https://launchpad.net/ubuntu/+source/iva/1.0.11+ds-5/+build/27738259 RUN: /usr/share/launchpad-buildd/bin/builder-prep Kernel version: Linux bos01-arm64-022 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[1928]: adjust time server 10.211.37.1 offset -0.000203 sec RUN: /usr/share/launchpad-buildd/bin/in-target unpack-chroot --backend=chroot --series=noble --arch=arm64 PACKAGEBUILD-27738259 --image-type chroot /home/buildd/filecache-default/0aaa0d191106d33e51979a9c6a062e50b7f5b3b2 Creating target for build PACKAGEBUILD-27738259 RUN: /usr/share/launchpad-buildd/bin/in-target mount-chroot --backend=chroot --series=noble --arch=arm64 PACKAGEBUILD-27738259 Starting target for build PACKAGEBUILD-27738259 RUN: /usr/share/launchpad-buildd/bin/in-target override-sources-list --backend=chroot --series=noble --arch=arm64 PACKAGEBUILD-27738259 '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-27738259 RUN: /usr/share/launchpad-buildd/bin/in-target update-debian-chroot --backend=chroot --series=noble --arch=arm64 PACKAGEBUILD-27738259 Updating target for build PACKAGEBUILD-27738259 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 arm64 Packages [1406 kB] Get:6 http://ftpmaster.internal/ubuntu noble/main Translation-en [518 kB] Get:7 http://ftpmaster.internal/ubuntu noble/universe arm64 Packages [15.3 MB] Get:8 http://ftpmaster.internal/ubuntu noble/universe Translation-en [6024 kB] Get:9 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 Packages [214 kB] Get:10 http://ftpmaster.internal/ubuntu noble-proposed/main Translation-en [76.0 kB] Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 Packages [1111 kB] Get:12 http://ftpmaster.internal/ubuntu noble-proposed/universe Translation-en [402 kB] Fetched 25.6 MB in 8s (3108 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-aarch64-linux-gnu cpp-aarch64-linux-gnu g++-13-aarch64-linux-gnu g++-aarch64-linux-gnu gcc-13-aarch64-linux-gnu gcc-14-base gcc-aarch64-linux-gnu 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-aarch64-linux-gnu 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 libgprofng0 libgssapi-krb5-2 libhwasan0 libidn2-0 libitm1 libk5crypto3 libkmod2 libkrb5-3 libkrb5support0 liblocale-gettext-perl liblsan0 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 libtsan2 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 148 upgraded, 10 newly installed, 0 to remove and 0 not upgraded. Need to get 118 MB of archives. After this operation, 75.8 MB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu noble/main arm64 libnsl-dev arm64 1.3.0-3 [71.9 kB] Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libcrypt-dev arm64 1:4.4.36-4 [136 kB] Get:3 http://ftpmaster.internal/ubuntu noble/main arm64 libc6-dev arm64 2.38-3ubuntu1 [1573 kB] Get:4 http://ftpmaster.internal/ubuntu noble/main arm64 libc-dev-bin arm64 2.38-3ubuntu1 [19.4 kB] Get:5 http://ftpmaster.internal/ubuntu noble/main arm64 libtirpc-common all 1.3.4+ds-1build1 [8566 B] Get:6 http://ftpmaster.internal/ubuntu noble/main arm64 libtirpc-dev arm64 1.3.4+ds-1build1 [232 kB] Get:7 http://ftpmaster.internal/ubuntu noble/main arm64 libgssapi-krb5-2 arm64 1.20.1-5build1 [139 kB] Get:8 http://ftpmaster.internal/ubuntu noble/main arm64 libkrb5-3 arm64 1.20.1-5build1 [347 kB] Get:9 http://ftpmaster.internal/ubuntu noble/main arm64 libk5crypto3 arm64 1.20.1-5build1 [85.5 kB] Get:10 http://ftpmaster.internal/ubuntu noble/main arm64 libkrb5support0 arm64 1.20.1-5build1 [33.5 kB] Get:11 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libssl3 arm64 3.0.10-1ubuntu4 [1764 kB] Get:12 http://ftpmaster.internal/ubuntu noble/main arm64 libtirpc3 arm64 1.3.4+ds-1build1 [99.3 kB] Get:13 http://ftpmaster.internal/ubuntu noble/main arm64 libnsl2 arm64 1.3.0-3 [40.9 kB] Get:14 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libcrypt1 arm64 1:4.4.36-4 [100 kB] Get:15 http://ftpmaster.internal/ubuntu noble/main arm64 linux-libc-dev arm64 6.6.0-14.14 [1554 kB] Get:16 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 gcc-14-base arm64 14-20240130-1ubuntu1 [46.2 kB] Get:17 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libgcc-s1 arm64 14-20240130-1ubuntu1 [49.8 kB] Get:18 http://ftpmaster.internal/ubuntu noble/main arm64 libc6 arm64 2.38-3ubuntu1 [2740 kB] Get:19 http://ftpmaster.internal/ubuntu noble/main arm64 base-files arm64 13ubuntu6 [84.1 kB] Get:20 http://ftpmaster.internal/ubuntu noble/main arm64 debianutils arm64 5.16 [93.7 kB] Get:21 http://ftpmaster.internal/ubuntu noble/main arm64 bash arm64 5.2.21-2ubuntu1 [777 kB] Get:22 http://ftpmaster.internal/ubuntu noble/main arm64 bsdutils arm64 1:2.39.2-6ubuntu1 [96.9 kB] Get:23 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 coreutils arm64 9.4-2ubuntu3 [1384 kB] Get:24 http://ftpmaster.internal/ubuntu noble/main arm64 diffutils arm64 1:3.10-1 [174 kB] Get:25 http://ftpmaster.internal/ubuntu noble/main arm64 libgpg-error-l10n all 1.47-3build1 [8024 B] Get:26 http://ftpmaster.internal/ubuntu noble/main arm64 libgpg-error0 arm64 1.47-3build1 [69.9 kB] Get:27 http://ftpmaster.internal/ubuntu noble/main arm64 libgcrypt20 arm64 1.10.3-2 [472 kB] Get:28 http://ftpmaster.internal/ubuntu noble/main arm64 liblzma5 arm64 5.4.5-0.3 [140 kB] Get:29 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libstdc++6 arm64 14-20240130-1ubuntu1 [749 kB] Get:30 http://ftpmaster.internal/ubuntu noble/main arm64 libacl1 arm64 2.3.1-4ubuntu1 [19.4 kB] Get:31 http://ftpmaster.internal/ubuntu noble/main arm64 libapparmor1 arm64 4.0.0~alpha2-0ubuntu8 [48.8 kB] Get:32 http://ftpmaster.internal/ubuntu noble/main arm64 libaudit-common all 1:3.1.2-2 [5594 B] Get:33 http://ftpmaster.internal/ubuntu noble/main arm64 libcap-ng0 