https://launchpad.net/ubuntu/+source/minimap2/2.27+dfsg-1/+build/28285771 RUN: /usr/share/launchpad-buildd/bin/builder-prep Kernel version: Linux bos02-arm64-014 5.4.0-177-generic #197-Ubuntu SMP Thu Mar 28 22:51:24 UTC 2024 aarch64 Buildd toolchain package versions: launchpad-buildd_237~660~ubuntu20.04.1 python3-lpbuildd_237~660~ubuntu20.04.1 sbuild_0.79.0-1ubuntu1 git-build-recipe_0.3.6 git_1:2.25.1-1ubuntu3.11 dpkg-dev_1.19.7ubuntu3.2 python3-debian_0.1.36ubuntu1.1. Syncing the system clock with the buildd NTP service... 3 May 11:59:38 ntpdate[1814]: adjust time server 10.211.37.1 offset -0.031311 sec RUN: /usr/share/launchpad-buildd/bin/in-target unpack-chroot --backend=chroot --series=oracular --arch=arm64 PACKAGEBUILD-28285771 --image-type chroot /home/buildd/filecache-default/0aaa0d191106d33e51979a9c6a062e50b7f5b3b2 Creating target for build PACKAGEBUILD-28285771 RUN: /usr/share/launchpad-buildd/bin/in-target mount-chroot --backend=chroot --series=oracular --arch=arm64 PACKAGEBUILD-28285771 Starting target for build PACKAGEBUILD-28285771 RUN: /usr/share/launchpad-buildd/bin/in-target override-sources-list --backend=chroot --series=oracular --arch=arm64 PACKAGEBUILD-28285771 'deb http://ftpmaster.internal/ubuntu oracular main universe' 'deb http://ftpmaster.internal/ubuntu oracular-security main universe' 'deb http://ftpmaster.internal/ubuntu oracular-updates main universe' 'deb http://ftpmaster.internal/ubuntu oracular-proposed main universe' Overriding sources.list in build-PACKAGEBUILD-28285771 RUN: /usr/share/launchpad-buildd/bin/in-target update-debian-chroot --backend=chroot --series=oracular --arch=arm64 PACKAGEBUILD-28285771 Updating target for build PACKAGEBUILD-28285771 Get:1 http://ftpmaster.internal/ubuntu oracular InRelease [64.6 kB] Get:2 http://ftpmaster.internal/ubuntu oracular-security InRelease [64.6 kB] Get:3 http://ftpmaster.internal/ubuntu oracular-updates InRelease [64.6 kB] Get:4 http://ftpmaster.internal/ubuntu oracular-proposed InRelease [64.7 kB] Get:5 http://ftpmaster.internal/ubuntu oracular/main arm64 Packages [1377 kB] Get:6 http://ftpmaster.internal/ubuntu oracular/main Translation-en [512 kB] Get:7 http://ftpmaster.internal/ubuntu oracular/universe arm64 Packages [14.8 MB] Get:8 http://ftpmaster.internal/ubuntu oracular/universe Translation-en [5980 kB] Get:9 http://ftpmaster.internal/ubuntu oracular-proposed/main arm64 Packages [207 kB] Get:10 http://ftpmaster.internal/ubuntu oracular-proposed/main Translation-en [73.7 kB] Get:11 http://ftpmaster.internal/ubuntu oracular-proposed/universe arm64 Packages [1004 kB] Get:12 http://ftpmaster.internal/ubuntu oracular-proposed/universe Translation-en [582 kB] Fetched 24.8 MB in 11s (2274 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-aarch64-linux-gnu cpp-aarch64-linux-gnu g++-13-aarch64-linux-gnu g++-aarch64-linux-gnu gcc-13-aarch64-linux-gnu gcc-14-base gcc-aarch64-linux-gnu libapt-pkg6.0t64 libdb5.3t64 libext2fs2t64 libgdbm-compat4t64 libgdbm6t64 libgnutls30t64 libhogweed6t64 libnettle8t64 libnpth0t64 libperl5.38t64 libpng16-16t64 libreadline8t64 libssl3t64 libtirpc3t64 libunistring5 perl-modules-5.38 The following packages will be upgraded: advancecomp apt apt-utils base-files base-passwd bash bash-completion binutils binutils-aarch64-linux-gnu binutils-common bsdextrautils bsdutils bzip2 ca-certificates coreutils cpp cpp-13 dash debconf debconf-i18n debianutils diffutils dpkg dpkg-dev e2fsprogs fakeroot findutils 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 libassuan0 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 libgmp10 libgomp1 libgpg-error-l10n libgpg-error0 libgpm2 libgprofng0 libgssapi-krb5-2 libhwasan0 libidn2-0 libip4tc2 libisl23 libitm1 libjansson4 libjson-c5 libk5crypto3 libkeyutils1 libkmod2 libkrb5-3 libkrb5support0 liblocale-gettext-perl liblockfile-bin liblockfile1 liblsan0 liblz4-1 liblzma5 libmd0 libmount1 libmpc3 libmpfr6 libncursesw6 libnsl-dev libnsl2 libnss-nis 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 libtasn1-6 libtext-charwidth-perl libtext-iconv-perl libtinfo6 libtirpc-common libtirpc-dev libtsan2 libubsan1 libudev1 libuuid1 libxxhash0 libzstd1 linux-libc-dev lockfile-progs login logsave lto-disabled-list make mawk mount ncurses-base ncurses-bin openssl optipng passwd patch perl perl-base pinentry-curses procps psmisc readline-common rpcsvc-proto sed sensible-utils systemd systemd-dev systemd-sysv sysvinit-utils tar tzdata ubuntu-keyring util-linux uuid-runtime xz-utils zlib1g 176 upgraded, 23 newly installed, 14 to remove and 0 not upgraded. Need to get 116 MB of archives. After this operation, 78.1 MB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu oracular-proposed/main arm64 libtirpc-common all 1.3.4+ds-1.3 [8106 B] Get:2 http://ftpmaster.internal/ubuntu oracular-proposed/main arm64 libtirpc-dev arm64 1.3.4+ds-1.3 [201 kB] Get:3 http://ftpmaster.internal/ubuntu oracular/main arm64 libnsl-dev arm64 1.3.0-3build3 [72.5 kB] Get:4 http://ftpmaster.internal/ubuntu oracular/main arm64 libnsl2 arm64 1.3.0-3build3 [41.6 kB] Get:5 http://ftpmaster.internal/ubuntu