https://launchpad.net/ubuntu/+source/iva/1.0.11+ds-5/+build/27738260 RUN: /usr/share/launchpad-buildd/bin/builder-prep Kernel version: Linux bos01-arm64-013 5.4.0-169-generic #187-Ubuntu SMP Thu Nov 23 14:53:38 UTC 2023 aarch64 Buildd toolchain package versions: launchpad-buildd_235~645~ubuntu20.04.1 python3-lpbuildd_235~645~ubuntu20.04.1 sbuild_0.79.0-1ubuntu1 git-build-recipe_0.3.6 git_1:2.25.1-1ubuntu3.11 dpkg-dev_1.19.7ubuntu3.2 python3-debian_0.1.36ubuntu1.1. Syncing the system clock with the buildd NTP service... 1 Feb 17:15:33 ntpdate[1926]: adjust time server 10.211.37.1 offset -0.017241 sec RUN: /usr/share/launchpad-buildd/bin/in-target unpack-chroot --backend=chroot --series=noble --arch=armhf PACKAGEBUILD-27738260 --image-type chroot /home/buildd/filecache-default/59612f0fc5bae33f6226b6e60c2e882b82c04bd0 Creating target for build PACKAGEBUILD-27738260 RUN: /usr/share/launchpad-buildd/bin/in-target mount-chroot --backend=chroot --series=noble --arch=armhf PACKAGEBUILD-27738260 Starting target for build PACKAGEBUILD-27738260 RUN: /usr/share/launchpad-buildd/bin/in-target override-sources-list --backend=chroot --series=noble --arch=armhf PACKAGEBUILD-27738260 'deb http://ftpmaster.internal/ubuntu noble main universe' 'deb http://ftpmaster.internal/ubuntu noble-security main universe' 'deb http://ftpmaster.internal/ubuntu noble-updates main universe' 'deb http://ftpmaster.internal/ubuntu noble-proposed main universe' Overriding sources.list in build-PACKAGEBUILD-27738260 RUN: /usr/share/launchpad-buildd/bin/in-target update-debian-chroot --backend=chroot --series=noble --arch=armhf PACKAGEBUILD-27738260 Updating target for build PACKAGEBUILD-27738260 Get:1 http://ftpmaster.internal/ubuntu noble InRelease [256 kB] Get:2 http://ftpmaster.internal/ubuntu noble-security InRelease [90.7 kB] Get:3 http://ftpmaster.internal/ubuntu noble-updates InRelease [90.7 kB] Get:4 http://ftpmaster.internal/ubuntu noble-proposed InRelease [118 kB] Get:5 http://ftpmaster.internal/ubuntu noble/main armhf Packages [1348 kB] Get:6 http://ftpmaster.internal/ubuntu noble/main Translation-en [518 kB] Get:7 http://ftpmaster.internal/ubuntu noble/universe armhf Packages [14.3 MB] Get:8 http://ftpmaster.internal/ubuntu noble/universe Translation-en [6024 kB] Get:9 http://ftpmaster.internal/ubuntu noble-proposed/main armhf Packages [207 kB] Get:10 http://ftpmaster.internal/ubuntu noble-proposed/main Translation-en [76.0 kB] Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe armhf Packages [1050 kB] Get:12 http://ftpmaster.internal/ubuntu noble-proposed/universe Translation-en [402 kB] Fetched 24.5 MB in 4s (6821 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: libperl5.36 libunistring2 perl-modules-5.36 Use 'sudo apt autoremove' to remove them. The following NEW packages will be installed: cpp-13-arm-linux-gnueabihf cpp-arm-linux-gnueabihf g++-13-arm-linux-gnueabihf g++-arm-linux-gnueabihf gcc-13-arm-linux-gnueabihf gcc-14-base gcc-arm-linux-gnueabihf libperl5.38 libunistring5 perl-modules-5.38 The following packages will be upgraded: apt apt-utils base-files base-passwd bash bash-completion binutils binutils-arm-linux-gnueabihf binutils-common bsdextrautils bsdutils coreutils cpp cpp-13 debconf debconf-i18n debianutils diffutils dpkg dpkg-dev fakeroot g++ g++-13 gcc gcc-13 gcc-13-base grep init init-system-helpers krb5-locales libacl1 libapparmor1 libapt-pkg6.0 libargon2-1 libasan8 libatomic1 libattr1 libaudit-common libaudit1 libbinutils libblkid1 libc-bin libc-dev-bin libc6 libc6-dev libcap-ng0 libcc1-0 libcrypt-dev libcrypt1 libcryptsetup12 libctf-nobfd0 libctf0 libdb5.3 libdebconfclient0 libdpkg-perl libfakeroot libfdisk1 libffi8 libgcc-13-dev libgcc-s1 libgcrypt20 libgdbm-compat4 libgdbm6 libgnutls30 libgomp1 libgpg-error-l10n libgpg-error0 libgssapi-krb5-2 libidn2-0 libk5crypto3 libkmod2 libkrb5-3 libkrb5support0 liblocale-gettext-perl liblzma5 libmd0 libmount1 libncursesw6 libnsl-dev libnsl2 libp11-kit0 libpam-modules libpam-modules-bin libpam-runtime libpam0g libpcre2-8-0 libperl5.36 libpng16-16 libproc2-0 libreadline8 libseccomp2 libselinux1 libsemanage-common libsemanage2 libsepol2 libsframe1 libsmartcols1 libsqlite3-0 libssl3 libstdc++-13-dev libstdc++6 libsystemd-shared libsystemd0 libtext-charwidth-perl libtext-iconv-perl libtinfo6 libtirpc-common libtirpc-dev libtirpc3 libubsan1 libudev1 libuuid1 libxxhash0 libzstd1 linux-libc-dev login lto-disabled-list mawk mount ncurses-base ncurses-bin openssl optipng passwd perl perl-base perl-modules-5.36 pinentry-curses procps psmisc readline-common sed systemd systemd-dev systemd-sysv sysvinit-utils tar tzdata ubuntu-keyring util-linux uuid-runtime xz-utils zlib1g 143 upgraded, 10 newly installed, 0 to remove and 0 not upgraded. Need to get 101 MB of archives. After this operation, 46.2 MB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu noble/main armhf libnsl-dev armhf 1.3.0-3 [65.8 kB] Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libcrypt-dev armhf 1:4.4.36-4 [136 kB] Get:3 http://ftpmaster.internal/ubuntu noble/main armhf libc6-dev armhf 2.38-3ubuntu1 [1347 kB] Get:4 http://ftpmaster.internal/ubuntu noble/main armhf libc-dev-bin armhf 2.38-3ubuntu1 [18.9 kB] Get:5 http://ftpmaster.internal/ubuntu noble/main armhf libtirpc-common all 1.3.4+ds-1build1 [8566 B] Get:6 http://ftpmaster.internal/ubuntu noble/main armhf libtirpc-dev armhf 1.3.4+ds-1build1 [207 kB] Get:7 http://ftpmaster.internal/ubuntu noble/main armhf libgssapi-krb5-2 armhf 1.20.1-5build1 [118 kB] Get:8 http://ftpmaster.internal/ubuntu noble/main armhf libkrb5-3 armhf 1.20.1-5build1 [320 kB] Get:9 http://ftpmaster.internal/ubuntu noble/main armhf libk5crypto3 armhf 1.20.1-5build1 [78.6 kB] Get:10 http://ftpmaster.internal/ubuntu noble/main armhf libkrb5support0 armhf 1.20.1-5build1 [31.3 kB] Get:11 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libssl3 armhf 3.0.10-1ubuntu4 [1553 kB] Get:12 http://ftpmaster.internal/ubuntu noble/main armhf libtirpc3 armhf 1.3.4+ds-1build1 [81.0 kB] Get:13 http://ftpmaster.internal/ubuntu noble/main armhf libnsl2 armhf 1.3.0-3 [35.9 kB] Get:14 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libcrypt1 armhf 1:4.4.36-4 [104 kB] Get:15 http://ftpmaster.internal/ubuntu noble/main armhf linux-libc-dev armhf 6.6.0-14.14 [1539 kB] Get:16 http://ftpmaster.internal/ubuntu noble-proposed/main armhf gcc-14-base armhf 14-20240130-1ubuntu1 [46.2 kB] Get:17 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libgcc-s1 armhf 14-20240130-1ubuntu1 [41.5 kB] Get:18 http://ftpmaster.internal/ubuntu noble/main armhf libc6 armhf 2.38-3ubuntu1 [2818 kB] Get:19 http://ftpmaster.internal/ubuntu noble/main armhf base-files armhf 13ubuntu6 [84.0 kB] Get:20 http://ftpmaster.internal/ubuntu noble/main armhf debianutils armhf 5.16 [93.1 kB] Get:21 http://ftpmaster.internal/ubuntu noble/main armhf bash armhf 5.2.21-2ubuntu1 [673 kB] Get:22 http://ftpmaster.internal/ubuntu noble/main armhf bsdutils armhf 1:2.39.2-6ubuntu1 [99.5 kB] Get:23 http://ftpmaster.internal/ubuntu noble-proposed/main armhf coreutils armhf 9.4-2ubuntu3 [1312 kB] Get:24 http://ftpmaster.internal/ubuntu noble/main armhf diffutils armhf 1:3.10-1 [167 kB] Get:25 http://ftpmaster.internal/ubuntu noble/main armhf libgpg-error-l10n all 1.47-3build1 [8024 B] Get:26 http://ftpmaster.internal/ubuntu noble/main armhf libgpg-error0 armhf 1.47-3build1 [61.6 kB] Get:27 http://ftpmaster.internal/ubuntu noble/main armhf libgcrypt20 armhf 1.10.3-2 [454 kB] Get:28 http://ftpmaster.internal/ubuntu noble/main armhf liblzma5 armhf 5.4.5-0.3 [120 kB] Get:29 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libstdc++6 armhf 14-20240130-1ubuntu1 [714 kB] Get:30 http://ftpmaster.internal/ubuntu noble/main armhf libacl1 armhf 2.3.1-4ubuntu1 [16.2 kB] Get:31 http://ftpmaster.internal/ubuntu noble/main armhf libapparmor1 armhf 4.0.0~alpha2-0ubuntu8 [43.9 kB] Get:32 http://ftpmaster.internal/ubuntu noble/main armhf libaudit-common all 1:3.1.2-2 [5594 B] Get:33 http://ftpmaster.internal/ubuntu noble/main armhf libcap-ng0 armhf 0.8.4-1 [14.5 kB] Get:34 http://ftpmaster.internal/ubuntu noble/main armhf libaudit1 armhf 1:3.1.2-2 [44.2 kB] Get:35 http://ftpmaster.internal/ubuntu noble/main armhf libblkid1 armhf 2.39.2-6ubuntu1 [159 kB] Get:36 http://ftpmaster.internal/ubuntu noble/main armhf libzstd1 armhf 1.5.5+dfsg2-2 [265 kB] Get:37 http://ftpmaster.internal/ubuntu noble/main armhf libkmod2 armhf 30+20230601-2ubuntu1 [43.9 kB] Get:38 http://ftpmaster.internal/ubuntu noble/main armhf libpcre2-8-0 armhf 10.42-4ubuntu1 [198 kB] Get:39 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libselinux1 armhf 3.5-2 [70.3 kB] Get:40 http://ftpmaster.internal/ubuntu noble/main armhf libmount1 armhf 2.39.2-6ubuntu1 [171 kB] Get:41 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libtext-iconv-perl armhf 1.7-8build1 [12.6 kB] Get:42 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libtext-charwidth-perl armhf 0.04-11build1 [8894 B] Get:43 http://ftpmaster.internal/ubuntu noble-proposed/main armhf perl-modules-5.38 all 5.38.2-3 [3110 kB] Get:44 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libperl5.38 armhf 5.38.2-3 [4105 kB] Get:45 http://ftpmaster.internal/ubuntu noble-proposed/main armhf perl armhf 5.38.2-3 [231 kB] Get:46 http://ftpmaster.internal/ubuntu noble-proposed/main armhf perl-base armhf 5.38.2-3 [1670 kB] Get:47 http://ftpmaster.internal/ubuntu noble-proposed/main armhf liblocale-gettext-perl armhf 1.07-6build1 [14.8 kB] Get:48 http://ftpmaster.internal/ubuntu noble/main armhf perl-modules-5.36 all 5.36.0-10ubuntu1 [2984 kB] Get:49 http://ftpmaster.internal/ubuntu noble/main armhf libperl5.36 armhf 5.36.0-10ubuntu1 [4019 kB] Get:50 http://ftpmaster.internal/ubuntu noble/main armhf libdb5.3 armhf 5.3.28+dfsg2-4 [652 kB] Get:51 http://ftpmaster.internal/ubuntu noble/main armhf libgdbm6 armhf 1.23-5 [29.8 kB] Get:52 http://ftpmaster.internal/ubuntu noble/main armhf libgdbm-compat4 armhf 1.23-5 [5970 B] Get:53 http://ftpmaster.internal/ubuntu noble/main armhf zlib1g armhf 1:1.3.dfsg-3ubuntu1 [50.6 kB] Get:54 http://ftpmaster.internal/ubuntu noble-proposed/main armhf debconf-i18n all 1.5.85 [205 kB] Get:55 http://ftpmaster.internal/ubuntu noble-proposed/main armhf debconf all 1.5.85 [124 kB] Get:56 http://ftpmaster.internal/ubuntu noble/main armhf libpam0g armhf 1.5.2-9.1ubuntu2 [60.2 kB] Get:57 http://ftpmaster.internal/ubuntu noble/main armhf libseccomp2 armhf 2.5.4-2ubuntu2 [49.0 kB] Get:58 http://ftpmaster.internal/ubuntu noble-proposed/main armhf systemd-sysv armhf 255.2-3ubuntu2 [11.9 kB] Get:59 http://ftpmaster.internal/ubuntu noble-proposed/main armhf systemd-dev all 255.2-3ubuntu2 [101 kB] Get:60 http://ftpmaster.internal/ubuntu noble-proposed/main armhf systemd armhf 255.2-3ubuntu2 [3495 kB] Get:61 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libsystemd-shared armhf 255.2-3ubuntu2 [2006 kB] Get:62 http://ftpmaster.internal/ubuntu noble/main armhf libargon2-1 armhf 0~20190702+dfsg-4 [22.3 kB] Get:63 http://ftpmaster.internal/ubuntu noble/main armhf libuuid1 armhf 2.39.2-6ubuntu1 [33.4 kB] Get:64 http://ftpmaster.internal/ubuntu noble/main armhf libcryptsetup12 armhf 2:2.6.1-6ubuntu1 [216 kB] Get:65 http://ftpmaster.internal/ubuntu noble/main armhf libfdisk1 armhf 2.39.2-6ubuntu1 [195 kB] Get:66 http://ftpmaster.internal/ubuntu noble/main armhf mount armhf 2.39.2-6ubuntu1 [132 kB] Get:67 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libsystemd0 armhf 255.2-3ubuntu2 [408 kB] Get:68 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libudev1 armhf 255.2-3ubuntu2 [164 kB] Get:69 http://ftpmaster.internal/ubuntu noble/main armhf libxxhash0 armhf 0.8.2-2 [31.3 kB] Get:70 http://ftpmaster.internal/ubuntu noble/main armhf libapt-pkg6.0 armhf 2.7.10 [984 kB] Get:71 http://ftpmaster.internal/ubuntu noble/main armhf tar armhf 1.35+dfsg-3 [236 kB] Get:72 http://ftpmaster.internal/ubuntu noble-proposed/main armhf dpkg armhf 1.22.2ubuntu3 [1234 kB] Get:73 http://ftpmaster.internal/ubuntu noble/main armhf grep armhf 3.11-4 [166 kB] Get:74 http://ftpmaster.internal/ubuntu noble/main armhf login armhf 1:4.13+dfsg1-3ubuntu1 [200 kB] Get:75 http://ftpmaster.internal/ubuntu noble-proposed/main armhf ncurses-bin armhf 6.4+20240113-1 [178 kB] Get:76 http://ftpmaster.internal/ubuntu noble/main armhf sed armhf 4.9-2 [198 kB] Get:77 http://ftpmaster.internal/ubuntu noble/main armhf util-linux armhf 2.39.2-6ubuntu1 [1211 kB] Get:78 http://ftpmaster.internal/ubuntu noble/main armhf libdebconfclient0 armhf 0.271ubuntu1 [10.8 kB] Get:79 http://ftpmaster.internal/ubuntu noble/main armhf base-passwd armhf 3.6.3 [51.0 kB] Get:80 http://ftpmaster.internal/ubuntu noble/main armhf init-system-helpers all 1.66ubuntu1 [39.4 kB] Get:81 http://ftpmaster.internal/ubuntu noble/main armhf libc-bin armhf 2.38-3ubuntu1 [532 kB] Get:82 http://ftpmaster.internal/ubuntu noble-proposed/main armhf ncurses-base all 6.4+20240113-1 [25.4 kB] Get:83 http://ftpmaster.internal/ubuntu noble/main armhf sysvinit-utils armhf 3.08-3ubuntu1 [33.4 kB] Get:84 http://ftpmaster.internal/ubuntu noble/main armhf apt armhf 2.7.10 [1362 kB] Get:85 http://ftpmaster.internal/ubuntu noble/main armhf apt-utils armhf 2.7.10 [211 kB] Get:86 http://ftpmaster.internal/ubuntu noble/main armhf ubuntu-keyring all 2023.11.28.1 [11.1 kB] Get:87 http://ftpmaster.internal/ubuntu noble/main armhf libffi8 armhf 3.4.4-2 [20.8 kB] Get:88 http://ftpmaster.internal/ubuntu noble/main armhf libp11-kit0 armhf 0.25.3-2ubuntu2 [261 kB] Get:89 http://ftpmaster.internal/ubuntu noble/main armhf libunistring5 armhf 1.1-2 [512 kB] Get:90 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libidn2-0 armhf 2.3.7-2 [96.1 kB] Get:91 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libgnutls30 armhf 3.8.3-1ubuntu1 [939 kB] Get:92 http://ftpmaster.internal/ubuntu noble/main armhf libpam-modules-bin armhf 1.5.2-9.1ubuntu2 [43.6 kB] Get:93 http://ftpmaster.internal/ubuntu noble/main armhf libpam-modules armhf 1.5.2-9.1ubuntu2 [265 kB] Get:94 http://ftpmaster.internal/ubuntu noble/main armhf init armhf 1.66ubuntu1 [6186 B] Get:95 http://ftpmaster.internal/ubuntu noble/main armhf libsmartcols1 armhf 2.39.2-6ubuntu1 [116 kB] Get:96 http://ftpmaster.internal/ubuntu