arm64 0.8.4-1 [16.4 kB] Get:34 http://ftpmaster.internal/ubuntu noble/main arm64 libaudit1 arm64 1:3.1.2-2 [47.4 kB] Get:35 http://ftpmaster.internal/ubuntu noble/main arm64 libblkid1 arm64 2.39.2-6ubuntu1 [121 kB] Get:36 http://ftpmaster.internal/ubuntu noble/main arm64 libzstd1 arm64 1.5.5+dfsg2-2 [270 kB] Get:37 http://ftpmaster.internal/ubuntu noble/main arm64 libkmod2 arm64 30+20230601-2ubuntu1 [49.8 kB] Get:38 http://ftpmaster.internal/ubuntu noble/main arm64 libpcre2-8-0 arm64 10.42-4ubuntu1 [211 kB] Get:39 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libselinux1 arm64 3.5-2 [79.4 kB] Get:40 http://ftpmaster.internal/ubuntu noble/main arm64 libmount1 arm64 2.39.2-6ubuntu1 [132 kB] Get:41 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libtext-iconv-perl arm64 1.7-8build1 [13.0 kB] Get:42 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libtext-charwidth-perl arm64 0.04-11build1 [9316 B] Get:43 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 perl-modules-5.38 all 5.38.2-3 [3110 kB] Get:44 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libperl5.38 arm64 5.38.2-3 [4772 kB] Get:45 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 perl arm64 5.38.2-3 [231 kB] Get:46 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 perl-base arm64 5.38.2-3 [1777 kB] Get:47 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 liblocale-gettext-perl arm64 1.07-6build1 [15.0 kB] Get:48 http://ftpmaster.internal/ubuntu noble/main arm64 perl-modules-5.36 all 5.36.0-10ubuntu1 [2984 kB] Get:49 http://ftpmaster.internal/ubuntu noble/main arm64 libperl5.36 arm64 5.36.0-10ubuntu1 [4673 kB] Get:50 http://ftpmaster.internal/ubuntu noble/main arm64 libdb5.3 arm64 5.3.28+dfsg2-4 [718 kB] Get:51 http://ftpmaster.internal/ubuntu noble/main arm64 libgdbm6 arm64 1.23-5 [33.8 kB] Get:52 http://ftpmaster.internal/ubuntu noble/main arm64 libgdbm-compat4 arm64 1.23-5 [6302 B] Get:53 http://ftpmaster.internal/ubuntu noble/main arm64 zlib1g arm64 1:1.3.dfsg-3ubuntu1 [61.6 kB] Get:54 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 debconf-i18n all 1.5.85 [205 kB] Get:55 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 debconf all 1.5.85 [124 kB] Get:56 http://ftpmaster.internal/ubuntu noble/main arm64 libpam0g arm64 1.5.2-9.1ubuntu2 [65.8 kB] Get:57 http://ftpmaster.internal/ubuntu noble/main arm64 libseccomp2 arm64 2.5.4-2ubuntu2 [50.7 kB] Get:58 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 systemd-sysv arm64 255.2-3ubuntu2 [11.9 kB] Get:59 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 systemd-dev all 255.2-3ubuntu2 [101 kB] Get:60 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 systemd arm64 255.2-3ubuntu2 [3397 kB] Get:61 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libsystemd-shared arm64 255.2-3ubuntu2 [2012 kB] Get:62 http://ftpmaster.internal/ubuntu noble/main arm64 libargon2-1 arm64 0~20190702+dfsg-4 [20.5 kB] Get:63 http://ftpmaster.internal/ubuntu noble/main arm64 libuuid1 arm64 2.39.2-6ubuntu1 [34.3 kB] Get:64 http://ftpmaster.internal/ubuntu noble/main arm64 libcryptsetup12 arm64 2:2.6.1-6ubuntu1 [240 kB] Get:65 http://ftpmaster.internal/ubuntu noble/main arm64 libfdisk1 arm64 2.39.2-6ubuntu1 [141 kB] Get:66 http://ftpmaster.internal/ubuntu noble/main arm64 mount arm64 2.39.2-6ubuntu1 [116 kB] Get:67 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libsystemd0 arm64 255.2-3ubuntu2 [421 kB] Get:68 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libudev1 arm64 255.2-3ubuntu2 [170 kB] Get:69 http://ftpmaster.internal/ubuntu noble/main arm64 libxxhash0 arm64 0.8.2-2 [21.2 kB] Get:70 http://ftpmaster.internal/ubuntu noble/main arm64 libapt-pkg6.0 arm64 2.7.10 [929 kB] Get:71 http://ftpmaster.internal/ubuntu noble/main arm64 tar arm64 1.35+dfsg-3 [248 kB] Get:72 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 dpkg arm64 1.22.2ubuntu3 [1271 kB] Get:73 http://ftpmaster.internal/ubuntu noble/main arm64 grep arm64 3.11-4 [174 kB] Get:74 http://ftpmaster.internal/ubuntu noble/main arm64 login arm64 1:4.13+dfsg1-3ubuntu1 [200 kB] Get:75 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 ncurses-bin arm64 6.4+20240113-1 [186 kB] Get:76 http://ftpmaster.internal/ubuntu noble/main arm64 sed arm64 4.9-2 [201 kB] Get:77 http://ftpmaster.internal/ubuntu noble/main arm64 util-linux arm64 2.39.2-6ubuntu1 [1113 kB] Get:78 http://ftpmaster.internal/ubuntu noble/main arm64 libdebconfclient0 arm64 0.271ubuntu1 [11.2 kB] Get:79 http://ftpmaster.internal/ubuntu noble/main arm64 base-passwd arm64 3.6.3 [51.1 kB] Get:80 http://ftpmaster.internal/ubuntu noble/main arm64 init-system-helpers all 1.66ubuntu1 [39.4 kB] Get:81 http://ftpmaster.internal/ubuntu noble/main arm64 libc-bin arm64 2.38-3ubuntu1 [590 kB] Get:82 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 ncurses-base all 6.4+20240113-1 [25.4 kB] Get:83 http://ftpmaster.internal/ubuntu noble/main arm64 sysvinit-utils arm64 3.08-3ubuntu1 [33.3 kB] Get:84 http://ftpmaster.internal/ubuntu noble/main arm64 apt arm64 2.7.10 [1333 kB] Get:85 http://ftpmaster.internal/ubuntu noble/main arm64 apt-utils arm64 2.7.10 [205 kB] Get:86 http://ftpmaster.internal/ubuntu noble/main arm64 ubuntu-keyring all 2023.11.28.1 [11.1 kB] Get:87 http://ftpmaster.internal/ubuntu noble/main arm64 libffi8 arm64 3.4.4-2 [22.2 kB] Get:88 http://ftpmaster.internal/ubuntu noble/main arm64 libp11-kit0 arm64 0.25.3-2ubuntu2 [274 kB] Get:89 http://ftpmaster.internal/ubuntu noble/main arm64 libunistring5 arm64 1.1-2 [528 kB] Get:90 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libidn2-0 arm64 2.3.7-2 [67.1 kB] Get:91 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libgnutls30 arm64 3.8.3-1ubuntu1 [942 kB] Get:92 http://ftpmaster.internal/ubuntu noble/main arm64 libpam-modules-bin arm64 1.5.2-9.1ubuntu2 [47.0 kB] Get:93 http://ftpmaster.internal/ubuntu noble/main arm64 libpam-modules arm64 1.5.2-9.1ubuntu2 [284 kB] Get:94 http://ftpmaster.internal/ubuntu noble/main arm64 init arm64 1.66ubuntu1 [6186 B] Get:95 http://ftpmaster.internal/ubuntu noble/main arm64 libsmartcols1 arm64 2.39.2-6ubuntu1 [62.9 kB] Get:96 http://ftpmaster.internal/ubuntu noble/main arm64 uuid-runtime arm64 2.39.2-6ubuntu1 [32.3 kB] Get:97 http://ftpmaster.internal/ubuntu noble/main arm64 libattr1 arm64 1:2.5.2-1 [11.0 kB] Get:98 http://ftpmaster.internal/ubuntu noble/main arm64 libmd0 arm64 1.1.0-2 [24.7 kB] Get:99 http://ftpmaster.internal/ubuntu noble/main arm64 libpam-runtime all 1.5.2-9.1ubuntu2 [40.6 kB] Get:100 http://ftpmaster.internal/ubuntu noble/main arm64 libsemanage-common all 3.5-1build1 [9982 B] Get:101 http://ftpmaster.internal/ubuntu noble/main arm64 libsepol2 arm64 3.5-2 [289 kB] Get:102 http://ftpmaster.internal/ubuntu noble/main arm64 libsemanage2 arm64 3.5-1build1 [90.0 kB] Get:103 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libncursesw6 arm64 6.4+20240113-1 [145 kB] Get:104 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libtinfo6 arm64 6.4+20240113-1 [104 kB] Get:105 http://ftpmaster.internal/ubuntu noble/main arm64 passwd arm64 1:4.13+dfsg1-3ubuntu1 [837 kB] Get:106 http://ftpmaster.internal/ubuntu noble/main arm64 g++-13 arm64 13.2.0-13ubuntu1 [14.0 kB] Get:107 http://ftpmaster.internal/ubuntu noble/main arm64 gcc-13 arm64 13.2.0-13ubuntu1 [463 kB] Get:108 http://ftpmaster.internal/ubuntu noble/main arm64 cpp-13 arm64 13.2.0-13ubuntu1 [1030 B] Get:109 http://ftpmaster.internal/ubuntu noble/main arm64 cpp-13-aarch64-linux-gnu arm64 13.2.0-13ubuntu1 [10.3 MB] Get:110 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libcc1-0 arm64 14-20240130-1ubuntu1 [44.8 kB] Get:111 http://ftpmaster.internal/ubuntu noble/main arm64 libgprofng0 arm64 2.42-2ubuntu1 [777 kB] Get:112 http://ftpmaster.internal/ubuntu noble/main arm64 libctf0 arm64 2.42-2ubuntu1 [95.7 kB] Get:113 http://ftpmaster.internal/ubuntu noble/main arm64 libctf-nobfd0 arm64 2.42-2ubuntu1 [99.5 kB] Get:114 http://ftpmaster.internal/ubuntu noble/main arm64 libsframe1 arm64 2.42-2ubuntu1 [14.1 kB] Get:115 http://ftpmaster.internal/ubuntu noble/main arm64 binutils-aarch64-linux-gnu arm64 2.42-2ubuntu1 [3294 kB] Get:116 http://ftpmaster.internal/ubuntu noble/main arm64 libbinutils arm64 2.42-2ubuntu1 [768 kB] Get:117 http://ftpmaster.internal/ubuntu noble/main arm64 binutils arm64 2.42-2ubuntu1 [18.1 kB] Get:118 http://ftpmaster.internal/ubuntu noble/main arm64 binutils-common arm64 2.42-2ubuntu1 [239 kB] Get:119 http://ftpmaster.internal/ubuntu noble/main arm64 libstdc++-13-dev arm64 13.2.0-13ubuntu1 [2319 kB] Get:120 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libgomp1 arm64 14-20240130-1ubuntu1 [144 kB] Get:121 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libitm1 arm64 14-20240130-1ubuntu1 [27.6 kB] Get:122 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libatomic1 arm64 14-20240130-1ubuntu1 [11.4 kB] Get:123 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libasan8 arm64 14-20240130-1ubuntu1 [2918 kB] Get:124 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 liblsan0 arm64 14-20240130-1ubuntu1 [1281 kB] Get:125 http://ftpmaster.internal/ubuntu noble/main arm64 libgcc-13-dev arm64 13.2.0-13ubuntu1 [2463 kB] Get:126 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libtsan2 arm64 14-20240130-1ubuntu1 [2687 kB] Get:127 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libubsan1 arm64 14-20240130-1ubuntu1 [1150 kB] Get:128 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libhwasan0 arm64 14-20240130-1ubuntu1 [1545 kB] Get:129 http://ftpmaster.internal/ubuntu noble/main arm64 gcc-13-aarch64-linux-gnu arm64 13.2.0-13ubuntu1 [20.1 MB] Get:130 http://ftpmaster.internal/ubuntu noble/main arm64 g++-13-aarch64-linux-gnu arm64 13.2.0-13ubuntu1 [11.7 MB] Get:131 http://ftpmaster.internal/ubuntu noble/main arm64 gcc-13-base arm64 13.2.0-13ubuntu1 [46.6 kB] Get:132 http://ftpmaster.internal/ubuntu noble/main arm64 libproc2-0 arm64 2:4.0.4-2ubuntu1 [56.5 kB] Get:133 http://ftpmaster.internal/ubuntu noble/main arm64 mawk arm64 1.3.4.20240123-1 [124 kB] Get:134 http://ftpmaster.internal/ubuntu noble/main arm64 procps arm64 2:4.0.4-2ubuntu1 [706 kB] Get:135 http://ftpmaster.internal/ubuntu noble/main arm64 krb5-locales all 1.20.1-5build1 [13.7 kB] Get:136 http://ftpmaster.internal/ubuntu noble/main arm64 readline-common all 8.2-3 [56.2 kB] Get:137 http://ftpmaster.internal/ubuntu noble/main arm64 libreadline8 arm64 8.2-3 [152 kB] Get:138 http://ftpmaster.internal/ubuntu noble/main arm64 libsqlite3-0 arm64 3.45.0-1 [703 kB] Get:139 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 openssl arm64 3.0.10-1ubuntu4 [983 kB] Get:140 http://ftpmaster.internal/ubuntu noble/main arm64 tzdata all 2023d-1ubuntu2 [321 kB] Get:141 http://ftpmaster.internal/ubuntu noble/main arm64 bash-completion all 1:2.11-8 [180 kB] Get:142 http://ftpmaster.internal/ubuntu noble/main arm64 bsdextrautils arm64 2.39.2-6ubuntu1 [71.4 kB] Get:143 http://ftpmaster.internal/ubuntu noble/main arm64 libpng16-16 arm64 1.6.42-1 [185 kB] Get:144 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 psmisc arm64 23.6-2 [178 kB] Get:145 http://ftpmaster.internal/ubuntu noble/main arm64 xz-utils arm64 5.4.5-0.3 [277 kB] Get:146 http://ftpmaster.internal/ubuntu noble/main arm64 g++ arm64 4:13.2.0-7ubuntu1 [1082 B] Get:147 http://ftpmaster.internal/ubuntu noble/main arm64 gcc arm64 4:13.2.0-7ubuntu1 [5018 B] Get:148 