oracular-proposed/main arm64 libtirpc3t64 arm64 1.3.4+ds-1.3 [83.6 kB] Get:6 http://ftpmaster.internal/ubuntu oracular/main arm64 libgssapi-krb5-2 arm64 1.20.1-6ubuntu2 [141 kB] Get:7 http://ftpmaster.internal/ubuntu oracular/main arm64 libkrb5-3 arm64 1.20.1-6ubuntu2 [349 kB] Get:8 http://ftpmaster.internal/ubuntu oracular/main arm64 libk5crypto3 arm64 1.20.1-6ubuntu2 [85.6 kB] Get:9 http://ftpmaster.internal/ubuntu oracular/main arm64 libkrb5support0 arm64 1.20.1-6ubuntu2 [33.9 kB] Get:10 http://ftpmaster.internal/ubuntu oracular-proposed/main arm64 libacl1 arm64 2.3.2-2 [17.1 kB] Get:11 http://ftpmaster.internal/ubuntu oracular/main arm64 libapparmor1 arm64 4.0.0-beta3-0ubuntu3 [50.0 kB] Get:12 http://ftpmaster.internal/ubuntu oracular/main arm64 libaudit-common all 1:3.1.2-2.1build1 [5736 B] Get:13 http://ftpmaster.internal/ubuntu oracular-proposed/main arm64 libcap-ng0 arm64 0.8.5-1 [14.8 kB] Get:14 http://ftpmaster.internal/ubuntu oracular/main arm64 libaudit1 arm64 1:3.1.2-2.1build1 [47.6 kB] Get:15 http://ftpmaster.internal/ubuntu oracular/main arm64 libblkid1 arm64 2.39.3-9ubuntu6 [123 kB] Get:16 http://ftpmaster.internal/ubuntu oracular/main arm64 libcap2 arm64 1:2.66-5ubuntu2 [30.2 kB] Get:17 http://ftpmaster.internal/ubuntu oracular/main arm64 libcrypt-dev arm64 1:4.4.36-4build1 [118 kB] Get:18 http://ftpmaster.internal/ubuntu oracular/main arm64 libcrypt1 arm64 1:4.4.36-4build1 [85.9 kB] Get:19 http://ftpmaster.internal/ubuntu oracular/main arm64 libgpg-error-l10n all 1.47-3build2 [8064 B] Get:20 http://ftpmaster.internal/ubuntu oracular/main arm64 libgpg-error0 arm64 1.47-3build2 [70.0 kB] Get:21 http://ftpmaster.internal/ubuntu oracular/main arm64 libgcrypt20 arm64 1.10.3-2build1 [472 kB] Get:22 http://ftpmaster.internal/ubuntu oracular/main arm64 liblzma5 arm64 5.6.1+really5.4.5-1 [125 kB] Get:23 http://ftpmaster.internal/ubuntu oracular/main arm64 libzstd1 arm64 1.5.5+dfsg2-2build1 [271 kB] Get:24 http://ftpmaster.internal/ubuntu oracular/main arm64 libkmod2 arm64 31+20240202-2ubuntu7 [51.8 kB] Get:25 http://ftpmaster.internal/ubuntu oracular-proposed/main arm64 liblz4-1 arm64 1.9.4-2 [64.1 kB] Get:26 http://ftpmaster.internal/ubuntu oracular/main arm64 libpcre2-8-0 arm64 10.42-4ubuntu2 [212 kB] Get:27 http://ftpmaster.internal/ubuntu oracular/main arm64 libselinux1 arm64 3.5-2ubuntu2 [79.9 kB] Get:28 http://ftpmaster.internal/ubuntu oracular/main arm64 libmount1 arm64 2.39.3-9ubuntu6 [133 kB] Get:29 http://ftpmaster.internal/ubuntu oracular-proposed/main arm64 perl-modules-5.38 all 5.38.2-4 [3110 kB] Get:30 http://ftpmaster.internal/ubuntu oracular/main arm64 libdb5.3t64 arm64 5.3.28+dfsg2-7 [732 kB] Get:31 http://ftpmaster.internal/ubuntu oracular/main arm64 libgdbm6t64 arm64 1.23-5.1build1 [34.4 kB] Get:32 http://ftpmaster.internal/ubuntu oracular/main arm64 libgdbm-compat4t64 arm64 1.23-5.1build1 [6578 B] Get:33 http://ftpmaster.internal/ubuntu oracular-proposed/main arm64 libperl5.38t64 arm64 5.38.2-4 [4771 kB] Get:34 http://ftpmaster.internal/ubuntu oracular-proposed/main arm64 perl arm64 5.38.2-4 [231 kB] Get:35 http://ftpmaster.internal/ubuntu oracular-proposed/main arm64 perl-base arm64 5.38.2-4 [1777 kB] Get:36 http://ftpmaster.internal/ubuntu oracular/main arm64 liblocale-gettext-perl arm64 1.07-6ubuntu5 [15.3 kB] Get:37 http://ftpmaster.internal/ubuntu oracular/main arm64 libtext-iconv-perl arm64 1.7-8build3 [13.1 kB] Get:38 http://ftpmaster.internal/ubuntu oracular/main arm64 libtext-charwidth-perl arm64 0.04-11build3 [9406 B] Get:39 http://ftpmaster.internal/ubuntu oracular/universe arm64 libnss-nisplus arm64 1.3-5build1 [22.5 kB] Get:40 http://ftpmaster.internal/ubuntu oracular/universe arm64 libnss-nis arm64 3.1-0ubuntu7 [26.6 kB] Get:41 http://ftpmaster.internal/ubuntu oracular-proposed/main arm64 libc-dev-bin arm64 2.39-0ubuntu8.1 [19.7 kB] Get:42 http://ftpmaster.internal/ubuntu oracular/main arm64 rpcsvc-proto arm64 1.4.2-0ubuntu7 [64.8 kB] Get:43 http://ftpmaster.internal/ubuntu oracular-proposed/main arm64 libc6-dev arm64 2.39-0ubuntu8.1 [1596 kB] Get:44 http://ftpmaster.internal/ubuntu oracular-proposed/main arm64 libc6 arm64 2.39-0ubuntu8.1 [2774 kB] Get:45 http://ftpmaster.internal/ubuntu oracular-proposed/main arm64 libc-bin arm64 2.39-0ubuntu8.1 [591 kB] Get:46 http://ftpmaster.internal/ubuntu oracular/main arm64 openssl arm64 3.0.13-0ubuntu3 [984 kB] Get:47 http://ftpmaster.internal/ubuntu oracular/main arm64 libsystemd-shared arm64 255.4-1ubuntu8 [2016 kB] Get:48 http://ftpmaster.internal/ubuntu oracular/main arm64 libcryptsetup12 arm64 2:2.7.0-1ubuntu4 [262 kB] Get:49 http://ftpmaster.internal/ubuntu oracular/main arm64 libssl3t64 arm64 3.0.13-0ubuntu3 [1793 kB] Get:50 http://ftpmaster.internal/ubuntu oracular/main arm64 systemd-dev all 255.4-1ubuntu8 [104 kB] Get:51 http://ftpmaster.internal/ubuntu oracular/main arm64 systemd-sysv arm64 255.4-1ubuntu8 [11.9 kB] Get:52 http://ftpmaster.internal/ubuntu oracular/main arm64 systemd arm64 255.4-1ubuntu8 [3403 kB] Get:53 http://ftpmaster.internal/ubuntu oracular/main arm64 libsystemd0 arm64 255.4-1ubuntu8 [424 kB] Get:54 