noble/main armhf uuid-runtime armhf 2.39.2-6ubuntu1 [40.7 kB] Get:97 http://ftpmaster.internal/ubuntu noble/main armhf libattr1 armhf 1:2.5.2-1 [10.3 kB] Get:98 http://ftpmaster.internal/ubuntu noble/main armhf libmd0 armhf 1.1.0-2 [23.1 kB] Get:99 http://ftpmaster.internal/ubuntu noble/main armhf libpam-runtime all 1.5.2-9.1ubuntu2 [40.6 kB] Get:100 http://ftpmaster.internal/ubuntu noble/main armhf libsemanage-common all 3.5-1build1 [9982 B] Get:101 http://ftpmaster.internal/ubuntu noble/main armhf libsepol2 armhf 3.5-2 [262 kB] Get:102 http://ftpmaster.internal/ubuntu noble/main armhf libsemanage2 armhf 3.5-1build1 [84.1 kB] Get:103 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libncursesw6 armhf 6.4+20240113-1 [118 kB] Get:104 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libtinfo6 armhf 6.4+20240113-1 [90.6 kB] Get:105 http://ftpmaster.internal/ubuntu noble/main armhf passwd armhf 1:4.13+dfsg1-3ubuntu1 [817 kB] Get:106 http://ftpmaster.internal/ubuntu noble/main armhf g++-13 armhf 13.2.0-13ubuntu1 [14.0 kB] Get:107 http://ftpmaster.internal/ubuntu noble/main armhf gcc-13 armhf 13.2.0-13ubuntu1 [443 kB] Get:108 http://ftpmaster.internal/ubuntu noble/main armhf cpp-13 armhf 13.2.0-13ubuntu1 [1032 B] Get:109 http://ftpmaster.internal/ubuntu noble/main armhf cpp-13-arm-linux-gnueabihf armhf 13.2.0-13ubuntu1 [8754 kB] Get:110 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libcc1-0 armhf 14-20240130-1ubuntu1 [39.2 kB] Get:111 http://ftpmaster.internal/ubuntu noble/main armhf libctf0 armhf 2.42-2ubuntu1 [87.6 kB] Get:112 http://ftpmaster.internal/ubuntu noble/main armhf libctf-nobfd0 armhf 2.42-2ubuntu1 [87.7 kB] Get:113 http://ftpmaster.internal/ubuntu noble/main armhf libsframe1 armhf 2.42-2ubuntu1 [12.8 kB] Get:114 http://ftpmaster.internal/ubuntu noble/main armhf binutils-arm-linux-gnueabihf armhf 2.42-2ubuntu1 [2924 kB] Get:115 http://ftpmaster.internal/ubuntu noble/main armhf libbinutils armhf 2.42-2ubuntu1 [460 kB] Get:116 http://ftpmaster.internal/ubuntu noble/main armhf binutils armhf 2.42-2ubuntu1 [3080 B] Get:117 http://ftpmaster.internal/ubuntu noble/main armhf binutils-common armhf 2.42-2ubuntu1 [216 kB] Get:118 http://ftpmaster.internal/ubuntu noble/main armhf libstdc++-13-dev armhf 13.2.0-13ubuntu1 [2401 kB] Get:119 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libgomp1 armhf 14-20240130-1ubuntu1 [126 kB] Get:120 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libatomic1 armhf 14-20240130-1ubuntu1 [7814 B] Get:121 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libasan8 armhf 14-20240130-1ubuntu1 [2940 kB] Get:122 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libubsan1 armhf 14-20240130-1ubuntu1 [1151 kB] Get:123 http://ftpmaster.internal/ubuntu noble/main armhf libgcc-13-dev armhf 13.2.0-13ubuntu1 [901 kB] Get:124 http://ftpmaster.internal/ubuntu noble/main armhf gcc-13-arm-linux-gnueabihf armhf 13.2.0-13ubuntu1 [16.8 MB] Get:125 http://ftpmaster.internal/ubuntu noble/main armhf g++-13-arm-linux-gnueabihf armhf 13.2.0-13ubuntu1 [9933 kB] Get:126 http://ftpmaster.internal/ubuntu noble/main armhf gcc-13-base armhf 13.2.0-13ubuntu1 [46.6 kB] Get:127 http://ftpmaster.internal/ubuntu noble/main armhf libproc2-0 armhf 2:4.0.4-2ubuntu1 [49.6 kB] Get:128 http://ftpmaster.internal/ubuntu noble/main armhf mawk armhf 1.3.4.20240123-1 [115 kB] Get:129 http://ftpmaster.internal/ubuntu noble/main armhf procps armhf 2:4.0.4-2ubuntu1 [699 kB] Get:130 http://ftpmaster.internal/ubuntu noble/main armhf krb5-locales all 1.20.1-5build1 [13.7 kB] Get:131 http://ftpmaster.internal/ubuntu noble/main armhf readline-common all 8.2-3 [56.2 kB] Get:132 http://ftpmaster.internal/ubuntu noble/main armhf libreadline8 armhf 8.2-3 [129 kB] Get:133 http://ftpmaster.internal/ubuntu noble/main armhf libsqlite3-0 armhf 3.45.0-1 [599 kB] Get:134 http://ftpmaster.internal/ubuntu noble-proposed/main armhf openssl armhf 3.0.10-1ubuntu4 [973 kB] Get:135 http://ftpmaster.internal/ubuntu noble/main armhf tzdata all 2023d-1ubuntu2 [321 kB] Get:136 http://ftpmaster.internal/ubuntu noble/main armhf bash-completion all 1:2.11-8 [180 kB] Get:137 http://ftpmaster.internal/ubuntu noble/main armhf bsdextrautils armhf 2.39.2-6ubuntu1 [77.7 kB] Get:138 http://ftpmaster.internal/ubuntu noble/main armhf libpng16-16 armhf 1.6.42-1 [166 kB] Get:139 http://ftpmaster.internal/ubuntu noble-proposed/main armhf psmisc armhf 23.6-2 [176 kB] Get:140 http://ftpmaster.internal/ubuntu noble/main armhf xz-utils armhf 5.4.5-0.3 [274 kB] Get:141 http://ftpmaster.internal/ubuntu noble/main armhf g++ armhf 4:13.2.0-7ubuntu1 [1090 B] Get:142 http://ftpmaster.internal/ubuntu noble/main armhf gcc armhf 4:13.2.0-7ubuntu1 [5022 B] Get:143 http://ftpmaster.internal/ubuntu noble/main armhf cpp armhf 4:13.2.0-7ubuntu1 [22.4 kB] Get:144 http://ftpmaster.internal/ubuntu noble/main armhf cpp-arm-linux-gnueabihf armhf 4:13.2.0-7ubuntu1 [5320 B] Get:145 http://ftpmaster.internal/ubuntu noble/main armhf gcc-arm-linux-gnueabihf armhf 4:13.2.0-7ubuntu1 [1220 B] Get:146 http://ftpmaster.internal/ubuntu noble/main armhf g++-arm-linux-gnueabihf armhf 4:13.2.0-7ubuntu1 [966 B] Get:147 http://ftpmaster.internal/ubuntu noble-proposed/main armhf dpkg-dev all 1.22.2ubuntu3 [1076 kB] Get:148 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libdpkg-perl all 1.22.2ubuntu3 [266 kB] Get:149 http://ftpmaster.internal/ubuntu noble/main armhf lto-disabled-list all 46 [12.3 kB] Get:150 http://ftpmaster.internal/ubuntu noble/main armhf libfakeroot armhf 1.33-1 [28.7 kB] Get:151 http://ftpmaster.internal/ubuntu noble/main armhf fakeroot armhf 1.33-1 [68.6 kB] Get:152 http://ftpmaster.internal/ubuntu noble-proposed/main armhf optipng armhf 0.7.8+ds-1 [109 kB] Get:153 http://ftpmaster.internal/ubuntu noble/main armhf pinentry-curses armhf 1.2.1-3ubuntu1 [36.4 kB] Preconfiguring packages ... 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Setting up libkrb5support0:armhf (1.20.1-5build1) ... Setting up tzdata (2023d-1ubuntu2) ... Current default time zone: 'Etc/UTC' Local time is now: Thu Feb 1 17:16:02 UTC 2024. Universal Time is now: Thu Feb 1 17:16:02 UTC 2024. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up fakeroot (1.33-1) ... Setting up perl-modules-5.36 (5.36.0-10ubuntu1) ... Setting up gcc-13-base:armhf (13.2.0-13ubuntu1) ... Setting up bash-completion (1:2.11-8) ... Setting up xz-utils (5.4.5-0.3) ... Setting up perl-modules-5.38 (5.38.2-3) ... Setting up libproc2-0:armhf (2:4.0.4-2ubuntu1) ... Setting up libpng16-16:armhf (1.6.42-1) ... Setting up libatomic1:armhf (14-20240130-1ubuntu1) ... Setting up libncursesw6:armhf (6.4+20240113-1) ... Setting up libk5crypto3:armhf (1.20.1-5build1) ... Setting up libubsan1:armhf (14-20240130-1ubuntu1) ... Setting up uuid-runtime (2.39.2-6ubuntu1) ... Running in chroot, ignoring request. invoke-rc.d: policy-rc.d denied execution of restart. Setting up libcrypt-dev:armhf (1:4.4.36-4) ... Setting up libasan8:armhf (14-20240130-1ubuntu1) ... Setting up procps (2:4.0.4-2ubuntu1) ... Installing new version of config file /etc/sysctl.conf ... Setting up mawk (1.3.4.20240123-1) ... Setting up libkrb5-3:armhf (1.20.1-5build1) ... Setting up libbinutils:armhf (2.42-2ubuntu1) ... Setting up libc-dev-bin (2.38-3ubuntu1) ... Setting up openssl (3.0.10-1ubuntu4) ... Setting up libgpg-error-l10n (1.47-3build1) ... Setting up readline-common (8.2-3) ... Setting up libcc1-0:armhf (14-20240130-1ubuntu1) ... Setting up liblocale-gettext-perl (1.07-6build1) ... Setting up libgdbm6:armhf (1.23-5) ... Setting up libctf0:armhf (2.42-2ubuntu1) ... Setting up pinentry-curses (1.2.1-3ubuntu1) ... Setting up cpp-13-arm-linux-gnueabihf (13.2.0-13ubuntu1) ... Setting up libreadline8:armhf (8.2-3) ... Setting up debconf-i18n (1.5.85) ... Setting up optipng (0.7.8+ds-1) ... Setting up libgssapi-krb5-2:armhf (1.20.1-5build1) ... Setting up libgdbm-compat4:armhf (1.23-5) ... Setting up libgcc-13-dev:armhf (13.2.0-13ubuntu1) ... Setting up binutils-arm-linux-gnueabihf (2.42-2ubuntu1) ... Setting up libperl5.36:armhf (5.36.0-10ubuntu1) ... Setting up cpp-arm-linux-gnueabihf (4:13.2.0-7ubuntu1) ... Setting up libtirpc3:armhf (1.3.4+ds-1build1) ... Setting up cpp-13 (13.2.0-13ubuntu1) ... Setting up libperl5.38:armhf (5.38.2-3) ... Setting up binutils (2.42-2ubuntu1) ... Setting up gcc-13-arm-linux-gnueabihf (13.2.0-13ubuntu1) ... Setting up perl (5.38.2-3) ... Setting up libtirpc-dev:armhf (1.3.4+ds-1build1) ... Setting up gcc-13 (13.2.0-13ubuntu1) ... Setting up libdpkg-perl (1.22.2ubuntu3) ... Setting up cpp (4:13.2.0-7ubuntu1) ... Setting up libnsl2:armhf (1.3.0-3) ... Setting up gcc-arm-linux-gnueabihf (4:13.2.0-7ubuntu1) ... Setting up gcc (4:13.2.0-7ubuntu1) ... Setting up dpkg-dev (1.22.2ubuntu3) ... Setting up libnsl-dev:armhf (1.3.0-3) ... Setting up libc6-dev:armhf (2.38-3ubuntu1) ... Setting up libstdc++-13-dev:armhf (13.2.0-13ubuntu1) ... Setting up g++-13-arm-linux-gnueabihf (13.2.0-13ubuntu1) ... Setting up g++-arm-linux-gnueabihf (4:13.2.0-7ubuntu1) ... Setting up g++-13 (13.2.0-13ubuntu1) ... Setting up g++ (4:13.2.0-7ubuntu1) ... Processing triggers for libc-bin (2.38-3ubuntu1) ... Processing triggers for debianutils (5.16) ... RUN: /usr/share/launchpad-buildd/bin/sbuild-package PACKAGEBUILD-27738260 armhf noble-proposed -c chroot:build-PACKAGEBUILD-27738260 --arch=armhf --dist=noble-proposed --nolog iva_1.0.11+ds-5.dsc Initiating build PACKAGEBUILD-27738260 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 5.4.0-169-generic #187-Ubuntu SMP Thu Nov 23 14:53:38 UTC 2023 armv7l sbuild (Debian sbuild) 0.79.0 (05 February 2020) on bos01-arm64-013.buildd +==============================================================================+ | iva 1.0.11+ds-5 (armhf) Thu, 01 Feb 2024 17:16:04 +0000 | +==============================================================================+ Package: iva Version: 1.0.11+ds-5 Source Version: 1.0.11+ds-5 Distribution: noble-proposed Machine Architecture: arm64 Host Architecture: armhf Build Architecture: armhf Build Type: any I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-27738260/chroot-autobuild' with '<>' I: NOTICE: Log filtering will replace 'build/iva-wA1pwP/resolver-9DmLvY' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- iva_1.0.11+ds-5.dsc exists in .; copying to chroot I: NOTICE: Log filtering will replace 'build/iva-wA1pwP/iva-1.0.11+ds' with '<>' I: NOTICE: Log filtering will replace 'build/iva-wA1pwP' with '<>' +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper-compat (= 13), dh-sequence-python3, libssl-dev, bioperl, fastaq, kmc, help2man, mummer, python3, python3-setuptools, python3-packaging, python3-numpy, python3-networkx, python3-pysam, python3-pytest, samtools, smalt, default-jdk-headless, build-essential, fakeroot Filtered Build-Depends: debhelper-compat (= 13), dh-sequence-python3, libssl-dev, bioperl, fastaq, kmc, help2man, mummer, python3, python3-setuptools, python3-packaging, python3-numpy, python3-networkx, python3-pysam, python3-pytest, samtools, smalt, default-jdk-headless, build-essential, fakeroot dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/<>/apt_archive/sbuild-build-depends-main-dummy.deb'. Ign:1 copy:/<>/apt_archive ./ InRelease Get:2 copy:/<>/apt_archive ./ Release [957 B] Ign:3 copy:/<>/apt_archive ./ Release.gpg Get:4 copy:/<>/apt_archive ./ Sources [481 B] Get:5 copy:/<>/apt_archive ./ Packages [560 B] Fetched 1998 B in 0s (132 kB/s) Reading package lists... Reading package lists... Install main build dependencies (apt-based resolver) ---------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following packages were automatically installed and are no longer required: apt-utils bash-completion debconf-i18n krb5-locales libgpg-error-l10n libgpm2 libip4tc2 libnss-nis libnss-nisplus libperl5.36 libtext-charwidth-perl libtext-iconv-perl libtext-wrapi18n-perl libunistring2 perl-modules-5.36 psmisc uuid-runtime Use 'apt autoremove' to remove them. The following additional packages will be installed: autoconf automake autopoint autotools-dev bioperl ca-certificates-java debhelper debugedit default-jdk-headless default-jre-headless dh-autoreconf dh-python dh-strip-nondeterminism dwz fastaq file fontconfig-config fonts-dejavu-core fonts-dejavu-mono gawk gettext gettext-base groff-base help2man intltool-debian java-common kmc libalgorithm-diff-perl libarchive-zip-perl libasound2 libasound2-data libavahi-client3 libavahi-common-data libavahi-common3 libbambamc0 libbio-perl-perl libblas3 libbrotli1 libcapture-tiny-perl libclass-data-inheritable-perl libcups2 libcurl3-gnutls libdata-stag-perl libdbus-1-3 libdebhelper-perl libdeflate0 libdevel-stacktrace-perl libdw1 libelf1 libexception-class-perl libexpat1 libfile-stripnondeterminism-perl libfontconfig1 libfreetype6 libgfortran5 libglib2.0-0 libgraphite2-3 libharfbuzz0b libhts3 libhtscodecs2 libicu74 libio-string-perl libjpeg-turbo8 libjpeg8 liblapack3 liblcms2-2 libldap2 libmagic-mgc libmagic1 libncurses6 libnghttp2-14 libnspr4 libnss3 libpcsclite1 libpipeline1 libpsl5 libpython3-stdlib libpython3.11-minimal libpython3.11-stdlib libpython3.12-minimal libpython3.12-stdlib librtmp1 libsasl2-2 libsasl2-modules-db libsigsegv2 libssh-4 libssl-dev libsub-override-perl libsub-uplevel-perl libtest-deep-perl libtest-differences-perl libtest-exception-perl libtest-most-perl libtest-warn-perl libtext-diff-perl libtool libuchardet0 libxml2 m4 man-db media-types mummer netbase openjdk-17-jdk-headless openjdk-17-jre-headless po-debconf python3 python3-distutils python3-iniconfig python3-lib2to3 python3-minimal python3-networkx python3-numpy python3-packaging python3-pkg-resources python3-pluggy python3-pysam python3-pytest python3-setuptools python3.11 python3.11-minimal python3.12 python3.12-minimal samtools smalt Suggested packages: autoconf-archive gnu-standards autoconf-doc dh-make default-jre flit python3-build python3-installer python3-wheel gawk-doc gettext-doc libasprintf-dev libgettextpo-dev groff libasound2-plugins alsa-utils libxml-sax-expatxs-perl cups-common low-memory-monitor liblcms2-utils pcscd libssl-doc libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc apparmor less www-browser openjdk-17-demo