https://launchpad.net/ubuntu/+source/iva/1.0.9+ds-6/+build/15221806 RUN: /usr/share/launchpad-buildd/slavebin/slave-prep Forking launchpad-buildd slave process... Kernel version: Linux lgw01-amd64-026 4.4.0-128-generic #154-Ubuntu SMP Fri May 25 14:15:18 UTC 2018 x86_64 Buildd toolchain package versions: launchpad-buildd_163 python-lpbuildd_163 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_0.3.4~git201611291343.dcee459~ubuntu16.04.1 git_1:2.7.4-0ubuntu1.4 dpkg-dev_1.18.4ubuntu1.4 python-debian_0.1.27ubuntu2. Syncing the system clock with the buildd NTP service... 2 Aug 05:09:53 ntpdate[1858]: adjust time server 10.211.37.1 offset 0.008594 sec RUN: /usr/share/launchpad-buildd/slavebin/in-target unpack-chroot --backend=chroot --series=cosmic --arch=amd64 PACKAGEBUILD-15221806 /home/buildd/filecache-default/b7d07d6b68ae68badf26a018a3a0291d50e41e42 Creating target for build PACKAGEBUILD-15221806 RUN: /usr/share/launchpad-buildd/slavebin/in-target mount-chroot --backend=chroot --series=cosmic --arch=amd64 PACKAGEBUILD-15221806 Starting target for build PACKAGEBUILD-15221806 RUN: /usr/share/launchpad-buildd/slavebin/in-target override-sources-list --backend=chroot --series=cosmic --arch=amd64 PACKAGEBUILD-15221806 'deb http://ftpmaster.internal/ubuntu cosmic main universe' 'deb http://ftpmaster.internal/ubuntu cosmic-security main universe' 'deb http://ftpmaster.internal/ubuntu cosmic-updates main universe' 'deb http://ftpmaster.internal/ubuntu cosmic-proposed main universe' Overriding sources.list in build-PACKAGEBUILD-15221806 RUN: /usr/share/launchpad-buildd/slavebin/in-target update-debian-chroot --backend=chroot --series=cosmic --arch=amd64 PACKAGEBUILD-15221806 Updating target for build PACKAGEBUILD-15221806 Get:1 http://ftpmaster.internal/ubuntu cosmic InRelease [242 kB] Get:2 http://ftpmaster.internal/ubuntu cosmic-security InRelease [65.4 kB] Get:3 http://ftpmaster.internal/ubuntu cosmic-updates InRelease [65.4 kB] Get:4 http://ftpmaster.internal/ubuntu cosmic-proposed InRelease [92.5 kB] Get:5 http://ftpmaster.internal/ubuntu cosmic/main amd64 Packages [1021 kB] Get:6 http://ftpmaster.internal/ubuntu cosmic/main Translation-en [515 kB] Get:7 http://ftpmaster.internal/ubuntu cosmic/universe amd64 Packages [8734 kB] Get:8 http://ftpmaster.internal/ubuntu cosmic/universe Translation-en [5036 kB] Get:9 http://ftpmaster.internal/ubuntu cosmic-proposed/main amd64 Packages [87.3 kB] Get:10 http://ftpmaster.internal/ubuntu cosmic-proposed/main Translation-en [42.2 kB] Get:11 http://ftpmaster.internal/ubuntu cosmic-proposed/universe amd64 Packages [468 kB] Get:12 http://ftpmaster.internal/ubuntu cosmic-proposed/universe Translation-en [220 kB] Fetched 16.6 MB in 4s (3722 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages were automatically installed and are no longer required: g++-7 libargon2-0 libncursesw5 libprocps6 libstdc++-7-dev Use 'sudo apt autoremove' to remove them. The following NEW packages will be installed: cpp-8 g++-8 gcc-8 libargon2-1 libasan5 libgcc-8-dev libncurses6 libncursesw6 libprocps7 libstdc++-8-dev libtinfo6 libubsan1 The following packages will be upgraded: adduser apt base-files base-passwd bash binutils binutils-common binutils-x86-64-linux-gnu bsdutils build-essential cpp cpp-7 debconf debianutils dpkg dpkg-dev e2fslibs e2fsprogs fdisk g++ g++-7 gcc gcc-7 gcc-7-base gcc-8-base gpg gpg-agent gpgconf gpgv libapparmor1 libapt-pkg5.0 libargon2-0 libasan4 libatomic1 libaudit-common libaudit1 libbinutils libblkid1 libcap-ng0 libcc1-0 libcilkrts5 libcom-err2 libcomerr2 libcryptsetup12 libdpkg-perl libext2fs2 libfdisk1 libgcc-7-dev libgcc1 libgcrypt20 libgmp10 libgomp1 libgpg-error0 libidn11 libidn2-0 libitm1 libkmod2 liblsan0 liblz4-1 libmount1 libmpx2 libncurses5 libncursesw5 libnpth0 libp11-kit0 libpcre3 libperl5.26 libpng16-16 libquadmath0 libreadline7 libseccomp2 libselinux1 libsemanage-common libsemanage1 libsepol1 libslang2 libsmartcols1 libsqlite3-0 libss2 libssl1.1 libstdc++-7-dev libstdc++6 libsystemd0 libtasn1-6 libtinfo5 libtsan0 libubsan0 libudev1 libunistring2 libusb-0.1-4 libuuid1 linux-libc-dev make mount ncurses-base ncurses-bin openssl perl perl-base perl-modules-5.26 pinentry-curses pkgbinarymangler procps readline-common sed systemd systemd-sysv tar tzdata util-linux 110 upgraded, 12 newly installed, 0 to remove and 0 not upgraded. Need to get 85.4 MB of archives. After this operation, 115 MB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu cosmic/main amd64 base-files amd64 10.1ubuntu4 [58.0 kB] Get:2 http://ftpmaster.internal/ubuntu cosmic/main amd64 libtinfo6 amd64 6.1+20180210-4ubuntu1 [84.0 kB] Get:3 http://ftpmaster.internal/ubuntu cosmic/main amd64 debianutils amd64 4.8.6 [85.6 kB] Get:4 http://ftpmaster.internal/ubuntu cosmic/main amd64 bash amd64 4.4.18-2ubuntu2 [614 kB] Get:5 http://ftpmaster.internal/ubuntu cosmic/main amd64 bsdutils amd64 1:2.32-0.1ubuntu1 [60.4 kB] Get:6 http://ftpmaster.internal/ubuntu cosmic/main amd64 tar amd64 1.30+dfsg-2 [240 kB] Get:7 http://ftpmaster.internal/ubuntu cosmic/main amd64 dpkg amd64 1.19.0.5ubuntu3 [1140 kB] Get:8 http://ftpmaster.internal/ubuntu cosmic/main amd64 libext2fs2 amd64 1.44.3-1 [158 kB] Get:9 http://ftpmaster.internal/ubuntu cosmic/main amd64 e2fsprogs amd64 1.44.3-1 [396 kB] Get:10 http://ftpmaster.internal/ubuntu cosmic/main amd64 ncurses-bin amd64 6.1+20180210-4ubuntu1 [163 kB] Get:11 http://ftpmaster.internal/ubuntu cosmic/main amd64 perl-modules-5.26 all 5.26.2-6 [2762 kB] Get:12 http://ftpmaster.internal/ubuntu cosmic/main amd64 libperl5.26 amd64 5.26.2-6 [3545 kB] Get:13 http://ftpmaster.internal/ubuntu cosmic/main amd64 perl amd64 5.26.2-6 [202 kB] Get:14 http://ftpmaster.internal/ubuntu cosmic/main amd64 perl-base amd64 5.26.2-6 [1391 kB] Get:15 http://ftpmaster.internal/ubuntu cosmic/main amd64 sed amd64 4.5-1 [184 kB] Get:16 http://ftpmaster.internal/ubuntu cosmic/main amd64 libuuid1 amd64 2.32-0.1ubuntu1 [19.9 kB] Get:17 http://ftpmaster.internal/ubuntu cosmic/main amd64 libblkid1 amd64 2.32-0.1ubuntu1 [128 kB] Get:18 http://ftpmaster.internal/ubuntu cosmic/main amd64 libfdisk1 amd64 2.32-0.1ubuntu1 [167 kB] Get:19 http://ftpmaster.internal/ubuntu cosmic/main amd64 libncursesw6 amd64 6.1+20180210-4ubuntu1 [130 kB] Get:20 http://ftpmaster.internal/ubuntu cosmic-proposed/main amd64 libpcre3 amd64 2:8.39-11 [230 kB] Get:21 http://ftpmaster.internal/ubuntu cosmic-proposed/main amd64 libselinux1 amd64 2.8-1build1 [68.5 kB] Get:22 http://ftpmaster.internal/ubuntu cosmic/main amd64 libmount1 amd64 2.32-0.1ubuntu1 [139 kB] Get:23 http://ftpmaster.internal/ubuntu cosmic/main amd64 libsmartcols1 amd64 2.32-0.1ubuntu1 [86.0 kB] Get:24 http://ftpmaster.internal/ubuntu cosmic/main amd64 fdisk amd64 2.32-0.1ubuntu1 [109 kB] Get:25 http://ftpmaster.internal/ubuntu cosmic/main amd64 util-linux amd64 2.32-0.1ubuntu1 [916 kB] Get:26 http://ftpmaster.internal/ubuntu cosmic/main amd64 base-passwd amd64 3.5.45 [47.4 kB] Get:27 http://ftpmaster.internal/ubuntu cosmic/main amd64 ncurses-base all 6.1+20180210-4ubuntu1 [18.4 kB] Get:28 http://ftpmaster.internal/ubuntu cosmic/main amd64 libquadmath0 amd64 8.2.0-1ubuntu2 [134 kB] Get:29 http://ftpmaster.internal/ubuntu cosmic/main amd64 libitm1 amd64 8.2.0-1ubuntu2 [28.1 kB] Get:30 http://ftpmaster.internal/ubuntu cosmic/main amd64 gcc-8-base amd64 8.2.0-1ubuntu2 [18.3 kB] Get:31 http://ftpmaster.internal/ubuntu cosmic/main amd64 libgcc1 amd64 1:8.2.0-1ubuntu2 [40.8 kB] Get:32 http://ftpmaster.internal/ubuntu cosmic/main amd64 libmpx2 amd64 8.2.0-1ubuntu2 [11.7 kB] Get:33 http://ftpmaster.internal/ubuntu cosmic/main amd64 liblsan0 amd64 8.2.0-1ubuntu2 [132 kB] Get:34 http://ftpmaster.internal/ubuntu cosmic/main amd64 libtsan0 amd64 8.2.0-1ubuntu2 [288 kB] Get:35 http://ftpmaster.internal/ubuntu cosmic/main amd64 libcc1-0 amd64 8.2.0-1ubuntu2 [39.5 kB] Get:36 http://ftpmaster.internal/ubuntu cosmic/main amd64 libatomic1 amd64 8.2.0-1ubuntu2 [9084 B] Get:37 http://ftpmaster.internal/ubuntu cosmic/main amd64 libgomp1 amd64 8.2.0-1ubuntu2 [76.4 kB] Get:38 http://ftpmaster.internal/ubuntu cosmic/main amd64 libstdc++6 amd64 8.2.0-1ubuntu2 [399 kB] Get:39 http://ftpmaster.internal/ubuntu cosmic/main amd64 liblz4-1 amd64 1.8.2-1ubuntu1 [86.1 kB] Get:40 http://ftpmaster.internal/ubuntu cosmic-proposed/main amd64 libudev1 amd64 239-7ubuntu1 [56.8 kB] Get:41 http://ftpmaster.internal/ubuntu cosmic/main amd64 libapt-pkg5.0 amd64 1.7.0~alpha2 [803 kB] Get:42 http://ftpmaster.internal/ubuntu cosmic-proposed/main amd64 debconf all 1.5.69 [121 kB] Get:43 http://ftpmaster.internal/ubuntu cosmic/main amd64 adduser all 3.117ubuntu1 [163 kB] Get:44 http://ftpmaster.internal/ubuntu cosmic/main amd64 libgpg-error0 amd64 1.32-1 [56.1 kB] Get:45 http://ftpmaster.internal/ubuntu cosmic/main amd64 libgcrypt20 amd64 1.8.3-1ubuntu1 [419 kB] Get:46 http://ftpmaster.internal/ubuntu cosmic/main amd64 gpgv amd64 2.2.8-1ubuntu1 [197 kB] Get:47 http://ftpmaster.internal/ubuntu cosmic/main amd64 libseccomp2 amd64 2.3.3-3ubuntu1 [38.9 kB] Get:48 http://ftpmaster.internal/ubuntu cosmic/main amd64 apt amd64 1.7.0~alpha2 [1172 kB] Get:49 http://ftpmaster.internal/ubuntu cosmic-proposed/main amd64 libapparmor1 amd64 2.12-4ubuntu7 [30.7 kB] Get:50 http://ftpmaster.internal/ubuntu cosmic/main amd64 libaudit-common all 1:2.8.3-1ubuntu2 [4064 B] Get:51 http://ftpmaster.internal/ubuntu cosmic/main amd64 libcap-ng0 amd64 0.7.9-1 [11.3 kB] Get:52 http://ftpmaster.internal/ubuntu cosmic/main amd64 libaudit1 amd64 1:2.8.3-1ubuntu2 [38.6 kB] Get:53 http://ftpmaster.internal/ubuntu cosmic/main amd64 libargon2-1 amd64 0~20171227-0.1 [20.2 kB] Get:54 http://ftpmaster.internal/ubuntu cosmic/main amd64 libcryptsetup12 amd64 2:2.0.3-6ubuntu1 [139 kB] Get:55 http://ftpmaster.internal/ubuntu cosmic/main amd64 libkmod2 amd64 25-1ubuntu1 [41.6 kB] Get:56 http://ftpmaster.internal/ubuntu cosmic/main amd64 mount amd64 2.32-0.1ubuntu1 [104 kB] Get:57 http://ftpmaster.internal/ubuntu cosmic/main amd64 libncurses6 amd64 6.1+20180210-4ubuntu1 [101 kB] Get:58 http://ftpmaster.internal/ubuntu cosmic/main amd64 libprocps7 amd64 2:3.3.15-2ubuntu1 [32.6 kB] Get:59 http://ftpmaster.internal/ubuntu cosmic/main amd64 procps amd64 2:3.3.15-2ubuntu1 [231 kB] Get:60 http://ftpmaster.internal/ubuntu cosmic-proposed/main amd64 systemd amd64 239-7ubuntu1 [2968 kB] Get:61 http://ftpmaster.internal/ubuntu cosmic-proposed/main amd64 libsystemd0 amd64 239-7ubuntu1 [214 kB] Get:62 http://ftpmaster.internal/ubuntu cosmic-proposed/main amd64 systemd-sysv amd64 239-7ubuntu1 [14.1 kB] Get:63 http://ftpmaster.internal/ubuntu cosmic/main amd64 libcom-err2 amd64 1.44.3-1 [9184 B] Get:64 http://ftpmaster.internal/ubuntu cosmic/main amd64 libsepol1 amd64 2.8-1 [252 kB] Get:65 http://ftpmaster.internal/ubuntu cosmic/main amd64 libsemanage-common all 2.8-1build1 [7000 B] Get:66 http://ftpmaster.internal/ubuntu cosmic/main amd64 libsemanage1 amd64 2.8-1build1 [85.3 kB] Get:67 http://ftpmaster.internal/ubuntu cosmic/main amd64 libss2 amd64 1.44.3-1 [11.1 kB] Get:68 http://ftpmaster.internal/ubuntu cosmic/main amd64 libgmp10 amd64 2:6.1.2+dfsg-3 [240 kB] Get:69 http://ftpmaster.internal/ubuntu cosmic/main amd64 libunistring2 amd64 0.9.10-1ubuntu1 [380 kB] Get:70 http://ftpmaster.internal/ubuntu cosmic/main amd64 libidn2-0 amd64 2.0.4-2.2 [48.3 kB] Get:71 http://ftpmaster.internal/ubuntu cosmic/main amd64 libp11-kit0 amd64 0.23.12-2 [184 kB] Get:72 http://ftpmaster.internal/ubuntu cosmic/main amd64 libtasn1-6 amd64 4.13-3 [36.1 kB] Get:73 http://ftpmaster.internal/ubuntu cosmic/universe amd64 libncurses5 amd64 6.1+20180210-4ubuntu1 [95.2 kB] Get:74 http://ftpmaster.internal/ubuntu cosmic/main amd64 libncursesw5 amd64 6.1+20180210-4ubuntu1 [117 kB] Get:75 http://ftpmaster.internal/ubuntu cosmic/main amd64 libtinfo5 amd64 6.1+20180210-4ubuntu1 [79.3 kB] Get:76 http://ftpmaster.internal/ubuntu cosmic/main amd64 libidn11 amd64 1.33-2.2ubuntu1 [46.1 kB] Get:77 http://ftpmaster.internal/ubuntu cosmic/main amd64 readline-common all 7.0-5 [52.2 kB] Get:78 http://ftpmaster.internal/ubuntu cosmic/main amd64 libreadline7 amd64 7.0-5 [123 kB] Get:79 http://ftpmaster.internal/ubuntu cosmic/main amd64 libslang2 amd64 2.3.2-1ubuntu1 [425 kB] Get:80 http://ftpmaster.internal/ubuntu cosmic-proposed/main amd64 libsqlite3-0 amd64 3.24.0-1 [506 kB] Get:81 http://ftpmaster.internal/ubuntu cosmic/main amd64 libssl1.1 amd64 1.1.0g-2ubuntu5 [1129 kB] Get:82 http://ftpmaster.internal/ubuntu cosmic/main amd64 openssl amd64 1.1.0g-2ubuntu5 [531 kB] Get:83 http://ftpmaster.internal/ubuntu cosmic/main amd64 tzdata all 2018e-1 [188 kB] Get:84 http://ftpmaster.internal/ubuntu cosmic-proposed/main amd64 libpng16-16 amd64 1.6.34-2 [176 kB] Get:85 http://ftpmaster.internal/ubuntu cosmic/main amd64 binutils-x86-64-linux-gnu amd64 2.31.1-2ubuntu1 [1831 kB] Get:86 http://ftpmaster.internal/ubuntu cosmic/main amd64 binutils-common amd64 2.31.1-2ubuntu1 [194 kB] Get:87 http://ftpmaster.internal/ubuntu cosmic/main amd64 binutils amd64 2.31.1-2ubuntu1 [3388 B] Get:88 http://ftpmaster.internal/ubuntu cosmic/main amd64 libbinutils amd64 2.31.1-2ubuntu1 [483 kB] Get:89 http://ftpmaster.internal/ubuntu cosmic/main amd64 cpp-8 amd64 8.2.0-1ubuntu2 [7213 kB] Get:90 http://ftpmaster.internal/ubuntu cosmic/main amd64 cpp amd64 4:8.1.0-2ubuntu1 [27.7 kB] Get:91 http://ftpmaster.internal/ubuntu cosmic/main amd64 libasan5 amd64 8.2.0-1ubuntu2 [364 kB] Get:92 http://ftpmaster.internal/ubuntu cosmic/main amd64 libubsan1 amd64 8.2.0-1ubuntu2 [122 kB] Get:93 http://ftpmaster.internal/ubuntu cosmic/main amd64 libgcc-8-dev amd64 8.2.0-1ubuntu2 [2307 kB] Get:94 http://ftpmaster.internal/ubuntu cosmic/main amd64 gcc-8 amd64 8.2.0-1ubuntu2 [7985 kB] Get:95 http://ftpmaster.internal/ubuntu cosmic/main amd64 gcc amd64 4:8.1.0-2ubuntu1 [5216 B] Get:96 http://ftpmaster.internal/ubuntu cosmic/main amd64 libstdc++-8-dev amd64 8.2.0-1ubuntu2 [1535 kB] Get:97 http://ftpmaster.internal/ubuntu cosmic/main amd64 g++-8 amd64 8.2.0-1ubuntu2 [8102 kB] Get:98 http://ftpmaster.internal/ubuntu cosmic/main amd64 g++ amd64 4:8.1.0-2ubuntu1 [1604 B] Get:99 http://ftpmaster.internal/ubuntu cosmic/main amd64 make amd64 4.2.1-1.1 [162 kB] Get:100 http://ftpmaster.internal/ubuntu cosmic/main amd64 dpkg-dev all 1.19.0.5ubuntu3 [608 kB] Get:101 http://ftpmaster.internal/ubuntu cosmic/main amd64 libdpkg-perl all 1.19.0.5ubuntu3 [211 kB] Get:102 http://ftpmaster.internal/ubuntu cosmic/main amd64 build-essential amd64 12.5ubuntu2 [4732 B] Get:103 http://ftpmaster.internal/ubuntu cosmic/main amd64 libasan4 amd64 7.3.0-27ubuntu1 [359 kB] Get:104 http://ftpmaster.internal/ubuntu cosmic/main amd64 libubsan0 amd64 7.3.0-27ubuntu1 [126 kB] Get:105 http://ftpmaster.internal/ubuntu cosmic/main amd64 libcilkrts5 amd64 7.3.0-27ubuntu1 [42.5 kB] Get:106 http://ftpmaster.internal/ubuntu cosmic/universe amd64 g++-7 amd64 7.3.0-27ubuntu1 [7572 kB] Get:107 http://ftpmaster.internal/ubuntu cosmic/main amd64 gcc-7 amd64 7.3.0-27ubuntu1 [7452 kB] Get:108 http://ftpmaster.internal/ubuntu cosmic/main amd64 libstdc++-7-dev amd64 7.3.0-27ubuntu1 [1463 kB] Get:109 http://ftpmaster.internal/ubuntu cosmic/main amd64 libgcc-7-dev amd64 7.3.0-27ubuntu1 [2379 kB] Get:110 http://ftpmaster.internal/ubuntu cosmic/main amd64 cpp-7 amd64 7.3.0-27ubuntu1 [6736 kB] Get:111 http://ftpmaster.internal/ubuntu cosmic/main amd64 gcc-7-base amd64 7.3.0-27ubuntu1 [18.9 kB] Get:112 http://ftpmaster.internal/ubuntu cosmic/main amd64 e2fslibs amd64 1.44.3-1 [2704 B] Get:113 http://ftpmaster.internal/ubuntu cosmic/main amd64 pinentry-curses amd64 1.1.0-1build2 [35.9 kB] Get:114 http://ftpmaster.internal/ubuntu cosmic/main amd64 libnpth0 amd64 1.6-1 [7736 B] Get:115 http://ftpmaster.internal/ubuntu cosmic/main amd64 gpg amd64 2.2.8-1ubuntu1 [470 kB] Get:116 http://ftpmaster.internal/ubuntu cosmic/main amd64 gpgconf amd64 2.2.8-1ubuntu1 [122 kB] Get:117 http://ftpmaster.internal/ubuntu cosmic/main amd64 gpg-agent amd64 2.2.8-1ubuntu1 [228 kB] Get:118 http://ftpmaster.internal/ubuntu cosmic/universe amd64 libargon2-0 amd64 0~20171227-0.1 [4532 B] Get:119 http://ftpmaster.internal/ubuntu cosmic/main amd64 libcomerr2 amd64 1.44.3-1 [2704 B] Get:120 http://ftpmaster.internal/ubuntu cosmic/main amd64 libusb-0.1-4 amd64 2:0.1.12-32 [17.4 kB] Get:121 http://ftpmaster.internal/ubuntu cosmic-proposed/main amd64 linux-libc-dev amd64 4.17.0-6.7 [1008 kB] Get:122 http://ftpmaster.internal/ubuntu cosmic/main amd64 pkgbinarymangler all 141 [53.4 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 85.4 MB in 10s (8525 kB/s) (Reading database ... 