http://ftpmaster.internal/ubuntu oracular-proposed/main arm64 libapt-pkg6.0t64 arm64 2.9.2 [938 kB] Get:55 http://ftpmaster.internal/ubuntu oracular/main arm64 libnettle8t64 arm64 3.9.1-2.2build1 [192 kB] Get:56 http://ftpmaster.internal/ubuntu oracular/main arm64 libhogweed6t64 arm64 3.9.1-2.2build1 [199 kB] Get:57 http://ftpmaster.internal/ubuntu oracular/main arm64 libp11-kit0 arm64 0.25.3-4ubuntu2 [276 kB] Get:58 http://ftpmaster.internal/ubuntu oracular-proposed/main arm64 libunistring5 arm64 1.2-1 [533 kB] Get:59 http://ftpmaster.internal/ubuntu oracular-proposed/main arm64 libgnutls30t64 arm64 3.8.3-1.1ubuntu3.1 [935 kB] Get:60 http://ftpmaster.internal/ubuntu oracular-proposed/main arm64 apt arm64 2.9.2 [1364 kB] Get:61 http://ftpmaster.internal/ubuntu oracular-proposed/main arm64 apt-utils arm64 2.9.2 [211 kB] Get:62 http://ftpmaster.internal/ubuntu oracular-proposed/main arm64 libpam-modules-bin arm64 1.5.3-7ubuntu1 [50.4 kB] Get:63 http://ftpmaster.internal/ubuntu oracular-proposed/main arm64 libpam-modules arm64 1.5.3-7ubuntu1 [284 kB] Get:64 http://ftpmaster.internal/ubuntu oracular/main arm64 bzip2 arm64 1.0.8-5.1 [34.0 kB] Get:65 http://ftpmaster.internal/ubuntu oracular/main arm64 libbz2-1.0 arm64 1.0.8-5.1 [35.7 kB] Get:66 http://ftpmaster.internal/ubuntu oracular/main arm64 gcc-14-base arm64 14-20240412-0ubuntu1 [47.6 kB] Get:67 http://ftpmaster.internal/ubuntu oracular/main arm64 libgcc-s1 arm64 14-20240412-0ubuntu1 [61.7 kB] Get:68 http://ftpmaster.internal/ubuntu oracular/main arm64 libstdc++6 arm64 14-20240412-0ubuntu1 [748 kB] Get:69 http://ftpmaster.internal/ubuntu oracular/main arm64 libudev1 arm64 255.4-1ubuntu8 [173 kB] Get:70 http://ftpmaster.internal/ubuntu oracular/main arm64 libxxhash0 arm64 0.8.2-2build1 [21.7 kB] Get:71 http://ftpmaster.internal/ubuntu oracular/main arm64 zlib1g arm64 1:1.3.dfsg-3.1ubuntu2 [61.7 kB] Get:72 http://ftpmaster.internal/ubuntu oracular/main arm64 libgmp10 arm64 2:6.3.0+dfsg-2ubuntu6 [243 kB] Get:73 http://ftpmaster.internal/ubuntu oracular/main arm64 libffi8 arm64 3.4.6-1build1 [22.7 kB] Get:74 http://ftpmaster.internal/ubuntu oracular/main arm64 libidn2-0 arm64 2.3.7-2build1 [67.2 kB] Get:75 http://ftpmaster.internal/ubuntu oracular/main arm64 libtasn1-6 arm64 4.19.0-3build1 [43.1 kB] Get:76 http://ftpmaster.internal/ubuntu oracular/main arm64 libdebconfclient0 arm64 0.271ubuntu3 [11.3 kB] Get:77 http://ftpmaster.internal/ubuntu oracular/main arm64 base-passwd arm64 3.6.3build1 [51.1 kB] Get:78 http://ftpmaster.internal/ubuntu oracular/main arm64 libassuan0 arm64 2.5.6-1build1 [36.8 kB] Get:79 http://ftpmaster.internal/ubuntu oracular-proposed/main arm64 libsqlite3-0 arm64 3.45.3-1 [705 kB] Get:80 http://ftpmaster.internal/ubuntu oracular/main arm64 gpg arm64 2.4.4-2ubuntu17 [548 kB] Get:81 http://ftpmaster.internal/ubuntu oracular/main arm64 libreadline8t64 arm64 8.2-4build1 [153 kB] Get:82 http://ftpmaster.internal/ubuntu oracular/main arm64 readline-common all 8.2-4build1 [56.5 kB] Get:83 http://ftpmaster.internal/ubuntu oracular/main arm64 libncursesw6 arm64 6.4+20240113-1ubuntu2 [145 kB] Get:84 http://ftpmaster.internal/ubuntu oracular/main arm64 libtinfo6 arm64 6.4+20240113-1ubuntu2 [104 kB] Get:85 http://ftpmaster.internal/ubuntu oracular/main arm64 gpg-agent arm64 2.4.4-2ubuntu17 [221 kB] Get:86 http://ftpmaster.internal/ubuntu oracular/main arm64 gpgconf arm64 2.4.4-2ubuntu17 [103 kB] Get:87 http://ftpmaster.internal/ubuntu oracular/main arm64 pinentry-curses arm64 1.2.1-3ubuntu5 [34.3 kB] Get:88 http://ftpmaster.internal/ubuntu oracular/main arm64 init-system-helpers all 1.66ubuntu1 [39.4 kB] Get:89 http://ftpmaster.internal/ubuntu oracular/main arm64 libnpth0t64 arm64 1.6-3.1build1 [8144 B] Get:90 http://ftpmaster.internal/ubuntu oracular/main arm64 gpgv arm64 2.4.4-2ubuntu17 [150 kB] Get:91 http://ftpmaster.internal/ubuntu oracular/main arm64 ubuntu-keyring all 2023.11.28.1 [11.1 kB] Get:92 http://ftpmaster.internal/ubuntu oracular/main arm64 libseccomp2 arm64 2.5.5-1ubuntu3 [51.1 kB] Get:93 http://ftpmaster.internal/ubuntu oracular/main arm64 debconf-i18n all 1.5.86ubuntu1 [205 kB] Get:94 http://ftpmaster.internal/ubuntu oracular/main arm64 debconf all 1.5.86ubuntu1 [124 kB] Get:95 http://ftpmaster.internal/ubuntu oracular-proposed/main arm64 libpam0g arm64 1.5.3-7ubuntu1 [68.0 kB] Get:96 http://ftpmaster.internal/ubuntu oracular/main arm64 libargon2-1 arm64 0~20190702+dfsg-4build1 [20.5 kB] Get:97 http://ftpmaster.internal/ubuntu oracular/main arm64 libdevmapper1.02.1 arm64 2:1.02.185-3ubuntu3 [128 kB] Get:98 http://ftpmaster.internal/ubuntu oracular/main arm64 libjson-c5 arm64 0.17-1build1 [36.4 kB] Get:99 http://ftpmaster.internal/ubuntu oracular/main arm64 libuuid1 arm64 2.39.3-9ubuntu6 [35.4 kB] Get:100 http://ftpmaster.internal/ubuntu oracular/main arm64 libfdisk1 arm64 2.39.3-9ubuntu6 [142 kB] Get:101 http://ftpmaster.internal/ubuntu oracular/main arm64 mount arm64 2.39.3-9ubuntu6 [116 kB] Get:102 http://ftpmaster.internal/ubuntu oracular/main arm64 libcom-err2 arm64 1.47.0-2.4~exp1ubuntu4 [22.4 kB] Get:103 http://ftpmaster.internal/ubuntu