http://ftpmaster.internal/ubuntu noble/main arm64 cpp arm64 4:13.2.0-7ubuntu1 [22.4 kB] Get:149 http://ftpmaster.internal/ubuntu noble/main arm64 cpp-aarch64-linux-gnu arm64 4:13.2.0-7ubuntu1 [5316 B] Get:150 http://ftpmaster.internal/ubuntu noble/main arm64 gcc-aarch64-linux-gnu arm64 4:13.2.0-7ubuntu1 [1198 B] Get:151 http://ftpmaster.internal/ubuntu noble/main arm64 g++-aarch64-linux-gnu arm64 4:13.2.0-7ubuntu1 [962 B] Get:152 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 dpkg-dev all 1.22.2ubuntu3 [1076 kB] Get:153 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libdpkg-perl all 1.22.2ubuntu3 [266 kB] Get:154 http://ftpmaster.internal/ubuntu noble/main arm64 lto-disabled-list all 46 [12.3 kB] Get:155 http://ftpmaster.internal/ubuntu noble/main arm64 libfakeroot arm64 1.33-1 [32.5 kB] Get:156 http://ftpmaster.internal/ubuntu noble/main arm64 fakeroot arm64 1.33-1 [66.9 kB] Get:157 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 optipng arm64 0.7.8+ds-1 [109 kB] Get:158 http://ftpmaster.internal/ubuntu noble/main arm64 pinentry-curses arm64 1.2.1-3ubuntu1 [34.0 kB] Preconfiguring packages ... 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Setting up dpkg-dev (1.22.2ubuntu3) ... Setting up libnsl-dev:arm64 (1.3.0-3) ... Setting up libc6-dev:arm64 (2.38-3ubuntu1) ... Setting up libstdc++-13-dev:arm64 (13.2.0-13ubuntu1) ... Setting up g++-13-aarch64-linux-gnu (13.2.0-13ubuntu1) ... Setting up g++-13 (13.2.0-13ubuntu1) ... Setting up g++-aarch64-linux-gnu (4:13.2.0-7ubuntu1) ... 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-27738259 arm64 noble-proposed -c chroot:build-PACKAGEBUILD-27738259 --arch=arm64 --dist=noble-proposed --nolog iva_1.0.11+ds-5.dsc Initiating build PACKAGEBUILD-27738259 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 aarch64 sbuild (Debian sbuild) 0.79.0 (05 February 2020) on bos01-arm64-022.buildd +==============================================================================+ | iva 1.0.11+ds-5 (arm64) Thu, 01 Feb 2024 17:16:27 +0000 | +==============================================================================+ Package: iva Version: 1.0.11+ds-5 Source Version: 1.0.11+ds-5 Distribution: noble-proposed Machine Architecture: arm64 Host Architecture: arm64 Build Architecture: arm64 Build Type: any I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-27738259/chroot-autobuild' with '<>' I: NOTICE: Log filtering will replace 'build/iva-ayabeL/resolver-vOWWXP' 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-ayabeL/iva-1.0.11+ds' with '<>' I: NOTICE: Log filtering will replace 'build/iva-ayabeL' 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 [562 B] Fetched 2000 B in 0s (118 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. Need to get 180 MB of archives. After this operation, 545 MB of additional disk space will be used. Get:1 copy:/<>/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [776 B] Get:2 http://ftpmaster.internal/ubuntu noble/main arm64 libpython3.12-minimal arm64 3.12.1-2 [827 kB] Get:3 http://ftpmaster.internal/ubuntu noble/main arm64 libexpat1 arm64 2.5.0-2 [72.2 kB] Get:4 http://ftpmaster.internal/ubuntu noble/main arm64 python3.12-minimal arm64 3.12.1-2 [2276 kB] Get:5 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 python3-minimal arm64 3.12.1-0ubuntu1 [26.9 kB] Get:6 http://ftpmaster.internal/ubuntu noble/main arm64 media-types all 10.1.0 [27.5 kB] Get:7 http://ftpmaster.internal/ubuntu noble/main arm64 netbase all 6.4 [13.1 kB] Get:8 http://ftpmaster.internal/ubuntu noble/main arm64 libpython3.12-stdlib arm64 3.12.1-2 [2005 kB] Get:9 http://ftpmaster.internal/ubuntu noble/main arm64 python3.12 arm64 3.12.1-2 [638 kB] Get:10 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libpython3-stdlib arm64 3.12.1-0ubuntu1 [9662 B] Get:11 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http://ftpmaster.internal/ubuntu noble/main arm64 fonts-dejavu-mono all 2.37-8 [502 kB] Get:82 http://ftpmaster.internal/ubuntu noble/main arm64 fonts-dejavu-core all 2.37-8 [835 kB] Get:83 http://ftpmaster.internal/ubuntu noble/main arm64 fontconfig-config arm64 2.14.2-6ubuntu1 [36.0 kB] Get:84 http://ftpmaster.internal/ubuntu noble/main arm64 libfontconfig1 arm64 2.14.2-6ubuntu1 [140 kB] Get:85 http://ftpmaster.internal/ubuntu noble/main arm64 libnspr4 arm64 2:4.35-1.1 [113 kB] Get:86 http://ftpmaster.internal/ubuntu noble/main arm64 libnss3 arm64 2:3.96.1-1 [1389 kB] Get:87 http://ftpmaster.internal/ubuntu noble/main arm64 libasound2-data all 1.2.10-3build1 [20.7 kB] Get:88 http://ftpmaster.internal/ubuntu noble/main arm64 libasound2 arm64 1.2.10-3build1 [386 kB] Get:89 http://ftpmaster.internal/ubuntu noble/main arm64 libgraphite2-3 arm64 1.3.14-2 [81.5 kB] Get:90 http://ftpmaster.internal/ubuntu noble/main arm64 libharfbuzz0b arm64 8.3.0-2 [463 kB] Get:91 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libpcsclite1 arm64 2.0.1-1 [21.4 kB] Get:92 http://ftpmaster.internal/ubuntu noble/main arm64 openjdk-17-jre-headless arm64 17.0.10+7-1 [47.3 MB] Get:93 http://ftpmaster.internal/ubuntu noble/main arm64 default-jre-headless arm64 2:1.17-75 [3046 B] Get:94 http://ftpmaster.internal/ubuntu noble/main arm64 openjdk-17-jdk-headless arm64 17.0.10+7-1 [70.5 MB] Get:95 http://ftpmaster.internal/ubuntu noble/main arm64 default-jdk-headless arm64 2:1.17-75 [956 B] Get:96 http://ftpmaster.internal/ubuntu noble/main arm64 python3-lib2to3 all 3.11.5-1 [79.0 kB] Get:97 http://ftpmaster.internal/ubuntu noble/main arm64 python3-distutils all 3.11.5-1 [131 kB] Get:98 http://ftpmaster.internal/ubuntu noble/main arm64 python3-setuptools all 68.1.2-2 [396 kB] Get:99 http://ftpmaster.internal/ubuntu noble/universe arm64 