12637 files and directories currently installed.) Preparing to unpack .../base-files_10.1ubuntu4_amd64.deb ... Unpacking base-files (10.1ubuntu4) over (10.1ubuntu2) ... Setting up base-files (10.1ubuntu4) ... Installing new version of config file /etc/issue ... Installing new version of config file /etc/issue.net ... Installing new version of config file /etc/lsb-release ... Selecting previously unselected package libtinfo6:amd64. (Reading database ... 12637 files and directories currently installed.) Preparing to unpack .../libtinfo6_6.1+20180210-4ubuntu1_amd64.deb ... Unpacking libtinfo6:amd64 (6.1+20180210-4ubuntu1) ... Setting up libtinfo6:amd64 (6.1+20180210-4ubuntu1) ... (Reading database ... 12646 files and directories currently installed.) Preparing to unpack .../debianutils_4.8.6_amd64.deb ... Unpacking debianutils (4.8.6) over (4.8.4) ... Setting up debianutils (4.8.6) ... (Reading database ... 12646 files and directories currently installed.) Preparing to unpack .../bash_4.4.18-2ubuntu2_amd64.deb ... Unpacking bash (4.4.18-2ubuntu2) over (4.4.18-2ubuntu1) ... Setting up bash (4.4.18-2ubuntu2) ... 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 ... 12646 files and directories currently installed.) Preparing to unpack .../bsdutils_1%3a2.32-0.1ubuntu1_amd64.deb ... Unpacking bsdutils (1:2.32-0.1ubuntu1) over (1:2.31.1-0.4ubuntu3) ... Setting up bsdutils (1:2.32-0.1ubuntu1) ... (Reading database ... 12646 files and directories currently installed.) Preparing to unpack .../tar_1.30+dfsg-2_amd64.deb ... Unpacking tar (1.30+dfsg-2) over (1.29b-2) ... Setting up tar (1.30+dfsg-2) ... (Reading database ... 12646 files and directories currently installed.) Preparing to unpack .../dpkg_1.19.0.5ubuntu3_amd64.deb ... Unpacking dpkg (1.19.0.5ubuntu3) over (1.19.0.5ubuntu2) ... Setting up dpkg (1.19.0.5ubuntu3) ... (Reading database ... 12646 files and directories currently installed.) 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Setting up systemd-sysv (239-7ubuntu1) ... Setting up libtsan0:amd64 (8.2.0-1ubuntu2) ... Setting up gpgconf (2.2.8-1ubuntu1) ... Setting up linux-libc-dev:amd64 (4.17.0-6.7) ... Setting up perl-modules-5.26 (5.26.2-6) ... Setting up liblsan0:amd64 (8.2.0-1ubuntu2) ... Setting up libargon2-0 (0~20171227-0.1) ... Setting up gcc-7-base:amd64 (7.3.0-27ubuntu1) ... Setting up binutils-common:amd64 (2.31.1-2ubuntu1) ... Setting up libmpx2:amd64 (8.2.0-1ubuntu2) ... Processing triggers for libc-bin (2.27-3ubuntu1) ... Setting up libperl5.26:amd64 (5.26.2-6) ... Setting up libssl1.1:amd64 (1.1.0g-2ubuntu5) ... Setting up openssl (1.1.0g-2ubuntu5) ... Setting up libsqlite3-0:amd64 (3.24.0-1) ... Setting up pinentry-curses (1.1.0-1build2) ... Setting up libcomerr2:amd64 (1.44.3-1) ... Setting up libslang2:amd64 (2.3.2-1ubuntu1) ... Setting up libasan5:amd64 (8.2.0-1ubuntu2) ... Setting up libusb-0.1-4:amd64 (2:0.1.12-32) ... Setting up libitm1:amd64 (8.2.0-1ubuntu2) ... Setting up libidn11:amd64 (1.33-2.2ubuntu1) ... Setting up gpg (2.2.8-1ubuntu1) ... Setting up libubsan1:amd64 (8.2.0-1ubuntu2) ... Setting up libasan4:amd64 (7.3.0-27ubuntu1) ... Setting up libbinutils:amd64 (2.31.1-2ubuntu1) ... Setting up libcilkrts5:amd64 (7.3.0-27ubuntu1) ... Setting up libubsan0:amd64 (7.3.0-27ubuntu1) ... Setting up gpg-agent (2.2.8-1ubuntu1) ... Setting up libgcc-7-dev:amd64 (7.3.0-27ubuntu1) ... Setting up cpp-7 (7.3.0-27ubuntu1) ... Setting up libstdc++-7-dev:amd64 (7.3.0-27ubuntu1) ... Setting up perl (5.26.2-6) ... Setting up libgcc-8-dev:amd64 (8.2.0-1ubuntu2) ... Setting up binutils-x86-64-linux-gnu (2.31.1-2ubuntu1) ... Setting up libstdc++-8-dev:amd64 (8.2.0-1ubuntu2) ... Setting up libdpkg-perl (1.19.0.5ubuntu3) ... Setting up binutils (2.31.1-2ubuntu1) ... Setting up gcc-7 (7.3.0-27ubuntu1) ... Setting up g++-7 (7.3.0-27ubuntu1) ... Setting up gcc-8 (8.2.0-1ubuntu2) ... Setting up g++-8 (8.2.0-1ubuntu2) ... Setting up dpkg-dev (1.19.0.5ubuntu3) ... Setting up gcc (4:8.1.0-2ubuntu1) ... Setting up g++ (4:8.1.0-2ubuntu1) ... Setting up build-essential (12.5ubuntu2) ... Processing triggers for libc-bin (2.27-3ubuntu1) ... RUN: /usr/share/launchpad-buildd/slavebin/sbuild-package PACKAGEBUILD-15221806 amd64 cosmic-proposed -c chroot:build-PACKAGEBUILD-15221806 --arch=amd64 --dist=cosmic-proposed --nolog -A iva_1.0.9+ds-6.dsc Initiating build PACKAGEBUILD-15221806 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 4.4.0-128-generic #154-Ubuntu SMP Fri May 25 14:15:18 UTC 2018 x86_64 sbuild (Debian sbuild) 0.67.0 (26 Dec 2015) on lgw01-amd64-026.buildd +==============================================================================+ | iva 1.0.9+ds-6 (amd64) 02 Aug 2018 05:10 | +==============================================================================+ Package: iva Version: 1.0.9+ds-6 Source Version: 1.0.9+ds-6 Distribution: cosmic-proposed Machine Architecture: amd64 Host Architecture: amd64 Build Architecture: amd64 I: NOTICE: Log filtering will replace 'build/iva-mLEubf/iva-1.0.9+ds' with '<>' I: NOTICE: Log filtering will replace 'build/iva-mLEubf' with '<>' I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-15221806/chroot-autobuild' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- iva_1.0.9+ds-6.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-gfSIBT/apt_archive/sbuild-build-depends-core-dummy.deb'. Ign:1 copy:/<>/resolver-gfSIBT/apt_archive ./ InRelease Get:2 copy:/<>/resolver-gfSIBT/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-gfSIBT/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-gfSIBT/apt_archive ./ Sources [214 B] Get:5 copy:/<>/resolver-gfSIBT/apt_archive ./ Packages [526 B] Fetched 2859 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: g++-7 libargon2-0 libncursesw5 libprocps6 libstdc++-7-dev 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-gfSIBT/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 ... 13730 files and directories currently installed.) Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_amd64.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~), dh-python, libssl-dev, bioperl, fastaq (>= 1.6), kmc, help2man, mummer, python3, python3-setuptools, python3-numpy, python3-nose, python3-networkx, python3-pysam, samtools, smalt, default-jdk-headless Filtered Build-Depends: debhelper (>= 11~), dh-python, libssl-dev, bioperl, fastaq (>= 1.6), kmc, help2man, mummer, python3, python3-setuptools, python3-numpy, python3-nose, python3-networkx, python3-pysam, samtools, smalt, default-jdk-headless dpkg-deb: building package 'sbuild-build-depends-iva-dummy' in '/<>/resolver-zOj6Pk/apt_archive/sbuild-build-depends-iva-dummy.deb'. Ign:1 copy:/<>/resolver-zOj6Pk/apt_archive ./ InRelease Get:2 copy:/<>/resolver-zOj6Pk/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-zOj6Pk/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-zOj6Pk/apt_archive ./ Sources [310 B] Get:5 copy:/<>/resolver-zOj6Pk/apt_archive ./ Packages [633 B] Fetched 3062 B in 0s (0 B/s) Reading package lists... Reading package lists... +------------------------------------------------------------------------------+ | Install iva build dependencies (apt-based resolver) | +------------------------------------------------------------------------------+ Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following packages were automatically installed and are no longer required: g++-7 libargon2-0 libncursesw5 libprocps6 libstdc++-7-dev Use 'apt autoremove' to remove them. The following additional packages will be installed: autoconf automake autopoint autotools-dev bioperl bsdmainutils ca-certificates-java debhelper default-jdk-headless default-jre-headless dh-autoreconf dh-python dh-strip-nondeterminism dwz fastaq file fontconfig-config fonts-dejavu-core gawk gettext gettext-base groff-base help2man intltool-debian java-common kmc libalgorithm-diff-perl libarchive-zip-perl libasn1-8-heimdal libavahi-client3 libavahi-common-data libavahi-common3 libbambamc0 libbio-perl-perl libblas3 libbsd0 libcapture-tiny-perl libclass-data-inheritable-perl libcroco3 libcups2 libcurl3-gnutls libdata-stag-perl libdbus-1-3 libdevel-stacktrace-perl libelf1 libexception-class-perl libexpat1 libfile-stripnondeterminism-perl libfontconfig1 libfreetype6 libgfortran5 libglib2.0-0 libgssapi-krb5-2 libgssapi3-heimdal libhcrypto4-heimdal libheimbase1-heimdal libheimntlm0-heimdal libhts2 libhx509-5-heimdal libicu60 libio-string-perl libjpeg-turbo8 libjpeg8 libk5crypto3 libkeyutils1 libkrb5-26-heimdal libkrb5-3 libkrb5support0 liblapack3 liblcms2-2 libldap-2.4-2 libldap-common liblocale-gettext-perl libmagic-mgc libmagic1 libmpdec2 libnghttp2-14 libnspr4 libnss3 libpcsclite1 libpipeline1 libpsl5 libpython3-stdlib libpython3.6-minimal libpython3.6-stdlib libpython3.7-minimal libpython3.7-stdlib libroken18-heimdal librtmp1 libsasl2-2 libsasl2-modules-db libsigsegv2 libssl-dev libsub-uplevel-perl libtest-deep-perl libtest-differences-perl libtest-exception-perl libtest-most-perl libtest-warn-perl libtext-diff-perl libtimedate-perl libtool libwind0-heimdal libx11-6 libx11-data libxau6 libxcb1 libxdmcp6 libxext6 libxi6 libxml2 libxrender1 libxtst6 m4 man-db mime-support mummer openjdk-11-jdk-headless openjdk-11-jre-headless po-debconf python3 python3-decorator python3-distutils python3-lib2to3 python3-minimal python3-networkx python3-nose python3-numpy python3-pkg-resources python3-pysam python3-setuptools python3.6 python3.6-minimal python3.7 python3.7-minimal samtools smalt ucf x11-common Suggested packages: autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois vacation dh-make default-jre gawk-doc gettext-doc libasprintf-dev libgettextpo-dev groff libxml-sax-expatxs-perl cups-common krb5-doc krb5-user liblcms2-utils pcscd libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc apparmor less www-browser openjdk-11-demo openjdk-11-source libnss-mdns fonts-dejavu-extra fonts-ipafont-gothic fonts-ipafont-mincho fonts-wqy-microhei | fonts-wqy-zenhei fonts-indic libmail-box-perl python3-doc python3-tk python3-venv python3-scipy python-nose-doc gfortran python-numpy-doc python3-dev python3-numpy-dbg python-setuptools-doc python3.6-venv python3.6-doc binfmt-support python3.7-venv python3.7-doc Recommended packages: bioperl-run perl-doc libhttp-message-perl libwww-perl libcache-cache-perl libbio-perl-run-perl libdbi-perl libgd-gd2-perl libapache-dbi-perl liburi-perl libxml-simple-perl libyaml-perl libace-perl liblist-moreutils-perl libxml-twig-perl libset-scalar-perl curl | wget | lynx libalgorithm-diff-xs-perl bioperl-run | libbio-perl-run-perl libalgorithm-munkres-perl libarray-compare-perl libbio-asn1-entrezgene-perl libclone-perl libconvert-binary-c-perl libdbd-sqlite3-perl libdbd-mysql-perl libdbd-pg-perl libgd-perl libgraph-perl libgraphviz-perl libhtml-parser-perl libhtml-tableextract-perl libpostscript-perl libsoap-lite-perl libsort-naturally-perl libspreadsheet-parseexcel-perl libspreadsheet-writeexcel-perl libsvg-perl libsvg-graph-perl libxml-dom-xpath-perl libxml-parser-perl libxml-sax-perl libxml-sax-writer-perl libxml-writer-perl libxml-libxml-perl perl-tk libgd-gd2-perl | libgd-gd2-noxpm-perl libxml-libxslt-perl libmldbm-perl libxml-perl dbus libarchive-cpio-perl libglib2.0-data shared-mime-info xdg-user-dirs krb5-locales publicsuffix libsasl2-modules libssl-doc libltdl-dev libmail-sendmail-perl python3-gdal python3-yaml python cwltool The following NEW packages will be installed: autoconf automake autopoint autotools-dev bioperl bsdmainutils ca-certificates-java debhelper default-jdk-headless default-jre-headless dh-autoreconf dh-python dh-strip-nondeterminism dwz fastaq file fontconfig-config fonts-dejavu-core gawk gettext gettext-base groff-base help2man intltool-debian java-common kmc libalgorithm-diff-perl libarchive-zip-perl libasn1-8-heimdal libavahi-client3 libavahi-common-data libavahi-common3 libbambamc0 libbio-perl-perl libblas3 libbsd0 libcapture-tiny-perl libclass-data-inheritable-perl libcroco3 libcups2 libcurl3-gnutls libdata-stag-perl libdbus-1-3 libdevel-stacktrace-perl libelf1 libexception-class-perl libexpat1 libfile-stripnondeterminism-perl libfontconfig1 libfreetype6 libgfortran5 libglib2.0-0 libgssapi-krb5-2 libgssapi3-heimdal libhcrypto4-heimdal libheimbase1-heimdal libheimntlm0-heimdal libhts2 libhx509-5-heimdal libicu60 libio-string-perl libjpeg-turbo8 libjpeg8 libk5crypto3 libkeyutils1 libkrb5-26-heimdal libkrb5-3 libkrb5support0 liblapack3 liblcms2-2 libldap-2.4-2 libldap-common liblocale-gettext-perl libmagic-mgc libmagic1 libmpdec2 libnghttp2-14 libnspr4 libnss3 libpcsclite1 libpipeline1 libpsl5 libpython3-stdlib libpython3.6-minimal libpython3.6-stdlib libpython3.7-minimal libpython3.7-stdlib libroken18-heimdal librtmp1 libsasl2-2 libsasl2-modules-db libsigsegv2 libssl-dev libsub-uplevel-perl libtest-deep-perl libtest-differences-perl libtest-exception-perl libtest-most-perl libtest-warn-perl libtext-diff-perl libtimedate-perl libtool libwind0-heimdal libx11-6 libx11-data libxau6 libxcb1 libxdmcp6 libxext6 libxi6 libxml2 libxrender1 libxtst6 m4 man-db mime-support mummer openjdk-11-jdk-headless openjdk-11-jre-headless po-debconf python3 python3-decorator python3-distutils python3-lib2to3 python3-minimal python3-networkx python3-nose python3-numpy python3-pkg-resources python3-pysam python3-setuptools python3.6 python3.6-minimal python3.7 python3.7-minimal samtools sbuild-build-depends-iva-dummy smalt ucf x11-common 0 upgraded, 140 newly installed, 0 to remove and 0 not upgraded. Need to get 283 MB of archives. After this operation, 597 MB of additional disk space will be used. Get:1 copy:/<>/resolver-zOj6Pk/apt_archive ./ sbuild-build-depends-iva-dummy 0.invalid.0 [960 B] Get:2 http://ftpmaster.internal/ubuntu cosmic/main amd64 liblocale-gettext-perl amd64 1.07-3build2 [16.6 kB] Get:3 http://ftpmaster.internal/ubuntu cosmic/main amd64 libpython3.6-minimal amd64 3.6.6-1 [531 kB] Get:4 http://ftpmaster.internal/ubuntu cosmic/main amd64 libexpat1 amd64 2.2.5-3 [80.2 kB] Get:5 http://ftpmaster.internal/ubuntu cosmic/main amd64 python3.6-minimal amd64 3.6.6-1 [1607 kB] Get:6 http://ftpmaster.internal/ubuntu cosmic/main amd64 python3-minimal amd64 3.6.6-1 [23.6 kB] Get:7 http://ftpmaster.internal/ubuntu cosmic/main amd64 mime-support all 3.60ubuntu1 [30.1 kB] Get:8 http://ftpmaster.internal/ubuntu cosmic/main amd64 libmpdec2 amd64 2.4.2-2 [84.1 kB] Get:9 http://ftpmaster.internal/ubuntu cosmic/main amd64 libpython3.6-stdlib amd64 3.6.6-1 [1708 kB] Get:10 http://ftpmaster.internal/ubuntu cosmic/main amd64 python3.6 amd64 3.6.6-1 [190 kB] Get:11 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groff-base amd64 1.22.3-10 [1153 kB] Get:22 http://ftpmaster.internal/ubuntu cosmic/main amd64 libpipeline1 amd64 1.5.0-1 [25.3 kB] Get:23 http://ftpmaster.internal/ubuntu cosmic/main amd64 man-db amd64 2.8.4-2 [1029 kB] Get:24 http://ftpmaster.internal/ubuntu cosmic/main amd64 libsigsegv2 amd64 2.12-2 [13.9 