/ubuntu focal/main s390x ruby-minitest all 5.13.0-1 [40.9 kB] Get:36 http://ftpmaster.internal/ubuntu focal/main s390x ruby-net-telnet all 0.1.1-2 [12.6 kB] Get:37 http://ftpmaster.internal/ubuntu focal/main s390x ruby-power-assert all 1.1.1-1 [11.0 kB] Get:38 http://ftpmaster.internal/ubuntu focal/main s390x ruby-test-unit all 3.3.4-1 [73.1 kB] Get:39 http://ftpmaster.internal/ubuntu focal/main s390x ruby-xmlrpc all 0.3.0-2 [23.8 kB] Get:40 http://ftpmaster.internal/ubuntu focal/main s390x libruby2.5 s390x 2.5.7-1ubuntu1 [2981 kB] Get:41 http://ftpmaster.internal/ubuntu focal/main s390x ruby2.5 s390x 2.5.7-1ubuntu1 [48.6 kB] Get:42 http://ftpmaster.internal/ubuntu focal/main s390x ruby s390x 1:2.5.2 [5788 B] Get:43 http://ftpmaster.internal/ubuntu focal/universe s390x ruby-asciidoctor all 2.0.10-2 [166 kB] Get:44 http://ftpmaster.internal/ubuntu focal/universe s390x asciidoctor all 2.0.10-2 [40.3 kB] Get:45 http://ftpmaster.internal/ubuntu focal/main s390x libsigsegv2 s390x 2.12-2 [13.8 kB] Get:46 http://ftpmaster.internal/ubuntu focal/main s390x m4 s390x 1.4.18-4 [196 kB] Get:47 http://ftpmaster.internal/ubuntu focal/main s390x autoconf all 2.69-11ubuntu1 [321 kB] Get:48 http://ftpmaster.internal/ubuntu focal/main s390x autotools-dev all 20180224.1 [39.6 kB] Get:49 http://ftpmaster.internal/ubuntu focal/main s390x automake all 1:1.16.1-4ubuntu3 [522 kB] Get:50 http://ftpmaster.internal/ubuntu focal/main s390x autopoint all 0.19.8.1-10 [412 kB] Get:51 http://ftpmaster.internal/ubuntu focal/universe s390x libbamtools2.5.1 s390x 2.5.1+dfsg-5 [139 kB] Get:52 http://ftpmaster.internal/ubuntu focal/main s390x libjsoncpp1 s390x 1.7.4-3 [70.8 kB] Get:53 http://ftpmaster.internal/ubuntu focal/universe s390x bamtools s390x 2.5.1+dfsg-5 [153 kB] Get:54 http://ftpmaster.internal/ubuntu focal/main s390x libtool all 2.4.6-11 [194 kB] Get:55 http://ftpmaster.internal/ubuntu focal/main s390x dh-autoreconf all 19 [16.1 kB] Get:56 http://ftpmaster.internal/ubuntu focal/main s390x libdebhelper-perl all 12.7.1ubuntu1 [52.0 kB] Get:57 http://ftpmaster.internal/ubuntu focal/main s390x libarchive-zip-perl all 1.67-1 [90.4 kB] Get:58 http://ftpmaster.internal/ubuntu focal/main s390x libsub-override-perl all 0.09-2 [9532 B] Get:59 http://ftpmaster.internal/ubuntu focal/main s390x libfile-stripnondeterminism-perl all 1.6.3-1 [16.0 kB] Get:60 http://ftpmaster.internal/ubuntu focal/main s390x dh-strip-nondeterminism all 1.6.3-1 [5224 B] Get:61 http://ftpmaster.internal/ubuntu focal/main s390x dwz s390x 0.13-5 [146 kB] Get:62 http://ftpmaster.internal/ubuntu focal/main s390x libcroco3 s390x 0.6.13-1 [73.7 kB] Get:63 http://ftpmaster.internal/ubuntu focal/main s390x gettext s390x 0.19.8.1-10 [867 kB] Get:64 http://ftpmaster.internal/ubuntu focal/main s390x intltool-debian all 0.35.0+20060710.5 [24.9 kB] Get:65 http://ftpmaster.internal/ubuntu focal/main s390x po-debconf all 1.0.21 [233 kB] Get:66 http://ftpmaster.internal/ubuntu focal/main s390x debhelper all 12.7.1ubuntu1 [875 kB] Get:67 http://ftpmaster.internal/ubuntu focal/main s390x libfreetype6 s390x 2.10.1-2 [319 kB] Get:68 http://ftpmaster.internal/ubuntu focal/main s390x fonts-dejavu-core all 2.37-1 [1041 kB] Get:69 http://ftpmaster.internal/ubuntu focal/main s390x fontconfig-config all 2.13.1-2ubuntu2 [28.9 kB] Get:70 http://ftpmaster.internal/ubuntu focal/main s390x libfontconfig1 s390x 2.13.1-2ubuntu2 [108 kB] Get:71 http://ftpmaster.internal/ubuntu focal/main s390x fontconfig s390x 2.13.1-2ubuntu2 [171 kB] Get:72 http://ftpmaster.internal/ubuntu focal/main s390x libroken18-heimdal s390x 7.7.0+dfsg-1 [40.0 kB] Get:73 http://ftpmaster.internal/ubuntu focal/main s390x libasn1-8-heimdal s390x 7.7.0+dfsg-1 [148 kB] Get:74 http://ftpmaster.internal/ubuntu focal/universe s390x libbambamc0 s390x 0.0.50-3 [34.1 kB] Get:75 http://ftpmaster.internal/ubuntu focal/universe s390x libbamtools-dev s390x 2.5.1+dfsg-5 [19.8 kB] Get:76 http://ftpmaster.internal/ubuntu focal/main s390x libblas3 s390x 3.9.0-1 [124 kB] Get:77 http://ftpmaster.internal/ubuntu focal/main s390x libbrotli1 s390x 1.0.7-5 [260 kB] Get:78 http://ftpmaster.internal/ubuntu focal/main s390x libpixman-1-0 s390x 0.38.4-0ubuntu1 [136 kB] Get:79 http://ftpmaster.internal/ubuntu focal/main s390x libxcb-render0 s390x 1.13.1-2 [14.6 kB] Get:80 http://ftpmaster.internal/ubuntu focal/main s390x libxcb-shm0 s390x 1.13.1-2 [5472 B] Get:81 http://ftpmaster.internal/ubuntu focal/main s390x libxrender1 s390x 1:0.9.10-1 [17.8 kB] Get:82 http://ftpmaster.internal/ubuntu focal/main s390x libcairo2 s390x 1.16.0-4ubuntu1 [535 kB] Get:83 http://ftpmaster.internal/ubuntu focal/main s390x libheimbase1-heimdal s390x 7.7.0+dfsg-1 [27.8 kB] Get:84 http://ftpmaster.internal/ubuntu focal/main s390x libhcrypto4-heimdal s390x 7.7.0+dfsg-1 [83.1 kB] Get:85 http://ftpmaster.internal/ubuntu focal/main s390x libwind0-heimdal s390x 7.7.0+dfsg-1 [47.4 kB] Get:86 http://ftpmaster.internal/ubuntu focal/main s390x libhx509-5-heimdal s390x 7.7.0+dfsg-1 [98.2 kB] Get:87 http://ftpmaster.internal/ubuntu focal/main s390x libkrb5-26-heimdal s390x 7.7.0+dfsg-1 [191 kB] Get:88 http://ftpmaster.internal/ubuntu focal/main s390x libheimntlm0-heimdal s390x 7.7.0+dfsg-1 [14.5 kB] Get:89 http://ftpmaster.internal/ubuntu focal/main s390x libgssapi3-heimdal s390x 7.7.0+dfsg-1 [87.6 kB] Get:90 http://ftpmaster.internal/ubuntu focal/main s390x libsasl2-modules-db s390x 2.1.27+dfsg-2 [14.6 kB] Get:91 http://ftpmaster.internal/ubuntu focal/main s390x libsasl2-2 s390x 2.1.27+dfsg-2 [47.7 kB] Get:92 http://ftpmaster.internal/ubuntu focal/main s390x libldap-common all 2.4.48+dfsg-1ubuntu3 [17.3 kB] Get:93 http://ftpmaster.internal/ubuntu focal/main s390x libldap-2.4-2 s390x 2.4.48+dfsg-1ubuntu3 [145 kB] Get:94 http://ftpmaster.internal/ubuntu focal/main s390x libnghttp2-14 s390x 1.40.0-1 [74.1 kB] Get:95 http://ftpmaster.internal/ubuntu focal/main s390x librtmp1 s390x 2.4+20151223.gitfa8646d.1-2build1 [50.9 kB] Get:96 http://ftpmaster.internal/ubuntu focal/main s390x libssh-4 s390x 0.9.0-1ubuntu5 [180 kB] Get:97 http://ftpmaster.internal/ubuntu focal/main s390x libcurl3-gnutls s390x 7.66.0-1ubuntu1 [215 kB] Get:98 http://ftpmaster.internal/ubuntu focal/main s390x libcurl4 s390x 7.66.0-1ubuntu1 [217 kB] Get:99 http://ftpmaster.internal/ubuntu focal/main s390x libdatrie1 s390x 0.2.12-3 [18.1 kB] Get:100 http://ftpmaster.internal/ubuntu focal/universe s390x libdeflate0 s390x 1.5-1 [98.5 kB] Get:101 http://ftpmaster.internal/ubuntu focal/universe s390x libfile-copy-link-perl all 0.140-2 [15.2 kB] Get:102 http://ftpmaster.internal/ubuntu focal/main s390x libgfortran5 s390x 9.2.1-21ubuntu1 [359 kB] Get:103 http://ftpmaster.internal/ubuntu focal/main s390x libgraphite2-3 s390x 1.3.13-11 [67.9 kB] Get:104 http://ftpmaster.internal/ubuntu focal/main s390x libharfbuzz0b s390x 2.6.4-1ubuntu1 [371 kB] Get:105 http://ftpmaster.internal/ubuntu focal/universe s390x libhts2 s390x 1.9-12 [290 kB] Get:106 http://ftpmaster.internal/ubuntu focal/main s390x liblzma-dev s390x 5.2.4-1 [145 kB] Get:107 http://ftpmaster.internal/ubuntu focal/main s390x zlib1g-dev s390x 1:1.2.11.dfsg-1ubuntu3 [173 kB] Get:108 http://ftpmaster.internal/ubuntu focal/universe s390x libhts-dev s390x 1.9-12 [71.8 kB] Get:109 http://ftpmaster.internal/ubuntu focal/main s390x x11-common all 1:7.7+19ubuntu12 [22.4 kB] Get:110 http://ftpmaster.internal/ubuntu focal/main s390x libice6 s390x 2:1.0.10-0ubuntu1 [36.8 kB] Get:111 http://ftpmaster.internal/ubuntu focal/main s390x libjpeg-turbo8 s390x 2.0.3-0ubuntu1 [102 kB] Get:112 http://ftpmaster.internal/ubuntu focal/main s390x libjpeg8 s390x 8c-2ubuntu8 [2142 B] Get:113 http://ftpmaster.internal/ubuntu focal/main s390x liblapack3 s390x 3.9.0-1 [1707 kB] Get:114 http://ftpmaster.internal/ubuntu