dh-python all 6.20231223 [128 kB] Get:100 http://ftpmaster.internal/ubuntu noble/main arm64 libsasl2-modules-db arm64 2.1.28+dfsg1-4 [21.1 kB] Get:101 http://ftpmaster.internal/ubuntu noble/main arm64 libsasl2-2 arm64 2.1.28+dfsg1-4 [54.5 kB] Get:102 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libldap2 arm64 2.6.6+dfsg-1~exp1ubuntu2 [193 kB] Get:103 http://ftpmaster.internal/ubuntu noble/main arm64 librtmp1 arm64 2.4+20151223.gitfa8646d.1-2build4 [59.2 kB] Get:104 http://ftpmaster.internal/ubuntu noble/main arm64 libssh-4 arm64 0.10.6-2 [226 kB] Get:105 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libcurl3-gnutls arm64 8.5.0-2ubuntu2 [326 kB] Get:106 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libdeflate0 arm64 1.19-1 [43.4 kB] Get:107 http://ftpmaster.internal/ubuntu noble/universe arm64 libhtscodecs2 arm64 1.6.0-1 [78.1 kB] Get:108 http://ftpmaster.internal/ubuntu noble/universe arm64 libhts3 arm64 1.18+ds-1 [422 kB] Get:109 http://ftpmaster.internal/ubuntu noble/universe arm64 samtools arm64 1.19-1 [584 kB] Get:110 http://ftpmaster.internal/ubuntu noble/universe arm64 fastaq all 3.17.0-6 [47.9 kB] Get:111 http://ftpmaster.internal/ubuntu noble/universe arm64 help2man arm64 1.49.3 [201 kB] Get:112 http://ftpmaster.internal/ubuntu noble/universe arm64 kmc arm64 3.2.3+dfsg-1 [942 kB] Get:113 http://ftpmaster.internal/ubuntu noble/universe arm64 libbambamc0 arm64 0.0.50-6 [37.2 kB] Get:114 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libblas3 arm64 3.12.0-2 [143 kB] Get:115 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libgfortran5 arm64 14-20240130-1ubuntu1 [441 kB] Get:116 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 liblapack3 arm64 3.12.0-2 [2242 kB] Get:117 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libssl-dev arm64 3.0.10-1ubuntu4 [2330 kB] Get:118 http://ftpmaster.internal/ubuntu noble/universe arm64 mummer arm64 3.23+dfsg-8 [673 kB] Get:119 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-iniconfig all 1.1.1-2 [6024 B] Get:120 http://ftpmaster.internal/ubuntu noble/main arm64 python3-networkx all 2.8.8-1ubuntu1 [1468 kB] Get:121 http://ftpmaster.internal/ubuntu noble/main arm64 python3-numpy arm64 1:1.24.2-2 [4525 kB] Get:122 http://ftpmaster.internal/ubuntu noble/main arm64 python3-packaging all 23.2-1 [40.6 kB] Get:123 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 python3-pluggy all 1.4.0-1 [20.4 kB] Get:124 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-pysam arm64 0.22.0+ds-1 [4399 kB] Get:125 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 python3-pytest all 7.4.4-2 [241 kB] Get:126 http://ftpmaster.internal/ubuntu noble/universe arm64 smalt arm64 0.7.6-13 [95.2 kB] Preconfiguring packages ... Fetched 180 MB in 34s (5268 kB/s) Selecting previously unselected package libpython3.12-minimal:arm64. (Reading database ... 15813 files and directories currently installed.) Preparing to unpack .../libpython3.12-minimal_3.12.1-2_arm64.deb ... Unpacking libpython3.12-minimal:arm64 (3.12.1-2) ... Selecting previously unselected package libexpat1:arm64. Preparing to unpack .../libexpat1_2.5.0-2_arm64.deb ... Unpacking libexpat1:arm64 (2.5.0-2) ... Selecting previously unselected package python3.12-minimal. Preparing to unpack .../python3.12-minimal_3.12.1-2_arm64.deb ... Unpacking python3.12-minimal (3.12.1-2) ... Setting up libpython3.12-minimal:arm64 (3.12.1-2) ... Setting up libexpat1:arm64 (2.5.0-2) ... Setting up python3.12-minimal (3.12.1-2) ... Selecting previously unselected package python3-minimal. (Reading database ... 16131 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.12.1-0ubuntu1_arm64.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_arm64.deb ... Unpacking sbuild-build-depends-main-dummy (0.invalid.0) ... Setting up libhtscodecs2:arm64 (1.6.0-1) ... Setting up media-types (10.1.0) ... Setting up libpipeline1:arm64 (1.5.7-1) ... Setting up libgraphite2-3:arm64 (1.3.14-2) ... Setting up liblcms2-2:arm64 (2.14-2) ... Setting up libpsl5:arm64 (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:arm64 (2.78.3-2) ... No schema files found: doing nothing. Setting up libdebhelper-perl (13.13ubuntu1) ... Setting up libbrotli1:arm64 (1.1.0-2) ... Setting up libnghttp2-14:arm64 (1.58.0-1) ... Setting up libmagic1:arm64 (1:5.45-2) ... Setting up libdeflate0:arm64 (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:arm64 (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:arm64 (3.12.0-2) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/aarch64-linux-gnu/libblas.so.3 (libblas.so.3-aarch64-linux-gnu) in auto mode Setting up libclass-data-inheritable-perl (0.08-3) ... Setting up libfreetype6:arm64 (2.13.2+dfsg-1) ... Setting up libnspr4:arm64 (2:4.35-1.1) ... Setting up libtext-diff-perl (1.45-2) ... Setting up librtmp1:arm64 (2.4+20151223.gitfa8646d.1-2build4) ... Setting up libavahi-common-data:arm64 (0.8-13ubuntu2) ... Setting up libncurses6:arm64 (6.4+20240113-1) ... Setting up libdbus-1-3:arm64 (1.14.10-3ubuntu1) ... Setting up libbambamc0:arm64 (0.0.50-6) ... Setting up fonts-dejavu-mono (2.37-8) ... Setting up libssl-dev:arm64 (3.0.10-1ubuntu4) ... Setting up autopoint (0.21-14ubuntu1) ... Setting up fonts-dejavu-core (2.37-8) ... Setting up libpcsclite1:arm64 (2.0.1-1) ... Setting up libjpeg-turbo8:arm64 (2.1.5-2ubuntu1) ... Setting up libsasl2-2:arm64 (2.1.28+dfsg1-4) ... Setting up libssh-4:arm64 (0.10.6-2) ... Setting up libgfortran5:arm64 (14-20240130-1ubuntu1) ... Setting up autoconf (2.71-3) ... Setting up libcapture-tiny-perl (0.48-2) ... Setting up libicu74:arm64 (74.2-1ubuntu1) ... Setting up libdata-stag-perl (0.14-3) ... Setting up libuchardet0:arm64 (0.0.8-1) ... Setting up libasound2:arm64 (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:arm64 (8.3.0-2) ... Setting up netbase (6.4) ... Setting up libdevel-stacktrace-perl (2.0500-1) ... Setting up libpython3.11-minimal:arm64 (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:arm64 (0.190-1) ... Setting up kmc (3.2.3+dfsg-1) ... Setting up libxml2:arm64 (2.9.14+dfsg-1.3build3) ... Setting up libldap2:arm64 (2.6.6+dfsg-1~exp1ubuntu2) ... Setting up libjpeg8:arm64 (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:arm64 (0.190-1) ... Setting up liblapack3:arm64 (3.12.0-2) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/aarch64-linux-gnu/liblapack.so.3 (liblapack.so.3-aarch64-linux-gnu) in auto mode Setting up gettext (0.21-14ubuntu1) ... Setting up libpython3.12-stdlib:arm64 (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:arm64 (3.11.7-2) ... Setting up python3.12 (3.12.1-2) ... Setting up libavahi-common3:arm64 (0.8-13ubuntu2) ... Setting up libtest-differences-perl (0.71-1) ... Setting up libcurl3-gnutls:arm64 (8.5.0-2ubuntu2) ... Setting up libnss3:arm64 (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:arm64 (2.14.2-6ubuntu1) ... Setting up libavahi-client3:arm64 (0.8-13ubuntu2) ... Setting up libpython3-stdlib:arm64 (3.12.1-0ubuntu1) ... Setting up python3.11 (3.11.7-2) ... Setting up libhts3:arm64 (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:arm64 (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:arm64 (17.0.10+7-1) ... update-alternatives: using /usr/lib/jvm/java-17-openjdk-arm64/bin/java to provide /usr/bin/java (java) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-arm64/bin/jpackage to provide /usr/bin/jpackage (jpackage) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-arm64/bin/keytool to provide /usr/bin/keytool (keytool) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-arm64/bin/rmiregistry to provide /usr/bin/rmiregistry (rmiregistry) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-arm64/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:arm64 (17.0.10+7-1) ... update-alternatives: using /usr/lib/jvm/java-17-openjdk-arm64/bin/jar to provide /usr/bin/jar (jar) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-arm64/bin/jarsigner to provide /usr/bin/jarsigner (jarsigner) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-arm64/bin/javac to provide /usr/bin/javac (javac) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-arm64/bin/javadoc to provide /usr/bin/javadoc (javadoc) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-arm64/bin/javap to provide /usr/bin/javap (javap) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-arm64/bin/jcmd to provide /usr/bin/jcmd (jcmd) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-arm64/bin/jdb to provide /usr/bin/jdb (jdb) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-arm64/bin/jdeprscan to provide /usr/bin/jdeprscan (jdeprscan) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-arm64/bin/jdeps to provide /usr/bin/jdeps (jdeps) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-arm64/bin/jfr to provide /usr/bin/jfr (jfr) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-arm64/bin/jimage to provide /usr/bin/jimage (jimage) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-arm64/bin/jinfo to provide /usr/bin/jinfo (jinfo) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-arm64/bin/jlink to provide /usr/bin/jlink (jlink) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-arm64/bin/jmap to provide /usr/bin/jmap (jmap) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-arm64/bin/jmod to provide /usr/bin/jmod (jmod) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-arm64/bin/jps to provide /usr/bin/jps (jps) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-arm64/bin/jrunscript to provide /usr/bin/jrunscript (jrunscript) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-arm64/bin/jshell to provide /usr/bin/jshell (jshell) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-arm64/bin/jstack to provide /usr/bin/jstack (jstack) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-arm64/bin/jstat to provide /usr/bin/jstat (jstat) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-arm64/bin/jstatd to provide /usr/bin/jstatd (jstatd) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-arm64/bin/serialver to provide /usr/bin/serialver (serialver) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-arm64/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 (arm64 included in any) +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 5.4.0-169-generic #187-Ubuntu SMP Thu Nov 23 14:53:38 UTC 2023 arm64 (aarch64) 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-aarch64-linux-gnu_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-aarch64-linux-gnu_13.2.0-13ubuntu1 cpp-aarch64-linux-gnu_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-aarch64-linux-gnu_13.2.0-13ubuntu1 g++-aarch64-linux-gnu_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-aarch64-linux-gnu_13.2.0-13ubuntu1 gcc-13-base_13.2.0-13ubuntu1 gcc-14-base_14-20240130-1ubuntu1 gcc-aarch64-linux-gnu_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 libassuan0_2.5.6-1 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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 libgprofng0_2.42-2ubuntu1 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 libhwasan0_14-20240130-1ubuntu1 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 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libpcre2-8-0_10.42-4ubuntu1 libpcsclite1_2.0.1-1 libperl5.36_5.36.0-10ubuntu1 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 libtsan2_14-20240130-1ubuntu1 