kB] Get:25 http://ftpmaster.internal/ubuntu cosmic/main amd64 gawk amd64 1:4.1.4+dfsg-1build1 [401 kB] Get:26 http://ftpmaster.internal/ubuntu cosmic/main amd64 libjpeg-turbo8 amd64 1.5.2-0ubuntu6 [110 kB] Get:27 http://ftpmaster.internal/ubuntu cosmic/main amd64 libpython3.7-minimal amd64 3.7.0-3 [548 kB] Get:28 http://ftpmaster.internal/ubuntu cosmic/main amd64 python3.7-minimal amd64 3.7.0-3 [1683 kB] Get:29 http://ftpmaster.internal/ubuntu cosmic/main amd64 libmagic-mgc amd64 1:5.33-3 [192 kB] Get:30 http://ftpmaster.internal/ubuntu cosmic/main amd64 libmagic1 amd64 1:5.33-3 [69.8 kB] Get:31 http://ftpmaster.internal/ubuntu cosmic/main amd64 file amd64 1:5.33-3 [22.9 kB] Get:32 http://ftpmaster.internal/ubuntu cosmic/main amd64 libdbus-1-3 amd64 1.12.2-1ubuntu1 [175 kB] Get:33 http://ftpmaster.internal/ubuntu cosmic/main amd64 libelf1 amd64 0.170-0.5 [44.1 kB] Get:34 http://ftpmaster.internal/ubuntu cosmic/main amd64 libglib2.0-0 amd64 2.56.1-2ubuntu1 [1167 kB] Get:35 http://ftpmaster.internal/ubuntu cosmic/main amd64 libicu60 amd64 60.2-6ubuntu1 [8055 kB] Get:36 http://ftpmaster.internal/ubuntu cosmic-proposed/main amd64 libxml2 amd64 2.9.4+dfsg1-7build1 [664 kB] Get:37 http://ftpmaster.internal/ubuntu cosmic/main amd64 ucf all 3.0038 [50.5 kB] Get:38 http://ftpmaster.internal/ubuntu cosmic/main amd64 gettext-base amd64 0.19.8.1-6build1 [50.0 kB] Get:39 http://ftpmaster.internal/ubuntu cosmic/main amd64 libkrb5support0 amd64 1.16-2build1 [31.1 kB] Get:40 http://ftpmaster.internal/ubuntu cosmic/main amd64 libk5crypto3 amd64 1.16-2build1 [85.6 kB] Get:41 http://ftpmaster.internal/ubuntu cosmic/main amd64 libkeyutils1 amd64 1.5.9-9.3 [9640 B] Get:42 http://ftpmaster.internal/ubuntu cosmic/main amd64 libkrb5-3 amd64 1.16-2build1 [279 kB] Get:43 http://ftpmaster.internal/ubuntu cosmic/main amd64 libgssapi-krb5-2 amd64 1.16-2build1 [122 kB] Get:44 http://ftpmaster.internal/ubuntu cosmic/main amd64 libpsl5 amd64 0.20.2-1 [49.3 kB] Get:45 http://ftpmaster.internal/ubuntu cosmic/main amd64 m4 amd64 1.4.18-1 [197 kB] Get:46 http://ftpmaster.internal/ubuntu cosmic/main amd64 autoconf all 2.69-11 [322 kB] Get:47 http://ftpmaster.internal/ubuntu cosmic/main amd64 autotools-dev all 20180224.1 [39.6 kB] Get:48 http://ftpmaster.internal/ubuntu cosmic/main amd64 automake all 1:1.15.1-3ubuntu2 [509 kB] Get:49 http://ftpmaster.internal/ubuntu cosmic/main amd64 autopoint all 0.19.8.1-6build1 [412 kB] Get:50 http://ftpmaster.internal/ubuntu cosmic/main amd64 libio-string-perl all 1.08-3 [11.1 kB] Get:51 http://ftpmaster.internal/ubuntu cosmic/universe amd64 libdata-stag-perl all 0.14-2 [369 kB] Get:52 http://ftpmaster.internal/ubuntu cosmic/universe amd64 libbio-perl-perl all 1.7.2-2 [4526 kB] Get:53 http://ftpmaster.internal/ubuntu cosmic/main amd64 libclass-data-inheritable-perl all 0.08-2 [8774 B] Get:54 http://ftpmaster.internal/ubuntu cosmic/main amd64 libdevel-stacktrace-perl all 2.0300-1 [22.4 kB] Get:55 http://ftpmaster.internal/ubuntu cosmic/main amd64 libexception-class-perl all 1.44-1 [25.9 kB] Get:56 http://ftpmaster.internal/ubuntu cosmic/universe amd64 libtest-deep-perl all 1.128-1 [41.3 kB] Get:57 http://ftpmaster.internal/ubuntu cosmic/universe amd64 libcapture-tiny-perl all 0.48-1 [20.4 kB] Get:58 http://ftpmaster.internal/ubuntu cosmic/main amd64 libalgorithm-diff-perl all 1.19.03-1 [47.6 kB] Get:59 http://ftpmaster.internal/ubuntu cosmic/universe amd64 libtext-diff-perl all 1.45-1 [25.7 kB] Get:60 http://ftpmaster.internal/ubuntu cosmic/universe amd64 libtest-differences-perl all 0.64-2 [16.5 kB] Get:61 http://ftpmaster.internal/ubuntu cosmic/universe amd64 libsub-uplevel-perl all 0.2800-1 [13.5 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http://ftpmaster.internal/ubuntu cosmic/main amd64 x11-common all 1:7.7+19ubuntu8 [22.5 kB] Get:83 http://ftpmaster.internal/ubuntu cosmic/main amd64 libxtst6 amd64 2:1.2.3-1 [12.8 kB] Get:84 http://ftpmaster.internal/ubuntu cosmic/main amd64 openjdk-11-jre-headless amd64 10.0.2+13-1ubuntu1 [39.3 MB] Get:85 http://ftpmaster.internal/ubuntu cosmic/main amd64 default-jre-headless amd64 2:1.10-63ubuntu1~02 [3412 B] Get:86 http://ftpmaster.internal/ubuntu cosmic/main amd64 ca-certificates-java all 20180516ubuntu1 [12.3 kB] Get:87 http://ftpmaster.internal/ubuntu cosmic/main amd64 libtool all 2.4.6-2.1build1 [196 kB] Get:88 http://ftpmaster.internal/ubuntu cosmic/main amd64 dh-autoreconf all 19 [16.1 kB] Get:89 http://ftpmaster.internal/ubuntu cosmic/main amd64 libarchive-zip-perl all 1.60-1ubuntu1 [84.6 kB] Get:90 http://ftpmaster.internal/ubuntu cosmic/main amd64 libfile-stripnondeterminism-perl all 0.042-1 [15.2 kB] Get:91 http://ftpmaster.internal/ubuntu cosmic/main amd64 libtimedate-perl all 2.3000-2 [37.5 kB] Get:92 http://ftpmaster.internal/ubuntu cosmic/main amd64 dh-strip-nondeterminism all 0.042-1 [5188 B] Get:93 http://ftpmaster.internal/ubuntu cosmic/main amd64 dwz amd64 0.12-2 [77.7 kB] Get:94 http://ftpmaster.internal/ubuntu cosmic/main amd64 libcroco3 amd64 0.6.12-2 [81.3 kB] Get:95 http://ftpmaster.internal/ubuntu cosmic/main amd64 gettext amd64 0.19.8.1-6build1 [895 kB] Get:96 http://ftpmaster.internal/ubuntu cosmic/main amd64 intltool-debian all 0.35.0+20060710.4 [24.9 kB] Get:97 http://ftpmaster.internal/ubuntu cosmic/main amd64 po-debconf all 1.0.20 [232 kB] Get:98 http://ftpmaster.internal/ubuntu cosmic/main amd64 debhelper all 11.3.2ubuntu1 [883 kB] Get:99 http://ftpmaster.internal/ubuntu cosmic/main amd64 openjdk-11-jdk-headless amd64 10.0.2+13-1ubuntu1 [193 MB] Get:100 http://ftpmaster.internal/ubuntu cosmic/main amd64 default-jdk-headless amd64 2:1.10-63ubuntu1~02 [1132 B] Get:101 http://ftpmaster.internal/ubuntu cosmic/main amd64 python3-lib2to3 all 3.6.6-1 [76.9 kB] Get:102 http://ftpmaster.internal/ubuntu cosmic/main amd64 python3-distutils all 3.6.6-1 [141 kB] Get:103 http://ftpmaster.internal/ubuntu cosmic/main amd64 dh-python all 3.20180723 [90.2 kB] Get:104 http://ftpmaster.internal/ubuntu cosmic/main amd64 python3-pkg-resources all 39.2.0-1 [98.8 kB] Get:105 http://ftpmaster.internal/ubuntu cosmic/main amd64 libroken18-heimdal amd64 7.5.0+dfsg-2 [41.3 kB] Get:106 http://ftpmaster.internal/ubuntu cosmic/main amd64 libasn1-8-heimdal amd64 7.5.0+dfsg-2 [174 kB] Get:107 http://ftpmaster.internal/ubuntu cosmic/main amd64 libheimbase1-heimdal amd64 7.5.0+dfsg-2 [29.3 kB] Get:108 http://ftpmaster.internal/ubuntu cosmic/main amd64 libhcrypto4-heimdal amd64 7.5.0+dfsg-2 [85.9 kB] Get:109 http://ftpmaster.internal/ubuntu cosmic/main amd64 libwind0-heimdal amd64 7.5.0+dfsg-2 [47.8 kB] Get:110 http://ftpmaster.internal/ubuntu cosmic/main amd64 libhx509-5-heimdal amd64 7.5.0+dfsg-2 [108 kB] Get:111 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http://ftpmaster.internal/ubuntu cosmic/main amd64 libcurl3-gnutls amd64 7.60.0-2ubuntu1 [214 kB] Get:121 http://ftpmaster.internal/ubuntu cosmic/universe amd64 libhts2 amd64 1.7-2 [300 kB] Get:122 http://ftpmaster.internal/ubuntu cosmic/universe amd64 samtools amd64 1.7-2 [406 kB] Get:123 http://ftpmaster.internal/ubuntu cosmic/universe amd64 fastaq all 3.17.0-2 [47.5 kB] Get:124 http://ftpmaster.internal/ubuntu cosmic/universe amd64 help2man amd64 1.47.6 [162 kB] Get:125 http://ftpmaster.internal/ubuntu cosmic/universe amd64 kmc amd64 2.3+dfsg-6 [500 kB] Get:126 http://ftpmaster.internal/ubuntu cosmic/universe amd64 libbambamc0 amd64 0.0.50-3 [36.9 kB] Get:127 http://ftpmaster.internal/ubuntu cosmic-proposed/main amd64 libblas3 amd64 3.8.0-1build1 [138 kB] Get:128 http://ftpmaster.internal/ubuntu cosmic/main amd64 libgfortran5 amd64 8.2.0-1ubuntu2 [589 kB] Get:129 http://ftpmaster.internal/ubuntu cosmic-proposed/main amd64 liblapack3 amd64 3.8.0-1build1 [2099 kB] Get:130 http://ftpmaster.internal/ubuntu cosmic/main amd64 libpython3.7-stdlib amd64 3.7.0-3 [1730 kB] Get:131 http://ftpmaster.internal/ubuntu cosmic/main amd64 libssl-dev amd64 1.1.0g-2ubuntu5 [1373 kB] Get:132 http://ftpmaster.internal/ubuntu cosmic/universe amd64 mummer amd64 3.23+dfsg-4 [811 kB] Get:133 http://ftpmaster.internal/ubuntu cosmic/main amd64 python3-decorator all 4.3.0-1 [9428 B] Get:134 http://ftpmaster.internal/ubuntu cosmic/universe amd64 python3-networkx all 2.1-1ubuntu2 [757 kB] Get:135 http://ftpmaster.internal/ubuntu cosmic/universe amd64 python3-nose all 1.3.7-4 [116 kB] Get:136 http://ftpmaster.internal/ubuntu cosmic/main amd64 python3.7 amd64 3.7.0-3 [264 kB] Get:137 http://ftpmaster.internal/ubuntu cosmic-proposed/main amd64 python3-numpy amd64 1:1.14.5-1ubuntu3 [2230 kB] Get:138 http://ftpmaster.internal/ubuntu cosmic/universe amd64 python3-pysam amd64 0.14+ds-2build1 [2230 kB] Get:139 http://ftpmaster.internal/ubuntu cosmic/main amd64 python3-setuptools all 39.2.0-1 [248 kB] Get:140 http://ftpmaster.internal/ubuntu cosmic/universe amd64 smalt amd64 0.7.6-7 [113 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 283 MB in 7s (38.7 MB/s) Selecting previously unselected package liblocale-gettext-perl. (Reading database ... 13730 files and directories currently installed.) Preparing to unpack .../liblocale-gettext-perl_1.07-3build2_amd64.deb ... Unpacking liblocale-gettext-perl (1.07-3build2) ... Selecting previously unselected package libpython3.6-minimal:amd64. Preparing to unpack .../libpython3.6-minimal_3.6.6-1_amd64.deb ... Unpacking libpython3.6-minimal:amd64 (3.6.6-1) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../libexpat1_2.2.5-3_amd64.deb ... Unpacking libexpat1:amd64 (2.2.5-3) ... Selecting previously unselected package python3.6-minimal. Preparing to unpack .../python3.6-minimal_3.6.6-1_amd64.deb ... Unpacking python3.6-minimal (3.6.6-1) ... Setting up libpython3.6-minimal:amd64 (3.6.6-1) ... Setting up libexpat1:amd64 (2.2.5-3) ... Setting up python3.6-minimal (3.6.6-1) ... Selecting previously unselected package python3-minimal. (Reading database ... 13991 files and directories currently installed.) 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Unpacking sbuild-build-depends-iva-dummy (0.invalid.0) ... Setting up libtest-deep-perl (1.128-1) ... Setting up libicu60:amd64 (60.2-6ubuntu1) ... Setting up libclass-data-inheritable-perl (0.08-2) ... Setting up libarchive-zip-perl (1.60-1ubuntu1) ... Setting up libnghttp2-14:amd64 (1.32.0-1) ... Setting up mime-support (3.60ubuntu1) ... Setting up libtimedate-perl (2.3000-2) ... Setting up liblcms2-2:amd64 (2.9-2) ... Setting up libpcsclite1:amd64 (1.8.23-3) ... Setting up libldap-common (2.4.46+dfsg-5ubuntu1) ... Setting up fonts-dejavu-core (2.37-1) ... Setting up libpsl5:amd64 (0.20.2-1) ... Setting up libdevel-stacktrace-perl (2.0300-1) ... Setting up libelf1:amd64 (0.170-0.5) ... Setting up libssl-dev:amd64 (1.1.0g-2ubuntu5) ... Setting up groff-base (1.22.3-10) ... Setting up libglib2.0-0:amd64 (2.56.1-2ubuntu1) ... No schema files found: doing nothing. Setting up libcapture-tiny-perl (0.48-1) ... Setting up libsasl2-modules-db:amd64 (2.1.27~101-g0780600+dfsg-3ubuntu2) ... Setting up java-common (0.63ubuntu1~02) ... Setting up libsasl2-2:amd64 (2.1.27~101-g0780600+dfsg-3ubuntu2) ... Setting up gettext-base (0.19.8.1-6build1) ... Setting up libjpeg-turbo8:amd64 (1.5.2-0ubuntu6) ... Setting up libpipeline1:amd64 (1.5.0-1) ... Setting up libroken18-heimdal:amd64 (7.5.0+dfsg-2) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2) ... Setting up kmc (2.3+dfsg-6) ... Setting up m4 (1.4.18-1) ... Setting up libpython3.7-minimal:amd64 (3.7.0-3) ... Setting up python3.7-minimal (3.7.0-3) ... Setting up gawk (1:4.1.4+dfsg-1build1) ... Setting up libbsd0:amd64 (0.9.1-1) ... Setting up libkrb5support0:amd64 (1.16-2build1) ... Setting up libnspr4:amd64 (2:4.18-1ubuntu1) ... Setting up ucf (3.0038) ... Setting up libxml2:amd64 (2.9.4+dfsg1-7build1) ... Setting up libfreetype6:amd64 (2.8.1-2ubuntu2) ... Setting up libmagic-mgc (1:5.33-3) ... Setting up libmagic1:amd64 (1:5.33-3) ... Setting up libcroco3:amd64 (0.6.12-2) ... Setting up libblas3:amd64 (3.8.0-1build1) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode Processing triggers for libc-bin (2.27-3ubuntu1) ... Setting up dwz (0.12-2) ... Setting up autotools-dev (20180224.1) ... Setting up libheimbase1-heimdal:amd64 (7.5.0+dfsg-2) ... Processing triggers for systemd (239-7ubuntu1) ... Setting up libio-string-perl (1.08-3) ... Setting up libalgorithm-diff-perl (1.19.03-1) ... Setting up liblocale-gettext-perl (1.07-3build2) ... Setting up libbambamc0 (0.0.50-3) ... Setting up libxdmcp6:amd64 (1:1.1.2-3) ... Setting up libkeyutils1:amd64 (1.5.9-9.3) ... 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 libsub-uplevel-perl (0.2800-1) ... Setting up x11-common (1:7.7+19ubuntu8) ... 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. Processing triggers for ca-certificates (20180409) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. Setting up libgfortran5:amd64 (8.2.0-1ubuntu2) ... Setting up libx11-data (2:1.6.5-1) ... Setting up libdata-stag-perl (0.14-2) ... Setting up libxau6:amd64 (1:1.0.8-1) ... Setting up autopoint (0.19.8.1-6build1) ... Setting up libmpdec2:amd64 (2.4.2-2) ... Setting up libdbus-1-3:amd64 (1.12.2-1ubuntu1) ... Setting up libavahi-common-data:amd64 (0.7-4ubuntu1) ... Setting up libtest-warn-perl (0.36-1) ... Setting up libfile-stripnondeterminism-perl (0.042-1) ... Setting up libjpeg8:amd64 (8c-2ubuntu8) ... Setting up libpython3.6-stdlib:amd64 (3.6.6-1) ... Setting up libk5crypto3:amd64 (1.16-2build1) ... Setting up libpython3.7-stdlib:amd64 (3.7.0-3) ... Setting up fontconfig-config (2.12.6-0ubuntu2) ... Setting up python3.6 (3.6.6-1) ... Setting up libbio-perl-perl (1.7.2-2) ... Setting up libexception-class-perl (1.44-1) ... Setting up libwind0-heimdal:amd64 (7.5.0+dfsg-2) ... Setting up gettext (0.19.8.1-6build1) ... Setting up libasn1-8-heimdal:amd64 (7.5.0+dfsg-2) ... Setting up mummer (3.23+dfsg-4) ... Setting up liblapack3:amd64 (3.8.0-1build1) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode Setting up libtext-diff-perl (1.45-1) ... Setting up libtest-exception-perl (0.43-1) ... Setting up libhcrypto4-heimdal:amd64 (7.5.0+dfsg-2) ... Setting up libnss3:amd64 (2:3.36.1-1ubuntu1) ... Setting up python3.7 (3.7.0-3) ... Setting up autoconf (2.69-11) ... Setting up file (1:5.33-3) ... Setting up libhx509-5-heimdal:amd64 (7.5.0+dfsg-2) ... Setting up smalt (0.7.6-7) ... Setting up intltool-debian (0.35.0+20060710.4) ... Setting up automake (1:1.15.1-3ubuntu2) ... update-alternatives: using /usr/bin/automake-1.15 to provide /usr/bin/automake (automake) in auto mode Setting up help2man (1.47.6) ... Setting up man-db (2.8.4-2) ... Not building database; man-db/auto-update is not 'true'. Setting up libkrb5-3:amd64 (1.16-2build1) ... Setting up libavahi-common3:amd64 (0.7-4ubuntu1) ... Setting up libkrb5-26-heimdal:amd64 (7.5.0+dfsg-2) ... Setting up libxcb1:amd64 (1.13-2) ... Setting up libheimntlm0-heimdal:amd64 (7.5.0+dfsg-2) ... Setting up libtool (2.4.6-2.1build1) ... Setting up libpython3-stdlib:amd64 (3.6.6-1) ... Setting up libfontconfig1:amd64 (2.12.6-0ubuntu2) ... Setting up libtest-differences-perl (0.64-2) ... Setting up po-debconf (1.0.20) ... Setting up python3 (3.6.6-1) ... Setting up python3-numpy (1:1.14.5-1ubuntu3) ... Setting up libx11-6:amd64 (2:1.6.5-1) ... Setting up python3-pkg-resources (39.2.0-1) ... Setting up libgssapi-krb5-2:amd64 (1.16-2build1) ... Setting up python3-nose (1.3.7-4) ... Setting up libxrender1:amd64 (1:0.9.10-1) ... Setting up libavahi-client3:amd64 (0.7-4ubuntu1) ... Setting up libgssapi3-heimdal:amd64 (7.5.0+dfsg-2) ... Setting up python3-lib2to3 (3.6.6-1) ... Setting up python3-decorator (4.3.0-1) ... Setting up python3-distutils (3.6.6-1) ... Setting up libcups2:amd64 (2.2.7-1ubuntu3) ... Setting up libtest-most-perl (0.35-1) ... Setting up