focal/main s390x libthai-data all 0.1.28-3 [134 kB] Get:115 http://ftpmaster.internal/ubuntu focal/main s390x libthai0 s390x 0.1.28-3 [18.1 kB] Get:116 http://ftpmaster.internal/ubuntu focal/main s390x libpango-1.0-0 s390x 1.44.7-1 [156 kB] Get:117 http://ftpmaster.internal/ubuntu focal/main s390x libpangoft2-1.0-0 s390x 1.44.7-1 [32.3 kB] Get:118 http://ftpmaster.internal/ubuntu focal/main s390x libpangocairo-1.0-0 s390x 1.44.7-1 [22.5 kB] Get:119 http://ftpmaster.internal/ubuntu focal/main s390x libpaper1 s390x 1.1.28 [12.7 kB] Get:120 http://ftpmaster.internal/ubuntu focal/main s390x libpaper-utils s390x 1.1.28 [8184 B] Get:121 http://ftpmaster.internal/ubuntu focal/main s390x libsm6 s390x 2:1.2.3-1 [15.2 kB] Get:122 http://ftpmaster.internal/ubuntu focal/universe s390x libtabixpp0 s390x 1.0.0-4 [7564 B] Get:123 http://ftpmaster.internal/ubuntu focal/universe s390x libtabixpp-dev s390x 1.0.0-4 [6456 B] Get:124 http://ftpmaster.internal/ubuntu focal/main s390x libtcl8.6 s390x 8.6.10+dfsg-1 [838 kB] Get:125 http://ftpmaster.internal/ubuntu focal/main s390x libjbig0 s390x 2.1-3.1build1 [26.3 kB] Get:126 http://ftpmaster.internal/ubuntu focal/main s390x libwebp6 s390x 0.6.1-2 [149 kB] Get:127 http://ftpmaster.internal/ubuntu focal/main s390x libtiff5 s390x 4.1.0+git191117-1 [151 kB] Get:128 http://ftpmaster.internal/ubuntu focal/main s390x libxft2 s390x 2.3.3-0ubuntu1 [36.8 kB] Get:129 http://ftpmaster.internal/ubuntu focal/main s390x libxss1 s390x 1:1.2.3-1 [7972 B] Get:130 http://ftpmaster.internal/ubuntu focal/main s390x libtk8.6 s390x 8.6.10-1 [672 kB] Get:131 http://ftpmaster.internal/ubuntu focal/main s390x libxt6 s390x 1:1.1.5-1 [147 kB] Get:132 http://ftpmaster.internal/ubuntu focal/main s390x zip s390x 3.0-11build1 [157 kB] Get:133 http://ftpmaster.internal/ubuntu focal/main s390x unzip s390x 6.0-25ubuntu1 [157 kB] Get:134 http://ftpmaster.internal/ubuntu focal/main s390x xdg-utils all 1.1.3-1ubuntu2 [60.5 kB] Get:135 http://ftpmaster.internal/ubuntu focal/universe s390x r-base-core s390x 3.6.1-7 [24.3 MB] Get:136 http://ftpmaster.internal/ubuntu focal/universe s390x r-cran-boot all 1.3-23-2 [616 kB] Get:137 http://ftpmaster.internal/ubuntu focal/universe s390x r-cran-cluster s390x 2.1.0-2 [523 kB] Get:138 http://ftpmaster.internal/ubuntu focal/universe s390x r-cran-foreign s390x 0.8.72-1 [228 kB] Get:139 http://ftpmaster.internal/ubuntu focal/universe s390x r-cran-mass s390x 7.3-51.4-2 [1111 kB] Get:140 http://ftpmaster.internal/ubuntu focal/universe s390x r-cran-kernsmooth s390x 2.23-16-1+1 [89.9 kB] Get:141 http://ftpmaster.internal/ubuntu focal/universe s390x r-cran-lattice s390x 0.20-38-1 [1109 kB] Get:142 http://ftpmaster.internal/ubuntu focal/universe s390x r-cran-nlme s390x 3.1.142-1 [2214 kB] Get:143 http://ftpmaster.internal/ubuntu focal/universe s390x r-cran-matrix s390x 1.2-18-1 [3431 kB] Get:144 http://ftpmaster.internal/ubuntu focal/universe s390x r-cran-mgcv s390x 1.8-31-1 [2712 kB] Get:145 http://ftpmaster.internal/ubuntu focal/universe s390x r-cran-survival s390x 3.1-7-1 [7389 kB] Get:146 http://ftpmaster.internal/ubuntu focal/universe s390x r-cran-rpart s390x 4.1-15-2 [678 kB] Get:147 http://ftpmaster.internal/ubuntu focal/universe s390x r-cran-class s390x 7.3-15-1 [86.4 kB] Get:148 http://ftpmaster.internal/ubuntu focal/universe s390x r-cran-nnet s390x 7.3-12-2build2 [110 kB] Get:149 http://ftpmaster.internal/ubuntu focal/universe s390x r-cran-spatial s390x 7.3-11-2build2 [126 kB] Get:150 http://ftpmaster.internal/ubuntu focal/universe s390x r-cran-codetools all 0.2-16-1 [89.3 kB] Get:151 http://ftpmaster.internal/ubuntu focal/universe s390x r-recommended all 3.6.1-7 [2816 B] Get:152 http://ftpmaster.internal/ubuntu focal/universe s390x r-base all 3.6.1-7 [9312 B] Get:153 http://ftpmaster.internal/ubuntu focal/universe s390x samtools s390x 1.9-7 [401 kB] Get:154 http://ftpmaster.internal/ubuntu focal/universe s390x smalt s390x 0.7.6-9 [107 kB] Get:155 http://ftpmaster.internal/ubuntu focal/universe s390x snpomatic s390x 1.0-4 [71.5 kB] Get:156 http://ftpmaster.internal/ubuntu focal/universe s390x tabix s390x 1.9-12 [275 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 78.4 MB in 5s (15.8 MB/s) Selecting previously unselected package libbsd0:s390x. (Reading database ... 14440 files and directories currently installed.) Preparing to unpack .../000-libbsd0_0.10.0-1_s390x.deb ... Unpacking libbsd0:s390x (0.10.0-1) ... Selecting previously unselected package bsdmainutils. Preparing to unpack .../001-bsdmainutils_11.1.2ubuntu2_s390x.deb ... Unpacking bsdmainutils (11.1.2ubuntu2) ... Selecting previously unselected package libuchardet0:s390x. Preparing to unpack .../002-libuchardet0_0.0.6-3_s390x.deb ... Unpacking libuchardet0:s390x (0.0.6-3) ... Selecting previously unselected package groff-base. Preparing to unpack .../003-groff-base_1.22.4-4_s390x.deb ... Unpacking groff-base (1.22.4-4) ... Selecting previously unselected package libpipeline1:s390x. Preparing to unpack .../004-libpipeline1_1.5.1-3_s390x.deb ... Unpacking libpipeline1:s390x (1.5.1-3) ... Selecting previously unselected package man-db. Preparing to unpack .../005-man-db_2.9.0-2_s390x.deb ... Unpacking man-db (2.9.0-2) ... 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Unpacking libcroco3:s390x (0.6.13-1) ... Selecting previously unselected package gettext. Preparing to unpack .../061-gettext_0.19.8.1-10_s390x.deb ... Unpacking gettext (0.19.8.1-10) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../062-intltool-debian_0.35.0+20060710.5_all.deb ... Unpacking intltool-debian (0.35.0+20060710.5) ... Selecting previously unselected package po-debconf. Preparing to unpack .../063-po-debconf_1.0.21_all.deb ... Unpacking po-debconf (1.0.21) ... Selecting previously unselected package debhelper. Preparing to unpack .../064-debhelper_12.7.1ubuntu1_all.deb ... Unpacking debhelper (12.7.1ubuntu1) ... Selecting previously unselected package libfreetype6:s390x. Preparing to unpack .../065-libfreetype6_2.10.1-2_s390x.deb ... Unpacking libfreetype6:s390x (2.10.1-2) ... Selecting previously unselected package fonts-dejavu-core. Preparing to unpack .../066-fonts-dejavu-core_2.37-1_all.deb ... 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Unpacking libxcb-render0:s390x (1.13.1-2) ... Selecting previously unselected package libxcb-shm0:s390x. Preparing to unpack .../078-libxcb-shm0_1.13.1-2_s390x.deb ... Unpacking libxcb-shm0:s390x (1.13.1-2) ... Selecting previously unselected package libxrender1:s390x. Preparing to unpack .../079-libxrender1_1%3a0.9.10-1_s390x.deb ... Unpacking libxrender1:s390x (1:0.9.10-1) ... Selecting previously unselected package libcairo2:s390x. Preparing to unpack .../080-libcairo2_1.16.0-4ubuntu1_s390x.deb ... Unpacking libcairo2:s390x (1.16.0-4ubuntu1) ... Selecting previously unselected package libheimbase1-heimdal:s390x. Preparing to unpack .../081-libheimbase1-heimdal_7.7.0+dfsg-1_s390x.deb ... Unpacking libheimbase1-heimdal:s390x (7.7.0+dfsg-1) ... Selecting previously unselected package libhcrypto4-heimdal:s390x. Preparing to unpack .../082-libhcrypto4-heimdal_7.7.0+dfsg-1_s390x.deb ... Unpacking libhcrypto4-heimdal:s390x (7.7.0+dfsg-1) ... Selecting previously unselected package libwind0-heimdal:s390x. Preparing to unpack .../083-libwind0-heimdal_7.7.0+dfsg-1_s390x.deb ... Unpacking libwind0-heimdal:s390x (7.7.0+dfsg-1) ... Selecting previously unselected package libhx509-5-heimdal:s390x. Preparing to unpack .../084-libhx509-5-heimdal_7.7.0+dfsg-1_s390x.deb ... Unpacking libhx509-5-heimdal:s390x (7.7.0+dfsg-1) ... Selecting previously unselected package libkrb5-26-heimdal:s390x. Preparing to unpack .../085-libkrb5-26-heimdal_7.7.0+dfsg-1_s390x.deb ... Unpacking libkrb5-26-heimdal:s390x (7.7.0+dfsg-1) ... Selecting previously unselected package libheimntlm0-heimdal:s390x. Preparing to unpack .../086-libheimntlm0-heimdal_7.7.0+dfsg-1_s390x.deb ... Unpacking libheimntlm0-heimdal:s390x (7.7.0+dfsg-1) ... Selecting previously unselected package libgssapi3-heimdal:s390x. Preparing to unpack .../087-libgssapi3-heimdal_7.7.0+dfsg-1_s390x.deb ... Unpacking libgssapi3-heimdal:s390x (7.7.0+dfsg-1) ... Selecting previously unselected package libsasl2-modules-db:s390x. Preparing to unpack .../088-libsasl2-modules-db_2.1.27+dfsg-2_s390x.deb ... Unpacking libsasl2-modules-db:s390x (2.1.27+dfsg-2) ... Selecting previously unselected package libsasl2-2:s390x. Preparing to unpack .../089-libsasl2-2_2.1.27+dfsg-2_s390x.deb ... Unpacking libsasl2-2:s390x (2.1.27+dfsg-2) ... Selecting previously unselected package libldap-common. Preparing to unpack .../090-libldap-common_2.4.48+dfsg-1ubuntu3_all.deb ... Unpacking libldap-common (2.4.48+dfsg-1ubuntu3) ... Selecting previously unselected package libldap-2.4-2:s390x. Preparing to unpack .../091-libldap-2.4-2_2.4.48+dfsg-1ubuntu3_s390x.deb ... Unpacking libldap-2.4-2:s390x (2.4.48+dfsg-1ubuntu3) ... Selecting previously unselected package libnghttp2-14:s390x. Preparing to unpack .../092-libnghttp2-14_1.40.0-1_s390x.deb ... Unpacking libnghttp2-14:s390x (1.40.0-1) ... Selecting previously unselected package librtmp1:s390x. Preparing to unpack .../093-librtmp1_2.4+20151223.gitfa8646d.1-2build1_s390x.deb ... Unpacking librtmp1:s390x (2.4+20151223.gitfa8646d.1-2build1) ... Selecting previously unselected package libssh-4:s390x. Preparing to unpack .../094-libssh-4_0.9.0-1ubuntu5_s390x.deb ... Unpacking libssh-4:s390x (0.9.0-1ubuntu5) ... Selecting previously unselected package libcurl3-gnutls:s390x. Preparing to unpack .../095-libcurl3-gnutls_7.66.0-1ubuntu1_s390x.deb ... Unpacking libcurl3-gnutls:s390x (7.66.0-1ubuntu1) ... Selecting previously unselected package libcurl4:s390x. Preparing to unpack .../096-libcurl4_7.66.0-1ubuntu1_s390x.deb ... Unpacking libcurl4:s390x (7.66.0-1ubuntu1) ... Selecting previously unselected package libdatrie1:s390x. Preparing to unpack .../097-libdatrie1_0.2.12-3_s390x.deb ... Unpacking libdatrie1:s390x (0.2.12-3) ... Selecting previously unselected package libdeflate0. Preparing to unpack .../098-libdeflate0_1.5-1_s390x.deb ... Unpacking libdeflate0 (1.5-1) ... 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Unpacking liblzma-dev:s390x (5.2.4-1) ... Selecting previously unselected package zlib1g-dev:s390x. Preparing to unpack .../105-zlib1g-dev_1%3a1.2.11.dfsg-1ubuntu3_s390x.deb ... Unpacking zlib1g-dev:s390x (1:1.2.11.dfsg-1ubuntu3) ... Selecting previously unselected package libhts-dev:s390x. Preparing to unpack .../106-libhts-dev_1.9-12_s390x.deb ... Unpacking libhts-dev:s390x (1.9-12) ... Selecting previously unselected package x11-common. Preparing to unpack .../107-x11-common_1%3a7.7+19ubuntu12_all.deb ... dpkg-query: no packages found matching nux-tools Unpacking x11-common (1:7.7+19ubuntu12) ... Selecting previously unselected package libice6:s390x. Preparing to unpack .../108-libice6_2%3a1.0.10-0ubuntu1_s390x.deb ... Unpacking libice6:s390x (2:1.0.10-0ubuntu1) ... Selecting previously unselected package libjpeg-turbo8:s390x. Preparing to unpack .../109-libjpeg-turbo8_2.0.3-0ubuntu1_s390x.deb ... Unpacking libjpeg-turbo8:s390x (2.0.3-0ubuntu1) ... 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Selecting previously unselected package libpangocairo-1.0-0:s390x. Preparing to unpack .../116-libpangocairo-1.0-0_1.44.7-1_s390x.deb ... Unpacking libpangocairo-1.0-0:s390x (1.44.7-1) ... Selecting previously unselected package libpaper1:s390x. Preparing to unpack .../117-libpaper1_1.1.28_s390x.deb ... Unpacking libpaper1:s390x (1.1.28) ... Selecting previously unselected package libpaper-utils. Preparing to unpack .../118-libpaper-utils_1.1.28_s390x.deb ... Unpacking libpaper-utils (1.1.28) ... Selecting previously unselected package libsm6:s390x. Preparing to unpack .../119-libsm6_2%3a1.2.3-1_s390x.deb ... Unpacking libsm6:s390x (2:1.2.3-1) ... Selecting previously unselected package libtabixpp0:s390x. Preparing to unpack .../120-libtabixpp0_1.0.0-4_s390x.deb ... Unpacking libtabixpp0:s390x (1.0.0-4) ... Selecting previously unselected package libtabixpp-dev:s390x. Preparing to unpack .../121-libtabixpp-dev_1.0.0-4_s390x.deb ... Unpacking libtabixpp-dev:s390x (1.0.0-4) ... 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Selecting previously unselected package libtk8.6:s390x. Preparing to unpack .../128-libtk8.6_8.6.10-1_s390x.deb ... Unpacking libtk8.6:s390x (8.6.10-1) ... Selecting previously unselected package libxt6:s390x. Preparing to unpack .../129-libxt6_1%3a1.1.5-1_s390x.deb ... Unpacking libxt6:s390x (1:1.1.5-1) ... Selecting previously unselected package zip. Preparing to unpack .../130-zip_3.0-11build1_s390x.deb ... Unpacking zip (3.0-11build1) ... Selecting previously unselected package unzip. Preparing to unpack .../131-unzip_6.0-25ubuntu1_s390x.deb ... Unpacking unzip (6.0-25ubuntu1) ... Selecting previously unselected package xdg-utils. Preparing to unpack .../132-xdg-utils_1.1.3-1ubuntu2_all.deb ... Unpacking xdg-utils (1.1.3-1ubuntu2) ... Selecting previously unselected package r-base-core. Preparing to unpack .../133-r-base-core_3.6.1-7_s390x.deb ... Unpacking r-base-core (3.6.1-7) ... Selecting previously unselected package r-cran-boot. 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Preparing to unpack .../146-r-cran-nnet_7.3-12-2build2_s390x.deb ... Unpacking r-cran-nnet (7.3-12-2build2) ... Selecting previously unselected package r-cran-spatial. Preparing to unpack .../147-r-cran-spatial_7.3-11-2build2_s390x.deb ... Unpacking r-cran-spatial (7.3-11-2build2) ... Selecting previously unselected package r-cran-codetools. Preparing to unpack .../148-r-cran-codetools_0.2-16-1_all.deb ... Unpacking r-cran-codetools (0.2-16-1) ... Selecting previously unselected package r-recommended. Preparing to unpack .../149-r-recommended_3.6.1-7_all.deb ... Unpacking r-recommended (3.6.1-7) ... Selecting previously unselected package r-base. Preparing to unpack .../150-r-base_3.6.1-7_all.deb ... Unpacking r-base (3.6.1-7) ... Selecting previously unselected package samtools. Preparing to unpack .../151-samtools_1.9-7_s390x.deb ... Unpacking samtools (1.9-7) ... Selecting previously unselected package smalt. Preparing to unpack .../152-smalt_0.7.6-9_s390x.deb ... Unpacking smalt (0.7.6-9) ... Selecting previously unselected package snpomatic. Preparing to unpack .../153-snpomatic_1.0-4_s390x.deb ... Unpacking snpomatic (1.0-4) ... Selecting previously unselected package tabix. Preparing to unpack .../154-tabix_1.9-12_s390x.deb ... Unpacking tabix (1.9-12) ... Selecting previously unselected package sbuild-build-depends-reapr-dummy. Preparing to unpack .../155-sbuild-build-depends-reapr-dummy_0.invalid.0_s390x.deb ... Unpacking sbuild-build-depends-reapr-dummy (0.invalid.0) ... Setting up libexpat1:s390x (2.2.9-1) ... Setting up libpipeline1:s390x (1.5.1-3) ... Setting up libgraphite2-3:s390x (1.3.13-11) ... Setting up libpixman-1-0:s390x (0.38.4-0ubuntu1) ... Setting up libxau6:s390x (1:1.0.9-0ubuntu1) ... Setting up libkeyutils1:s390x (1.6-6ubuntu1) ... Setting up libpsl5:s390x (0.20.2-2) ... Setting up libfile-copy-link-perl (0.140-2) ... Setting up libdatrie1:s390x (0.2.12-3) ... Setting up ruby-power-assert (1.1.1-1) ... Setting up libmagic-mgc (1:5.37-6) ... Setting up libarchive-zip-perl (1.67-1) ... Setting up libyaml-0-2:s390x (0.2.2-1) ... Setting up libglib2.0-0:s390x (2.63.3-1) ... No schema files found: doing nothing. Setting up unzip (6.0-25ubuntu1) ... Setting up libdebhelper-perl (12.7.1ubuntu1) ... Setting up libbrotli1:s390x (1.0.7-5) ... Setting up x11-common (1:7.7+19ubuntu12) ... 