https://launchpad.net/ubuntu/+source/nanopolish/0.14.0-1ubuntu3/+build/28007361 RUN: /usr/share/launchpad-buildd/bin/builder-prep Kernel version: Linux bos03-riscv64-009 6.5.0-26-generic #26.1~22.04.1-Ubuntu SMP Thu Mar 14 04:00:07 UTC 2024 riscv64 Buildd toolchain package versions: launchpad-buildd_236~650~ubuntu22.04.1 python3-lpbuildd_236~650~ubuntu22.04.1 sbuild_0.81.2ubuntu6 git-build-recipe_0.3.6 git_1:2.34.1-1ubuntu1.10 dpkg-dev_1.21.1ubuntu2.3 python3-debian_0.1.43ubuntu1.1. Syncing the system clock with the buildd NTP service... 2 Apr 00:48:27 ntpdate[2311]: adjust time server 10.211.37.1 offset -0.003296 sec RUN: /usr/share/launchpad-buildd/bin/in-target unpack-chroot --backend=chroot --series=noble --arch=riscv64 PACKAGEBUILD-28007361 --image-type chroot /home/buildd/filecache-default/20a3246b7a16d5658607d7f37229fcda30a33651 Creating target for build PACKAGEBUILD-28007361 RUN: /usr/share/launchpad-buildd/bin/in-target mount-chroot --backend=chroot --series=noble --arch=riscv64 PACKAGEBUILD-28007361 Starting target for build PACKAGEBUILD-28007361 RUN: /usr/share/launchpad-buildd/bin/in-target override-sources-list --backend=chroot --series=noble --arch=riscv64 PACKAGEBUILD-28007361 '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-28007361 RUN: /usr/share/launchpad-buildd/bin/in-target update-debian-chroot --backend=chroot --series=noble --arch=riscv64 PACKAGEBUILD-28007361 Updating target for build PACKAGEBUILD-28007361 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 riscv64 Packages [1351 kB] Get:6 http://ftpmaster.internal/ubuntu noble/main Translation-en [512 kB] Get:7 http://ftpmaster.internal/ubuntu noble/universe riscv64 Packages [14.5 MB] Get:8 http://ftpmaster.internal/ubuntu noble/universe Translation-en [6118 kB] Get:9 http://ftpmaster.internal/ubuntu noble-updates/main riscv64 Packages [667 kB] Get:10 http://ftpmaster.internal/ubuntu noble-updates/main Translation-en [242 kB] Get:11 http://ftpmaster.internal/ubuntu noble-updates/universe riscv64 Packages [4442 kB] Get:12 http://ftpmaster.internal/ubuntu noble-updates/universe Translation-en [1693 kB] Get:13 http://ftpmaster.internal/ubuntu noble-proposed/main riscv64 Packages [623 kB] Get:14 http://ftpmaster.internal/ubuntu noble-proposed/main Translation-en [247 kB] Get:15 http://ftpmaster.internal/ubuntu noble-proposed/universe riscv64 Packages [2873 kB] Get:16 http://ftpmaster.internal/ubuntu noble-proposed/universe Translation-en [1744 kB] Fetched 35.6 MB in 46s (777 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* libgdbm-compat4* libgdbm6* libgnutls30* libhogweed6* libnettle8* libnpth0* libpng16-16* libreadline8* libssl3* libtirpc3* usrmerge* The following NEW packages will be installed: cpp-13-riscv64-linux-gnu cpp-riscv64-linux-gnu g++-13-riscv64-linux-gnu g++-riscv64-linux-gnu gcc-13-riscv64-linux-gnu gcc-14-base gcc-riscv64-linux-gnu libapt-pkg6.0t64 libdb5.3t64 libext2fs2t64 libgdbm-compat4t64 libgdbm6t64 libgnutls30t64 libhogweed6t64 libnettle8t64 libnpth0t64 libperl5.38t64 libpng16-16t64 libreadline8t64 libssl3t64 libtirpc3t64 libubsan1 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-riscv64-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 libgomp1 libgpg-error-l10n libgpg-error0 libgpm2 libgssapi-krb5-2 libidn2-0 libip4tc2 libjansson4 libk5crypto3 libkeyutils1 libkmod2 libkrb5-3 libkrb5support0 liblocale-gettext-perl liblzma5 libmd0 libmount1 libncursesw6 libnsl-dev libnsl2 libnss-nisplus libp11-kit0 libpam-modules libpam-modules-bin libpam-runtime libpam0g libpcre2-8-0 libproc2-0 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 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 153 upgraded, 24 newly installed, 14 to remove and 0 not upgraded. Need to get 113 MB of archives. After this operation, 70.1 MB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu noble-proposed/main riscv64 libnsl-dev riscv64 1.3.0-3build3 [137 kB] Get:2 http://ftpmaster.internal/ubuntu noble/main riscv64 libcrypt-dev riscv64 1:4.4.36-4 [322 kB] Get:3 http://ftpmaster.internal/ubuntu noble-proposed/main riscv64 libc6-dev riscv64 2.39-0ubuntu8 [3458 kB] Get:4 http://ftpmaster.internal/ubuntu noble-proposed/main riscv64 libc-dev-bin riscv64 2.39-0ubuntu8 [20.0 kB] Get:5 http://ftpmaster.internal/ubuntu noble-proposed/main riscv64 libtirpc-common all 1.3.4+ds-1.1build1 [8094 B] Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main riscv64 libtirpc-dev riscv64 1.3.4+ds-1.1build1 [350 kB] Get:7 http://ftpmaster.internal/ubuntu noble-proposed/universe riscv64 libnss-nisplus riscv64 1.3-5build1 [23.8 kB] Get:8 http://ftpmaster.internal/ubuntu noble-proposed/main riscv64 libtirpc3t64 riscv64 1.3.4+ds-1.1build1 [92.3 kB] Get:9 http://ftpmaster.internal/ubuntu noble-proposed/main riscv64 libgssapi-krb5-2 riscv64 1.20.1-6ubuntu2 [153 kB] Get:10 http://ftpmaster.internal/ubuntu noble-proposed/main riscv64 libkrb5-3 riscv64 1.20.1-6ubuntu2 [385 kB] Get:11 http://ftpmaster.internal/ubuntu noble-proposed/main riscv64 libk5crypto3 riscv64 1.20.1-6ubuntu2 [108 kB] Get:12 http://ftpmaster.internal/ubuntu noble-proposed/main riscv64 libkrb5support0 riscv64 1.20.1-6ubuntu2 [36.7 kB] Get:13 http://ftpmaster.internal/ubuntu noble/main riscv64 libacl1 riscv64 2.3.2-1 [18.7 kB] Get:14 http://ftpmaster.internal/ubuntu noble-proposed/main riscv64 libapparmor1 riscv64 4.0.0-beta3-0ubuntu3 [51.2 kB] Get:15 http://ftpmaster.internal/ubuntu noble-proposed/main riscv64 libaudit-common all 1:3.1.2-2.1build1 [5736 B] Get:16 http://ftpmaster.internal/ubuntu noble-proposed/main riscv64 libcap-ng0 riscv64 0.8.4-2build2 [15.5 kB] Get:17 http://ftpmaster.internal/ubuntu noble-proposed/main riscv64 libaudit1 riscv64 1:3.1.2-2.1build1 [47.9 kB] Get:18 http://ftpmaster.internal/ubuntu noble-proposed/main riscv64 libblkid1 riscv64 2.39.3-9ubuntu4 [204 kB] Get:19 http://ftpmaster.internal/ubuntu noble/main riscv64 libcap2 riscv64 1:2.66-5ubuntu1 [31.7 kB] Get:20 http://ftpmaster.internal/ubuntu noble/main riscv64 libcrypt1 riscv64 1:4.4.36-4 [115 kB] Get:21 http://ftpmaster.internal/ubuntu noble/main riscv64 libgpg-error-l10n all 1.47-3build1 [8024 B] Get:22 http://ftpmaster.internal/ubuntu noble/main riscv64 libgpg-error0 riscv64 1.47-3build1 [75.7 kB] Get:23 http://ftpmaster.internal/ubuntu noble/main riscv64 libgcrypt20 riscv64 1.10.3-2 [564 kB] Get:24 http://ftpmaster.internal/ubuntu noble-proposed/main riscv64 liblzma5 riscv64 5.6.1+really5.4.5-1build1 [130 kB] Get:25 http://ftpmaster.internal/ubuntu noble/main riscv64 libzstd1 riscv64 1.5.5+dfsg2-2 [349 kB] Get:26 http://ftpmaster.internal/ubuntu noble-proposed/main riscv64 libkmod2 riscv64 31+20240202-2ubuntu5 [55.0 kB] Get:27 http://ftpmaster.internal/ubuntu noble/main riscv64 libpcre2-8-0 riscv64 10.42-4ubuntu1 [149 kB] Get:28 http://ftpmaster.internal/ubuntu noble-proposed/main riscv64 libselinux1 riscv64 3.5-2ubuntu2 [86.1 kB] Get:29 http://ftpmaster.internal/ubuntu noble-proposed/main riscv64 libmount1 riscv64 2.39.3-9ubuntu4 [212 kB] Get:30 http://ftpmaster.internal/ubuntu noble-proposed/main riscv64 libtext-iconv-perl riscv64 1.7-8build3 [13.5 kB] Get:31 http://ftpmaster.internal/ubuntu noble-proposed/main riscv64 libtext-charwidth-perl riscv64 0.04-11build3 [9272 B] Get:32 http://ftpmaster.internal/ubuntu noble-proposed/main riscv64 perl-modules-5.38 all 5.38.2-3.2build1 [3110 kB] Get:33 http://ftpmaster.internal/ubuntu noble-proposed/main riscv64 libdb5.3t64 riscv64 5.3.28+dfsg2-6build1 [779 kB] Get:34 http://ftpmaster.internal/ubuntu noble-proposed/main riscv64 libgdbm6t64 riscv64 1.23-5.1build1 [35.9 kB] Get:35 http://ftpmaster.internal/ubuntu noble-proposed/main riscv64 libgdbm-compat4t64 riscv64 1.23-5.1build1 [6884 B] Get:36 http://ftpmaster.internal/ubuntu noble-proposed/main riscv64 libperl5.38t64 riscv64 5.38.2-3.2build1 [4467 kB] Get:37 http://ftpmaster.internal/ubuntu noble-proposed/main riscv64 perl riscv64 5.38.2-3.2build1 [231 kB] Get:38 http://ftpmaster.internal/ubuntu noble-proposed/main riscv64 perl-base riscv64 5.38.2-3.2build1 [1833 kB] Get:39 http://ftpmaster.internal/ubuntu noble-proposed/main riscv64 liblocale-gettext-perl riscv64 1.07-6ubuntu5 [15.7 kB] Get:40 http://ftpmaster.internal/ubuntu noble-proposed/main riscv64 openssl riscv64 3.0.13-0ubuntu3 [992 kB] Get:41 http://ftpmaster.internal/ubuntu noble-proposed/main riscv64 libsystemd-shared riscv64 255.4-1ubuntu6 [2180 kB] Get:42 http://ftpmaster.internal/ubuntu noble-proposed/main riscv64 libcryptsetup12 riscv64 2:2.7.0-1ubuntu3 [274 kB] Get:43 http://ftpmaster.internal/ubuntu noble-proposed/main riscv64 libssl3t64 riscv64 3.0.13-0ubuntu3 [1735 kB] Get:44 http://ftpmaster.internal/ubuntu noble-proposed/main riscv64 systemd-dev all 255.4-1ubuntu6 [104 kB] Get:45 http://ftpmaster.internal/ubuntu noble-proposed/main riscv64 systemd-sysv riscv64 255.4-1ubuntu6 [11.9 kB] Get:46 http://ftpmaster.internal/ubuntu noble-proposed/main riscv64 systemd riscv64 255.4-1ubuntu6 [3552 kB] Get:47 http://ftpmaster.internal/ubuntu noble-proposed/main riscv64 libsystemd0 riscv64 255.4-1ubuntu6 [458 kB] Get:48 http://ftpmaster.internal/ubuntu noble-proposed/main riscv64 libpam-modules-bin riscv64 1.5.3-5ubuntu4 [55.1 kB] Get:49 http://ftpmaster.internal/ubuntu noble-proposed/main riscv64 libpam-modules riscv64 1.5.3-5ubuntu4 [284 kB] Get:50 http://ftpmaster.internal/ubuntu noble-proposed/main riscv64 libnettle8t64 riscv64 3.9.1-2.2build1 [217 kB] Get:51 http://ftpmaster.internal/ubuntu noble-proposed/main riscv64 libhogweed6t64 riscv64 3.9.1-2.2build1 [200 kB] Get:52 http://ftpmaster.internal/ubuntu noble/main riscv64 libp11-kit0 riscv64 0.25.3-4ubuntu1 [318 kB] Get:53 http://ftpmaster.internal/ubuntu noble/main riscv64 libunistring5 riscv64 1.1-2 [544 kB] Get:54 http://ftpmaster.internal/ubuntu noble-proposed/main riscv64 libgnutls30t64 riscv64 3.8.3-1.1ubuntu3 [1012 kB] Get:55 http://ftpmaster.internal/ubuntu noble/main riscv64 libapt-pkg6.0t64 riscv64 2.7.14 [1051 kB] Get:56 http://ftpmaster.internal/ubuntu noble-proposed/main riscv64 bzip2 riscv64 1.0.8-5.1 [35.0 kB] Get:57 http://ftpmaster.internal/ubuntu noble-proposed/main riscv64 libbz2-1.0 riscv64 1.0.8-5.1 [40.2 kB] Get:58 http://ftpmaster.internal/ubuntu noble/main riscv64 gcc-14-base riscv64 14-20240315-1ubuntu1 [47.0 kB] Get:59 http://ftpmaster.internal/ubuntu noble/main riscv64 libgcc-s1 riscv64 14-20240315-1ubuntu1 [61.1 kB] Get:60 http://ftpmaster.internal/ubuntu noble/main riscv64 libstdc++6 riscv64 14-20240315-1ubuntu1 [807 kB] Get:61 