oracular/main arm64 libkeyutils1 arm64 1.6.3-3build1 [9654 B] Get:104 http://ftpmaster.internal/ubuntu oracular/main arm64 linux-libc-dev arm64 6.8.0-31.31 [1572 kB] Get:105 http://ftpmaster.internal/ubuntu oracular/main arm64 base-files arm64 13.1ubuntu1 [74.0 kB] Get:106 http://ftpmaster.internal/ubuntu oracular/main arm64 debianutils arm64 5.17build1 [90.2 kB] Get:107 http://ftpmaster.internal/ubuntu oracular/main arm64 bash arm64 5.2.21-2ubuntu4 [780 kB] Get:108 http://ftpmaster.internal/ubuntu oracular/main arm64 bsdutils arm64 1:2.39.3-9ubuntu6 [97.7 kB] Get:109 http://ftpmaster.internal/ubuntu oracular/main arm64 coreutils arm64 9.4-3ubuntu6 [1363 kB] Get:110 http://ftpmaster.internal/ubuntu oracular/main arm64 tar arm64 1.35+dfsg-3build1 [248 kB] Get:111 http://ftpmaster.internal/ubuntu oracular-proposed/main arm64 dpkg arm64 1.22.6ubuntu10 [1264 kB] Get:112 http://ftpmaster.internal/ubuntu oracular/main arm64 dash arm64 0.5.12-6ubuntu5 [90.4 kB] Get:113 http://ftpmaster.internal/ubuntu oracular/main arm64 diffutils arm64 1:3.10-1build1 [175 kB] Get:114 http://ftpmaster.internal/ubuntu oracular/main arm64 findutils arm64 4.9.0-5build1 [300 kB] Get:115 http://ftpmaster.internal/ubuntu oracular/main arm64 grep arm64 3.11-4build1 [159 kB] Get:116 http://ftpmaster.internal/ubuntu oracular/main arm64 gzip arm64 1.12-1ubuntu3 [97.2 kB] Get:117 http://ftpmaster.internal/ubuntu oracular/main arm64 hostname arm64 3.23+nmu2ubuntu2 [11.0 kB] Get:118 http://ftpmaster.internal/ubuntu oracular/main arm64 login arm64 1:4.13+dfsg1-4ubuntu3 [200 kB] Get:119 http://ftpmaster.internal/ubuntu oracular/main arm64 ncurses-bin arm64 6.4+20240113-1ubuntu2 [186 kB] Get:120 http://ftpmaster.internal/ubuntu oracular/main arm64 sed arm64 4.9-2build1 [191 kB] Get:121 http://ftpmaster.internal/ubuntu oracular/main arm64 util-linux arm64 2.39.3-9ubuntu6 [1114 kB] Get:122 http://ftpmaster.internal/ubuntu oracular/main arm64 ncurses-base all 6.4+20240113-1ubuntu2 [25.5 kB] Get:123 http://ftpmaster.internal/ubuntu oracular/main arm64 sysvinit-utils arm64 3.08-6ubuntu3 [33.8 kB] Get:124 http://ftpmaster.internal/ubuntu oracular/main arm64 logsave arm64 1.47.0-2.4~exp1ubuntu4 [22.2 kB] Get:125 http://ftpmaster.internal/ubuntu oracular/main arm64 libext2fs2t64 arm64 1.47.0-2.4~exp1ubuntu4 [225 kB] Get:126 http://ftpmaster.internal/ubuntu oracular/main arm64 e2fsprogs arm64 1.47.0-2.4~exp1ubuntu4 [594 kB] Get:127 http://ftpmaster.internal/ubuntu oracular/main arm64 optipng arm64 0.7.8+ds-1build2 [109 kB] Get:128 http://ftpmaster.internal/ubuntu oracular/main arm64 libpng16-16t64 arm64 1.6.43-5build1 [185 kB] Get:129 http://ftpmaster.internal/ubuntu oracular/main arm64 init arm64 1.66ubuntu1 [6186 B] Get:130 http://ftpmaster.internal/ubuntu oracular/main arm64 libsmartcols1 arm64 2.39.3-9ubuntu6 [64.4 kB] Get:131 http://ftpmaster.internal/ubuntu oracular/main arm64 uuid-runtime arm64 2.39.3-9ubuntu6 [32.5 kB] Get:132 http://ftpmaster.internal/ubuntu oracular/main arm64 libattr1 arm64 1:2.5.2-1build1 [11.0 kB] Get:133 http://ftpmaster.internal/ubuntu oracular/main arm64 libmd0 arm64 1.1.0-2build1 [24.6 kB] Get:134 http://ftpmaster.internal/ubuntu oracular-proposed/main arm64 libpam-runtime all 1.5.3-7ubuntu1 [40.8 kB] Get:135 http://ftpmaster.internal/ubuntu oracular/main arm64 libsemanage-common all 3.5-1build5 [10.1 kB] Get:136 http://ftpmaster.internal/ubuntu oracular/main arm64 libsepol2 arm64 3.5-2build1 [291 kB] Get:137 http://ftpmaster.internal/ubuntu oracular/main arm64 libsemanage2 arm64 3.5-1build5 [90.8 kB] Get:138 http://ftpmaster.internal/ubuntu oracular/main arm64 passwd arm64 1:4.13+dfsg1-4ubuntu3 [839 kB] Get:139 http://ftpmaster.internal/ubuntu oracular/main arm64 libproc2-0 arm64 2:4.0.4-4ubuntu3 [58.5 kB] Get:140 http://ftpmaster.internal/ubuntu oracular/main arm64 libss2 arm64 1.47.0-2.4~exp1ubuntu4 [16.5 kB] Get:141 http://ftpmaster.internal/ubuntu oracular/main arm64 mawk arm64 1.3.4.20240123-1build1 [124 kB] Get:142 http://ftpmaster.internal/ubuntu oracular/main arm64 procps arm64 2:4.0.4-4ubuntu3 [708 kB] Get:143 http://ftpmaster.internal/ubuntu oracular/main arm64 sensible-utils all 0.0.22 [22.5 kB] Get:144 http://ftpmaster.internal/ubuntu oracular/main arm64 ca-certificates all 20240203 [159 kB] Get:145 http://ftpmaster.internal/ubuntu oracular/main arm64 krb5-locales all 1.20.1-6ubuntu2 [13.8 kB] Get:146 http://ftpmaster.internal/ubuntu oracular-proposed/main arm64 tzdata all 2024a-4ubuntu1 [274 kB] Get:147 http://ftpmaster.internal/ubuntu oracular-proposed/main arm64 bash-completion all 1:2.13.0-1 [205 kB] Get:148 http://ftpmaster.internal/ubuntu oracular/main arm64 bsdextrautils arm64 2.39.3-9ubuntu6 [71.5 kB] Get:149 http://ftpmaster.internal/ubuntu oracular/main arm64 libgpm2 arm64 1.20.7-11 [14.7 kB] Get:150 http://ftpmaster.internal/ubuntu oracular/main arm64 libip4tc2 arm64 1.8.10-3ubuntu2 [23.4 kB] Get:151 http://ftpmaster.internal/ubuntu oracular/main arm64 libjansson4 arm64 2.14-2build2 [34.4 kB] Get:152 http://ftpmaster.internal/ubuntu oracular/main arm64 psmisc arm64 23.7-1build1 [178 kB] Get:153 