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 lIoHTpRXnIaWGWcxJfs132HoJeeUjWuqrt7UG7apx61aB0P3imVpZYFbvyvROuN5 zxnj0ga+hw/pqBikfRQCnQu1Me3aMOurE7Q42N2CSO8A2VCFzCX3DYGhRCFKZuE0 cTOxmwO88ZUN80fAbm7mTMOrQpwMFsMtbVEIHk6o8hx8IiUn43gbf1pMRaKLhKK8 BMncd8ME+zVpI8F/Ag5209h1Eawibwd+dM4J+cHN2ENe4M1P3Qc2bw4a5vhi2+H/ p0mhCyYpNG2XU0VnnoNhpCU5dLrX7mYaEbjR19y9A98kCFFqSQ6yJmIyC8icm5HI 9SVS0U6tU6qbC1jmhqI313VlYYN+qH5t1z71ktLo4Uq5khmdC/Qrv2XVhARkS+Tr ZmOMQGJIwgC0hkKFpuNtzcocTIlAQSyo7QQCPVsNYh//UCyk1RPO9Ta1LpsNQ0hN Q33gwdEqgMMrZW30A9qyR71bno5aRznYe8FeNt/razi5XHm5U2eipEcmwCEU4jN5 0Eq06ewO6c0= =RITE -----END PGP SIGNATURE----- gpgv: Signature made Thu Feb 1 12:52:13 2024 UTC gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./iva_1.0.11+ds-5.dsc: no acceptable signature found dpkg-source: info: extracting iva in /<> dpkg-source: info: unpacking iva_1.0.11+ds.orig.tar.xz dpkg-source: info: unpacking 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-27738259 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-27738259 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-27738259 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 arm64 debian/rules clean dh clean --buildsystem=pybuild 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 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 57ms] [parsing started SimpleFileObject[/<>/iva/gage/SizeFasta.java]] [parsing completed 3ms] [parsing started SimpleFileObject[/<>/iva/gage/SplitFastaByLetter.java]] [parsing completed 2ms] [parsing started SimpleFileObject[/<>/iva/gage/Utils.java]] [parsing completed 35ms] [parsing started SimpleFileObject[/<>/iva/gage/getScaffoldStats.java]] [parsing completed 11ms] [loading /modules/java.prefs/module-info.class] [loading /modules/jdk.xml.dom/module-info.class] [loading /modules/java.smartcardio/module-info.class] [loading /modules/jdk.internal.jvmstat/module-info.class] [loading /modules/java.xml/module-info.class] [loading /modules/jdk.internal.vm.ci/module-info.class] [loading /modules/jdk.nio.mapmode/module-info.class] [loading /modules/java.scripting/module-info.class] [loading /modules/jdk.jsobject/module-info.class] [loading /modules/jdk.jlink/module-info.class] [loading /modules/jdk.naming.rmi/module-info.class] [loading /modules/jdk.zipfs/module-info.class] [loading /modules/jdk.net/module-info.class] [loading /modules/jdk.security.jgss/module-info.class] [loading /modules/jdk.unsupported.desktop/module-info.class] [loading /modules/jdk.naming.dns/module-info.class] [loading /modules/jdk.accessibility/module-info.class] [loading /modules/jdk.jartool/module-info.class] [loading /modules/jdk.incubator.vector/module-info.class] [loading /modules/jdk.jshell/module-info.class] [loading /modules/jdk.management.agent/module-info.class] [loading /modules/jdk.dynalink/module-info.class] [loading /modules/java.logging/module-info.class] [loading /modules/java.xml.crypto/module-info.class] [loading /modules/java.management.rmi/module-info.class] [loading /modules/jdk.jfr/module-info.class] [loading /modules/jdk.javadoc/module-info.class] [loading /modules/jdk.internal.vm.compiler/module-info.class] [loading /modules/java.instrument/module-info.class] [loading /modules/jdk.management/module-info.class] [loading /modules/jdk.localedata/module-info.class] [loading /modules/java.net.http/module-info.class] [loading /modules/jdk.crypto.ec/module-info.class] [loading /modules/jdk.jcmd/module-info.class] [loading /modules/jdk.jdeps/module-info.class] [loading /modules/jdk.internal.vm.compiler.management/module-info.class] [loading /modules/java.sql.rowset/module-info.class] [loading /modules/jdk.internal.le/module-info.class] [loading /modules/jdk.internal.opt/module-info.class] [loading /modules/java.sql/module-info.class] [loading /modules/jdk.jdwp.agent/module-info.class] [loading /modules/java.rmi/module-info.class] [loading /modules/java.management/module-info.class] [loading /modules/jdk.hotspot.agent/module-info.class] [loading /modules/jdk.management.jfr/module-info.class] [loading /modules/java.security.sasl/module-info.class] [loading /modules/jdk.editpad/module-info.class] [loading /modules/jdk.random/module-info.class] [loading /modules/jdk.attach/module-info.class] [loading /modules/jdk.security.auth/module-info.class] [loading /modules/jdk.jstatd/module-info.class] [loading /modules/jdk.unsupported/module-info.class] [loading /modules/jdk.jpackage/module-info.class] [loading /modules/jdk.jconsole/module-info.class] [loading /modules/jdk.jdi/module-info.class] [loading /modules/jdk.compiler/module-info.class] [loading /modules/java.transaction.xa/module-info.class] [loading /modules/java.datatransfer/module-info.class] [loading /modules/jdk.httpserver/module-info.class] [loading /modules/jdk.internal.ed/module-info.class] [loading /modules/java.desktop/module-info.class] [loading /modules/jdk.incubator.foreign/module-info.class] [loading /modules/jdk.charsets/module-info.class] [loading /modules/java.security.jgss/module-info.class] [loading /modules/java.se/module-info.class] [loading /modules/jdk.crypto.cryptoki/module-info.class] [loading /modules/java.naming/module-info.class] [loading /modules/java.base/module-info.class] [loading /modules/java.compiler/module-info.class] [loading /modules/jdk.sctp/module-info.class] [search path for source files: .] [search path for class files: /usr/lib/jvm/java-17-openjdk-arm64/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$Scaffold.class] [wrote /<>/iva/gage/getScaffoldStats.class] [total 890ms] dh_auto_build -- I: pybuild base:305: /usr/bin/python3 setup.py build Checking dependencies found in path: OK kmc OK kmc_dump OK nucmer OK delta-filter OK