libxext6:amd64 (2:1.3.3-1) ... Setting up libxtst6:amd64 (2:1.2.3-1) ... Setting up libldap-2.4-2:amd64 (2.4.46+dfsg-5ubuntu1) ... Setting up python3-networkx (2.1-1ubuntu2) ... Setting up bioperl (1.7.2-2) ... Setting up python3-setuptools (39.2.0-1) ... Setting up dh-python (3.20180723) ... Setting up libxi6:amd64 (2:1.7.9-1) ... Setting up libcurl3-gnutls:amd64 (7.60.0-2ubuntu1) ... Setting up libhts2:amd64 (1.7-2) ... Setting up python3-pysam (0.14+ds-2build1) ... Setting up samtools (1.7-2) ... Setting up fastaq (3.17.0-2) ... Setting up dh-autoreconf (19) ... Setting up openjdk-11-jre-headless:amd64 (10.0.2+13-1ubuntu1) ... update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/rmid to provide /usr/bin/rmid (rmid) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/java to provide /usr/bin/java (java) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/keytool to provide /usr/bin/keytool (keytool) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/jjs to provide /usr/bin/jjs (jjs) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/pack200 to provide /usr/bin/pack200 (pack200) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/rmiregistry to provide /usr/bin/rmiregistry (rmiregistry) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/unpack200 to provide /usr/bin/unpack200 (unpack200) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/orbd to provide /usr/bin/orbd (orbd) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/servertool to provide /usr/bin/servertool (servertool) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/tnameserv to provide /usr/bin/tnameserv (tnameserv) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/lib/jexec to provide /usr/bin/jexec (jexec) in auto mode Setting up openjdk-11-jdk-headless:amd64 (10.0.2+13-1ubuntu1) ... update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/jlink to provide /usr/bin/jlink (jlink) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/idlj to provide /usr/bin/idlj (idlj) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/jdeps to provide /usr/bin/jdeps (jdeps) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/wsimport to provide /usr/bin/wsimport (wsimport) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/rmic to provide /usr/bin/rmic (rmic) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/jinfo to provide /usr/bin/jinfo (jinfo) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/jstat to provide /usr/bin/jstat (jstat) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/javac to provide /usr/bin/javac (javac) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/jhsdb to provide /usr/bin/jhsdb (jhsdb) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/jps to provide /usr/bin/jps (jps) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/jstack to provide /usr/bin/jstack (jstack) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/jrunscript to provide /usr/bin/jrunscript (jrunscript) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/javadoc to provide /usr/bin/javadoc (javadoc) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/jmod to provide /usr/bin/jmod (jmod) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/javap to provide /usr/bin/javap (javap) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/jar to provide /usr/bin/jar (jar) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/jaotc to provide /usr/bin/jaotc (jaotc) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/schemagen to provide /usr/bin/schemagen (schemagen) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/jshell to provide /usr/bin/jshell (jshell) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/xjc to provide /usr/bin/xjc (xjc) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/jmap to provide /usr/bin/jmap (jmap) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/jdeprscan to provide /usr/bin/jdeprscan (jdeprscan) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/jimage to provide /usr/bin/jimage (jimage) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/jstatd to provide /usr/bin/jstatd (jstatd) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/jdb to provide /usr/bin/jdb (jdb) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/serialver to provide /usr/bin/serialver (serialver) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/wsgen to provide /usr/bin/wsgen (wsgen) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/jcmd to provide /usr/bin/jcmd (jcmd) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/jarsigner to provide /usr/bin/jarsigner (jarsigner) in auto mode Setting up dh-strip-nondeterminism (0.042-1) ... Setting up default-jre-headless (2:1.10-63ubuntu1~02) ... Setting up default-jdk-headless (2:1.10-63ubuntu1~02) ... Setting up debhelper (11.3.2ubuntu1) ... Setting up ca-certificates-java (20180516ubuntu1) ... head: cannot open '/etc/ssl/certs/java/cacerts' for reading: No such file or directory Adding debian:IdenTrust_Public_Sector_Root_CA_1.pem Adding debian:DST_Root_CA_X3.pem Adding debian:thawte_Primary_Root_CA_-_G2.pem Adding debian:GlobalSign_Root_CA_-_R3.pem Adding debian:T-TeleSec_GlobalRoot_Class_3.pem Adding debian:Starfield_Class_2_CA.pem Adding debian:Global_Chambersign_Root_-_2008.pem Adding debian:QuoVadis_Root_CA_2.pem Adding debian:GeoTrust_Universal_CA.pem Adding debian:Certum_Trusted_Network_CA.pem Adding debian:DigiCert_Assured_ID_Root_G2.pem Adding debian:AffirmTrust_Networking.pem Adding debian:Actalis_Authentication_Root_CA.pem Adding debian:AC_RAIZ_FNMT-RCM.pem Adding debian:Buypass_Class_3_Root_CA.pem Adding debian:EC-ACC.pem Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2015.pem Adding debian:TeliaSonera_Root_CA_v1.pem Adding debian:TWCA_Global_Root_CA.pem Adding debian:GlobalSign_ECC_Root_CA_-_R5.pem Adding debian:COMODO_Certification_Authority.pem Adding debian:GeoTrust_Primary_Certification_Authority_-_G3.pem Adding debian:Certigna.pem Adding debian:Deutsche_Telekom_Root_CA_2.pem Adding debian:Sonera_Class_2_Root_CA.pem Adding debian:TrustCor_RootCert_CA-1.pem Adding debian:Security_Communication_Root_CA.pem Adding debian:Izenpe.com.pem Adding debian:Amazon_Root_CA_3.pem Adding debian:DigiCert_Assured_ID_Root_G3.pem Adding debian:OISTE_WISeKey_Global_Root_GB_CA.pem Adding debian:ACCVRAIZ1.pem Adding debian:Cybertrust_Global_Root.pem Adding debian:Security_Communication_RootCA2.pem Adding debian:Secure_Global_CA.pem Adding debian:Entrust.net_Premium_2048_Secure_Server_CA.pem Adding debian:Amazon_Root_CA_1.pem Adding debian:TÜRKTRUST_Elektronik_Sertifika_Hizmet_Sağlayıcısı_H5.pem Adding debian:ePKI_Root_Certification_Authority.pem Adding debian:Go_Daddy_Class_2_CA.pem Adding debian:D-TRUST_Root_Class_3_CA_2_2009.pem Adding debian:Comodo_AAA_Services_root.pem Adding debian:OISTE_WISeKey_Global_Root_GA_CA.pem Adding debian:USERTrust_ECC_Certification_Authority.pem Adding debian:CA_Disig_Root_R2.pem Adding debian:SecureTrust_CA.pem Adding debian:SecureSign_RootCA11.pem Adding debian:OpenTrust_Root_CA_G1.pem Adding debian:Certplus_Root_CA_G1.pem Adding debian:Staat_der_Nederlanden_Root_CA_-_G3.pem Adding debian:VeriSign_Universal_Root_Certification_Authority.pem Adding debian:DigiCert_Global_Root_CA.pem Adding debian:Go_Daddy_Root_Certificate_Authority_-_G2.pem Adding debian:TrustCor_ECA-1.pem Adding debian:E-Tugra_Certification_Authority.pem Adding debian:GeoTrust_Universal_CA_2.pem Adding debian:SSL.com_EV_Root_Certification_Authority_ECC.pem Adding debian:XRamp_Global_CA_Root.pem Adding debian:AffirmTrust_Commercial.pem Adding debian:Atos_TrustedRoot_2011.pem Adding debian:EE_Certification_Centre_Root_CA.pem Adding debian:Trustis_FPS_Root_CA.pem Adding debian:Baltimore_CyberTrust_Root.pem Adding debian:Certplus_Class_2_Primary_CA.pem Adding debian:DigiCert_Trusted_Root_G4.pem Adding debian:SwissSign_Silver_CA_-_G2.pem Adding debian:VeriSign_Class_3_Public_Primary_Certification_Authority_-_G5.pem Adding debian:Starfield_Services_Root_Certificate_Authority_-_G2.pem Adding debian:GlobalSign_ECC_Root_CA_-_R4.pem Adding debian:ISRG_Root_X1.pem Adding debian:thawte_Primary_Root_CA_-_G3.pem Adding debian:Hellenic_Academic_and_Research_Institutions_ECC_RootCA_2015.pem Adding debian:CFCA_EV_ROOT.pem Adding debian:Certum_Trusted_Network_CA_2.pem Adding debian:AffirmTrust_Premium_ECC.pem Adding debian:QuoVadis_Root_CA.pem Adding debian:NetLock_Arany_=Class_Gold=_Főtanúsítvány.pem Adding debian:GDCA_TrustAUTH_R5_ROOT.pem Adding debian:certSIGN_ROOT_CA.pem Adding debian:USERTrust_RSA_Certification_Authority.pem Adding debian:Visa_eCommerce_Root.pem Adding debian:AddTrust_External_Root.pem Adding debian:GeoTrust_Primary_Certification_Authority_-_G2.pem Adding debian:Entrust_Root_Certification_Authority_-_EC1.pem Adding debian:SSL.com_Root_Certification_Authority_RSA.pem Adding debian:Hongkong_Post_Root_CA_1.pem Adding debian:T-TeleSec_GlobalRoot_Class_2.pem Adding debian:Chambers_of_Commerce_Root_-_2008.pem Adding debian:LuxTrust_Global_Root_2.pem Adding debian:thawte_Primary_Root_CA.pem Adding debian:COMODO_ECC_Certification_Authority.pem Adding debian:TWCA_Root_Certification_Authority.pem Adding debian:DigiCert_Global_Root_G2.pem Adding debian:Network_Solutions_Certificate_Authority.pem Adding debian:Certplus_Root_CA_G2.pem Adding debian:IdenTrust_Commercial_Root_CA_1.pem Adding debian:Amazon_Root_CA_2.pem Adding debian:GlobalSign_Root_CA_-_R2.pem Adding debian:QuoVadis_Root_CA_3.pem Adding debian:GeoTrust_Primary_Certification_Authority.pem Adding debian:Buypass_Class_2_Root_CA.pem Adding debian:GlobalSign_Root_CA.pem Adding debian:TUBITAK_Kamu_SM_SSL_Kok_Sertifikasi_-_Surum_1.pem Adding debian:QuoVadis_Root_CA_2_G3.pem Adding debian:AffirmTrust_Premium.pem Adding debian:QuoVadis_Root_CA_1_G3.pem Adding debian:Staat_der_Nederlanden_EV_Root_CA.pem Adding debian:Amazon_Root_CA_4.pem Adding debian:SSL.com_Root_Certification_Authority_ECC.pem Adding debian:Microsec_e-Szigno_Root_CA_2009.pem Adding debian:DigiCert_Assured_ID_Root_CA.pem Adding debian:D-TRUST_Root_Class_3_CA_2_EV_2009.pem Adding debian:DigiCert_Global_Root_G3.pem Adding debian:Staat_der_Nederlanden_Root_CA_-_G2.pem Adding debian:Autoridad_de_Certificacion_Firmaprofesional_CIF_A62634068.pem Adding debian:Taiwan_GRCA.pem Adding debian:Entrust_Root_Certification_Authority_-_G2.pem Adding debian:Entrust_Root_Certification_Authority.pem Adding debian:DigiCert_High_Assurance_EV_Root_CA.pem Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2011.pem Adding debian:GeoTrust_Global_CA.pem Adding debian:OpenTrust_Root_CA_G3.pem Adding debian:SSL.com_EV_Root_Certification_Authority_RSA_R2.pem Adding debian:Verisign_Class_3_Public_Primary_Certification_Authority_-_G3.pem Adding debian:SwissSign_Gold_CA_-_G2.pem Adding debian:COMODO_RSA_Certification_Authority.pem Adding debian:Certinomis_-_Root_CA.pem Adding debian:TrustCor_RootCert_CA-2.pem Adding debian:QuoVadis_Root_CA_3_G3.pem Adding debian:OpenTrust_Root_CA_G2.pem Adding debian:VeriSign_Class_3_Public_Primary_Certification_Authority_-_G4.pem Adding debian:Starfield_Root_Certificate_Authority_-_G2.pem Adding debian:SZAFIR_ROOT_CA2.pem done. Setting up sbuild-build-depends-iva-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.27-3ubuntu1) ... Processing triggers for systemd (239-7ubuntu1) ... Processing triggers for ca-certificates (20180409) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. done. +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 4.4.0-128-generic amd64 (x86_64) Toolchain package versions: binutils_2.31.1-2ubuntu1 dpkg-dev_1.19.0.5ubuntu3 g++-7_7.3.0-27ubuntu1 g++-8_8.2.0-1ubuntu2 gcc-7_7.3.0-27ubuntu1 gcc-8_8.2.0-1ubuntu2 libc6-dev_2.27-3ubuntu1 libstdc++-7-dev_7.3.0-27ubuntu1 libstdc++-8-dev_8.2.0-1ubuntu2 libstdc++6_8.2.0-1ubuntu2 linux-libc-dev_4.17.0-6.7 Package versions: adduser_3.117ubuntu1 advancecomp_2.1-1 apt_1.7.0~alpha2 autoconf_2.69-11 automake_1:1.15.1-3ubuntu2 autopoint_0.19.8.1-6build1 autotools-dev_20180224.1 base-files_10.1ubuntu4 base-passwd_3.5.45 bash_4.4.18-2ubuntu2 binutils_2.31.1-2ubuntu1 binutils-common_2.31.1-2ubuntu1 binutils-x86-64-linux-gnu_2.31.1-2ubuntu1 bioperl_1.7.2-2 bsdmainutils_11.1.2ubuntu2 bsdutils_1:2.32-0.1ubuntu1 build-essential_12.5ubuntu2 bzip2_1.0.6-8.1 ca-certificates_20180409 ca-certificates-java_20180516ubuntu1 coreutils_8.28-1ubuntu1 cpp_4:8.1.0-2ubuntu1 cpp-7_7.3.0-27ubuntu1 cpp-8_8.2.0-1ubuntu2 dash_0.5.8-2.10 debconf_1.5.69 debhelper_11.3.2ubuntu1 debianutils_4.8.6 default-jdk-headless_2:1.10-63ubuntu1~02 default-jre-headless_2:1.10-63ubuntu1~02 dh-autoreconf_19 dh-python_3.20180723 dh-strip-nondeterminism_0.042-1 diffutils_1:3.6-1 dmsetup_2:1.02.145-4.1ubuntu3 dpkg_1.19.0.5ubuntu3 dpkg-dev_1.19.0.5ubuntu3 dwz_0.12-2 e2fslibs_1.44.3-1 e2fsprogs_1.44.3-1 fakeroot_1.22-2ubuntu1 fastaq_3.17.0-2 fdisk_2.32-0.1ubuntu1 file_1:5.33-3 findutils_4.6.0+git+20170828-2 fontconfig-config_2.12.6-0ubuntu2 fonts-dejavu-core_2.37-1 g++_4:8.1.0-2ubuntu1 g++-7_7.3.0-27ubuntu1 g++-8_8.2.0-1ubuntu2 gawk_1:4.1.4+dfsg-1build1 gcc_4:8.1.0-2ubuntu1 gcc-7_7.3.0-27ubuntu1 gcc-7-base_7.3.0-27ubuntu1 gcc-8_8.2.0-1ubuntu2 gcc-8-base_8.2.0-1ubuntu2 gettext_0.19.8.1-6build1 gettext-base_0.19.8.1-6build1 gpg_2.2.8-1ubuntu1 gpg-agent_2.2.8-1ubuntu1 gpgconf_2.2.8-1ubuntu1 gpgv_2.2.8-1ubuntu1 grep_3.1-2 groff-base_1.22.3-10 gzip_1.6-5ubuntu1 help2man_1.47.6 hostname_3.20 init_1.51 init-system-helpers_1.51 initscripts_2.88dsf-59.3ubuntu2 insserv_1.14.0-5ubuntu3 intltool-debian_0.35.0+20060710.4 java-common_0.63ubuntu1~02 kmc_2.3+dfsg-6 libacl1_2.2.52-3build1 libalgorithm-diff-perl_1.19.03-1 libapparmor1_2.12-4ubuntu7 libapt-pkg5.0_1.7.0~alpha2 libarchive-zip-perl_1.60-1ubuntu1 libargon2-0_0~20171227-0.1 libargon2-1_0~20171227-0.1 libasan4_7.3.0-27ubuntu1 libasan5_8.2.0-1ubuntu2 libasn1-8-heimdal_7.5.0+dfsg-2 libassuan0_2.5.1-2 libatomic1_8.2.0-1ubuntu2 libattr1_1:2.4.47-2build1 libaudit-common_1:2.8.3-1ubuntu2 libaudit1_1:2.8.3-1ubuntu2 libavahi-client3_0.7-4ubuntu1 libavahi-common-data_0.7-4ubuntu1 libavahi-common3_0.7-4ubuntu1 libbambamc0_0.0.50-3 libbinutils_2.31.1-2ubuntu1 libbio-perl-perl_1.7.2-2 libblas3_3.8.0-1build1 libblkid1_2.32-0.1ubuntu1 libbsd0_0.9.1-1 libbz2-1.0_1.0.6-8.1 libc-bin_2.27-3ubuntu1 libc-dev-bin_2.27-3ubuntu1 libc6_2.27-3ubuntu1 libc6-dev_2.27-3ubuntu1 libcap-ng0_0.7.9-1 libcap2_1:2.25-1.2 libcapture-tiny-perl_0.48-1 libcc1-0_8.2.0-1ubuntu2 libcilkrts5_7.3.0-27ubuntu1 libclass-data-inheritable-perl_0.08-2 libcom-err2_1.44.3-1 libcomerr2_1.44.3-1 libcroco3_0.6.12-2 libcryptsetup12_2:2.0.3-6ubuntu1 libcups2_2.2.7-1ubuntu3 libcurl3-gnutls_7.60.0-2ubuntu1 libdata-stag-perl_0.14-2 libdb5.3_5.3.28-13.1ubuntu1 libdbus-1-3_1.12.2-1ubuntu1 libdebconfclient0_0.213ubuntu1 libdevel-stacktrace-perl_2.0300-1 libdevmapper1.02.1_2:1.02.145-4.1ubuntu3 libdpkg-perl_1.19.0.5ubuntu3 libelf1_0.170-0.5 libexception-class-perl_1.44-1 libexpat1_2.2.5-3 libext2fs2_1.44.3-1 libfakeroot_1.22-2ubuntu1 libfdisk1_2.32-0.1ubuntu1 libffi6_3.2.1-8 libfile-stripnondeterminism-perl_0.042-1 libfontconfig1_2.12.6-0ubuntu2 libfreetype6_2.8.1-2ubuntu2 libgcc-7-dev_7.3.0-27ubuntu1 libgcc-8-dev_8.2.0-1ubuntu2 libgcc1_1:8.2.0-1ubuntu2 libgcrypt20_1.8.3-1ubuntu1 libgdbm-compat4_1.14.1-6 libgdbm5_1.14.1-6 libgfortran5_8.2.0-1ubuntu2 libglib2.0-0_2.56.1-2ubuntu1 libgmp10_2:6.1.2+dfsg-3 libgnutls30_3.5.18-1ubuntu1 libgomp1_8.2.0-1ubuntu2 libgpg-error0_1.32-1 libgssapi-krb5-2_1.16-2build1 libgssapi3-heimdal_7.5.0+dfsg-2 libhcrypto4-heimdal_7.5.0+dfsg-2 libheimbase1-heimdal_7.5.0+dfsg-2 libheimntlm0-heimdal_7.5.0+dfsg-2 libhogweed4_3.4-1 libhts2_1.7-2 libhx509-5-heimdal_7.5.0+dfsg-2 libicu60_60.2-6ubuntu1 libidn11_1.33-2.2ubuntu1 libidn2-0_2.0.4-2.2 libio-string-perl_1.08-3 libip4tc0_1.6.1-2ubuntu2 libisl19_0.19-1 libitm1_8.2.0-1ubuntu2 libjpeg-turbo8_1.5.2-0ubuntu6 