https://launchpad.net/ubuntu/+source/reapr/1.0.18+dfsg-5ubuntu2/+build/28010610 RUN: /usr/share/launchpad-buildd/bin/builder-prep Kernel version: Linux lcy02-amd64-070 5.4.0-173-generic #191-Ubuntu SMP Fri Feb 2 13:55:07 UTC 2024 x86_64 Buildd toolchain package versions: launchpad-buildd_236~650~ubuntu20.04.1 python3-lpbuildd_236~650~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 Apr 10:24:50 ntpdate[1845]: adjust time server 10.131.248.1 offset -0.003793 sec RUN: /usr/share/launchpad-buildd/bin/in-target unpack-chroot --backend=chroot --series=noble --arch=amd64 PACKAGEBUILD-28010610 --image-type chroot /home/buildd/filecache-default/1fe94ca8758119221c8de2550665a1bb335bd6a9 Creating target for build PACKAGEBUILD-28010610 RUN: /usr/share/launchpad-buildd/bin/in-target mount-chroot --backend=chroot --series=noble --arch=amd64 PACKAGEBUILD-28010610 Starting target for build PACKAGEBUILD-28010610 RUN: /usr/share/launchpad-buildd/bin/in-target override-sources-list --backend=chroot --series=noble --arch=amd64 PACKAGEBUILD-28010610 '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-28010610 RUN: /usr/share/launchpad-buildd/bin/in-target update-debian-chroot --backend=chroot --series=noble --arch=amd64 PACKAGEBUILD-28010610 Updating target for build PACKAGEBUILD-28010610 Get:1 http://ftpmaster.internal/ubuntu noble InRelease [255 kB] Get:2 http://ftpmaster.internal/ubuntu noble-security InRelease [90.7 kB] Get:3 http://ftpmaster.internal/ubuntu noble-updates InRelease [89.7 kB] Get:4 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] Get:5 http://ftpmaster.internal/ubuntu noble/main amd64 Packages [867 kB] Get:6 http://ftpmaster.internal/ubuntu noble/main Translation-en [512 kB] Get:7 http://ftpmaster.internal/ubuntu noble/universe amd64 Packages [11.4 MB] Get:8 http://ftpmaster.internal/ubuntu noble/universe Translation-en [6118 kB] Get:9 http://ftpmaster.internal/ubuntu noble-updates/main amd64 Packages [705 kB] Get:10 http://ftpmaster.internal/ubuntu noble-updates/main Translation-en [242 kB] Get:11 http://ftpmaster.internal/ubuntu noble-updates/universe amd64 Packages [4722 kB] Get:12 http://ftpmaster.internal/ubuntu noble-updates/universe Translation-en [1693 kB] Get:13 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 Packages [665 kB] Get:14 http://ftpmaster.internal/ubuntu noble-proposed/main Translation-en [239 kB] Get:15 http://ftpmaster.internal/ubuntu noble-proposed/universe amd64 Packages [3869 kB] Get:16 http://ftpmaster.internal/ubuntu noble-proposed/universe Translation-en [1363 kB] Fetched 32.9 MB in 4s (9243 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: libnsl-dev libperl5.36 libtirpc-dev libunistring2 perl-modules-5.36 Use 'sudo apt autoremove' to remove them. The following packages will be REMOVED: libapt-pkg6.0* libdb5.3* libext2fs2* libgnutls30* libhogweed6* libnettle8* libpng16-16* libssl3* libtirpc3* usrmerge* The following NEW packages will be installed: cpp-13-x86-64-linux-gnu cpp-x86-64-linux-gnu g++-13-x86-64-linux-gnu g++-x86-64-linux-gnu gcc-13-x86-64-linux-gnu gcc-14-base gcc-x86-64-linux-gnu libapt-pkg6.0t64 libdb5.3t64 libext2fs2t64 libgnutls30t64 libhogweed6t64 libnettle8t64 libperl5.38t64 libpng16-16t64 libssl3t64 libtirpc3t64 libunistring5 perl-modules-5.38 The following packages will be upgraded: apt apt-utils base-files base-passwd bash bash-completion binutils binutils-common binutils-x86-64-linux-gnu bsdextrautils bsdutils bzip2 ca-certificates coreutils cpp cpp-13 dash debconf debconf-i18n debianutils diffutils dpkg dpkg-dev e2fsprogs fakeroot g++ g++-13 gcc gcc-13 gcc-13-base gpg gpg-agent gpgconf gpgv grep gzip hostname init init-system-helpers krb5-locales libacl1 libapparmor1 libargon2-1 libasan8 libatomic1 libattr1 libaudit-common libaudit1 libbinutils libblkid1 libbz2-1.0 libc-bin libc-dev-bin libc6 libc6-dev libcap-ng0 libcap2 libcc1-0 libcom-err2 libcrypt-dev libcrypt1 libcryptsetup12 libctf-nobfd0 libctf0 libdebconfclient0 libdevmapper1.02.1 libdpkg-perl libfakeroot libfdisk1 libffi8 libgcc-13-dev libgcc-s1 libgcrypt20 libgdbm-compat4 libgdbm6 libgomp1 libgpg-error-l10n libgpg-error0 libgpm2 libgprofng0 libgssapi-krb5-2 libhwasan0 libidn2-0 libip4tc2 libitm1 libjansson4 libk5crypto3 libkeyutils1 libkmod2 libkrb5-3 libkrb5support0 liblocale-gettext-perl liblsan0 liblzma5 libmd0 libmount1 libncursesw6 libnsl-dev libnsl2 libnss-nisplus libp11-kit0 libpam-modules libpam-modules-bin libpam-runtime libpam0g libpcre2-8-0 libproc2-0 libquadmath0 libreadline8 libseccomp2 libselinux1 libsemanage-common libsemanage2 libsepol2 libsframe1 libsmartcols1 libsqlite3-0 libss2 libstdc++-13-dev libstdc++6 libsystemd-shared libsystemd0 libtext-charwidth-perl libtext-iconv-perl libtinfo6 libtirpc-common libtirpc-dev libtsan2 libubsan1 libudev1 libuuid1 libxxhash0 libzstd1 linux-libc-dev login logsave lto-disabled-list mawk mount ncurses-base ncurses-bin openssl optipng passwd perl perl-base pinentry-curses procps psmisc readline-common sed sensible-utils systemd systemd-dev systemd-sysv sysvinit-utils tar tzdata ubuntu-keyring util-linux uuid-runtime xz-utils zlib1g 163 upgraded, 19 newly installed, 10 to remove and 0 not upgraded. Need to get 119 MB of archives. After this operation, 78.3 MB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libnsl-dev amd64 1.3.0-3build3 [70.5 kB] Get:2 http://ftpmaster.internal/ubuntu noble/main amd64 libcrypt-dev amd64 1:4.4.36-4 [128 kB] Get:3 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libc6-dev amd64 2.39-0ubuntu8 [2124 kB] Get:4 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libc-dev-bin amd64 2.39-0ubuntu8 [20.4 kB] Get:5 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libtirpc-common all 1.3.4+ds-1.1build1 [8094 B] Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libtirpc-dev amd64 1.3.4+ds-1.1build1 [193 kB] Get:7 http://ftpmaster.internal/ubuntu noble-proposed/universe amd64 libnss-nisplus amd64 1.3-5build1 [22.4 kB] Get:8 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libtirpc3t64 amd64 1.3.4+ds-1.1build1 [82.6 kB] Get:9 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libgssapi-krb5-2 amd64 1.20.1-6ubuntu2 [142 kB] Get:10 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libkrb5-3 amd64 1.20.1-6ubuntu2 [347 kB] Get:11 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libk5crypto3 amd64 1.20.1-6ubuntu2 [81.7 kB] Get:12 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libkrb5support0 amd64 1.20.1-6ubuntu2 [33.5 kB] Get:13 http://ftpmaster.internal/ubuntu noble/main amd64 libacl1 amd64 2.3.2-1 [16.7 kB] Get:14 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libapparmor1 amd64 4.0.0-beta3-0ubuntu3 [49.5 kB] Get:15 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libaudit-common all 1:3.1.2-2.1build1 [5736 B] Get:16 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libcap-ng0 amd64 0.8.4-2build2 [15.2 kB] Get:17 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libaudit1 amd64 1:3.1.2-2.1build1 [46.9 kB] Get:18 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libblkid1 amd64 2.39.3-9ubuntu4 [122 kB] Get:19 http://ftpmaster.internal/ubuntu noble/main amd64 libcap2 amd64 1:2.66-5ubuntu1 [29.9 kB] Get:20 http://ftpmaster.internal/ubuntu noble/main amd64 libcrypt1 amd64 1:4.4.36-4 [95.3 kB] Get:21 http://ftpmaster.internal/ubuntu noble/main amd64 libgpg-error-l10n all 1.47-3build1 [8024 B] Get:22 http://ftpmaster.internal/ubuntu noble/main amd64 libgpg-error0 amd64 1.47-3build1 [70.0 kB] Get:23 http://ftpmaster.internal/ubuntu noble/main amd64 libgcrypt20 amd64 1.10.3-2 [532 kB] Get:24 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 liblzma5 amd64 5.6.1+really5.4.5-1build1 [127 kB] Get:25 http://ftpmaster.internal/ubuntu noble/main amd64 libzstd1 amd64 1.5.5+dfsg2-2 [297 kB] Get:26 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libkmod2 amd64 31+20240202-2ubuntu5 [51.5 kB] Get:27 http://ftpmaster.internal/ubuntu noble/main amd64 libpcre2-8-0 amd64 10.42-4ubuntu1 [228 kB] Get:28 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libselinux1 amd64 3.5-2ubuntu2 [79.6 kB] Get:29 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libmount1 amd64 2.39.3-9ubuntu4 [134 kB] Get:30 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 perl-modules-5.38 all 5.38.2-3.2build1 [3110 kB] Get:31 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libperl5.38t64 amd64 5.38.2-3.2build1 [4870 kB] Get:32 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 perl amd64 5.38.2-3.2build1 [231 kB] Get:33 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 perl-base amd64 5.38.2-3.2build1 [1823 kB] Get:34 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 liblocale-gettext-perl amd64 1.07-6ubuntu5 [15.8 kB] Get:35 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libtext-iconv-perl amd64 1.7-8build3 [13.5 kB] Get:36 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libtext-charwidth-perl amd64 0.04-11build3 [9358 B] Get:37 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 bzip2 amd64 1.0.8-5.1 [34.5 kB] Get:38 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libbz2-1.0 amd64 1.0.8-5.1 [34.3 kB] Get:39 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libc6 amd64 2.39-0ubuntu8 [3265 kB] Get:40 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libc-bin amd64 2.39-0ubuntu8 [682 kB] Get:41 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libsystemd-shared amd64 255.4-1ubuntu6 [2070 kB] Get:42 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 systemd-dev all 255.4-1ubuntu6 [104 kB] Get:43 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 systemd-sysv amd64 255.4-1ubuntu6 [11.9 kB] Get:44 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 systemd amd64 255.4-1ubuntu6 [3471 kB] Get:45 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libsystemd0 amd64 255.4-1ubuntu6 [432 kB] Get:46 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libpam-modules-bin amd64 1.5.3-5ubuntu4 [51.9 kB] Get:47 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libpam-modules amd64 1.5.3-5ubuntu4 [279 kB] Get:48 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libnettle8t64 amd64 3.9.1-2.2build1 [182 kB] Get:49 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libhogweed6t64 amd64 3.9.1-2.2build1 [199 kB] Get:50 http://ftpmaster.internal/ubuntu noble/main amd64 libp11-kit0 amd64 0.25.3-4ubuntu1 [299 kB] Get:51 http://ftpmaster.internal/ubuntu noble/main amd64 libunistring5 amd64 1.1-2 [537 kB] Get:52 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libgnutls30t64 amd64 3.8.3-1.1ubuntu3 [998 kB] Get:53 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libapt-pkg6.0t64 amd64 2.7.14build2 [985 kB] Get:54 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 gcc-14-base amd64 14-20240330-1ubuntu2 [47.5 kB] Get:55 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libgcc-s1 amd64 14-20240330-1ubuntu2 [77.7 kB] Get:56 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libstdc++6 amd64 14-20240330-1ubuntu2 [795 kB] Get:57 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libudev1 amd64 255.4-1ubuntu6 [174 kB] Get:58 http://ftpmaster.internal/ubuntu noble/main amd64 libxxhash0 amd64 0.8.2-2 [25.5 kB] Get:59 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 zlib1g amd64 1:1.3.dfsg-3.1ubuntu2 [62.8 kB] Get:60 http://ftpmaster.internal/ubuntu noble/main amd64 libffi8 amd64 3.4.6-1 [24.7 kB] Get:61 http://ftpmaster.internal/ubuntu noble/main amd64 libidn2-0 amd64 2.3.7-2 [66.0 kB] Get:62 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libdebconfclient0 amd64 0.271ubuntu3 [11.4 kB] Get:63 http://ftpmaster.internal/ubuntu noble/main amd64 base-passwd amd64 3.6.3 [51.2 kB] Get:64 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 gpgv amd64 2.4.4-2ubuntu16 [157 kB] Get:65 http://ftpmaster.internal/ubuntu noble/main amd64 ubuntu-keyring all 2023.11.28.1 [11.1 kB] Get:66 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libseccomp2 amd64 2.5.5-1ubuntu3 [50.3 kB] Get:67 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libdb5.3t64 amd64 5.3.28+dfsg2-6build1 [734 kB] Get:68 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 apt-utils amd64 2.7.14build2 [217 kB] Get:69 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 apt amd64 2.7.14build2 [1375 kB] Get:70 http://ftpmaster.internal/ubuntu noble-updates/main amd64 libgdbm6 amd64 1.23-5 [33.3 kB] Get:71 http://ftpmaster.internal/ubuntu noble-updates/main amd64 libgdbm-compat4 amd64 1.23-5 [6498 B] Get:72 http://ftpmaster.internal/ubuntu noble/main amd64 debconf-i18n all 1.5.86 [205 kB] Get:73 http://ftpmaster.internal/ubuntu noble/main amd64 debconf all 1.5.86 [124 kB] Get:74 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libpam0g amd64 1.5.3-5ubuntu4 [67.6 kB] Get:75 http://ftpmaster.internal/ubuntu noble/main amd64 libargon2-1 amd64 0~20190702+dfsg-4 [21.4 kB] Get:76 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libdevmapper1.02.1 amd64 2:1.02.185-3ubuntu3 [139 kB] Get:77 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libuuid1 amd64 2.39.3-9ubuntu4 [35.1 kB] Get:78 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libcryptsetup12 amd64 2:2.7.0-1ubuntu3 [266 kB] Get:79 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libfdisk1 amd64 2.39.3-9ubuntu4 [146 kB] Get:80 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 mount amd64 2.39.3-9ubuntu4 [118 kB] Get:81 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 openssl amd64 3.0.13-0ubuntu3 [1002 kB] Get:82 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libssl3t64 amd64 3.0.13-0ubuntu3 [1936 kB] Get:83 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libcom-err2 amd64 1.47.0-2.4~exp1ubuntu3 [22.7 kB] Get:84 http://ftpmaster.internal/ubuntu noble/main amd64 libkeyutils1 amd64 1.6.3-3 [9386 B] Get:85 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libnsl2 amd64 1.3.0-3build3 [41.4 