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 (1.40.0-1) ... Setting up libmagic1:s390x (1:5.37-6) ... Setting up libdeflate0 (1.5-1) ... Setting up gettext-base (0.19.8.1-10) ... Setting up rubygems-integration (1.14) ... Setting up file (1:5.37-6) ... Setting up libldap-common (2.4.48+dfsg-1ubuntu3) ... Setting up libjbig0:s390x (2.1-3.1build1) ... Setting up libicu63:s390x (63.2-2) ... Setting up libkrb5support0:s390x (1.17-6) ... Setting up libsasl2-modules-db:s390x (2.1.27+dfsg-2) ... Setting up ruby-minitest (5.13.0-1) ... Setting up zip (3.0-11build1) ... Setting up autotools-dev (20180224.1) ... Setting up libblas3:s390x (3.9.0-1) ... 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 (2.10.1-2) ... Setting up ruby-test-unit (3.3.4-1) ... Setting up libx11-data (2:1.6.8-1) ... Setting up librtmp1:s390x (2.4+20151223.gitfa8646d.1-2build1) ... Setting up ruby-net-telnet (0.1.1-2) ... Setting up libsigsegv2:s390x (2.12-2) ... Setting up libfribidi0:s390x (1.0.7-1.1) ... Setting up libbambamc0 (0.0.50-3) ... Setting up libbamtools2.5.1:s390x (2.5.1+dfsg-5) ... Setting up libtcl8.6:s390x (8.6.10+dfsg-1) ... Setting up autopoint (0.19.8.1-10) ... Setting up libwebp6:s390x (0.6.1-2) ... Setting up fonts-dejavu-core (2.37-1) ... Setting up ucf (3.0038+nmu1) ... Setting up libk5crypto3:s390x (1.17-6) ... Setting up libjpeg-turbo8:s390x (2.0.3-0ubuntu1) ... Setting up libsasl2-2:s390x (2.1.27+dfsg-2) ... Setting up libgfortran5:s390x (9.2.1-21ubuntu1) ... Setting up libroken18-heimdal:s390x (7.7.0+dfsg-1) ... Setting up liblzma-dev:s390x (5.2.4-1) ... Setting up zlib1g-dev:s390x (1:1.2.11.dfsg-1ubuntu3) ... Setting up snpomatic (1.0-4) ... Setting up libuchardet0:s390x (0.0.6-3) ... Setting up libsub-override-perl (0.09-2) ... Setting up libharfbuzz0b:s390x (2.6.4-1ubuntu1) ... Setting up libthai-data (0.1.28-3) ... Setting up libkrb5-3:s390x (1.17-6) ... Setting up ruby-did-you-mean (1.2.1-1) ... Setting up libbsd0:s390x (0.10.0-1) ... Setting up libelf1:s390x (0.176-1.1) ... Setting up ruby-xmlrpc (0.3.0-2) ... Setting up libxml2:s390x (2.9.4+dfsg1-8ubuntu1) ... Setting up xdg-utils (1.1.3-1ubuntu2) ... Setting up libjsoncpp1:s390x (1.7.4-3) ... Setting up libheimbase1-heimdal:s390x (7.7.0+dfsg-1) ... Setting up libjpeg8:s390x (8c-2ubuntu8) ... Setting up libfile-stripnondeterminism-perl (1.6.3-1) ... 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 (2:1.0.10-0ubuntu1) ... Setting up libxdmcp6:s390x (1:1.1.3-0ubuntu1) ... Setting up liblapack3:s390x (3.9.0-1) ... 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 (1.13.1-2) ... Setting up libtool (2.4.6-11) ... Setting up libxcb-render0:s390x (1.13.1-2) ... Setting up fontconfig-config (2.13.1-2ubuntu2) ... Setting up libasn1-8-heimdal:s390x (7.7.0+dfsg-1) ... Setting up m4 (1.4.18-4) ... Setting up libxcb-shm0:s390x (1.13.1-2) ... Setting up libpaper-utils (1.1.28) ... Setting up libhcrypto4-heimdal:s390x (7.7.0+dfsg-1) ... Setting up libthai0:s390x (0.1.28-3) ... Setting up libwind0-heimdal:s390x (7.7.0+dfsg-1) ... Setting up libbamtools-dev:s390x (2.5.1+dfsg-5) ... Setting up bsdmainutils (11.1.2ubuntu2) ... update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode Setting up libgssapi-krb5-2:s390x (1.17-6) ... Setting up libcroco3:s390x (0.6.13-1) ... Setting up libssh-4:s390x (0.9.0-1ubuntu5) ... Setting up autoconf (2.69-11ubuntu1) ... Setting up dh-strip-nondeterminism (1.6.3-1) ... Setting up dwz (0.13-5) ... Setting up groff-base (1.22.4-4) ... Setting up bamtools (2.5.1+dfsg-5) ... Setting up libx11-6:s390x (2:1.6.8-1) ... Setting up libtiff5:s390x (4.1.0+git191117-1) ... Setting up libfontconfig1:s390x (2.13.1-2ubuntu2) ... Setting up libsm6:s390x (2:1.2.3-1) ... Setting up automake (1:1.16.1-4ubuntu3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up fontconfig (2.13.1-2ubuntu2) ... Regenerating fonts cache... done. Setting up gettext (0.19.8.1-10) ... Setting up libxrender1:s390x (1:0.9.10-1) ... Setting up libhx509-5-heimdal:s390x (7.7.0+dfsg-1) ... Setting up libpango-1.0-0:s390x (1.44.7-1) ... Setting up libxext6:s390x (2:1.3.4-0ubuntu1) ... Setting up man-db (2.9.0-2) ... 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 (1.16.0-4ubuntu1) ... Setting up intltool-debian (0.35.0+20060710.5) ... Setting up libxt6:s390x (1:1.1.5-1) ... Setting up libxss1:s390x (1:1.2.3-1) ... Setting up libpangoft2-1.0-0:s390x (1.44.7-1) ... Setting up libpangocairo-1.0-0:s390x (1.44.7-1) ... Setting up libkrb5-26-heimdal:s390x (7.7.0+dfsg-1) ... Setting up libxft2:s390x (2.3.3-0ubuntu1) ... Setting up po-debconf (1.0.21) ... Setting up libtk8.6:s390x (8.6.10-1) ... Setting up libheimntlm0-heimdal:s390x (7.7.0+dfsg-1) ... Setting up libgssapi3-heimdal:s390x (7.7.0+dfsg-1) ... Setting up libldap-2.4-2:s390x (2.4.48+dfsg-1ubuntu3) ... Setting up libcurl3-gnutls:s390x (7.66.0-1ubuntu1) ... Setting up libcurl4:s390x (7.66.0-1ubuntu1) ... Setting up tabix (1.9-12) ... Setting up libhts2:s390x (1.9-12) ... Setting up libhts-dev:s390x (1.9-12) ... Setting up samtools (1.9-7) ... Setting up r-base-core (3.6.1-7) ... Creating config file /etc/R/Renviron with new version Setting up r-cran-lattice (0.20-38-1) ... Setting up r-cran-nlme (3.1.142-1) ... Setting up r-cran-cluster (2.1.0-2) ... Setting up libtabixpp0:s390x (1.0.0-4) ... Setting up r-cran-nnet (7.3-12-2build2) ... Setting up r-cran-codetools (0.2-16-1) ... Setting up r-cran-boot (1.3-23-2) ... Setting up r-cran-spatial (7.3-11-2build2) ... Setting up r-cran-mass (7.3-51.4-2) ... Setting up r-cran-foreign (0.8.72-1) ... Setting up r-cran-matrix (1.2-18-1) ... Setting up r-cran-kernsmooth (2.23-16-1+1) ... Setting up r-cran-mgcv (1.8-31-1) ... Setting up libtabixpp-dev:s390x (1.0.0-4) ... Setting up r-cran-class (7.3-15-1) ... Setting up r-cran-survival (3.1-7-1) ... Setting up r-cran-rpart (4.1-15-2) ... Setting up r-recommended (3.6.1-7) ... Setting up r-base (3.6.1-7) ... Setting up libruby2.5:s390x (2.5.7-1ubuntu1) ... Setting up dh-autoreconf (19) ... Setting up ruby2.5 (2.5.7-1ubuntu1) ... Setting up debhelper (12.7.1ubuntu1) ... Setting up ruby (1:2.5.2) ... Setting up ruby-asciidoctor (2.0.10-2) ... Setting up rake (12.3.3-1) ... Setting up asciidoctor (2.0.10-2) ... Setting up sbuild-build-depends-reapr-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.30-0ubuntu3) ... Processing triggers for systemd (244-3ubuntu1) ... +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 4.4.0-170-generic s390x (s390x) Toolchain package versions: binutils_2.33.1-6ubuntu3 dpkg-dev_1.19.7ubuntu2 g++-9_9.2.1-21ubuntu1 gcc-9_9.2.1-21ubuntu1 libc6-dev_2.30-0ubuntu3 libstdc++-9-dev_9.2.1-21ubuntu1 libstdc++6_9.2.1-21ubuntu1 linux-libc-dev_5.3.0-24.26 Package versions: adduser_3.118ubuntu1 advancecomp_2.1-2.1 apt_1.9.5 asciidoctor_2.0.10-2 autoconf_2.69-11ubuntu1 automake_1:1.16.1-4ubuntu3 autopoint_0.19.8.1-10 autotools-dev_20180224.1 bamtools_2.5.1+dfsg-5 base-files_11ubuntu2 base-passwd_3.5.47 bash_5.0-5ubuntu1 binutils_2.33.1-6ubuntu3 binutils-common_2.33.1-6ubuntu3 binutils-s390x-linux-gnu_2.33.1-6ubuntu3 bsdmainutils_11.1.2ubuntu2 bsdutils_1:2.34-0.1ubuntu4 build-essential_12.8ubuntu1 bzip2_1.0.8-2 ca-certificates_20190110 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libuuid1_2.34-0.1ubuntu4 libwebp6_0.6.1-2 libwind0-heimdal_7.7.0+dfsg-1 libx11-6_2:1.6.8-1 libx11-data_2:1.6.8-1 libxau6_1:1.0.9-0ubuntu1 libxcb-render0_1.13.1-2 libxcb-shm0_1.13.1-2 libxcb1_1.13.1-2 libxdmcp6_1:1.1.3-0ubuntu1 libxext6_2:1.3.4-0ubuntu1 libxft2_2.3.3-0ubuntu1 libxml2_2.9.4+dfsg1-8ubuntu1 libxrender1_1:0.9.10-1 libxss1_1:1.2.3-1 libxt6_1:1.1.5-1 libyaml-0-2_0.2.2-1 libzstd1_1.4.4+dfsg-1 linux-libc-dev_5.3.0-24.26 lockfile-progs_0.1.18 login_1:4.5-1.1ubuntu4 