http://ftpmaster.internal/ubuntu noble-proposed/main riscv64 libudev1 riscv64 255.4-1ubuntu6 [181 kB] Get:62 http://ftpmaster.internal/ubuntu noble/main riscv64 libxxhash0 riscv64 0.8.2-2 [43.7 kB] Get:63 http://ftpmaster.internal/ubuntu noble-proposed/main riscv64 zlib1g riscv64 1:1.3.dfsg-3.1ubuntu2 [60.8 kB] Get:64 http://ftpmaster.internal/ubuntu noble/main riscv64 libffi8 riscv64 3.4.6-1 [23.0 kB] Get:65 http://ftpmaster.internal/ubuntu noble/main riscv64 libidn2-0 riscv64 2.3.7-2 [102 kB] Get:66 http://ftpmaster.internal/ubuntu noble-proposed/main riscv64 libdebconfclient0 riscv64 0.271ubuntu3 [11.2 kB] Get:67 http://ftpmaster.internal/ubuntu noble/main riscv64 base-passwd riscv64 3.6.3 [52.1 kB] Get:68 http://ftpmaster.internal/ubuntu noble-proposed/main riscv64 libsqlite3-0 riscv64 3.45.1-1ubuntu2 [739 kB] Get:69 http://ftpmaster.internal/ubuntu noble-proposed/main riscv64 gpg riscv64 2.4.4-2ubuntu16 [607 kB] Get:70 http://ftpmaster.internal/ubuntu noble-proposed/main riscv64 libreadline8t64 riscv64 8.2-4build1 [156 kB] Get:71 http://ftpmaster.internal/ubuntu noble-proposed/main riscv64 readline-common all 8.2-4build1 [56.5 kB] Get:72 http://ftpmaster.internal/ubuntu noble/main riscv64 libncursesw6 riscv64 6.4+20240113-1ubuntu1 [155 kB] Get:73 http://ftpmaster.internal/ubuntu noble/main riscv64 libtinfo6 riscv64 6.4+20240113-1ubuntu1 [108 kB] Get:74 http://ftpmaster.internal/ubuntu noble-proposed/main riscv64 gpg-agent riscv64 2.4.4-2ubuntu16 [282 kB] Get:75 http://ftpmaster.internal/ubuntu noble-proposed/main riscv64 gpgconf riscv64 2.4.4-2ubuntu16 [133 kB] Get:76 http://ftpmaster.internal/ubuntu noble-proposed/main riscv64 pinentry-curses riscv64 1.2.1-3ubuntu5 [40.6 kB] Get:77 http://ftpmaster.internal/ubuntu noble/main riscv64 init-system-helpers all 1.66ubuntu1 [39.4 kB] Get:78 http://ftpmaster.internal/ubuntu noble-proposed/main riscv64 libnpth0t64 riscv64 1.6-3.1build1 [8144 B] Get:79 http://ftpmaster.internal/ubuntu noble-proposed/main riscv64 gpgv riscv64 2.4.4-2ubuntu16 [276 kB] Get:80 http://ftpmaster.internal/ubuntu noble/main riscv64 ubuntu-keyring all 2023.11.28.1 [11.1 kB] Get:81 http://ftpmaster.internal/ubuntu noble/main riscv64 apt-utils riscv64 2.7.14 [226 kB] Get:82 http://ftpmaster.internal/ubuntu noble/main riscv64 apt riscv64 2.7.14 [1349 kB] Get:83 http://ftpmaster.internal/ubuntu noble/main riscv64 debconf-i18n all 1.5.86 [205 kB] Get:84 http://ftpmaster.internal/ubuntu noble/main riscv64 debconf all 1.5.86 [124 kB] Get:85 http://ftpmaster.internal/ubuntu noble-proposed/main riscv64 libpam0g riscv64 1.5.3-5ubuntu4 [69.0 kB] Get:86 http://ftpmaster.internal/ubuntu noble-proposed/main riscv64 libseccomp2 riscv64 2.5.5-1ubuntu3 [52.9 kB] Get:87 http://ftpmaster.internal/ubuntu noble/main riscv64 libargon2-1 riscv64 0~20190702+dfsg-4 [23.7 kB] Get:88 http://ftpmaster.internal/ubuntu noble-proposed/main riscv64 libdevmapper1.02.1 riscv64 2:1.02.185-3ubuntu3 [145 kB] Get:89 http://ftpmaster.internal/ubuntu noble-proposed/main riscv64 libuuid1 riscv64 2.39.3-9ubuntu4 [37.6 kB] Get:90 http://ftpmaster.internal/ubuntu noble-proposed/main riscv64 libfdisk1 riscv64 2.39.3-9ubuntu4 [238 kB] Get:91 http://ftpmaster.internal/ubuntu noble-proposed/main riscv64 mount riscv64 2.39.3-9ubuntu4 [152 kB] Get:92 http://ftpmaster.internal/ubuntu noble-proposed/main riscv64 libcom-err2 riscv64 1.47.0-2.4~exp1ubuntu3 [22.5 kB] Get:93 http://ftpmaster.internal/ubuntu noble/main riscv64 libkeyutils1 riscv64 1.6.3-3 [9694 B] Get:94 http://ftpmaster.internal/ubuntu noble-proposed/main riscv64 libnsl2 riscv64 1.3.0-3build3 [43.3 kB] Get:95 http://ftpmaster.internal/ubuntu noble/main riscv64 linux-libc-dev riscv64 6.8.0-20.20 [1567 kB] Get:96 http://ftpmaster.internal/ubuntu noble-proposed/main riscv64 libc6 riscv64 2.39-0ubuntu8 [2776 kB] Get:97 http://ftpmaster.internal/ubuntu noble-proposed/main riscv64 libc-bin riscv64 2.39-0ubuntu8 [609 kB] Get:98 http://ftpmaster.internal/ubuntu noble-proposed/main riscv64 base-files riscv64 13ubuntu9 [73.6 kB] Get:99 http://ftpmaster.internal/ubuntu noble-proposed/main riscv64 debianutils riscv64 5.17build1 [89.8 kB] Get:100 http://ftpmaster.internal/ubuntu noble-proposed/main riscv64 bash riscv64 5.2.21-2ubuntu4 [745 kB] Get:101 http://ftpmaster.internal/ubuntu noble-proposed/main riscv64 bsdutils riscv64 1:2.39.3-9ubuntu4 [115 kB] Get:102 http://ftpmaster.internal/ubuntu noble-proposed/main riscv64 coreutils riscv64 9.4-3ubuntu5 [1458 kB] Get:103 http://ftpmaster.internal/ubuntu noble/main riscv64 tar riscv64 1.35+dfsg-3 [269 kB] Get:104 http://ftpmaster.internal/ubuntu noble-proposed/main riscv64 dpkg riscv64 1.22.6ubuntu6 [1285 kB] Get:105 http://ftpmaster.internal/ubuntu noble-proposed/main riscv64 dash riscv64 0.5.12-6ubuntu5 [93.2 kB] Get:106 http://ftpmaster.internal/ubuntu noble/main riscv64 diffutils riscv64 1:3.10-1 [180 kB] Get:107 http://ftpmaster.internal/ubuntu noble/main riscv64 grep riscv64 3.11-4 [182 kB] Get:108 http://ftpmaster.internal/ubuntu noble/main riscv64 gzip riscv64 1.12-1ubuntu2 [102 kB] Get:109 http://ftpmaster.internal/ubuntu noble/main riscv64 hostname riscv64 3.23+nmu2ubuntu1 [11.3 kB] Get:110 http://ftpmaster.internal/ubuntu noble/main riscv64 login riscv64 1:4.13+dfsg1-4ubuntu1 [203 kB] Get:111 http://ftpmaster.internal/ubuntu noble/main riscv64 ncurses-bin riscv64 6.4+20240113-1ubuntu1 [186 kB] Get:112 http://ftpmaster.internal/ubuntu noble/main riscv64 sed riscv64 4.9-2 [211 kB] Get:113 http://ftpmaster.internal/ubuntu noble-proposed/main riscv64 util-linux riscv64 2.39.3-9ubuntu4 [1330 kB] Get:114 http://ftpmaster.internal/ubuntu noble/main riscv64 ncurses-base all 6.4+20240113-1ubuntu1 [25.4 kB] Get:115 http://ftpmaster.internal/ubuntu noble/main riscv64 sysvinit-utils riscv64 3.08-6ubuntu2 [35.0 kB] Get:116 http://ftpmaster.internal/ubuntu noble-proposed/main riscv64 logsave riscv64 1.47.0-2.4~exp1ubuntu3 [22.2 kB] Get:117 http://ftpmaster.internal/ubuntu noble-proposed/main riscv64 libext2fs2t64 riscv64 1.47.0-2.4~exp1ubuntu3 [243 kB] Get:118 http://ftpmaster.internal/ubuntu noble-proposed/main riscv64 e2fsprogs riscv64 1.47.0-2.4~exp1ubuntu3 [604 kB] Get:119 http://ftpmaster.internal/ubuntu noble-proposed/main riscv64 optipng riscv64 0.7.8+ds-1build2 [115 kB] Get:120 http://ftpmaster.internal/ubuntu noble-proposed/main riscv64 libpng16-16t64 riscv64 1.6.43-5build1 [193 kB] Get:121 http://ftpmaster.internal/ubuntu noble/main riscv64 init riscv64 1.66ubuntu1 [6190 B] Get:122 http://ftpmaster.internal/ubuntu noble-proposed/main riscv64 libsmartcols1 riscv64 2.39.3-9ubuntu4 [146 kB] Get:123 http://ftpmaster.internal/ubuntu noble-proposed/main riscv64 uuid-runtime riscv64 2.39.3-9ubuntu4 [49.2 kB] Get:124 http://ftpmaster.internal/ubuntu noble/main riscv64 libattr1 riscv64 1:2.5.2-1 [11.5 kB] Get:125 http://ftpmaster.internal/ubuntu noble/main riscv64 libmd0 riscv64 1.1.0-2 [30.6 kB] Get:126 http://ftpmaster.internal/ubuntu noble-proposed/main riscv64 libpam-runtime all 1.5.3-5ubuntu4 [40.8 kB] Get:127 http://ftpmaster.internal/ubuntu noble-proposed/main riscv64 libsemanage-common all 3.5-1build5 [10.1 kB] Get:128 http://ftpmaster.internal/ubuntu noble/main riscv64 libsepol2 riscv64 3.5-2 [312 kB] Get:129 http://ftpmaster.internal/ubuntu noble-proposed/main riscv64 libsemanage2 riscv64 3.5-1build5 [101 kB] Get:130 http://ftpmaster.internal/ubuntu noble/main riscv64 passwd riscv64 1:4.13+dfsg1-4ubuntu1 [864 kB] Get:131 http://ftpmaster.internal/ubuntu noble-proposed/main riscv64 libproc2-0 riscv64 2:4.0.4-4ubuntu3 [60.9 kB] Get:132 http://ftpmaster.internal/ubuntu noble-proposed/main riscv64 libss2 riscv64 1.47.0-2.4~exp1ubuntu3 [17.1 kB] Get:133 http://ftpmaster.internal/ubuntu noble/main riscv64 mawk riscv64 1.3.4.20240123-1 [129 kB] Get:134 http://ftpmaster.internal/ubuntu noble-proposed/main riscv64 procps riscv64 2:4.0.4-4ubuntu3 [715 kB] Get:135 http://ftpmaster.internal/ubuntu noble/main riscv64 sensible-utils all 0.0.22 [22.5 kB] Get:136 http://ftpmaster.internal/ubuntu noble/main riscv64 ca-certificates all 20240203 [159 kB] Get:137 http://ftpmaster.internal/ubuntu noble-proposed/main riscv64 krb5-locales all 1.20.1-6ubuntu2 [13.8 kB] Get:138 http://ftpmaster.internal/ubuntu noble/main riscv64 tzdata all 2024a-1ubuntu1 [273 kB] Get:139 http://ftpmaster.internal/ubuntu noble/main riscv64 bash-completion all 1:2.11-8 [180 kB] Get:140 http://ftpmaster.internal/ubuntu noble-proposed/main riscv64 bsdextrautils riscv64 2.39.3-9ubuntu4 [92.1 kB] Get:141 http://ftpmaster.internal/ubuntu noble-proposed/main riscv64 libgpm2 riscv64 1.20.7-11 [15.0 kB] Get:142 http://ftpmaster.internal/ubuntu noble/main riscv64 libip4tc2 riscv64 1.8.10-3ubuntu1 [23.9 kB] Get:143 http://ftpmaster.internal/ubuntu noble-proposed/main riscv64 libjansson4 riscv64 2.14-2build2 [34.7 kB] Get:144 http://ftpmaster.internal/ubuntu noble-proposed/main riscv64 psmisc riscv64 23.7-1build1 [177 kB] Get:145 http://ftpmaster.internal/ubuntu noble-proposed/main riscv64 xz-utils riscv64 5.6.1+really5.4.5-1build1 [269 kB] Get:146 http://ftpmaster.internal/ubuntu noble/main riscv64 libctf0 riscv64 2.42-4ubuntu2 [104 kB] Get:147 http://ftpmaster.internal/ubuntu noble/main riscv64 libctf-nobfd0 riscv64 2.42-4ubuntu2 [106 kB] Get:148 http://ftpmaster.internal/ubuntu noble/main riscv64 binutils-riscv64-linux-gnu riscv64 2.42-4ubuntu2 [899 kB] Get:149 http://ftpmaster.internal/ubuntu noble/main riscv64 libbinutils riscv64 2.42-4ubuntu2 [566 kB] Get:150 http://ftpmaster.internal/ubuntu noble/main riscv64 binutils riscv64 2.42-4ubuntu2 [2984 B] Get:151 http://ftpmaster.internal/ubuntu noble/main riscv64 binutils-common riscv64 2.42-4ubuntu2 [209 kB] Get:152 http://ftpmaster.internal/ubuntu noble/main riscv64 libsframe1 riscv64 2.42-4ubuntu2 [15.7 kB] Get:153 http://ftpmaster.internal/ubuntu noble/main riscv64 libgomp1 riscv64 14-20240315-1ubuntu1 [145 kB] Get:154 http://ftpmaster.internal/ubuntu noble/main riscv64 libatomic1 riscv64 14-20240315-1ubuntu1 [9496 B] Get:155 http://ftpmaster.internal/ubuntu noble/main riscv64 libasan8 riscv64 14-20240315-1ubuntu1 [2621 kB] Get:156 http://ftpmaster.internal/ubuntu noble/main riscv64 libubsan1 riscv64 14-20240315-1ubuntu1 [1075 kB] Get:157 http://ftpmaster.internal/ubuntu noble-proposed/main riscv64 g++-13 riscv64 13.2.0-23ubuntu3 [14.5 kB] Get:158 http://ftpmaster.internal/ubuntu noble-proposed/main riscv64 gcc-13 riscv64 13.2.0-23ubuntu3 [450 kB] Get:159 http://ftpmaster.internal/ubuntu noble-proposed/main riscv64 libstdc++-13-dev