openjdk-17-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 python-networkx-doc python3-gdal python3-matplotlib python3-pydot python3-pygraphviz python3-scipy gfortran python3-dev python-setuptools-doc python3.11-venv python3.11-doc binfmt-support python3.12-venv python3.12-doc cwltool 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 alsa-ucm-conf alsa-topology-conf 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 libldap-common publicsuffix libsasl2-modules libltdl-dev libmail-sendmail-perl python3-yaml python3-pygments The following NEW packages will be installed: autoconf automake autopoint autotools-dev bioperl ca-certificates-java debhelper debugedit default-jdk-headless default-jre-headless dh-autoreconf dh-python dh-strip-nondeterminism dwz fastaq file fontconfig-config fonts-dejavu-core fonts-dejavu-mono gawk gettext gettext-base groff-base help2man intltool-debian java-common kmc libalgorithm-diff-perl libarchive-zip-perl libasound2 libasound2-data libavahi-client3 libavahi-common-data libavahi-common3 libbambamc0 libbio-perl-perl libblas3 libbrotli1 libcapture-tiny-perl libclass-data-inheritable-perl libcups2 libcurl3-gnutls libdata-stag-perl libdbus-1-3 libdebhelper-perl libdeflate0 libdevel-stacktrace-perl libdw1 libelf1 libexception-class-perl libexpat1 libfile-stripnondeterminism-perl libfontconfig1 libfreetype6 libgfortran5 libglib2.0-0 libgraphite2-3 libharfbuzz0b libhts3 libhtscodecs2 libicu74 libio-string-perl libjpeg-turbo8 libjpeg8 liblapack3 liblcms2-2 libldap2 libmagic-mgc libmagic1 libncurses6 libnghttp2-14 libnspr4 libnss3 libpcsclite1 libpipeline1 libpsl5 libpython3-stdlib libpython3.11-minimal libpython3.11-stdlib libpython3.12-minimal libpython3.12-stdlib librtmp1 libsasl2-2 libsasl2-modules-db libsigsegv2 libssh-4 libssl-dev libsub-override-perl libsub-uplevel-perl libtest-deep-perl libtest-differences-perl libtest-exception-perl libtest-most-perl libtest-warn-perl libtext-diff-perl libtool libuchardet0 libxml2 m4 man-db media-types mummer netbase openjdk-17-jdk-headless openjdk-17-jre-headless po-debconf python3 python3-distutils python3-iniconfig python3-lib2to3 python3-minimal python3-networkx python3-numpy python3-packaging python3-pkg-resources python3-pluggy python3-pysam python3-pytest python3-setuptools python3.11 python3.11-minimal python3.12 python3.12-minimal samtools sbuild-build-depends-main-dummy smalt 0 upgraded, 126 newly installed, 0 to remove and 0 not upgraded. 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http://ftpmaster.internal/ubuntu noble/main armhf python3-networkx all 2.8.8-1ubuntu1 [1468 kB] Get:121 http://ftpmaster.internal/ubuntu noble/main armhf python3-numpy armhf 1:1.24.2-2 [4410 kB] Get:122 http://ftpmaster.internal/ubuntu noble/main armhf python3-packaging all 23.2-1 [40.6 kB] Get:123 http://ftpmaster.internal/ubuntu noble-proposed/universe armhf python3-pluggy all 1.4.0-1 [20.4 kB] Get:124 http://ftpmaster.internal/ubuntu noble/universe armhf python3-pysam armhf 0.22.0+ds-1 [4378 kB] Get:125 http://ftpmaster.internal/ubuntu noble-proposed/universe armhf python3-pytest all 7.4.4-2 [241 kB] Get:126 http://ftpmaster.internal/ubuntu noble/universe armhf smalt armhf 0.7.6-13 [106 kB] Preconfiguring packages ... Fetched 169 MB in 11s (15.1 MB/s) Selecting previously unselected package libpython3.12-minimal:armhf. (Reading database ... 15501 files and directories currently installed.) Preparing to unpack .../libpython3.12-minimal_3.12.1-2_armhf.deb ... Unpacking libpython3.12-minimal:armhf (3.12.1-2) ... Selecting previously unselected package libexpat1:armhf. Preparing to unpack .../libexpat1_2.5.0-2_armhf.deb ... Unpacking libexpat1:armhf (2.5.0-2) ... Selecting previously unselected package python3.12-minimal. Preparing to unpack .../python3.12-minimal_3.12.1-2_armhf.deb ... Unpacking python3.12-minimal (3.12.1-2) ... Setting up libpython3.12-minimal:armhf (3.12.1-2) ... Setting up libexpat1:armhf (2.5.0-2) ... Setting up python3.12-minimal (3.12.1-2) ... Selecting previously unselected package python3-minimal. (Reading database ... 15819 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.12.1-0ubuntu1_armhf.deb ... 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Selecting previously unselected package sbuild-build-depends-main-dummy. Preparing to unpack .../112-sbuild-build-depends-main-dummy_0.invalid.0_armhf.deb ... Unpacking sbuild-build-depends-main-dummy (0.invalid.0) ... Setting up libhtscodecs2:armhf (1.6.0-1) ... Setting up media-types (10.1.0) ... Setting up libpipeline1:armhf (1.5.7-1) ... Setting up libgraphite2-3:armhf (1.3.14-2) ... Setting up liblcms2-2:armhf (2.14-2) ... Setting up libpsl5:armhf (0.21.2-1build1) ... Setting up java-common (0.75) ... Setting up libtest-deep-perl (1.204-1) ... Setting up libmagic-mgc (1:5.45-2) ... Setting up gawk (1:5.2.1-2) ... Setting up libalgorithm-diff-perl (1.201-1) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libglib2.0-0:armhf (2.78.3-2) ... No schema files found: doing nothing. Setting up libdebhelper-perl (13.13ubuntu1) ... Setting up libbrotli1:armhf (1.1.0-2) ... Setting up libnghttp2-14:armhf (1.58.0-1) ... Setting up libmagic1:armhf (1:5.45-2) ... Setting up libdeflate0:armhf (1.19-1) ... Setting up gettext-base (0.21-14ubuntu1) ... Setting up m4 (1.4.19-4) ... Setting up file (1:5.45-2) ... Setting up libsasl2-modules-db:armhf (2.1.28+dfsg1-4) ... Setting up help2man (1.49.3) ... Setting up libasound2-data (1.2.10-3build1) ... Setting up libio-string-perl (1.08-4) ... Setting up autotools-dev (20220109.1) ... Setting up libblas3:armhf (3.12.0-2) ... update-alternatives: using /usr/lib/arm-linux-gnueabihf/blas/libblas.so.3 to provide /usr/lib/arm-linux-gnueabihf/libblas.so.3 (libblas.so.3-arm-linux-gnueabihf) in auto mode Setting up libclass-data-inheritable-perl (0.08-3) ... Setting up libfreetype6:armhf (2.13.2+dfsg-1) ... Setting up libnspr4:armhf (2:4.35-1.1) ... Setting up libtext-diff-perl (1.45-2) ... Setting up librtmp1:armhf (2.4+20151223.gitfa8646d.1-2build4) ... Setting up libavahi-common-data:armhf (0.8-13ubuntu2) ... Setting up libncurses6:armhf (6.4+20240113-1) ... Setting up libdbus-1-3:armhf (1.14.10-3ubuntu1) ... Setting up libbambamc0:armhf (0.0.50-6) ... Setting up fonts-dejavu-mono (2.37-8) ... Setting up libssl-dev:armhf (3.0.10-1ubuntu4) ... Setting up autopoint (0.21-14ubuntu1) ... Setting up fonts-dejavu-core (2.37-8) ... Setting up libpcsclite1:armhf (2.0.1-1) ... Setting up libjpeg-turbo8:armhf (2.1.5-2ubuntu1) ... Setting up libsasl2-2:armhf (2.1.28+dfsg1-4) ... Setting up libssh-4:armhf (0.10.6-2) ... Setting up libgfortran5:armhf (14-20240130-1ubuntu1) ... Setting up autoconf (2.71-3) ... Setting up libcapture-tiny-perl (0.48-2) ... Setting up libicu74:armhf (74.2-1ubuntu1) ... Setting up libdata-stag-perl (0.14-3) ... Setting up libuchardet0:armhf (0.0.8-1) ... Setting up libasound2:armhf (1.2.10-3build1) ... Setting up mummer (3.23+dfsg-8) ... Setting up libsub-uplevel-perl (0.2800-3) ... Setting up libsub-override-perl (0.10-1) ... Setting up libharfbuzz0b:armhf (8.3.0-2) ... Setting up netbase (6.4) ... Setting up libdevel-stacktrace-perl (2.0500-1) ... Setting up libpython3.11-minimal:armhf (3.11.7-2) ... Setting up libbio-perl-perl (1.7.8-1) ... Setting up ca-certificates-java (20240118) ... No JRE found. Skipping Java certificates setup. Setting up libelf1:armhf (0.190-1) ... Setting up kmc (3.2.3+dfsg-1) ... Setting up libxml2:armhf (2.9.14+dfsg-1.3build3) ... Setting up libldap2:armhf (2.6.6+dfsg-1~exp1ubuntu2) ... Setting up libjpeg8:armhf (8c-2ubuntu11) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.13.1-1) ... Setting up python3.11-minimal (3.11.7-2) ... Setting up smalt (0.7.6-13) ... Setting up libdw1:armhf (0.190-1) ... Setting up liblapack3:armhf (3.12.0-2) ... update-alternatives: using /usr/lib/arm-linux-gnueabihf/lapack/liblapack.so.3 to provide /usr/lib/arm-linux-gnueabihf/liblapack.so.3 (liblapack.so.3-arm-linux-gnueabihf) in auto mode Setting up gettext (0.21-14ubuntu1) ... Setting up libpython3.12-stdlib:armhf (3.12.1-2) ... Setting up libtool (2.4.7-7) ... Setting up fontconfig-config (2.14.2-6ubuntu1) ... Setting up libtest-warn-perl (0.37-2) ... Setting up libpython3.11-stdlib:armhf (3.11.7-2) ... Setting up python3.12 (3.12.1-2) ... Setting up libavahi-common3:armhf (0.8-13ubuntu2) ... Setting up libtest-differences-perl (0.71-1) ... Setting up libcurl3-gnutls:armhf (8.5.0-2ubuntu2) ... Setting up libnss3:armhf (2:3.96.1-1) ... Setting up libexception-class-perl (1.45-1) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up libtest-exception-perl (0.43-3) ... Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up dwz (0.15-1) ... Setting up groff-base (1.23.0-3) ... Setting up debugedit (1:5.0-5) ... Setting up libfontconfig1:armhf (2.14.2-6ubuntu1) ... Setting up libavahi-client3:armhf (0.8-13ubuntu2) ... Setting up libpython3-stdlib:armhf (3.12.1-0ubuntu1) ... Setting up python3.11 (3.11.7-2) ... Setting up libhts3:armhf (1.18+ds-1) ... Setting up libtest-most-perl (0.38-1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up python3 (3.12.1-0ubuntu1) ... Setting up man-db (2.12.0-3) ... Not building database; man-db/auto-update is not 'true'. Created symlink /etc/systemd/system/timers.target.wants/man-db.timer → /usr/lib/systemd/system/man-db.timer. Setting up samtools (1.19-1) ... Setting up python3-packaging (23.2-1) ... Setting up python3-pluggy (1.4.0-1) ... Setting up libcups2:armhf (2.4.6-0ubuntu3) ... Setting up python3-lib2to3 (3.11.5-1) ... Setting up python3-pkg-resources (68.1.2-2) ... Setting up python3-distutils (3.11.5-1) ... python3.12: can't get files for byte-compilation Setting up bioperl (1.7.8-1) ... Setting up python3-iniconfig (1.1.1-2) ... Setting up python3-pysam (0.22.0+ds-1) ... Setting up python3-setuptools (68.1.2-2) ... Setting up python3-pytest (7.4.4-2) ... Setting up fastaq (3.17.0-6) ... /usr/lib/python3/dist-packages/pyfastaq/sequences.py:37: SyntaxWarning: invalid escape sequence '\s' phylip_regex = re.compile('^\s*[0-9]+\s+[0-9]+$') /usr/lib/python3/dist-packages/pyfastaq/sequences.py:38: SyntaxWarning: invalid escape sequence '\s' gbk_regex = re.compile('^LOCUS\s+\S') Setting up debhelper (13.13ubuntu1) ... Setting up python3-networkx (2.8.8-1ubuntu1) ... /usr/lib/python3/dist-packages/networkx/readwrite/tests/test_gml.py:556: SyntaxWarning: invalid octal escape sequence '\420' "graph [edge [ source u'u\4200' target u'u\4200' ] " /usr/lib/python3/dist-packages/networkx/readwrite/tests/test_gml.py:557: SyntaxWarning: invalid octal escape sequence '\420' + "node [ id u'u\4200' label b ] ]" Setting up python3-numpy (1:1.24.2-2) ... Setting up openjdk-17-jre-headless:armhf (17.0.10+7-1) ... update-alternatives: using /usr/lib/jvm/java-17-openjdk-armhf/bin/java to provide /usr/bin/java (java) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-armhf/bin/jpackage to provide /usr/bin/jpackage (jpackage) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-armhf/bin/keytool to provide /usr/bin/keytool (keytool) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-armhf/bin/rmiregistry to provide /usr/bin/rmiregistry (rmiregistry) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-armhf/lib/jexec to provide /usr/bin/jexec (jexec) in auto mode Setting up dh-python (6.20231223) ... Processing triggers for libc-bin (2.38-3ubuntu1) ... Processing triggers for systemd (255.2-3ubuntu2) ... Processing triggers for ca-certificates-java (20240118) ... Adding debian:ACCVRAIZ1.pem Adding debian:AC_RAIZ_FNMT-RCM.pem Adding debian:AC_RAIZ_FNMT-RCM_SERVIDORES_SEGUROS.pem Adding debian:ANF_Secure_Server_Root_CA.pem Adding debian:Actalis_Authentication_Root_CA.pem Adding debian:AffirmTrust_Commercial.pem Adding debian:AffirmTrust_Networking.pem Adding debian:AffirmTrust_Premium.pem Adding debian:AffirmTrust_Premium_ECC.pem Adding debian:Amazon_Root_CA_1.pem Adding debian:Amazon_Root_CA_2.pem Adding debian:Amazon_Root_CA_3.pem Adding debian:Amazon_Root_CA_4.pem Adding debian:Atos_TrustedRoot_2011.pem Adding debian:Autoridad_de_Certificacion_Firmaprofesional_CIF_A62634068.pem Adding debian:Autoridad_de_Certificacion_Firmaprofesional_CIF_A62634068_2.pem Adding debian:Baltimore_CyberTrust_Root.pem Adding debian:Buypass_Class_2_Root_CA.pem Adding debian:Buypass_Class_3_Root_CA.pem Adding debian:CA_Disig_Root_R2.pem Adding debian:CFCA_EV_ROOT.pem Adding debian:COMODO_Certification_Authority.pem Adding debian:COMODO_ECC_Certification_Authority.pem Adding debian:COMODO_RSA_Certification_Authority.pem Adding debian:Certainly_Root_E1.pem Adding debian:Certainly_Root_R1.pem Adding debian:Certigna.pem Adding debian:Certigna_Root_CA.pem Adding debian:Certum_EC-384_CA.pem Adding debian:Certum_Trusted_Network_CA.pem Adding debian:Certum_Trusted_Network_CA_2.pem Adding debian:Certum_Trusted_Root_CA.pem Adding debian:Comodo_AAA_Services_root.pem Adding debian:D-TRUST_BR_Root_CA_1_2020.pem Adding debian:D-TRUST_EV_Root_CA_1_2020.pem Adding debian:D-TRUST_Root_Class_3_CA_2_2009.pem Adding debian:D-TRUST_Root_Class_3_CA_2_EV_2009.pem Adding debian:DigiCert_Assured_ID_Root_CA.pem Adding debian:DigiCert_Assured_ID_Root_G2.pem Adding debian:DigiCert_Assured_ID_Root_G3.pem Adding debian:DigiCert_Global_Root_CA.pem Adding debian:DigiCert_Global_Root_G2.pem Adding debian:DigiCert_Global_Root_G3.pem Adding debian:DigiCert_High_Assurance_EV_Root_CA.pem Adding debian:DigiCert_TLS_ECC_P384_Root_G5.pem Adding debian:DigiCert_TLS_RSA4096_Root_G5.pem Adding debian:DigiCert_Trusted_Root_G4.pem Adding debian:E-Tugra_Certification_Authority.pem Adding debian:E-Tugra_Global_Root_CA_ECC_v3.pem Adding debian:E-Tugra_Global_Root_CA_RSA_v3.pem Adding debian:Entrust.net_Premium_2048_Secure_Server_CA.pem Adding debian:Entrust_Root_Certification_Authority.pem Adding debian:Entrust_Root_Certification_Authority_-_EC1.pem Adding debian:Entrust_Root_Certification_Authority_-_G2.pem Adding debian:Entrust_Root_Certification_Authority_-_G4.pem Adding debian:GDCA_TrustAUTH_R5_ROOT.pem Adding debian:GLOBALTRUST_2020.pem Adding debian:GTS_Root_R1.pem Adding debian:GTS_Root_R2.pem Adding debian:GTS_Root_R3.pem Adding debian:GTS_Root_R4.pem Adding debian:GlobalSign_ECC_Root_CA_-_R4.pem Adding debian:GlobalSign_ECC_Root_CA_-_R5.pem