logsave_1.45.3-4ubuntu2 lsb-base_11.1.0ubuntu2 m4_1.4.18-4 make_4.2.1-1.2 man-db_2.9.0-2 mawk_1.3.3-17ubuntu3 mount_2.34-0.1ubuntu4 ncurses-base_6.1+20191019-1ubuntu1 ncurses-bin_6.1+20191019-1ubuntu1 openssl_1.1.1c-1ubuntu4 optipng_0.7.7-1 passwd_1:4.5-1.1ubuntu4 patch_2.7.6-6 perl_5.30.0-9 perl-base_5.30.0-9 perl-modules-5.28_5.28.1-6build1 perl-modules-5.30_5.30.0-9 pinentry-curses_1.1.0-3 pkgbinarymangler_144 po-debconf_1.0.21 policyrcd-script-zg2_0.1-3 procps_2:3.3.15-2ubuntu3 r-base_3.6.1-7 r-base-core_3.6.1-7 r-cran-boot_1.3-23-2 r-cran-class_7.3-15-1 r-cran-cluster_2.1.0-2 r-cran-codetools_0.2-16-1 r-cran-foreign_0.8.72-1 r-cran-kernsmooth_2.23-16-1+1 r-cran-lattice_0.20-38-1 r-cran-mass_7.3-51.4-2 r-cran-matrix_1.2-18-1 r-cran-mgcv_1.8-31-1 r-cran-nlme_3.1.142-1 r-cran-nnet_7.3-12-2build2 r-cran-rpart_4.1-15-2 r-cran-spatial_7.3-11-2build2 r-cran-survival_3.1-7-1 r-recommended_3.6.1-7 rake_12.3.3-1 readline-common_8.0-3 ruby_1:2.5.2 ruby-asciidoctor_2.0.10-2 ruby-did-you-mean_1.2.1-1 ruby-minitest_5.13.0-1 ruby-net-telnet_0.1.1-2 ruby-power-assert_1.1.1-1 ruby-test-unit_3.3.4-1 ruby-xmlrpc_0.3.0-2 ruby2.5_2.5.7-1ubuntu1 rubygems-integration_1.14 samtools_1.9-7 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-reapr-dummy_0.invalid.0 sed_4.7-1 sensible-utils_0.0.12+nmu1 smalt_0.7.6-9 snpomatic_1.0-4 systemd_244-3ubuntu1 systemd-sysv_244-3ubuntu1 sysvinit-utils_2.96-1ubuntu1 tabix_1.9-12 tar_1.30+dfsg-6 tzdata_2019c-3 ubuntu-keyring_2018.09.18.1 ucf_3.0038+nmu1 unzip_6.0-25ubuntu1 util-linux_2.34-0.1ubuntu4 x11-common_1:7.7+19ubuntu12 xdg-utils_1.1.3-1ubuntu2 xz-utils_5.2.4-1 zip_3.0-11build1 zlib1g_1:1.2.11.dfsg-1ubuntu3 zlib1g-dev_1:1.2.11.dfsg-1ubuntu3 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- gpgv: Signature made Sat Jul 14 14:50:00 2018 UTC gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./reapr_1.0.18+dfsg-4.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-4.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying spelling dpkg-source: info: applying use_shared_libs dpkg-source: info: applying hardening dpkg-source: info: applying fix_sort_samtools13 dpkg-source: info: applying ld_as_needed Check disc space ---------------- Sufficient free space for build User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf DEB_BUILD_OPTIONS=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-18348607 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-18348607 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-18348607 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-4 dpkg-buildpackage: info: source distribution unstable 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 -fdebug-prefix-map=/<>/reapr-1.0.18+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -I /usr/include/bamtools -I /usr/include -c errorWindow.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/reapr-1.0.18+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -I /usr/include/bamtools -I /usr/include -c utils.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/reapr-1.0.18+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -I /usr/include/bamtools -I /usr/include -c histogram.cpp 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 -fdebug-prefix-map=/<>/reapr-1.0.18+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -I /usr/include/bamtools -I /usr/include -c task_score.cpp task_score.cpp: In function ‘int main(int, char**)’: task_score.cpp:235:79: warning: variable ‘p’ set but not used [-Wunused-but-set-variable] 235 | map > >::iterator p = globalGaps.find(currentRefID); | ^ g++ -o task_score -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/reapr-1.0.18+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -I /usr/include/bamtools -I /usr/include task_score.o errorWindow.o utils.o histogram.o -lbamtools -ltabixpp -lhts -lz -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/reapr-1.0.18+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -I /usr/include/bamtools -I /usr/include -c trianglePlot.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/reapr-1.0.18+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -I /usr/include/bamtools -I /usr/include -c coveragePlot.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/reapr-1.0.18+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -I /usr/include/bamtools -I /usr/include -c fasta.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/reapr-1.0.18+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -I /usr/include/bamtools -I /usr/include -c task_stats.cpp task_stats.cpp: In function ‘int main(int, char**)’: task_stats.cpp:441:16: warning: ‘ti_perfect’ may be used uninitialized in this function [-Wmaybe-uninitialized] 441 | delete ti_perfect; | ^~~~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/reapr-1.0.18+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -I /usr/include/bamtools -I /usr/include task_stats.o trianglePlot.o coveragePlot.o fasta.o histogram.o utils.o -lbamtools -ltabixpp -lhts -lz -o task_stats -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/reapr-1.0.18+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -I /usr/include/bamtools -I /usr/include -c task_break.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/reapr-1.0.18+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -I /usr/include/bamtools -I /usr/include task_break.o -lbamtools fasta.o utils.o -lbamtools -ltabixpp -lhts -lz -o task_break -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/reapr-1.0.18+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -I /usr/include/bamtools -I /usr/include -c bam2fragCov.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/reapr-1.0.18+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -I /usr/include/bamtools -I /usr/include bam2fragCov.o -lbamtools coveragePlot.o utils.o -lbamtools -ltabixpp -lhts -lz -o bam2fragCov -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/reapr-1.0.18+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -I /usr/include/bamtools -I /usr/include -c bam2insert.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/reapr-1.0.18+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -I /usr/include/bamtools -I /usr/include bam2insert.o -lbamtools histogram.o utils.o -lbamtools -ltabixpp -lhts -lz -o bam2insert -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/reapr-1.0.18+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -I /usr/include/bamtools -I /usr/include -c bam2fcdEstimate.cpp bam2fcdEstimate.cpp: In function ‘int main(int, char**)’: bam2fcdEstimate.cpp:84:34: warning: comparison of integer expressions of different signedness: ‘int32_t’ {aka ‘int’} and ‘long unsigned int’ [-Wsign-compare] 84 | while (bamAlign.Position > triplot.centreCoord()) | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ bam2fcdEstimate.cpp: In function ‘void initialiseFCDHists(std::vector&, CmdLineOptions&)’: bam2fcdEstimate.cpp:210:33: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘long int’ [-Wsign-compare] 210 | for (unsigned long i = 0; i <= ops.maxInsert; i++) | ~~^~~~~~~~~~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/reapr-1.0.18+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -I /usr/include/bamtools -I /usr/include bam2fcdEstimate.o -lbamtools histogram.o utils.o trianglePlot.o -ltabixpp -lhts -lz -o bam2fcdEstimate -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/reapr-1.0.18+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -I /usr/include/bamtools -I /usr/include -c make_plots.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/reapr-1.0.18+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -I /usr/include/bamtools -I /usr/include make_plots.o -o make_plots -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/reapr-1.0.18+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -I /usr/include/bamtools -I /usr/include -c fa2gaps.