riscv64 13.2.0-23ubuntu3 [5666 kB] Get:160 http://ftpmaster.internal/ubuntu noble-proposed/main riscv64 libgcc-13-dev riscv64 13.2.0-23ubuntu3 [3858 kB] Get:161 http://ftpmaster.internal/ubuntu noble/main riscv64 libcc1-0 riscv64 14-20240315-1ubuntu1 [45.2 kB] Get:162 http://ftpmaster.internal/ubuntu noble-proposed/main riscv64 cpp-13 riscv64 13.2.0-23ubuntu3 [1030 B] Get:163 http://ftpmaster.internal/ubuntu noble-proposed/main riscv64 gcc-13-base riscv64 13.2.0-23ubuntu3 [48.7 kB] Get:164 http://ftpmaster.internal/ubuntu noble-proposed/main riscv64 gcc-13-riscv64-linux-gnu riscv64 13.2.0-23ubuntu3 [19.7 MB] Get:165 http://ftpmaster.internal/ubuntu noble-proposed/main riscv64 g++-13-riscv64-linux-gnu riscv64 13.2.0-23ubuntu3 [11.6 MB] Get:166 http://ftpmaster.internal/ubuntu noble-proposed/main riscv64 cpp-13-riscv64-linux-gnu riscv64 13.2.0-23ubuntu3 [10.3 MB] Get:167 http://ftpmaster.internal/ubuntu noble/main riscv64 g++ riscv64 4:13.2.0-7ubuntu1 [1082 B] Get:168 http://ftpmaster.internal/ubuntu noble/main riscv64 gcc riscv64 4:13.2.0-7ubuntu1 [5016 B] Get:169 http://ftpmaster.internal/ubuntu noble/main riscv64 cpp riscv64 4:13.2.0-7ubuntu1 [22.4 kB] Get:170 http://ftpmaster.internal/ubuntu noble/main riscv64 cpp-riscv64-linux-gnu riscv64 4:13.2.0-7ubuntu1 [5316 B] Get:171 http://ftpmaster.internal/ubuntu noble/main riscv64 gcc-riscv64-linux-gnu riscv64 4:13.2.0-7ubuntu1 [1202 B] Get:172 http://ftpmaster.internal/ubuntu noble/main riscv64 g++-riscv64-linux-gnu riscv64 4:13.2.0-7ubuntu1 [960 B] Get:173 http://ftpmaster.internal/ubuntu noble-proposed/main riscv64 dpkg-dev all 1.22.6ubuntu6 [1074 kB] Get:174 http://ftpmaster.internal/ubuntu noble-proposed/main riscv64 libdpkg-perl all 1.22.6ubuntu6 [268 kB] Get:175 http://ftpmaster.internal/ubuntu noble/main riscv64 lto-disabled-list all 47 [12.4 kB] Get:176 http://ftpmaster.internal/ubuntu noble/main riscv64 libfakeroot riscv64 1.33-1 [34.6 kB] Get:177 http://ftpmaster.internal/ubuntu noble/main riscv64 fakeroot riscv64 1.33-1 [78.4 kB] Preconfiguring packages ... Fetched 113 MB in 19s (6073 kB/s) (Reading database ... 13552 files and directories currently installed.) Preparing to unpack .../0-libnsl-dev_1.3.0-3build3_riscv64.deb ... Unpacking libnsl-dev:riscv64 (1.3.0-3build3) over (1.3.0-2build2) ... Preparing to unpack .../1-libcrypt-dev_1%3a4.4.36-4_riscv64.deb ... Unpacking libcrypt-dev:riscv64 (1:4.4.36-4) over (1:4.4.36-2) ... Preparing to unpack .../2-libc6-dev_2.39-0ubuntu8_riscv64.deb ... Unpacking libc6-dev:riscv64 (2.39-0ubuntu8) over (2.38-1ubuntu6) ... Preparing to unpack .../3-libc-dev-bin_2.39-0ubuntu8_riscv64.deb ... Unpacking libc-dev-bin (2.39-0ubuntu8) over (2.38-1ubuntu6) ... Preparing to unpack .../4-libtirpc-common_1.3.4+ds-1.1build1_all.deb ... Unpacking libtirpc-common (1.3.4+ds-1.1build1) over (1.3.3+ds-1) ... Preparing to unpack .../5-libtirpc-dev_1.3.4+ds-1.1build1_riscv64.deb ... Unpacking libtirpc-dev:riscv64 (1.3.4+ds-1.1build1) over (1.3.3+ds-1) ... 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(Reading database ... 14971 files and directories currently installed.) Preparing to unpack .../libgdbm-compat4t64_1.23-5.1build1_riscv64.deb ... Unpacking libgdbm-compat4t64:riscv64 (1.23-5.1build1) ... Selecting previously unselected package libperl5.38t64:riscv64. Preparing to unpack .../libperl5.38t64_5.38.2-3.2build1_riscv64.deb ... Unpacking libperl5.38t64:riscv64 (5.38.2-3.2build1) ... Preparing to unpack .../perl-base_5.38.2-3.2build1_riscv64.deb ... Unpacking perl-base (5.38.2-3.2build1) over (5.36.0-9ubuntu1) ... Setting up perl-base (5.38.2-3.2build1) ... (Reading database ... 15497 files and directories currently installed.) Preparing to unpack .../liblocale-gettext-perl_1.07-6ubuntu5_riscv64.deb ... Unpacking liblocale-gettext-perl (1.07-6ubuntu5) over (1.07-6) ... Preparing to unpack .../openssl_3.0.13-0ubuntu3_riscv64.deb ... Unpacking openssl (3.0.13-0ubuntu3) over (3.0.10-1ubuntu2) ... Preparing to unpack .../libsystemd-shared_255.4-1ubuntu6_riscv64.deb ... 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Unpacking systemd (255.4-1ubuntu6) over (253.5-1ubuntu6) ... dpkg: warning: unable to delete old directory '/lib/systemd/system-preset': Directory not empty dpkg: warning: unable to delete old directory '/lib/systemd/system-generators': Directory not empty dpkg: warning: unable to delete old directory '/lib/systemd/system/user@0.service.d': Directory not empty dpkg: warning: unable to delete old directory '/lib/systemd/system/user@.service.d': Directory not empty dpkg: warning: unable to delete old directory '/lib/systemd/system/user-.slice.d': Directory not empty dpkg: warning: unable to delete old directory '/lib/systemd/system/timers.target.wants': Directory not empty dpkg: warning: unable to delete old directory '/lib/systemd/system/systemd-localed.service.d': Directory not empty dpkg: warning: unable to delete old directory '/lib/systemd/system/sysinit.target.wants': Directory not empty dpkg: warning: unable to delete old directory '/lib/systemd/system/sockets.target.wants': Directory not empty dpkg: warning: unable to delete old directory '/lib/systemd/system/rescue.target.wants': Directory not empty dpkg: warning: unable to delete old directory '/lib/systemd/system/rc-local.service.d': Directory not empty dpkg: warning: unable to delete old directory '/lib/systemd/system/multi-user.target.wants': Directory not empty dpkg: warning: unable to delete old directory '/lib/systemd/system/initrd.target.wants': Directory not empty dpkg: warning: unable to delete old directory '/lib/systemd/system/initrd-root-fs.target.wants': Directory not empty dpkg: warning: unable to delete old directory '/lib/systemd/system/initrd-root-device.target.wants': Directory not empty dpkg: warning: unable to delete old directory '/lib/systemd/system/graphical.target.wants': Directory not empty dpkg: warning: unable to delete old directory '/lib/systemd/system/getty.target.wants': Directory not empty dpkg: warning: unable to delete old directory '/lib/systemd/network': Directory not empty dpkg: warning: unable to delete old directory '/lib/systemd/journald.conf.d': Directory not empty dpkg: warning: unable to delete old directory '/lib/modprobe.d': Directory not empty Preparing to unpack .../libsystemd0_255.4-1ubuntu6_riscv64.deb ... 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(both '/usr/bin/bunzip2' and '/usr/bin/bzcat') dpkg: warning: old file '/bin/bzip2' is the same as several new files! (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_riscv64.deb ... Unpacking libbz2-1.0:riscv64 (1.0.8-5.1) over (1.0.8-5build1) ... Setting up libbz2-1.0:riscv64 (1.0.8-5.1) ... Selecting previously unselected package gcc-14-base:riscv64. (Reading database ... 15664 files and directories currently installed.) 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Selecting previously unselected package libext2fs2t64:riscv64. (Reading database ... 15664 files and directories currently installed.) Preparing to unpack .../libext2fs2t64_1.47.0-2.4~exp1ubuntu3_riscv64.deb ... Adding 'diversion of /lib/riscv64-linux-gnu/libe2p.so.2 to /lib/riscv64-linux-gnu/libe2p.so.2.usr-is-merged by libext2fs2t64' Adding 'diversion of /lib/riscv64-linux-gnu/libe2p.so.2.3 to /lib/riscv64-linux-gnu/libe2p.so.2.3.usr-is-merged by libext2fs2t64' Adding 'diversion of /lib/riscv64-linux-gnu/libext2fs.so.2 to /lib/riscv64-linux-gnu/libext2fs.so.2.usr-is-merged by libext2fs2t64' Adding 'diversion of /lib/riscv64-linux-gnu/libext2fs.so.2.4 to /lib/riscv64-linux-gnu/libext2fs.so.2.4.usr-is-merged by libext2fs2t64' Unpacking libext2fs2t64:riscv64 (1.47.0-2.4~exp1ubuntu3) ... Setting up libcom-err2:riscv64 (1.47.0-2.4~exp1ubuntu3) ... Setting up libext2fs2t64:riscv64 (1.47.0-2.4~exp1ubuntu3) ... (Reading database ... 15680 files and directories currently installed.) 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Setting up libcryptsetup12:riscv64 (2:2.7.0-1ubuntu3) ... Setting up libfdisk1:riscv64 (2.39.3-9ubuntu4) ... Setting up libkmod2:riscv64 (31+20240202-2ubuntu5) ... Setting up libseccomp2:riscv64 (2.5.5-1ubuntu3) ... Setting up libsystemd-shared:riscv64 (255.4-1ubuntu6) ... Setting up systemd-dev (255.4-1ubuntu6) ... Setting up mount (2.39.3-9ubuntu4) ... Setting up systemd (255.4-1ubuntu6) ... Installing new version of config file /etc/systemd/journald.conf ... Installing new version of config file /etc/systemd/logind.conf ... Installing new version of config file /etc/systemd/networkd.conf ... Installing new version of config file /etc/systemd/pstore.conf ... Installing new version of config file /etc/systemd/sleep.conf ... Installing new version of config file /etc/systemd/system.conf ... Installing new version of config file /etc/systemd/user.conf ... Initializing machine ID from random generator. Setting up systemd-sysv (255.4-1ubuntu6) ... (Reading database ... 15679 files and directories currently installed.) Preparing to unpack .../init_1.66ubuntu1_riscv64.deb ... Unpacking init (1.66ubuntu1) over (1.65.2ubuntu1) ... Preparing to unpack .../libsmartcols1_2.39.3-9ubuntu4_riscv64.deb ... Unpacking libsmartcols1:riscv64 (2.39.3-9ubuntu4) over (2.39.1-4ubuntu2) ... Setting up libsmartcols1:riscv64 (2.39.3-9ubuntu4) ... (Reading database ... 15680 files and directories currently installed.) Preparing to unpack .../uuid-runtime_2.39.3-9ubuntu4_riscv64.deb ... Unpacking uuid-runtime (2.39.3-9ubuntu4) over (2.39.1-4ubuntu2) ... dpkg: warning: unable to delete old directory '/lib/systemd/system': Directory not empty dpkg: warning: unable to delete old directory '/lib/systemd': Directory not empty Preparing to unpack .../libattr1_1%3a2.5.2-1_riscv64.deb ... Unpacking libattr1:riscv64 (1:2.5.2-1) over (1:2.5.1-4) ... Setting up libattr1:riscv64 (1:2.5.2-1) ... 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Setting up libgpm2:riscv64 (1.20.7-11) ... Setting up libgdbm6t64:riscv64 (1.23-5.1build1) ... Setting up bsdextrautils (2.39.3-9ubuntu4) ... Setting up init (1.66ubuntu1) ... Setting up libgdbm-compat4t64:riscv64 (1.23-5.1build1) ... Setting up psmisc (23.7-1build1) ... Setting up libtirpc-common (1.3.4+ds-1.1build1) ... Setting up libsqlite3-0:riscv64 (3.45.1-1ubuntu2) ... Setting up binutils-common:riscv64 (2.42-4ubuntu2) ... Setting up linux-libc-dev:riscv64 (6.8.0-20.20) ... Setting up libctf-nobfd0:riscv64 (2.42-4ubuntu2) ... Setting up krb5-locales (1.20.1-6ubuntu2) ... Setting up libgomp1:riscv64 (14-20240315-1ubuntu1) ... Setting up bzip2 (1.0.8-5.1) ... Setting up libsframe1:riscv64 (2.42-4ubuntu2) ... Setting up libfakeroot:riscv64 (1.33-1) ... Setting up libjansson4:riscv64 (2.14-2build2) ... Setting up libkrb5support0:riscv64 (1.20.1-6ubuntu2) ... Setting up tzdata (2024a-1ubuntu1) ... Current default time zone: 'Etc/UTC' Local time is now: Tue Apr 2 00:58:24 UTC 2024. Universal Time is now: Tue Apr 2 00:58:24 UTC 2024. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up fakeroot (1.33-1) ... Setting up gcc-13-base:riscv64 (13.2.0-23ubuntu3) ... Setting up bash-completion (1:2.11-8) ... Setting up xz-utils (5.6.1+really5.4.5-1build1) ... Setting up perl-modules-5.38 (5.38.2-3.2build1) ... Setting up libproc2-0:riscv64 (2:4.0.4-4ubuntu3) ... Setting up libpng16-16t64:riscv64 (1.6.43-5build1) ... Setting up libatomic1:riscv64 (14-20240315-1ubuntu1) ... Setting up libss2:riscv64 (1.47.0-2.4~exp1ubuntu3) ... Setting up libncursesw6:riscv64 (6.4+20240113-1ubuntu1) ... Setting up libk5crypto3:riscv64 (1.20.1-6ubuntu2) ... Setting up logsave (1.47.0-2.4~exp1ubuntu3) ... Setting up libdb5.3t64:riscv64 (5.3.28+dfsg2-6build1) ... Setting up libubsan1:riscv64 (14-20240315-1ubuntu1) ... Setting up sensible-utils (0.0.22) ... Setting up uuid-runtime (2.39.3-9ubuntu4) ... Running in chroot, ignoring request. invoke-rc.d: policy-rc.d denied execution of restart. Setting up libcrypt-dev:riscv64 (1:4.4.36-4) ... Setting up libasan8:riscv64 (14-20240315-1ubuntu1) ... Setting up procps (2:4.0.4-4ubuntu3) ... Installing new version of config file /etc/sysctl.conf ... Setting up mawk (1.3.4.20240123-1) ... Setting up libkrb5-3:riscv64 (1.20.1-6ubuntu2) ... Setting up libperl5.38t64:riscv64 (5.38.2-3.2build1) ... Setting up libbinutils:riscv64 (2.42-4ubuntu2) ... Setting up libc-dev-bin (2.39-0ubuntu8) ... Setting up openssl (3.0.13-0ubuntu3) ... Setting up libgpg-error-l10n (1.47-3build1) ... Setting up readline-common (8.2-4build1) ... Setting up libcc1-0:riscv64 (14-20240315-1ubuntu1) ... Setting up liblocale-gettext-perl (1.07-6ubuntu5) ... Setting up libctf0:riscv64 (2.42-4ubuntu2) ... Setting up pinentry-curses (1.2.1-3ubuntu5) ... Setting up apt-utils (2.7.14) ... Setting up cpp-13-riscv64-linux-gnu (13.2.0-23ubuntu3) ... Setting up binutils-riscv64-linux-gnu (2.42-4ubuntu2) ... Setting up debconf-i18n (1.5.86) ... Setting up e2fsprogs (1.47.0-2.4~exp1ubuntu3) ... Setting up binutils (2.42-4ubuntu2) ... Setting up ca-certificates (20240203) ... Updating certificates in /etc/ssl/certs... rehash: warning: skipping ca-certificates.crt,it does not contain exactly one certificate or CRL 14 added, 5 removed; done. Setting up perl (5.38.2-3.2build1) ... Setting up optipng (0.7.8+ds-1build2) ... Setting up libgssapi-krb5-2:riscv64 (1.20.1-6ubuntu2) ... Setting up libdpkg-perl (1.22.6ubuntu6) ... Setting up libreadline8t64:riscv64 (8.2-4build1) ... Setting up libgcc-13-dev:riscv64 (13.2.0-23ubuntu3) ... Setting up gpgconf (2.4.4-2ubuntu16) ... Setting up libc6-dev:riscv64 (2.39-0ubuntu8) ... Setting up cpp-riscv64-linux-gnu (4:13.2.0-7ubuntu1) ... Setting up gpg (2.4.4-2ubuntu16) ... Setting up libstdc++-13-dev:riscv64 (13.2.0-23ubuntu3) ... Setting up gpg-agent (2.4.4-2ubuntu16) ... Setting up cpp-13 (13.2.0-23ubuntu3) ... Setting up libtirpc3t64:riscv64 (1.3.4+ds-1.1build1) ... Setting up gcc-13-riscv64-linux-gnu (13.2.0-23ubuntu3) ... Setting up dpkg-dev (1.22.6ubuntu6) ... Setting up gcc-riscv64-linux-gnu (4:13.2.0-7ubuntu1) ... Setting up libtirpc-dev:riscv64 (1.3.4+ds-1.1build1) ... Setting up gcc-13 (13.2.0-23ubuntu3) ... Setting up cpp (4:13.2.0-7ubuntu1) ... Setting up libnsl2:riscv64 (1.3.0-3build3) ... Setting up g++-13-riscv64-linux-gnu (13.2.0-23ubuntu3) ... Setting up g++-13 (13.2.0-23ubuntu3) ... Setting up libnss-nisplus:riscv64 (1.3-5build1) ... Setting up gcc (4:13.2.0-7ubuntu1) ... Setting up g++-riscv64-linux-gnu (4:13.2.0-7ubuntu1) ... Setting up g++ (4:13.2.0-7ubuntu1) ... Setting up libnsl-dev:riscv64 (1.3.0-3build3) ... Processing triggers for libc-bin (2.39-0ubuntu8) ... Processing triggers for debianutils (5.17build1) ... (Reading database ... 15732 files and directories currently installed.) Purging configuration files for libssl3:riscv64 (3.0.10-1ubuntu2) ... 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-28007361 riscv64 noble-proposed -c chroot:build-PACKAGEBUILD-28007361 --arch=riscv64 --dist=noble-proposed --nolog nanopolish_0.14.0-1ubuntu3.dsc Initiating build PACKAGEBUILD-28007361 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 6.5.0-26-generic #26.1~22.04.1-Ubuntu SMP Thu Mar 14 04:00:07 UTC 2024 riscv64 sbuild (Debian sbuild) 0.81.2ubuntu6 (16 February 2022) on bos03-riscv64-009.buildd +==============================================================================+ | nanopolish 0.14.0-1ubuntu3 (riscv64) Tue, 02 Apr 2024 01:01:31 +0000 | +==============================================================================+ Package: nanopolish Version: 0.14.0-1ubuntu3 Source Version: 0.14.0-1ubuntu3 Distribution: noble-proposed Machine Architecture: riscv64 Host Architecture: riscv64 Build Architecture: riscv64 Build Type: any I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-28007361/chroot-autobuild' with '<>' I: NOTICE: Log filtering will replace 'build/nanopolish-BxljmO/resolver-iNFv0b' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- nanopolish_0.14.0-1ubuntu3.dsc exists in .; copying to chroot I: NOTICE: Log filtering will replace 'build/nanopolish-BxljmO/nanopolish-0.14.0' with '<>' I: NOTICE: Log filtering will replace 'build/nanopolish-BxljmO' with '<>' +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper-compat (= 13), dh-python, python3, zlib1g-dev, libfast5-dev, libhts-dev, libeigen3-dev, libminimap2-dev, libstreamvbyte-dev, libslow5-dev, build-essential, fakeroot Filtered Build-Depends: debhelper-compat (= 13), dh-python, python3, zlib1g-dev, libfast5-dev, libhts-dev, libeigen3-dev, libminimap2-dev, libstreamvbyte-dev, libslow5-dev, 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 [425 B] Get:5 copy:/<>/apt_archive ./ Packages [512 B] Fetched 1894 B in 0s (4475 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 ca-certificates 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-common libtirpc-dev libtirpc3t64 libunistring2 openssl perl-modules-5.36 psmisc uuid-runtime Use 'apt autoremove' to remove them. The following additional packages will be installed: autoconf automake autopoint autotools-dev debhelper debugedit dh-autoreconf dh-python dh-strip-nondeterminism dwz file gettext gettext-base groff-base hdf5-helpers intltool-debian libaec-dev libaec0 libarchive-zip-perl libbrotli1 libcurl3t64-gnutls libcurl4-gnutls-dev libcurl4t64 libdebhelper-perl libdeflate-dev libdeflate0 libdw1t64 libeigen3-dev libelf1t64 libexpat1 libfast5-dev libfile-stripnondeterminism-perl libgfortran5 libhdf5-103-1t64 libhdf5-cpp-103-1t64 libhdf5-dev libhdf5-fortran-102t64 libhdf5-hl-100t64 libhdf5-hl-cpp-100t64 libhdf5-hl-fortran-100t64 libhts-dev libhts3t64 libhtscodecs2 libicu74 libjpeg-dev libjpeg-turbo8 libjpeg-turbo8-dev libjpeg8 libjpeg8-dev libldap2 liblzma-dev libmagic-mgc libmagic1t64 libminimap2-dev libnghttp2-14 libpipeline1 libpkgconf3 libpsl5t64 libpython3-stdlib libpython3.12-minimal libpython3.12-stdlib librtmp1 libsasl2-2 libsasl2-modules-db libslow5-0t64 libslow5-dev libssh-4 libssl-dev libstreamvbyte-dev libstreamvbyte0 libsub-override-perl libsz2 libtool libuchardet0 libxml2 m4 man-db media-types netbase pkg-config pkgconf pkgconf-bin po-debconf python3 python3-minimal python3-pkg-resources python3-setuptools python3.12 python3.12-minimal zlib1g-dev Suggested packages: autoconf-archive gnu-standards autoconf-doc dh-make flit python3-build python3-installer python3-wheel gettext-doc libasprintf-dev libgettextpo-dev groff libcurl4-doc libgnutls28-dev libidn-dev libkrb5-dev libldap2-dev librtmp-dev libssh2-1-dev libeigen3-doc libmpfrc++-dev libhdf5-doc liblzma-doc libssl-doc libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc apparmor less www-browser libmail-box-perl python3-doc python3-tk python3-venv python-setuptools-doc python3.12-venv python3.12-doc binfmt-support Recommended packages: curl | wget | lynx libarchive-cpio-perl libldap-common publicsuffix libsasl2-modules libltdl-dev libmail-sendmail-perl The following NEW packages will be installed: autoconf automake autopoint autotools-dev debhelper debugedit dh-autoreconf dh-python dh-strip-nondeterminism dwz file gettext gettext-base groff-base hdf5-helpers intltool-debian libaec-dev libaec0 libarchive-zip-perl libbrotli1 libcurl3t64-gnutls libcurl4-gnutls-dev libcurl4t64 libdebhelper-perl libdeflate-dev libdeflate0 libdw1t64 libeigen3-dev libelf1t64 libexpat1 libfast5-dev libfile-stripnondeterminism-perl libgfortran5 libhdf5-103-1t64 libhdf5-cpp-103-1t64 libhdf5-dev libhdf5-fortran-102t64 libhdf5-hl-100t64 libhdf5-hl-cpp-100t64 libhdf5-hl-fortran-100t64 libhts-dev libhts3t64 libhtscodecs2 libicu74 libjpeg-dev libjpeg-turbo8 libjpeg-turbo8-dev libjpeg8 libjpeg8-dev libldap2 liblzma-dev libmagic-mgc libmagic1t64 libminimap2-dev libnghttp2-14 libpipeline1 libpkgconf3 libpsl5t64 libpython3-stdlib libpython3.12-minimal libpython3.12-stdlib librtmp1 libsasl2-2 libsasl2-modules-db libslow5-0t64 libslow5-dev libssh-4 libssl-dev libstreamvbyte-dev libstreamvbyte0 libsub-override-perl libsz2 libtool libuchardet0 libxml2 m4 man-db media-types netbase pkg-config pkgconf pkgconf-bin po-debconf python3 python3-minimal python3-pkg-resources python3-setuptools python3.12 python3.12-minimal sbuild-build-depends-main-dummy zlib1g-dev 0 upgraded, 91 newly installed, 0 to remove and 0 not upgraded. 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Fetched 51.3 MB in 8s (6158 kB/s) Selecting previously unselected package libpython3.12-minimal:riscv64. (Reading database ... 15732 files and directories currently installed.) Preparing to unpack .../libpython3.12-minimal_3.12.2-4build4_riscv64.deb ... Unpacking libpython3.12-minimal:riscv64 (3.12.2-4build4) ... Selecting previously unselected package libexpat1:riscv64. Preparing to unpack .../libexpat1_2.6.1-2build1_riscv64.deb ... Unpacking libexpat1:riscv64 (2.6.1-2build1) ... Selecting previously unselected package python3.12-minimal. Preparing to unpack .../python3.12-minimal_3.12.2-4build4_riscv64.deb ... Unpacking python3.12-minimal (3.12.2-4build4) ... Setting up libpython3.12-minimal:riscv64 (3.12.2-4build4) ... Setting up libexpat1:riscv64 (2.6.1-2build1) ... Setting up python3.12-minimal (3.12.2-4build4) ... Selecting previously unselected package python3-minimal. (Reading database ... 