http://ftpmaster.internal/ubuntu oracular/main arm64 xz-utils arm64 5.6.1+really5.4.5-1 [268 kB] Get:154 http://ftpmaster.internal/ubuntu oracular/main arm64 advancecomp arm64 2.5-1build1 [177 kB] Get:155 http://ftpmaster.internal/ubuntu oracular/main arm64 libgprofng0 arm64 2.42-4ubuntu2 [777 kB] Get:156 http://ftpmaster.internal/ubuntu oracular/main arm64 libctf0 arm64 2.42-4ubuntu2 [95.7 kB] Get:157 http://ftpmaster.internal/ubuntu oracular/main arm64 libctf-nobfd0 arm64 2.42-4ubuntu2 [99.8 kB] Get:158 http://ftpmaster.internal/ubuntu oracular/main arm64 binutils-aarch64-linux-gnu arm64 2.42-4ubuntu2 [3291 kB] Get:159 http://ftpmaster.internal/ubuntu oracular/main arm64 libbinutils arm64 2.42-4ubuntu2 [767 kB] Get:160 http://ftpmaster.internal/ubuntu oracular/main arm64 binutils arm64 2.42-4ubuntu2 [18.1 kB] Get:161 http://ftpmaster.internal/ubuntu oracular/main arm64 binutils-common arm64 2.42-4ubuntu2 [239 kB] Get:162 http://ftpmaster.internal/ubuntu oracular/main arm64 libsframe1 arm64 2.42-4ubuntu2 [14.4 kB] Get:163 http://ftpmaster.internal/ubuntu oracular/main arm64 libubsan1 arm64 14-20240412-0ubuntu1 [1155 kB] Get:164 http://ftpmaster.internal/ubuntu oracular/main arm64 g++-13 arm64 13.2.0-23ubuntu4 [14.5 kB] Get:165 http://ftpmaster.internal/ubuntu oracular/main arm64 libstdc++-13-dev arm64 13.2.0-23ubuntu4 [2379 kB] Get:166 http://ftpmaster.internal/ubuntu oracular/main arm64 libgomp1 arm64 14-20240412-0ubuntu1 [144 kB] Get:167 http://ftpmaster.internal/ubuntu oracular/main arm64 libitm1 arm64 14-20240412-0ubuntu1 [27.9 kB] Get:168 http://ftpmaster.internal/ubuntu oracular/main arm64 libatomic1 arm64 14-20240412-0ubuntu1 [11.4 kB] Get:169 http://ftpmaster.internal/ubuntu oracular/main arm64 libasan8 arm64 14-20240412-0ubuntu1 [2921 kB] Get:170 http://ftpmaster.internal/ubuntu oracular/main arm64 liblsan0 arm64 14-20240412-0ubuntu1 [1286 kB] Get:171 http://ftpmaster.internal/ubuntu oracular/main arm64 libhwasan0 arm64 14-20240412-0ubuntu1 [1604 kB] Get:172 http://ftpmaster.internal/ubuntu oracular/main arm64 gcc-13 arm64 13.2.0-23ubuntu4 [472 kB] Get:173 http://ftpmaster.internal/ubuntu oracular/main arm64 libgcc-13-dev arm64 13.2.0-23ubuntu4 [2470 kB] Get:174 http://ftpmaster.internal/ubuntu oracular/main arm64 libtsan2 arm64 14-20240412-0ubuntu1 [2692 kB] Get:175 http://ftpmaster.internal/ubuntu oracular/main arm64 libcc1-0 arm64 14-20240412-0ubuntu1 [44.7 kB] Get:176 http://ftpmaster.internal/ubuntu oracular/main arm64 cpp-13 arm64 13.2.0-23ubuntu4 [1032 B] Get:177 http://ftpmaster.internal/ubuntu oracular/main arm64 gcc-13-base arm64 13.2.0-23ubuntu4 [49.0 kB] Get:178 http://ftpmaster.internal/ubuntu oracular/main arm64 libisl23 arm64 0.26-3build1 [669 kB] Get:179 http://ftpmaster.internal/ubuntu oracular/main arm64 libmpfr6 arm64 4.2.1-1build1 [329 kB] Get:180 http://ftpmaster.internal/ubuntu oracular/main arm64 libmpc3 arm64 1.3.1-1build1 [56.4 kB] Get:181 http://ftpmaster.internal/ubuntu oracular/main arm64 gcc-13-aarch64-linux-gnu arm64 13.2.0-23ubuntu4 [20.1 MB] Get:182 http://ftpmaster.internal/ubuntu oracular/main arm64 g++-13-aarch64-linux-gnu arm64 13.2.0-23ubuntu4 [11.7 MB] Get:183 http://ftpmaster.internal/ubuntu oracular/main arm64 cpp-13-aarch64-linux-gnu arm64 13.2.0-23ubuntu4 [10.3 MB] Get:184 http://ftpmaster.internal/ubuntu oracular/main arm64 g++ arm64 4:13.2.0-7ubuntu1 [1082 B] Get:185 http://ftpmaster.internal/ubuntu oracular/main arm64 gcc arm64 4:13.2.0-7ubuntu1 [5018 B] Get:186 http://ftpmaster.internal/ubuntu oracular/main arm64 cpp arm64 4:13.2.0-7ubuntu1 [22.4 kB] Get:187 http://ftpmaster.internal/ubuntu oracular/main arm64 cpp-aarch64-linux-gnu arm64 4:13.2.0-7ubuntu1 [5316 B] Get:188 http://ftpmaster.internal/ubuntu oracular/main arm64 gcc-aarch64-linux-gnu arm64 4:13.2.0-7ubuntu1 [1198 B] Get:189 http://ftpmaster.internal/ubuntu oracular/main arm64 g++-aarch64-linux-gnu arm64 4:13.2.0-7ubuntu1 [962 B] Get:190 http://ftpmaster.internal/ubuntu oracular-proposed/main arm64 dpkg-dev all 1.22.6ubuntu10 [1074 kB] Get:191 http://ftpmaster.internal/ubuntu oracular-proposed/main arm64 libdpkg-perl all 1.22.6ubuntu10 [269 kB] Get:192 http://ftpmaster.internal/ubuntu oracular/main arm64 patch arm64 2.7.6-7build3 [101 kB] Get:193 http://ftpmaster.internal/ubuntu oracular/main arm64 make arm64 4.3-4.1build2 [178 kB] Get:194 http://ftpmaster.internal/ubuntu oracular/main arm64 lto-disabled-list all 47 [12.4 kB] Get:195 http://ftpmaster.internal/ubuntu oracular/main arm64 libfakeroot arm64 1.34-1 [32.5 kB] Get:196 http://ftpmaster.internal/ubuntu oracular/main arm64 fakeroot arm64 1.34-1 [66.9 kB] Get:197 http://ftpmaster.internal/ubuntu oracular/main arm64 liblockfile-bin arm64 1.17-1build3 [11.0 kB] Get:198 http://ftpmaster.internal/ubuntu oracular/main arm64 liblockfile1 arm64 1.17-1build3 [6874 B] Get:199 http://ftpmaster.internal/ubuntu oracular-proposed/main arm64 lockfile-progs arm64 0.1.19+nmu1 [8780 B] Preconfiguring packages ... 