libjpeg8_8c-2ubuntu8 libjson-c3_0.12.1-1.3 libk5crypto3_1.16-2build1 libkeyutils1_1.5.9-9.3 libkmod2_25-1ubuntu1 libkrb5-26-heimdal_7.5.0+dfsg-2 libkrb5-3_1.16-2build1 libkrb5support0_1.16-2build1 liblapack3_3.8.0-1build1 liblcms2-2_2.9-2 libldap-2.4-2_2.4.46+dfsg-5ubuntu1 libldap-common_2.4.46+dfsg-5ubuntu1 liblocale-gettext-perl_1.07-3build2 liblockfile-bin_1.14-1.1 liblockfile1_1.14-1.1 liblsan0_8.2.0-1ubuntu2 liblz4-1_1.8.2-1ubuntu1 liblzma5_5.2.2-1.3 libmagic-mgc_1:5.33-3 libmagic1_1:5.33-3 libmount1_2.32-0.1ubuntu1 libmpc3_1.1.0-1 libmpdec2_2.4.2-2 libmpfr6_4.0.1-1 libmpx2_8.2.0-1ubuntu2 libncurses5_6.1+20180210-4ubuntu1 libncurses6_6.1+20180210-4ubuntu1 libncursesw5_6.1+20180210-4ubuntu1 libncursesw6_6.1+20180210-4ubuntu1 libnettle6_3.4-1 libnghttp2-14_1.32.0-1 libnpth0_1.6-1 libnspr4_2:4.18-1ubuntu1 libnss3_2:3.36.1-1ubuntu1 libp11-kit0_0.23.12-2 libpam-modules_1.1.8-3.6ubuntu2 libpam-modules-bin_1.1.8-3.6ubuntu2 libpam-runtime_1.1.8-3.6ubuntu2 libpam0g_1.1.8-3.6ubuntu2 libpcre3_2:8.39-11 libpcsclite1_1.8.23-3 libperl5.26_5.26.2-6 libpipeline1_1.5.0-1 libpng16-16_1.6.34-2 libprocps6_2:3.3.12-3ubuntu1 libprocps7_2:3.3.15-2ubuntu1 libpsl5_0.20.2-1 libpython3-stdlib_3.6.6-1 libpython3.6-minimal_3.6.6-1 libpython3.6-stdlib_3.6.6-1 libpython3.7-minimal_3.7.0-3 libpython3.7-stdlib_3.7.0-3 libquadmath0_8.2.0-1ubuntu2 libreadline7_7.0-5 libroken18-heimdal_7.5.0+dfsg-2 librtmp1_2.4+20151223.gitfa8646d.1-2 libsasl2-2_2.1.27~101-g0780600+dfsg-3ubuntu2 libsasl2-modules-db_2.1.27~101-g0780600+dfsg-3ubuntu2 libseccomp2_2.3.3-3ubuntu1 libselinux1_2.8-1build1 libsemanage-common_2.8-1build1 libsemanage1_2.8-1build1 libsepol1_2.8-1 libsigsegv2_2.12-2 libslang2_2.3.2-1ubuntu1 libsmartcols1_2.32-0.1ubuntu1 libsqlite3-0_3.24.0-1 libss2_1.44.3-1 libssl-dev_1.1.0g-2ubuntu5 libssl1.1_1.1.0g-2ubuntu5 libstdc++-7-dev_7.3.0-27ubuntu1 libstdc++-8-dev_8.2.0-1ubuntu2 libstdc++6_8.2.0-1ubuntu2 libsub-uplevel-perl_0.2800-1 libsystemd0_239-7ubuntu1 libtasn1-6_4.13-3 libtest-deep-perl_1.128-1 libtest-differences-perl_0.64-2 libtest-exception-perl_0.43-1 libtest-most-perl_0.35-1 libtest-warn-perl_0.36-1 libtext-diff-perl_1.45-1 libtimedate-perl_2.3000-2 libtinfo5_6.1+20180210-4ubuntu1 libtinfo6_6.1+20180210-4ubuntu1 libtool_2.4.6-2.1build1 libtsan0_8.2.0-1ubuntu2 libubsan0_7.3.0-27ubuntu1 libubsan1_8.2.0-1ubuntu2 libudev1_239-7ubuntu1 libunistring2_0.9.10-1ubuntu1 libusb-0.1-4_2:0.1.12-32 libuuid1_2.32-0.1ubuntu1 libwind0-heimdal_7.5.0+dfsg-2 libx11-6_2:1.6.5-1 libx11-data_2:1.6.5-1 libxau6_1:1.0.8-1 libxcb1_1.13-2 libxdmcp6_1:1.1.2-3 libxext6_2:1.3.3-1 libxi6_2:1.7.9-1 libxml2_2.9.4+dfsg1-7build1 libxrender1_1:0.9.10-1 libxtst6_2:1.2.3-1 libzstd1_1.3.3+dfsg-2ubuntu1 linux-libc-dev_4.17.0-6.7 lockfile-progs_0.1.17build1 login_1:4.5-1ubuntu1 lsb-base_9.20170808ubuntu1 m4_1.4.18-1 make_4.2.1-1.1 man-db_2.8.4-2 mawk_1.3.3-17ubuntu3 mime-support_3.60ubuntu1 mount_2.32-0.1ubuntu1 multiarch-support_2.27-3ubuntu1 mummer_3.23+dfsg-4 ncurses-base_6.1+20180210-4ubuntu1 ncurses-bin_6.1+20180210-4ubuntu1 openjdk-11-jdk-headless_10.0.2+13-1ubuntu1 openjdk-11-jre-headless_10.0.2+13-1ubuntu1 openssl_1.1.0g-2ubuntu5 optipng_0.7.6-1.1 passwd_1:4.5-1ubuntu1 patch_2.7.6-2ubuntu1 perl_5.26.2-6 perl-base_5.26.2-6 perl-modules-5.26_5.26.2-6 pinentry-curses_1.1.0-1build2 pkgbinarymangler_141 po-debconf_1.0.20 policyrcd-script-zg2_0.1-3 procps_2:3.3.15-2ubuntu1 python3_3.6.6-1 python3-decorator_4.3.0-1 python3-distutils_3.6.6-1 python3-lib2to3_3.6.6-1 python3-minimal_3.6.6-1 python3-networkx_2.1-1ubuntu2 python3-nose_1.3.7-4 python3-numpy_1:1.14.5-1ubuntu3 python3-pkg-resources_39.2.0-1 python3-pysam_0.14+ds-2build1 python3-setuptools_39.2.0-1 python3.6_3.6.6-1 python3.6-minimal_3.6.6-1 python3.7_3.7.0-3 python3.7-minimal_3.7.0-3 readline-common_7.0-5 samtools_1.7-2 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-iva-dummy_0.invalid.0 sed_4.5-1 sensible-utils_0.0.12 smalt_0.7.6-7 systemd_239-7ubuntu1 systemd-sysv_239-7ubuntu1 sysv-rc_2.88dsf-59.3ubuntu2 sysvinit-utils_2.88dsf-59.10ubuntu1 tar_1.30+dfsg-2 tzdata_2018e-1 ubuntu-keyring_2018.02.28 ucf_3.0038 util-linux_2.32-0.1ubuntu1 x11-common_1:7.7+19ubuntu8 xz-utils_5.2.2-1.3 zlib1g_1:1.2.11.dfsg-0ubuntu2 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- gpgv: Signature made Wed Aug 1 19:53:01 2018 UTC gpgv: using RSA key 8451F9178172E7E2DC73F79551F84A8FECCA7E09 gpgv: issuer "satta@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./iva_1.0.9+ds-6.dsc dpkg-source: info: extracting iva in iva-1.0.9+ds dpkg-source: info: unpacking iva_1.0.9+ds.orig.tar.xz dpkg-source: info: unpacking iva_1.0.9+ds-6.debian.tar.xz dpkg-source: info: applying disable-multithreaded-test.patch dpkg-source: info: applying perl-shebang.patch Check disc space ---------------- Sufficient free space for build User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf DEB_BUILD_OPTIONS=parallel=4 HOME=/sbuild-nonexistent LANG=C.UTF-8 LC_ALL=C.UTF-8 LOGNAME=buildd PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games SCHROOT_ALIAS_NAME=build-PACKAGEBUILD-15221806 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-15221806 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-15221806 SCHROOT_UID=2001 SCHROOT_USER=buildd SHELL=/bin/sh TERM=unknown USER=buildd V=1 dpkg-buildpackage ----------------- dpkg-buildpackage: info: source package iva dpkg-buildpackage: info: source version 1.0.9+ds-6 dpkg-buildpackage: info: source distribution unstable dpkg-source --before-build iva-1.0.9+ds dpkg-buildpackage: info: host architecture amd64 fakeroot debian/rules clean dh clean --with python3 --buildsystem=pybuild debian/rules override_dh_auto_clean make[1]: Entering directory '/<>/iva-1.0.9+ds' rm -rf .pybuild rm -f iva/gage/*.class rm -rf /<>/iva-1.0.9+ds/debian/man find . -name __pycache__ | xargs rm -rf make[1]: Leaving directory '/<>/iva-1.0.9+ds' dh_clean -O--buildsystem=pybuild debian/rules build dh build --with python3 --buildsystem=pybuild dh_update_autotools_config -O--buildsystem=pybuild dh_autoreconf -O--buildsystem=pybuild dh_auto_configure -O--buildsystem=pybuild I: pybuild base:217: python3.6 setup.py config Checking dependencies found in path: OK kmc OK kmc_dump OK nucmer OK delta-filter OK show-coords OK samtools OK smalt running config debian/rules override_dh_auto_build make[1]: Entering directory '/<>/iva-1.0.9+ds' chmod a-x /<>/iva-1.0.9+ds/iva/read_trim/adapters.fasta chmod a+x /<>/iva-1.0.9+ds/iva/gage/getCorrectnessStats.sh chmod a+x /<>/iva-1.0.9+ds/iva/ratt/main.ratt.pl chmod a+x scripts/* javac -verbose /<>/iva-1.0.9+ds/iva/gage/*.java [parsing started SimpleFileObject[/<>/iva-1.0.9+ds/iva/gage/GetFastaStats.java]] [parsing completed 66ms] [parsing started SimpleFileObject[/<>/iva-1.0.9+ds/iva/gage/SizeFasta.java]] [parsing completed 4ms] [parsing started SimpleFileObject[/<>/iva-1.0.9+ds/iva/gage/SplitFastaByLetter.java]] [parsing completed 2ms] [parsing started SimpleFileObject[/<>/iva-1.0.9+ds/iva/gage/Utils.java]] [parsing completed 10ms] [parsing started SimpleFileObject[/<>/iva-1.0.9+ds/iva/gage/getScaffoldStats.java]] [parsing completed 30ms] [loading /modules/jdk.naming.rmi/module-info.class] [loading /modules/jdk.internal.le/module-info.class] [loading /modules/jdk.naming.dns/module-info.class] [loading /modules/jdk.jartool/module-info.class] [loading /modules/java.datatransfer/module-info.class] [loading /modules/jdk.charsets/module-info.class] [loading /modules/java.sql/module-info.class] [loading /modules/java.se.ee/module-info.class] [loading /modules/java.sql.rowset/module-info.class] [loading /modules/jdk.jdwp.agent/module-info.class] [loading /modules/java.xml.ws.annotation/module-info.class] [loading /modules/java.naming/module-info.class] [loading /modules/jdk.httpserver/module-info.class] [loading /modules/jdk.jconsole/module-info.class] [loading /modules/jdk.xml.dom/module-info.class] [loading /modules/java.xml.crypto/module-info.class] [loading /modules/java.prefs/module-info.class] [loading 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[loading /modules/jdk.compiler/module-info.class] [loading /modules/jdk.internal.vm.compiler/module-info.class] [loading /modules/java.desktop/module-info.class] [loading /modules/jdk.internal.vm.ci/module-info.class] [loading /modules/jdk.rmic/module-info.class] [loading /modules/jdk.hotspot.agent/module-info.class] [loading /modules/java.base/module-info.class] [loading /modules/java.rmi/module-info.class] [loading /modules/jdk.jsobject/module-info.class] [loading /modules/jdk.scripting.nashorn.shell/module-info.class] [loading /modules/jdk.management.agent/module-info.class] [loading /modules/java.xml.ws/module-info.class] [loading /modules/jdk.security.jgss/module-info.class] [loading /modules/jdk.crypto.cryptoki/module-info.class] [loading /modules/jdk.sctp/module-info.class] [loading /modules/java.compiler/module-info.class] [loading /modules/java.xml.bind/module-info.class] [loading /modules/jdk.internal.ed/module-info.class] [loading /modules/jdk.jstatd/module-info.class] [loading /modules/jdk.attach/module-info.class] [loading /modules/jdk.dynalink/module-info.class] [loading /modules/jdk.jlink/module-info.class] [loading /modules/jdk.crypto.ec/module-info.class] [loading /modules/jdk.xml.ws/module-info.class] [loading /modules/jdk.jdeps/module-info.class] [loading /modules/jdk.zipfs/module-info.class] [loading /modules/jdk.unsupported/module-info.class] [loading /modules/jdk.net/module-info.class] [loading /modules/java.logging/module-info.class] [loading /modules/jdk.management/module-info.class] [loading /modules/jdk.jcmd/module-info.class] [loading /modules/jdk.internal.vm.compiler.management/module-info.class] [loading /modules/jdk.xml.bind/module-info.class] [loading /modules/jdk.aot/module-info.class] [loading /modules/java.se/module-info.class] [loading /modules/jdk.internal.opt/module-info.class] [loading /modules/jdk.pack/module-info.class] [loading /modules/jdk.editpad/module-info.class] [loading /modules/jdk.incubator.httpclient/module-info.class] [search path for source files: .] [search path for class files: /usr/lib/jvm/java-11-openjdk-amd64/lib/modules,.] [search path for source files: .] [search path for class files: /usr/lib/jvm/java-11-openjdk-amd64/lib/modules,.] [loading /modules/java.base/java/io/BufferedReader.class] [loading /modules/java.base/java/io/FileInputStream.class] [loading /modules/java.base/java/io/InputStreamReader.class] [loading /modules/java.base/java/text/DecimalFormat.class] [loading /modules/java.base/java/text/NumberFormat.class] [loading /modules/java.base/java/util/ArrayList.class] [loading /modules/java.base/java/util/Arrays.class] [loading /modules/java.base/java/util/HashMap.class] [loading /modules/java.base/java/lang/Object.class] [loading /modules/java.base/java/lang/String.class] [loading /modules/java.base/java/lang/Integer.class] [loading /modules/java.base/java/lang/Exception.class] [loading /modules/java.base/java/lang/StringBuffer.class] [loading /modules/java.management/java/lang/management/ManagementFactory.class] [loading /modules/java.management/java/lang/management/MemoryMXBean.class] [loading /modules/java.base/java/io/File.class] [loading /modules/java.base/java/io/FileReader.class] [loading /modules/java.base/java/lang/Boolean.class] [loading /modules/java.base/java/lang/Enum.class] [loading /modules/java.base/java/lang/Comparable.class] [loading /modules/java.base/java/io/Serializable.class] [loading /modules/java.base/java/util/Collections.class] [loading /modules/java.base/java/lang/Deprecated.class] [loading /modules/java.base/java/lang/annotation/Retention.class] [loading /modules/java.base/java/lang/annotation/RetentionPolicy.class] [loading /modules/java.base/java/lang/annotation/Target.class] [loading /modules/java.base/java/lang/annotation/ElementType.class] [checking GetFastaStats] [loading /modules/java.base/java/lang/AutoCloseable.class] [loading /modules/java.base/java/util/Map.class] [loading /modules/java.base/java/lang/Throwable.class] [loading /modules/java.base/java/lang/CharSequence.class] [loading /modules/java.base/java/io/Reader.class] [loading /modules/java.base/java/lang/Readable.class] [loading /modules/java.base/java/io/Closeable.class] [loading /modules/java.base/java/lang/Number.class] [loading /modules/java.base/java/lang/Cloneable.class] [loading /modules/java.base/java/util/AbstractMap.class] [loading /modules/java.base/java/lang/AbstractStringBuilder.class] [loading /modules/java.base/java/lang/Appendable.class] [loading /modules/java.base/java/lang/Byte.class] [loading /modules/java.base/java/lang/Character.class] [loading /modules/java.base/java/lang/Short.class] [loading /modules/java.base/java/lang/Long.class] [loading /modules/java.base/java/lang/Float.class] [loading /modules/java.base/java/lang/Double.class] [loading /modules/java.base/java/lang/Void.class] [loading /modules/java.base/java/io/FileDescriptor.class] [loading /modules/java.base/java/lang/System.class] [loading /modules/java.base/java/io/PrintStream.class] [loading /modules/java.base/java/io/FilterOutputStream.class] [loading /modules/java.base/java/io/OutputStream.class] [loading /modules/java.base/java/io/Flushable.class] [loading /modules/java.base/java/util/Set.class] [loading /modules/java.base/java/lang/Iterable.class] [loading /modules/java.base/java/util/Collection.class] [loading /modules/java.base/java/lang/Math.class] [loading /modules/java.base/java/util/List.class] [loading /modules/java.base/java/util/RandomAccess.class] [loading /modules/java.base/java/util/AbstractList.class] [loading /modules/java.base/java/util/AbstractCollection.class] [loading /modules/java.base/java/util/Comparator.class] [loading /modules/java.base/java/text/Format.class] [loading /modules/java.base/java/lang/Error.class] [loading /modules/java.base/java/lang/RuntimeException.class] [loading /modules/java.base/java/io/IOException.class] [loading /modules/java.base/java/lang/NumberFormatException.class] [loading /modules/java.base/java/lang/IllegalArgumentException.class] [loading /modules/java.base/java/io/FileNotFoundException.class] [loading /modules/java.base/java/util/Iterator.class] [wrote SimpleFileObject[/<>/iva-1.0.9+ds/iva/gage/GetFastaStats$ContigAt.class]] [loading /modules/java.base/java/lang/invoke/StringConcatFactory.class] [loading /modules/java.base/java/lang/invoke/MethodHandles.class] [loading /modules/java.base/java/lang/invoke/MethodHandles$Lookup.class] [loading /modules/java.base/java/lang/invoke/MethodType.class] [loading /modules/java.base/java/io/InputStream.class] [loading /modules/java.base/java/lang/invoke/CallSite.class] [wrote SimpleFileObject[/<>/iva-1.0.9+ds/iva/gage/GetFastaStats.class]] [checking SizeFasta] [wrote SimpleFileObject[/<>/iva-1.0.9+ds/iva/gage/SizeFasta.class]] [checking SplitFastaByLetter] [wrote SimpleFileObject[/<>/iva-1.0.9+ds/iva/gage/SplitFastaByLetter.class]] [checking Utils] [loading /modules/java.base/java/lang/CloneNotSupportedException.class] [loading /modules/java.base/java/lang/Class.class] [loading /modules/java.base/java/net/URI.class] [loading /modules/java.base/java/lang/Process.class] [loading /modules/java.base/java/lang/Runtime.class] [loading /modules/java.base/java/lang/StringBuilder.class] [loading /modules/java.base/java/lang/reflect/GenericDeclaration.class] [loading /modules/java.base/java/lang/reflect/AnnotatedElement.class] [loading /modules/java.base/java/lang/reflect/Type.class] [loading /modules/java.base/java/lang/AssertionError.class] [wrote SimpleFileObject[/<>/iva-1.0.9+ds/iva/gage/Utils$Pair.class]] [wrote SimpleFileObject[/<>/iva-1.0.9+ds/iva/gage/Utils$Translate.class]] [wrote SimpleFileObject[/<>/iva-1.0.9+ds/iva/gage/Utils$ToProtein.class]] [wrote