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/reapr-1.0.18+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -I /usr/include/bamtools -I /usr/include fa2gaps.o fasta.o -o fa2gaps -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/reapr-1.0.18+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -I /usr/include/bamtools -I /usr/include -c fa2gc.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/reapr-1.0.18+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -I /usr/include/bamtools -I /usr/include fa2gc.o fasta.o -o fa2gc -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/reapr-1.0.18+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -I /usr/include/bamtools -I /usr/include -c scaff2contig.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/reapr-1.0.18+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -I /usr/include/bamtools -I /usr/include scaff2contig.o fasta.o -o scaff2contig -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/reapr-1.0.18+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -I /usr/include/bamtools -I /usr/include -c n50.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/reapr-1.0.18+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -I /usr/include/bamtools -I /usr/include n50.o fasta.o -o n50 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/reapr-1.0.18+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -I /usr/include/bamtools -I /usr/include -c task_gapresize.cpp task_gapresize.cpp: In function ‘int main(int, char**)’: task_gapresize.cpp:129:127: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘int64_t’ {aka ‘long int’} [-Wsign-compare] 129 | if (!bamAlign.IsReverseStrand() && pairOrientation == INNIE && bamAlign.InsertSize > 0 && gapIter->second < fragEnd && fragEnd <= gapIter->second + options.maxFragLength) | ~~~~~~~~~~~~~~~~^~~~~~~~~ task_gapresize.cpp:129:148: warning: comparison of integer expressions of different signedness: ‘int64_t’ {aka ‘long int’} and ‘long unsigned int’ [-Wsign-compare] 129 | if (!bamAlign.IsReverseStrand() && pairOrientation == INNIE && bamAlign.InsertSize > 0 && gapIter->second < fragEnd && fragEnd <= gapIter->second + options.maxFragLength) | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/reapr-1.0.18+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -I /usr/include/bamtools -I /usr/include task_gapresize.o -lbamtools utils.o trianglePlot.o fasta.o -ltabixpp -lhts -lz -o task_gapresize -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/reapr-1.0.18+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -I /usr/include/bamtools -I /usr/include -c task_fcdrate.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/reapr-1.0.18+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -I /usr/include/bamtools -I /usr/include task_fcdrate.o -ltabixpp -lhts -lz histogram.o utils.o -lbamtools -o task_fcdrate -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/reapr-1.0.18+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -I /usr/include/bamtools -I /usr/include -c bam2perfect.cpp bam2perfect.cpp: In function ‘void writeAlignments(std::multimap&, BamTools::BamWriter&, long unsigned int)’: bam2perfect.cpp:213:32: warning: comparison of integer expressions of different signedness: ‘int32_t’ {aka ‘int’} and ‘long unsigned int’ [-Wsign-compare] 213 | if (p->second.Position >= endPos) break; | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/reapr-1.0.18+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -I /usr/include/bamtools -I /usr/include bam2perfect.o -lbamtools utils.o -lbamtools -ltabixpp -lhts -lz -o bam2perfect -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now make[2]: Leaving directory '/<>/reapr-1.0.18+dfsg/src' make[1]: Leaving directory '/<>/reapr-1.0.18+dfsg' debian/rules override_dh_auto_test make[1]: Entering directory '/<>/reapr-1.0.18+dfsg' mkdir /<>/reapr-1.0.18+dfsg/debian/test ln -s /<>/reapr-1.0.18+dfsg/src/reapr.pl /<>/reapr-1.0.18+dfsg/debian/test/reapr PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/<>/reapr-1.0.18+dfsg/src:/<>/reapr-1.0.18+dfsg/debian/test /<>/reapr-1.0.18+dfsg/debian/tests/test-example [wgsim] seed = 42 [wgsim_core] calculating the total length of the reference sequence... [wgsim_core] 1 sequences, total length: 1000111 foo 1384 T K + foo 4961 T W + foo 5885 - T - foo 9598 A C - foo 10177 G R + foo 11305 G K + foo 11592 G R + foo 13931 T - - foo 15907 C A - foo 17264 G K + foo 17780 A - - foo 18711 A W + foo 19249 T W + foo 19522 C S + foo 23053 T K + foo 23681 A R + foo 23730 C S + foo 24075 G S + foo 24555 G C - foo 26775 G K + foo 26896 C M + foo 27253 G K + foo 28210 T Y + foo 28224 A W + foo 28377 - G + foo 29035 G K + foo 29898 C M + foo 30274 A R + foo 30542 G K + foo 31566 A C - foo 32252 - A - foo 33303 T K + foo 33390 - G + foo 34073 A R + foo 34171 G R + foo 34718 T Y + foo 34801 - C + foo 35204 T W + foo 35342 G S + foo 35489 G T - foo 36153 A M + foo 36273 C S + foo 37356 G T - foo 37596 C S + foo 39308 T - - foo 40333 C G - foo 42295 T K + foo 42372 T Y + foo 44433 C G - foo 44630 - AG + foo 44902 T C - foo 47156 C A - foo 48210 C M + foo 48390 A R + foo 49652 C M + foo 52739 T Y + foo 52858 A M + foo 54737 A G - foo 55306 C T - foo 55434 C T - foo 59204 A W + foo 59300 G C - foo 59335 T Y + foo 59444 T - - foo 59531 C S + foo 59766 C Y + foo 61950 C S + foo 62887 G S + foo 63390 A G - foo 64365 G K + foo 64703 C S + foo 64932 C Y + foo 68383 - CG + foo 68464 A W + foo 68727 A W + foo 69080 A M + foo 72071 T C - foo 72720 - G - foo 73354 C T - foo 73637 G T - foo 74741 A M + foo 75101 C T - foo 75207 T K + foo 76400 T Y + foo 76780 A C - foo 77172 A W + foo 78385 C Y + foo 80705 C M + foo 82440 A R + foo 83021 G K + foo 83116 A - - foo 83846 T K + foo 84633 G S + foo 85891 G S + foo 87759 A C - foo 87778 T W + foo 88581 T K + foo 88606 T Y + foo 88880 A G - foo 89945 G C - foo 90728 T K + foo 91798 G R + foo 95957 G C - foo 96173 T W + foo 96665 A M + foo 98019 - G + foo 98131 A M + foo 98669 A R + foo 98719 G T - foo 99062 A W + foo 99590 A T - foo 100532 - TC + foo 103015 A W + foo 103172 G S + foo 103609 G R + foo 106549 T Y + foo 108808 C Y + foo 109191 G C - foo 111686 C G - foo 113436 C A - foo 113763 A W + foo 115671 C T - foo 117460 - A - foo 118193 G - - foo 118585 T K + foo 121219 A M + foo 121876 T K + foo 122071 T A - foo 124918 C G - foo 125300 G S + foo 125967 C S + foo 127443 G S + foo 127565 C Y + foo 128700 C A - foo 129912 G A - foo 130847 T W + foo 131677 G S + foo 132189 T C - foo 135878 CGGC - - foo 136825 T K + foo 138881 TGT - - foo 139288 A W + foo 141054 A W + foo 141055 - T + foo 141101 C S + foo 141404 A R + foo 142698 T C - foo 143990 C A - foo 144167 T Y + foo 144814 C Y + foo 146381 T Y + foo 146393 C A - foo 146510 A C - foo 147182 A W + foo 148783 T C - foo 149068 G S + foo 150208 T K + foo 151554 T W + foo 151709 C G - foo 153072 G R + foo 153307 T Y + foo 154050 G S + foo 154415 C S + foo 154594 G R + foo 155839 G T - foo 156106 G A - foo 159356 T W + foo 159926 A W + foo 160303 T K + foo 161323 C Y + foo 161904 G S + foo 162533 - ACC - foo 164738 C G - foo 165413 A R + foo 166944 C M + foo 167464 T Y + foo 168420 T C - foo 168579 A M + foo 168787 T W + foo 168959 A T - foo 169884 G S + foo 170032 G T - foo 172058 G K + foo 174942 A R + foo 175014 G K + foo 178406 G A - foo 179028 - A + foo 182394 C M + foo 182735 T Y + foo 183384 T K + foo 183893 - AT - foo 185360 G A - foo 185538 - G - foo 187948 G S + foo 188120 T G - foo 188179 T W + foo 188316 T Y + foo 189963 - G + foo 190093 C Y + foo 192220 C M + foo 192368 A W + foo 192782 T K + foo 193307 A R + foo 193501 G K + foo 194276 G S + foo 194930 C