kB] Get:86 http://ftpmaster.internal/ubuntu noble-updates/main amd64 linux-libc-dev amd64 6.8.0-11.11 [1595 kB] Get:87 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 base-files amd64 13ubuntu9 [73.7 kB] Get:88 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 debianutils amd64 5.17build1 [89.9 kB] Get:89 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 bash amd64 5.2.21-2ubuntu4 [794 kB] Get:90 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 bsdutils amd64 1:2.39.3-9ubuntu4 [95.2 kB] Get:91 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 coreutils amd64 9.4-3ubuntu5 [1412 kB] Get:92 http://ftpmaster.internal/ubuntu noble/main amd64 tar amd64 1.35+dfsg-3 [253 kB] Get:93 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 dpkg amd64 1.22.6ubuntu6 [1283 kB] Get:94 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 dash amd64 0.5.12-6ubuntu5 [89.8 kB] Get:95 http://ftpmaster.internal/ubuntu noble/main amd64 diffutils amd64 1:3.10-1 [176 kB] Get:96 http://ftpmaster.internal/ubuntu noble/main amd64 grep amd64 3.11-4 [176 kB] Get:97 http://ftpmaster.internal/ubuntu noble/main amd64 gzip amd64 1.12-1ubuntu2 [98.8 kB] Get:98 http://ftpmaster.internal/ubuntu noble/main amd64 hostname amd64 3.23+nmu2ubuntu1 [11.0 kB] Get:99 http://ftpmaster.internal/ubuntu noble/main amd64 login amd64 1:4.13+dfsg1-4ubuntu1 [201 kB] Get:100 http://ftpmaster.internal/ubuntu noble/main amd64 ncurses-bin amd64 6.4+20240113-1ubuntu1 [188 kB] Get:101 http://ftpmaster.internal/ubuntu noble/main amd64 sed amd64 4.9-2 [204 kB] Get:102 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 util-linux amd64 2.39.3-9ubuntu4 [1127 kB] Get:103 http://ftpmaster.internal/ubuntu noble/main amd64 init-system-helpers all 1.66ubuntu1 [39.4 kB] Get:104 http://ftpmaster.internal/ubuntu noble/main amd64 ncurses-base all 6.4+20240113-1ubuntu1 [25.4 kB] Get:105 http://ftpmaster.internal/ubuntu noble/main amd64 sysvinit-utils amd64 3.08-6ubuntu2 [34.1 kB] Get:106 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 logsave amd64 1.47.0-2.4~exp1ubuntu3 [22.5 kB] Get:107 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libext2fs2t64 amd64 1.47.0-2.4~exp1ubuntu3 [222 kB] Get:108 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 e2fsprogs amd64 1.47.0-2.4~exp1ubuntu3 [601 kB] Get:109 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 optipng amd64 0.7.8+ds-1build2 [110 kB] Get:110 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libpng16-16t64 amd64 1.6.43-5build1 [187 kB] Get:111 http://ftpmaster.internal/ubuntu noble/main amd64 init amd64 1.66ubuntu1 [6186 B] Get:112 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libsmartcols1 amd64 2.39.3-9ubuntu4 [64.7 kB] Get:113 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 uuid-runtime amd64 2.39.3-9ubuntu4 [33.1 kB] Get:114 http://ftpmaster.internal/ubuntu noble/main amd64 libattr1 amd64 1:2.5.2-1 [11.4 kB] Get:115 http://ftpmaster.internal/ubuntu noble/main amd64 libmd0 amd64 1.1.0-2 [27.1 kB] Get:116 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libpam-runtime all 1.5.3-5ubuntu4 [40.8 kB] Get:117 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libsemanage-common all 3.5-1build5 [10.1 kB] Get:118 http://ftpmaster.internal/ubuntu noble/main amd64 libsepol2 amd64 3.5-2 [300 kB] Get:119 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libsemanage2 amd64 3.5-1build5 [93.2 kB] Get:120 http://ftpmaster.internal/ubuntu noble/main amd64 libncursesw6 amd64 6.4+20240113-1ubuntu1 [148 kB] Get:121 http://ftpmaster.internal/ubuntu noble/main amd64 libtinfo6 amd64 6.4+20240113-1ubuntu1 [108 kB] Get:122 http://ftpmaster.internal/ubuntu noble/main amd64 passwd amd64 1:4.13+dfsg1-4ubuntu1 [844 kB] Get:123 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libproc2-0 amd64 2:4.0.4-4ubuntu3 [59.1 kB] Get:124 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libss2 amd64 1.47.0-2.4~exp1ubuntu3 [17.0 kB] Get:125 http://ftpmaster.internal/ubuntu noble/main amd64 mawk amd64 1.3.4.20240123-1 [127 kB] Get:126 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 procps amd64 2:4.0.4-4ubuntu3 [708 kB] Get:127 http://ftpmaster.internal/ubuntu noble/main amd64 sensible-utils all 0.0.22 [22.5 kB] Get:128 http://ftpmaster.internal/ubuntu noble/main amd64 ca-certificates all 20240203 [159 kB] Get:129 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 krb5-locales all 1.20.1-6ubuntu2 [13.8 kB] Get:130 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libsqlite3-0 amd64 3.45.1-1ubuntu2 [701 kB] Get:131 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 readline-common all 8.2-4build1 [56.5 kB] Get:132 http://ftpmaster.internal/ubuntu noble/main amd64 tzdata all 2024a-1ubuntu1 [273 kB] Get:133 http://ftpmaster.internal/ubuntu noble/main amd64 bash-completion all 1:2.11-8 [180 kB] Get:134 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 bsdextrautils amd64 2.39.3-9ubuntu4 [73.9 kB] Get:135 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libgpm2 amd64 1.20.7-11 [14.1 kB] Get:136 http://ftpmaster.internal/ubuntu noble/main amd64 libip4tc2 amd64 1.8.10-3ubuntu1 [23.3 kB] Get:137 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libjansson4 amd64 2.14-2build2 [32.8 kB] Get:138 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 psmisc amd64 23.7-1build1 [179 kB] Get:139 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 xz-utils amd64 5.6.1+really5.4.5-1build1 [267 kB] Get:140 http://ftpmaster.internal/ubuntu noble/main amd64 libgprofng0 amd64 2.42-4ubuntu2 [851 kB] Get:141 http://ftpmaster.internal/ubuntu noble/main amd64 libctf0 amd64 2.42-4ubuntu2 [94.5 kB] Get:142 http://ftpmaster.internal/ubuntu noble/main amd64 libctf-nobfd0 amd64 2.42-4ubuntu2 [97.1 kB] Get:143 http://ftpmaster.internal/ubuntu noble/main amd64 binutils-x86-64-linux-gnu amd64 2.42-4ubuntu2 [2469 kB] Get:144 http://ftpmaster.internal/ubuntu noble/main amd64 libbinutils amd64 2.42-4ubuntu2 [572 kB] Get:145 http://ftpmaster.internal/ubuntu noble/main amd64 binutils amd64 2.42-4ubuntu2 [18.0 kB] Get:146 http://ftpmaster.internal/ubuntu noble/main amd64 binutils-common amd64 2.42-4ubuntu2 [239 kB] Get:147 http://ftpmaster.internal/ubuntu noble/main amd64 libsframe1 amd64 2.42-4ubuntu2 [14.8 kB] Get:148 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libubsan1 amd64 14-20240330-1ubuntu2 [1172 kB] Get:149 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 g++-13 amd64 13.2.0-23ubuntu3 [14.5 kB] Get:150 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libstdc++-13-dev amd64 13.2.0-23ubuntu3 [2398 kB] Get:151 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libgomp1 amd64 14-20240330-1ubuntu2 [147 kB] Get:152 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libitm1 amd64 14-20240330-1ubuntu2 [29.1 kB] Get:153 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libatomic1 amd64 14-20240330-1ubuntu2 [10.4 kB] Get:154 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libasan8 amd64 14-20240330-1ubuntu2 [3020 kB] Get:155 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 liblsan0 amd64 14-20240330-1ubuntu2 [1310 kB] Get:156 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libhwasan0 amd64 14-20240330-1ubuntu2 [1629 kB] Get:157 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libquadmath0 amd64 14-20240330-1ubuntu2 [155 kB] Get:158 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 gcc-13 amd64 13.2.0-23ubuntu3 [479 kB] Get:159 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libgcc-13-dev amd64 13.2.0-23ubuntu3 [2687 kB] Get:160 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libtsan2 amd64 14-20240330-1ubuntu2 [2731 kB] Get:161 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libcc1-0 amd64 14-20240330-1ubuntu2 [47.7 kB] Get:162 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 cpp-13 amd64 13.2.0-23ubuntu3 [1034 B] Get:163 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 gcc-13-base amd64 13.2.0-23ubuntu3 [48.6 kB] Get:164 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 gcc-13-x86-64-linux-gnu amd64 13.2.0-23ubuntu3 [21.9 MB] Get:165 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 g++-13-x86-64-linux-gnu amd64 13.2.0-23ubuntu3 [12.5 MB] Get:166 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 cpp-13-x86-64-linux-gnu amd64 13.2.0-23ubuntu3 [11.2 MB] Get:167 http://ftpmaster.internal/ubuntu noble/main amd64 g++ amd64 4:13.2.0-7ubuntu1 [1100 B] Get:168 http://ftpmaster.internal/ubuntu noble/main amd64 gcc amd64 4:13.2.0-7ubuntu1 [5018 B] Get:169 http://ftpmaster.internal/ubuntu noble/main amd64 cpp amd64 4:13.2.0-7ubuntu1 [22.4 kB] Get:170 http://ftpmaster.internal/ubuntu noble/main amd64 cpp-x86-64-linux-gnu amd64 4:13.2.0-7ubuntu1 [5326 B] Get:171 http://ftpmaster.internal/ubuntu noble/main amd64 gcc-x86-64-linux-gnu amd64 4:13.2.0-7ubuntu1 [1212 B] Get:172 http://ftpmaster.internal/ubuntu noble/main amd64 g++-x86-64-linux-gnu amd64 4:13.2.0-7ubuntu1 [964 B] Get:173 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 dpkg-dev all 1.22.6ubuntu6 [1074 kB] Get:174 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libdpkg-perl all 1.22.6ubuntu6 [268 kB] Get:175 http://ftpmaster.internal/ubuntu noble/main amd64 lto-disabled-list all 47 [12.4 kB] Get:176 http://ftpmaster.internal/ubuntu noble/main amd64 libfakeroot amd64 1.33-1 [32.4 kB] Get:177 http://ftpmaster.internal/ubuntu noble/main amd64 fakeroot amd64 1.33-1 [67.2 kB] Get:178 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 pinentry-curses amd64 1.2.1-3ubuntu5 [35.2 kB] Get:179 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 gpg amd64 2.4.4-2ubuntu16 [565 kB] Get:180 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 gpgconf amd64 2.4.4-2ubuntu16 [103 kB] Get:181 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 gpg-agent amd64 2.4.4-2ubuntu16 [227 kB] Get:182 http://ftpmaster.internal/ubuntu noble-updates/universe amd64 libreadline8 amd64 8.2-3 [152 kB] Preconfiguring packages ... 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(both '/usr/bin/bzcat' and '/usr/bin/bzip2') dpkg: warning: old file '/bin/bzcat' is the same as several new files! (both '/usr/bin/bunzip2' and '/usr/bin/bzcat') dpkg: warning: old file '/bin/bzcat' is the same as several new files! (both '/usr/bin/bzcat' and '/usr/bin/bzip2') dpkg: warning: old file '/bin/bunzip2' is the same as several new files! (both '/usr/bin/bunzip2' and '/usr/bin/bzcat') dpkg: warning: old file '/bin/bunzip2' is the same as several new files! (both '/usr/bin/bzcat' and '/usr/bin/bzip2') Preparing to unpack .../libbz2-1.0_1.0.8-5.1_amd64.deb ... Unpacking libbz2-1.0:amd64 (1.0.8-5.1) over (1.0.8-5build1) ... Setting up libbz2-1.0:amd64 (1.0.8-5.1) ... (Reading database ... 15595 files and directories currently installed.) Preparing to unpack .../libc6_2.39-0ubuntu8_amd64.deb ... Unpacking libc6:amd64 (2.39-0ubuntu8) over (2.38-1ubuntu6) ... Setting up libc6:amd64 (2.39-0ubuntu8) ... (Reading database ... 15599 files and directories currently installed.) 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Processing triggers for ca-certificates (20240203) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. RUN: /usr/share/launchpad-buildd/bin/sbuild-package PACKAGEBUILD-28010610 amd64 noble-proposed -c chroot:build-PACKAGEBUILD-28010610 --arch=amd64 --dist=noble-proposed --nolog -A reapr_1.0.18+dfsg-5ubuntu2.dsc Initiating build PACKAGEBUILD-28010610 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 5.4.0-173-generic #191-Ubuntu SMP Fri Feb 2 13:55:07 UTC 2024 x86_64 sbuild (Debian sbuild) 0.79.0 (05 February 2020) on lcy02-amd64-070.buildd +==============================================================================+ | reapr 1.0.18+dfsg-5ubuntu2 (amd64) Mon, 01 Apr 2024 10:25:22 +0000 | +==============================================================================+ Package: reapr Version: 1.0.18+dfsg-5ubuntu2 Source Version: 1.0.18+dfsg-5ubuntu2 Distribution: noble-proposed Machine Architecture: amd64 Host Architecture: amd64 Build Architecture: amd64 Build Type: binary I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-28010610/chroot-autobuild' with '<>' I: NOTICE: Log filtering will replace 'build/reapr-sLoMir/resolver-PLSt1m' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- reapr_1.0.18+dfsg-5ubuntu2.dsc exists in .; copying to chroot I: NOTICE: Log filtering will replace 'build/reapr-sLoMir/reapr-1.0.18+dfsg' with '<>' I: NOTICE: Log filtering will replace 'build/reapr-sLoMir' with '<>' +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper-compat (= 12), libbamtools-dev, libtabixpp-dev, libhts-dev (>= 1.3), zlib1g-dev, asciidoctor, samtools (>= 1.3), bamtools, smalt, r-base, snpomatic, tabix, libfile-copy-link-perl, build-essential, fakeroot Filtered Build-Depends: debhelper-compat (= 12), libbamtools-dev, libtabixpp-dev, libhts-dev (>= 1.3), zlib1g-dev, asciidoctor, samtools (>= 1.3), bamtools, smalt, r-base, snpomatic, tabix, libfile-copy-link-perl, 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 [453 B] Get:5 copy:/<>/apt_archive ./ Packages [535 B] Fetched 1945 B in 0s (0 B/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 liblocale-gettext-perl libnsl-dev libnsl2 libnss-nis libnss-nisplus libperl5.36 libtext-charwidth-perl libtext-iconv-perl libtext-wrapi18n-perl libtirpc-dev libunistring2 perl-modules-5.36 psmisc uuid-runtime Use 'apt autoremove' to remove them. The following additional packages will be installed: asciidoctor autoconf automake autopoint autotools-dev bamtools debhelper debugedit dh-autoreconf dh-strip-nondeterminism dwz file fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono gettext gettext-base groff-base intltool-debian libarchive-zip-perl libbambamc0 libbamtools-dev libbamtools2.5.2 libblas3 libbrotli1 libbsd0 libcairo2 libcurl3t64-gnutls libcurl4-gnutls-dev libcurl4t64 libdatrie1 libdebhelper-perl libdeflate-dev