SimpleFileObject[/<>/iva-1.0.9+ds/iva/gage/Utils.class]] [checking getScaffoldStats] [wrote SimpleFileObject[/<>/iva-1.0.9+ds/iva/gage/getScaffoldStats$Scaffold.class]] [wrote SimpleFileObject[/<>/iva-1.0.9+ds/iva/gage/getScaffoldStats$1.class]] [wrote SimpleFileObject[/<>/iva-1.0.9+ds/iva/gage/getScaffoldStats.class]] [total 1531ms] dh_auto_build -- I: pybuild base:217: /usr/bin/python3 setup.py build Checking dependencies found in path: OK kmc OK kmc_dump OK nucmer OK delta-filter OK show-coords OK samtools OK smalt running build running build_py creating /<>/iva-1.0.9+ds/.pybuild/cpython3_3.6_iva/build/iva copying iva/kcount.py -> /<>/iva-1.0.9+ds/.pybuild/cpython3_3.6_iva/build/iva copying iva/contig_trim.py -> /<>/iva-1.0.9+ds/.pybuild/cpython3_3.6_iva/build/iva copying iva/contig.py -> /<>/iva-1.0.9+ds/.pybuild/cpython3_3.6_iva/build/iva copying iva/seed.py -> /<>/iva-1.0.9+ds/.pybuild/cpython3_3.6_iva/build/iva copying iva/kraken.py -> /<>/iva-1.0.9+ds/.pybuild/cpython3_3.6_iva/build/iva copying iva/assembly.py -> /<>/iva-1.0.9+ds/.pybuild/cpython3_3.6_iva/build/iva copying iva/graph.py -> /<>/iva-1.0.9+ds/.pybuild/cpython3_3.6_iva/build/iva copying iva/egg_extract.py -> /<>/iva-1.0.9+ds/.pybuild/cpython3_3.6_iva/build/iva copying iva/qc.py -> /<>/iva-1.0.9+ds/.pybuild/cpython3_3.6_iva/build/iva copying iva/kmers.py -> /<>/iva-1.0.9+ds/.pybuild/cpython3_3.6_iva/build/iva copying iva/mummer.py -> /<>/iva-1.0.9+ds/.pybuild/cpython3_3.6_iva/build/iva copying iva/read_trim.py -> /<>/iva-1.0.9+ds/.pybuild/cpython3_3.6_iva/build/iva copying iva/mapping.py -> /<>/iva-1.0.9+ds/.pybuild/cpython3_3.6_iva/build/iva copying iva/qc_external.py -> /<>/iva-1.0.9+ds/.pybuild/cpython3_3.6_iva/build/iva copying iva/__init__.py -> /<>/iva-1.0.9+ds/.pybuild/cpython3_3.6_iva/build/iva copying iva/external_progs.py -> /<>/iva-1.0.9+ds/.pybuild/cpython3_3.6_iva/build/iva copying iva/seed_processor.py -> /<>/iva-1.0.9+ds/.pybuild/cpython3_3.6_iva/build/iva copying iva/test_data_runner.py -> /<>/iva-1.0.9+ds/.pybuild/cpython3_3.6_iva/build/iva copying iva/common.py -> /<>/iva-1.0.9+ds/.pybuild/cpython3_3.6_iva/build/iva copying iva/edge.py -> /<>/iva-1.0.9+ds/.pybuild/cpython3_3.6_iva/build/iva creating /<>/iva-1.0.9+ds/.pybuild/cpython3_3.6_iva/build/iva/gage copying iva/gage/getMummerStats.sh -> /<>/iva-1.0.9+ds/.pybuild/cpython3_3.6_iva/build/iva/gage copying iva/gage/Utils.class -> /<>/iva-1.0.9+ds/.pybuild/cpython3_3.6_iva/build/iva/gage copying iva/gage/getScaffoldStats$Scaffold.class -> /<>/iva-1.0.9+ds/.pybuild/cpython3_3.6_iva/build/iva/gage copying iva/gage/getScaffoldStats.class -> /<>/iva-1.0.9+ds/.pybuild/cpython3_3.6_iva/build/iva/gage copying iva/gage/GetFastaStats.class -> /<>/iva-1.0.9+ds/.pybuild/cpython3_3.6_iva/build/iva/gage copying iva/gage/GetFastaStats$ContigAt.class -> /<>/iva-1.0.9+ds/.pybuild/cpython3_3.6_iva/build/iva/gage copying iva/gage/Utils$Translate.class -> /<>/iva-1.0.9+ds/.pybuild/cpython3_3.6_iva/build/iva/gage copying iva/gage/SplitFastaByLetter.class -> /<>/iva-1.0.9+ds/.pybuild/cpython3_3.6_iva/build/iva/gage copying iva/gage/getCorrectnessStats.sh -> /<>/iva-1.0.9+ds/.pybuild/cpython3_3.6_iva/build/iva/gage copying iva/gage/SizeFasta.class -> /<>/iva-1.0.9+ds/.pybuild/cpython3_3.6_iva/build/iva/gage copying iva/gage/SizeFasta.java -> /<>/iva-1.0.9+ds/.pybuild/cpython3_3.6_iva/build/iva/gage copying iva/gage/Utils.java -> /<>/iva-1.0.9+ds/.pybuild/cpython3_3.6_iva/build/iva/gage copying iva/gage/getScaffoldStats$1.class -> /<>/iva-1.0.9+ds/.pybuild/cpython3_3.6_iva/build/iva/gage copying iva/gage/GetFastaStats.java -> /<>/iva-1.0.9+ds/.pybuild/cpython3_3.6_iva/build/iva/gage copying iva/gage/colsum.pl -> /<>/iva-1.0.9+ds/.pybuild/cpython3_3.6_iva/build/iva/gage copying iva/gage/Utils$Pair.class -> /<>/iva-1.0.9+ds/.pybuild/cpython3_3.6_iva/build/iva/gage copying iva/gage/SplitFastaByLetter.java -> /<>/iva-1.0.9+ds/.pybuild/cpython3_3.6_iva/build/iva/gage copying iva/gage/getScaffoldStats.java -> /<>/iva-1.0.9+ds/.pybuild/cpython3_3.6_iva/build/iva/gage copying iva/gage/Utils$ToProtein.class -> /<>/iva-1.0.9+ds/.pybuild/cpython3_3.6_iva/build/iva/gage creating /<>/iva-1.0.9+ds/.pybuild/cpython3_3.6_iva/build/iva/ratt copying iva/ratt/ratt.config -> /<>/iva-1.0.9+ds/.pybuild/cpython3_3.6_iva/build/iva/ratt copying iva/ratt/embl2gff.pl -> /<>/iva-1.0.9+ds/.pybuild/cpython3_3.6_iva/build/iva/ratt copying iva/ratt/ratt_correction.pm -> /<>/iva-1.0.9+ds/.pybuild/cpython3_3.6_iva/build/iva/ratt copying iva/ratt/start.ratt.sh -> /<>/iva-1.0.9+ds/.pybuild/cpython3_3.6_iva/build/iva/ratt copying iva/ratt/ratt.config.hiv -> /<>/iva-1.0.9+ds/.pybuild/cpython3_3.6_iva/build/iva/ratt copying iva/ratt/genbank2embl.pl -> /<>/iva-1.0.9+ds/.pybuild/cpython3_3.6_iva/build/iva/ratt copying iva/ratt/main.ratt.pl -> /<>/iva-1.0.9+ds/.pybuild/cpython3_3.6_iva/build/iva/ratt creating /<>/iva-1.0.9+ds/.pybuild/cpython3_3.6_iva/build/iva/read_trim copying iva/read_trim/adapters.fasta -> /<>/iva-1.0.9+ds/.pybuild/cpython3_3.6_iva/build/iva/read_trim creating /<>/iva-1.0.9+ds/.pybuild/cpython3_3.6_iva/build/iva/test_run_data copying iva/test_run_data/reference.fasta -> /<>/iva-1.0.9+ds/.pybuild/cpython3_3.6_iva/build/iva/test_run_data copying iva/test_run_data/reads_2.fq.gz -> /<>/iva-1.0.9+ds/.pybuild/cpython3_3.6_iva/build/iva/test_run_data copying iva/test_run_data/hiv_pcr_primers.fa -> /<>/iva-1.0.9+ds/.pybuild/cpython3_3.6_iva/build/iva/test_run_data copying iva/test_run_data/iva_contigs_with_trimmomatic.fasta -> /<>/iva-1.0.9+ds/.pybuild/cpython3_3.6_iva/build/iva/test_run_data copying iva/test_run_data/iva_contigs_no_trimmomatic.fasta -> /<>/iva-1.0.9+ds/.pybuild/cpython3_3.6_iva/build/iva/test_run_data copying iva/test_run_data/reads_1.fq.gz -> /<>/iva-1.0.9+ds/.pybuild/cpython3_3.6_iva/build/iva/test_run_data running build_scripts creating build creating build/scripts-3.6 copying and adjusting scripts/iva_qc -> build/scripts-3.6 copying and adjusting scripts/iva -> build/scripts-3.6 copying and adjusting scripts/iva_qc_make_db -> build/scripts-3.6 changing mode of build/scripts-3.6/iva_qc from 664 to 775 changing mode of build/scripts-3.6/iva from 664 to 775 changing mode of build/scripts-3.6/iva_qc_make_db from 664 to 775 make[1]: Leaving directory '/<>/iva-1.0.9+ds' debian/rules override_dh_auto_test make[1]: Entering directory '/<>/iva-1.0.9+ds' python3 setup.py test Checking dependencies found in path: OK kmc OK kmc_dump OK nucmer OK delta-filter OK show-coords OK samtools OK smalt running test running egg_info creating iva.egg-info writing iva.egg-info/PKG-INFO writing dependency_links to iva.egg-info/dependency_links.txt writing requirements to iva.egg-info/requires.txt writing top-level names to iva.egg-info/top_level.txt writing manifest file 'iva.egg-info/SOURCES.txt' reading manifest file 'iva.egg-info/SOURCES.txt' writing manifest file 'iva.egg-info/SOURCES.txt' running build_ext /usr/lib/python3.6/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__ return f(*args, **kwds) /<>/iva-1.0.9+ds/iva/mapping.py:157: DeprecationWarning: invalid escape sequence \^ s = re.sub('\^.', '', s) /<>/iva-1.0.9+ds/iva/external_progs.py:33: DeprecationWarning: invalid escape sequence \( 'kmc': ('kmc', re.compile('^K-Mer Counter \(KMC\) ver\. (.*) \(.*\)$')), /<>/iva-1.0.9+ds/iva/external_progs.py:34: DeprecationWarning: invalid escape sequence \( 'kmc_dump': ('kmc_dump', re.compile('^KMC dump ver. (.*) \(.*\)$')), /<>/iva-1.0.9+ds/iva/external_progs.py:37: DeprecationWarning: invalid escape sequence \( 'nucmer': ('nucmer --version', re.compile('^NUCmer \(NUCleotide MUMmer\) version (.*)$')), /<>/iva-1.0.9+ds/iva/external_progs.py:38: DeprecationWarning: invalid escape sequence \( 'R': ('R --version', re.compile('^R version (.*) \(.*\) --')), /<>/iva-1.0.9+ds/iva/external_progs.py:40: DeprecationWarning: invalid escape sequence \d 'samtools': ('samtools', re.compile('(\d+\.\d+[\.\d]*)')), /<>/iva-1.0.9+ds/iva/kraken.py:360: DeprecationWarning: invalid escape sequence \. self._genbank2embl(fname, re.sub('\.gbk$', '', fname) + '.embl') /<>/iva-1.0.9+ds/iva/kraken.py:415: DeprecationWarning: invalid escape sequence \W return re.sub('\W', '_', s).strip('_') test_add_new_seed_contig (assembly_test.TestAssembly) Test add_new_seed_contig ... ok test_contig_contained_in_nucmer_hits (assembly_test.TestAssembly) Test _contig_contained_in_nucmer_hits ... ok test_contig_names_size_order (assembly_test.TestAssembly) Test _contig_names_size_order ... ok test_contig_worth_extending (assembly_test.TestAssembly) Test _contig_worth_extending ... ok test_coords_to_new_contig (assembly_test.TestAssembly) Test _coords_to_new_contig ... ok test_extend_contigs_with_bam (assembly_test.TestAssembly) test _extend_contigs_with_bam ... ok test_get_contig_order_by_orfs (assembly_test.TestAssembly) Test get_contig_order_by_orfs ... ok test_get_ref_length (assembly_test.TestAssembly) Test _get_ref_length ... ok test_get_ref_length_sam_pair (assembly_test.TestAssembly) Test _get_ref_length_sam_pair ... ok test_get_unmapped_pairs (assembly_test.TestAssembly) Test _get_unmapped_pairs ... ok test_good_intervals_from_strand_coverage (assembly_test.TestAssembly) Test good_intervals_from_strand_coverage ... ok test_init_and_write (assembly_test.TestAssembly) test assembly initialise and write to file ... ok test_map_reads (assembly_test.TestAssembly) test _map_reads ... ok test_merge_overlapping_contigs (assembly_test.TestAssembly) Test _merge_overlapping_contigs ... ok test_read_pair_extend (assembly_test.TestAssembly) Test read_pair_extend ... ok test_remove_contained_contigs (assembly_test.TestAssembly) Test _remove_contained_contigs ... ok test_remove_contig (assembly_test.TestAssembly) Test _remove_contig ... ok test_remove_contig_from_nucmer_hits (assembly_test.TestAssembly) Test _remove_contig_from_nucmer_hits ... ok test_subcontigs_from_strand_bias (assembly_test.TestAssembly) Test _subcontigs_from_strand_bias ... ok test_trim_contig_for_strand_bias (assembly_test.TestAssembly) Test _trim_contig_for_strand_bias ... ok test_trim_contigs (assembly_test.TestAssembly) Test trim_contigs ... ok test_trim_strand_biased_ends (assembly_test.TestAssembly) Test _trim_strand_biased_ends ... ok test_worth_extending (assembly_test.TestAssembly) Test worth_extending ... ok test_add_left_kmer (contig_test.TestContig) Test add_left_kmer ... ok test_add_right_kmer (contig_test.TestContig) Test add_right_kmer ... ok test_extend (contig_test.TestContig) Test extend ... ok test_init (contig_test.TestContig) Test init ... ok test_len (contig_test.TestContig) Test len ... ok test_coverage_to_trimmed_coords (contig_trim_test.TestContigTrim) Test _coverage_to_trimmed_coords ... ok test_trim_ends (contig_trim_test.TestContigTrim) Test _trim_ends ... ok test_trim_primers_and_adapters (contig_trim_test.TestContigTrim) Test trim_primers_and_adapters ... ok test_change_hit_coords_with_intersection (edge_test.TestEdge) test test_change_hit_coords_with_intersection ... ok test_make_contig_first (edge_test.TestEdge) test make_contig_first ... ok test_make_contig_forwards (edge_test.TestEdge) test make_contig_forwards ... ok test_merge_into (edge_test.TestEdge) test merge_into ... ok test_open_end (edge_test.TestEdge) test open_end ... ok test_reverse (edge_test.TestEdge) test reverse ... ok test_copy_dir (egg_extract_test.TestEggExtract) test copy_dir ... ok test_copy_dir_unzipped (egg_extract_test.TestEggExtract) test copy_dir_unzipped ... ok test_copy_dir_zipped (egg_extract_test.TestEggExtract) test copy_dir_zipped ... ok test_copy_file (egg_extract_test.TestEggExtract) test copy_file ... ok test_copy_file_unzipped (egg_extract_test.TestEggExtract) test _copy_file_unzipped ... ok test_copy_file_zipped (egg_extract_test.TestEggExtract) test _copy_file_zipped ... ok test_init_and_write (egg_extract_test.TestEggExtract) test __init__ ... ok test_blastn_version (external_progs_test.TestExternalProgs) Test blastn version ... ok test_delta_filter_in_path (external_progs_test.TestExternalProgs) Test delta-filter in path ... ok test_kmc_dump_in_path (external_progs_test.TestExternalProgs) Test kmc_dump in path ... ok test_kmc_dump_version (external_progs_test.TestExternalProgs) Test kmc_dump version ... ok test_kmc_in_path (external_progs_test.TestExternalProgs) Test kmc in path ... ok test_kmc_version (external_progs_test.TestExternalProgs) Test kmc version ... ok test_makeblastdb_version (external_progs_test.TestExternalProgs) Test makeblastdb version ... ok test_nucmer_in_path (external_progs_test.TestExternalProgs) Test nucmer in path ... ok test_nucmer_version (external_progs_test.TestExternalProgs) Test nucmer version ... ok test_r_version (external_progs_test.TestExternalProgs) Test R versions ... ok test_samtools_in_path (external_progs_test.TestExternalProgs) Test samtools in path ... ok test_samtools_original_version (external_progs_test.TestExternalProgs) Test samtools original version ... ok test_samtools_version (external_progs_test.TestExternalProgs) Test samtools version ... ok test_show_coords_in_path (external_progs_test.TestExternalProgs) Test show-coords in path ... ok test_smalt_in_path (external_progs_test.TestExternalProgs) Test smalt in path ... ok test_smalt_version (external_progs_test.TestExternalProgs) Test smalt version ... ok test_add_and_get_edges (graph_test.TestGraph) test adding and getting edges ... ok test_connected_components (graph_test.TestGraph) test connected_components ... ok test_degree (graph_test.TestGraph) test degree ... ok test_edges_are_consistent (graph_test.TestGraph) test edges_are_consistent ... ok test_find_simple_path (graph_test.TestGraph) test find_simple_path ... ok test_get_nodes (graph_test.TestGraph) test get_nodes ... ok test_merged_coords_from_simple_nonredundant_path (graph_test.TestGraph) test merged_coords_from_simple_nonredundant_path ... ok test_node_to_coords (graph_test.TestGraph) test _node_to_coords ... ok test_remove_middle_node (graph_test.TestGraph) test remove_middle_node ... ok test_remove_node (graph_test.TestGraph) test remove_node ... ok test_remove_redundant_nodes_from_simple_path (graph_test.TestGraph) test remove_redundant_nodes_from_simple_path ... ok test_simple_path_is_consistent (graph_test.TestGraph) test simple_path_is_consistent ... ok test_counts_file_to_fasta (kcount_test.TestKcount) Test _counts_file_to_fasta ... ok test_get_most_common_kmers (kcount_test.TestKcount) Test get_most_common_kmers ... ok test_head_fastaq_fa (kcount_test.TestKcount) Test head_fastaq with FASTA input ... ok test_head_fastaq_fq (kcount_test.TestKcount) Test head_fastaq with FASTQ input ... ok test_kmc_to_kmer_counts (kcount_test.TestKcount) Test _kmc_to_kmer_counts ... ok test_median (kcount_test.TestKcount) Test _median() ... ok test_run_kmc (kcount_test.TestKcount) Test test_run_kmc ... ok test_run_kmc_two_threads (kcount_test.TestKcount) Test test_run_kmc with two threads ... ok test_append (kmers_test.TestKmers) Test append ... ok test_commonest_kmers (kmers_test.TestKmers) ... ok test_extend (kmers_test.TestKmers) Test extend ... ok test_extension (kmers_test.TestKmers) Test extension ... ok test_init (kmers_test.TestKmers) Test __init__ ... ok test_kmer_dict (kmers_test.TestKmers) Test kmer_dict ... ok test_append_to_file (kraken_test.TestKraken) test _append_to_file ... ok test_count_cds_from_embl (kraken_test.TestKraken) test count_cds_from_embl ... ok test_genbank_to_taxon_and_gi (kraken_test.TestKraken) test _genbank_to_taxon_and_gi ... ok test_get_most_common_species_dir (kraken_test.TestKraken) Test get_most_common_species ... ok test_get_parent_taxons (kraken_test.TestKraken) test _get_parent_taxons ... ok test_load_extra_ref_info (kraken_test.TestKraken) test _load_extra_ref_info ... ok test_replace_fasta_header (kraken_test.TestKraken) test _replace_fasta_header ... ok test_species_to_dir (kraken_test.TestKraken) test species_to_dir ... ok test_bam_file_to_fasta_pair_files (mapping_test.TestMapping) Test bam_file_to_fasta_pair_files ... ok test_bam_file_to_fasta_pair_files_region (mapping_test.TestMapping) Test bam_file_to_fasta_pair_files with a region ... ok test_bam_file_to_region_fasta (mapping_test.TestMapping) Test bam_file_to_region_fasta ... ok test_bam_to_fasta (mapping_test.TestMapping) Test bam_to_fasta ... ok test_can_extend (mapping_test.TestMapping) Test can_extend ... ok test_consensus_base (mapping_test.TestMapping) Test consensus_base ... ok test_consensus_base_both_strands (mapping_test.TestMapping) Test consensus_base_both_strands ... ok test_find_incorrect_ref_bases (mapping_test.TestMapping) Test find_incorrect_ref_bases ... ok test_get_bam_region_coverage_fwd (mapping_test.TestMapping) Test get_bam_region_coverage forward strand ... ok test_get_bam_region_coverage_fwd_And_rev (mapping_test.TestMapping) Test get_bam_region_coverage both strands ... ok test_get_bam_region_coverage_rev (mapping_test.TestMapping) Test get_bam_region_coverage reverse strand ... ok test_get_pair_type (mapping_test.TestMapping) Test get_pair_type ... ok test_get_ref_name (mapping_test.TestMapping) Test get_ref_name ... ok test_map_reads (mapping_test.TestMapping) Test mapping reads ... ok test_map_reads_and_sort (mapping_test.TestMapping) Test mapping reads and sort BAM ... ok test_map_reads_wth_flag (mapping_test.TestMapping) Test map_reads with required flag ... ok test_remove_indels (mapping_test.TestMapping) Test _remove_indels ... ok test_sam_to_fasta (mapping_test.TestMapping) Test sam_to_fasta ... ok test_smalt_in_path (mapping_test.TestMapping) Test that samtools is in the user's path ... ok test_soft_clipped (mapping_test.TestMapping) Test soft_clipped ... ok test_strip_mpileup_coverage_string (mapping_test.TestMapping) Test strip_mpileup_coverage_string ... ok test_total_ref_length_from_bam (mapping_test.TestMapping) Test _total_ref_length_from_bam ... ok test_file_read (mummer_test.TestMummer) test file_read ... ok test_is_at_ends (mummer_test.TestMummer) Test is_at_ends ... ok test_is_self_hit (mummer_test.TestMummer) Test is_self_hit ... ok test_on_same_strand (mummer_test.TestMummer) test on_same_strand ... ok test_qry_coords (mummer_test.TestMummer) Test qry_coords ... ok test_ref_coords (mummer_test.TestMummer) Test ref_coords ... ok test_run_nucmer (mummer_test.TestMummer) test run_nucmer ... ok test_sort (mummer_test.TestMummer) test sort ... ok test_swap (mummer_test.TestMummer) test swap ... ok test_to_graph_edge (mummer_test.TestMummer) Test to_graph_edge ... ok test_run_gage (qc_external_test.TestQcExternal) test run_gage ... ok test_run_ratt (qc_external_test.TestQcExternal) test run_ratt ... ok test_calculate_cds_assembly_stats (qc_test.TestQc) test _calculate_cds_assembly_stats ... ok test_calculate_contig_placement (qc_test.TestQc) test calculate_contig_placement ... ok test_calculate_ref_positions_covered_by_contigs (qc_test.TestQc) test _calculate_ref_positions_covered_by_contigs ... ok test_calculate_ref_read_coverage (qc_test.TestQc) test _calculate_ref_read_coverage ... ok test_calculate_ref_read_region_coverage (qc_test.TestQc) test _calculate_ref_read_region_coverage ... ok test_calculate_refseq_assembly_stats (qc_test.TestQc) test _calculate_refseq_assembly_stats ... ok test_calculate_should_have_assembled (qc_test.TestQc) test _calculate_should_have_assembled ... ok test_contig_placement_in_reference (qc_test.TestQc) test _contig_placement_in_reference ... ok test_contigs_and_bases_that_hit_ref (qc_test.TestQc) test _contigs_and_bases_that_hit_ref ... ok test_cov_to_R_string (qc_test.TestQc) test _cov_to_R_string ... ok test_coverage_list_to_low_cov_intervals (qc_test.TestQc) test _coverage_list_to_low_cov_intervals ... ok test_get_R_plot_contig_order_from_contig_placement (qc_test.TestQc) test _get_R_plot_contig_order_from_contig_placement ... ok test_get_contig_hits_to_reference (qc_test.TestQc) test _get_contig_hits_to_reference ... ok test_get_overlapping_qry_hits (qc_test.TestQc) test _get_overlapping_qry_hits ... ok test_get_ref_cds_from_gff (qc_test.TestQc) test _get_ref_cds_from_gff ... ok test_get_unique_and_repetitive_from_contig_hits (qc_test.TestQc) test _get_unique_and_repetitive_from_contig_hits ... ok test_gff_and_fasta_to_cds (qc_test.TestQc) test _gff_and_fasta_to_cds ... ok test_has_orf (qc_test.TestQc) test _has_orf ... ok test_hash_nucmer_hits_by_ref (qc_test.TestQc) test _hash_nucmer_hits_by_ref ... ok test_ids_in_order_from_fai (qc_test.TestQc) test _ids_in_order_from_fai ... ok test_invert_list (qc_test.TestQc) test _invert_list ... ok test_map_cds_to_assembly (qc_test.TestQc) test _map_cds_to_assembly ... ok test_mummer_coords_file_to_dict (qc_test.TestQc) test _mummer_coords_file_to_dict ... ok test_write_cds_seqs (qc_test.TestQc) test _write_cds_seqs ... ok test_write_fasta_contigs_hit_ref (qc_test.TestQc) test _write_fasta_contigs_hit_ref ... ok test_write_fasta_contigs_not_hit_ref (qc_test.TestQc) test _write_fasta_contigs_not_hit_ref ... ok test_write_ref_coverage_to_files_for_R (qc_test.TestQc) test _write_ref_coverage_to_files_for_R ... ok test_run_trimmomatic (read_trim_test.TestReadTrim) Test run_trimmomatic ... ok test_extend (seed_test.TestSeed) Test extend ... ok test_extend_with_reads_as_single_end (seed_test.TestSeed) Test _extend_with_reads_as_single_end ... ok test_extension_from_read (seed_test.TestSeed) Test _test_extension_from_read ... ok test_extensions_from_reads_file (seed_test.TestSeed) Test _extensions_from_reads_file ... ok test_init (seed_test.TestSeed) test init ... ok test_kmc_in_path (seed_test.TestSeed) Test that kmc is in the user's path ... ok test_len (seed_test.TestSeed) Test len ... ok test_write_fasta (seed_test.TestSeed) Test write_fasta ... ok ---------------------------------------------------------------------- Ran 164 tests in 6.610s OK make[1]: Leaving directory '/<>/iva-1.0.9+ds' create-stamp debian/debhelper-build-stamp fakeroot debian/rules binary dh binary --with python3 --buildsystem=pybuild dh_testroot -O--buildsystem=pybuild dh_prep -O--buildsystem=pybuild dh_auto_install -O--buildsystem=pybuild I: pybuild base:217: /usr/bin/python3 setup.py install --root /<>/iva-1.0.9+ds/debian/iva Checking dependencies found in path: OK kmc OK kmc_dump OK nucmer OK delta-filter OK show-coords OK samtools OK smalt running install running build running build_py running build_scripts running install_lib creating /<>/iva-1.0.9+ds/debian/iva/usr creating /<>/iva-1.0.9+ds/debian/iva/usr/lib creating /<>/iva-1.0.9+ds/debian/iva/usr/lib/python3.6 creating /<>/iva-1.0.9+ds/debian/iva/usr/lib/python3.6/dist-packages creating /<>/iva-1.0.9+ds/debian/iva/usr/lib/python3.6/dist-packages/iva creating /<>/iva-1.0.9+ds/debian/iva/usr/lib/python3.6/dist-packages/iva/ratt copying /<>/iva-1.0.9+ds/.pybuild/cpython3_3.6_iva/build/iva/ratt/ratt.config -> /<>/iva-1.0.9+ds/debian/iva/usr/lib/python3.6/dist-packages/iva/ratt copying /<>/iva-1.0.9+ds/.pybuild/cpython3_3.6_iva/build/iva/ratt/embl2gff.pl -> /<>/iva-1.0.9+ds/debian/iva/usr/lib/python3.6/dist-packages/iva/ratt copying /<>/iva-1.0.9+ds/.pybuild/cpython3_3.6_iva/build/iva/ratt/ratt_correction.pm -> /<>/iva-1.0.9+ds/debian/iva/usr/lib/python3.6/dist-packages/iva/ratt copying /<>/iva-1.0.9+ds/.pybuild/cpython3_3.6_iva/build/iva/ratt/start.ratt.sh -> /<>/iva-1.0.9+ds/debian/iva/usr/lib/python3.6/dist-packages/iva/ratt copying /<>/iva-1.0.9+ds/.pybuild/cpython3_3.6_iva/build/iva/ratt/ratt.config.hiv -> /<>/iva-1.0.9+ds/debian/iva/usr/lib/python3.6/dist-packages/iva/ratt copying /<>/iva-1.0.9+ds/.pybuild/cpython3_3.6_iva/build/iva/ratt/genbank2embl.pl -> /<>/iva-1.0.9+ds/debian/iva/usr/lib/python3.6/dist-packages/iva/ratt copying /<>/iva-1.0.9+ds/.pybuild/cpython3_3.6_iva/build/iva/ratt/main.ratt.pl -> /<>/iva-1.0.9+ds/debian/iva/usr/lib/python3.6/dist-packages/iva/ratt copying /<>/iva-1.0.9+ds/.pybuild/cpython3_3.6_iva/build/iva/kcount.py -> /<>/iva-1.0.9+ds/debian/iva/usr/lib/python3.6/dist-packages/iva copying /<>/iva-1.0.9+ds/.pybuild/cpython3_3.6_iva/build/iva/contig_trim.py -> /<>/iva-1.0.9+ds/debian/iva/usr/lib/python3.6/dist-packages/iva creating /<>/iva-1.0.9+ds/debian/iva/usr/lib/python3.6/dist-packages/iva/read_trim copying /<>/iva-1.0.9+ds/.pybuild/cpython3_3.6_iva/build/iva/read_trim/adapters.fasta -> /<>/iva-1.0.9+ds/debian/iva/usr/lib/python3.6/dist-packages/iva/read_trim copying /<>/iva-1.0.9+ds/.pybuild/cpython3_3.6_iva/build/iva/contig.py -> /<>/iva-1.0.9+ds/debian/iva/usr/lib/python3.6/dist-packages/iva copying /<>/iva-1.0.9+ds/.pybuild/cpython3_3.6_iva/build/iva/seed.py -> /<>/iva-1.0.9+ds/debian/iva/usr/lib/python3.6/dist-packages/iva copying /<>/iva-1.0.9+ds/.pybuild/cpython3_3.6_iva/build/iva/kraken.py -> /<>/iva-1.0.9+ds/debian/iva/usr/lib/python3.6/dist-packages/iva copying /<>/iva-1.0.9+ds/.pybuild/cpython3_3.6_iva/build/iva/assembly.py -> /<>/iva-1.0.9+ds/debian/iva/usr/lib/python3.6/dist-packages/iva copying /<>/iva-1.0.9+ds/.pybuild/cpython3_3.6_iva/build/iva/graph.py -> /<>/iva-1.0.9+ds/debian/iva/usr/lib/python3.6/dist-packages/iva copying /<>/iva-1.0.9+ds/.pybuild/cpython3_3.6_iva/build/iva/egg_extract.py -> /<>/iva-1.0.9+ds/debian/iva/usr/lib/python3.6/dist-packages/iva copying /<>/iva-1.0.9+ds/.pybuild/cpython3_3.6_iva/build/iva/qc.py -> /<>/iva-1.0.9+ds/debian/iva/usr/lib/python3.6/dist-packages/iva copying /<>/iva-1.0.9+ds/.pybuild/cpython3_3.6_iva/build/iva/kmers.py -> /<>/iva-1.0.9+ds/debian/iva/usr/lib/python3.6/dist-packages/iva creating /<>/iva-1.0.9+ds/debian/iva/usr/lib/python3.6/dist-packages/iva/gage copying /<>/iva-1.0.9+ds/.pybuild/cpython3_3.6_iva/build/iva/gage/getMummerStats.sh -> /<>/iva-1.0.9+ds/debian/iva/usr/lib/python3.6/dist-packages/iva/gage copying /<>/iva-1.0.9+ds/.pybuild/cpython3_3.6_iva/build/iva/gage/Utils.class -> /<>/iva-1.0.9+ds/debian/iva/usr/lib/python3.6/dist-packages/iva/gage copying /<>/iva-1.0.9+ds/.pybuild/cpython3_3.6_iva/build/iva/gage/getScaffoldStats$Scaffold.class -> /<>/iva-1.0.9+ds/debian/iva/usr/lib/python3.6/dist-packages/iva/gage copying /<>/iva-1.0.9+ds/.pybuild/cpython3_3.6_iva/build/iva/gage/getScaffoldStats.class -> /<>/iva-1.0.9+ds/debian/iva/usr/lib/python3.6/dist-packages/iva/gage copying /<>/iva-1.0.9+ds/.pybuild/cpython3_3.6_iva/build/iva/gage/GetFastaStats.class -> /<>/iva-1.0.9+ds/debian/iva/usr/lib/python3.6/dist-packages/iva/gage copying /<>/iva-1.0.9+ds/.pybuild/cpython3_3.6_iva/build/iva/gage/GetFastaStats$ContigAt.class -> /<>/iva-1.0.9+ds/debian/iva/usr/lib/python3.6/dist-packages/iva/gage copying /<>/iva-1.0.9+ds/.pybuild/cpython3_3.6_iva/build/iva/gage/Utils$Translate.class -> /<>/iva-1.0.9+ds/debian/iva/usr/lib/python3.6/dist-packages/iva/gage copying /<>/iva-1.0.9+ds/.pybuild/cpython3_3.6_iva/build/iva/gage/SplitFastaByLetter.class -> /<>/iva-1.0.9+ds/debian/iva/usr/lib/python3.6/dist-packages/iva/gage copying /<>/iva-1.0.9+ds/.pybuild/cpython3_3.6_iva/build/iva/gage/getCorrectnessStats.sh -> /<>/iva-1.0.9+ds/debian/iva/usr/lib/python3.6/dist-packages/iva/gage copying /<>/iva-1.0.9+ds/.pybuild/cpython3_3.6_iva/build/iva/gage/SizeFasta.class -> /<>/iva-1.0.9+ds/debian/iva/usr/lib/python3.6/dist-packages/iva/gage copying /<>/iva-1.0.9+ds/.pybuild/cpython3_3.6_iva/build/iva/gage/SizeFasta.java -> /<>/iva-1.0.9+ds/debian/iva/usr/lib/python3.6/dist-packages/iva/gage copying /<>/iva-1.0.9+ds/.pybuild/cpython3_3.6_iva/build/iva/gage/Utils.java -> /<>/iva-1.0.9+ds/debian/iva/usr/lib/python3.6/dist-packages/iva/gage copying /<>/iva-1.0.9+ds/.pybuild/cpython3_3.6_iva/build/iva/gage/getScaffoldStats$1.class -> /<>/iva-1.0.9+ds/debian/iva/usr/lib/python3.6/dist-packages/iva/gage copying /<>/iva-1.0.9+ds/.pybuild/cpython3_3.6_iva/build/iva/gage/GetFastaStats.java -> /<>/iva-1.0.9+ds/debian/iva/usr/lib/python3.6/dist-packages/iva/gage copying /<>/iva-1.0.9+ds/.pybuild/cpython3_3.6_iva/build/iva/gage/colsum.pl -> /<>/iva-1.0.9+ds/debian/iva/usr/lib/python3.6/dist-packages/iva/gage copying /<>/iva-1.0.9+ds/.pybuild/cpython3_3.6_iva/build/iva/gage/Utils$Pair.class -> /<>/iva-1.0.9+ds/debian/iva/usr/lib/python3.6/dist-packages/iva/gage copying /<>/iva-1.0.9+ds/.pybuild/cpython3_3.6_iva/build/iva/gage/SplitFastaByLetter.java -> /<>/iva-1.0.9+ds/debian/iva/usr/lib/python3.6/dist-packages/iva/gage copying /<>/iva-1.0.9+ds/.pybuild/cpython3_3.6_iva/build/iva/gage/getScaffoldStats.java -> /<>/iva-1.0.9+ds/debian/iva/usr/lib/python3.6/dist-packages/iva/gage copying /<>/iva-1.0.9+ds/.pybuild/cpython3_3.6_iva/build/iva/gage/Utils$ToProtein.class -> /<>/iva-1.0.9+ds/debian/iva/usr/lib/python3.6/dist-packages/iva/gage copying /<>/iva-1.0.9+ds/.pybuild/cpython3_3.6_iva/build/iva/mummer.py -> /<>/iva-1.0.9+ds/debian/iva/usr/lib/python3.6/dist-packages/iva copying /<>/iva-1.0.9+ds/.pybuild/cpython3_3.6_iva/build/iva/read_trim.py -> /<>/iva-1.0.9+ds/debian/iva/usr/lib/python3.6/dist-packages/iva copying /<>/iva-1.0.9+ds/.pybuild/cpython3_3.6_iva/build/iva/mapping.py -> /<>/iva-1.0.9+ds/debian/iva/usr/lib/python3.6/dist-packages/iva copying /<>/iva-1.0.9+ds/.pybuild/cpython3_3.6_iva/build/iva/qc_external.py -> /<>/iva-1.0.9+ds/debian/iva/usr/lib/python3.6/dist-packages/iva copying /<>/iva-1.0.9+ds/.pybuild/cpython3_3.6_iva/build/iva/__init__.py -> /<>/iva-1.0.9+ds/debian/iva/usr/lib/python3.6/dist-packages/iva creating /<>/iva-1.0.9+ds/debian/iva/usr/lib/python3.6/dist-packages/iva/test_run_data copying /<>/iva-1.0.9+ds/.pybuild/cpython3_3.6_iva/build/iva/test_run_data/reference.fasta -> /<>/iva-1.0.9+ds/debian/iva/usr/lib/python3.6/dist-packages/iva/test_run_data copying /<>/iva-1.0.9+ds/.pybuild/cpython3_3.6_iva/build/iva/test_run_data/reads_2.fq.gz -> /<>/iva-1.0.9+ds/debian/iva/usr/lib/python3.6/dist-packages/iva/test_run_data copying /<>/iva-1.0.9+ds/.pybuild/cpython3_3.6_iva/build/iva/test_run_data/hiv_pcr_primers.fa -> /<>/iva-1.0.9+ds/debian/iva/usr/lib/python3.6/dist-packages/iva/test_run_data copying /<>/iva-1.0.9+ds/.pybuild/cpython3_3.6_iva/build/iva/test_run_data/iva_contigs_with_trimmomatic.fasta -> /<>/iva-1.0.9+ds/debian/iva/usr/lib/python3.6/dist-packages/iva/test_run_data copying /<>/iva-1.0.9+ds/.pybuild/cpython3_3.6_iva/build/iva/test_run_data/iva_contigs_no_trimmomatic.fasta -> /<>/iva-1.0.9+ds/debian/iva/usr/lib/python3.6/dist-packages/iva/test_run_data copying /<>/iva-1.0.9+ds/.pybuild/cpython3_3.6_iva/build/iva/test_run_data/reads_1.fq.gz -> /<>/iva-1.0.9+ds/debian/iva/usr/lib/python3.6/dist-packages/iva/test_run_data copying /<>/iva-1.0.9+ds/.pybuild/cpython3_3.6_iva/build/iva/external_progs.py -> /<>/iva-1.0.9+ds/debian/iva/usr/lib/python3.6/dist-packages/iva copying /<>/iva-1.0.9+ds/.pybuild/cpython3_3.6_iva/build/iva/seed_processor.py -> /<>/iva-1.0.9+ds/debian/iva/usr/lib/python3.6/dist-packages/iva copying /<>/iva-1.0.9+ds/.pybuild/cpython3_3.6_iva/build/iva/test_data_runner.py -> /<>/iva-1.0.9+ds/debian/iva/usr/lib/python3.6/dist-packages/iva copying /<>/iva-1.0.9+ds/.pybuild/cpython3_3.6_iva/build/iva/common.py -> /<>/iva-1.0.9+ds/debian/iva/usr/lib/python3.6/dist-packages/iva copying /<>/iva-1.0.9+ds/.pybuild/cpython3_3.6_iva/build/iva/edge.py -> /<>/iva-1.0.9+ds/debian/iva/usr/lib/python3.6/dist-packages/iva byte-compiling /<>/iva-1.0.9+ds/debian/iva/usr/lib/python3.6/dist-packages/iva/kcount.py to kcount.cpython-36.pyc byte-compiling /<>/iva-1.0.9+ds/debian/iva/usr/lib/python3.6/dist-packages/iva/contig_trim.py to contig_trim.cpython-36.pyc byte-compiling /<>/iva-1.0.9+ds/debian/iva/usr/lib/python3.6/dist-packages/iva/contig.py to contig.cpython-36.pyc