S + foo 196728 A W + foo 197559 G C - foo 198467 T W + foo 199042 C Y + foo 199259 AA - - foo 199687 TT - - foo 200287 C A - foo 200678 A R + foo 201208 C T - foo 201882 A - - foo 204456 T K + foo 206327 G R + foo 207311 G T - foo 209184 G A - foo 209279 C Y + foo 211459 C Y + foo 213807 T Y + foo 213846 T Y + foo 214635 A G - foo 214884 C A - foo 216244 A M + foo 216652 A M + foo 216745 T - - foo 216909 A T - foo 217579 A G - foo 217895 C Y + foo 218870 G K + foo 223098 T A - foo 223283 - C + foo 223666 C A - foo 224011 - C + foo 225681 C S + foo 227345 T C - foo 228778 T G - foo 229926 C - - foo 230778 T K + foo 230939 CG - - foo 231988 CT - - foo 234593 T W + foo 235496 C S + foo 235705 G K + foo 235758 A G - foo 236852 T C - foo 238790 A M + foo 238865 T K + foo 239329 A M + foo 239576 - C + foo 243058 G S + foo 244147 T - - foo 244462 C G - foo 245443 - A + foo 246544 C Y + foo 246744 T W + foo 247473 C M + foo 248129 C T - foo 249060 A C - foo 249515 G T - foo 250138 G S + foo 250567 C A - foo 254381 G R + foo 257864 C M + foo 257879 C Y + foo 259859 A M + foo 260643 C S + foo 261681 C G - foo 262645 T Y + foo 263279 A R + foo 263575 A - - foo 264587 - TA + foo 264689 T K + foo 265758 G K + foo 266272 A M + foo 268550 C M + foo 269986 G S + foo 270321 AC - - foo 273346 C S + foo 275367 C A - foo 277334 C G - foo 277629 G T - foo 278431 C Y + foo 281456 T Y + foo 281556 T G - foo 281737 G K + foo 282290 AC - - foo 282851 - C - foo 284405 A C - foo 288751 A C - foo 290501 TAAA - - foo 291315 A W + foo 291368 C - - foo 292154 A C - foo 292385 C M + foo 292555 G K + foo 297709 G C - foo 298183 A W + foo 298228 T W + foo 299902 T G - foo 302575 A T - foo 304823 G R + foo 305308 T Y + foo 305487 G S + foo 305697 G T - foo 306098 C G - foo 306882 T Y + foo 308201 A M + foo 308833 A T - foo 312033 A - - foo 312895 C G - foo 313889 C - - foo 315109 A R + foo 316083 C - - foo 316466 A R + foo 318040 G C - foo 319446 T C - foo 320236 C S + foo 320652 A - - foo 320716 T K + foo 323644 A - - foo 325359 G T - foo 329476 - CA + foo 329706 T G - foo 330181 T Y + foo 330703 C Y + foo 331315 G S + foo 332351 C A - foo 333408 A R + foo 333468 C S + foo 336247 A G - foo 336586 A M + foo 337364 G K + foo 337686 A T - foo 338043 A - - foo 338292 C G - foo 338962 A C - foo 339353 G K + foo 340647 - A + foo 341705 G R + foo 344283 C M + foo 345898 - AG - foo 347959 T - - foo 349162 C M + foo 352072 T Y + foo 354614 C Y + foo 359304 T - - foo 359312 - G + foo 360972 C S + foo 363857 C Y + foo 366226 A C - foo 367259 C M + foo 372502 T Y + foo 372747 A M + foo 375140 C S + foo 376298 T W + foo 376313 C - - foo 376760 T W + foo 378494 A W + foo 381137 T G - foo 381186 A R + foo 381701 A G - foo 382614 A W + foo 382761 C T - foo 382854 T C - foo 383201 C T - foo 385104 G S + foo 385233 - A + foo 386138 C T - foo 386316 A W + foo 387072 A R + foo 387642 - A + foo 388232 T C - foo 388890 GGG - - foo 390508 C S + foo 390625 C M + foo 391921 C G - foo 395256 G T - foo 395542 G S + foo 397015 A - - foo 397516 C Y + foo 397528 GC - - foo 398152 C T - foo 399802 A W + foo 400972 T K + foo 401419 - T + foo 401477 T W + foo 402437 A M + foo 402722 G R + foo 403452 C M + foo 404234 - A + foo 405344 A W + foo 407040 G S + foo 408483 G R + foo 408586 A C - foo 408721 A R + foo 409494 A M + foo 410078 A G - foo 411170 C A - foo 415342 T Y + foo 416265 C G - foo 417740 C A - foo 418622 C S + foo 420232 A W + foo 420288 T Y + foo 420908 A W + foo 421109 T A - foo 421357 A R + foo 422799 G A - foo 424383 C S + foo 424871 - GCA + foo 427273 T A - foo 429822 C M + foo 429846 T W + foo 432015 A G - foo 432414 G K + foo 433606 C Y + foo 433831 T Y + foo 437721 - A - foo 438402 G - - foo 438799 A T - foo 439422 C M + foo 440734 C A - foo 441840 T G - foo 442021 - C + foo 445021 T A - foo 445591 G A - foo 446138 T W + foo 447757 A W + foo 449156 T - - foo 449161 G K + foo 450114 A W + foo 450688 A W + foo 454421 C G - foo 454718 T Y + foo 455675 TC - - foo 461721 G R + foo 462526 G S + foo 467296 G A - foo 467510 G K + foo 468267 T K + foo 469118 G R + foo 469830 C Y + foo 471073 G T - foo 472056 G A - foo 472773 - A + foo 473046 G R + foo 473188 G A - foo 473742 C - - foo 474789 T A - foo 477763 G R + foo 478246 T W + foo 478975 T G - foo 479038 A R + foo 480275 T Y + foo 480317 G A - foo 481512 T K + foo 482069 G S + foo 482534 A R + foo 483760 C Y + foo 485281 T W + foo 486255 T C - foo 487038 T K + foo 487225 T A - foo 488012 C Y + foo 488795 T C - foo 490241 A R + foo 492595 - CGG + foo 493224 C A - foo 494284 A T - foo 495990 - T - foo 497306 A R + foo 497403 T Y + foo 499569 C Y + foo 499651 T K + foo 503139 T C - foo 504660 A R + foo 508679 C - - foo 513643 G K + foo 515668 CC - - foo 515836 G R + foo 516488 C S + foo 517602 G R + foo 517962 G K + foo 517975 T K + foo 519144 A T - foo 520068 T K + foo 520926 A W + foo 521562 C S + foo 522076 CG - - foo 522838 T Y + foo 523513 - C + foo 523907 - TA + foo 526271 T A - foo 526533 AC - - foo 526767 C Y + foo 528217 C Y + foo 531924 G S + foo 532333 - TT + foo 533132 C M + foo 534689 A T - foo 534779 A W + foo 535594 C A - foo 535795 G R + foo 538368 A R + foo 540879 G K + foo 542530 A - - foo 543620 G R + foo 544733 - C - foo 546300 - TT + foo 548196 A T - foo 548878 C M + foo 548885 G R + foo 549459 T K + foo 550908 A G - foo 551170 A - - foo 553130 T Y + foo 555293 T G - foo 556198 G R + foo 556355 A T - foo 557688 G K + foo 558415 G C - foo 558461 - G + foo 559287 T Y + foo 559465 C M + foo 560184 T W + foo 560252 T W + foo 562579 A M + foo 562961 G A - foo 566986 C A - foo 568134 C A - foo 569698 T C - foo 570180 T K + foo 570451 TG - - foo 570832 - A - foo 571589 A W + foo 572208 C M + foo 572871 C S + foo 574334 G - - foo 575673 T Y + foo 576797 G S + foo 578486 - C - foo 578494 C S + foo 579257 G A - foo 580103 G T - foo 580872 A W + foo 580925 G S + foo 580950 G C - foo 581637 T Y + foo 581654 A G - foo 582538 A T - foo 582691 C M + foo 582938 A W + foo 583104 T K + foo 584763 T W + foo 585723 T W + foo 588253 T Y + foo 588972 T C - foo 589438 - C - foo 591131 C Y + foo 591950 G R + foo 592194 T G - foo 592310 G S + foo 593892 G A - foo 598556 A - - foo 601660 G S + foo 602112 G T - foo 602412 T Y + foo 607282 - C + foo 607394 A M + foo 608438 A T - foo 609255 A W + foo 609365 - T + foo 611161 G K + foo 612224 C G - foo 614493 G R + foo 614601 G A - foo 614607 C Y + foo 619507 C M + foo 619798 T C - foo 621872 C T - foo 622375 C Y + foo 623208 - G - foo 624366 C A - foo 625320 - ACA - foo 626664 - G + foo 627140 T C - foo 627353 G T - foo 628714 T Y + foo 628744 A - - foo 629152 A G - foo 630110 T G - foo 631744 G K + foo 632763 C S + foo 634419 G - - foo 634459 A G - foo 634571 G A - foo 635366 - A + foo 635604 G T - foo 637057 T C - foo 637525 A T - foo 638412 A R + foo 640547 A W + foo 641514 T K + foo 642219 A R + foo 642427 A G - foo 642612 A R + foo 643553 T W + foo 647316 - T + foo 647598 C - - foo 651093 G A - foo 651718 G R + foo 652235 A G - foo 652579 A C - foo 653355 A W + foo 655174 C M + foo 655487 A M + foo 656849 G S + foo 661081 T K + foo 661134 G C - foo 661935 A W + foo 662010 A M + foo 662040 G R + foo 663030 A W + foo 663268 - C + foo 664991 T - - foo 665489 T K + foo 665555 C M + foo 665965 C Y + foo 668725 A C - foo 668834 - G - foo 668873 C S + foo 669654 T W + foo 671041 G S + foo 671485 T W + foo 671690 C M + foo 673022 G R + foo 674137 - T + foo 674782 A C - foo 676373 G T - foo 676793 T C - foo 677409 G S + foo 677536 - AA - foo 677620 G K + foo 677686 C Y + foo 678327 G S + foo 678704 G S + foo 678771 A C - foo 678866 C T - foo 679960 A W + foo 680447 - C + foo 682102 C T - foo 685497 T A - foo 686884 G S + foo 687324 ACA - - foo 687684 - AC + foo 687823 T C - foo 688590 G