16050 files and directories currently installed.) 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Setting up libdeflate0:riscv64 (1.19-1) ... Setting up gettext-base (0.21-14ubuntu1) ... Setting up m4 (1.4.19-4) ... Setting up file (1:5.45-3build1) ... Setting up libaec0:riscv64 (1.1.2-1) ... Setting up libelf1t64:riscv64 (0.190-1.1build3) ... Setting up libdw1t64:riscv64 (0.190-1.1build3) ... Setting up libsasl2-modules-db:riscv64 (2.1.28+dfsg1-5ubuntu2) ... Setting up autotools-dev (20220109.1) ... Setting up libpkgconf3:riscv64 (1.8.1-2) ... Setting up librtmp1:riscv64 (2.4+20151223.gitfa8646d.1-2build7) ... Setting up libstreamvbyte-dev:riscv64 (0.4.1-4ubuntu1) ... Setting up libssl-dev:riscv64 (3.0.13-0ubuntu3) ... Setting up autopoint (0.21-14ubuntu1) ... Setting up libslow5-0t64:riscv64 (0.7.0+dfsg-2.1) ... Setting up pkgconf-bin (1.8.1-2) ... Setting up libjpeg-turbo8:riscv64 (2.1.5-2ubuntu1) ... Setting up libsasl2-2:riscv64 (2.1.28+dfsg1-5ubuntu2) ... Setting up libssh-4:riscv64 (0.10.6-2build1) ... Setting up libgfortran5:riscv64 (14-20240315-1ubuntu1) ... Setting up autoconf (2.71-3) ... Setting up liblzma-dev:riscv64 (5.6.1+really5.4.5-1build1) ... Setting up libicu74:riscv64 (74.2-1ubuntu1) ... Setting up zlib1g-dev:riscv64 (1:1.3.dfsg-3.1ubuntu2) ... Setting up dwz (0.15-1build6) ... Setting up libuchardet0:riscv64 (0.0.8-1) ... Setting up debugedit (1:5.0-5build1) ... Setting up libsub-override-perl (0.10-1) ... Setting up netbase (6.4) ... Setting up libdeflate-dev:riscv64 (1.19-1) ... Setting up libxml2:riscv64 (2.9.14+dfsg-1.3ubuntu3) ... Setting up libldap2:riscv64 (2.6.7+dfsg-1~exp1ubuntu7) ... Setting up libsz2:riscv64 (1.1.2-1) ... Setting up libjpeg8:riscv64 (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 libjpeg-turbo8-dev:riscv64 (2.1.5-2ubuntu1) ... Setting up gettext (0.21-14ubuntu1) ... Setting up libpython3.12-stdlib:riscv64 (3.12.2-4build4) ... Setting up libcurl4t64:riscv64 (8.5.0-2ubuntu9) ... Setting up libtool (2.4.7-7) ... Setting up python3.12 (3.12.2-4build4) ... Setting up libaec-dev:riscv64 (1.1.2-1) ... Setting up libcurl3t64-gnutls:riscv64 (8.5.0-2ubuntu9) ... Setting up libslow5-dev:riscv64 (0.7.0+dfsg-2.1) ... Setting up libcurl4-gnutls-dev:riscv64 (8.5.0-2ubuntu9) ... Setting up pkgconf:riscv64 (1.8.1-2) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up libminimap2-dev (2.26+dfsg-1build1) ... Setting up libeigen3-dev (3.4.0-4) ... Setting up pkg-config:riscv64 (1.8.1-2) ... Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up groff-base (1.23.0-3build2) ... Setting up libhts3t64:riscv64 (1.19+ds-1.1build3) ... Setting up libjpeg8-dev:riscv64 (8c-2ubuntu11) ... Setting up libhdf5-103-1t64:riscv64 (1.10.10+repack-3.1ubuntu4) ... Setting up libpython3-stdlib:riscv64 (3.12.2-0ubuntu2) ... Setting up libhdf5-hl-100t64:riscv64 (1.10.10+repack-3.1ubuntu4) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libhdf5-cpp-103-1t64:riscv64 (1.10.10+repack-3.1ubuntu4) ... Setting up libjpeg-dev:riscv64 (8c-2ubuntu11) ... Setting up libhts-dev:riscv64 (1.19+ds-1.1build3) ... Setting up libhdf5-fortran-102t64:riscv64 (1.10.10+repack-3.1ubuntu4) ... Setting up python3 (3.12.2-0ubuntu2) ... 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 libhdf5-hl-cpp-100t64:riscv64 (1.10.10+repack-3.1ubuntu4) ... Setting up python3-pkg-resources (68.1.2-2ubuntu1) ... Setting up python3-setuptools (68.1.2-2ubuntu1) ... Setting up libhdf5-hl-fortran-100t64:riscv64 (1.10.10+repack-3.1ubuntu4) ... Setting up debhelper (13.14.1ubuntu5) ... Setting up libhdf5-dev (1.10.10+repack-3.1ubuntu4) ... update-alternatives: using /usr/lib/riscv64-linux-gnu/pkgconfig/hdf5-serial.pc to provide /usr/lib/riscv64-linux-gnu/pkgconfig/hdf5.pc (hdf5.pc) in auto mode Setting up dh-python (6.20240401) ... Setting up libfast5-dev (0.6.5-7build5) ... Setting up sbuild-build-depends-main-dummy (0.invalid.0) ... Processing triggers for systemd (255.4-1ubuntu6) ... Processing triggers for libc-bin (2.39-0ubuntu8) ... +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (riscv64 included in amd64 arm64 armhf ppc64el riscv64) +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 6.5.0-26-generic #26.1~22.04.1-Ubuntu SMP Thu Mar 14 04:00:07 UTC 2024 riscv64 (riscv64) 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_14-20240315-1ubuntu1 linux-libc-dev_6.8.0-20.20 Package versions: adduser_3.137ubuntu1 advancecomp_2.5-1 apt_2.7.14 apt-utils_2.7.14 autoconf_2.71-3 automake_1:1.16.5-1.3ubuntu1 autopoint_0.21-14ubuntu1 autotools-dev_20220109.1 base-files_13ubuntu9 base-passwd_3.6.3 bash_5.2.21-2ubuntu4 bash-completion_1:2.11-8 binutils_2.42-4ubuntu2 binutils-common_2.42-4ubuntu2 binutils-riscv64-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-riscv64-linux-gnu_13.2.0-23ubuntu3 cpp-riscv64-linux-gnu_4:13.2.0-7ubuntu1 dash_0.5.12-6ubuntu5 debconf_1.5.86 debconf-i18n_1.5.86 debhelper_13.14.1ubuntu5 debianutils_5.17build1 debugedit_1:5.0-5build1 dh-autoreconf_20 dh-python_6.20240401 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 e2fsprogs_1.47.0-2.4~exp1ubuntu3 fakeroot_1.33-1 file_1:5.45-3build1 findutils_4.9.0-5 g++_4:13.2.0-7ubuntu1 g++-13_13.2.0-23ubuntu3 g++-13-riscv64-linux-gnu_13.2.0-23ubuntu3 g++-riscv64-linux-gnu_4:13.2.0-7ubuntu1 gcc_4:13.2.0-7ubuntu1 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+------------------------------------------------------------------------------+ Unpack source ------------- -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: nanopolish Binary: nanopolish Architecture: amd64 arm64 armhf ppc64el riscv64 Version: 0.14.0-1ubuntu3 Maintainer: Ubuntu Developers Uploaders: Andreas Tille Homepage: https://github.com/jts/nanopolish Standards-Version: 4.6.1 Vcs-Browser: https://salsa.debian.org/med-team/nanopolish Vcs-Git: https://salsa.debian.org/med-team/nanopolish.git Testsuite: autopkgtest Build-Depends: debhelper-compat (= 13), dh-python, python3, zlib1g-dev, libfast5-dev, libhts-dev, libeigen3-dev, libminimap2-dev, libstreamvbyte-dev, libslow5-dev Package-List: nanopolish deb science optional arch=amd64,arm64,armhf,ppc64el,riscv64 Checksums-Sha1: a26c2a1a0f41a0e3fef52dee3d6ef1aea11e0266 4073583 nanopolish_0.14.0.orig.tar.gz bf62914c8b77702b3dd91ec1877b2538a2786314 9212 nanopolish_0.14.0-1ubuntu3.debian.tar.xz Checksums-Sha256: bcc1a7e2d23941592d817da3af9165b3843ae52b11a3ca5983d6417f1614ef78 4073583 nanopolish_0.14.0.orig.tar.gz ab1d2f95e3d1117b6122b3afd0d3ae4264153c1f45ab17107466438898e526d2 9212 nanopolish_0.14.0-1ubuntu3.debian.tar.xz Files: 90b445d40348427fd009bea3e04f0249 4073583 nanopolish_0.14.0.orig.tar.gz 01704c02240716bc34d99a863d7e62e6 9212 nanopolish_0.14.0-1ubuntu3.debian.tar.xz Original-Maintainer: Debian Med Packaging Team -----BEGIN PGP SIGNATURE----- iQIzBAEBCgAdFiEEoIn7Nqr72tWswTJQafeQFxohCYQFAmYKW7EACgkQafeQFxoh CYQcGhAAxzBt6XmIn63nUIQQyTEx4z8nsg/oJDSG0h6PBtm5dHVbAmVdVOPuV3hM YflSKN3s1vFgrk5VmT8q3P+xL7YeQjrRNmM0PsJ4tQ38iHcMBUY4hEBO3yPgOBN8 xOm3zdoafWOpiz1vw/cWHmshz51jEUTHtV7HTrAP66GqWTOoxVXSA37rY7XYYMQ2 CfYosz8wazCN+CN6oAyDLPKbQyk2TN0C0uKtKw0zIJlEPk/ObD2eXdEfgpes0Eul qrQX2trjcvTNMitBV2Z/VLUQOCFkTuzmlSZfUN3+T17+b2LAO/8Md0Fcs2V6vWG0 FBYSbvmaOAtNz4PpXstv68Ko8blCZS5N/s+pPfMNEujtC9kQbgs/b4pyFv5Z+UUs qQYoo2IR81cD0fs5TDiNmXGHFK3kKGHPwNxkcj299yL8tu7Re6JGA/OqIERvMjjJ 4xhb5oRyD/G85qFxIBcsXDqHgDhCaIyIpBQszhStR2GwLdGwSYsBdbAi2dLxdfBW Ljymd3xY+DYuxIVSdnExjGxo2XHGn0X1W+qOEbN2cRMUH8h5nYPrCZjYpOoX96kL dRmvrfe4vGTY3OMIEovV6LM9dfqW05cQQ6YH+5w5WHH9+oGBYfayLUfTOmHVXjke OxRJy+Z7AhHMqZlgn9n0S0rhMZogNeEydcCmBqPY74EsrEfxmL4= =POyj -----END PGP SIGNATURE----- gpgv: Signature made Mon Apr 1 07:01:05 2024 UTC gpgv: using RSA key A089FB36AAFBDAD5ACC1325069F790171A210984 gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./nanopolish_0.14.0-1ubuntu3.dsc: no acceptable signature found dpkg-source: info: extracting nanopolish in /<> dpkg-source: info: unpacking nanopolish_0.14.0.orig.tar.gz dpkg-source: info: unpacking nanopolish_0.14.0-1ubuntu3.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying add-shebang-to-script.patch dpkg-source: info: applying reproducible.patch dpkg-source: info: applying fix_remaining_python_interpreters.patch dpkg-source: info: applying staticMinimap2Library.patch dpkg-source: info: applying link_ext_slow5lib.patch Check disk space ---------------- Sufficient free space for build User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf DEB_BUILD_OPTIONS=parallel=4 HOME=/sbuild-nonexistent LANG=C.UTF-8 LC_ALL=C.UTF-8 LOGNAME=buildd PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games SCHROOT_ALIAS_NAME=build-PACKAGEBUILD-28007361 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-28007361 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-28007361 SCHROOT_UID=2001 SCHROOT_USER=buildd SHELL=/bin/sh TERM=unknown USER=buildd V=1 dpkg-buildpackage ----------------- Command: dpkg-buildpackage --sanitize-env -us -uc -mLaunchpad Build Daemon -B -rfakeroot dpkg-buildpackage: info: source package nanopolish dpkg-buildpackage: info: source version 0.14.0-1ubuntu3 dpkg-buildpackage: info: source distribution noble dpkg-source --before-build . dpkg-buildpackage: info: host architecture riscv64 debian/rules clean dh clean --with python3 debian/rules override_dh_auto_clean make[1]: Entering directory '/<>' sed -i~ 's/^.depend: .