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(both '/usr/bin/bzcat' and '/usr/bin/bzip2') dpkg: warning: old file '/bin/bzcat' is the same as several new files! (both '/usr/bin/bunzip2' and '/usr/bin/bzcat') dpkg: warning: old file '/bin/bzcat' is the same as several new files! (both '/usr/bin/bzcat' and '/usr/bin/bzip2') dpkg: warning: old file '/bin/bunzip2' is the same as several new files! (both '/usr/bin/bunzip2' and '/usr/bin/bzcat') dpkg: warning: old file '/bin/bunzip2' is the same as several new files! (both '/usr/bin/bzcat' and '/usr/bin/bzip2') Preparing to unpack .../libbz2-1.0_1.0.8-5.1_arm64.deb ... Unpacking libbz2-1.0:arm64 (1.0.8-5.1) over (1.0.8-5build1) ... Setting up libbz2-1.0:arm64 (1.0.8-5.1) ... Selecting previously unselected package gcc-14-base:arm64. (Reading database ... 15791 files and directories currently installed.) Preparing to unpack .../gcc-14-base_14-20240412-0ubuntu1_arm64.deb ... Unpacking gcc-14-base:arm64 (14-20240412-0ubuntu1) ... Setting up gcc-14-base:arm64 (14-20240412-0ubuntu1) ... 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Setting up debconf-i18n (1.5.86ubuntu1) ... Setting up e2fsprogs (1.47.0-2.4~exp1ubuntu4) ... 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 (5.38.2-4) ... Setting up cpp-aarch64-linux-gnu (4:13.2.0-7ubuntu1) ... Setting up libgprofng0:arm64 (2.42-4ubuntu2) ... Setting up optipng (0.7.8+ds-1build2) ... Setting up lockfile-progs (0.1.19+nmu1) ... Setting up libgssapi-krb5-2:arm64 (1.20.1-6ubuntu2) ... Setting up libdpkg-perl (1.22.6ubuntu10) ... Setting up libreadline8t64:arm64 (8.2-4build1) ... Setting up libgcc-13-dev:arm64 (13.2.0-23ubuntu4) ... Setting up gpgconf (2.4.4-2ubuntu17) ... Setting up libc6-dev:arm64 (2.39-0ubuntu8.1) ... Setting up gpg (2.4.4-2ubuntu17) ... Setting up libstdc++-13-dev:arm64 (13.2.0-23ubuntu4) ... Setting up gpg-agent (2.4.4-2ubuntu17) ... Setting up cpp-13 (13.2.0-23ubuntu4) ... Setting up libtirpc3t64:arm64 (1.3.4+ds-1.3) ... Setting up binutils-aarch64-linux-gnu (2.42-4ubuntu2) ... Setting up binutils (2.42-4ubuntu2) ... Setting up gcc-13-aarch64-linux-gnu (13.2.0-23ubuntu4) ... Setting up dpkg-dev (1.22.6ubuntu10) ... Setting up libtirpc-dev:arm64 (1.3.4+ds-1.3) ... Setting up gcc-13 (13.2.0-23ubuntu4) ... Setting up cpp (4:13.2.0-7ubuntu1) ... Setting up libnsl2:arm64 (1.3.0-3build3) ... Setting up g++-13-aarch64-linux-gnu (13.2.0-23ubuntu4) ... Setting up gcc-aarch64-linux-gnu (4:13.2.0-7ubuntu1) ... Setting up g++-13 (13.2.0-23ubuntu4) ... Setting up libnss-nisplus:arm64 (1.3-5build1) ... Setting up gcc (4:13.2.0-7ubuntu1) ... Setting up libnss-nis:arm64 (3.1-0ubuntu7) ... Setting up libnsl-dev:arm64 (1.3.0-3build3) ... Setting up g++-aarch64-linux-gnu (4:13.2.0-7ubuntu1) ... Setting up g++ (4:13.2.0-7ubuntu1) ... Processing triggers for libc-bin (2.39-0ubuntu8.1) ... Processing triggers for debianutils (5.17build1) ... (Reading database ... 16019 files and directories currently installed.) Purging configuration files for libssl3:arm64 (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-28285771 arm64 oracular-proposed -c chroot:build-PACKAGEBUILD-28285771 --arch=arm64 --dist=oracular-proposed --nolog minimap2_2.27+dfsg-1.dsc Initiating build PACKAGEBUILD-28285771 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 5.4.0-177-generic #197-Ubuntu SMP Thu Mar 28 22:51:24 UTC 2024 aarch64 sbuild (Debian sbuild) 0.79.0 (05 February 2020) on bos02-arm64-014.buildd +==============================================================================+ | minimap2 2.27+dfsg-1 (arm64) Fri, 03 May 2024 12:01:53 +0000 | +==============================================================================+ Package: minimap2 Version: 2.27+dfsg-1 Source Version: 2.27+dfsg-1 Distribution: oracular-proposed Machine Architecture: arm64 Host Architecture: arm64 Build Architecture: arm64 Build Type: any I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-28285771/chroot-autobuild' with '<>' I: NOTICE: Log filtering will replace 'build/minimap2-4ILu0w/resolver-eqXj1l' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- minimap2_2.27+dfsg-1.dsc exists in .; copying to chroot I: NOTICE: Log filtering will replace 'build/minimap2-4ILu0w/minimap2-2.27+dfsg' with '<>' I: NOTICE: Log filtering will replace 'build/minimap2-4ILu0w' with '<>' +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper-compat (= 13), python3-setuptools, dh-sequence-python3, cython3, python3-all-dev, d-shlibs, zlib1g-dev, texlive-latex-extra, texlive-science, texlive-font-utils, ghostscript, gnuplot-nox | gnuplot, libsimde-dev, build-essential, fakeroot Filtered Build-Depends: debhelper-compat (= 13), python3-setuptools, dh-sequence-python3, cython3, python3-all-dev, d-shlibs, zlib1g-dev, texlive-latex-extra, texlive-science, texlive-font-utils, ghostscript, gnuplot-nox | gnuplot, libsimde-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 [471 B] Get:5 copy:/<>/apt_archive ./ Packages [553 B] Fetched 1981 B in 0s (17.3 kB/s) Reading package lists... Reading package lists... Install main build dependencies (apt-based resolver) ---------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following packages were automatically installed and are no longer required: apt-utils bash-completion 