Adding debian:GlobalSign_Root_CA.pem Adding debian:GlobalSign_Root_CA_-_R3.pem Adding debian:GlobalSign_Root_CA_-_R6.pem Adding debian:GlobalSign_Root_E46.pem Adding debian:GlobalSign_Root_R46.pem Adding debian:Go_Daddy_Class_2_CA.pem Adding debian:Go_Daddy_Root_Certificate_Authority_-_G2.pem Adding debian:HARICA_TLS_ECC_Root_CA_2021.pem Adding debian:HARICA_TLS_RSA_Root_CA_2021.pem Adding debian:Hellenic_Academic_and_Research_Institutions_ECC_RootCA_2015.pem Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2015.pem Adding debian:HiPKI_Root_CA_-_G1.pem Adding debian:Hongkong_Post_Root_CA_1.pem Adding debian:Hongkong_Post_Root_CA_3.pem Adding debian:ISRG_Root_X1.pem Adding debian:ISRG_Root_X2.pem Adding debian:IdenTrust_Commercial_Root_CA_1.pem Adding debian:IdenTrust_Public_Sector_Root_CA_1.pem Adding debian:Izenpe.com.pem Adding debian:Microsec_e-Szigno_Root_CA_2009.pem Adding debian:Microsoft_ECC_Root_Certificate_Authority_2017.pem Adding debian:Microsoft_RSA_Root_Certificate_Authority_2017.pem Adding debian:NAVER_Global_Root_Certification_Authority.pem Adding debian:NetLock_Arany_=Class_Gold=_Főtanúsítvány.pem Adding debian:OISTE_WISeKey_Global_Root_GB_CA.pem Adding debian:OISTE_WISeKey_Global_Root_GC_CA.pem Adding debian:QuoVadis_Root_CA_1_G3.pem Adding debian:QuoVadis_Root_CA_2.pem Adding debian:QuoVadis_Root_CA_2_G3.pem Adding debian:QuoVadis_Root_CA_3.pem Adding debian:QuoVadis_Root_CA_3_G3.pem Adding debian:SSL.com_EV_Root_Certification_Authority_ECC.pem Adding debian:SSL.com_EV_Root_Certification_Authority_RSA_R2.pem Adding debian:SSL.com_Root_Certification_Authority_ECC.pem Adding debian:SSL.com_Root_Certification_Authority_RSA.pem Adding debian:SZAFIR_ROOT_CA2.pem Adding debian:SecureSign_RootCA11.pem Adding debian:SecureTrust_CA.pem Adding debian:Secure_Global_CA.pem Adding debian:Security_Communication_ECC_RootCA1.pem Adding debian:Security_Communication_RootCA2.pem Adding debian:Security_Communication_RootCA3.pem Adding debian:Security_Communication_Root_CA.pem Adding debian:Starfield_Class_2_CA.pem Adding debian:Starfield_Root_Certificate_Authority_-_G2.pem Adding debian:Starfield_Services_Root_Certificate_Authority_-_G2.pem Adding debian:SwissSign_Gold_CA_-_G2.pem Adding debian:SwissSign_Silver_CA_-_G2.pem Adding debian:T-TeleSec_GlobalRoot_Class_2.pem Adding debian:T-TeleSec_GlobalRoot_Class_3.pem Adding debian:TUBITAK_Kamu_SM_SSL_Kok_Sertifikasi_-_Surum_1.pem Adding debian:TWCA_Global_Root_CA.pem Adding debian:TWCA_Root_Certification_Authority.pem Adding debian:TeliaSonera_Root_CA_v1.pem Adding debian:Telia_Root_CA_v2.pem Adding debian:Trustwave_Global_Certification_Authority.pem Adding debian:Trustwave_Global_ECC_P256_Certification_Authority.pem Adding debian:Trustwave_Global_ECC_P384_Certification_Authority.pem Adding debian:TunTrust_Root_CA.pem Adding debian:UCA_Extended_Validation_Root.pem Adding debian:UCA_Global_G2_Root.pem Adding debian:USERTrust_ECC_Certification_Authority.pem Adding debian:USERTrust_RSA_Certification_Authority.pem Adding debian:XRamp_Global_CA_Root.pem Adding debian:certSIGN_ROOT_CA.pem Adding debian:certSIGN_Root_CA_G2.pem Adding debian:e-Szigno_Root_CA_2017.pem Adding debian:ePKI_Root_Certification_Authority.pem Adding debian:emSign_ECC_Root_CA_-_C3.pem Adding debian:emSign_ECC_Root_CA_-_G3.pem Adding debian:emSign_Root_CA_-_C1.pem Adding debian:emSign_Root_CA_-_G1.pem Adding debian:vTrus_ECC_Root_CA.pem Adding debian:vTrus_Root_CA.pem done. Setting up openjdk-17-jdk-headless:armhf (17.0.10+7-1) ... update-alternatives: using /usr/lib/jvm/java-17-openjdk-armhf/bin/jar to provide /usr/bin/jar (jar) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-armhf/bin/jarsigner to provide /usr/bin/jarsigner (jarsigner) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-armhf/bin/javac to provide /usr/bin/javac (javac) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-armhf/bin/javadoc to provide /usr/bin/javadoc (javadoc) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-armhf/bin/javap to provide /usr/bin/javap (javap) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-armhf/bin/jcmd to provide /usr/bin/jcmd (jcmd) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-armhf/bin/jdb to provide /usr/bin/jdb (jdb) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-armhf/bin/jdeprscan to provide /usr/bin/jdeprscan (jdeprscan) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-armhf/bin/jdeps to provide /usr/bin/jdeps (jdeps) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-armhf/bin/jfr to provide /usr/bin/jfr (jfr) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-armhf/bin/jimage to provide /usr/bin/jimage (jimage) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-armhf/bin/jinfo to provide /usr/bin/jinfo (jinfo) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-armhf/bin/jlink to provide /usr/bin/jlink (jlink) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-armhf/bin/jmap to provide /usr/bin/jmap (jmap) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-armhf/bin/jmod to provide /usr/bin/jmod (jmod) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-armhf/bin/jps to provide /usr/bin/jps (jps) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-armhf/bin/jrunscript to provide /usr/bin/jrunscript (jrunscript) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-armhf/bin/jshell to provide /usr/bin/jshell (jshell) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-armhf/bin/jstack to provide /usr/bin/jstack (jstack) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-armhf/bin/jstat to provide /usr/bin/jstat (jstat) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-armhf/bin/jstatd to provide /usr/bin/jstatd (jstatd) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-armhf/bin/serialver to provide /usr/bin/serialver (serialver) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-armhf/bin/jhsdb to provide /usr/bin/jhsdb (jhsdb) in auto mode Setting up default-jre-headless (2:1.17-75) ... Setting up default-jdk-headless (2:1.17-75) ... Setting up sbuild-build-depends-main-dummy (0.invalid.0) ... +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (armhf included in any) +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 5.4.0-169-generic #187-Ubuntu SMP Thu Nov 23 14:53:38 UTC 2023 arm64 (armv7l) Toolchain package versions: binutils_2.42-2ubuntu1 dpkg-dev_1.22.2ubuntu3 g++-13_13.2.0-13ubuntu1 gcc-13_13.2.0-13ubuntu1 libc6-dev_2.38-3ubuntu1 libstdc++-13-dev_13.2.0-13ubuntu1 libstdc++6_14-20240130-1ubuntu1 linux-libc-dev_6.6.0-14.14 Package versions: adduser_3.137ubuntu1 advancecomp_2.5-1 apt_2.7.10 apt-utils_2.7.10 autoconf_2.71-3 automake_1:1.16.5-1.3 autopoint_0.21-14ubuntu1 autotools-dev_20220109.1 base-files_13ubuntu6 base-passwd_3.6.3 bash_5.2.21-2ubuntu1 bash-completion_1:2.11-8 binutils_2.42-2ubuntu1 binutils-arm-linux-gnueabihf_2.42-2ubuntu1 binutils-common_2.42-2ubuntu1 bioperl_1.7.8-1 bsdextrautils_2.39.2-6ubuntu1 bsdutils_1:2.39.2-6ubuntu1 build-essential_12.10ubuntu1 bzip2_1.0.8-5build1 ca-certificates_20230311ubuntu1 ca-certificates-java_20240118 coreutils_9.4-2ubuntu3 cpp_4:13.2.0-7ubuntu1 cpp-13_13.2.0-13ubuntu1 cpp-13-arm-linux-gnueabihf_13.2.0-13ubuntu1 cpp-arm-linux-gnueabihf_4:13.2.0-7ubuntu1 dash_0.5.12-6ubuntu1 debconf_1.5.85 debconf-i18n_1.5.85 debhelper_13.13ubuntu1 debianutils_5.16 debugedit_1:5.0-5 default-jdk-headless_2:1.17-75 default-jre-headless_2:1.17-75 dh-autoreconf_20 dh-python_6.20231223 dh-strip-nondeterminism_1.13.1-1 diffutils_1:3.10-1 dpkg_1.22.2ubuntu3 dpkg-dev_1.22.2ubuntu3 dwz_0.15-1 e2fsprogs_1.47.0-2ubuntu1 fakeroot_1.33-1 fastaq_3.17.0-6 file_1:5.45-2 findutils_4.9.0-5 fontconfig-config_2.14.2-6ubuntu1 fonts-dejavu-core_2.37-8 fonts-dejavu-mono_2.37-8 g++_4:13.2.0-7ubuntu1 g++-13_13.2.0-13ubuntu1 g++-13-arm-linux-gnueabihf_13.2.0-13ubuntu1 g++-arm-linux-gnueabihf_4:13.2.0-7ubuntu1 gawk_1:5.2.1-2 gcc_4:13.2.0-7ubuntu1 gcc-13_13.2.0-13ubuntu1 gcc-13-arm-linux-gnueabihf_13.2.0-13ubuntu1 gcc-13-base_13.2.0-13ubuntu1 gcc-14-base_14-20240130-1ubuntu1 gcc-arm-linux-gnueabihf_4:13.2.0-7ubuntu1 gettext_0.21-14ubuntu1 gettext-base_0.21-14ubuntu1 gpg_2.2.40-1.1ubuntu1 gpg-agent_2.2.40-1.1ubuntu1 gpgconf_2.2.40-1.1ubuntu1 gpgv_2.2.40-1.1ubuntu1 grep_3.11-4 groff-base_1.23.0-3 gzip_1.12-1ubuntu1 help2man_1.49.3 hostname_3.23+nmu1ubuntu1 init_1.66ubuntu1 init-system-helpers_1.66ubuntu1 intltool-debian_0.35.0+20060710.6 java-common_0.75 kmc_3.2.3+dfsg-1 krb5-locales_1.20.1-5build1 libacl1_2.3.1-4ubuntu1 libalgorithm-diff-perl_1.201-1 libapparmor1_4.0.0~alpha2-0ubuntu8 libapt-pkg6.0_2.7.10 libarchive-zip-perl_1.68-1 libargon2-1_0~20190702+dfsg-4 libasan8_14-20240130-1ubuntu1 libasound2_1.2.10-3build1 libasound2-data_1.2.10-3build1 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libdevel-stacktrace-perl_2.0500-1 libdevmapper1.02.1_2:1.02.185-2ubuntu1 libdpkg-perl_1.22.2ubuntu3 libdw1_0.190-1 libelf1_0.190-1 libexception-class-perl_1.45-1 libexpat1_2.5.0-2 libext2fs2_1.47.0-2ubuntu1 libfakeroot_1.33-1 libfdisk1_2.39.2-6ubuntu1 libffi8_3.4.4-2 libfile-stripnondeterminism-perl_1.13.1-1 libfontconfig1_2.14.2-6ubuntu1 libfreetype6_2.13.2+dfsg-1 libgcc-13-dev_13.2.0-13ubuntu1 libgcc-s1_14-20240130-1ubuntu1 libgcrypt20_1.10.3-2 libgdbm-compat4_1.23-5 libgdbm6_1.23-5 libgfortran5_14-20240130-1ubuntu1 libglib2.0-0_2.78.3-2 libgmp10_2:6.3.0+dfsg-2ubuntu4 libgnutls30_3.8.3-1ubuntu1 libgomp1_14-20240130-1ubuntu1 libgpg-error-l10n_1.47-3build1 libgpg-error0_1.47-3build1 libgpm2_1.20.7-10build1 libgraphite2-3_1.3.14-2 libgssapi-krb5-2_1.20.1-5build1 libharfbuzz0b_8.3.0-2 libhogweed6_3.9.1-2 libhts3_1.18+ds-1 libhtscodecs2_1.6.0-1 libicu74_74.2-1ubuntu1 libidn2-0_2.3.7-2 libio-string-perl_1.08-4 libip4tc2_1.8.9-2ubuntu2 libisl23_0.26-3 libjansson4_2.14-2 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libperl5.38_5.38.2-3 libpipeline1_1.5.7-1 libpng16-16_1.6.42-1 libproc2-0_2:4.0.4-2ubuntu1 libpsl5_0.21.2-1build1 libpython3-stdlib_3.12.1-0ubuntu1 libpython3.11-minimal_3.11.7-2 libpython3.11-stdlib_3.11.7-2 libpython3.12-minimal_3.12.1-2 libpython3.12-stdlib_3.12.1-2 libreadline8_8.2-3 librtmp1_2.4+20151223.gitfa8646d.1-2build4 libsasl2-2_2.1.28+dfsg1-4 libsasl2-modules-db_2.1.28+dfsg1-4 libseccomp2_2.5.4-2ubuntu2 libselinux1_3.5-2 libsemanage-common_3.5-1build1 libsemanage2_3.5-1build1 libsepol2_3.5-2 libsframe1_2.42-2ubuntu1 libsigsegv2_2.14-1ubuntu1 libsmartcols1_2.39.2-6ubuntu1 libsqlite3-0_3.45.0-1 libss2_1.47.0-2ubuntu1 libssh-4_0.10.6-2 libssl-dev_3.0.10-1ubuntu4 libssl3_3.0.10-1ubuntu4 libstdc++-13-dev_13.2.0-13ubuntu1 libstdc++6_14-20240130-1ubuntu1 libsub-override-perl_0.10-1 libsub-uplevel-perl_0.2800-3 libsystemd-shared_255.2-3ubuntu2 libsystemd0_255.2-3ubuntu2 libtasn1-6_4.19.0-3 libtest-deep-perl_1.204-1 libtest-differences-perl_0.71-1 libtest-exception-perl_0.43-3 libtest-most-perl_0.38-1 libtest-warn-perl_0.37-2 libtext-charwidth-perl_0.04-11build1 libtext-diff-perl_1.45-2 libtext-iconv-perl_1.7-8build1 libtext-wrapi18n-perl_0.06-10 libtinfo6_6.4+20240113-1 libtirpc-common_1.3.4+ds-1build1 libtirpc-dev_1.3.4+ds-1build1 libtirpc3_1.3.4+ds-1build1 libtool_2.4.7-7 libubsan1_14-20240130-1ubuntu1 libuchardet0_0.0.8-1 libudev1_255.2-3ubuntu2 libunistring2_1.0-2 libunistring5_1.1-2 libuuid1_2.39.2-6ubuntu1 libxml2_2.9.14+dfsg-1.3build3 libxxhash0_0.8.2-2 libzstd1_1.5.5+dfsg2-2 linux-libc-dev_6.6.0-14.14 lockfile-progs_0.1.19build1 login_1:4.13+dfsg1-3ubuntu1 logsave_1.47.0-2ubuntu1 lto-disabled-list_46 m4_1.4.19-4 make_4.3-4.1build1 man-db_2.12.0-3 mawk_1.3.4.20240123-1 media-types_10.1.0 mount_2.39.2-6ubuntu1 mummer_3.23+dfsg-8 ncurses-base_6.4+20240113-1 ncurses-bin_6.4+20240113-1 netbase_6.4 openjdk-17-jdk-headless_17.0.10+7-1 openjdk-17-jre-headless_17.0.10+7-1 openssl_3.0.10-1ubuntu4 optipng_0.7.8+ds-1 passwd_1:4.13+dfsg1-3ubuntu1 patch_2.7.6-7build2 perl_5.38.2-3 perl-base_5.38.2-3 perl-modules-5.36_5.36.0-10ubuntu1 perl-modules-5.38_5.38.2-3 pinentry-curses_1.2.1-3ubuntu1 pkgbinarymangler_154 po-debconf_1.0.21+nmu1 policyrcd-script-zg2_0.1-3.1 procps_2:4.0.4-2ubuntu1 psmisc_23.6-2 python3_3.12.1-0ubuntu1 python3-distutils_3.11.5-1 python3-iniconfig_1.1.1-2 python3-lib2to3_3.11.5-1 python3-minimal_3.12.1-0ubuntu1 python3-networkx_2.8.8-1ubuntu1 python3-numpy_1:1.24.2-2 python3-packaging_23.2-1 python3-pkg-resources_68.1.2-2 python3-pluggy_1.4.0-1 python3-pysam_0.22.0+ds-1 python3-pytest_7.4.4-2 python3-setuptools_68.1.2-2 python3.11_3.11.7-2 python3.11-minimal_3.11.7-2 python3.12_3.12.1-2 python3.12-minimal_3.12.1-2 readline-common_8.2-3 rpcsvc-proto_1.4.2-0ubuntu6 samtools_1.19-1 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.9-2 sensible-utils_0.0.20 smalt_0.7.6-13 systemd_255.2-3ubuntu2 systemd-dev_255.2-3ubuntu2 systemd-sysv_255.2-3ubuntu2 sysvinit-utils_3.08-3ubuntu1 tar_1.35+dfsg-3 tzdata_2023d-1ubuntu2 ubuntu-keyring_2023.11.28.1 usrmerge_35ubuntu1 util-linux_2.39.2-6ubuntu1 uuid-runtime_2.39.2-6ubuntu1 xz-utils_5.4.5-0.3 zlib1g_1:1.3.dfsg-3ubuntu1 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: iva Binary: iva Architecture: any Version: 1.0.11+ds-5 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille , Jorge Soares , Sascha Steinbiss Homepage: https://github.com/sanger-pathogens/iva Standards-Version: 4.6.2 Vcs-Browser: https://salsa.debian.org/med-team/iva Vcs-Git: https://salsa.debian.org/med-team/iva.git Testsuite: autopkgtest Testsuite-Triggers: python3-packaging, trimmomatic Build-Depends: debhelper-compat (= 13), dh-sequence-python3, libssl-dev, bioperl, fastaq, kmc, help2man, mummer, python3, python3-setuptools, python3-packaging, python3-numpy, python3-networkx, python3-pysam, python3-pytest, samtools, smalt, default-jdk-headless Package-List: iva deb science optional arch=any Checksums-Sha1: f333165445174c86c83460fe990b625f7ae3aff5 8680588 iva_1.0.11+ds.orig.tar.xz 30c67565ccddfecdcac0a5e1fe6da1278ef3481c 5992 iva_1.0.11+ds-5.debian.tar.xz Checksums-Sha256: 0835a11746deaa4067aeb1bc9817ed8d415f36de51ae4fc122ea5b287c5ecf1d 8680588 iva_1.0.11+ds.orig.tar.xz aea1686cc3a60ec0fbfd9340b5332cf0430cd814f96ae1ac6992cb8e6f8a6467 5992 iva_1.0.11+ds-5.debian.tar.xz Files: e7b6c8d9cc2adb23b0d90168122c33b3 8680588 iva_1.0.11+ds.orig.tar.xz 0ef1450aea819feff2cd1b7b0edb906a 5992 iva_1.0.11+ds-5.