*/.depend:/' Makefile touch .depend /usr/bin/make clean make[2]: Entering directory '/<>' rm -f nanopolish nanopolish_test src/alignment/nanopolish_alignment_db.o src/alignment/nanopolish_anchor.o src/alignment/nanopolish_eventalign.o src/basemods/nanopolish_basemods.o src/common/fs_support.o src/common/logsum.o src/common/nanopolish_alphabet.o src/common/nanopolish_bam_processor.o src/common/nanopolish_bam_utils.o src/common/nanopolish_common.o src/common/nanopolish_iupac.o src/common/nanopolish_klcs.o src/common/nanopolish_variant.o src/hmm/nanopolish_duration_model.o src/hmm/nanopolish_profile_hmm.o src/hmm/nanopolish_profile_hmm_r7.o src/hmm/nanopolish_profile_hmm_r9.o src/hmm/nanopolish_transition_parameters.o src/io/nanopolish_fast5_io.o src/io/nanopolish_fast5_loader.o src/io/nanopolish_fast5_processor.o src/nanopolish_call_methylation.o src/nanopolish_call_variants.o src/nanopolish_detect_polyi.o src/nanopolish_fast5_check.o src/nanopolish_haplotype.o src/nanopolish_index.o src/nanopolish_methyltrain.o src/nanopolish_phase_reads.o src/nanopolish_polya_estimator.o src/nanopolish_raw_loader.o src/nanopolish_read_db.o src/nanopolish_scorereads.o src/nanopolish_squiggle_read.o src/nanopolish_train_poremodel_from_basecalls.o src/nanopolish_variant_db.o src/nanopolish_vcf2fasta.o src/pore_model/nanopolish_model_names.o src/pore_model/nanopolish_pore_model_set.o src/pore_model/nanopolish_poremodel.o src/training_core.o src/thirdparty/fet.o src/thirdparty/scrappie/event_detection.o src/thirdparty/scrappie/scrappie_common.o src/thirdparty/stdaln.o \ src/main/nanopolish.o src/test/nanopolish_test.o make[2]: Leaving directory '/<>' rm -f .depend mv Makefile~ Makefile make[1]: Leaving directory '/<>' dh_clean debian/rules binary-arch dh binary-arch --with python3 dh_update_autotools_config -a dh_autoreconf -a dh_auto_configure -a debian/rules override_dh_auto_build make[1]: Entering directory '/<>' dh_auto_build make -j4 "INSTALL=install --strip-program=true" make[2]: Entering directory '/<>' rm -f ./.depend g++ -o src/main/nanopolish.o -c -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/nanopolish-0.14.0-1ubuntu3 -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./src/basemods -fPIC src/main/nanopolish.cpp g++ -o src/alignment/nanopolish_alignment_db.o -c -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/nanopolish-0.14.0-1ubuntu3 -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./src/basemods -fPIC src/alignment/nanopolish_alignment_db.cpp g++ -o src/alignment/nanopolish_anchor.o -c -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/nanopolish-0.14.0-1ubuntu3 -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./src/basemods -fPIC src/alignment/nanopolish_anchor.cpp g++ -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/nanopolish-0.14.0-1ubuntu3 -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./src/basemods -MM src/alignment/nanopolish_alignment_db.cpp src/alignment/nanopolish_anchor.cpp src/alignment/nanopolish_eventalign.cpp src/basemods/nanopolish_basemods.cpp src/common/fs_support.cpp src/common/logsum.cpp src/common/nanopolish_alphabet.cpp src/common/nanopolish_bam_processor.cpp src/common/nanopolish_bam_utils.cpp src/common/nanopolish_common.cpp src/common/nanopolish_iupac.cpp src/common/nanopolish_klcs.cpp src/common/nanopolish_variant.cpp src/hmm/nanopolish_duration_model.cpp src/hmm/nanopolish_profile_hmm.cpp src/hmm/nanopolish_profile_hmm_r7.cpp src/hmm/nanopolish_profile_hmm_r9.cpp src/hmm/nanopolish_transition_parameters.cpp src/io/nanopolish_fast5_io.cpp src/io/nanopolish_fast5_loader.cpp src/io/nanopolish_fast5_processor.cpp src/nanopolish_call_methylation.cpp src/nanopolish_call_variants.cpp src/nanopolish_detect_polyi.cpp src/nanopolish_fast5_check.cpp src/nanopolish_haplotype.cpp src/nanopolish_index.cpp src/nanopolish_methyltrain.cpp src/nanopolish_phase_reads.cpp src/nanopolish_polya_estimator.cpp src/nanopolish_raw_loader.cpp src/nanopolish_read_db.cpp src/nanopolish_scorereads.cpp src/nanopolish_squiggle_read.cpp src/nanopolish_train_poremodel_from_basecalls.cpp src/nanopolish_variant_db.cpp src/nanopolish_vcf2fasta.cpp src/pore_model/nanopolish_model_names.cpp src/pore_model/nanopolish_pore_model_set.cpp src/pore_model/nanopolish_poremodel.cpp src/training_core.cpp src/thirdparty/fet.c src/thirdparty/scrappie/event_detection.c src/thirdparty/scrappie/scrappie_common.c src/thirdparty/stdaln.c > ./.depend; g++ -o src/alignment/nanopolish_eventalign.o -c -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/nanopolish-0.14.0-1ubuntu3 -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./src/basemods -fPIC src/alignment/nanopolish_eventalign.cpp g++ -o src/basemods/nanopolish_basemods.o -c -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/nanopolish-0.14.0-1ubuntu3 -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./src/basemods -fPIC src/basemods/nanopolish_basemods.cpp g++ -o src/common/fs_support.o -c -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/nanopolish-0.14.0-1ubuntu3 -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./src/basemods -fPIC src/common/fs_support.cpp g++ -o src/common/logsum.o -c -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/nanopolish-0.14.0-1ubuntu3 -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./src/basemods -fPIC src/common/logsum.cpp g++ -o src/common/nanopolish_alphabet.o -c -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/nanopolish-0.14.0-1ubuntu3 -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./src/basemods -fPIC src/common/nanopolish_alphabet.cpp g++ -o src/common/nanopolish_bam_processor.o -c -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/nanopolish-0.14.0-1ubuntu3 -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./src/basemods -fPIC src/common/nanopolish_bam_processor.cpp g++ -o src/common/nanopolish_bam_utils.o -c -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/nanopolish-0.14.0-1ubuntu3 -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./src/basemods -fPIC src/common/nanopolish_bam_utils.cpp g++ -o src/common/nanopolish_common.o -c -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/nanopolish-0.14.0-1ubuntu3 -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./src/basemods -fPIC src/common/nanopolish_common.cpp g++ -o src/common/nanopolish_iupac.o -c -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/nanopolish-0.14.0-1ubuntu3 -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./src/basemods -fPIC src/common/nanopolish_iupac.cpp g++ -o src/common/nanopolish_klcs.o -c -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/nanopolish-0.14.0-1ubuntu3 -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./src/basemods -fPIC src/common/nanopolish_klcs.cpp g++ -o src/common/nanopolish_variant.o -c -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/nanopolish-0.14.0-1ubuntu3 -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./src/basemods -fPIC src/common/nanopolish_variant.cpp g++ -o src/hmm/nanopolish_duration_model.o -c -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/nanopolish-0.14.0-1ubuntu3 -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./src/basemods -fPIC src/hmm/nanopolish_duration_model.cpp g++ -o src/hmm/nanopolish_profile_hmm.o -c -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/nanopolish-0.14.0-1ubuntu3 -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./src/basemods -fPIC src/hmm/nanopolish_profile_hmm.cpp g++ -o src/hmm/nanopolish_profile_hmm_r7.o -c -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/nanopolish-0.14.0-1ubuntu3 -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./src/basemods -fPIC src/hmm/nanopolish_profile_hmm_r7.cpp g++ -o src/hmm/nanopolish_profile_hmm_r9.o -c -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/nanopolish-0.14.0-1ubuntu3 -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./src/basemods -fPIC src/hmm/nanopolish_profile_hmm_r9.cpp g++ -o src/hmm/nanopolish_transition_parameters.o -c -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/nanopolish-0.14.0-1ubuntu3 -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./src/basemods -fPIC src/hmm/nanopolish_transition_parameters.cpp g++ -o src/io/nanopolish_fast5_io.o -c -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/nanopolish-0.14.0-1ubuntu3 -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./src/basemods -fPIC src/io/nanopolish_fast5_io.cpp g++ -o src/io/nanopolish_fast5_loader.o -c -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/nanopolish-0.14.0-1ubuntu3 -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./src/basemods -fPIC src/io/nanopolish_fast5_loader.cpp g++ -o src/io/nanopolish_fast5_processor.o -c -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/nanopolish-0.14.0-1ubuntu3 -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./src/basemods -fPIC src/io/nanopolish_fast5_processor.cpp g++ -o src/nanopolish_call_methylation.o -c -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/nanopolish-0.14.0-1ubuntu3 -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./src/basemods -fPIC src/nanopolish_call_methylation.cpp g++ -o src/nanopolish_call_variants.o -c -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/nanopolish-0.14.0-1ubuntu3 -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./src/basemods -fPIC src/nanopolish_call_variants.cpp g++ -o src/nanopolish_detect_polyi.o -c -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/nanopolish-0.14.0-1ubuntu3 -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./src/basemods -fPIC src/nanopolish_detect_polyi.cpp g++ -o src/nanopolish_fast5_check.o -c -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/nanopolish-0.14.0-1ubuntu3 -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./src/basemods -fPIC src/nanopolish_fast5_check.cpp src/nanopolish_detect_polyi.cpp: In function ‘void dpi_estimate_polya_for_single_read(const ReadDB&, const faidx_t*, FILE*, const bam_hdr_t*, const bam1_t*, size_t, int, int)’: src/nanopolish_detect_polyi.cpp:1040:39: warning: format ‘%d’ expects argument of type ‘int’, but argument 5 has type ‘long int’ [-Wformat=] 1040 | fprintf(out_fp, "%s\t%s\t%d\t-1.0\t-1.0\t-1.0\t-1.0\t-1.00\t-1.00\tREAD_FAILED_LOAD\n", | ~^ | | | int | %ld 1041 | read_name.c_str(), ref_name.c_str(), record->core.pos); | ~~~~~~~~~~~~~~~~ | | | long int src/nanopolish_detect_polyi.cpp:1105:35: warning: format ‘%d’ expects argument of type ‘int’, but argument 5 has type ‘long int’ [-Wformat=] 1105 | fprintf(out_fp, "%s\t%s\t%d\t%.1lf\t%.1lf\t%.1lf\t%.1lf\t%.2lf\t%.2lf\t%s\t%s\n", | ~^ | | | int | %ld 1106 | read_name.c_str(), ref_name.c_str(), record->core.pos, | ~~~~~~~~~~~~~~~~ | | | long int g++ -o src/nanopolish_haplotype.o -c -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/nanopolish-0.14.0-1ubuntu3 -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./src/basemods -fPIC src/nanopolish_haplotype.cpp g++ -o src/nanopolish_index.o -c -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/nanopolish-0.14.0-1ubuntu3 -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./src/basemods -fPIC src/nanopolish_index.cpp g++ -o src/nanopolish_methyltrain.o -c -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/nanopolish-0.14.0-1ubuntu3 -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./src/basemods -fPIC src/nanopolish_methyltrain.cpp g++ -o src/nanopolish_phase_reads.o -c -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/nanopolish-0.14.0-1ubuntu3 -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./src/basemods -fPIC