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: aglfn autoconf automake autopoint autotools-dev cython3 d-shlibs debhelper debugedit dh-autoreconf dh-python dh-strip-nondeterminism dwz file fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono fonts-gfs-baskerville fonts-gfs-porson fonts-lmodern fonts-urw-base35 gettext gettext-base ghostscript gnuplot-data gnuplot-nox groff-base intltool-debian libaom3 libapache-pom-java libarchive-zip-perl libavahi-client3 libavahi-common-data libavahi-common3 libbrotli1 libbsd0 libcairo2 libcommons-logging-java libcommons-parent-java libcups2t64 libdatrie1 libdbus-1-3 libde265-0 libdebhelper-perl libdeflate0 libdw1t64 libedit2 libelf1t64 libexpat1 libexpat1-dev libfile-stripnondeterminism-perl libfontbox-java libfontconfig1 libfontenc1 libfreetype6 libfribidi0 libgd3 libglib2.0-0t64 libgraphite2-3 libgs-common libgs10 libgs10-common libharfbuzz0b libheif-plugin-aomdec libheif-plugin-libde265 libheif1 libice6 libicu74 libidn12 libijs-0.35 libjbig0 libjbig2dec0 libjpeg-turbo8 libjpeg8 libjs-jquery libjs-sphinxdoc libjs-underscore libkpathsea6 liblerc4 liblua5.4-0 libmagic-mgc libmagic1t64 libopenjp2-7 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper1 libpdfbox-java libpipeline1 libpixman-1-0 libpotrace0 libptexenc1 libpython3-all-dev libpython3-dev libpython3-stdlib libpython3.12-dev libpython3.12-minimal libpython3.12-stdlib libpython3.12t64 libsharpyuv0 libsimde-dev libsm6 libsub-override-perl libsynctex2 libteckit0 libtexlua53-5 libthai-data libthai0 libtiff6 libtool libuchardet0 libwebp7 libwebpmux3 libx11-6 libx11-data libxau6 libxaw7 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxi6 libxml2 libxmu6 libxpm4 libxrender1 libxt6t64 libzzip-0-13t64 m4 man-db media-types netbase po-debconf poppler-data preview-latex-style python3 python3-all python3-all-dev python3-dev python3-minimal python3-pkg-resources python3-setuptools python3.12 python3.12-dev python3.12-minimal t1utils tex-common texlive-base texlive-binaries texlive-font-utils texlive-fonts-recommended texlive-lang-greek texlive-latex-base texlive-latex-extra texlive-latex-recommended texlive-pictures texlive-science ucf x11-common xdg-utils xfonts-encodings xfonts-utils zlib1g-dev Suggested packages: autoconf-archive gnu-standards autoconf-doc cython-doc dh-make flit python3-build python3-installer python3-wheel fonts-freefont-otf | fonts-freefont-ttf fonts-texgyre gettext-doc libasprintf-dev libgettextpo-dev gnuplot-doc groff libavalon-framework-java libexcalibur-logkit-java liblog4j1.2-java cups-common libgd-tools low-memory-monitor libheif-plugin-x265 libheif-plugin-ffmpegdec libheif-plugin-jpegdec libheif-plugin-jpegenc libheif-plugin-j2kdec libheif-plugin-j2kenc libheif-plugin-rav1e libheif-plugin-svtenc libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc apparmor less www-browser libmail-box-perl poppler-utils fonts-japanese-mincho | fonts-ipafont-mincho fonts-japanese-gothic | fonts-ipafont-gothic fonts-arphic-ukai fonts-arphic-uming fonts-nanum python3-doc python3-tk python3-venv python-setuptools-doc python3.12-venv python3.12-doc binfmt-support perl-tk xpdf | pdf-viewer xzdec texlive-binaries-sse2 hintview lcdf-typetools psutils texlive-fonts-recommended-doc texlive-latex-base-doc wp2latex python3-pygments icc-profiles libfile-which-perl texlive-latex-extra-doc texlive-latex-recommended-doc texlive-luatex texlive-pstricks dot2tex prerex texlive-pictures-doc vprerex texlive-science-doc Recommended packages: curl | wget | lynx fonts-liberation groff dbus libarchive-cpio-perl libglib2.0-data shared-mime-info xdg-user-dirs fonts-droid-fallback libheif-plugin-aomenc javascript-common libltdl-dev libmail-sendmail-perl lmodern dvisvgm ps2eps tex-gyre tipa default-jre libspreadsheet-parseexcel-perl texlive-plain-generic ruby tk libfile-mimeinfo-perl libnet-dbus-perl libx11-protocol-perl x11-utils x11-xserver-utils The following NEW packages will be installed: aglfn autoconf automake autopoint autotools-dev cython3 d-shlibs debhelper debugedit dh-autoreconf dh-python dh-strip-nondeterminism dwz file fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono fonts-gfs-baskerville fonts-gfs-porson fonts-lmodern fonts-urw-base35 gettext gettext-base ghostscript gnuplot-data gnuplot-nox groff-base intltool-debian libaom3 libapache-pom-java libarchive-zip-perl libavahi-client3 libavahi-common-data libavahi-common3 libbrotli1 libbsd0 libcairo2 libcommons-logging-java libcommons-parent-java libcups2t64 libdatrie1 libdbus-1-3 libde265-0 libdebhelper-perl libdeflate0 libdw1t64 libedit2 libelf1t64 libexpat1 libexpat1-dev libfile-stripnondeterminism-perl libfontbox-java libfontconfig1 libfontenc1 libfreetype6 libfribidi0 libgd3 libglib2.0-0t64 libgraphite2-3 libgs-common libgs10 libgs10-common libharfbuzz0b libheif-plugin-aomdec libheif-plugin-libde265 libheif1 libice6 libicu74 libidn12 libijs-0.35 libjbig0 libjbig2dec0 libjpeg-turbo8 libjpeg8 libjs-jquery libjs-sphinxdoc libjs-underscore libkpathsea6 liblerc4 liblua5.4-0 libmagic-mgc libmagic1t64 libopenjp2-7 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper1 