K + foo 690802 C M + foo 691388 T C - foo 691403 T G - foo 691790 G A - foo 692973 C A - foo 694058 G S + foo 694550 G R + foo 694968 T W + foo 695898 A T - foo 696721 C S + foo 696787 C S + foo 696935 A M + foo 698024 - C + foo 699813 A - - foo 700179 G R + foo 701421 A M + foo 701989 T A - foo 702862 C A - foo 707020 G A - foo 708420 A - - foo 708669 C G - foo 710521 T W + foo 711801 G C - foo 711913 T G - foo 715830 C M + foo 717664 TC - - foo 718845 A W + foo 719069 T Y + foo 719565 A W + foo 721136 T K + foo 726116 T K + foo 727809 T K + foo 728864 G K + foo 728918 G A - foo 730296 - T + foo 731988 C Y + foo 734658 A M + foo 734715 A W + foo 736618 C G - foo 737257 T Y + foo 740864 C A - foo 741640 G - - foo 741859 - TA - foo 742011 T K + foo 742237 A R + foo 742960 G K + foo 743731 G R + foo 743971 A W + foo 744635 T K + foo 746430 C G - foo 746489 - GC - foo 746881 C M + foo 756997 TC - - foo 757776 A M + foo 759870 A T - foo 760224 G K + foo 760799 G C - foo 761692 T C - foo 762569 G S + foo 763140 A G - foo 763842 - T - foo 764192 A M + foo 764334 G A - foo 764889 - AAT + foo 766464 G S + foo 768226 G A - foo 770272 T G - foo 771145 C Y + foo 772209 T A - foo 773672 T K + foo 773932 G C - foo 774658 C S + foo 775969 A M + foo 776816 T G - foo 777591 C Y + foo 777891 A M + foo 778164 C M + foo 778219 T W + foo 779260 G T - foo 779465 A W + foo 779779 G S + foo 780033 G K + foo 783243 C M + foo 783860 A R + foo 788345 A M + foo 789554 G - - foo 790025 G K + foo 791454 T K + foo 792009 C A - foo 792872 C G - foo 794616 T W + foo 795031 G R + foo 796919 C M + foo 797020 G S + foo 797042 G C - foo 797149 G A - foo 797177 A C - foo 799076 G C - foo 799580 G S + foo 800356 A R + foo 802297 G T - foo 802309 T Y + foo 802343 - C + foo 802769 A W + foo 803104 C G - foo 805819 C Y + foo 805972 T Y + foo 807503 T K + foo 807950 C M + foo 807994 - A - foo 809167 A G - foo 809658 A W + foo 810152 A M + foo 811506 G R + foo 813494 A M + foo 814035 G T - foo 814476 A W + foo 819399 T K + foo 820171 T W + foo 820445 G C - foo 822178 C G - foo 822504 C T - foo 823378 C M + foo 823591 CG - - foo 824229 C M + foo 824579 C T - foo 824858 C M + foo 826101 T K + foo 827593 C G - foo 827794 T Y + foo 828228 A M + foo 828367 T K + foo 828788 C M + foo 829002 C Y + foo 830345 C M + foo 831018 C A - foo 831459 T K + foo 832413 A T - foo 832782 T Y + foo 832908 T Y + foo 833130 T - - foo 833142 G S + foo 833241 G A - foo 836727 A T - foo 836829 G S + foo 838452 T G - foo 838543 A T - foo 838605 C M + foo 838954 G C - foo 841829 G K + foo 842324 - TC + foo 842996 - C + foo 844390 C A - foo 844793 A C - foo 844925 C A - foo 845082 G C - foo 846202 G R + foo 846707 A G - foo 848713 G A - foo 849372 C S + foo 849742 G A - foo 850499 C - - foo 850927 GT - - foo 851084 - G + foo 852247 A R + foo 852972 C A - foo 854808 T W + foo 855956 G K + foo 856225 G A - foo 856582 T K + foo 857351 C M + foo 857504 AC - - foo 858324 A T - foo 858858 T C - foo 859488 T Y + foo 862441 T Y + foo 863827 C Y + foo 864165 C A - foo 865997 C M + foo 866370 G S + foo 867653 G S + foo 867722 C Y + foo 868696 C M + foo 869005 T W + foo 869791 T Y + foo 875339 C Y + foo 875347 C M + foo 875584 T G - foo 876780 C T - foo 878368 A C - foo 878916 - CAG + foo 879005 A R + foo 880112 G T - foo 881021 - T - foo 881175 T W + foo 882168 - GGG + foo 882223 - G - foo 883033 TG - - foo 883381 C G - foo 884378 C - - foo 885075 A M + foo 885190 A W + foo 885568 A W + foo 885827 T Y + foo 887610 TG - - foo 889139 G R + foo 890978 T - - foo 891500 C Y + foo 892257 G C - foo 892642 G R + foo 892644 T W + foo 892757 C A - foo 893222 T - - foo 893348 T W + foo 894161 - C - foo 894447 A G - foo 894614 A W + foo 897817 T W + foo 899408 C S + foo 902450 A T - foo 902970 AT - - foo 905836 G K + foo 906524 GA - - foo 907484 A W + foo 907537 C M + foo 908515 G R + foo 908642 C T - foo 911145 T C - foo 912220 T Y + foo 912682 C Y + foo 914260 C S + foo 914757 T Y + foo 916413 G C - foo 916783 T G - foo 917033 G C - foo 917218 A - - foo 918225 G - - foo 918459 A - - foo 918732 A M + foo 919640 TC - - foo 920824 T W + foo 920836 G C - foo 924560 G R + foo 924659 GA - - foo 925868 T A - foo 928254 T G - foo 928369 - A - foo 928641 - AG + foo 929857 C M + foo 930211 T W + foo 930935 C T - foo 931986 A M + foo 932852 G T - foo 933965 T A - foo 935564 A W + foo 936034 T Y + foo 936221 AC - - foo 936670 C S + foo 936704 T A - foo 936786 T W + foo 939218 C S + foo 939312 A W + foo 939467 A W + foo 939934 C S + foo 941603 C Y + foo 942910 A W + foo 944654 T Y + foo 945301 A C - foo 945770 C T - foo 946078 G S + foo 948833 G K + foo 948999 A W + foo 949193 A R + foo 950276 C M + foo 950414 A W + foo 951285 G C - foo 953158 G R + foo 953287 A W + foo 954150 C G - foo 954258 G - - foo 955396 CC - - foo 956490 - AC + foo 958129 A R + foo 959027 T A - foo 959964 A W + foo 962042 A G - foo 962742 C G - foo 963306 T W + foo 963422 G K + foo 964082 G S + foo 965561 C S + foo 966531 T K + foo 967324 T W + foo 968419 - C - foo 969054 G - - foo 969158 G S + foo 972658 C M + foo 974266 T W + foo 974629 G K + foo 975034 A R + foo 975636 T W + foo 977078 - A - foo 978321 G T - foo 978595 C G - foo 979090 C M + foo 983855 TA - - foo 985725 T A - foo 988497 C Y + foo 990171 C M + foo 990804 - CA - foo 990941 T W + foo 991797 A W + foo 992469 A M + foo 994610 C Y + foo 998107 - T + foo 999725 G R + [REAPR smaltmap] Running: smalt index -k 13 -s 2 out.bam.tmp.5478.smaltmap.smalt_index foo1.fasta # Command line: smalt index -k 13 -s 2 out.bam.tmp.5478.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.5478.smaltmap.smalt_sample out.bam.tmp.5478.smaltmap.smalt_index foofq.1.fastq foofq.2.fastq # Command line: smalt sample -u 1000 -o out.bam.tmp.5478.smaltmap.smalt_sample out.bam.tmp.5478.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.5478.smaltmap.smalt_sample -f samsoft out.bam.tmp.5478.smaltmap.smalt_index foofq.1.fastq foofq.2.fastq | awk '$1!~/^#/' | samtools view -S -T foo1.fasta -b - > out.bam.tmp.5478.smaltmap.raw.bam # Command line: smalt map -r 0 -x -y 0.5 -g out.bam.tmp.5478.smaltmap.smalt_sample -f samsoft out.bam.tmp.5478.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.5478.smaltmap.raw.bam -O bam -o out.bam.tmp.5478.smaltmap.raw.bam.sort.bam [REAPR smaltmap] Running: samtools rmdup out.bam.tmp.5478.smaltmap.raw.bam.sort.bam out.bam.tmp.5478.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.5478.smaltmap.header [REAPR smaltmap] Running: samtools view -H out.bam.tmp.5478.smaltmap.rmdup.bam >> out.bam.tmp.5478.smaltmap.header [REAPR smaltmap] Running: samtools reheader out.bam.tmp.5478.smaltmap.header out.bam.tmp.5478.smaltmap.rmdup.bam > out.bam [REAPR smaltmap] Running: samtools index out.bam [REAPR smaltmap] Running: rm out.bam.tmp.5478.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:36: 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 20200105-1044 Finished -------- E: Build failure (dpkg-buildpackage died) +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not removing build depends: as requested +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: s390x Build-Space: 53824 Build-Time: 57 Distribution: focal Fail-Stage: build Host Architecture: s390x Install-Time: 18 Job: reapr_1.0.18+dfsg-4.dsc Machine Architecture: s390x Package: reapr Package-Time: 76 Source-Version: 1.0.18+dfsg-4 Space: 53824 Status: attempted Version: 1.0.18+dfsg-4 -------------------------------------------------------------------------------- Finished at 20200105-1044 Build needed 00:01:16, 53824k disc space RUN: /usr/share/launchpad-buildd/bin/in-target scan-for-processes --backend=chroot --series=focal --arch=s390x PACKAGEBUILD-18348607 Scanning for processes to kill in build PACKAGEBUILD-18348607