libdeflate0 libdw1t64 libedit2 libelf1t64 libexpat1 libfile-copy-link-perl libfile-stripnondeterminism-perl libfontconfig1 libfreetype6 libfribidi0 libgfortran5 libglib2.0-0t64 libgraphite2-3 libharfbuzz0b libhts-dev libhts3t64 libhtscodecs2 libice6 libicu74 libjbig0 libjpeg-turbo8 libjpeg8 libjsoncpp25 liblapack3 libldap2 liblerc4 liblzma-dev libmagic-mgc libmagic1t64 libncurses6 libnghttp2-14 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper1 libpipeline1 libpixman-1-0 libpsl5 libreadline8t64 librtmp1 libruby libruby3.2 libsasl2-2 libsasl2-modules-db libsharpyuv0 libsm6 libssh-4 libsub-override-perl libtabixpp-dev libtabixpp0t64 libtcl8.6 libthai-data libthai0 libtiff6 libtk8.6 libtool libuchardet0 libwebp7 libx11-6 libx11-data libxau6 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxft2 libxml2 libxrender1 libxss1 libxt6t64 libyaml-0-2 m4 man-db po-debconf r-base r-base-core r-cran-boot r-cran-class r-cran-cluster r-cran-codetools r-cran-foreign r-cran-kernsmooth r-cran-lattice r-cran-mass r-cran-matrix r-cran-mgcv r-cran-nlme r-cran-nnet r-cran-rpart r-cran-spatial r-cran-survival r-recommended rake ruby ruby-asciidoctor ruby-net-telnet ruby-rubygems ruby-sdbm ruby-webrick ruby-xmlrpc ruby3.2 rubygems-integration samtools smalt snpomatic tabix ucf unzip x11-common xdg-utils zip zlib1g-dev Suggested packages: autoconf-archive gnu-standards autoconf-doc dh-make gettext-doc libasprintf-dev libgettextpo-dev groff libbamtools-doc libcurl4-doc libgnutls28-dev libidn-dev libkrb5-dev libldap2-dev librtmp-dev libssh2-1-dev pkg-config low-memory-monitor liblzma-doc tcl8.6 tk8.6 libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc apparmor less www-browser libmail-box-perl elpa-ess r-doc-info | r-doc-pdf r-mathlib r-base-html ri ruby-dev bundler cwltool Recommended packages: curl | wget | lynx libarchive-cpio-perl libglib2.0-data shared-mime-info xdg-user-dirs libldap-common publicsuffix libsasl2-modules libltdl-dev libmail-sendmail-perl r-base-html r-doc-html r-base-dev fonts-lato libjs-jquery libfile-mimeinfo-perl libnet-dbus-perl libx11-protocol-perl x11-utils x11-xserver-utils The following packages will be REMOVED: libreadline8* The following NEW packages will be installed: asciidoctor autoconf automake autopoint autotools-dev bamtools debhelper debugedit dh-autoreconf dh-strip-nondeterminism dwz file fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono gettext gettext-base groff-base intltool-debian libarchive-zip-perl libbambamc0 libbamtools-dev libbamtools2.5.2 libblas3 libbrotli1 libbsd0 libcairo2 libcurl3t64-gnutls libcurl4-gnutls-dev libcurl4t64 libdatrie1 libdebhelper-perl libdeflate-dev libdeflate0 libdw1t64 libedit2 libelf1t64 libexpat1 libfile-copy-link-perl libfile-stripnondeterminism-perl libfontconfig1 libfreetype6 libfribidi0 libgfortran5 libglib2.0-0t64 libgraphite2-3 libharfbuzz0b libhts-dev libhts3t64 libhtscodecs2 libice6 libicu74 libjbig0 libjpeg-turbo8 libjpeg8 libjsoncpp25 liblapack3 libldap2 liblerc4 liblzma-dev libmagic-mgc libmagic1t64 libncurses6 libnghttp2-14 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper1 libpipeline1 libpixman-1-0 libpsl5 libreadline8t64 librtmp1 libruby libruby3.2 libsasl2-2 libsasl2-modules-db libsharpyuv0 libsm6 libssh-4 libsub-override-perl libtabixpp-dev libtabixpp0t64 libtcl8.6 libthai-data libthai0 libtiff6 libtk8.6 libtool libuchardet0 libwebp7 libx11-6 libx11-data libxau6 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxft2 libxml2 libxrender1 libxss1 libxt6t64 libyaml-0-2 m4 man-db po-debconf r-base r-base-core r-cran-boot r-cran-class r-cran-cluster r-cran-codetools r-cran-foreign r-cran-kernsmooth r-cran-lattice r-cran-mass r-cran-matrix r-cran-mgcv r-cran-nlme r-cran-nnet r-cran-rpart r-cran-spatial r-cran-survival r-recommended rake ruby ruby-asciidoctor ruby-net-telnet ruby-rubygems ruby-sdbm ruby-webrick ruby-xmlrpc ruby3.2 rubygems-integration samtools sbuild-build-depends-main-dummy smalt snpomatic tabix ucf unzip x11-common xdg-utils zip zlib1g-dev 0 upgraded, 149 newly installed, 1 to remove and 0 not upgraded. Need to get 98.2 MB of archives. After this operation, 243 MB of additional disk space will be used. Get:1 copy:/<>/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [752 B] Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libreadline8t64 amd64 8.2-4build1 [153 kB] Get:3 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libbsd0 amd64 0.12.1-1build1 [41.2 kB] Get:4 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libelf1t64 amd64 0.190-1.1build3 [57.6 kB] Get:5 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libexpat1 amd64 2.6.1-2build1 [87.0 kB] Get:6 http://ftpmaster.internal/ubuntu noble/main amd64 libfribidi0 amd64 1.0.13-3 [26.1 kB] Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libglib2.0-0t64 amd64 2.80.0-6build1 [1311 kB] Get:8 http://ftpmaster.internal/ubuntu noble/main amd64 libicu74 amd64 74.2-1ubuntu1 [10.9 MB] Get:9 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libxml2 amd64 2.9.14+dfsg-1.3ubuntu3 [762 kB] Get:10 http://ftpmaster.internal/ubuntu noble/main amd64 libyaml-0-2 amd64 0.2.5-1 [52.8 kB] Get:11 http://ftpmaster.internal/ubuntu noble/main amd64 ucf all 3.0043+nmu1 [56.5 kB] Get:12 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libmagic-mgc amd64 1:5.45-3build1 [307 kB] Get:13 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libmagic1t64 amd64 1:5.45-3build1 [87.2 kB] Get:14 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 file amd64 1:5.45-3build1 [22.0 kB] Get:15 http://ftpmaster.internal/ubuntu noble/main amd64 gettext-base amd64 0.21-14ubuntu1 [38.3 kB] Get:16 http://ftpmaster.internal/ubuntu noble/main amd64 libuchardet0 amd64 0.0.8-1 [75.3 kB] Get:17 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 groff-base amd64 1.23.0-3build2 [1020 kB] Get:18 http://ftpmaster.internal/ubuntu noble/main amd64 libedit2 amd64 3.1-20230828-1 [95.8 kB] Get:19 http://ftpmaster.internal/ubuntu noble/main amd64 libncurses6 amd64 6.4+20240113-1ubuntu1 [112 kB] Get:20 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libnghttp2-14 amd64 1.59.0-1build2 [73.8 kB] Get:21 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libpipeline1 amd64 1.5.7-2 [23.6 kB] Get:22 http://ftpmaster.internal/ubuntu noble/main amd64 libxau6 amd64 1:1.0.9-1build5 [7634 B] Get:23 http://ftpmaster.internal/ubuntu noble/main amd64 libxdmcp6 amd64 1:1.1.3-0ubuntu5 [10.9 kB] Get:24 http://ftpmaster.internal/ubuntu noble/main amd64 libxcb1 amd64 1.15-1 [48.0 kB] Get:25 http://ftpmaster.internal/ubuntu noble/main amd64 libx11-data all 2:1.8.7-1 [115 kB] Get:26 http://ftpmaster.internal/ubuntu noble/main amd64 libx11-6 amd64 2:1.8.7-1 [642 kB] Get:27 http://ftpmaster.internal/ubuntu noble/main amd64 libxext6 amd64 2:1.3.4-1build1 [31.8 kB] Get:28 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 man-db amd64 2.12.0-4build1 [1237 kB] Get:29 http://ftpmaster.internal/ubuntu noble/main amd64 rubygems-integration all 1.18 [5336 B] Get:30 http://ftpmaster.internal/ubuntu noble/main amd64 rake all 13.0.6-3 [61.6 kB] Get:31 http://ftpmaster.internal/ubuntu noble/main amd64 ruby-net-telnet all 0.2.0-1 [13.3 kB] Get:32 http://ftpmaster.internal/ubuntu noble/main amd64 ruby-webrick all 1.8.1-1 [52.3 kB] Get:33 http://ftpmaster.internal/ubuntu noble/main amd64 ruby-xmlrpc all 0.3.2-2 [24.8 kB] Get:34 http://ftpmaster.internal/ubuntu noble/main amd64 libruby amd64 1:3.2~ubuntu1 [4694 B] Get:35 http://ftpmaster.internal/ubuntu noble/main amd64 ruby-sdbm amd64 1.0.0-5build4 [16.2 kB] Get:36 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libruby3.2 amd64 3.2.3-1build3 [5339 kB] Get:37 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 ruby3.2 amd64 3.2.3-1build3 [50.7 kB] Get:38 http://ftpmaster.internal/ubuntu noble/main amd64 ruby-rubygems all 3.4.20-1 [238 kB] Get:39 http://ftpmaster.internal/ubuntu noble/main amd64 ruby amd64 1:3.2~ubuntu1 [3466 B] Get:40 http://ftpmaster.internal/ubuntu noble/universe amd64 ruby-asciidoctor all 2.0.20-1 [174 kB] Get:41 http://ftpmaster.internal/ubuntu noble/universe amd64 asciidoctor all 2.0.20-1 [44.2 kB] Get:42 http://ftpmaster.internal/ubuntu noble/main amd64 m4 amd64 1.4.19-4 [243 kB] Get:43 http://ftpmaster.internal/ubuntu noble/main amd64 autoconf all 2.71-3 [339 kB] Get:44 http://ftpmaster.internal/ubuntu noble/main amd64 autotools-dev all 20220109.1 [44.9 kB] Get:45 http://ftpmaster.internal/ubuntu noble/main amd64 automake all 1:1.16.5-1.3ubuntu1 [558 kB] Get:46 http://ftpmaster.internal/ubuntu noble/main amd64 autopoint all 0.21-14ubuntu1 [422 kB] Get:47 http://ftpmaster.internal/ubuntu noble-proposed/universe amd64 libbamtools2.5.2 amd64 2.5.2+dfsg-5 [137 kB] Get:48 http://ftpmaster.internal/ubuntu noble/main amd64 libjsoncpp25 amd64 1.9.5-6 [82.3 kB] Get:49 http://ftpmaster.internal/ubuntu noble-proposed/universe amd64 bamtools amd64 2.5.2+dfsg-5 [174 kB] Get:50 http://ftpmaster.internal/ubuntu noble/main amd64 libdebhelper-perl all 13.14.1ubuntu5 [89.8 kB] Get:51 http://ftpmaster.internal/ubuntu noble/main amd64 libtool all 2.4.7-7 [166 kB] Get:52 http://ftpmaster.internal/ubuntu noble/main amd64 dh-autoreconf all 20 [16.1 kB] Get:53 http://ftpmaster.internal/ubuntu noble/main amd64 libarchive-zip-perl all 1.68-1 [90.2 kB] Get:54 http://ftpmaster.internal/ubuntu noble/main amd64 libsub-override-perl all 0.10-1 [10.0 kB] Get:55 http://ftpmaster.internal/ubuntu noble/main amd64 libfile-stripnondeterminism-perl all 1.13.1-1 [18.1 kB] Get:56 http://ftpmaster.internal/ubuntu noble/main amd64 dh-strip-nondeterminism all 1.13.1-1 [5362 B] Get:57 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libdw1t64 amd64 0.190-1.1build3 [261 kB] Get:58 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 debugedit amd64 1:5.0-5build1 [46.1 kB] Get:59 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 dwz amd64 0.15-1build6 [115 kB] Get:60 http://ftpmaster.internal/ubuntu noble/main amd64 gettext amd64 0.21-14ubuntu1 [864 kB] Get:61 http://ftpmaster.internal/ubuntu noble/main amd64 intltool-debian all 0.35.0+20060710.6 [23.2 kB] Get:62 http://ftpmaster.internal/ubuntu noble/main amd64 po-debconf all 1.0.21+nmu1 [233 kB] Get:63 http://ftpmaster.internal/ubuntu noble/main amd64 debhelper all 13.14.1ubuntu5 [869 kB] Get:64 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libbrotli1 amd64 1.1.0-2build2 [331 kB] Get:65 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libfreetype6 amd64 2.13.2+dfsg-1build3 [402 kB] Get:66 http://ftpmaster.internal/ubuntu noble/main amd64 fonts-dejavu-mono all 2.37-8 [502 kB] Get:67 http://ftpmaster.internal/ubuntu noble/main amd64 fonts-dejavu-core all 2.37-8 [835 kB] Get:68 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 fontconfig-config amd64 2.15.0-1.1ubuntu2 [37.3 kB] Get:69 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libfontconfig1 amd64 2.15.0-1.1ubuntu2 [139 kB] Get:70 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 fontconfig amd64 2.15.0-1.1ubuntu2 [180 kB] Get:71 http://ftpmaster.internal/ubuntu noble/universe amd64 libbambamc0 amd64 0.0.50-6 [39.4 kB] Get:72 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 zlib1g-dev amd64 1:1.3.dfsg-3.1ubuntu2 [894 kB] Get:73 http://ftpmaster.internal/ubuntu noble-proposed/universe amd64 libbamtools-dev amd64 2.5.2+dfsg-5 [240 kB] Get:74 http://ftpmaster.internal/ubuntu noble/main amd64 libblas3 amd64 3.12.0-3 [238 kB] Get:75 http://ftpmaster.internal/ubuntu noble/main amd64 libpixman-1-0 amd64 0.42.2-1 [268 kB] Get:76 http://ftpmaster.internal/ubuntu noble/main amd64 libxcb-render0 amd64 1.15-1 [16.3 kB] Get:77 http://ftpmaster.internal/ubuntu noble/main amd64 libxcb-shm0 amd64 1.15-1 [5740 B] Get:78 http://ftpmaster.internal/ubuntu noble/main amd64 libxrender1 amd64 1:0.9.10-1.1 [20.0 kB] Get:79 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libcairo2 amd64 1.18.0-3 [566 kB] Get:80 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-5ubuntu2 [20.2 kB] Get:81 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-5ubuntu2 [53.2 kB] Get:82 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libldap2 amd64 2.6.7+dfsg-1~exp1ubuntu7 [195 kB] Get:83 http://ftpmaster.internal/ubuntu noble-updates/main amd64 libpsl5 amd64 0.21.2-1build1 [56.8 kB] Get:84 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2build7 [56.3 kB] Get:85 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libssh-4 amd64 0.10.6-2build2 [188 kB] Get:86 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libcurl3t64-gnutls amd64 8.5.0-2ubuntu9 [333 kB] Get:87 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libcurl4-gnutls-dev amd64 8.5.0-2ubuntu9 [438 kB] Get:88 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libcurl4t64 amd64 8.5.0-2ubuntu9 [340 kB] Get:89 http://ftpmaster.internal/ubuntu noble/main amd64 libdatrie1 amd64 0.2.13-3 [20.9 kB] Get:90 http://ftpmaster.internal/ubuntu noble/main amd64 libdeflate0 amd64 1.19-1 [43.7 kB] Get:91 http://ftpmaster.internal/ubuntu noble/main amd64 libdeflate-dev amd64 1.19-1 [50.9 kB] Get:92 http://ftpmaster.internal/ubuntu noble/universe amd64 libfile-copy-link-perl all 0.140-5 [12.3 kB] Get:93 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libgfortran5 amd64 14-20240330-1ubuntu2 [930 kB] Get:94 http://ftpmaster.internal/ubuntu noble/main amd64 libgraphite2-3 amd64 1.3.14-2 [83.1 kB] Get:95 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libharfbuzz0b amd64 8.3.0-2build2 [469 kB] Get:96 http://ftpmaster.internal/ubuntu noble/universe amd64 libhtscodecs2 amd64 1.6.0-1 [98.9 kB] Get:97 http://ftpmaster.internal/ubuntu noble-proposed/universe amd64 libhts3t64 amd64 1.19+ds-1.1build3 [437 kB] Get:98 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 liblzma-dev amd64 5.6.1+really5.4.5-1build1 [176 kB] Get:99 http://ftpmaster.internal/ubuntu noble-proposed/universe amd64 libhts-dev amd64 1.19+ds-1.1build3 [5916 kB] Get:100 http://ftpmaster.internal/ubuntu noble/main amd64 x11-common all 1:7.7+23ubuntu2 [23.4 kB] Get:101 http://ftpmaster.internal/ubuntu noble/main amd64 libice6 amd64 2:1.0.10-1build2 [42.6 kB] Get:102 http://ftpmaster.internal/ubuntu noble/main amd64 libjpeg-turbo8 amd64 2.1.5-2ubuntu1 [147 kB] Get:103 http://ftpmaster.internal/ubuntu noble/main amd64 libjpeg8 amd64 8c-2ubuntu11 [2148 B] Get:104 http://ftpmaster.internal/ubuntu noble/main amd64 liblapack3 amd64 3.12.0-3 [2649 kB] Get:105 http://ftpmaster.internal/ubuntu noble/main amd64 liblerc4 amd64 4.0.0+ds-4ubuntu1 [184 kB] Get:106 http://ftpmaster.internal/ubuntu noble/main amd64 libthai-data all 0.1.29-2 [158 kB] Get:107 http://ftpmaster.internal/ubuntu noble/main amd64 libthai0 amd64 0.1.29-2 [18.8 kB] Get:108 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libpango-1.0-0 amd64 1.52.1+ds-1build1 [231 kB] Get:109 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libpangoft2-1.0-0 amd64 1.52.1+ds-1build1 [42.5 kB] Get:110 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libpangocairo-1.0-0 amd64 1.52.1+ds-1build1 [28.8 kB] Get:111 http://ftpmaster.internal/ubuntu noble/main amd64 libpaper1 amd64 1.1.29 [13.4 kB] Get:112 http://ftpmaster.internal/ubuntu noble/main amd64 libpaper-utils amd64 1.1.29 [8658 B] Get:113 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libsharpyuv0 amd64 1.3.2-0.4build3 [15.8 kB] Get:114 http://ftpmaster.internal/ubuntu noble/main amd64 libsm6 amd64 2:1.2.3-1build2 [16.7 kB] Get:115 http://ftpmaster.internal/ubuntu noble-proposed/universe amd64 libtabixpp0t64 amd64 1.1.2-2.1build1 [10.8 kB] Get:116 http://ftpmaster.internal/ubuntu noble-proposed/universe amd64 libtabixpp-dev amd64 1.1.2-2.1build1 [8960 B] Get:117 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libtcl8.6 amd64 8.6.14+dfsg-1build1 [988 kB] Get:118 http://ftpmaster.internal/ubuntu noble/main amd64 libjbig0 amd64 2.1-6.1ubuntu1 [29.3 kB] Get:119 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libwebp7 amd64 1.3.2-0.4build3 [230 kB] Get:120 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libtiff6 amd64 4.5.1+git230720-4ubuntu2 [199 kB] Get:121 http://ftpmaster.internal/ubuntu noble/main amd64 libxft2 amd64 2.3.6-1 [44.5 kB] Get:122 http://ftpmaster.internal/ubuntu noble/main amd64 libxss1 amd64 1:1.2.3-1build2 [8476 B] Get:123 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libtk8.6 amd64 8.6.14-1build1 [779 kB] Get:124 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libxt6t64 amd64 1:1.2.1-1.2build1 [171 kB] Get:125 http://ftpmaster.internal/ubuntu noble/main amd64 zip amd64 3.0-13 [176 kB] Get:126 http://ftpmaster.internal/ubuntu noble/main amd64 unzip amd64 6.0-28ubuntu3 [174 kB] Get:127 http://ftpmaster.internal/ubuntu noble/main amd64 xdg-utils all 1.1.3-4.1ubuntu3 [62.0 kB] Get:128 http://ftpmaster.internal/ubuntu noble-proposed/universe amd64 r-base-core amd64 4.3.3-2build2 [27.1 MB] Get:129 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-boot all 1.3-30-1 [619 kB] Get:130 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-cluster amd64 2.1.6-1 [554 kB] Get:131 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-foreign amd64 0.8.86-1 [242 kB] Get:132 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-mass amd64 7.3-60.0.1-1 [1119 kB] Get:133 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-kernsmooth amd64 2.23-22-1 [91.7 kB] Get:134 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-lattice amd64 0.22-5-1 [1342 kB] Get:135 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-nlme amd64 3.1.164-1 [2260 kB] Get:136 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-matrix amd64 1.6-5-1 [3830 kB] Get:137 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-mgcv amd64 1.9-1-1 [3252 kB] Get:138 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-survival amd64 3.5-8-1 [6120 kB] Get:139 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-rpart amd64 4.1.23-1 [661 kB] Get:140 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-class amd64 7.3-22-2 [88.3 kB] Get:141 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-nnet amd64 7.3-19-2 [112 kB] Get:142 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-spatial amd64 7.3-17-1 [132 kB] Get:143 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-codetools all 0.2-19-1 [90.5 kB] Get:144 http://ftpmaster.internal/ubuntu noble-proposed/universe amd64 r-recommended all 4.3.3-2build2 [2636 B] Get:145 http://ftpmaster.internal/ubuntu noble-proposed/universe amd64 r-base all 4.3.3-2build2 [9304 B] Get:146 http://ftpmaster.internal/ubuntu noble-updates/universe amd64 samtools amd64 1.19.2-1 [593 kB] Get:147 http://ftpmaster.internal/ubuntu noble/universe amd64 smalt amd64 0.7.6-13 [101 kB] Get:148 http://ftpmaster.internal/ubuntu noble/universe amd64 snpomatic amd64 1.0-7 [82.4 kB] Get:149 http://ftpmaster.internal/ubuntu noble-proposed/universe amd64 tabix amd64 1.19+ds-1.1build3 [510 kB] Preconfiguring packages ... Fetched 98.2 MB in 1s (88.5 MB/s) dpkg: libreadline8:amd64: dependency problems, but removing anyway as you requested: gpgconf depends on libreadline8 (>= 6.0). gpg depends on libreadline8 (>= 6.0). (Reading database ... 15814 files and directories currently installed.) Removing libreadline8:amd64 (8.2-3) ... Selecting previously unselected package libreadline8t64:amd64. (Reading database ... 15802 files and directories currently installed.) Preparing to unpack .../000-libreadline8t64_8.2-4build1_amd64.deb ... Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8 to /lib/x86_64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8.2 to /lib/x86_64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8 to /lib/x86_64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8.2 to /lib/x86_64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:amd64 (8.2-4build1) ... Selecting previously unselected package libbsd0:amd64. Preparing to unpack .../001-libbsd0_0.12.1-1build1_amd64.deb ... Unpacking libbsd0:amd64 (0.12.1-1build1) ... Selecting previously unselected package libelf1t64:amd64. Preparing to unpack .../002-libelf1t64_0.190-1.1build3_amd64.deb ... Unpacking libelf1t64:amd64 (0.190-1.1build3) ... Selecting previously unselected package libexpat1:amd64. 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Setting up libbrotli1:amd64 (1.1.0-2build2) ... Setting up libmagic1t64:amd64 (1:5.45-3build1) ... Setting up x11-common (1:7.7+23ubuntu2) ... Running in chroot, ignoring request. invoke-rc.d: policy-rc.d denied execution of start. Setting up libnghttp2-14:amd64 (1.59.0-1build2) ... Setting up libdeflate0:amd64 (1.19-1) ... Setting up gettext-base (0.21-14ubuntu1) ... Setting up m4 (1.4.19-4) ... Setting up rubygems-integration (1.18) ... Setting up file (1:5.45-3build1) ... Setting up libjbig0:amd64 (2.1-6.1ubuntu1) ... Setting up libelf1t64:amd64 (0.190-1.1build3) ... Setting up libdw1t64:amd64 (0.190-1.1build3) ... Setting up libsasl2-modules-db:amd64 (2.1.28+dfsg1-5ubuntu2) ... Setting up zip (3.0-13) ... Setting up autotools-dev (20220109.1) ... Setting up libglib2.0-0t64:amd64 (2.80.0-6build1) ... No schema files found: doing nothing. 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Setting up xdg-utils (1.1.3-4.1ubuntu3) ... update-alternatives: using /usr/bin/xdg-open to provide /usr/bin/open (open) in auto mode Setting up libldap2:amd64 (2.6.7+dfsg-1~exp1ubuntu7) ... Setting up libjpeg8:amd64 (8c-2ubuntu11) ... Setting up automake (1:1.16.5-1.3ubuntu1) ... 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 smalt (0.7.6-13) ... Setting up libpaper1:amd64 (1.1.29) ... Creating config file /etc/papersize with new version Setting up libice6:amd64 (2:1.0.10-1build2) ... Setting up libxdmcp6:amd64 (1:1.1.3-0ubuntu5) ... Setting up liblapack3:amd64 (3.12.0-3) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode Setting up libxcb1:amd64 (1.15-1) ... Setting up gettext (0.21-14ubuntu1) ... Setting up libcurl4t64:amd64 (8.5.0-2ubuntu9) ... Setting up libtool (2.4.7-7) ... Setting up libxcb-render0:amd64 (1.15-1) ... Setting up fontconfig-config (2.15.0-1.1ubuntu2) ... Setting up libedit2:amd64 (3.1-20230828-1) ... Setting up libcurl3t64-gnutls:amd64 (8.5.0-2ubuntu9) ... Setting up libxcb-shm0:amd64 (1.15-1) ... Setting up libpaper-utils (1.1.29) ... Setting up libcurl4-gnutls-dev:amd64 (8.5.0-2ubuntu9) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up libthai0:amd64 (0.1.29-2) ... Setting up libbamtools-dev:amd64 (2.5.2+dfsg-5) ... Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up groff-base (1.23.0-3build2) ... Setting up libtiff6:amd64 (4.5.1+git230720-4ubuntu2) ... Setting up libhts3t64:amd64 (1.19+ds-1.1build3) ... Setting up libx11-6:amd64 (2:1.8.7-1) ... Setting up libfontconfig1:amd64 (2.15.0-1.1ubuntu2) ... Setting up libsm6:amd64 (2:1.2.3-1build2) ... Setting up fontconfig (2.15.0-1.1ubuntu2) ... Regenerating fonts cache... done. Setting up libxrender1:amd64 (1:0.9.10-1.1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libpango-1.0-0:amd64 (1.52.1+ds-1build1) ... Setting up libxext6:amd64 (2:1.3.4-1build1) ... Setting up libhts-dev:amd64 (1.19+ds-1.1build3) ... Setting up man-db (2.12.0-4build1) ... 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 libcairo2:amd64 (1.18.0-3) ... Setting up samtools (1.19.2-1) ... Setting up libxt6t64:amd64 (1:1.2.1-1.2build1) ... Setting up libtabixpp0t64:amd64 (1.1.2-2.1build1) ... Setting up libxss1:amd64 (1:1.2.3-1build2) ... Setting up libpangoft2-1.0-0:amd64 (1.52.1+ds-1build1) ... Setting up libpangocairo-1.0-0:amd64 (1.52.1+ds-1build1) ... Setting up libxft2:amd64 (2.3.6-1) ... Setting up libtk8.6:amd64 (8.6.14-1build1) ... Setting up debhelper (13.14.1ubuntu5) ... Setting up r-base-core (4.3.3-2build2) ... Creating config file /etc/R/Renviron with new version Setting up r-cran-lattice (0.22-5-1) ... Setting up r-cran-nlme (3.1.164-1) ... Setting up libtabixpp-dev:amd64 (1.1.2-2.1build1) ... Setting up r-cran-cluster (2.1.6-1) ... Setting up r-cran-nnet (7.3-19-2) ... Setting up r-cran-codetools (0.2-19-1) ... Setting up r-cran-boot (1.3-30-1) ... Setting up r-cran-spatial (7.3-17-1) ... Setting up r-cran-mass (7.3-60.0.1-1) ... Setting up r-cran-foreign (0.8.86-1) ... Setting up r-cran-matrix (1.6-5-1) ... Setting up r-cran-kernsmooth (2.23-22-1) ... Setting up r-cran-mgcv (1.9-1-1) ... Setting up r-cran-class (7.3-22-2) ... Setting up r-cran-survival (3.5-8-1) ... Setting up r-cran-rpart (4.1.23-1) ... Setting up r-recommended (4.3.3-2build2) ... Setting up r-base (4.3.3-2build2) ... Setting up libruby:amd64 (1:3.2~ubuntu1) ... Setting up ruby-sdbm:amd64 (1.0.0-5build4) ... Setting up libruby3.2:amd64 (3.2.3-1build3) ... Setting up ruby3.2 (3.2.3-1build3) ... Setting up ruby (1:3.2~ubuntu1) ... Setting up ruby-asciidoctor (2.0.20-1) ... Setting up rake (13.0.6-3) ... Setting up asciidoctor (2.0.20-1) ... Setting up sbuild-build-depends-main-dummy (0.invalid.0) ... Setting up ruby-rubygems (3.4.20-1) ... Processing triggers for libc-bin (2.39-0ubuntu8) ... +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (amd64 included in any) +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 5.4.0-173-generic #191-Ubuntu SMP Fri Feb 2 13:55:07 UTC 2024 amd64 (x86_64) Toolchain package versions: binutils_2.42-4ubuntu2 dpkg-dev_1.22.6ubuntu6 g++-13_13.2.0-23ubuntu3 gcc-13_13.2.0-23ubuntu3 libc6-dev_2.39-0ubuntu8 libstdc++-13-dev_13.2.0-23ubuntu3 libstdc++6_14-20240330-1ubuntu2 linux-libc-dev_6.8.0-11.11 Package versions: adduser_3.137ubuntu1 advancecomp_2.5-1 apt_2.7.14build2 apt-utils_2.7.14build2 asciidoctor_2.0.20-1 autoconf_2.71-3 automake_1:1.16.5-1.3ubuntu1 autopoint_0.21-14ubuntu1 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xdg-utils_1.1.3-4.1ubuntu3 xz-utils_5.6.1+really5.4.5-1build1 zip_3.0-13 zlib1g_1:1.3.dfsg-3.1ubuntu2 zlib1g-dev_1:1.3.dfsg-3.1ubuntu2 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: reapr Binary: reapr Architecture: any Version: 1.0.18+dfsg-5ubuntu2 Maintainer: Ubuntu Developers Uploaders: Sascha Steinbiss Homepage: https://www.sanger.ac.uk/science/tools/reapr Standards-Version: 4.4.0 Vcs-Browser: https://salsa.debian.org/med-team/reapr Vcs-Git: https://salsa.debian.org/med-team/reapr.git Testsuite: autopkgtest Testsuite-Triggers: samtools Build-Depends: debhelper-compat (= 12), libbamtools-dev, libtabixpp-dev, libhts-dev (>= 1.3), zlib1g-dev, asciidoctor, samtools (>= 1.3), bamtools, smalt, r-base, snpomatic, tabix, libfile-copy-link-perl Package-List: reapr deb science optional arch=any Checksums-Sha1: 3534f93653fc8eb621226e51ef212835b1281af9 74636 reapr_1.0.18+dfsg.orig.tar.gz f9b3b0b928b81a5564c0490b2c3e6a95f6b9ba1d 319936 reapr_1.0.18+dfsg-5ubuntu2.debian.tar.xz Checksums-Sha256: 70a9c252474fbbd36360c49589af18ca1599289eff2e98fb8cb7614583cb28a6 74636 reapr_1.0.18+dfsg.orig.tar.gz b342659df4cc757c69916aef85aeed91147e34ca9ef43fa61d727b29ad2d4e6e 319936 reapr_1.0.18+dfsg-5ubuntu2.debian.tar.xz Files: 061dfbfe97a0bdffe3a4b9e4be8142d3 74636 reapr_1.0.18+dfsg.orig.tar.gz 5de139cf1bf149e6c91f6a9cde5d21b0 319936 reapr_1.0.18+dfsg-5ubuntu2.debian.tar.xz Original-Maintainer: Debian Med Packaging Team -----BEGIN PGP SIGNATURE----- iQIzBAEBCgAdFiEEoIn7Nqr72tWswTJQafeQFxohCYQFAmYKYVwACgkQafeQFxoh CYQk+w/9GTdwf6KENxr3s0OEapD7si5GwOtQMqf7ky4oo2RIObIDXyGf971kAADc 5CBH2APxkuhG53Fxx1C+NqM2VvQIH/bTqQpDu4WBAbfstnx1r1DaRVAtGBqEhdU+ 42eOmm4NDybRNm9Uo3RUF89SmjyGuPHA6vv0JtLoGYdSX8FAyP+n/6gRxf4qth64 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info: using patch list from debian/patches/series dpkg-source: info: applying spelling dpkg-source: info: applying use_shared_libs dpkg-source: info: applying hardening dpkg-source: info: applying fix_sort_samtools13 dpkg-source: info: applying ld_as_needed Check disk space ---------------- Sufficient free space for build User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf DEB_BUILD_OPTIONS=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-28010610 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-28010610 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-28010610 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 reapr dpkg-buildpackage: info: source version 1.0.18+dfsg-5ubuntu2 dpkg-buildpackage: info: source distribution noble dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 fakeroot debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/<>' rm -rf /<>/debian/man_src/*.html /<>/debian/man_src/*.? rm -rf /<>/debian/man rm -rf /<>/debian/test dh_auto_clean -- make[1]: Leaving directory '/<>' dh_clean debian/rules build dh build dh_update_autotools_config dh_autoreconf debian/rules override_dh_auto_build make[1]: Entering directory '/<>' cd src && /usr/bin/make make[2]: Entering directory '/<>/src' g++ -Wdate-time -D_FORTIFY_SOURCE=3 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/reapr-1.0.18+dfsg-5ubuntu2 -Wall -O3 -I /usr/include/bamtools -I /usr/include -c errorWindow.