byte-compiling /<>/iva-1.0.9+ds/debian/iva/usr/lib/python3.6/dist-packages/iva/seed.py to seed.cpython-36.pyc byte-compiling /<>/iva-1.0.9+ds/debian/iva/usr/lib/python3.6/dist-packages/iva/kraken.py to kraken.cpython-36.pyc byte-compiling /<>/iva-1.0.9+ds/debian/iva/usr/lib/python3.6/dist-packages/iva/assembly.py to assembly.cpython-36.pyc byte-compiling /<>/iva-1.0.9+ds/debian/iva/usr/lib/python3.6/dist-packages/iva/graph.py to graph.cpython-36.pyc byte-compiling /<>/iva-1.0.9+ds/debian/iva/usr/lib/python3.6/dist-packages/iva/egg_extract.py to egg_extract.cpython-36.pyc byte-compiling /<>/iva-1.0.9+ds/debian/iva/usr/lib/python3.6/dist-packages/iva/qc.py to qc.cpython-36.pyc byte-compiling /<>/iva-1.0.9+ds/debian/iva/usr/lib/python3.6/dist-packages/iva/kmers.py to kmers.cpython-36.pyc byte-compiling /<>/iva-1.0.9+ds/debian/iva/usr/lib/python3.6/dist-packages/iva/mummer.py to mummer.cpython-36.pyc byte-compiling /<>/iva-1.0.9+ds/debian/iva/usr/lib/python3.6/dist-packages/iva/read_trim.py to read_trim.cpython-36.pyc byte-compiling /<>/iva-1.0.9+ds/debian/iva/usr/lib/python3.6/dist-packages/iva/mapping.py to mapping.cpython-36.pyc byte-compiling /<>/iva-1.0.9+ds/debian/iva/usr/lib/python3.6/dist-packages/iva/qc_external.py to qc_external.cpython-36.pyc byte-compiling /<>/iva-1.0.9+ds/debian/iva/usr/lib/python3.6/dist-packages/iva/__init__.py to __init__.cpython-36.pyc byte-compiling /<>/iva-1.0.9+ds/debian/iva/usr/lib/python3.6/dist-packages/iva/external_progs.py to external_progs.cpython-36.pyc byte-compiling /<>/iva-1.0.9+ds/debian/iva/usr/lib/python3.6/dist-packages/iva/seed_processor.py to seed_processor.cpython-36.pyc byte-compiling /<>/iva-1.0.9+ds/debian/iva/usr/lib/python3.6/dist-packages/iva/test_data_runner.py to test_data_runner.cpython-36.pyc byte-compiling /<>/iva-1.0.9+ds/debian/iva/usr/lib/python3.6/dist-packages/iva/common.py to common.cpython-36.pyc byte-compiling /<>/iva-1.0.9+ds/debian/iva/usr/lib/python3.6/dist-packages/iva/edge.py to edge.cpython-36.pyc running install_egg_info running egg_info writing iva.egg-info/PKG-INFO writing dependency_links to iva.egg-info/dependency_links.txt writing requirements to iva.egg-info/requires.txt writing top-level names to iva.egg-info/top_level.txt reading manifest file 'iva.egg-info/SOURCES.txt' writing manifest file 'iva.egg-info/SOURCES.txt' Copying iva.egg-info to /<>/iva-1.0.9+ds/debian/iva/usr/lib/python3.6/dist-packages/iva-1.0.9.egg-info Skipping SOURCES.txt running install_scripts creating /<>/iva-1.0.9+ds/debian/iva/usr/bin copying build/scripts-3.6/iva_qc -> /<>/iva-1.0.9+ds/debian/iva/usr/bin copying build/scripts-3.6/iva -> /<>/iva-1.0.9+ds/debian/iva/usr/bin copying build/scripts-3.6/iva_qc_make_db -> /<>/iva-1.0.9+ds/debian/iva/usr/bin changing mode of /<>/iva-1.0.9+ds/debian/iva/usr/bin/iva_qc to 775 changing mode of /<>/iva-1.0.9+ds/debian/iva/usr/bin/iva to 775 changing mode of /<>/iva-1.0.9+ds/debian/iva/usr/bin/iva_qc_make_db to 775 dh_installdocs -O--buildsystem=pybuild dh_installchangelogs -O--buildsystem=pybuild debian/rules override_dh_installman make[1]: Entering directory '/<>/iva-1.0.9+ds' mkdir -p /<>/iva-1.0.9+ds/debian/man PYTHONPATH=. help2man -N -o /<>/iva-1.0.9+ds/debian/man/iva.1 \ -n 'iterative virus assembler' \ --no-discard-stderr ./scripts/iva PYTHONPATH=. help2man -N -o /<>/iva-1.0.9+ds/debian/man/iva_qc.1 \ -n 'compare an assembly to a reference' \ --no-discard-stderr ./scripts/iva_qc PYTHONPATH=. help2man -N -o /<>/iva-1.0.9+ds/debian/man/iva_qc_make_db.1 \ -n 'make a database as input for iva_qc' \ --no-discard-stderr ./scripts/iva_qc_make_db dh_installman -- make[1]: Leaving directory '/<>/iva-1.0.9+ds' dh_python3 -O--buildsystem=pybuild dh_perl -O--buildsystem=pybuild dh_link -O--buildsystem=pybuild dh_strip_nondeterminism -O--buildsystem=pybuild dh_compress -O--buildsystem=pybuild dh_fixperms -O--buildsystem=pybuild dh_missing -O--buildsystem=pybuild dh_strip -O--buildsystem=pybuild dh_makeshlibs -O--buildsystem=pybuild dh_shlibdeps -O--buildsystem=pybuild dh_installdeb -O--buildsystem=pybuild dh_gencontrol -O--buildsystem=pybuild dpkg-gencontrol: warning: package iva: unused substitution variable ${perl:Depends} dh_md5sums -O--buildsystem=pybuild dh_builddeb -O--buildsystem=pybuild INFO: pkgstriptranslations version 141 pkgstriptranslations: processing iva (in debian/iva); do_strip: , oemstrip: pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/iva/DEBIAN/control, package iva, directory debian/iva pkgstripfiles: Truncating usr/share/doc/iva/changelog.Debian.gz to topmost ten records pkgstripfiles: Running PNG optimization (using 4 cpus) for package iva ... pkgstripfiles: No PNG files. dpkg-deb: building package 'iva' in '../iva_1.0.9+ds-6_amd64.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary -mLaunchpad Build Daemon >../iva_1.0.9+ds-6_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build iva-1.0.9+ds dpkg-buildpackage: info: binary-only upload (no source included) -------------------------------------------------------------------------------- Build finished at 20180802-0512 Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Post Build Chroot | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ iva_1.0.9+ds-6_amd64.changes: ----------------------------- Format: 1.8 Date: Wed, 01 Aug 2018 21:19:30 +0200 Source: iva Binary: iva Architecture: amd64 Version: 1.0.9+ds-6 Distribution: cosmic-proposed Urgency: medium Maintainer: Launchpad Build Daemon Changed-By: Sascha Steinbiss Description: iva - iterative virus sequence assembler Changes: iva (1.0.9+ds-6) unstable; urgency=medium . * Use correct Vcs-Git URL. * Remove ancient X-Python3-Version field. * Use Debian's Perl path in RATT scripts. Checksums-Sha1: 174c8a678a34d7a0807c422abd8ee9687d83de9e 8936 iva_1.0.9+ds-6_amd64.buildinfo 2e654f0138171b62f69e9d3a357052e853a26b1e 8578192 iva_1.0.9+ds-6_amd64.deb Checksums-Sha256: 7ec2ed099b9ef1739bfe2a621775c9298ac0d753ca1635704bc6888895bbd196 8936 iva_1.0.9+ds-6_amd64.buildinfo 7a18b0ef79d8d1050587b842cb59d1bb0d561db8f0dec7f19628ee48a7fc0213 8578192 iva_1.0.9+ds-6_amd64.deb Files: 925e590e29903bd28e619d1b5c6362cf 8936 science optional iva_1.0.9+ds-6_amd64.buildinfo de1e1a24e3506f074f974366064821f4 8578192 science optional iva_1.0.9+ds-6_amd64.deb +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ iva_1.0.9+ds-6_amd64.deb ------------------------ new debian package, version 2.0. size 8578192 bytes: control archive=3040 bytes. 1009 bytes, 22 lines control 5575 bytes, 65 lines md5sums 155 bytes, 9 lines * postinst #!/bin/sh 381 bytes, 12 lines * prerm #!/bin/sh Package: iva Version: 1.0.9+ds-6 Architecture: amd64 Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 8766 Depends: fastaq (>= 1.6), python3-networkx, python3-pysam, python3:any, kmc, mummer, smalt, samtools, python3-numpy, default-jre-headless Recommends: r-base-core, bioperl, trimmomatic Section: science Priority: optional Homepage: https://github.com/sanger-pathogens/iva Description: iterative virus sequence assembler IVA is a de novo assembler designed to assemble virus genomes that have no repeat sequences, using Illumina read pairs sequenced from mixed populations at extremely high depth. . IVA's main algorithm works by iteratively extending contigs using aligned read pairs. Its input can be just read pairs, or additionally you can provide an existing set of contigs to be extended. Alternatively, it can take reads together with a reference sequence. drwxr-xr-x root/root 0 2018-08-01 19:19 ./ drwxr-xr-x root/root 0 2018-08-01 19:19 ./usr/ drwxr-xr-x root/root 0 2018-08-01 19:19 ./usr/bin/ -rwxr-xr-x root/root 17240 2018-08-01 19:19 ./usr/bin/iva -rwxr-xr-x root/root 6228 2018-08-01 19:19 ./usr/bin/iva_qc -rwxr-xr-x root/root 2406 2018-08-01 19:19 ./usr/bin/iva_qc_make_db drwxr-xr-x root/root 0 2018-08-01 19:19 ./usr/lib/ drwxr-xr-x root/root 0 2018-08-01 19:19 ./usr/lib/python3/ drwxr-xr-x root/root 0 2018-08-01 19:19 ./usr/lib/python3/dist-packages/ drwxr-xr-x root/root 0 2018-08-01 19:19 ./usr/lib/python3/dist-packages/iva-1.0.9.egg-info/ -rw-r--r-- root/root 483 2018-08-01 19:19 ./usr/lib/python3/dist-packages/iva-1.0.9.egg-info/PKG-INFO -rw-r--r-- root/root 1 2018-08-01 19:19 ./usr/lib/python3/dist-packages/iva-1.0.9.egg-info/dependency_links.txt -rw-r--r-- root/root 0 2018-08-01 19:19 ./usr/lib/python3/dist-packages/iva-1.0.9.egg-info/requires.txt -rw-r--r-- root/root 4 2018-08-01 19:19 ./usr/lib/python3/dist-packages/iva-1.0.9.egg-info/top_level.txt drwxr-xr-x root/root 0 2018-08-01 19:19 ./usr/lib/python3/dist-packages/iva/ -rw-r--r-- root/root 1033 2018-01-25 10:57 ./usr/lib/python3/dist-packages/iva/__init__.py -rw-r--r-- root/root 28055 2018-01-25 10:57 ./usr/lib/python3/dist-packages/iva/assembly.py -rw-r--r-- root/root 1856 2018-01-25 10:57 ./usr/lib/python3/dist-packages/iva/common.py -rw-r--r-- root/root 1960 2018-01-25 10:57 ./usr/lib/python3/dist-packages/iva/contig.py -rw-r--r-- root/root 4391 2018-01-25 10:57 ./usr/lib/python3/dist-packages/iva/contig_trim.py -rw-r--r-- root/root 4903 2018-01-25 10:57 ./usr/lib/python3/dist-packages/iva/edge.py -rw-r--r-- root/root 3077 2018-01-25 10:57 ./usr/lib/python3/dist-packages/iva/egg_extract.py -rw-r--r-- root/root 4110 2018-01-25 10:57 ./usr/lib/python3/dist-packages/iva/external_progs.py drwxr-xr-x root/root 0 2018-08-01 19:19 ./usr/lib/python3/dist-packages/iva/gage/ -rw-r--r-- root/root 489 2018-08-01 19:19 ./usr/lib/python3/dist-packages/iva/gage/GetFastaStats$ContigAt.class -rw-r--r-- root/root 10168 2018-08-01 19:19 ./usr/lib/python3/dist-packages/iva/gage/GetFastaStats.class -rw-r--r-- root/root 14839 2018-01-25 10:57 ./usr/lib/python3/dist-packages/iva/gage/GetFastaStats.java -rw-r--r-- root/root 3689 2018-08-01 19:19 ./usr/lib/python3/dist-packages/iva/gage/SizeFasta.class -rw-r--r-- root/root 3611 2018-01-25 10:57 ./usr/lib/python3/dist-packages/iva/gage/SizeFasta.java -rw-r--r-- root/root 2898 2018-08-01 19:19 ./usr/lib/python3/dist-packages/iva/gage/SplitFastaByLetter.class -rw-r--r-- root/root 2229 2018-01-25 10:57 ./usr/lib/python3/dist-packages/iva/gage/SplitFastaByLetter.java -rw-r--r-- root/root 621 2018-08-01 19:19 ./usr/lib/python3/dist-packages/iva/gage/Utils$Pair.class -rw-r--r-- root/root 4564 2018-08-01 19:19 ./usr/lib/python3/dist-packages/iva/gage/Utils$ToProtein.class -rw-r--r-- root/root 1225 2018-08-01 19:19 ./usr/lib/python3/dist-packages/iva/gage/Utils$Translate.class -rw-r--r-- root/root 5892 2018-08-01 19:19 ./usr/lib/python3/dist-packages/iva/gage/Utils.class -rw-r--r-- root/root 9230 2018-01-25 10:57 ./usr/lib/python3/dist-packages/iva/gage/Utils.java -rwxr-xr-x root/root 80 2018-01-25 10:57 ./usr/lib/python3/dist-packages/iva/gage/colsum.pl -rwxr-xr-x root/root 1773 2018-01-25 10:57 ./usr/lib/python3/dist-packages/iva/gage/getCorrectnessStats.sh -rwxr-xr-x root/root 1430 2018-01-25 10:57 ./usr/lib/python3/dist-packages/iva/gage/getMummerStats.sh -rw-r--r-- root/root 196 2018-08-01 19:19 ./usr/lib/python3/dist-packages/iva/gage/getScaffoldStats$1.class -rw-r--r-- root/root 1229 2018-08-01 19:19 ./usr/lib/python3/dist-packages/iva/gage/getScaffoldStats$Scaffold.class -rw-r--r-- root/root 13840 2018-08-01 19:19 ./usr/lib/python3/dist-packages/iva/gage/getScaffoldStats.class -rw-r--r-- root/root 19111 2018-01-25 10:57 ./usr/lib/python3/dist-packages/iva/gage/getScaffoldStats.java -rw-r--r-- root/root 7133 2018-01-25 10:57 ./usr/lib/python3/dist-packages/iva/graph.py -rw-r--r-- root/root 9487 2018-01-25 10:57 ./usr/lib/python3/dist-packages/iva/kcount.py -rw-r--r-- root/root 3466 2018-01-25 10:57 ./usr/lib/python3/dist-packages/iva/kmers.py -rw-r--r-- root/root 16961 2018-01-25 10:57 ./usr/lib/python3/dist-packages/iva/kraken.py -rw-r--r-- root/root 13238 2018-01-25 10:57 ./usr/lib/python3/dist-packages/iva/mapping.py -rw-r--r-- root/root 8365 2018-01-25 10:57 ./usr/lib/python3/dist-packages/iva/mummer.py -rw-r--r-- root/root 36646 2018-01-25 10:57 ./usr/lib/python3/dist-packages/iva/qc.py -rw-r--r-- root/root 8190 2018-01-25 10:57 ./usr/lib/python3/dist-packages/iva/qc_external.py drwxr-xr-x root/root 0 2018-08-01 19:19 ./usr/lib/python3/dist-packages/iva/ratt/ -rwxr-xr-x root/root 1008 2018-08-01 19:19 ./usr/lib/python3/dist-packages/iva/ratt/embl2gff.pl -rwxr-xr-x root/root 1045 2018-08-01 19:19 ./usr/lib/python3/dist-packages/iva/ratt/genbank2embl.pl -rwxr-xr-x root/root 41988 2018-01-25 10:57 ./usr/lib/python3/dist-packages/iva/ratt/main.ratt.pl -rw-r--r-- root/root 90 2018-01-25 10:57 ./usr/lib/python3/dist-packages/iva/ratt/ratt.config -rw-r--r-- root/root 90 2018-01-25 10:57 ./usr/lib/python3/dist-packages/iva/ratt/ratt.config.hiv -rw-r--r-- root/root 57611 2018-01-25 10:57 ./usr/lib/python3/dist-packages/iva/ratt/ratt_correction.pm -rwxr-xr-x root/root 13201 2018-01-25 10:57 ./usr/lib/python3/dist-packages/iva/ratt/start.ratt.sh -rw-r--r-- root/root 1428 2018-01-25 10:57 ./usr/lib/python3/dist-packages/iva/read_trim.py drwxr-xr-x root/root 0 2018-08-01 19:19 ./usr/lib/python3/dist-packages/iva/read_trim/ -rw-r--r-- root/root 3143 2018-01-25 10:57 ./usr/lib/python3/dist-packages/iva/read_trim/adapters.fasta -rw-r--r-- root/root 6056 2018-01-25 10:57 ./usr/lib/python3/dist-packages/iva/seed.py -rw-r--r-- root/root 5586 2018-01-25 10:57 ./usr/lib/python3/dist-packages/iva/seed_processor.py -rw-r--r-- root/root 2443 2018-01-25 10:57 ./usr/lib/python3/dist-packages/iva/test_data_runner.py drwxr-xr-x root/root 0 2018-08-01 19:19 ./usr/lib/python3/dist-packages/iva/test_run_data/ -rw-r--r-- root/root 672 2018-01-25 10:57 ./usr/lib/python3/dist-packages/iva/test_run_data/hiv_pcr_primers.fa -rw-r--r-- root/root 9981 2018-01-25 10:57 ./usr/lib/python3/dist-packages/iva/test_run_data/iva_contigs_no_trimmomatic.fasta -rw-r--r-- root/root 9200 2018-01-25 10:57 ./usr/lib/python3/dist-packages/iva/test_run_data/iva_contigs_with_trimmomatic.fasta -rw-r--r-- root/root 3813239 2018-08-01 19:19 ./usr/lib/python3/dist-packages/iva/test_run_data/reads_1.fq.gz -rw-r--r-- root/root 4661713 2018-08-01 19:19 ./usr/lib/python3/dist-packages/iva/test_run_data/reads_2.fq.gz -rw-r--r-- root/root 9217 2018-01-25 10:57 ./usr/lib/python3/dist-packages/iva/test_run_data/reference.fasta drwxr-xr-x root/root 0 2018-08-01 19:19 ./usr/share/ drwxr-xr-x root/root 0 2018-08-01 19:19 ./usr/share/doc/ drwxr-xr-x root/root 0 2018-08-01 19:19 ./usr/share/doc/iva/ -rw-r--r-- root/root 960 2018-08-01 19:19 ./usr/share/doc/iva/changelog.Debian.gz -rw-r--r-- root/root 1488 2018-08-01 19:18 ./usr/share/doc/iva/copyright drwxr-xr-x root/root 0 2018-08-01 19:19 ./usr/share/man/ drwxr-xr-x root/root 0 2018-08-01 19:19 ./usr/share/man/man1/ -rw-r--r-- root/root 2254 2018-08-01 19:19 ./usr/share/man/man1/iva.1.gz -rw-r--r-- root/root 1281 2018-08-01 19:19 ./usr/share/man/man1/iva_qc.1.gz -rw-r--r-- root/root 643 2018-08-01 19:19 ./usr/share/man/man1/iva_qc_make_db.1.gz +------------------------------------------------------------------------------+ | Post Build | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not removing build depends: as requested +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: amd64 Build-Space: 37320 Build-Time: 27 Distribution: cosmic-proposed Host Architecture: amd64 Install-Time: 70 Job: iva_1.0.9+ds-6.dsc Machine Architecture: amd64 Package: iva Package-Time: 99 Source-Version: 1.0.9+ds-6 Space: 37320 Status: successful Version: 1.0.9+ds-6 -------------------------------------------------------------------------------- Finished at 20180802-0512 Build needed 00:01:39, 37320k disc space RUN: /usr/share/launchpad-buildd/slavebin/in-target scan-for-processes --backend=chroot --series=cosmic --arch=amd64 PACKAGEBUILD-15221806 Scanning for processes to kill in build PACKAGEBUILD-15221806