show-coords OK samtools OK smalt running build running build_py creating /<>/.pybuild/cpython3_3.12_iva/build/iva copying iva/seed_processor.py -> /<>/.pybuild/cpython3_3.12_iva/build/iva copying iva/kraken.py -> /<>/.pybuild/cpython3_3.12_iva/build/iva copying iva/contig_trim.py -> /<>/.pybuild/cpython3_3.12_iva/build/iva copying iva/kmers.py -> /<>/.pybuild/cpython3_3.12_iva/build/iva copying iva/mapping.py -> /<>/.pybuild/cpython3_3.12_iva/build/iva copying iva/edge.py -> /<>/.pybuild/cpython3_3.12_iva/build/iva copying iva/test_data_runner.py -> /<>/.pybuild/cpython3_3.12_iva/build/iva copying iva/assembly.py -> /<>/.pybuild/cpython3_3.12_iva/build/iva copying iva/__init__.py -> /<>/.pybuild/cpython3_3.12_iva/build/iva copying iva/graph.py -> /<>/.pybuild/cpython3_3.12_iva/build/iva copying iva/external_progs.py -> /<>/.pybuild/cpython3_3.12_iva/build/iva copying iva/read_trim.py -> /<>/.pybuild/cpython3_3.12_iva/build/iva copying iva/qc_external.py -> /<>/.pybuild/cpython3_3.12_iva/build/iva copying iva/egg_extract.py -> /<>/.pybuild/cpython3_3.12_iva/build/iva copying iva/contig.py -> /<>/.pybuild/cpython3_3.12_iva/build/iva copying iva/qc.py -> /<>/.pybuild/cpython3_3.12_iva/build/iva copying iva/mummer.py -> /<>/.pybuild/cpython3_3.12_iva/build/iva copying iva/kcount.py -> /<>/.pybuild/cpython3_3.12_iva/build/iva copying iva/seed.py -> /<>/.pybuild/cpython3_3.12_iva/build/iva copying iva/common.py -> /<>/.pybuild/cpython3_3.12_iva/build/iva creating /<>/.pybuild/cpython3_3.12_iva/build/iva/gage copying iva/gage/GetFastaStats$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 3.50s ======================= 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_arm64.deb'. dpkg-genbuildinfo --build=any -O../iva_1.0.11+ds-5_arm64.buildinfo dpkg-genchanges --build=any -mLaunchpad Build Daemon -O../iva_1.0.11+ds-5_arm64.changes dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) -------------------------------------------------------------------------------- Build finished at 2024-02-01T17:17:41Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ iva_1.0.11+ds-5_arm64.changes: ------------------------------ Format: 1.8 Date: Thu, 01 Feb 2024 13:34:57 +0100 Source: iva Binary: iva Built-For-Profiles: noudeb Architecture: arm64 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: a8391d289cc46f64ece53eec22ec9d9116a3291f 9134 iva_1.0.11+ds-5_arm64.buildinfo 2f50f155d0eeb15b6a5d6f88b0ceed80291e6ea5 8581856 iva_1.0.11+ds-5_arm64.deb Checksums-Sha256: 047c6b33eef7d2cda259131b15a890fedd1802dba1c33b58a923d6303154823b 9134 iva_1.0.11+ds-5_arm64.buildinfo 8591bba295e138be95475b549121f7683bf9c5a143e6ca8c2e6733ae5b78055f 8581856 iva_1.0.11+ds-5_arm64.deb Files: 7d706cc2499c8ab6a2c34c3342ee840f 9134 science optional iva_1.0.11+ds-5_arm64.buildinfo 7ec60a66f4065316beb24d7a917d5a13 8581856 science optional iva_1.0.11+ds-5_arm64.deb /<>/iva_1.0.11+ds-5_arm64.changes.new could not be renamed to /<>/iva_1.0.11+ds-5_arm64.changes: Illegal seek Distribution field may be wrong!!! +------------------------------------------------------------------------------+ | Buildinfo | +------------------------------------------------------------------------------+ Format: 1.0 Source: iva Binary: iva Architecture: arm64 Version: 1.0.11+ds-5 Checksums-Md5: 7ec60a66f4065316beb24d7a917d5a13 8581856 iva_1.0.11+ds-5_arm64.deb Checksums-Sha1: 2f50f155d0eeb15b6a5d6f88b0ceed80291e6ea5 8581856 iva_1.0.11+ds-5_arm64.deb Checksums-Sha256: 8591bba295e138be95475b549121f7683bf9c5a143e6ca8c2e6733ae5b78055f 8581856 iva_1.0.11+ds-5_arm64.deb Build-Origin: Ubuntu Build-Architecture: arm64 Build-Date: Thu, 01 Feb 2024 17:17:40 +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-aarch64-linux-gnu (= 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-aarch64-linux-gnu (= 13.2.0-13ubuntu1), cpp-aarch64-linux-gnu (= 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-aarch64-linux-gnu (= 13.2.0-13ubuntu1), g++-aarch64-linux-gnu (= 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-aarch64-linux-gnu (= 13.2.0-13ubuntu1), gcc-13-base (= 13.2.0-13ubuntu1), gcc-14-base (= 14-20240130-1ubuntu1), gcc-aarch64-linux-gnu (= 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), libgprofng0 (= 2.42-2ubuntu1), 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), libhwasan0 (= 14-20240130-1ubuntu1), libicu74 (= 74.2-1ubuntu1), libidn2-0 (= 2.3.7-2), libio-string-perl (= 1.08-4), libisl23 (= 0.26-3), libitm1 (= 14-20240130-1ubuntu1), 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), liblsan0 (= 14-20240130-1ubuntu1), 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), libtsan2 (= 14-20240130-1ubuntu1), 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_arm64.deb ------------------------- new Debian package, version 2.0. size 8581856 bytes: control archive=2969 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: arm64 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-- 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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: arm64 Build Type: any Build-Space: 37708 Build-Time: 15 Distribution: noble-proposed Host Architecture: arm64 Install-Time: 58 Job: iva_1.0.11+ds-5.dsc Machine Architecture: arm64 Package: iva Package-Time: 74 Source-Version: 1.0.11+ds-5 Space: 37708 Status: successful Version: 1.0.11+ds-5 -------------------------------------------------------------------------------- Finished at 2024-02-01T17:17:41Z Build needed 00:01:14, 37708k disk space RUN: /usr/share/launchpad-buildd/bin/in-target scan-for-processes --backend=chroot --series=noble --arch=arm64 PACKAGEBUILD-27738259 Scanning for processes to kill in build PACKAGEBUILD-27738259