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=3 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/reapr-1.0.18+dfsg-5ubuntu2 -Wall -O3 -I /usr/include/bamtools -I /usr/include -c utils.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=3 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/reapr-1.0.18+dfsg-5ubuntu2 -Wall -O3 -I /usr/include/bamtools -I /usr/include -c histogram.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=3 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/reapr-1.0.18+dfsg-5ubuntu2 -Wall -O3 -I /usr/include/bamtools -I /usr/include -c task_score.cpp task_score.cpp: In function ‘int main(int, char**)’: task_score.cpp:235:79: warning: variable ‘p’ set but not used [-Wunused-but-set-variable] 235 | map > >::iterator p = globalGaps.find(currentRefID); | ^ g++ -o task_score -Wdate-time -D_FORTIFY_SOURCE=3 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/reapr-1.0.18+dfsg-5ubuntu2 -Wall -O3 -I /usr/include/bamtools -I /usr/include task_score.o errorWindow.o utils.o histogram.o -lbamtools -ltabixpp -lhts -lz -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now g++ -Wdate-time -D_FORTIFY_SOURCE=3 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/reapr-1.0.18+dfsg-5ubuntu2 -Wall -O3 -I /usr/include/bamtools -I /usr/include -c trianglePlot.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=3 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/reapr-1.0.18+dfsg-5ubuntu2 -Wall -O3 -I /usr/include/bamtools -I /usr/include -c coveragePlot.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=3 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/reapr-1.0.18+dfsg-5ubuntu2 -Wall -O3 -I /usr/include/bamtools -I /usr/include -c fasta.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=3 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/reapr-1.0.18+dfsg-5ubuntu2 -Wall -O3 -I /usr/include/bamtools -I /usr/include -c task_stats.cpp task_stats.cpp: In function ‘main’: task_stats.cpp:262:34: warning: ‘ti_perfect’ may be used uninitialized [-Wmaybe-uninitialized] 262 | getPerfectMapping(ti_perfect, currentRefIDstring, stats.perfectCov, references[currentRefID].RefLength); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ task_stats.cpp:150:12: note: ‘ti_perfect’ was declared here 150 | Tabix* ti_perfect; | ^~~~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=3 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/reapr-1.0.18+dfsg-5ubuntu2 -Wall -O3 -I /usr/include/bamtools -I /usr/include task_stats.o trianglePlot.o coveragePlot.o fasta.o histogram.o utils.o -lbamtools -ltabixpp -lhts -lz -o task_stats -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now g++ -Wdate-time -D_FORTIFY_SOURCE=3 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/reapr-1.0.18+dfsg-5ubuntu2 -Wall -O3 -I /usr/include/bamtools -I /usr/include -c task_break.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=3 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/reapr-1.0.18+dfsg-5ubuntu2 -Wall -O3 -I /usr/include/bamtools -I /usr/include task_break.o -lbamtools fasta.o utils.o -lbamtools -ltabixpp -lhts -lz -o task_break -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now g++ -Wdate-time -D_FORTIFY_SOURCE=3 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/reapr-1.0.18+dfsg-5ubuntu2 -Wall -O3 -I /usr/include/bamtools -I /usr/include -c bam2fragCov.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=3 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/reapr-1.0.18+dfsg-5ubuntu2 -Wall -O3 -I /usr/include/bamtools -I /usr/include bam2fragCov.o -lbamtools coveragePlot.o utils.o -lbamtools -ltabixpp -lhts -lz -o bam2fragCov -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now g++ -Wdate-time -D_FORTIFY_SOURCE=3 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/reapr-1.0.18+dfsg-5ubuntu2 -Wall -O3 -I /usr/include/bamtools -I /usr/include -c bam2insert.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=3 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/reapr-1.0.18+dfsg-5ubuntu2 -Wall -O3 -I /usr/include/bamtools -I /usr/include bam2insert.o -lbamtools histogram.o utils.o -lbamtools -ltabixpp -lhts -lz -o bam2insert -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now g++ -Wdate-time -D_FORTIFY_SOURCE=3 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/reapr-1.0.18+dfsg-5ubuntu2 -Wall -O3 -I /usr/include/bamtools -I /usr/include -c bam2fcdEstimate.cpp bam2fcdEstimate.cpp: In function ‘int main(int, char**)’: bam2fcdEstimate.cpp:84:34: warning: comparison of integer expressions of different signedness: ‘int32_t’ {aka ‘int’} and ‘long unsigned int’ [-Wsign-compare] 84 | while (bamAlign.Position > triplot.centreCoord()) | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ bam2fcdEstimate.cpp: In function ‘void initialiseFCDHists(std::vector&, CmdLineOptions&)’: bam2fcdEstimate.cpp:210:33: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘long int’ [-Wsign-compare] 210 | for (unsigned long i = 0; i <= ops.maxInsert; i++) | ~~^~~~~~~~~~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=3 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/reapr-1.0.18+dfsg-5ubuntu2 -Wall -O3 -I /usr/include/bamtools -I /usr/include bam2fcdEstimate.o -lbamtools histogram.o utils.o trianglePlot.o -ltabixpp -lhts -lz -o bam2fcdEstimate -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now g++ -Wdate-time -D_FORTIFY_SOURCE=3 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/reapr-1.0.18+dfsg-5ubuntu2 -Wall -O3 -I /usr/include/bamtools -I /usr/include -c make_plots.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=3 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/reapr-1.0.18+dfsg-5ubuntu2 -Wall -O3 -I /usr/include/bamtools -I /usr/include make_plots.o -o make_plots -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now g++ -Wdate-time -D_FORTIFY_SOURCE=3 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/reapr-1.0.18+dfsg-5ubuntu2 -Wall -O3 -I /usr/include/bamtools -I /usr/include -c fa2gaps.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=3 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/reapr-1.0.18+dfsg-5ubuntu2 -Wall -O3 -I /usr/include/bamtools -I /usr/include fa2gaps.o fasta.o -o fa2gaps -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now g++ -Wdate-time -D_FORTIFY_SOURCE=3 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/reapr-1.0.18+dfsg-5ubuntu2 -Wall -O3 -I /usr/include/bamtools -I /usr/include -c fa2gc.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=3 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/reapr-1.0.18+dfsg-5ubuntu2 -Wall -O3 -I /usr/include/bamtools -I /usr/include fa2gc.o fasta.o -o fa2gc -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now g++ -Wdate-time -D_FORTIFY_SOURCE=3 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/reapr-1.0.18+dfsg-5ubuntu2 -Wall -O3 -I /usr/include/bamtools -I /usr/include -c scaff2contig.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=3 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/reapr-1.0.18+dfsg-5ubuntu2 -Wall -O3 -I /usr/include/bamtools -I /usr/include scaff2contig.o fasta.o -o scaff2contig -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now g++ -Wdate-time -D_FORTIFY_SOURCE=3 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/reapr-1.0.18+dfsg-5ubuntu2 -Wall -O3 -I /usr/include/bamtools -I /usr/include -c n50.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=3 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/reapr-1.0.18+dfsg-5ubuntu2 -Wall -O3 -I /usr/include/bamtools -I /usr/include n50.o fasta.o -o n50 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now g++ -Wdate-time -D_FORTIFY_SOURCE=3 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/reapr-1.0.18+dfsg-5ubuntu2 -Wall -O3 -I /usr/include/bamtools -I /usr/include -c task_gapresize.cpp task_gapresize.cpp: In function ‘int main(int, char**)’: task_gapresize.cpp:129:127: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘int64_t’ {aka ‘long int’} [-Wsign-compare] 129 | if (!bamAlign.IsReverseStrand() && pairOrientation == INNIE && bamAlign.InsertSize > 0 && gapIter->second < fragEnd && fragEnd <= gapIter->second + options.maxFragLength) | ~~~~~~~~~~~~~~~~^~~~~~~~~ task_gapresize.cpp:129:148: warning: comparison of integer expressions of different signedness: ‘int64_t’ {aka ‘long int’} and ‘long unsigned int’ [-Wsign-compare] 129 | if (!bamAlign.IsReverseStrand() && pairOrientation == INNIE && bamAlign.InsertSize > 0 && gapIter->second < fragEnd && fragEnd <= gapIter->second + options.maxFragLength) | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=3 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/reapr-1.0.18+dfsg-5ubuntu2 -Wall -O3 -I /usr/include/bamtools -I /usr/include task_gapresize.o -lbamtools utils.o trianglePlot.o fasta.o -ltabixpp -lhts -lz -o task_gapresize -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now g++ -Wdate-time -D_FORTIFY_SOURCE=3 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/reapr-1.0.18+dfsg-5ubuntu2 -Wall -O3 -I /usr/include/bamtools -I /usr/include -c task_fcdrate.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=3 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/reapr-1.0.18+dfsg-5ubuntu2 -Wall -O3 -I /usr/include/bamtools -I /usr/include task_fcdrate.o -ltabixpp -lhts -lz histogram.o utils.o -lbamtools -o task_fcdrate -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now g++ -Wdate-time -D_FORTIFY_SOURCE=3 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/reapr-1.0.18+dfsg-5ubuntu2 -Wall -O3 -I /usr/include/bamtools -I /usr/include -c bam2perfect.cpp bam2perfect.cpp: In function ‘void writeAlignments(std::multimap&, BamTools::BamWriter&, long unsigned int)’: bam2perfect.cpp:213:32: warning: comparison of integer expressions of different signedness: ‘int32_t’ {aka ‘int’} and ‘long unsigned int’ [-Wsign-compare] 213 | if (p->second.Position >= endPos) break; | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=3 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/reapr-1.0.18+dfsg-5ubuntu2 -Wall -O3 -I /usr/include/bamtools -I /usr/include bam2perfect.o -lbamtools utils.o -lbamtools -ltabixpp -lhts -lz -o bam2perfect -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now make[2]: Leaving directory '/<>/src' make[1]: Leaving directory '/<>' debian/rules override_dh_auto_test make[1]: Entering directory '/<>' mkdir /<>/debian/test ln -s /<>/src/reapr.pl /<>/debian/test/reapr PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/<>/src:/<>/debian/test /<>/debian/tests/test-example [wgsim] seed = 42 [wgsim_core] calculating the total length of the reference sequence... [wgsim_core] 1 sequences, total length: 1000111 foo 1384 T K + foo 4961 T W + foo 5885 - T - foo 9598 A C - foo 10177 G R + foo 11305 G K + foo 11592 G R + foo 13931 T - - foo 15907 C A - foo 17264 G K + foo 17780 A - - foo 18711 A W + foo 19249 T W + foo 19522 C S + foo 23053 T K + foo 23681 A R + foo 23730 C S + foo 24075 G S + foo 24555 G C - foo 26775 G K + foo 26896 C M + foo 27253 G K + foo 28210 T Y + foo 28224 A W + foo 28377 - G + foo 29035 G K + foo 29898 C M + foo 30274 A R + foo 30542 G K + foo 31566 A C - foo 32252 - A - foo 33303 T K + foo 33390 - G + foo 34073 A R + foo 34171 G R + foo 34718 T Y + foo 34801 - C + foo 35204 T W + foo 35342 G S + foo 35489 G T - foo 36153 A M + foo 36273 C S + foo 37356 G T - foo 37596 C S + foo 39308 T - - foo 40333 C G - foo 42295 T K + foo 42372 T Y + foo 44433 C G - foo 44630 - AG + foo 44902 T C - foo 47156 C A - foo 48210 C M + foo 48390 A R + foo 49652 C M + foo 52739 T Y + foo 52858 A M + foo 54737 A G - foo 55306 C T - foo 55434 C T - foo 59204 A W + foo 59300 G C - foo 59335 T Y + foo 59444 T - - foo 59531 C S + foo 59766 C Y + foo 61950 C S + foo 62887 G S + foo 63390 A G - foo 64365 G K + foo 64703 C S + foo 64932 C Y + foo 68383 - CG + foo 68464 A W + foo 68727 A W + foo 69080 A M + foo 72071 T C - foo 72720 - G - foo 73354 C T - foo 73637 G T - foo 74741 A M + foo 75101 C T - foo 75207 T K + foo 76400 T Y + foo 76780 A C - foo 77172 A W + foo 78385 C Y + foo 80705 C M + foo 82440 A R + foo 83021 G K + foo 83116 A - - foo 83846 T K + foo 84633 G S + foo 85891 G S + foo 87759 A C - foo 87778 T W + foo 88581 T K + foo 88606 T Y + foo 88880 A G - foo 89945 G C - foo 90728 T K + foo 91798 G R + foo 95957 G C - foo 96173 T W + foo 96665 A M + foo 98019 - G + foo 98131 A M + foo 98669 A R + foo 98719 G T - foo 99062 A W + foo 99590 A T - foo 100532 - TC + foo 103015 A W + foo 103172 G S + foo 103609 G R + foo 106549 T Y + foo 108808 C Y + foo 109191 G C - foo 111686 C G - foo 113436 C A - foo 113763 A W + foo 115671 C T - foo 117460 - A - foo 118193 G - - foo 118585 T K + foo 121219 A M + foo 121876 T K + foo 122071 T A - foo 124918 C G - foo 125300 G S + foo 125967 C S + foo 127443 G S + foo 127565 C