src/nanopolish_phase_reads.cpp g++ -o src/nanopolish_polya_estimator.o -c -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/nanopolish-0.14.0-1ubuntu3 -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./src/basemods -fPIC src/nanopolish_polya_estimator.cpp src/nanopolish_polya_estimator.cpp: In function ‘void estimate_polya_for_single_read(const ReadDB&, const faidx_t*, FILE*, const bam_hdr_t*, const bam1_t*, size_t, int, int)’: src/nanopolish_polya_estimator.cpp:765:39: warning: format ‘%d’ expects argument of type ‘int’, but argument 5 has type ‘long int’ [-Wformat=] 765 | fprintf(out_fp, "%s\t%s\t%d\t-1.0\t-1.0\t-1.0\t-1.0\t-1.00\t-1.00\tREAD_FAILED_LOAD\n", | ~^ | | | int | %ld 766 | read_name.c_str(), ref_name.c_str(), record->core.pos); | ~~~~~~~~~~~~~~~~ | | | long int src/nanopolish_polya_estimator.cpp:823:35: warning: format ‘%d’ expects argument of type ‘int’, but argument 5 has type ‘long int’ [-Wformat=] 823 | fprintf(out_fp, "%s\t%s\t%d\t%.1lf\t%.1lf\t%.1lf\t%.1lf\t%.2lf\t%.2lf\t%s\n", | ~^ | | | int | %ld 824 | read_name.c_str(), ref_name.c_str(), record->core.pos, | ~~~~~~~~~~~~~~~~ | | | long int g++ -o src/nanopolish_raw_loader.o -c -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/nanopolish-0.14.0-1ubuntu3 -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./src/basemods -fPIC src/nanopolish_raw_loader.cpp g++ -o src/nanopolish_read_db.o -c -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/nanopolish-0.14.0-1ubuntu3 -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./src/basemods -fPIC src/nanopolish_read_db.cpp g++ -o src/nanopolish_scorereads.o -c -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/nanopolish-0.14.0-1ubuntu3 -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./src/basemods -fPIC src/nanopolish_scorereads.cpp g++ -o src/nanopolish_squiggle_read.o -c -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/nanopolish-0.14.0-1ubuntu3 -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./src/basemods -fPIC src/nanopolish_squiggle_read.cpp g++ -o src/nanopolish_train_poremodel_from_basecalls.o -c -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/nanopolish-0.14.0-1ubuntu3 -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./src/basemods -fPIC src/nanopolish_train_poremodel_from_basecalls.cpp g++ -o src/nanopolish_variant_db.o -c -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/nanopolish-0.14.0-1ubuntu3 -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./src/basemods -fPIC src/nanopolish_variant_db.cpp g++ -o src/nanopolish_vcf2fasta.o -c -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/nanopolish-0.14.0-1ubuntu3 -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./src/basemods -fPIC src/nanopolish_vcf2fasta.cpp g++ -o src/pore_model/nanopolish_model_names.o -c -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/nanopolish-0.14.0-1ubuntu3 -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./src/basemods -fPIC src/pore_model/nanopolish_model_names.cpp g++ -o src/pore_model/nanopolish_pore_model_set.o -c -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/nanopolish-0.14.0-1ubuntu3 -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./src/basemods -fPIC src/pore_model/nanopolish_pore_model_set.cpp g++ -o src/pore_model/nanopolish_poremodel.o -c -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/nanopolish-0.14.0-1ubuntu3 -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./src/basemods -fPIC src/pore_model/nanopolish_poremodel.cpp g++ -o src/training_core.o -c -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/nanopolish-0.14.0-1ubuntu3 -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./src/basemods -fPIC src/training_core.cpp cc -o src/thirdparty/fet.o -c -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/nanopolish-0.14.0-1ubuntu3 -O3 -flto -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./src/basemods -fPIC src/thirdparty/fet.c cc -o src/thirdparty/scrappie/event_detection.o -c -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/nanopolish-0.14.0-1ubuntu3 -O3 -flto -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./src/basemods -fPIC src/thirdparty/scrappie/event_detection.c cc -o src/thirdparty/scrappie/scrappie_common.o -c -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/nanopolish-0.14.0-1ubuntu3 -O3 -flto -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./src/basemods -fPIC src/thirdparty/scrappie/scrappie_common.c cc -o src/thirdparty/stdaln.o -c -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/nanopolish-0.14.0-1ubuntu3 -O3 -flto -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./src/basemods -fPIC src/thirdparty/stdaln.c g++ -o nanopolish -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/nanopolish-0.14.0-1ubuntu3 -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./src/basemods -fPIC src/main/nanopolish.o src/alignment/nanopolish_alignment_db.o src/alignment/nanopolish_anchor.o src/alignment/nanopolish_eventalign.o src/basemods/nanopolish_basemods.o src/common/fs_support.o src/common/logsum.o src/common/nanopolish_alphabet.o src/common/nanopolish_bam_processor.o src/common/nanopolish_bam_utils.o src/common/nanopolish_common.o src/common/nanopolish_iupac.o src/common/nanopolish_klcs.o src/common/nanopolish_variant.o src/hmm/nanopolish_duration_model.o src/hmm/nanopolish_profile_hmm.o src/hmm/nanopolish_profile_hmm_r7.o src/hmm/nanopolish_profile_hmm_r9.o src/hmm/nanopolish_transition_parameters.o src/io/nanopolish_fast5_io.o src/io/nanopolish_fast5_loader.o src/io/nanopolish_fast5_processor.o src/nanopolish_call_methylation.o src/nanopolish_call_variants.o src/nanopolish_detect_polyi.o src/nanopolish_fast5_check.o src/nanopolish_haplotype.o src/nanopolish_index.o src/nanopolish_methyltrain.o src/nanopolish_phase_reads.o src/nanopolish_polya_estimator.o src/nanopolish_raw_loader.o src/nanopolish_read_db.o src/nanopolish_scorereads.o src/nanopolish_squiggle_read.o src/nanopolish_train_poremodel_from_basecalls.o src/nanopolish_variant_db.o src/nanopolish_vcf2fasta.o src/pore_model/nanopolish_model_names.o src/pore_model/nanopolish_pore_model_set.o src/pore_model/nanopolish_poremodel.o src/training_core.o src/thirdparty/fet.o src/thirdparty/scrappie/event_detection.o src/thirdparty/scrappie/scrappie_common.o src/thirdparty/stdaln.o -lz -lrt -lhdf5 -lhts -lminimap2 -lslow5 -lstreamvbyte -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -L/usr/lib/riscv64-linux-gnu/hdf5/serial lto-wrapper: warning: using serial compilation of 10 LTRANS jobs lto-wrapper: note: see the ‘-flto’ option documentation for more information make[2]: Leaving directory '/<>' /usr/bin/make nanopolish_test make[2]: Entering directory '/<>' g++ -o src/test/nanopolish_test.o -c -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/nanopolish-0.14.0-1ubuntu3 -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./src/basemods -fPIC src/test/nanopolish_test.cpp g++ -o nanopolish_test -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<>=/usr/src/nanopolish-0.14.0-1ubuntu3 -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=3 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./src/basemods -fPIC src/test/nanopolish_test.o src/alignment/nanopolish_alignment_db.o src/alignment/nanopolish_anchor.o src/alignment/nanopolish_eventalign.o src/basemods/nanopolish_basemods.o src/common/fs_support.o src/common/logsum.o src/common/nanopolish_alphabet.o src/common/nanopolish_bam_processor.o src/common/nanopolish_bam_utils.o src/common/nanopolish_common.o src/common/nanopolish_iupac.o src/common/nanopolish_klcs.o src/common/nanopolish_variant.o src/hmm/nanopolish_duration_model.o src/hmm/nanopolish_profile_hmm.o src/hmm/nanopolish_profile_hmm_r7.o src/hmm/nanopolish_profile_hmm_r9.o src/hmm/nanopolish_transition_parameters.o src/io/nanopolish_fast5_io.o src/io/nanopolish_fast5_loader.o src/io/nanopolish_fast5_processor.o src/nanopolish_call_methylation.o src/nanopolish_call_variants.o src/nanopolish_detect_polyi.o src/nanopolish_fast5_check.o src/nanopolish_haplotype.o src/nanopolish_index.o src/nanopolish_methyltrain.o src/nanopolish_phase_reads.o src/nanopolish_polya_estimator.o src/nanopolish_raw_loader.o src/nanopolish_read_db.o src/nanopolish_scorereads.o src/nanopolish_squiggle_read.o src/nanopolish_train_poremodel_from_basecalls.o src/nanopolish_variant_db.o src/nanopolish_vcf2fasta.o src/pore_model/nanopolish_model_names.o src/pore_model/nanopolish_pore_model_set.o src/pore_model/nanopolish_poremodel.o src/training_core.o src/thirdparty/fet.o src/thirdparty/scrappie/event_detection.o src/thirdparty/scrappie/scrappie_common.o src/thirdparty/stdaln.o -lz -lrt -lhdf5 -lhts -lminimap2 -lslow5 -lstreamvbyte -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -L/usr/lib/riscv64-linux-gnu/hdf5/serial lto-wrapper: warning: using serial compilation of 8 LTRANS jobs lto-wrapper: note: see the ‘-flto’ option documentation for more information make[2]: Leaving directory '/<>' make[1]: Leaving directory '/<>' create-stamp debian/debhelper-build-stamp dh_prep -a dh_auto_install --destdir=debian/nanopolish/ -a debian/rules override_dh_install make[1]: Entering directory '/<>' dh_install for pl in `find debian -name "*.pl"` ; do \ sed -i '1s?^#!/usr/bin/env.*perl?#!/usr/bin/perl?' ${pl} ; \ done for pl in `grep -Rl '#![[:space:]]*/usr/bin/env *python' debian/*/usr/*` ; do \ sed -i '1s?^#!.*python.*?#!