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCgAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAmW7k/0RHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtEx8g/9GbdcWmPxrT733yvQimaZFg00Iy6yqAmj +K7oOvPXC4nkJ5Ft/5KR8bRueC3DIPLL5VmrttD14SICFi0Be8VcP8I4I7TOQi0z xkiC80VAIUSKJ9GDo+jMRWkB93bFnsnuCILAgC2b6eIfWeyGB4xX+qv/qqNpaY+s 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iva_1.0.11+ds-5.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying disable-multithreaded-test.patch dpkg-source: info: applying perl-shebang.patch dpkg-source: info: applying samtools1.10 dpkg-source: info: applying disable-ram-test.patch dpkg-source: info: applying python3.12.patch Check disk 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-27738260 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-27738260 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-27738260 SCHROOT_UID=2001 SCHROOT_USER=buildd SHELL=/bin/sh TERM=unknown USER=buildd V=1 dpkg-buildpackage ----------------- Command: dpkg-buildpackage -us -uc -mLaunchpad Build Daemon -B -rfakeroot dpkg-buildpackage: info: source package iva dpkg-buildpackage: info: source version 1.0.11+ds-5 dpkg-buildpackage: info: source distribution unstable dpkg-source --before-build . dpkg-buildpackage: info: host architecture armhf debian/rules clean dh clean --buildsystem=pybuild Use of uninitialized value $value in concatenation (.) or string at /usr/share/perl5/Dpkg/BuildFlags.pm line 389. Use of uninitialized value $value in concatenation (.) or string at /usr/share/perl5/Dpkg/BuildFlags.pm line 389. Use of uninitialized value $value in concatenation (.) or string at /usr/share/perl5/Dpkg/BuildFlags.pm line 389. Use of uninitialized value $value in concatenation (.) or string at /usr/share/perl5/Dpkg/BuildFlags.pm line 389. Use of uninitialized value $value in concatenation (.) or string at /usr/share/perl5/Dpkg/BuildFlags.pm line 389. Use of uninitialized value $value in concatenation (.) or string at /usr/share/perl5/Dpkg/BuildFlags.pm line 389. debian/rules override_dh_auto_clean make[1]: Entering directory '/<>' rm -rf .pybuild *.egg-info .pytest_cache build rm -f iva/gage/*.class rm -rf /<>/debian/man find . -name __pycache__ | xargs rm -rf make[1]: Leaving directory '/<>' dh_autoreconf_clean -O--buildsystem=pybuild dh_clean -O--buildsystem=pybuild debian/rules binary-arch dh binary-arch --buildsystem=pybuild Use of uninitialized value $value in concatenation (.) or string at /usr/share/perl5/Dpkg/BuildFlags.pm line 389. Use of uninitialized value $value in concatenation (.) or string at /usr/share/perl5/Dpkg/BuildFlags.pm line 389. Use of uninitialized value $value in concatenation (.) or string at /usr/share/perl5/Dpkg/BuildFlags.pm line 389. Use of uninitialized value $value in concatenation (.) or string at /usr/share/perl5/Dpkg/BuildFlags.pm line 389. Use of uninitialized value $value in concatenation (.) or string at /usr/share/perl5/Dpkg/BuildFlags.pm line 389. Use of uninitialized value $value in concatenation (.) or string at /usr/share/perl5/Dpkg/BuildFlags.pm line 389. dh_update_autotools_config -a -O--buildsystem=pybuild dh_autoreconf -a -O--buildsystem=pybuild dh_auto_configure -a -O--buildsystem=pybuild I: pybuild base:305: python3.12 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 '/<>' chmod a-x /<>/iva/read_trim/adapters.fasta chmod a+x /<>/iva/gage/getCorrectnessStats.sh chmod a+x /<>/iva/ratt/main.ratt.pl chmod a+x scripts/* javac -verbose /<>/iva/gage/*.java [parsing started SimpleFileObject[/<>/iva/gage/GetFastaStats.java]] [parsing completed 49ms] [parsing started SimpleFileObject[/<>/iva/gage/SizeFasta.java]] [parsing completed 4ms] [parsing started SimpleFileObject[/<>/iva/gage/SplitFastaByLetter.java]] [parsing completed 3ms] [parsing started SimpleFileObject[/<>/iva/gage/Utils.java]] [parsing completed 8ms] [parsing started SimpleFileObject[/<>/iva/gage/getScaffoldStats.java]] [parsing completed 17ms] [loading /modules/jdk.management.agent/module-info.class] [loading /modules/java.naming/module-info.class] [loading /modules/jdk.jconsole/module-info.class] [loading /modules/jdk.internal.le/module-info.class] [loading /modules/jdk.dynalink/module-info.class] [loading /modules/jdk.net/module-info.class] [loading /modules/jdk.editpad/module-info.class] [loading /modules/jdk.unsupported.desktop/module-info.class] [loading /modules/jdk.jcmd/module-info.class] [loading /modules/jdk.security.jgss/module-info.class] [loading /modules/jdk.zipfs/module-info.class] [loading /modules/jdk.jstatd/module-info.class] [loading /modules/jdk.crypto.cryptoki/module-info.class] [loading /modules/jdk.management/module-info.class] [loading /modules/java.desktop/module-info.class] [loading /modules/jdk.localedata/module-info.class] [loading /modules/jdk.compiler/module-info.class] [loading /modules/java.compiler/module-info.class] [loading /modules/java.datatransfer/module-info.class] [loading /modules/jdk.incubator.vector/module-info.class] [loading /modules/jdk.nio.mapmode/module-info.class] [loading /modules/jdk.incubator.foreign/module-info.class] [loading /modules/java.se/module-info.class] [loading /modules/jdk.xml.dom/module-info.class] [loading /modules/jdk.jpackage/module-info.class] [loading /modules/jdk.naming.dns/module-info.class] [loading /modules/jdk.management.jfr/module-info.class] [loading /modules/java.smartcardio/module-info.class] [loading /modules/java.security.sasl/module-info.class] [loading /modules/java.management.rmi/module-info.class] [loading /modules/jdk.jsobject/module-info.class] [loading /modules/java.sql/module-info.class] [loading /modules/java.transaction.xa/module-info.class] [loading /modules/jdk.httpserver/module-info.class] [loading /modules/jdk.security.auth/module-info.class] [loading /modules/java.xml.crypto/module-info.class] [loading /modules/java.security.jgss/module-info.class] [loading /modules/java.net.http/module-info.class] [loading /modules/jdk.jartool/module-info.class] [loading /modules/jdk.javadoc/module-info.class] [loading /modules/java.sql.rowset/module-info.class] [loading /modules/java.instrument/module-info.class] [loading /modules/jdk.jdwp.agent/module-info.class] [loading /modules/java.prefs/module-info.class] [loading /modules/jdk.jdeps/module-info.class] [loading /modules/jdk.jlink/module-info.class] [loading /modules/jdk.charsets/module-info.class] [loading /modules/jdk.internal.ed/module-info.class] [loading /modules/jdk.unsupported/module-info.class] [loading /modules/java.rmi/module-info.class] [loading /modules/java.management/module-info.class] [loading /modules/jdk.crypto.ec/module-info.class] [loading /modules/jdk.jfr/module-info.class] [loading /modules/java.xml/module-info.class] [loading /modules/java.logging/module-info.class] [loading /modules/java.base/module-info.class] [loading /modules/jdk.jshell/module-info.class] [loading /modules/java.scripting/module-info.class] [loading /modules/jdk.internal.jvmstat/module-info.class] [loading /modules/jdk.sctp/module-info.class] [loading /modules/jdk.naming.rmi/module-info.class] [loading /modules/jdk.attach/module-info.class] [loading /modules/jdk.jdi/module-info.class] [loading /modules/jdk.internal.opt/module-info.class] [loading /modules/jdk.accessibility/module-info.class] [loading /modules/jdk.hotspot.agent/module-info.class] [loading /modules/jdk.random/module-info.class] [search path for source files: .] [search path for class files: /usr/lib/jvm/java-17-openjdk-armhf/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/constant/Constable.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/lang/constant/ConstantDesc.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/util/Iterator.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/function/IntFunction.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] [wrote /<>/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$Lookup.class] [loading /modules/java.base/java/lang/invoke/MethodType.class] [loading /modules/java.base/java/io/InputStream.class] [loading /modules/java.base/java/lang/invoke/CallSite.class] [wrote /<>/iva/gage/GetFastaStats.class] [checking SizeFasta] [wrote /<>/iva/gage/SizeFasta.class] [checking SplitFastaByLetter] [wrote /<>/iva/gage/SplitFastaByLetter.class] [checking Utils] [loading /modules/java.base/java/util/Optional.class] [loading /modules/java.base/java/lang/Enum$EnumDesc.class] [loading /modules/java.base/java/lang/constant/DynamicConstantDesc.class] [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/invoke/TypeDescriptor.class] [loading /modules/java.base/java/lang/invoke/TypeDescriptor$OfField.class] [loading /modules/java.base/java/lang/AssertionError.class] [wrote /<>/iva/gage/Utils$Pair.class] [wrote /<>/iva/gage/Utils$Translate.class] [wrote /<>/iva/gage/Utils$ToProtein.class] [wrote /<>/iva/gage/Utils.class] [checking getScaffoldStats] [wrote /<>/iva/gage/getScaffoldStats$Scaffold.class] [wrote /<>/iva/gage/getScaffoldStats.class] [total 920ms] dh_auto_build -- I: pybuild base:305: /usr/bin/python3 setup.py build Checking dependencies found in path: OK kmc OK kmc_dump OK nucmer OK delta-filter OK show-coords OK samtools OK smalt running build running build_py creating /<>/.pybuild/cpython3_3.12_iva/build/iva copying iva/seed_processor.py -> /<>/.pybuild/cpython3_3.12_iva/build/iva copying iva/kraken.py -> /<>/.pybuild/cpython3_3.12_iva/build/iva copying iva/contig_trim.py -> /<>/.pybuild/cpython3_3.12_iva/build/iva copying iva/kmers.py -> /<>/.pybuild/cpython3_3.12_iva/build/iva copying iva/mapping.py -> /<>/.pybuild/cpython3_3.12_iva/build/iva copying iva/edge.py -> /<>/.pybuild/cpython3_3.12_iva/build/iva copying iva/test_data_runner.py -> /<>/.pybuild/cpython3_3.12_iva/build/iva copying iva/assembly.py -> /<>/.pybuild/cpython3_3.12_iva/build/iva copying iva/__init__.py -> /<>/.pybuild/cpython3_3.12_iva/build/iva copying iva/graph.py -> /<>/.pybuild/cpython3_3.12_iva/build/iva copying iva/external_progs.py -> /<>/.pybuild/cpython3_3.12_iva/build/iva copying iva/read_trim.py -> /<>/.pybuild/cpython3_3.12_iva/build/iva copying iva/qc_external.py -> /<>/.pybuild/cpython3_3.12_iva/build/iva copying iva/egg_extract.py -> /<>/.pybuild/cpython3_3.12_iva/build/iva copying iva/contig.py -> /<>/.pybuild/cpython3_3.12_iva/build/iva copying iva/qc.py -> /<>/.pybuild/cpython3_3.12_iva/build/iva copying iva/mummer.py -> /<>/.pybuild/cpython3_3.12_iva/build/iva copying iva/kcount.py -> /<>/.pybuild/cpython3_3.12_iva/build/iva copying iva/seed.py -> /<>/.pybuild/cpython3_3.12_iva/build/iva copying iva/common.py -> /<>/.pybuild/cpython3_3.12_iva/build/iva creating /<>/.pybuild/cpython3_3.12_iva/build/iva/gage copying iva/gage/GetFastaStats$ContigAt.class -> /<>/.pybuild/cpython3_3.12_iva/build/iva/gage copying iva/gage/Utils$Translate.class -> /<>/.pybuild/cpython3_3.12_iva/build/iva/gage copying iva/gage/GetFastaStats.class -> /<>/.pybuild/cpython3_3.12_iva/build/iva/gage copying iva/gage/getCorrectnessStats.sh -> /<>/.pybuild/cpython3_3.12_iva/build/iva/gage copying iva/gage/SizeFasta.java -> /<>/.pybuild/cpython3_3.12_iva/build/iva/gage copying iva/gage/colsum.pl -> /<>/.pybuild/cpython3_3.12_iva/build/iva/gage copying iva/gage/getScaffoldStats.class -> /<>/.pybuild/cpython3_3.12_iva/build/iva/gage copying iva/gage/SizeFasta.class -> /<>/.pybuild/cpython3_3.12_iva/build/iva/gage copying iva/gage/Utils.java -> /<>/.pybuild/cpython3_3.12_iva/build/iva/gage copying iva/gage/Utils.class -> /<>/.pybuild/cpython3_3.12_iva/build/iva/gage copying iva/gage/getScaffoldStats$Scaffold.class -> /<>/.pybuild/cpython3_3.12_iva/build/iva/gage copying iva/gage/SplitFastaByLetter.java -> /<>/.pybuild/cpython3_3.12_iva/build/iva/gage copying iva/gage/Utils$Pair.class -> /<>/.pybuild/cpython3_3.12_iva/build/iva/gage copying iva/gage/Utils$ToProtein.class -> /<>/.pybuild/cpython3_3.12_iva/build/iva/gage copying iva/gage/getMummerStats.sh -> /<>/.pybuild/cpython3_3.12_iva/build/iva/gage copying iva/gage/SplitFastaByLetter.class -> /<>/.pybuild/cpython3_3.12_iva/build/iva/gage copying iva/gage/getScaffoldStats.java -> /<>/.pybuild/cpython3_3.12_iva/build/iva/gage copying iva/gage/GetFastaStats.java -> /<>/.pybuild/cpython3_3.12_iva/build/iva/gage creating /<>/.pybuild/cpython3_3.12_iva/build/iva/ratt copying iva/ratt/genbank2embl.pl -> /<>/.pybuild/cpython3_3.12_iva/build/iva/ratt copying iva/ratt/embl2gff.pl -> /<>/.pybuild/cpython3_3.12_iva/build/iva/ratt copying iva/ratt/main.ratt.pl -> /<>/.pybuild/cpython3_3.12_iva/build/iva/ratt copying iva/ratt/start.ratt.sh -> /<>/.pybuild/cpython3_3.12_iva/build/iva/ratt copying iva/ratt/ratt_correction.pm -> /<>/.pybuild/cpython3_3.12_iva/build/iva/ratt copying iva/ratt/ratt.config -> /<>/.pybuild/cpython3_3.12_iva/build/iva/ratt copying iva/ratt/ratt.config.hiv -> /<>/.pybuild/cpython3_3.12_iva/build/iva/ratt creating /<>/.pybuild/cpython3_3.12_iva/build/iva/read_trim copying iva/read_trim/adapters.fasta -> /<>/.pybuild/cpython3_3.12_iva/build/iva/read_trim creating /<>/.pybuild/cpython3_3.12_iva/build/iva/test_run_data copying iva/test_run_data/hiv_pcr_primers.fa -> /<>/.pybuild/cpython3_3.12_iva/build/iva/test_run_data copying iva/test_run_data/reads_2.fq.gz -> /<>/.pybuild/cpython3_3.12_iva/build/iva/test_run_data copying iva/test_run_data/iva_contigs_with_trimmomatic.fasta -> /<>/.pybuild/cpython3_3.12_iva/build/iva/test_run_data copying iva/test_run_data/iva_contigs_no_trimmomatic.fasta -> /<>/.pybuild/cpython3_3.12_iva/build/iva/test_run_data copying iva/test_run_data/reads_1.fq.gz -> /<>/.pybuild/cpython3_3.12_iva/build/iva/test_run_data copying iva/test_run_data/reference.fasta -> /<>/.pybuild/cpython3_3.12_iva/build/iva/test_run_data running build_scripts creating build creating build/scripts-3.12 copying and adjusting scripts/iva_qc_make_db -> build/scripts-3.12 copying and adjusting scripts/iva_qc -> build/scripts-3.12 copying and adjusting scripts/iva -> build/scripts-3.12 changing mode of build/scripts-3.12/iva_qc_make_db from 644 to 755 changing mode of build/scripts-3.12/iva_qc from 644 to 755 changing mode of build/scripts-3.12/iva from 644 to 755 make[1]: Leaving directory '/<>' debian/rules override_dh_auto_test make[1]: Entering directory '/<>' python3 -m pytest --verbose ============================= test session starts ============================== platform linux -- Python 3.12.1, pytest-7.4.4, pluggy-1.4.0 -- /usr/bin/python3 cachedir: .pytest_cache rootdir: /<> collecting ... collected 160 items iva/tests/assembly_test.py::TestAssembly::test_contig_contained_in_nucmer_hits PASSED [ 0%] iva/tests/assembly_test.py::TestAssembly::test_contig_names_size_order PASSED [ 1%] iva/tests/assembly_test.py::TestAssembly::test_contig_worth_extending PASSED [ 1%] iva/tests/assembly_test.py::TestAssembly::test_coords_to_new_contig PASSED [ 2%] iva/tests/assembly_test.py::TestAssembly::test_extend_contigs_with_bam PASSED [ 3%] iva/tests/assembly_test.py::TestAssembly::test_get_contig_order_by_orfs PASSED [ 3%] iva/tests/assembly_test.py::TestAssembly::test_get_ref_length PASSED [ 4%] iva/tests/assembly_test.py::TestAssembly::test_get_ref_length_sam_pair PASSED [ 5%] iva/tests/assembly_test.py::TestAssembly::test_get_unmapped_pairs PASSED [ 5%] iva/tests/assembly_test.py::TestAssembly::test_good_intervals_from_strand_coverage PASSED [ 6%] iva/tests/assembly_test.py::TestAssembly::test_init_and_write PASSED [ 6%] iva/tests/assembly_test.py::TestAssembly::test_map_reads PASSED [ 7%] iva/tests/assembly_test.py::TestAssembly::test_merge_overlapping_contigs PASSED [ 8%] iva/tests/assembly_test.py::TestAssembly::test_read_pair_extend PASSED [ 8%] iva/tests/assembly_test.py::TestAssembly::test_remove_contained_contigs PASSED [ 9%] iva/tests/assembly_test.py::TestAssembly::test_remove_contig PASSED [ 10%] iva/tests/assembly_test.py::TestAssembly::test_remove_contig_from_nucmer_hits PASSED [ 10%] iva/tests/assembly_test.py::TestAssembly::test_subcontigs_from_strand_bias PASSED [ 11%] iva/tests/assembly_test.py::TestAssembly::test_trim_contig_for_strand_bias PASSED [ 11%] iva/tests/assembly_test.py::TestAssembly::test_trim_contigs PASSED [ 12%] iva/tests/assembly_test.py::TestAssembly::test_trim_strand_biased_ends PASSED [ 13%] iva/tests/assembly_test.py::TestAssembly::test_worth_extending PASSED [ 13%] iva/tests/contig_test.py::TestContig::test_add_left_kmer PASSED [ 14%] iva/tests/contig_test.py::TestContig::test_add_right_kmer PASSED [ 15%] iva/tests/contig_test.py::TestContig::test_extend PASSED [ 15%] iva/tests/contig_test.py::TestContig::test_init PASSED [ 16%] iva/tests/contig_test.py::TestContig::test_len PASSED [ 16%] iva/tests/contig_trim_test.py::TestContigTrim::test_coverage_to_trimmed_coords PASSED [ 17%] iva/tests/contig_trim_test.py::TestContigTrim::test_trim_ends PASSED [ 18%] iva/tests/contig_trim_test.py::TestContigTrim::test_trim_primers_and_adapters PASSED [ 18%] iva/tests/edge_test.py::TestEdge::test_change_hit_coords_with_intersection PASSED [ 19%] iva/tests/edge_test.py::TestEdge::test_make_contig_first PASSED [ 20%] iva/tests/edge_test.py::TestEdge::test_make_contig_forwards PASSED [ 20%] iva/tests/edge_test.py::TestEdge::test_merge_into PASSED [ 21%] iva/tests/edge_test.py::TestEdge::test_open_end PASSED [ 21%] iva/tests/edge_test.py::TestEdge::test_reverse PASSED [ 22%] iva/tests/egg_extract_test.py::TestEggExtract::test_copy_dir PASSED [ 23%] iva/tests/egg_extract_test.py::TestEggExtract::test_copy_dir_unzipped PASSED [ 23%] iva/tests/egg_extract_test.py::TestEggExtract::test_copy_dir_zipped PASSED [ 24%] iva/tests/egg_extract_test.py::TestEggExtract::test_copy_file PASSED [ 25%] iva/tests/egg_extract_test.py::TestEggExtract::test_copy_file_unzipped PASSED [ 25%] iva/tests/egg_extract_test.py::TestEggExtract::test_copy_file_zipped PASSED [ 26%] iva/tests/egg_extract_test.py::TestEggExtract::test_init_and_write PASSED [ 26%] iva/tests/external_progs_test.py::TestExternalProgs::test_blastn_version PASSED [ 27%] iva/tests/external_progs_test.py::TestExternalProgs::test_delta_filter_in_path PASSED [ 28%] iva/tests/external_progs_test.py::TestExternalProgs::test_kmc_dump_in_path PASSED [ 28%] iva/tests/external_progs_test.py::TestExternalProgs::test_kmc_dump_version PASSED [ 29%] iva/tests/external_progs_test.py::TestExternalProgs::test_kmc_in_path PASSED [ 30%] iva/tests/external_progs_test.py::TestExternalProgs::test_kmc_version PASSED [ 30%] iva/tests/external_progs_test.py::TestExternalProgs::test_makeblastdb_version PASSED [ 31%] iva/tests/external_progs_test.py::TestExternalProgs::test_nucmer_in_path PASSED [ 31%] iva/tests/external_progs_test.py::TestExternalProgs::test_nucmer_version PASSED [ 32%] iva/tests/external_progs_test.py::TestExternalProgs::test_r_version PASSED [ 33%] iva/tests/external_progs_test.py::TestExternalProgs::test_samtools_in_path PASSED [ 33%] iva/tests/external_progs_test.py::TestExternalProgs::test_samtools_original_version PASSED [ 34%] iva/tests/external_progs_test.py::TestExternalProgs::test_samtools_version PASSED [ 35%] iva/tests/external_progs_test.py::TestExternalProgs::test_show_coords_in_path PASSED [ 35%] iva/tests/external_progs_test.py::TestExternalProgs::test_smalt_in_path PASSED [ 36%] iva/tests/external_progs_test.py::TestExternalProgs::test_smalt_version PASSED [ 36%] iva/tests/graph_test.py::TestGraph::test_add_and_get_edges PASSED [ 37%] iva/tests/graph_test.py::TestGraph::test_connected_components PASSED [ 38%] iva/tests/graph_test.py::TestGraph::test_degree PASSED [ 38%] iva/tests/graph_test.py::TestGraph::test_edges_are_consistent PASSED [ 39%] iva/tests/graph_test.py::TestGraph::test_find_simple_path PASSED [ 40%] iva/tests/graph_test.py::TestGraph::test_get_nodes PASSED [ 40%] iva/tests/graph_test.py::TestGraph::test_merged_coords_from_simple_nonredundant_path PASSED [ 41%] iva/tests/graph_test.py::TestGraph::test_node_to_coords PASSED [ 41%] iva/tests/graph_test.py::TestGraph::test_remove_middle_node PASSED [ 42%] iva/tests/graph_test.py::TestGraph::test_remove_node PASSED [ 43%] iva/tests/graph_test.py::TestGraph::test_remove_redundant_nodes_from_simple_path PASSED [ 43%] iva/tests/graph_test.py::TestGraph::test_simple_path_is_consistent PASSED [ 44%] iva/tests/kcount_test.py::TestKcount::test_counts_file_to_fasta PASSED [ 45%] iva/tests/kcount_test.py::TestKcount::test_head_fastaq_fa PASSED [ 45%] iva/tests/kcount_test.py::TestKcount::test_head_fastaq_fq PASSED [ 46%] iva/tests/kcount_test.py::TestKcount::test_kmc_to_kmer_counts PASSED [ 46%] iva/tests/kcount_test.py::TestKcount::test_median PASSED [ 47%] iva/tests/kmers_test.py::TestKmers::test_append PASSED [ 48%] iva/tests/kmers_test.py::TestKmers::test_commonest_kmers PASSED [ 48%] iva/tests/kmers_test.py::TestKmers::test_extend PASSED [ 49%] iva/tests/kmers_test.py::TestKmers::test_extension PASSED [ 50%] iva/tests/kmers_test.py::TestKmers::test_init PASSED [ 50%] iva/tests/kmers_test.py::TestKmers::test_kmer_dict PASSED [ 51%] iva/tests/kraken_test.py::TestKraken::test_append_to_file PASSED [ 51%] iva/tests/kraken_test.py::TestKraken::test_count_cds_from_embl PASSED [ 52%] iva/tests/kraken_test.py::TestKraken::test_genbank_to_taxon_and_gi PASSED [ 53%] iva/tests/kraken_test.py::TestKraken::test_get_most_common_species_dir PASSED [ 53%] iva/tests/kraken_test.py::TestKraken::test_get_parent_taxons PASSED [ 54%] iva/tests/kraken_test.py::TestKraken::test_load_extra_ref_info PASSED [ 55%] iva/tests/kraken_test.py::TestKraken::test_replace_fasta_header PASSED [ 55%] iva/tests/kraken_test.py::TestKraken::test_species_to_dir PASSED [ 56%] iva/tests/mapping_test.py::TestMapping::test_bam_file_to_fasta_pair_files PASSED [ 56%] iva/tests/mapping_test.py::TestMapping::test_bam_file_to_fasta_pair_files_region PASSED [ 57%] iva/tests/mapping_test.py::TestMapping::test_bam_file_to_region_fasta PASSED [ 58%] iva/tests/mapping_test.py::TestMapping::test_bam_to_fasta PASSED [ 58%] iva/tests/mapping_test.py::TestMapping::test_can_extend PASSED [ 59%] iva/tests/mapping_test.py::TestMapping::test_consensus_base PASSED [ 60%] iva/tests/mapping_test.py::TestMapping::test_consensus_base_both_strands PASSED [ 60%] iva/tests/mapping_test.py::TestMapping::test_find_incorrect_ref_bases PASSED [ 61%] iva/tests/mapping_test.py::TestMapping::test_get_bam_region_coverage_fwd PASSED [ 61%] iva/tests/mapping_test.py::TestMapping::test_get_bam_region_coverage_fwd_And_rev PASSED [ 62%] iva/tests/mapping_test.py::TestMapping::test_get_bam_region_coverage_rev PASSED [ 63%] iva/tests/mapping_test.py::TestMapping::test_get_pair_type PASSED [ 63%] iva/tests/mapping_test.py::TestMapping::test_get_ref_name PASSED [ 64%] iva/tests/mapping_test.py::TestMapping::test_map_reads PASSED [ 65%] iva/tests/mapping_test.py::TestMapping::test_map_reads_and_sort PASSED [ 65%] iva/tests/mapping_test.py::TestMapping::test_map_reads_wth_flag PASSED [ 66%] iva/tests/mapping_test.py::TestMapping::test_remove_indels PASSED [ 66%] iva/tests/mapping_test.py::TestMapping::test_sam_to_fasta PASSED [ 67%] iva/tests/mapping_test.py::TestMapping::test_smalt_in_path PASSED [ 68%] iva/tests/mapping_test.py::TestMapping::test_soft_clipped PASSED [ 68%] iva/tests/mapping_test.py::TestMapping::test_strip_mpileup_coverage_string PASSED [ 69%] iva/tests/mapping_test.py::TestMapping::test_total_ref_length_from_bam PASSED [ 70%] iva/tests/mummer_test.py::TestMummer::test_file_read PASSED [ 70%] iva/tests/mummer_test.py::TestMummer::test_is_at_ends PASSED [ 71%] iva/tests/mummer_test.py::TestMummer::test_is_self_hit PASSED [ 71%] iva/tests/mummer_test.py::TestMummer::test_on_same_strand PASSED [ 72%] iva/tests/mummer_test.py::TestMummer::test_qry_coords PASSED [ 73%] iva/tests/mummer_test.py::TestMummer::test_ref_coords PASSED [ 73%] iva/tests/mummer_test.py::TestMummer::test_run_nucmer PASSED [ 74%] iva/tests/mummer_test.py::TestMummer::test_sort PASSED [ 75%] iva/tests/mummer_test.py::TestMummer::test_swap PASSED [ 75%] iva/tests/mummer_test.py::TestMummer::test_to_graph_edge PASSED [ 76%] iva/tests/qc_external_test.py::TestQcExternal::test_run_gage PASSED [ 76%] iva/tests/qc_external_test.py::TestQcExternal::test_run_ratt PASSED [ 77%] iva/tests/qc_test.py::TestQc::test_calculate_cds_assembly_stats PASSED [ 78%] iva/tests/qc_test.py::TestQc::test_calculate_contig_placement PASSED [ 78%] iva/tests/qc_test.py::TestQc::test_calculate_ref_positions_covered_by_contigs PASSED [ 79%] iva/tests/qc_test.py::TestQc::test_calculate_ref_read_coverage PASSED [ 80%] iva/tests/qc_test.py::TestQc::test_calculate_ref_read_region_coverage PASSED [ 80%] iva/tests/qc_test.py::TestQc::test_calculate_refseq_assembly_stats PASSED [ 81%] iva/tests/qc_test.py::TestQc::test_calculate_should_have_assembled PASSED [ 81%] iva/tests/qc_test.py::TestQc::test_contig_placement_in_reference PASSED [ 82%] iva/tests/qc_test.py::TestQc::test_contigs_and_bases_that_hit_ref PASSED [ 83%] iva/tests/qc_test.py::TestQc::test_cov_to_R_string PASSED [ 83%] iva/tests/qc_test.py::TestQc::test_coverage_list_to_low_cov_intervals PASSED [ 84%] iva/tests/qc_test.py::TestQc::test_get_R_plot_contig_order_from_contig_placement PASSED [ 85%] iva/tests/qc_test.py::TestQc::test_get_contig_hits_to_reference PASSED [ 85%] iva/tests/qc_test.py::TestQc::test_get_overlapping_qry_hits PASSED [ 86%] iva/tests/qc_test.py::TestQc::test_get_ref_cds_from_gff PASSED [ 86%] iva/tests/qc_test.py::TestQc::test_get_unique_and_repetitive_from_contig_hits PASSED [ 87%] iva/tests/qc_test.py::TestQc::test_gff_and_fasta_to_cds PASSED [ 88%] iva/tests/qc_test.py::TestQc::test_has_orf PASSED [ 88%] iva/tests/qc_test.py::TestQc::test_hash_nucmer_hits_by_ref PASSED [ 89%] iva/tests/qc_test.py::TestQc::test_ids_in_order_from_fai PASSED [ 90%] iva/tests/qc_test.py::TestQc::test_invert_list PASSED [ 90%] iva/tests/qc_test.py::TestQc::test_map_cds_to_assembly PASSED [ 91%] iva/tests/qc_test.py::TestQc::test_mummer_coords_file_to_dict PASSED [ 91%] iva/tests/qc_test.py::TestQc::test_write_cds_seqs PASSED [ 92%] iva/tests/qc_test.py::TestQc::test_write_fasta_contigs_hit_ref PASSED [ 93%] iva/tests/qc_test.py::TestQc::test_write_fasta_contigs_not_hit_ref PASSED [ 93%] iva/tests/qc_test.py::TestQc::test_write_ref_coverage_to_files_for_R PASSED [ 94%] iva/tests/read_trim_test.py::TestReadTrim::test_run_trimmomatic PASSED [ 95%] iva/tests/seed_test.py::TestSeed::test_extend PASSED [ 95%] iva/tests/seed_test.py::TestSeed::test_extend_with_reads_as_single_end PASSED [ 96%] iva/tests/seed_test.py::TestSeed::test_extension_from_read PASSED [ 96%] iva/tests/seed_test.py::TestSeed::test_extensions_from_reads_file PASSED [ 97%] iva/tests/seed_test.py::TestSeed::test_init PASSED [ 98%] iva/tests/seed_test.py::TestSeed::test_kmc_in_path PASSED [ 98%] iva/tests/seed_test.py::TestSeed::test_len PASSED [ 99%] iva/tests/seed_test.py::TestSeed::test_write_fasta PASSED [100%] =============================== warnings summary =============================== iva/mapping.py:161 /<>/iva/mapping.py:161: SyntaxWarning: invalid escape sequence '\^' s = re.sub('\^.', '', s) ../../../usr/lib/python3/dist-packages/pyfastaq/__init__.py:1 /usr/lib/python3/dist-packages/pyfastaq/__init__.py:1: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html from pkg_resources import get_distribution iva/external_progs.py:33 /<>/iva/external_progs.py:33: SyntaxWarning: invalid escape sequence '\(' 'kmc': ('kmc', re.compile('^K-Mer Counter \(KMC\) ver\. (.*) \(.*\)$')), iva/external_progs.py:34 /<>/iva/external_progs.py:34: SyntaxWarning: invalid escape sequence '\(' 'kmc_dump': ('kmc_dump', re.compile('^KMC dump ver. (.*) \(.*\)$')), iva/external_progs.py:37 /<>/iva/external_progs.py:37: SyntaxWarning: invalid escape sequence '\(' 'nucmer': ('nucmer --version', re.compile('^NUCmer \(NUCleotide MUMmer\) version (.*)$')), iva/external_progs.py:38 /<>/iva/external_progs.py:38: SyntaxWarning: invalid escape sequence '\(' 'R': ('R --version', re.compile('^R version (.*) \(.*\) --')), iva/external_progs.py:40 /<>/iva/external_progs.py:40: SyntaxWarning: invalid escape sequence '\d' 'samtools': ('samtools', re.compile('(\d+\.\d+[\.