Y + foo 128700 C A - foo 129912 G A - foo 130847 T W + foo 131677 G S + foo 132189 T C - foo 135878 CGGC - - foo 136825 T K + foo 138881 TGT - - foo 139288 A W + foo 141054 A W + foo 141055 - T + foo 141101 C S + foo 141404 A R + foo 142698 T C - foo 143990 C A - foo 144167 T Y + foo 144814 C Y + foo 146381 T Y + foo 146393 C A - foo 146510 A C - foo 147182 A W + foo 148783 T C - foo 149068 G S + foo 150208 T K + foo 151554 T W + foo 151709 C G - foo 153072 G R + foo 153307 T Y + foo 154050 G S + foo 154415 C S + foo 154594 G R + foo 155839 G T - foo 156106 G A - foo 159356 T W + foo 159926 A W + foo 160303 T K + foo 161323 C Y + foo 161904 G S + foo 162533 - ACC - foo 164738 C G - foo 165413 A R + foo 166944 C M + foo 167464 T Y + foo 168420 T C - foo 168579 A M + foo 168787 T W + foo 168959 A T - foo 169884 G S + foo 170032 G T - foo 172058 G K + foo 174942 A R + foo 175014 G K + foo 178406 G A - foo 179028 - A + foo 182394 C M + foo 182735 T Y + foo 183384 T K + foo 183893 - AT - foo 185360 G A - foo 185538 - G - foo 187948 G S + foo 188120 T G - foo 188179 T W + foo 188316 T Y + foo 189963 - G + foo 190093 C Y + foo 192220 C M + foo 192368 A W + foo 192782 T K + foo 193307 A R + foo 193501 G K + foo 194276 G S + foo 194930 C S + foo 196728 A W + foo 197559 G C - foo 198467 T W + foo 199042 C Y + foo 199259 AA - - foo 199687 TT - - foo 200287 C A - foo 200678 A R + foo 201208 C T - foo 201882 A - - foo 204456 T K + foo 206327 G R + foo 207311 G T - foo 209184 G A - foo 209279 C Y + foo 211459 C Y + foo 213807 T Y + foo 213846 T Y + foo 214635 A G - foo 214884 C A - foo 216244 A M + foo 216652 A M + foo 216745 T - - foo 216909 A T - foo 217579 A G - foo 217895 C Y + foo 218870 G K + foo 223098 T A - foo 223283 - C + foo 223666 C A - foo 224011 - C + foo 225681 C S + foo 227345 T C - foo 228778 T G - foo 229926 C - - foo 230778 T K + foo 230939 CG - - foo 231988 CT - - foo 234593 T W + foo 235496 C S + foo 235705 G K + foo 235758 A G - foo 236852 T C - foo 238790 A M + foo 238865 T K + foo 239329 A M + foo 239576 - C + foo 243058 G S + foo 244147 T - - foo 244462 C G - foo 245443 - A + foo 246544 C Y + foo 246744 T W + foo 247473 C M + foo 248129 C T - foo 249060 A C - foo 249515 G T - foo 250138 G S + foo 250567 C A - foo 254381 G R + foo 257864 C M + foo 257879 C Y + foo 259859 A M + foo 260643 C S + foo 261681 C G - foo 262645 T Y + foo 263279 A R + foo 263575 A - - foo 264587 - TA + foo 264689 T K + foo 265758 G K + foo 266272 A M + foo 268550 C M + foo 269986 G S + foo 270321 AC - - foo 273346 C S + foo 275367 C A - foo 277334 C G - foo 277629 G T - foo 278431 C Y + foo 281456 T Y + foo 281556 T G - foo 281737 G K + foo 282290 AC - - foo 282851 - C - foo 284405 A C - foo 288751 A C - foo 290501 TAAA - - foo 291315 A W + foo 291368 C - - foo 292154 A C - foo 292385 C M + foo 292555 G K + foo 297709 G C - foo 298183 A W + foo 298228 T W + foo 299902 T G - foo 302575 A T - foo 304823 G R + foo 305308 T Y + foo 305487 G S + foo 305697 G T - foo 306098 C G - foo 306882 T Y + foo 308201 A M + foo 308833 A T - foo 312033 A - - foo 312895 C G - foo 313889 C - - foo 315109 A R + foo 316083 C - - foo 316466 A R + foo 318040 G C - foo 319446 T C - foo 320236 C S + foo 320652 A - - foo 320716 T K + foo 323644 A - - foo 325359 G T - foo 329476 - CA + foo 329706 T G - foo 330181 T Y + foo 330703 C Y + foo 331315 G S + foo 332351 C A - foo 333408 A R + foo 333468 C S + foo 336247 A G - foo 336586 A M + foo 337364 G K + foo 337686 A T - foo 338043 A - - foo 338292 C G - foo 338962 A C - foo 339353 G K + foo 340647 - A + foo 341705 G R + foo 344283 C M + foo 345898 - AG - foo 347959 T - - foo 349162 C M + foo 352072 T Y + foo 354614 C Y + foo 359304 T - - foo 359312 - G + foo 360972 C S + foo 363857 C Y + foo 366226 A C - foo 367259 C M + foo 372502 T Y + foo 372747 A M + foo 375140 C S + foo 376298 T W + foo 376313 C - - foo 376760 T W + foo 378494 A W + foo 381137 T G - foo 381186 A R + foo 381701 A G - foo 382614 A W + foo 382761 C T - foo 382854 T C - foo 383201 C T - foo 385104 G S + foo 385233 - A + foo 386138 C T - foo 386316 A W + foo 387072 A R + foo 387642 - A + foo 388232 T C - foo 388890 GGG - - foo 390508 C S + foo 390625 C M + foo 391921 C G - foo 395256 G T - foo 395542 G S + foo 397015 A - - foo 397516 C Y + foo 397528 GC - - foo 398152 C T - foo 399802 A W + foo 400972 T K + foo 401419 - T + foo 401477 T W + foo 402437 A M + foo 402722 G R + foo 403452 C M + foo 404234 - A + foo 405344 A W + foo 407040 G S + foo 408483 G R + foo 408586 A C - foo 408721 A R + foo 409494 A M + foo 410078 A G - foo 411170 C A - foo 415342 T Y + foo 416265 C G - foo 417740 C A - foo 418622 C S + foo 420232 A W + foo 420288 T Y + foo 420908 A W + foo 421109 T A - foo 421357 A R + foo 422799 G A - foo 424383 C S + foo 424871 - GCA + foo 427273 T A - foo 429822 C M + foo 429846 T W + foo 432015 A G - foo 432414 G K + foo 433606 C Y + foo 433831 T Y + foo 437721 - A - foo 438402 G - - foo 438799 A T - foo 439422 C M + foo 440734 C A - foo 441840 T G - foo 442021 - C + foo 445021 T A - foo 445591 G A - foo 446138 T W + foo 447757 A W + foo 449156 T - - foo 449161 G K + foo 450114 A W + foo 450688 A W + foo 454421 C G - foo 454718 T Y + foo 455675 TC - - foo 461721 G R + foo 462526 G S + foo 467296 G A - foo 467510 G K + foo 468267 T K + foo 469118 G R + foo 469830 C Y + foo 471073 G T - foo 472056 G A - foo 472773 - A + foo 473046 G R + foo 473188 G A - foo 473742 C - - foo 474789 T A - foo 477763 G R + foo 478246 T W + foo 478975 T G - foo 479038 A R + foo 480275 T Y + foo 480317 G A - foo 481512 T K + foo 482069 G S + foo 482534 A R + foo 483760 C Y + foo 485281 T W + foo 486255 T C - foo 487038 T K + foo 487225 T A - foo 488012 C Y + foo 488795 T C - foo 490241 A R + foo 492595 - CGG + foo 493224 C A - foo 494284 A T - foo 495990 - T - foo 497306 A R + foo 497403 T Y + foo 499569 C Y + foo 499651 T K + foo 503139 T C - foo 504660 A R + foo 508679 C - - foo 513643 G K + foo 515668 CC - - foo 515836 G R + foo 516488 C S + foo 517602 G R + foo 517962 G K + foo 517975 T K + foo 519144 A T - foo 520068 T K + foo 520926 A W + foo 521562 C S + foo 522076 CG - - foo 522838 T Y + foo 523513 - C + foo 523907 - TA + foo 526271 T A - foo 526533 AC - - foo 526767 C Y + foo 528217 C Y + foo 531924 G S + foo 532333 - TT + foo 533132 C M + foo 534689 A T - foo 534779 A W + foo 535594 C A - foo 535795 G R + foo 538368 A R + foo 540879 G K + foo 542530 A - - foo 543620 G R + foo 544733 - C - foo 546300 - TT + foo 548196 A T - foo 548878 C M + foo 548885 G R + foo 549459 T K + foo 550908 A G - foo 551170 A - - foo 553130 T Y + foo 555293 T G - foo 556198 G R + foo 556355 A T - foo 557688 G K + foo 558415 G C - foo 558461 - G + foo 559287 T Y + foo 559465 C M + foo 560184 T W + foo 560252 T W + foo 562579 A M + foo 562961 G A - foo 566986 C A - foo 568134 C A - foo 569698 T C - foo 570180 T K + foo 570451 TG - - foo 570832 - A - foo 571589 A W + foo 572208 C M + foo 572871 C S + foo 574334 G - - foo 575673 T Y + foo 576797 G S + foo 578486 - C - foo 578494 C S + foo 579257 G A - foo 580103 G T - foo 580872 A W + foo 580925 G S + foo 580950 G C - foo 581637 T Y + foo 581654 A G - foo 582538 A T - foo 582691 C M + foo 582938 A W + foo 583104 T K + foo 584763 T W + foo 585723 T W + foo 588253 T Y + foo 588972 T C - foo 589438 - C - foo 591131 C Y + foo 591950 G R + foo 592194 T G - foo 592310 G S + foo 593892 G A - foo 598556 A - - foo 601660 G S + foo 602112 G T - foo 602412 T Y + foo 607282 - C + foo 607394 A M + foo 608438 A T - foo 609255 A W + foo 609365 - T + foo 611161 G K + foo 612224 C G - foo 614493 G R + foo 614601 G A - foo 614607 C Y + foo 619507 C M + foo 619798 T C - foo 621872 C T - foo 622375 C Y + foo 623208 - G - foo 624366 C A - foo 625320 - ACA - foo 626664 - G + foo 627140 T C - foo 627353 G T - foo 628714 T Y + foo 628744 A - - foo 629152 A G - foo 630110 T G - foo 631744 G K + foo 632763 C S + foo 634419 G - - foo 634459 A G - foo 634571 G A - foo 635366 - A + foo 635604 G T - foo 637057 T C - foo 637525 A T - foo 638412 A R + foo 640547 A W + foo 641514 T K + foo 642219 A R + foo 642427 A G - foo 642612 A R + foo 643553 T W + foo 647316 - T + foo 647598 C - - foo 651093 G A - foo 651718 G R + foo 652235 A G - foo 652579 A C - foo 653355 A W + foo 655174 C M + foo 655487 A M + foo 656849 G S + foo 661081 T K + foo 661134 G C - foo 661935 A W + foo 662010 A M + foo 662040 G R + foo 663030 A W + foo 663268 - C + foo 664991 T - - foo 665489 T K + foo 665555 C M + foo 665965 C Y + foo 668725 A C - foo 668834 - G - foo 668873 C S + foo 669654 T W + foo 671041 G S + foo 671485 T W + foo 671690 C M + foo 673022 G R + foo 674137 - T + foo 674782 A C - foo 676373 G T - foo 676793 T C - foo 677409 G S + foo 677536 - AA - foo 677620 G K + foo 677686 C Y + foo 678327 G S + foo 678704 G S + foo 678771 A C - foo 678866 C T - foo 679960 A W + foo 680447 - C + foo 682102 C T - foo 685497 T A - foo 686884 G S + foo 687324 ACA - - foo 687684 - AC + foo 687823 T C - foo 688590 G K + foo 690802 C M + foo 691388 T C - foo 691403 T G - foo 691790 G A - foo 692973 C A - foo 694058 G S + foo 694550 G R + foo 694968 T W + foo 695898 A T - foo 696721 C S + foo 696787 C S + foo 696935 A M + foo 698024 - C + foo 699813 A - - foo 700179 G R + foo 701421 A M + foo 701989 T A - foo 702862 C A - foo 707020 G A - foo 708420 A - - foo 708669 C G - foo 710521 T W + foo 711801 G C - foo 711913 T G - foo 715830 C M + foo 717664 TC - - foo 718845 A W + foo 719069 T Y + foo 719565 A W + foo 721136 T K + foo 726116 T K + foo 727809 T K + foo 728864 G K + foo 728918 G A - foo 730296 - T + foo 731988 C Y + foo 734658 A M + foo 734715 A W + foo 736618 C G - foo 737257 T Y + foo 740864 C A - foo 741640 G - - foo 741859 - TA - foo 742011 T K + foo 742237 A R + foo 742960 G K + foo 743731 G R + foo 743971 A W + foo 744635 T K + foo 746430 C G - foo 746489 - GC - foo 746881 C M + foo 756997 TC - - foo 757776 A M + foo 759870 A T - foo 760224 G K + foo 760799 G C - foo 761692 T C - foo 762569 G S + foo 763140 A G - foo 763842 - T - foo 764192 A M + foo 764334 G A - foo 764889 - AAT + foo 766464 G S + foo 768226 G A - foo 770272 T G - foo 771145 C Y + foo 772209 T A - foo 773672 T K + foo 773932 G C - foo 774658 C S + foo 775969 A M + foo 776816 T G - foo 777591 C Y + foo 777891 A M + foo 778164 C M + foo 778219 T W + foo 779260 G T - foo 779465 A W + foo 779779 G S + foo 780033 G K + foo 783243 C M + foo 783860 A R + foo 788345 A M + foo 789554 G - - foo 790025 G K + foo 791454 T K + foo 792009 C A - foo 792872 C G - foo 794616 T W + foo 795031 G R + foo 796919 C M + foo 797020 G S + foo 797042 G C - foo 797149 G A - foo 797177 A C - foo 799076 G C - foo 799580 G S + foo 800356 A R + foo 802297 G T - foo 802309 T Y + foo 802343 - C + foo 802769 A W + foo 803104 C G - foo 805819 C Y + foo 805972 T Y + foo 807503 T K + foo 807950 C M + foo 807994 - A - foo 809167 A G - foo 809658 A W + foo 810152 A M + foo 811506 G R + foo 813494 A M + foo 814035 G T - foo 814476 A W + foo 819399 T K + foo 820171 T W + foo 820445 G C - foo 822178 C G - foo 822504 C T - foo 823378 C M + foo 823591 CG - - foo 824229 C M + foo 824579 C T - foo 824858 C M + foo 826101 T K + foo 827593 C G - foo 827794 T Y + foo 828228 A M + foo 828367 T K + foo 828788 C M + foo 829002 C Y + foo 830345 C M + foo 831018 C A - foo 831459 T K + foo 832413 A T - foo 832782 T Y + foo 832908 T Y + foo 833130 T - - foo 833142 G S + foo 833241 G A - foo 836727 A T - foo 836829 G S + foo 838452 T G - foo 838543 A T - foo 838605 C M + foo 838954 G C - foo 841829 G K + foo 842324 - TC + foo 842996 - C + foo 844390 C A - foo 844793 A C - foo 844925 C A - foo 845082 G C - foo 846202 G R + foo 846707 A G - foo 848713 G A - foo 849372 C S + foo 849742 G A - foo 850499 C - - foo 850927 GT - - foo 851084 - G + foo 852247 A R + foo 852972 C A - foo 854808 T W + foo 855956 G K + foo 856225 G A - foo 856582 T K + foo 857351 C M + foo 857504 AC - - foo 858324 A T - foo 858858 T C - foo 859488 T Y + foo 862441 T Y + foo 863827 C Y + foo 864165 C A - foo 865997 C M + foo 866370 G S + foo 867653 G S + foo 867722 C Y + foo 868696 C M + foo 869005 T W + foo 869791 T Y + foo 875339 C Y + foo 875347 C M + foo 875584 T G - foo 876780 C T - foo 878368 A C - foo 878916 - CAG + foo 879005 A R + foo 880112 G T - foo 881021 - T - foo 881175 T W + foo 882168 - GGG + foo 882223 - G - foo 883033 TG - - foo 883381 C G - foo 884378 C - - foo 885075 A M + foo 885190 A W + foo 885568 A W + foo 885827 T Y + foo 887610 TG - - foo 889139 G R + foo 890978 T - - foo 891500 C Y + foo 892257 G C - foo 892642 G R + foo 892644 T W + foo 892757 C A - foo 893222 T - - foo 893348 T W + foo 894161 - C - foo 894447 A G - foo 894614 A W + foo 897817 T W + foo 899408 C S + foo 902450 A T - foo 902970 AT - - foo 905836 G K + foo 906524 GA - - foo 907484 A W + foo 907537 C M + foo 908515 G R + foo 908642 C T - foo 911145 T C - foo 912220 T Y + foo 912682 C Y + foo 914260 C S + foo 914757 T Y + foo 916413 G C - foo 916783 T G - foo 917033 G C - foo 917218 A - - foo 918225 G - - foo 918459 A - - foo 918732 A M + foo 919640 TC - - foo 920824 T W + foo 920836 G C - foo 924560 G R + foo 924659 GA - - foo 925868 T A - foo 928254 T G - foo 928369 - A - foo 928641 - AG + foo 929857 C M + foo 930211 T W + foo 930935 C T - foo 931986 A M + foo 932852 G T - foo 933965 T A - foo 935564 A W + foo 936034 T Y + foo 936221 AC - - foo 936670 C S + foo 936704 T A - foo 936786 T W + foo 939218 C S + foo 939312 A W + foo 939467 A W + foo 939934 C S + foo 941603 C Y + foo 942910 A W + foo 944654 T Y + foo 945301 A C - foo 945770 C T - foo 946078 G S + foo 948833 G K + foo 948999 A W + foo 949193 A R + foo 950276 C M + foo 950414 A W + foo 951285 G C - foo 953158 G R + foo 953287 A W + foo 954150 C G - foo 954258 G - - foo 955396 CC - - foo 956490 - AC + foo 958129 A R + foo 959027 T A - foo 