/usr/bin/python3?' ${pl} ; \ done make[1]: Leaving directory '/<>' dh_installdocs -a dh_installchangelogs -a dh_installexamples -a dh_installman -a dh_python3 -a dh_perl -a dh_link -a dh_strip_nondeterminism -a dh_compress -a debian/rules override_dh_fixperms make[1]: Entering directory '/<>' dh_fixperms find debian -name *.fast5 -exec chmod -x \{\} \; make[1]: Leaving directory '/<>' dh_missing -a dh_dwz -a dh_strip -a debugedit: debian/nanopolish/usr/lib/nanopolish/nanopolish_test: Unknown DWARF DW_FORM_0x1f20 b6684364df2bac615a62cc2249db932a3e813808 debugedit: debian/nanopolish/usr/bin/nanopolish: Unknown DWARF DW_FORM_0x1f21 c4c6b04d8fc9e10a677dc0e8785abcac0c7ef3ec dh_makeshlibs -a dh_shlibdeps -a dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 from: /lib/ld-linux-riscv64-lp64d.so.1 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 to: /lib/ld-linux-riscv64-lp64d.so.1.usr-is-merged dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/nanopolish/usr/lib/nanopolish/nanopolish_test debian/nanopolish/usr/bin/nanopolish were not linked against libstreamvbyte.so.0 (they use none of the library's symbols) dh_installdeb -a dh_gencontrol -a dh_md5sums -a dh_builddeb -a INFO: pkgstriptranslations version 154 INFO: pkgstriptranslations version 154 pkgstriptranslations: processing nanopolish-dbgsym (in debian/.debhelper/nanopolish/dbgsym-root); do_strip: , oemstrip: pkgstriptranslations: processing nanopolish (in debian/nanopolish); 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/.debhelper/nanopolish/dbgsym-root/DEBIAN/control, package nanopolish-dbgsym, directory debian/.debhelper/nanopolish/dbgsym-root dpkg-deb: building package 'nanopolish-dbgsym' in 'debian/.debhelper/scratch-space/build-nanopolish/nanopolish-dbgsym_0.14.0-1ubuntu3_riscv64.deb'. pkgstripfiles: processing control file: debian/nanopolish/DEBIAN/control, package nanopolish, directory debian/nanopolish pkgstripfiles: Running PNG optimization (using 4 cpus) for package nanopolish ... pkgstripfiles: No PNG files. dpkg-deb: building package 'nanopolish' in '../nanopolish_0.14.0-1ubuntu3_riscv64.deb'. Renaming nanopolish-dbgsym_0.14.0-1ubuntu3_riscv64.deb to nanopolish-dbgsym_0.14.0-1ubuntu3_riscv64.ddeb dpkg-genbuildinfo --build=any -O../nanopolish_0.14.0-1ubuntu3_riscv64.buildinfo dpkg-genchanges --build=any -mLaunchpad Build Daemon -O../nanopolish_0.14.0-1ubuntu3_riscv64.changes dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) -------------------------------------------------------------------------------- Build finished at 2024-04-02T01:27:43Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ nanopolish_0.14.0-1ubuntu3_riscv64.changes: ------------------------------------------- Format: 1.8 Date: Mon, 01 Apr 2024 18:01:04 +1100 Source: nanopolish Binary: nanopolish Built-For-Profiles: noudeb Architecture: riscv64 Version: 0.14.0-1ubuntu3 Distribution: noble-proposed Urgency: medium Maintainer: Launchpad Build Daemon Changed-By: William Grant Description: nanopolish - consensus caller for nanopore sequencing data Changes: nanopolish (0.14.0-1ubuntu3) noble; urgency=medium . * No-change rebuild for CVE-2024-3094 Checksums-Sha1: dfffe3791d266ba7fd16010f53e009dfaf81f8a0 6522106 nanopolish-dbgsym_0.14.0-1ubuntu3_riscv64.ddeb 9cb85653e023e45916876663c53a876933469ab2 8503 nanopolish_0.14.0-1ubuntu3_riscv64.buildinfo 21cbfba639568f7967b90762b28aad55a59f2184 2392800 nanopolish_0.14.0-1ubuntu3_riscv64.deb Checksums-Sha256: f60be0fb37bc0cfdf83a01664edbe8ee4c9520af8b0e857f50cabc5d59e1ae22 6522106 nanopolish-dbgsym_0.14.0-1ubuntu3_riscv64.ddeb ca5833508c3c0aab606a5a6f0ecdbdb08efdfc97ac12eda526097d94f1c24ada 8503 nanopolish_0.14.0-1ubuntu3_riscv64.buildinfo efa732f9f4922f69e99ef19ea7558a68aa30739786e44ffc36aa0446b98faca8 2392800 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nanopolish_0.14.0-1ubuntu3_riscv64.deb Checksums-Sha1: dfffe3791d266ba7fd16010f53e009dfaf81f8a0 6522106 nanopolish-dbgsym_0.14.0-1ubuntu3_riscv64.ddeb 21cbfba639568f7967b90762b28aad55a59f2184 2392800 nanopolish_0.14.0-1ubuntu3_riscv64.deb Checksums-Sha256: f60be0fb37bc0cfdf83a01664edbe8ee4c9520af8b0e857f50cabc5d59e1ae22 6522106 nanopolish-dbgsym_0.14.0-1ubuntu3_riscv64.ddeb efa732f9f4922f69e99ef19ea7558a68aa30739786e44ffc36aa0446b98faca8 2392800 nanopolish_0.14.0-1ubuntu3_riscv64.deb Build-Origin: Ubuntu Build-Architecture: riscv64 Build-Date: Tue, 02 Apr 2024 01:27:36 +0000 Build-Path: /<> Build-Tainted-By: merged-usr-via-aliased-dirs usr-local-has-programs Installed-Build-Depends: autoconf (= 2.71-3), automake (= 1:1.16.5-1.3ubuntu1), autopoint (= 0.21-14ubuntu1), autotools-dev (= 20220109.1), base-files (= 13ubuntu9), base-passwd (= 3.6.3), bash (= 5.2.21-2ubuntu4), binutils (= 2.42-4ubuntu2), binutils-common (= 2.42-4ubuntu2), binutils-riscv64-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), coreutils (= 9.4-3ubuntu5), cpp (= 4:13.2.0-7ubuntu1), cpp-13 (= 13.2.0-23ubuntu3), cpp-13-riscv64-linux-gnu (= 13.2.0-23ubuntu3), cpp-riscv64-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-python (= 6.20240401), 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), g++ (= 4:13.2.0-7ubuntu1), g++-13 (= 13.2.0-23ubuntu3), g++-13-riscv64-linux-gnu (= 13.2.0-23ubuntu3), g++-riscv64-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-riscv64-linux-gnu (= 13.2.0-23ubuntu3), gcc-14-base (= 14-20240315-1ubuntu1), gcc-riscv64-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), hdf5-helpers (= 1.10.10+repack-3.1ubuntu4), hostname (= 3.23+nmu2ubuntu1), init-system-helpers (= 1.66ubuntu1), intltool-debian (= 0.35.0+20060710.6), libacl1 (= 2.3.2-1), libaec-dev (= 1.1.2-1), libaec0 (= 1.1.2-1), libarchive-zip-perl (= 1.68-1), libasan8 (= 14-20240315-1ubuntu1), libatomic1 (= 14-20240315-1ubuntu1), libattr1 (= 1:2.5.2-1), libaudit-common (= 1:3.1.2-2.1build1), libaudit1 (= 1:3.1.2-2.1build1), libbinutils (= 2.42-4ubuntu2), libblkid1 (= 2.39.3-9ubuntu4), libbrotli1 (= 1.1.0-2build1), 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), libcap-ng0 (= 0.8.4-2build2), libcap2 (= 1:2.66-5ubuntu1), libcc1-0 (= 14-20240315-1ubuntu1), 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), 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), libeigen3-dev (= 3.4.0-4), libelf1t64 (= 0.190-1.1build3), libexpat1 (= 2.6.1-2build1), libfast5-dev (= 0.6.5-7build5), libffi8 (= 3.4.6-1), libfile-stripnondeterminism-perl (= 1.13.1-1), libgcc-13-dev (= 13.2.0-23ubuntu3), libgcc-s1 (= 14-20240315-1ubuntu1), libgcrypt20 (= 1.10.3-2), libgdbm-compat4t64 (= 1.23-5.1build1), libgdbm6t64 (= 1.23-5.1build1), libgfortran5 (= 14-20240315-1ubuntu1), libgmp10 (= 2:6.3.0+dfsg-2ubuntu4), libgnutls30t64 (= 3.8.3-1.1ubuntu3), libgomp1 (= 14-20240315-1ubuntu1), libgpg-error0 (= 1.47-3build1), libgssapi-krb5-2 (= 1.20.1-6ubuntu2), libhdf5-103-1t64 (= 1.10.10+repack-3.1ubuntu4), libhdf5-cpp-103-1t64 (= 1.10.10+repack-3.1ubuntu4), libhdf5-dev (= 1.10.10+repack-3.1ubuntu4), libhdf5-fortran-102t64 (= 1.10.10+repack-3.1ubuntu4), libhdf5-hl-100t64 (= 1.10.10+repack-3.1ubuntu4), libhdf5-hl-cpp-100t64 (= 1.10.10+repack-3.1ubuntu4), libhdf5-hl-fortran-100t64 (= 1.10.10+repack-3.1ubuntu4), libhogweed6t64 (= 3.9.1-2.2build1), libhts-dev (= 1.19+ds-1.1build3), libhts3t64 (= 1.19+ds-1.1build3), libhtscodecs2 (= 1.6.0-1), libicu74 (= 74.2-1ubuntu1), libidn2-0 (= 2.3.7-2), libisl23 (= 0.26-3), libjansson4 (= 2.14-2build2), libjpeg-dev (= 8c-2ubuntu11), libjpeg-turbo8 (= 2.1.5-2ubuntu1), libjpeg-turbo8-dev (= 2.1.5-2ubuntu1), libjpeg8 (= 8c-2ubuntu11), libjpeg8-dev (= 8c-2ubuntu11), libk5crypto3 (= 1.20.1-6ubuntu2), libkeyutils1 (= 1.6.3-3), libkrb5-3 (= 1.20.1-6ubuntu2), libkrb5support0 (= 1.20.1-6ubuntu2), libldap2 (= 2.6.7+dfsg-1~exp1ubuntu7), 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), libminimap2-dev (= 2.26+dfsg-1build1), libmount1 (= 2.39.3-9ubuntu4), libmpc3 (= 1.3.1-1), libmpfr6 (= 4.2.1-1), libncursesw6 (= 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), libpcre2-8-0 (= 10.42-4ubuntu1), libperl5.38t64 (= 5.38.2-3.2build1), libpipeline1 (= 1.5.7-2), libpkgconf3 (= 1.8.1-2), libpsl5t64 (= 0.21.2-1.1build1), libpython3-stdlib (= 3.12.2-0ubuntu2), libpython3.12-minimal (= 3.12.2-4build4), libpython3.12-stdlib (= 3.12.2-4build4), libreadline8t64 (= 8.2-4build1), librtmp1 (= 2.4+20151223.gitfa8646d.1-2build7), libsasl2-2 (= 2.1.28+dfsg1-5ubuntu2), libsasl2-modules-db (= 2.1.28+dfsg1-5ubuntu2), libselinux1 (= 3.5-2ubuntu2), libsframe1 (= 2.42-4ubuntu2), libslow5-0t64 (= 0.7.0+dfsg-2.1), libslow5-dev (= 0.7.0+dfsg-2.1), libsmartcols1 (= 2.39.3-9ubuntu4), libsqlite3-0 (= 3.45.1-1ubuntu2), libssh-4 (= 0.10.6-2build1), libssl-dev (= 3.0.13-0ubuntu3), libssl3t64 (= 3.0.13-0ubuntu3), libstdc++-13-dev (= 13.2.0-23ubuntu3), libstdc++6 (= 14-20240315-1ubuntu1), libstreamvbyte-dev (= 0.4.1-4ubuntu1), libstreamvbyte0 (= 0.4.1-4ubuntu1), libsub-override-perl (= 0.10-1), libsystemd0 (= 255.4-1ubuntu6), libsz2 (= 1.1.2-1), libtasn1-6 (= 4.19.0-3), libtinfo6 (= 6.4+20240113-1ubuntu1), libtool (= 2.4.7-7), libubsan1 (= 14-20240315-1ubuntu1), libuchardet0 (= 0.0.8-1), libudev1 (= 255.4-1ubuntu6), libunistring5 (= 1.1-2), libuuid1 (= 2.39.3-9ubuntu4), libxml2 (= 2.9.14+dfsg-1.3ubuntu3), libzstd1 (= 1.5.5+dfsg2-2), linux-libc-dev (= 6.8.0-20.20), 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), media-types (= 10.1.0), ncurses-base (= 6.4+20240113-1ubuntu1), ncurses-bin (= 6.4+20240113-1ubuntu1), netbase (= 6.4), 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), pkg-config (= 1.8.1-2), pkgconf (= 1.8.1-2), pkgconf-bin (= 1.8.1-2), po-debconf (= 1.0.21+nmu1), python3 (= 3.12.2-0ubuntu2), python3-minimal (= 3.12.2-0ubuntu2), python3-pkg-resources (= 68.1.2-2ubuntu1), python3-setuptools (= 68.1.2-2ubuntu1), python3.12 (= 3.12.2-4build4), python3.12-minimal (= 3.12.2-4build4), readline-common (= 8.2-4build1), rpcsvc-proto (= 1.4.2-0ubuntu6), sed (= 4.9-2), sensible-utils (= 0.0.22), sysvinit-utils (= 3.08-6ubuntu2), tar (= 1.35+dfsg-3), tzdata (= 2024a-1ubuntu1), util-linux (= 2.39.3-9ubuntu4), xz-utils (= 5.6.1+really5.4.5-1build1), zlib1g (= 1:1.3.dfsg-3.1ubuntu2), zlib1g-dev (= 1:1.3.dfsg-3.1ubuntu2) Environment: DEB_BUILD_OPTIONS="nocheck parallel=4" DEB_BUILD_PROFILES="noudeb" LANG="C.UTF-8" LC_ALL="C.UTF-8" LC_COLLATE="C.UTF-8" SOURCE_DATE_EPOCH="1711954864" +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ nanopolish_0.14.0-1ubuntu3_riscv64.deb -------------------------------------- new Debian package, version 2.0. size 2392800 bytes: control archive=2091 bytes. 1045 bytes, 19 lines control 2320 bytes, 30 lines md5sums 309 bytes, 12 lines * postinst #!/bin/sh 384 bytes, 12 lines * prerm #!/bin/sh Package: nanopolish Version: 0.14.0-1ubuntu3 Architecture: riscv64 Maintainer: Ubuntu Developers Installed-Size: 9158 Depends: libc6 (>= 2.38), libgcc-s1 (>= 3.4), libgomp1 (>= 6), libhdf5-103-1t64, libhts3t64 (>= 1.17), libslow5-0t64 (>= 0.5.1), libstdc++6 (>= 13.1), libstreamvbyte0 (>= 0.4.1), zlib1g (>= 1:1.1.4), python3:any, perl:any Recommends: python3-biopython, python3-pysam Suggests: perl, make Section: science Priority: optional Homepage: https://github.com/jts/nanopolish Description: consensus caller for nanopore sequencing data Nanopolish uses a signal-level hidden Markov model for consensus calling of nanopore genome sequencing data. It can perform signal-level analysis of Oxford Nanopore sequencing data. Nanopolish can calculate an improved consensus sequence for a draft genome assembly, detect base modifications, call SNPs and indels with respect to a reference genome and more. 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