\d]*)')), iva/kraken.py:360 /<>/iva/kraken.py:360: SyntaxWarning: invalid escape sequence '\.' self._genbank2embl(fname, re.sub('\.gbk$', '', fname) + '.embl') iva/kraken.py:415 /<>/iva/kraken.py:415: SyntaxWarning: invalid escape sequence '\W' return re.sub('\W', '_', s).strip('_') iva/test_data_runner.py:20 /<>/iva/test_data_runner.py:20: PytestCollectionWarning: cannot collect test class 'Tester' because it has a __init__ constructor (from: iva/test_data_runner.py) class Tester: -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html ======================= 160 passed, 10 warnings in 3.57s ======================= make[1]: Leaving directory '/<>' create-stamp debian/debhelper-build-stamp dh_testroot -a -O--buildsystem=pybuild dh_prep -a -O--buildsystem=pybuild dh_auto_install --destdir=debian/iva/ -a -O--buildsystem=pybuild I: pybuild base:305: /usr/bin/python3 setup.py install --root /<>/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 /usr/lib/python3/dist-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated. !! ******************************************************************************** Please avoid running ``setup.py`` directly. Instead, use pypa/build, pypa/installer or other standards-based tools. See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. ******************************************************************************** !! self.initialize_options() running build running build_py running build_scripts running install_lib creating /<>/debian/iva/usr creating /<>/debian/iva/usr/lib creating /<>/debian/iva/usr/lib/python3.12 creating /<>/debian/iva/usr/lib/python3.12/dist-packages creating /<>/debian/iva/usr/lib/python3.12/dist-packages/iva copying /<>/.pybuild/cpython3_3.12_iva/build/iva/seed_processor.py -> /<>/debian/iva/usr/lib/python3.12/dist-packages/iva copying /<>/.pybuild/cpython3_3.12_iva/build/iva/kraken.py -> /<>/debian/iva/usr/lib/python3.12/dist-packages/iva copying /<>/.pybuild/cpython3_3.12_iva/build/iva/contig_trim.py -> /<>/debian/iva/usr/lib/python3.12/dist-packages/iva copying /<>/.pybuild/cpython3_3.12_iva/build/iva/kmers.py -> /<>/debian/iva/usr/lib/python3.12/dist-packages/iva creating /<>/debian/iva/usr/lib/python3.12/dist-packages/iva/ratt copying /<>/.pybuild/cpython3_3.12_iva/build/iva/ratt/genbank2embl.pl -> /<>/debian/iva/usr/lib/python3.12/dist-packages/iva/ratt copying /<>/.pybuild/cpython3_3.12_iva/build/iva/ratt/embl2gff.pl -> /<>/debian/iva/usr/lib/python3.12/dist-packages/iva/ratt copying /<>/.pybuild/cpython3_3.12_iva/build/iva/ratt/main.ratt.pl -> /<>/debian/iva/usr/lib/python3.12/dist-packages/iva/ratt copying /<>/.pybuild/cpython3_3.12_iva/build/iva/ratt/start.ratt.sh -> /<>/debian/iva/usr/lib/python3.12/dist-packages/iva/ratt copying /<>/.pybuild/cpython3_3.12_iva/build/iva/ratt/ratt_correction.pm -> /<>/debian/iva/usr/lib/python3.12/dist-packages/iva/ratt copying /<>/.pybuild/cpython3_3.12_iva/build/iva/ratt/ratt.config -> /<>/debian/iva/usr/lib/python3.12/dist-packages/iva/ratt copying /<>/.pybuild/cpython3_3.12_iva/build/iva/ratt/ratt.config.hiv -> /<>/debian/iva/usr/lib/python3.12/dist-packages/iva/ratt creating /<>/debian/iva/usr/lib/python3.12/dist-packages/iva/test_run_data copying /<>/.pybuild/cpython3_3.12_iva/build/iva/test_run_data/hiv_pcr_primers.fa -> /<>/debian/iva/usr/lib/python3.12/dist-packages/iva/test_run_data copying /<>/.pybuild/cpython3_3.12_iva/build/iva/test_run_data/reads_2.fq.gz -> /<>/debian/iva/usr/lib/python3.12/dist-packages/iva/test_run_data copying /<>/.pybuild/cpython3_3.12_iva/build/iva/test_run_data/iva_contigs_with_trimmomatic.fasta -> /<>/debian/iva/usr/lib/python3.12/dist-packages/iva/test_run_data copying /<>/.pybuild/cpython3_3.12_iva/build/iva/test_run_data/iva_contigs_no_trimmomatic.fasta -> /<>/debian/iva/usr/lib/python3.12/dist-packages/iva/test_run_data copying /<>/.pybuild/cpython3_3.12_iva/build/iva/test_run_data/reads_1.fq.gz -> /<>/debian/iva/usr/lib/python3.12/dist-packages/iva/test_run_data copying /<>/.pybuild/cpython3_3.12_iva/build/iva/test_run_data/reference.fasta -> /<>/debian/iva/usr/lib/python3.12/dist-packages/iva/test_run_data copying /<>/.pybuild/cpython3_3.12_iva/build/iva/mapping.py -> /<>/debian/iva/usr/lib/python3.12/dist-packages/iva copying /<>/.pybuild/cpython3_3.12_iva/build/iva/edge.py -> /<>/debian/iva/usr/lib/python3.12/dist-packages/iva copying /<>/.pybuild/cpython3_3.12_iva/build/iva/test_data_runner.py -> /<>/debian/iva/usr/lib/python3.12/dist-packages/iva copying /<>/.pybuild/cpython3_3.12_iva/build/iva/assembly.py -> /<>/debian/iva/usr/lib/python3.12/dist-packages/iva copying /<>/.pybuild/cpython3_3.12_iva/build/iva/__init__.py -> /<>/debian/iva/usr/lib/python3.12/dist-packages/iva copying /<>/.pybuild/cpython3_3.12_iva/build/iva/graph.py -> /<>/debian/iva/usr/lib/python3.12/dist-packages/iva copying /<>/.pybuild/cpython3_3.12_iva/build/iva/external_progs.py -> /<>/debian/iva/usr/lib/python3.12/dist-packages/iva copying /<>/.pybuild/cpython3_3.12_iva/build/iva/read_trim.py -> /<>/debian/iva/usr/lib/python3.12/dist-packages/iva copying /<>/.pybuild/cpython3_3.12_iva/build/iva/qc_external.py -> /<>/debian/iva/usr/lib/python3.12/dist-packages/iva copying /<>/.pybuild/cpython3_3.12_iva/build/iva/egg_extract.py -> /<>/debian/iva/usr/lib/python3.12/dist-packages/iva copying /<>/.pybuild/cpython3_3.12_iva/build/iva/contig.py -> /<>/debian/iva/usr/lib/python3.12/dist-packages/iva copying /<>/.pybuild/cpython3_3.12_iva/build/iva/qc.py -> /<>/debian/iva/usr/lib/python3.12/dist-packages/iva copying /<>/.pybuild/cpython3_3.12_iva/build/iva/mummer.py -> /<>/debian/iva/usr/lib/python3.12/dist-packages/iva copying /<>/.pybuild/cpython3_3.12_iva/build/iva/kcount.py -> /<>/debian/iva/usr/lib/python3.12/dist-packages/iva copying /<>/.pybuild/cpython3_3.12_iva/build/iva/seed.py -> /<>/debian/iva/usr/lib/python3.12/dist-packages/iva copying /<>/.pybuild/cpython3_3.12_iva/build/iva/common.py -> /<>/debian/iva/usr/lib/python3.12/dist-packages/iva creating /<>/debian/iva/usr/lib/python3.12/dist-packages/iva/gage copying /<>/.pybuild/cpython3_3.12_iva/build/iva/gage/GetFastaStats$ContigAt.class -> /<>/debian/iva/usr/lib/python3.12/dist-packages/iva/gage copying /<>/.pybuild/cpython3_3.12_iva/build/iva/gage/Utils$Translate.class -> /<>/debian/iva/usr/lib/python3.12/dist-packages/iva/gage copying /<>/.pybuild/cpython3_3.12_iva/build/iva/gage/GetFastaStats.class -> /<>/debian/iva/usr/lib/python3.12/dist-packages/iva/gage copying /<>/.pybuild/cpython3_3.12_iva/build/iva/gage/getCorrectnessStats.sh -> /<>/debian/iva/usr/lib/python3.12/dist-packages/iva/gage copying /<>/.pybuild/cpython3_3.12_iva/build/iva/gage/SizeFasta.java -> /<>/debian/iva/usr/lib/python3.12/dist-packages/iva/gage copying /<>/.pybuild/cpython3_3.12_iva/build/iva/gage/colsum.pl -> /<>/debian/iva/usr/lib/python3.12/dist-packages/iva/gage copying /<>/.pybuild/cpython3_3.12_iva/build/iva/gage/getScaffoldStats.class -> /<>/debian/iva/usr/lib/python3.12/dist-packages/iva/gage copying /<>/.pybuild/cpython3_3.12_iva/build/iva/gage/SizeFasta.class -> /<>/debian/iva/usr/lib/python3.12/dist-packages/iva/gage copying /<>/.pybuild/cpython3_3.12_iva/build/iva/gage/Utils.java -> /<>/debian/iva/usr/lib/python3.12/dist-packages/iva/gage copying /<>/.pybuild/cpython3_3.12_iva/build/iva/gage/Utils.class -> /<>/debian/iva/usr/lib/python3.12/dist-packages/iva/gage copying /<>/.pybuild/cpython3_3.12_iva/build/iva/gage/getScaffoldStats$Scaffold.class -> /<>/debian/iva/usr/lib/python3.12/dist-packages/iva/gage copying /<>/.pybuild/cpython3_3.12_iva/build/iva/gage/SplitFastaByLetter.java -> /<>/debian/iva/usr/lib/python3.12/dist-packages/iva/gage copying /<>/.pybuild/cpython3_3.12_iva/build/iva/gage/Utils$Pair.class -> /<>/debian/iva/usr/lib/python3.12/dist-packages/iva/gage copying /<>/.pybuild/cpython3_3.12_iva/build/iva/gage/Utils$ToProtein.class -> /<>/debian/iva/usr/lib/python3.12/dist-packages/iva/gage copying /<>/.pybuild/cpython3_3.12_iva/build/iva/gage/getMummerStats.sh -> /<>/debian/iva/usr/lib/python3.12/dist-packages/iva/gage copying /<>/.pybuild/cpython3_3.12_iva/build/iva/gage/SplitFastaByLetter.class -> /<>/debian/iva/usr/lib/python3.12/dist-packages/iva/gage copying /<>/.pybuild/cpython3_3.12_iva/build/iva/gage/getScaffoldStats.java -> /<>/debian/iva/usr/lib/python3.12/dist-packages/iva/gage copying /<>/.pybuild/cpython3_3.12_iva/build/iva/gage/GetFastaStats.java -> /<>/debian/iva/usr/lib/python3.12/dist-packages/iva/gage creating /<>/debian/iva/usr/lib/python3.12/dist-packages/iva/read_trim copying /<>/.pybuild/cpython3_3.12_iva/build/iva/read_trim/adapters.fasta -> /<>/debian/iva/usr/lib/python3.12/dist-packages/iva/read_trim byte-compiling /<>/debian/iva/usr/lib/python3.12/dist-packages/iva/seed_processor.py to seed_processor.cpython-312.pyc byte-compiling /<>/debian/iva/usr/lib/python3.12/dist-packages/iva/kraken.py to kraken.cpython-312.pyc /usr/lib/python3.12/dist-packages/iva/kraken.py:360: SyntaxWarning: invalid escape sequence '\.' /usr/lib/python3.12/dist-packages/iva/kraken.py:415: SyntaxWarning: invalid escape sequence '\W' byte-compiling /<>/debian/iva/usr/lib/python3.12/dist-packages/iva/contig_trim.py to contig_trim.cpython-312.pyc byte-compiling /<>/debian/iva/usr/lib/python3.12/dist-packages/iva/kmers.py to kmers.cpython-312.pyc byte-compiling /<>/debian/iva/usr/lib/python3.12/dist-packages/iva/mapping.py to mapping.cpython-312.pyc /usr/lib/python3.12/dist-packages/iva/mapping.py:161: SyntaxWarning: invalid escape sequence '\^' byte-compiling /<>/debian/iva/usr/lib/python3.12/dist-packages/iva/edge.py to edge.cpython-312.pyc byte-compiling /<>/debian/iva/usr/lib/python3.12/dist-packages/iva/test_data_runner.py to test_data_runner.cpython-312.pyc byte-compiling /<>/debian/iva/usr/lib/python3.12/dist-packages/iva/assembly.py to assembly.cpython-312.pyc byte-compiling /<>/debian/iva/usr/lib/python3.12/dist-packages/iva/__init__.py to __init__.cpython-312.pyc byte-compiling /<>/debian/iva/usr/lib/python3.12/dist-packages/iva/graph.py to graph.cpython-312.pyc byte-compiling /<>/debian/iva/usr/lib/python3.12/dist-packages/iva/external_progs.py to external_progs.cpython-312.pyc /usr/lib/python3.12/dist-packages/iva/external_progs.py:33: SyntaxWarning: invalid escape sequence '\(' /usr/lib/python3.12/dist-packages/iva/external_progs.py:34: SyntaxWarning: invalid escape sequence '\(' /usr/lib/python3.12/dist-packages/iva/external_progs.py:37: SyntaxWarning: invalid escape sequence '\(' /usr/lib/python3.12/dist-packages/iva/external_progs.py:38: SyntaxWarning: invalid escape sequence '\(' /usr/lib/python3.12/dist-packages/iva/external_progs.py:40: SyntaxWarning: invalid escape sequence '\d' byte-compiling /<>/debian/iva/usr/lib/python3.12/dist-packages/iva/read_trim.py to read_trim.cpython-312.pyc byte-compiling /<>/debian/iva/usr/lib/python3.12/dist-packages/iva/qc_external.py to qc_external.cpython-312.pyc byte-compiling /<>/debian/iva/usr/lib/python3.12/dist-packages/iva/egg_extract.py to egg_extract.cpython-312.pyc byte-compiling /<>/debian/iva/usr/lib/python3.12/dist-packages/iva/contig.py to contig.cpython-312.pyc byte-compiling /<>/debian/iva/usr/lib/python3.12/dist-packages/iva/qc.py to qc.cpython-312.pyc byte-compiling /<>/debian/iva/usr/lib/python3.12/dist-packages/iva/mummer.py to mummer.cpython-312.pyc byte-compiling /<>/debian/iva/usr/lib/python3.12/dist-packages/iva/kcount.py to kcount.cpython-312.pyc byte-compiling /<>/debian/iva/usr/lib/python3.12/dist-packages/iva/seed.py to seed.cpython-312.pyc byte-compiling /<>/debian/iva/usr/lib/python3.12/dist-packages/iva/common.py to common.cpython-312.pyc running install_egg_info 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' adding license file 'LICENSE' adding license file 'AUTHORS' writing manifest file 'iva.egg-info/SOURCES.txt' Copying iva.egg-info to /<>/debian/iva/usr/lib/python3.12/dist-packages/iva-1.0.9.egg-info Skipping SOURCES.txt running install_scripts creating /<>/debian/iva/usr/bin copying build/scripts-3.12/iva_qc_make_db -> /<>/debian/iva/usr/bin copying build/scripts-3.12/iva_qc -> /<>/debian/iva/usr/bin copying build/scripts-3.12/iva -> /<>/debian/iva/usr/bin changing mode of /<>/debian/iva/usr/bin/iva_qc_make_db to 755 changing mode of /<>/debian/iva/usr/bin/iva_qc to 755 changing mode of /<>/debian/iva/usr/bin/iva to 755 dh_installdocs -a -O--buildsystem=pybuild dh_installchangelogs -a -O--buildsystem=pybuild debian/rules override_dh_installman make[1]: Entering directory '/<>' mkdir -p /<>/debian/man PYTHONPATH=. help2man -N -o /<>/debian/man/iva.1 \ -n 'iterative virus assembler' \ --no-discard-stderr ./scripts/iva PYTHONPATH=. help2man -N -o /<>/debian/man/iva_qc.1 \ -n 'compare an assembly to a reference' \ --no-discard-stderr ./scripts/iva_qc PYTHONPATH=. help2man -N -o /<>/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 '/<>' dh_python3 -a -O--buildsystem=pybuild dh_installsystemduser -a -O--buildsystem=pybuild dh_perl -a -O--buildsystem=pybuild dh_link -a -O--buildsystem=pybuild dh_strip_nondeterminism -a -O--buildsystem=pybuild dh_compress -a -O--buildsystem=pybuild dh_fixperms -a -O--buildsystem=pybuild dh_missing -a -O--buildsystem=pybuild dh_dwz -a -O--buildsystem=pybuild dh_strip -a -O--buildsystem=pybuild dh_makeshlibs -a -O--buildsystem=pybuild dh_shlibdeps -a -O--buildsystem=pybuild dh_installdeb -a -O--buildsystem=pybuild dh_gencontrol -a -O--buildsystem=pybuild dh_md5sums -a -O--buildsystem=pybuild dh_builddeb -a -O--buildsystem=pybuild INFO: pkgstriptranslations version 154 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: Running PNG optimization (using 4 cpus) for package iva ... pkgstripfiles: No PNG files. dpkg-deb: building package 'iva' in '../iva_1.0.11+ds-5_armhf.deb'. dpkg-genbuildinfo --build=any -O../iva_1.0.11+ds-5_armhf.buildinfo Use of uninitialized value $value in concatenation (.) or string at /usr/share/perl5/Dpkg/BuildFlags.pm line 389. Use of uninitialized value $value in concatenation (.) or string at /usr/share/perl5/Dpkg/BuildFlags.pm line 389. Use of uninitialized value $value in concatenation (.) or string at /usr/share/perl5/Dpkg/BuildFlags.pm line 389. Use of uninitialized value $value in concatenation (.) or string at /usr/share/perl5/Dpkg/BuildFlags.pm line 389. Use of uninitialized value $value in concatenation (.) or string at /usr/share/perl5/Dpkg/BuildFlags.pm line 389. Use of uninitialized value $value in concatenation (.) or string at /usr/share/perl5/Dpkg/BuildFlags.pm line 389. dpkg-genchanges --build=any -mLaunchpad Build Daemon -O../iva_1.0.11+ds-5_armhf.changes dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) -------------------------------------------------------------------------------- Build finished at 2024-02-01T17:16:55Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ iva_1.0.11+ds-5_armhf.changes: ------------------------------ Format: 1.8 Date: Thu, 01 Feb 2024 13:34:57 +0100 Source: iva Binary: iva Built-For-Profiles: noudeb Architecture: armhf Version: 1.0.11+ds-5 Distribution: noble-proposed Urgency: medium Maintainer: Launchpad Build Daemon Changed-By: Andreas Tille Description: iva - iterative virus sequence assembler Closes: 1061804 Changes: iva (1.0.11+ds-5) unstable; urgency=medium . * Python3.12 compatibility by avoiding usage of distutils Closes: #1061804 * Build-Depends: s/dh-python/dh-sequence-python3/ (routine-update) Remove patch reduce-ram.patch that is missing from debian/patches/series. Checksums-Sha1: 201bc5634717b675ba3d84dc7ea146c3b0c53782 8971 iva_1.0.11+ds-5_armhf.buildinfo 76629046f4e69c019955080cd91e2b0602682b3f 8581856 iva_1.0.11+ds-5_armhf.deb Checksums-Sha256: beffbb490fb50de630ce1ba0ed3c2d987bd20e72bd5437d1df968adc725b37a2 8971 iva_1.0.11+ds-5_armhf.buildinfo 4b22677fe3b36d9f142059554d498b0032dea15d3fa591c2c46e56763e37fc8f 8581856 iva_1.0.11+ds-5_armhf.deb Files: 2eb776e70052205bb9f113b4e28e9080 8971 science optional iva_1.0.11+ds-5_armhf.buildinfo 6a35b9c9b2ee330355f482f23e255804 8581856 science optional iva_1.0.11+ds-5_armhf.deb /<>/iva_1.0.11+ds-5_armhf.changes.new could not be renamed to /<>/iva_1.0.11+ds-5_armhf.changes: Illegal seek Distribution field may be wrong!!! +------------------------------------------------------------------------------+ | Buildinfo | +------------------------------------------------------------------------------+ Format: 1.0 Source: iva Binary: iva Architecture: armhf Version: 1.0.11+ds-5 Checksums-Md5: 6a35b9c9b2ee330355f482f23e255804 8581856 iva_1.0.11+ds-5_armhf.deb Checksums-Sha1: 76629046f4e69c019955080cd91e2b0602682b3f 8581856 iva_1.0.11+ds-5_armhf.deb Checksums-Sha256: 4b22677fe3b36d9f142059554d498b0032dea15d3fa591c2c46e56763e37fc8f 8581856 iva_1.0.11+ds-5_armhf.deb Build-Origin: Ubuntu Build-Architecture: armhf Build-Date: Thu, 01 Feb 2024 17:16:55 +0000 Build-Path: /<> Build-Tainted-By: merged-usr-via-aliased-dirs usr-local-has-programs Installed-Build-Depends: autoconf (= 2.71-3), automake (= 1:1.16.5-1.3), autopoint (= 0.21-14ubuntu1), autotools-dev (= 20220109.1), base-files (= 13ubuntu6), base-passwd (= 3.6.3), bash (= 5.2.21-2ubuntu1), binutils (= 2.42-2ubuntu1), binutils-arm-linux-gnueabihf (= 2.42-2ubuntu1), binutils-common (= 2.42-2ubuntu1), bioperl (= 1.7.8-1), bsdextrautils (= 2.39.2-6ubuntu1), bsdutils (= 1:2.39.2-6ubuntu1), build-essential (= 12.10ubuntu1), bzip2 (= 1.0.8-5build1), ca-certificates (= 20230311ubuntu1), ca-certificates-java (= 20240118), coreutils (= 9.4-2ubuntu3), cpp (= 4:13.2.0-7ubuntu1), cpp-13 (= 13.2.0-13ubuntu1), cpp-13-arm-linux-gnueabihf (= 13.2.0-13ubuntu1), cpp-arm-linux-gnueabihf (= 4:13.2.0-7ubuntu1), dash (= 0.5.12-6ubuntu1), debconf (= 1.5.85), debhelper (= 13.13ubuntu1), debianutils (= 5.16), debugedit (= 1:5.0-5), default-jdk-headless (= 2:1.17-75), default-jre-headless (= 2:1.17-75), dh-autoreconf (= 20), dh-python (= 6.20231223), dh-strip-nondeterminism (= 1.13.1-1), diffutils (= 1:3.10-1), dpkg (= 1.22.2ubuntu3), dpkg-dev (= 1.22.2ubuntu3), dwz (= 0.15-1), fastaq (= 3.17.0-6), file (= 1:5.45-2), findutils (= 4.9.0-5), fontconfig-config (= 2.14.2-6ubuntu1), fonts-dejavu-core (= 2.37-8), fonts-dejavu-mono (= 2.37-8), g++ (= 4:13.2.0-7ubuntu1), g++-13 (= 13.2.0-13ubuntu1), g++-13-arm-linux-gnueabihf (= 13.2.0-13ubuntu1), g++-arm-linux-gnueabihf (= 4:13.2.0-7ubuntu1), gawk (= 1:5.2.1-2), gcc (= 4:13.2.0-7ubuntu1), gcc-13 (= 13.2.0-13ubuntu1), gcc-13-arm-linux-gnueabihf (= 13.2.0-13ubuntu1), gcc-13-base (= 13.2.0-13ubuntu1), gcc-14-base (= 14-20240130-1ubuntu1), gcc-arm-linux-gnueabihf (= 4:13.2.0-7ubuntu1), gettext (= 0.21-14ubuntu1), gettext-base (= 0.21-14ubuntu1), grep (= 3.11-4), groff-base (= 1.23.0-3), gzip (= 1.12-1ubuntu1), help2man (= 1.49.3), hostname (= 3.23+nmu1ubuntu1), init-system-helpers (= 1.66ubuntu1), intltool-debian (= 0.35.0+20060710.6), java-common (= 0.75), kmc (= 3.2.3+dfsg-1), libacl1 (= 2.3.1-4ubuntu1), libalgorithm-diff-perl (= 1.201-1), libarchive-zip-perl (= 1.68-1), libasan8 (= 14-20240130-1ubuntu1), libasound2 (= 1.2.10-3build1), libasound2-data (= 1.2.10-3build1), libatomic1 (= 14-20240130-1ubuntu1), libattr1 (= 1:2.5.2-1), libaudit-common (= 1:3.1.2-2), libaudit1 (= 1:3.1.2-2), libavahi-client3 (= 0.8-13ubuntu2), libavahi-common-data (= 0.8-13ubuntu2), libavahi-common3 (= 0.8-13ubuntu2), libbambamc0 (= 0.0.50-6), libbinutils (= 2.42-2ubuntu1), libbio-perl-perl (= 1.7.8-1), libblas3 (= 3.12.0-2), libblkid1 (= 2.39.2-6ubuntu1), libbrotli1 (= 1.1.0-2), libbz2-1.0 (= 1.0.8-5build1), libc-bin (= 2.38-3ubuntu1), libc-dev-bin (= 2.38-3ubuntu1), libc6 (= 2.38-3ubuntu1), libc6-dev (= 2.38-3ubuntu1), libcap-ng0 (= 0.8.4-1), libcap2 (= 1:2.66-4ubuntu1), libcapture-tiny-perl (= 0.48-2), libcc1-0 (= 14-20240130-1ubuntu1), libclass-data-inheritable-perl (= 0.08-3), libcom-err2 (= 1.47.0-2ubuntu1), libcrypt-dev (= 1:4.4.36-4), libcrypt1 (= 1:4.4.36-4), libctf-nobfd0 (= 2.42-2ubuntu1), libctf0 (= 2.42-2ubuntu1), libcups2 (= 2.4.6-0ubuntu3), libcurl3-gnutls (= 8.5.0-2ubuntu2), libdata-stag-perl (= 0.14-3), libdb5.3 (= 5.3.28+dfsg2-4), libdbus-1-3 (= 1.14.10-3ubuntu1), libdebconfclient0 (= 0.271ubuntu1), libdebhelper-perl (= 13.13ubuntu1), libdeflate0 (= 1.19-1), libdevel-stacktrace-perl (= 2.0500-1), libdpkg-perl (= 1.22.2ubuntu3), libdw1 (= 0.190-1), libelf1 (= 0.190-1), libexception-class-perl (= 1.45-1), libexpat1 (= 2.5.0-2), libffi8 (= 3.4.4-2), libfile-stripnondeterminism-perl (= 1.13.1-1), libfontconfig1 (= 2.14.2-6ubuntu1), libfreetype6 (= 2.13.2+dfsg-1), libgcc-13-dev (= 13.2.0-13ubuntu1), libgcc-s1 (= 14-20240130-1ubuntu1), libgcrypt20 (= 1.10.3-2), libgdbm-compat4 (= 1.23-5), libgdbm6 (= 1.23-5), libgfortran5 (= 14-20240130-1ubuntu1), libglib2.0-0 (= 2.78.3-2), libgmp10 (= 2:6.3.0+dfsg-2ubuntu4), libgnutls30 (= 3.8.3-1ubuntu1), libgomp1 (= 14-20240130-1ubuntu1), libgpg-error0 (= 1.47-3build1), libgraphite2-3 (= 1.3.14-2), libgssapi-krb5-2 (= 1.20.1-5build1), libharfbuzz0b (= 8.3.0-2), libhogweed6 (= 3.9.1-2), libhts3 (= 1.18+ds-1), libhtscodecs2 (= 1.6.0-1), libicu74 (= 74.2-1ubuntu1), libidn2-0 (= 2.3.7-2), libio-string-perl (= 1.08-4), libisl23 (= 0.26-3), libjansson4 (= 2.14-2), libjpeg-turbo8 (= 2.1.5-2ubuntu1), libjpeg8 (= 8c-2ubuntu11), libk5crypto3 (= 1.20.1-5build1), libkeyutils1 (= 1.6.3-2), libkrb5-3 (= 1.20.1-5build1), libkrb5support0 (= 1.20.1-5build1), liblapack3 (= 3.12.0-2), liblcms2-2 (= 2.14-2), libldap2 (= 2.6.6+dfsg-1~exp1ubuntu2), liblocale-gettext-perl (= 1.07-6build1), liblz4-1 (= 1.9.4-1), liblzma5 (= 5.4.5-0.3), libmagic-mgc (= 1:5.45-2), libmagic1 (= 1:5.45-2), libmd0 (= 1.1.0-2), libmount1 (= 2.39.2-6ubuntu1), libmpc3 (= 1.3.1-1), libmpfr6 (= 4.2.1-1), libncurses6 (= 6.4+20240113-1), libncursesw6 (= 6.4+20240113-1), libnettle8 (= 3.9.1-2), libnghttp2-14 (= 1.58.0-1), libnsl-dev (= 1.3.0-3), libnsl2 (= 1.3.0-3), libnspr4 (= 2:4.35-1.1), libnss3 (= 2:3.96.1-1), libp11-kit0 (= 0.25.3-2ubuntu2), libpam-modules (= 1.5.2-9.1ubuntu2), libpam-modules-bin (= 1.5.2-9.1ubuntu2), libpam-runtime (= 1.5.2-9.1ubuntu2), libpam0g (= 1.5.2-9.1ubuntu2), libpcre2-8-0 (= 10.42-4ubuntu1), libpcsclite1 (= 2.0.1-1), libperl5.38 (= 5.38.2-3), libpipeline1 (= 1.5.7-1), libpng16-16 (= 1.6.42-1), libpsl5 (= 0.21.2-1build1), libpython3-stdlib (= 3.12.1-0ubuntu1), libpython3.11-minimal (= 3.11.7-2), libpython3.11-stdlib (= 3.11.7-2), libpython3.12-minimal (= 3.12.1-2), libpython3.12-stdlib (= 3.12.1-2), libreadline8 (= 8.2-3), librtmp1 (= 2.4+20151223.gitfa8646d.1-2build4), libsasl2-2 (= 2.1.28+dfsg1-4), libsasl2-modules-db (= 2.1.28+dfsg1-4), libseccomp2 (= 2.5.4-2ubuntu2), libselinux1 (= 3.5-2), libsframe1 (= 2.42-2ubuntu1), libsigsegv2 (= 2.14-1ubuntu1), libsmartcols1 (= 2.39.2-6ubuntu1), libsqlite3-0 (= 3.45.0-1), libssh-4 (= 0.10.6-2), libssl-dev (= 3.0.10-1ubuntu4), libssl3 (= 3.0.10-1ubuntu4), libstdc++-13-dev (= 13.2.0-13ubuntu1), libstdc++6 (= 14-20240130-1ubuntu1), libsub-override-perl (= 0.10-1), libsub-uplevel-perl (= 0.2800-3), libsystemd0 (= 255.2-3ubuntu2), libtasn1-6 (= 4.19.0-3), libtest-deep-perl (= 1.204-1), libtest-differences-perl (= 0.71-1), libtest-exception-perl (= 0.43-3), libtest-most-perl (= 0.38-1), libtest-warn-perl (= 0.37-2), libtext-diff-perl (= 1.45-2), libtinfo6 (= 6.4+20240113-1), libtirpc-common (= 1.3.4+ds-1build1), libtirpc-dev (= 1.3.4+ds-1build1), libtirpc3 (= 1.3.4+ds-1build1), libtool (= 2.4.7-7), libubsan1 (= 14-20240130-1ubuntu1), libuchardet0 (= 0.0.8-1), libudev1 (= 255.2-3ubuntu2), libunistring5 (= 1.1-2), libuuid1 (= 2.39.2-6ubuntu1), libxml2 (= 2.9.14+dfsg-1.3build3), libzstd1 (= 1.5.5+dfsg2-2), linux-libc-dev (= 6.6.0-14.14), login (= 1:4.13+dfsg1-3ubuntu1), lto-disabled-list (= 46), m4 (= 1.4.19-4), make (= 4.3-4.1build1), man-db (= 2.12.0-3), mawk (= 1.3.4.20240123-1), media-types (= 10.1.0), mummer (= 3.23+dfsg-8), ncurses-base (= 6.4+20240113-1), ncurses-bin (= 6.4+20240113-1), netbase (= 6.4), openjdk-17-jdk-headless (= 17.0.10+7-1), openjdk-17-jre-headless (= 17.0.10+7-1), openssl (= 3.0.10-1ubuntu4), patch (= 2.7.6-7build2), perl (= 5.38.2-3), perl-base (= 5.38.2-3), perl-modules-5.38 (= 5.38.2-3), po-debconf (= 1.0.21+nmu1), python3 (= 3.12.1-0ubuntu1), python3-distutils (= 3.11.5-1), python3-iniconfig (= 1.1.1-2), python3-lib2to3 (= 3.11.5-1), python3-minimal (= 3.12.1-0ubuntu1), python3-networkx (= 2.8.8-1ubuntu1), python3-numpy (= 1:1.24.2-2), python3-packaging (= 23.2-1), python3-pkg-resources (= 68.1.2-2), python3-pluggy (= 1.4.0-1), python3-pysam (= 0.22.0+ds-1), python3-pytest (= 7.4.4-2), python3-setuptools (= 68.1.2-2), python3.11 (= 3.11.7-2), python3.11-minimal (= 3.11.7-2), python3.12 (= 3.12.1-2), python3.12-minimal (= 3.12.1-2), readline-common (= 8.2-3), rpcsvc-proto (= 1.4.2-0ubuntu6), samtools (= 1.19-1), sed (= 4.9-2), sensible-utils (= 0.0.20), smalt (= 0.7.6-13), sysvinit-utils (= 3.08-3ubuntu1), tar (= 1.35+dfsg-3), tzdata (= 2023d-1ubuntu2), util-linux (= 2.39.2-6ubuntu1), xz-utils (= 5.4.5-0.3), zlib1g (= 1:1.3.dfsg-3ubuntu1) Environment: DEB_BUILD_OPTIONS="parallel=4" DEB_BUILD_PROFILES="noudeb" LANG="C.UTF-8" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1706790897" +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ iva_1.0.11+ds-5_armhf.deb ------------------------- new Debian package, version 2.0. size 8581856 bytes: control archive=2970 bytes. 1030 bytes, 22 lines control 5477 bytes, 64 lines md5sums 253 bytes, 12 lines * postinst #!/bin/sh 366 bytes, 12 lines * prerm #!/bin/sh Package: iva Version: 1.0.11+ds-5 Architecture: armhf Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 8767 Depends: fastaq, python3-networkx, python3-packaging, python3-pysam, python3:any, perl: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 2024-02-01 12:34 ./ drwxr-xr-x root/root 0 2024-02-01 12:34 ./usr/ drwxr-xr-x root/root 0 2024-02-01 12:34 ./usr/bin/ -rwxr-xr-x root/root 17240 2024-02-01 12:34 ./usr/bin/iva -rwxr-xr-x root/root 6228 2024-02-01 12:34 ./usr/bin/iva_qc -rwxr-xr-x root/root 2406 2024-02-01 12:34 ./usr/bin/iva_qc_make_db drwxr-xr-x root/root 0 2024-02-01 12:34 ./usr/lib/ drwxr-xr-x root/root 0 2024-02-01 12:34 ./usr/lib/python3/ drwxr-xr-x root/root 0 2024-02-01 12:34 ./usr/lib/python3/dist-packages/ drwxr-xr-x root/root 0 2024-02-01 12:34 ./usr/lib/python3/dist-packages/iva-1.0.9.egg-info/ -rw-r--r-- root/root 488 2024-02-01 12:34 ./usr/lib/python3/dist-packages/iva-1.0.9.egg-info/PKG-INFO -rw-r--r-- root/root 1 2024-02-01 12:34 ./usr/lib/python3/dist-packages/iva-1.0.9.egg-info/dependency_links.txt -rw-r--r-- root/root 0 2024-02-01 12:34 ./usr/lib/python3/dist-packages/iva-1.0.9.egg-info/requires.txt -rw-r--r-- root/root 4 2024-02-01 12:34 ./usr/lib/python3/dist-packages/iva-1.0.9.egg-info/top_level.txt drwxr-xr-x root/root 0 2024-02-01 12:34 ./usr/lib/python3/dist-packages/iva/ -rw-r--r-- root/root 1033 2021-03-25 08:41 ./usr/lib/python3/dist-packages/iva/__init__.py -rw-r--r-- root/root 29056 2021-03-25 08:41 ./usr/lib/python3/dist-packages/iva/assembly.py -rw-r--r-- root/root 1856 2021-03-25 08:41 ./usr/lib/python3/dist-packages/iva/common.py -rw-r--r-- root/root 1960 2021-03-25 08:41 ./usr/lib/python3/dist-packages/iva/contig.py -rw-r--r-- root/root 4391 2021-03-25 08:41 ./usr/lib/python3/dist-packages/iva/contig_trim.py -rw-r--r-- root/root 4903 2021-03-25 08:41 ./usr/lib/python3/dist-packages/iva/edge.py -rw-r--r-- root/root 3077 2021-03-25 08:41 ./usr/lib/python3/dist-packages/iva/egg_extract.py -rw-r--r-- root/root 4121 2024-02-01 12:34 ./usr/lib/python3/dist-packages/iva/external_progs.py drwxr-xr-x root/root 0 2024-02-01 12:34 ./usr/lib/python3/dist-packages/iva/gage/ -rw-r--r-- 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-rw-r--r-- root/root 1493 2024-02-01 12:34 ./usr/share/doc/iva/copyright drwxr-xr-x root/root 0 2024-02-01 12:34 ./usr/share/man/ drwxr-xr-x root/root 0 2024-02-01 12:34 ./usr/share/man/man1/ -rw-r--r-- root/root 2254 2024-02-01 12:34 ./usr/share/man/man1/iva.1.gz -rw-r--r-- root/root 1282 2024-02-01 12:34 ./usr/share/man/man1/iva_qc.1.gz -rw-r--r-- root/root 643 2024-02-01 12:34 ./usr/share/man/man1/iva_qc_make_db.1.gz +------------------------------------------------------------------------------+ | Post Build | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not removing build depends: as requested +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: armhf Build Type: any Build-Space: 37708 Build-Time: 15 Distribution: noble-proposed Host Architecture: armhf Install-Time: 35 Job: iva_1.0.11+ds-5.dsc Machine Architecture: arm64 Package: iva Package-Time: 51 Source-Version: 1.0.11+ds-5 Space: 37708 Status: successful Version: 1.0.11+ds-5 -------------------------------------------------------------------------------- Finished at 2024-02-01T17:16:55Z Build needed 00:00:51, 37708k disk space RUN: /usr/share/launchpad-buildd/bin/in-target scan-for-processes --backend=chroot --series=noble --arch=armhf PACKAGEBUILD-27738260 Scanning for processes to kill in build PACKAGEBUILD-27738260