959964 A W + foo 962042 A G - foo 962742 C G - foo 963306 T W + foo 963422 G K + foo 964082 G S + foo 965561 C S + foo 966531 T K + foo 967324 T W + foo 968419 - C - foo 969054 G - - foo 969158 G S + foo 972658 C M + foo 974266 T W + foo 974629 G K + foo 975034 A R + foo 975636 T W + foo 977078 - A - foo 978321 G T - foo 978595 C G - foo 979090 C M + foo 983855 TA - - foo 985725 T A - foo 988497 C Y + foo 990171 C M + foo 990804 - CA - foo 990941 T W + foo 991797 A W + foo 992469 A M + foo 994610 C Y + foo 998107 - T + foo 999725 G R + [REAPR smaltmap] Running: smalt index -k 13 -s 2 out.bam.tmp.12717.smaltmap.smalt_index foo1.fasta # Command line: smalt index -k 13 -s 2 out.bam.tmp.12717.smaltmap.smalt_index foo1.fasta # Reading sequences ... # Writing sequence set ... # Setting up hash index with collisions ... # word length = 13 bases, skip step = 2 bases ... # number of bits for key = 18 with 0 perfect bits # Counting keys ... # Counting k-tuples ... # Allocating k-tuple arrays ... # Counting k-tuple occurrences ... # Setting the k-tuple positions in index ... # Hash table is set up. # =-=-=-=-= Hash Index Stats =-=-=-=-= # Hash index with collisions. # Word length: 13 bases # Skip step: 2 bases # Number of hash keys: 262144 # Number of word positions: 499970 # Number of different words: 498076 # Maximum number of words per key: 11 # Number of keys without words: 39377 # =-=-= End of Hash Index Stats =-=-= # Writing table to file ... # smalt: Total elapsed wall clock time: 0 seconds [REAPR smaltmap] Running: smalt sample -u 1000 -o out.bam.tmp.12717.smaltmap.smalt_sample out.bam.tmp.12717.smaltmap.smalt_index foofq.1.fastq foofq.2.fastq # Command line: smalt sample -u 1000 -o out.bam.tmp.12717.smaltmap.smalt_sample out.bam.tmp.12717.smaltmap.smalt_index foofq.1.fastq foofq.2.fastq # Opening read files ... # Reading reference sequences ... # Reading hash table ... # =-=-=-=-= Hash Index Stats =-=-=-=-= # Hash index with collisions. # Word length: 13 bases # Skip step: 2 bases # Number of hash keys: 262144 # Number of word positions: 499970 # Number of different words: 498076 # Maximum number of words per key: 11 # Number of keys without words: 39377 # =-=-= End of Hash Index Stats =-=-= # Check of read pairs ok ... # Mate names match ... # Sampling insert size distribution ... # Processed 9999 read pairs. # smalt: Time spent setting up hash index:0 seconds # smalt: Time spent mapping reads:2 seconds # smalt: Total elapsed wall clock time: 2 seconds [REAPR smaltmap] Running: smalt map -r 0 -x -y 0.5 -g out.bam.tmp.12717.smaltmap.smalt_sample -f samsoft out.bam.tmp.12717.smaltmap.smalt_index foofq.1.fastq foofq.2.fastq | awk '$1!~/^#/' | samtools view -S -T foo1.fasta -b - > out.bam.tmp.12717.smaltmap.raw.bam # Command line: smalt map -r 0 -x -y 0.5 -g out.bam.tmp.12717.smaltmap.smalt_sample -f samsoft out.bam.tmp.12717.smaltmap.smalt_index foofq.1.fastq foofq.2.fastq # Reading distribution of insert sizes from file ... # Sampled histogram # Smoothed histogram # Opening read files ... # Reading reference sequences ... # Reading hash table ... # =-=-=-=-= Hash Index Stats =-=-=-=-= # Hash index with collisions. # Word length: 13 bases # Skip step: 2 bases # Number of hash keys: 262144 # Number of word positions: 499970 # Number of different words: 498076 # Maximum number of words per key: 11 # Number of keys without words: 39377 # =-=-= End of Hash Index Stats =-=-= # Processing query reads ... # Processed 10000 read pairs. # smalt: Time spent setting up hash index:0 seconds # smalt: Time spent mapping reads:11 seconds # smalt: Total elapsed wall clock time: 11 seconds [REAPR smaltmap] Running: samtools sort out.bam.tmp.12717.smaltmap.raw.bam -O bam -o out.bam.tmp.12717.smaltmap.raw.bam.sort.bam [REAPR smaltmap] Running: samtools rmdup out.bam.tmp.12717.smaltmap.raw.bam.sort.bam out.bam.tmp.12717.smaltmap.rmdup.bam [bam_rmdup_core] processing reference foo... [bam_rmdup_core] 1 / 10000 = 0.0001 in library ' ' [REAPR smaltmap] Running: echo "@HD VN:1.0 SO:coordinate" | awk '{OFS="\t"; $1=$1; print}' > out.bam.tmp.12717.smaltmap.header [REAPR smaltmap] Running: samtools view -H out.bam.tmp.12717.smaltmap.rmdup.bam >> out.bam.tmp.12717.smaltmap.header [REAPR smaltmap] Running: samtools reheader out.bam.tmp.12717.smaltmap.header out.bam.tmp.12717.smaltmap.rmdup.bam > out.bam [REAPR smaltmap] Running: samtools index out.bam [REAPR smaltmap] Running: rm out.bam.tmp.12717.smaltmap.* Running reapr version 1.0.18 pipeline: reapr foo1.fasta out.bam result [REAPR pipeline] Running facheck [REAPR pipeline] Running preprocess [REAPR preprocess] sampling region foo:1169-3476. Already sampled 0 bases [REAPR preprocess] sampling region foo:3492-5726. Already sampled 2308 bases [REAPR preprocess] sampling region foo:5756-12551. Already sampled 4543 bases [REAPR preprocess] sampling region foo:12591-998105. Already sampled 11339 bases [REAPR preprocess] Sampled 996854 bases for GC/coverage estimation [REAPR pipeline] Running stats [REAPR pipeline] Running fcdrate [REAPR pipeline] Running score [REAPR pipeline] Running break [REAPR pipeline] Running summary rm -rf /<>/debian/test make[1]: Leaving directory '/<>' create-stamp debian/debhelper-build-stamp fakeroot debian/rules binary dh binary dh_testroot dh_prep debian/rules override_dh_auto_install make[1]: Entering directory '/<>' mkdir -p debian/reapr/usr/lib/reapr install src/reapr.pl debian/reapr/usr/lib/reapr/reapr.pl chmod -x src/*.cpp find src -executable -exec install {} debian/reapr/usr/lib/reapr \; install: omitting directory 'src' dh_auto_install -- make[1]: Leaving directory '/<>' debian/rules override_dh_install make[1]: Entering directory '/<>' for pl in `grep -Rl '#!/usr/bin/env' debian/*/usr/*` ; do \ sed -i '1s?^#!/usr/bin/env[[:space:]]\+perl?#!/usr/bin/perl?' ${pl} ; \ done make[1]: Leaving directory '/<>' dh_installdocs dh_installchangelogs debian/rules override_dh_installman make[1]: Entering directory '/<>' mkdir -p /<>/debian/man asciidoctor -a docdate='' -b manpage /<>/debian/man_src/*.adoc cp /<>/debian/man_src/*.? /<>/debian/man dh_installman -- make[1]: Leaving directory '/<>' dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_dwz dh_strip debugedit: debian/reapr/usr/lib/reapr/task_gapresize: Unknown DWARF DW_FORM_0x1f20 a62209aac74857831c4d5be711a6010bfe550763 debugedit: debian/reapr/usr/lib/reapr/bam2fragCov: Unknown DWARF DW_FORM_0x1f20 ae6c9e85ca13a1e9b8407d3fa6d83706d0f4156d debugedit: debian/reapr/usr/lib/reapr/fa2gaps: Unknown DWARF DW_FORM_0x1f20 9d0b10ec11bad728183480395fc2914384504be5 debugedit: debian/reapr/usr/lib/reapr/task_fcdrate: Unknown DWARF DW_FORM_0x1f20 042613e9ceab103a97a0681af0f72d880cd8a0e0 debugedit: debian/reapr/usr/lib/reapr/fa2gc: Unknown DWARF DW_FORM_0x1f20 d73493ea08802a0e89cfdd34065d028683fe1632 debugedit: debian/reapr/usr/lib/reapr/task_break: Unknown DWARF DW_FORM_0x1f20 dafb2222dab65c57ffd8d109d5dcf217ce6f3ed0 debugedit: debian/reapr/usr/lib/reapr/bam2perfect: Unknown DWARF DW_FORM_0x1f20 1baf54ca59b912f64963a5204badf7368cf60b37 debugedit: debian/reapr/usr/lib/reapr/task_stats: Unknown DWARF DW_FORM_0x1f20 7a00c46e2125b91f01c49fe03c0424a4db3160c3 debugedit: debian/reapr/usr/lib/reapr/n50: Unknown DWARF DW_FORM_0x1f20 61770543f91ff2f5aceba11a82efed084e32a47d debugedit: debian/reapr/usr/lib/reapr/task_score: Unknown DWARF DW_FORM_0x1f21 f5f7f9cfe9eafb2b68d2ab87eb8305e6e597d198 debugedit: debian/reapr/usr/lib/reapr/make_plots: Unknown DWARF DW_FORM_0x1f20 788f5ff070fe56ccf2eb27d11ba9672298ec06fb debugedit: debian/reapr/usr/lib/reapr/bam2fcdEstimate: Unknown DWARF DW_FORM_0x1f20 fca4d02d9d9c56f25a06e82d936a45599031cea6 debugedit: debian/reapr/usr/lib/reapr/scaff2contig: Unknown DWARF DW_FORM_0x1f20 d6c2a1ad2370a6ef78622b4b29cbcd2ac5d93942 debugedit: debian/reapr/usr/lib/reapr/bam2insert: Unknown DWARF DW_FORM_0x1f20 764d47baba45b00aff450ae4623a1383a78e0e73 dh_makeshlibs dh_shlibdeps dh_installdeb dh_gencontrol dpkg-gencontrol: warning: package reapr: substitution variable ${perl:Depends} unused, but is defined dpkg-gencontrol: warning: package reapr: substitution variable ${perl:Depends} unused, but is defined dh_md5sums dh_builddeb INFO: pkgstriptranslations version 154 INFO: pkgstriptranslations version 154 pkgstriptranslations: processing reapr (in debian/reapr); do_strip: , oemstrip: pkgstriptranslations: processing reapr-dbgsym (in debian/.debhelper/reapr/dbgsym-root); do_strip: , oemstrip: pkgmaintainermangler: Not overriding Maintainer for domain lists.ubuntu.com pkgmaintainermangler: Not overriding Maintainer for domain lists.ubuntu.com pkgstripfiles: processing control file: debian/reapr/DEBIAN/control, package reapr, directory debian/reapr pkgstripfiles: processing control file: debian/.debhelper/reapr/dbgsym-root/DEBIAN/control, package reapr-dbgsym, directory debian/.debhelper/reapr/dbgsym-root dpkg-deb: building package 'reapr-dbgsym' in 'debian/.debhelper/scratch-space/build-reapr/reapr-dbgsym_1.0.18+dfsg-5ubuntu2_amd64.deb'. pkgstripfiles: Running PNG optimization (using 4 cpus) for package reapr ... pkgstripfiles: No PNG files. dpkg-deb: building package 'reapr' in '../reapr_1.0.18+dfsg-5ubuntu2_amd64.deb'. Renaming reapr-dbgsym_1.0.18+dfsg-5ubuntu2_amd64.deb to reapr-dbgsym_1.0.18+dfsg-5ubuntu2_amd64.ddeb dpkg-genbuildinfo --build=binary -O../reapr_1.0.18+dfsg-5ubuntu2_amd64.buildinfo dpkg-genchanges --build=binary -mLaunchpad Build Daemon -O../reapr_1.0.18+dfsg-5ubuntu2_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) -------------------------------------------------------------------------------- Build finished at 2024-04-01T10:27:07Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ reapr_1.0.18+dfsg-5ubuntu2_amd64.changes: ----------------------------------------- Format: 1.8 Date: Mon, 01 Apr 2024 18:25:15 +1100 Source: reapr Binary: reapr Built-For-Profiles: noudeb Architecture: amd64 Version: 1.0.18+dfsg-5ubuntu2 Distribution: noble-proposed Urgency: medium Maintainer: Launchpad Build Daemon Changed-By: William Grant Description: reapr - universal tool for genome assembly evaluation Changes: reapr (1.0.18+dfsg-5ubuntu2) noble; urgency=medium . * No-change rebuild for CVE-2024-3094 Checksums-Sha1: 1dca4e750950c10b97a3ecf7c4edcaa9cb893ea6 2297874 reapr-dbgsym_1.0.18+dfsg-5ubuntu2_amd64.ddeb 44437a78d1f23f0cc1a7dc17838accce83c9570f 10226 reapr_1.0.18+dfsg-5ubuntu2_amd64.buildinfo 5a58b9a50c0d0a24ef21b60a034ea3b5dd4d5fd4 193656 reapr_1.0.18+dfsg-5ubuntu2_amd64.deb Checksums-Sha256: fe5b981e2de1191a4c98e911d93ce3c0a8d566e1d260a9120880c084fba1550a 2297874 reapr-dbgsym_1.0.18+dfsg-5ubuntu2_amd64.ddeb 1596646eddc627de738f4ecc10089f54be8b0bea327dc71de37d597210ebcdf0 10226 reapr_1.0.18+dfsg-5ubuntu2_amd64.buildinfo d92e61785eb0ecae0ecc381369c2a98188bff3a10bfc9ea0a51451bc030d3294 193656 reapr_1.0.18+dfsg-5ubuntu2_amd64.deb Files: 21edc1cb6ed39043aab1e25dceef318b 2297874 debug optional reapr-dbgsym_1.0.18+dfsg-5ubuntu2_amd64.ddeb d79ee89425fb2f79ef8dbe40d875b70c 10226 science optional reapr_1.0.18+dfsg-5ubuntu2_amd64.buildinfo 3fc609c5e380f78cf0f20a067c85cc6a 193656 science optional reapr_1.0.18+dfsg-5ubuntu2_amd64.deb Original-Maintainer: Debian Med Packaging Team /<>/reapr_1.0.18+dfsg-5ubuntu2_amd64.changes.new could not be renamed to /<>/reapr_1.0.18+dfsg-5ubuntu2_amd64.changes: Illegal seek Distribution field may be wrong!!! +------------------------------------------------------------------------------+ | Buildinfo | +------------------------------------------------------------------------------+ Format: 1.0 Source: reapr Binary: reapr reapr-dbgsym Architecture: amd64 Version: 1.0.18+dfsg-5ubuntu2 Checksums-Md5: 21edc1cb6ed39043aab1e25dceef318b 2297874 reapr-dbgsym_1.0.18+dfsg-5ubuntu2_amd64.ddeb 3fc609c5e380f78cf0f20a067c85cc6a 193656 reapr_1.0.18+dfsg-5ubuntu2_amd64.deb Checksums-Sha1: 1dca4e750950c10b97a3ecf7c4edcaa9cb893ea6 2297874 reapr-dbgsym_1.0.18+dfsg-5ubuntu2_amd64.ddeb 5a58b9a50c0d0a24ef21b60a034ea3b5dd4d5fd4 193656 reapr_1.0.18+dfsg-5ubuntu2_amd64.deb Checksums-Sha256: fe5b981e2de1191a4c98e911d93ce3c0a8d566e1d260a9120880c084fba1550a 2297874 reapr-dbgsym_1.0.18+dfsg-5ubuntu2_amd64.ddeb d92e61785eb0ecae0ecc381369c2a98188bff3a10bfc9ea0a51451bc030d3294 193656 reapr_1.0.18+dfsg-5ubuntu2_amd64.deb Build-Origin: Ubuntu Build-Architecture: amd64 Build-Date: Mon, 01 Apr 2024 10:27:06 +0000 Build-Path: /<> Build-Tainted-By: merged-usr-via-aliased-dirs usr-local-has-programs Installed-Build-Depends: asciidoctor (= 2.0.20-1), autoconf (= 2.71-3), automake (= 1:1.16.5-1.3ubuntu1), autopoint (= 0.21-14ubuntu1), autotools-dev (= 20220109.1), bamtools (= 2.5.2+dfsg-5), base-files (= 13ubuntu9), base-passwd (= 3.6.3), bash (= 5.2.21-2ubuntu4), binutils (= 2.42-4ubuntu2), binutils-common (= 2.42-4ubuntu2), binutils-x86-64-linux-gnu (= 2.42-4ubuntu2), bsdextrautils (= 2.39.3-9ubuntu4), bsdutils (= 1:2.39.3-9ubuntu4), build-essential (= 12.10ubuntu1), bzip2 (= 1.0.8-5.1), ca-certificates (= 20240203), coreutils (= 9.4-3ubuntu5), cpp (= 4:13.2.0-7ubuntu1), cpp-13 (= 13.2.0-23ubuntu3), cpp-13-x86-64-linux-gnu (= 13.2.0-23ubuntu3), cpp-x86-64-linux-gnu (= 4:13.2.0-7ubuntu1), dash (= 0.5.12-6ubuntu5), debconf (= 1.5.86), debhelper (= 13.14.1ubuntu5), debianutils (= 5.17build1), debugedit (= 1:5.0-5build1), dh-autoreconf (= 20), dh-strip-nondeterminism (= 1.13.1-1), diffutils (= 1:3.10-1), dpkg (= 1.22.6ubuntu6), dpkg-dev (= 1.22.6ubuntu6), dwz (= 0.15-1build6), file (= 1:5.45-3build1), findutils (= 4.9.0-5), fontconfig (= 2.15.0-1.1ubuntu2), fontconfig-config (= 2.15.0-1.1ubuntu2), fonts-dejavu-core (= 2.37-8), fonts-dejavu-mono (= 2.37-8), g++ (= 4:13.2.0-7ubuntu1), g++-13 (= 13.2.0-23ubuntu3), g++-13-x86-64-linux-gnu (= 13.2.0-23ubuntu3), g++-x86-64-linux-gnu (= 4:13.2.0-7ubuntu1), gcc (= 4:13.2.0-7ubuntu1), gcc-13 (= 13.2.0-23ubuntu3), gcc-13-base (= 13.2.0-23ubuntu3), gcc-13-x86-64-linux-gnu (= 13.2.0-23ubuntu3), gcc-14-base (= 14-20240330-1ubuntu2), gcc-x86-64-linux-gnu (= 4:13.2.0-7ubuntu1), gettext (= 0.21-14ubuntu1), gettext-base (= 0.21-14ubuntu1), grep (= 3.11-4), groff-base (= 1.23.0-3build2), gzip (= 1.12-1ubuntu2), hostname (= 3.23+nmu2ubuntu1), init-system-helpers (= 1.66ubuntu1), intltool-debian (= 0.35.0+20060710.6), libacl1 (= 2.3.2-1), libarchive-zip-perl (= 1.68-1), libasan8 (= 14-20240330-1ubuntu2), libatomic1 (= 14-20240330-1ubuntu2), libattr1 (= 1:2.5.2-1), libaudit-common (= 1:3.1.2-2.1build1), libaudit1 (= 1:3.1.2-2.1build1), libbambamc0 (= 0.0.50-6), libbamtools-dev (= 2.5.2+dfsg-5), libbamtools2.5.2 (= 2.5.2+dfsg-5), libbinutils (= 2.42-4ubuntu2), libblas3 (= 3.12.0-3), libblkid1 (= 2.39.3-9ubuntu4), libbrotli1 (= 1.1.0-2build2), libbsd0 (= 0.12.1-1build1), libbz2-1.0 (= 1.0.8-5.1), libc-bin (= 2.39-0ubuntu8), libc-dev-bin (= 2.39-0ubuntu8), libc6 (= 2.39-0ubuntu8), libc6-dev (= 2.39-0ubuntu8), libcairo2 (= 1.18.0-3), libcap-ng0 (= 0.8.4-2build2), libcap2 (= 1:2.66-5ubuntu1), libcc1-0 (= 14-20240330-1ubuntu2), libcom-err2 (= 1.47.0-2.4~exp1ubuntu3), libcrypt-dev (= 1:4.4.36-4), libcrypt1 (= 1:4.4.36-4), libctf-nobfd0 (= 2.42-4ubuntu2), libctf0 (= 2.42-4ubuntu2), libcurl3t64-gnutls (= 8.5.0-2ubuntu9), libcurl4-gnutls-dev (= 8.5.0-2ubuntu9), libcurl4t64 (= 8.5.0-2ubuntu9), libdatrie1 (= 0.2.13-3), libdb5.3t64 (= 5.3.28+dfsg2-6build1), libdebconfclient0 (= 0.271ubuntu3), libdebhelper-perl (= 13.14.1ubuntu5), libdeflate-dev (= 1.19-1), libdeflate0 (= 1.19-1), libdpkg-perl (= 1.22.6ubuntu6), libdw1t64 (= 0.190-1.1build3), libedit2 (= 3.1-20230828-1), libelf1t64 (= 0.190-1.1build3), libexpat1 (= 2.6.1-2build1), libffi8 (= 3.4.6-1), libfile-copy-link-perl (= 0.140-5), libfile-stripnondeterminism-perl (= 1.13.1-1), libfontconfig1 (= 2.15.0-1.1ubuntu2), libfreetype6 (= 2.13.2+dfsg-1build3), libfribidi0 (= 1.0.13-3), libgcc-13-dev (= 13.2.0-23ubuntu3), libgcc-s1 (= 14-20240330-1ubuntu2), libgcrypt20 (= 1.10.3-2), libgdbm-compat4 (= 1.23-5), libgdbm6 (= 1.23-5), libgfortran5 (= 14-20240330-1ubuntu2), libglib2.0-0t64 (= 2.80.0-6build1), libgmp10 (= 2:6.3.0+dfsg-2ubuntu4), libgnutls30t64 (= 3.8.3-1.1ubuntu3), libgomp1 (= 14-20240330-1ubuntu2), libgpg-error0 (= 1.47-3build1), libgprofng0 (= 2.42-4ubuntu2), libgraphite2-3 (= 1.3.14-2), libgssapi-krb5-2 (= 1.20.1-6ubuntu2), libharfbuzz0b (= 8.3.0-2build2), libhogweed6t64 (= 3.9.1-2.2build1), libhts-dev (= 1.19+ds-1.1build3), libhts3t64 (= 1.19+ds-1.1build3), libhtscodecs2 (= 1.6.0-1), libhwasan0 (= 14-20240330-1ubuntu2), libice6 (= 2:1.0.10-1build2), libicu74 (= 74.2-1ubuntu1), libidn2-0 (= 2.3.7-2), libisl23 (= 0.26-3), libitm1 (= 14-20240330-1ubuntu2), libjansson4 (= 2.14-2build2), libjbig0 (= 2.1-6.1ubuntu1), libjpeg-turbo8 (= 2.1.5-2ubuntu1), libjpeg8 (= 8c-2ubuntu11), libjsoncpp25 (= 1.9.5-6), libk5crypto3 (= 1.20.1-6ubuntu2), libkeyutils1 (= 1.6.3-3), libkrb5-3 (= 1.20.1-6ubuntu2), libkrb5support0 (= 1.20.1-6ubuntu2), liblapack3 (= 3.12.0-3), libldap2 (= 2.6.7+dfsg-1~exp1ubuntu7), liblerc4 (= 4.0.0+ds-4ubuntu1), liblsan0 (= 14-20240330-1ubuntu2), liblz4-1 (= 1.9.4-1), liblzma-dev (= 5.6.1+really5.4.5-1build1), liblzma5 (= 5.6.1+really5.4.5-1build1), libmagic-mgc (= 1:5.45-3build1), libmagic1t64 (= 1:5.45-3build1), libmd0 (= 1.1.0-2), libmount1 (= 2.39.3-9ubuntu4), libmpc3 (= 1.3.1-1), libmpfr6 (= 4.2.1-1), libncurses6 (= 6.4+20240113-1ubuntu1), libnettle8t64 (= 3.9.1-2.2build1), libnghttp2-14 (= 1.59.0-1build2), libp11-kit0 (= 0.25.3-4ubuntu1), libpam-modules (= 1.5.3-5ubuntu4), libpam-modules-bin (= 1.5.3-5ubuntu4), libpam-runtime (= 1.5.3-5ubuntu4), libpam0g (= 1.5.3-5ubuntu4), libpango-1.0-0 (= 1.52.1+ds-1build1), libpangocairo-1.0-0 (= 1.52.1+ds-1build1), libpangoft2-1.0-0 (= 1.52.1+ds-1build1), libpaper-utils (= 1.1.29), libpaper1 (= 1.1.29), libpcre2-8-0 (= 10.42-4ubuntu1), libperl5.38t64 (= 5.38.2-3.2build1), libpipeline1 (= 1.5.7-2), libpixman-1-0 (= 0.42.2-1), libpng16-16t64 (= 1.6.43-5build1), libpsl5 (= 0.21.2-1build1), libquadmath0 (= 14-20240330-1ubuntu2), libreadline8t64 (= 8.2-4build1), librtmp1 (= 2.4+20151223.gitfa8646d.1-2build7), libruby (= 1:3.2~ubuntu1), libruby3.2 (= 3.2.3-1build3), libsasl2-2 (= 2.1.28+dfsg1-5ubuntu2), libsasl2-modules-db (= 2.1.28+dfsg1-5ubuntu2), libseccomp2 (= 2.5.5-1ubuntu3), libselinux1 (= 3.5-2ubuntu2), libsframe1 (= 2.42-4ubuntu2), libsharpyuv0 (= 1.3.2-0.4build3), libsm6 (= 2:1.2.3-1build2), libsmartcols1 (= 2.39.3-9ubuntu4), libssh-4 (= 0.10.6-2build2), libssl3t64 (= 3.0.13-0ubuntu3), libstdc++-13-dev (= 13.2.0-23ubuntu3), libstdc++6 (= 14-20240330-1ubuntu2), libsub-override-perl (= 0.10-1), libsystemd0 (= 255.4-1ubuntu6), libtabixpp-dev (= 1.1.2-2.1build1), libtabixpp0t64 (= 1.1.2-2.1build1), libtasn1-6 (= 4.19.0-3), libtcl8.6 (= 8.6.14+dfsg-1build1), libthai-data (= 0.1.29-2), libthai0 (= 0.1.29-2), libtiff6 (= 4.5.1+git230720-4ubuntu2), libtinfo6 (= 6.4+20240113-1ubuntu1), libtirpc-common (= 1.3.4+ds-1.1build1), libtirpc3t64 (= 1.3.4+ds-1.1build1), libtk8.6 (= 8.6.14-1build1), libtool (= 2.4.7-7), libtsan2 (= 14-20240330-1ubuntu2), libubsan1 (= 14-20240330-1ubuntu2), libuchardet0 (= 0.0.8-1), libudev1 (= 255.4-1ubuntu6), libunistring5 (= 1.1-2), libuuid1 (= 2.39.3-9ubuntu4), libwebp7 (= 1.3.2-0.4build3), libx11-6 (= 2:1.8.7-1), libx11-data (= 2:1.8.7-1), libxau6 (= 1:1.0.9-1build5), libxcb-render0 (= 1.15-1), libxcb-shm0 (= 1.15-1), libxcb1 (= 1.15-1), libxdmcp6 (= 1:1.1.3-0ubuntu5), libxext6 (= 2:1.3.4-1build1), libxft2 (= 2.3.6-1), libxml2 (= 2.9.14+dfsg-1.3ubuntu3), libxrender1 (= 1:0.9.10-1.1), libxss1 (= 1:1.2.3-1build2), libxt6t64 (= 1:1.2.1-1.2build1), libyaml-0-2 (= 0.2.5-1), libzstd1 (= 1.5.5+dfsg2-2), linux-libc-dev (= 6.8.0-11.11), login (= 1:4.13+dfsg1-4ubuntu1), lto-disabled-list (= 47), m4 (= 1.4.19-4), make (= 4.3-4.1build1), man-db (= 2.12.0-4build1), mawk (= 1.3.4.20240123-1), ncurses-base (= 6.4+20240113-1ubuntu1), ncurses-bin (= 6.4+20240113-1ubuntu1), openssl (= 3.0.13-0ubuntu3), patch (= 2.7.6-7build2), perl (= 5.38.2-3.2build1), perl-base (= 5.38.2-3.2build1), perl-modules-5.38 (= 5.38.2-3.2build1), po-debconf (= 1.0.21+nmu1), r-base (= 4.3.3-2build2), r-base-core (= 4.3.3-2build2), r-cran-boot (= 1.3-30-1), r-cran-class (= 7.3-22-2), r-cran-cluster (= 2.1.6-1), r-cran-codetools (= 0.2-19-1), r-cran-foreign (= 0.8.86-1), r-cran-kernsmooth (= 2.23-22-1), r-cran-lattice (= 0.22-5-1), r-cran-mass (= 7.3-60.0.1-1), r-cran-matrix (= 1.6-5-1), r-cran-mgcv (= 1.9-1-1), r-cran-nlme (= 3.1.164-1), r-cran-nnet (= 7.3-19-2), r-cran-rpart (= 4.1.23-1), r-cran-spatial (= 7.3-17-1), r-cran-survival (= 3.5-8-1), r-recommended (= 4.3.3-2build2), rake (= 13.0.6-3), readline-common (= 8.2-4build1), rpcsvc-proto (= 1.4.2-0ubuntu6), ruby (= 1:3.2~ubuntu1), ruby-asciidoctor (= 2.0.20-1), ruby-net-telnet (= 0.2.0-1), ruby-rubygems (= 3.4.20-1), ruby-sdbm (= 1.0.0-5build4), ruby-webrick (= 1.8.1-1), ruby-xmlrpc (= 0.3.2-2), ruby3.2 (= 3.2.3-1build3), rubygems-integration (= 1.18), samtools (= 1.19.2-1), sed (= 4.9-2), sensible-utils (= 0.0.22), smalt (= 0.7.6-13), snpomatic (= 1.0-7), sysvinit-utils (= 3.08-6ubuntu2), tabix (= 1.19+ds-1.1build3), tar (= 1.35+dfsg-3), tzdata (= 2024a-1ubuntu1), ucf (= 3.0043+nmu1), unzip (= 6.0-28ubuntu3), util-linux (= 2.39.3-9ubuntu4), x11-common (= 1:7.7+23ubuntu2), xdg-utils (= 1.1.3-4.1ubuntu3), xz-utils (= 5.6.1+really5.4.5-1build1), zip (= 3.0-13), zlib1g (= 1:1.3.dfsg-3.1ubuntu2), zlib1g-dev (= 1:1.3.dfsg-3.1ubuntu2) Environment: DEB_BUILD_OPTIONS="parallel=4" DEB_BUILD_PROFILES="noudeb" LANG="C.UTF-8" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1711956315" +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ reapr_1.0.18+dfsg-5ubuntu2_amd64.deb ------------------------------------ new Debian package, version 2.0. size 193656 bytes: control archive=2120 bytes. 1528 bytes, 25 lines control 2623 bytes, 40 lines md5sums Package: reapr Version: 1.0.18+dfsg-5ubuntu2 Architecture: amd64 Maintainer: Ubuntu Developers Installed-Size: 758 Depends: libbamtools2.5.2 (>= 2.5.2+dfsg), libc6 (>= 2.38), libgcc-s1 (>= 3.3.1), libstdc++6 (>= 13.1), libtabixpp0t64 (>= 1.0.0), samtools (>= 1.3), bamtools, smalt, r-base, snpomatic, tabix, libfile-copy-link-perl Section: science Priority: optional Homepage: https://www.sanger.ac.uk/science/tools/reapr Description: universal tool for genome assembly evaluation REAPR is a tool that evaluates the accuracy of a genome assembly using mapped paired end reads, without the use of a reference genome for comparison. It can be used in any stage of an assembly pipeline to automatically break incorrect scaffolds and flag other errors in an assembly for manual inspection. It reports mis-assemblies and other warnings, and produces a new broken assembly based on the error calls. . The software requires as input an assembly in FASTA format and paired reads mapped to the assembly in a BAM file. Mapping information such as the fragment coverage and insert size distribution is analysed to locate mis-assemblies. REAPR works best using mapped read pairs from a large insert library (at least 1000bp). Additionally, if a short insert Illumina library is also available, REAPR can combine this with the large insert library in order to score each base of the assembly. Original-Maintainer: Debian Med Packaging Team drwxr-xr-x root/root 0 2024-04-01 07:25 ./ drwxr-xr-x root/root 0 2024-04-01 07:25 ./usr/ drwxr-xr-x root/root 0 2024-04-01 07:25 ./usr/bin/ lrwxrwxrwx root/root 0 2024-04-01 07:25 ./usr/bin/reapr -> ../lib/reapr/reapr.pl drwxr-xr-x root/root 0 2024-04-01 07:25 ./usr/lib/ drwxr-xr-x root/root 0 2024-04-01 07:25 ./usr/lib/reapr/ -rwxr-xr-x root/root 43408 2024-04-01 07:25 ./usr/lib/reapr/bam2fcdEstimate -rwxr-xr-x root/root 31120 2024-04-01 07:25 ./usr/lib/reapr/bam2fragCov -rwxr-xr-x root/root 55696 2024-04-01 07:25 ./usr/lib/reapr/bam2insert -rwxr-xr-x root/root 47504 2024-04-01 07:25 ./usr/lib/reapr/bam2perfect -rwxr-xr-x root/root 22920 2024-04-01 07:25 ./usr/lib/reapr/fa2gaps -rwxr-xr-x root/root 22920 2024-04-01 07:25 ./usr/lib/reapr/fa2gc -rwxr-xr-x root/root 35208 2024-04-01 07:25 ./usr/lib/reapr/make_plots -rwxr-xr-x root/root 31112 2024-04-01 07:25 ./usr/lib/reapr/n50 -rwxr-xr-x root/root 3505 2024-04-01 07:25 ./usr/lib/reapr/reapr.pl -rwxr-xr-x root/root 27016 2024-04-01 07:25 ./usr/lib/reapr/scaff2contig -rwxr-xr-x root/root 55696 2024-04-01 07:25 ./usr/lib/reapr/task_break -rwxr-xr-x root/root 2457 2024-04-01 07:25 ./usr/lib/reapr/task_facheck.pl -rwxr-xr-x root/root 55696 2024-04-01 07:25 ./usr/lib/reapr/task_fcdrate -rwxr-xr-x root/root 47504 2024-04-01 07:25 ./usr/lib/reapr/task_gapresize -rwxr-xr-x root/root 6007 2024-04-01 07:25 ./usr/lib/reapr/task_perfectfrombam.pl -rwxr-xr-x root/root 4471 2024-04-01 07:25 ./usr/lib/reapr/task_perfectmap.pl -rwxr-xr-x root/root 4060 2024-04-01 07:25 ./usr/lib/reapr/task_pipeline.pl -rwxr-xr-x root/root 3043 2024-04-01 07:25 ./usr/lib/reapr/task_plots.pl -rwxr-xr-x root/root 14801 2024-04-01 07:25 ./usr/lib/reapr/task_preprocess.pl -rwxr-xr-x root/root 117136 2024-04-01 07:25 ./usr/lib/reapr/task_score -rwxr-xr-x root/root 1373 2024-04-01 07:25 ./usr/lib/reapr/task_seqrename.pl -rwxr-xr-x root/root 5520 2024-04-01 07:25 ./usr/lib/reapr/task_smaltmap.pl -rwxr-xr-x root/root 84368 2024-04-01 07:25 ./usr/lib/reapr/task_stats -rwxr-xr-x root/root 8924 2024-04-01 07:25 ./usr/lib/reapr/task_summary.pl drwxr-xr-x root/root 0 2024-04-01 07:25 ./usr/share/ drwxr-xr-x root/root 0 2024-04-01 07:25 ./usr/share/doc/ drwxr-xr-x root/root 0 2024-04-01 07:25 ./usr/share/doc/reapr/ -rw-r--r-- root/root 698 2024-04-01 07:25 ./usr/share/doc/reapr/changelog.Debian.gz -rw-r--r-- root/root 1112 2019-12-26 15:22 ./usr/share/doc/reapr/copyright drwxr-xr-x root/root 0 2024-04-01 07:25 ./usr/share/man/ drwxr-xr-x root/root 0 2024-04-01 07:25 ./usr/share/man/man1/ -rw-r--r-- root/root 923 2024-04-01 07:25 ./usr/share/man/man1/reapr-break.1.gz -rw-r--r-- root/root 611 2024-04-01 07:25 ./usr/share/man/man1/reapr-facheck.1.gz -rw-r--r-- root/root 504 2024-04-01 07:25 ./usr/share/man/man1/reapr-gapresize.1.gz -rw-r--r-- root/root 944 2024-04-01 07:25 ./usr/share/man/man1/reapr-perfectfrombam.1.gz -rw-r--r-- root/root 644 2024-04-01 07:25 ./usr/share/man/man1/reapr-perfectmap.1.gz -rw-r--r-- root/root 900 2024-04-01 07:25 ./usr/share/man/man1/reapr-pipeline.1.gz -rw-r--r-- root/root 494 2024-04-01 07:25 ./usr/share/man/man1/reapr-plots.1.gz -rw-r--r-- root/root 410 2024-04-01 07:25 ./usr/share/man/man1/reapr-preprocess.1.gz -rw-r--r-- root/root 936 2024-04-01 07:25 ./usr/share/man/man1/reapr-score.1.gz -rw-r--r-- root/root 477 2024-04-01 07:25 ./usr/share/man/man1/reapr-seqrename.1.gz -rw-r--r-- root/root 1026 2024-04-01 07:25 ./usr/share/man/man1/reapr-smaltmap.1.gz -rw-r--r-- root/root 748 2024-04-01 07:25 ./usr/share/man/man1/reapr-stats.1.gz -rw-r--r-- root/root 519 2024-04-01 07:25 ./usr/share/man/man1/reapr-summary.1.gz -rw-r--r-- root/root 1108 2024-04-01 07:25 ./usr/share/man/man1/reapr.1.gz +------------------------------------------------------------------------------+ | Post Build | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not removing build depends: as requested +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: amd64 Build Type: binary Build-Space: 55388 Build-Time: 91 Distribution: noble-proposed Host Architecture: amd64 Install-Time: 13 Job: reapr_1.0.18+dfsg-5ubuntu2.dsc Machine Architecture: amd64 Package: reapr Package-Time: 105 Source-Version: 1.0.18+dfsg-5ubuntu2 Space: 55388 Status: successful Version: 1.0.18+dfsg-5ubuntu2 -------------------------------------------------------------------------------- Finished at 2024-04-01T10:27:07Z Build needed 00:01:45, 55388k disk space RUN: /usr/share/launchpad-buildd/bin/in-target scan-for-processes --backend=chroot --series=noble --arch=amd64 PACKAGEBUILD-28010610 Scanning for processes to kill in build PACKAGEBUILD-28010610