libpdfbox-java libpipeline1 libpixman-1-0 libpotrace0 libptexenc1 libpython3-all-dev libpython3-dev libpython3-stdlib libpython3.12-dev libpython3.12-minimal libpython3.12-stdlib libpython3.12t64 libsharpyuv0 libsimde-dev libsm6 libsub-override-perl libsynctex2 libteckit0 libtexlua53-5 libthai-data libthai0 libtiff6 libtool libuchardet0 libwebp7 libwebpmux3 libx11-6 libx11-data libxau6 libxaw7 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxi6 libxml2 libxmu6 libxpm4 libxrender1 libxt6t64 libzzip-0-13t64 m4 man-db media-types netbase po-debconf poppler-data preview-latex-style python3 python3-all python3-all-dev python3-dev python3-minimal python3-pkg-resources python3-setuptools python3.12 python3.12-dev python3.12-minimal sbuild-build-depends-main-dummy t1utils tex-common texlive-base texlive-binaries texlive-font-utils texlive-fonts-recommended texlive-lang-greek texlive-latex-base texlive-latex-extra texlive-latex-recommended texlive-pictures texlive-science ucf x11-common xdg-utils xfonts-encodings xfonts-utils zlib1g-dev 0 upgraded, 167 newly installed, 0 to remove and 0 not upgraded. Need to get 253 MB of archives. After this operation, 718 MB of additional disk space will be used. 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oracular/main arm64 libavahi-client3 arm64 0.8-13ubuntu6 [27.2 kB] Get:80 http://ftpmaster.internal/ubuntu oracular/main arm64 libcups2t64 arm64 2.4.7-1.2ubuntu7 [273 kB] Get:81 http://ftpmaster.internal/ubuntu oracular-proposed/main arm64 libidn12 arm64 1.42-2 [56.9 kB] Get:82 http://ftpmaster.internal/ubuntu oracular/main arm64 libijs-0.35 arm64 0.35-15.1build1 [15.3 kB] Get:83 http://ftpmaster.internal/ubuntu oracular/main arm64 libjbig2dec0 arm64 0.20-1build3 [63.2 kB] Get:84 http://ftpmaster.internal/ubuntu oracular/main arm64 libjpeg-turbo8 arm64 2.1.5-2ubuntu2 [163 kB] Get:85 http://ftpmaster.internal/ubuntu oracular/main arm64 libjpeg8 arm64 8c-2ubuntu11 [2148 B] Get:86 http://ftpmaster.internal/ubuntu oracular/main arm64 libopenjp2-7 arm64 2.5.0-2build3 [171 kB] Get:87 http://ftpmaster.internal/ubuntu oracular/main arm64 libpaper1 arm64 1.1.29build1 [13.4 kB] Get:88 http://ftpmaster.internal/ubuntu oracular-proposed/main arm64 libdeflate0 arm64 1.20-1 [45.3 kB] Get:89 http://ftpmaster.internal/ubuntu oracular/main arm64 libjbig0 arm64 2.1-6.1ubuntu2 [29.3 kB] Get:90 http://ftpmaster.internal/ubuntu oracular/main arm64 liblerc4 arm64 4.0.0+ds-4ubuntu2 [154 kB] Get:91 http://ftpmaster.internal/ubuntu oracular/main arm64 libsharpyuv0 arm64 1.3.2-0.4build3 [14.5 kB] Get:92 http://ftpmaster.internal/ubuntu oracular/main arm64 libwebp7 arm64 1.3.2-0.4build3 [191 kB] Get:93 http://ftpmaster.internal/ubuntu oracular/main arm64 libtiff6 arm64 4.5.1+git230720-4ubuntu2 [191 kB] Get:94 http://ftpmaster.internal/ubuntu oracular/main arm64 libice6 arm64 2:1.0.10-1build3 [41.1 kB] Get:95 http://ftpmaster.internal/ubuntu oracular/main arm64 libsm6 arm64 2:1.2.3-1build3 [15.6 kB] Get:96 http://ftpmaster.internal/ubuntu oracular/main arm64 libxt6t64 arm64 1:1.2.1-1.2build1 [168 kB] Get:97 http://ftpmaster.internal/ubuntu oracular/main arm64 libgs10 arm64 10.02.1~dfsg1-0ubuntu7 [3773 kB] Get:98 http://ftpmaster.internal/ubuntu oracular/main arm64 ghostscript arm64 10.02.1~dfsg1-0ubuntu7 [43.5 kB] Get:99 http://ftpmaster.internal/ubuntu oracular/universe arm64 aglfn all 1.7+git20191031.4036a9c-2 [30.6 kB] Get:100 http://ftpmaster.internal/ubuntu oracular/universe arm64 gnuplot-data all 6.0.0+dfsg1-1ubuntu3 [75.3 kB] Get:101 http://ftpmaster.internal/ubuntu oracular/main arm64 libpixman-1-0 arm64 0.42.2-1build1 [204 kB] Get:102 http://ftpmaster.internal/ubuntu oracular/main arm64 libxcb-render0 arm64 1.15-1ubuntu2 [16.6 kB] Get:103 http://ftpmaster.internal/ubuntu oracular/main arm64 libxcb-shm0 arm64 1.15-1ubuntu2 [5876 B] Get:104 http://ftpmaster.internal/ubuntu oracular/main arm64 libxrender1 arm64 1:0.9.10-1.1build1 [18.8 kB] Get:105 http://ftpmaster.internal/ubuntu oracular/main arm64 libcairo2 arm64 1.18.0-3build1 [555 kB] Get:106 http://ftpmaster.internal/ubuntu oracular/main arm64 libaom3 arm64 3.8.2-2build1 [1617 kB] Get:107 http://ftpmaster.internal/ubuntu oracular/main arm64 libheif-plugin-aomdec arm64 1.17.6-1ubuntu4 [10.1 kB] Get:108 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Get:136 http://ftpmaster.internal/ubuntu oracular/main arm64 zlib1g-dev arm64 1:1.3.dfsg-3.1ubuntu2 [894 kB] Get:137 http://ftpmaster.internal/ubuntu oracular/main arm64 libpython3.12-dev arm64 3.12.3-1 [5532 kB] Get:138 http://ftpmaster.internal/ubuntu oracular/main arm64 libpython3-dev arm64 3.12.3-0ubuntu1 [10.2 kB] Get:139 http://ftpmaster.internal/ubuntu oracular/main arm64 libpython3-all-dev arm64 3.12.3-0ubuntu1 [910 B] Get:140 http://ftpmaster.internal/ubuntu oracular-proposed/universe arm64 libsimde-dev all 0.8.2-1 [466 kB] Get:141 http://ftpmaster.internal/ubuntu oracular/main arm64 libsynctex2 arm64 2023.20230311.66589-9build3 [59.2 kB] Get:142 http://ftpmaster.internal/ubuntu oracular/universe arm64 libteckit0 arm64 2.5.12+ds1-1 [405 kB] Get:143 http://ftpmaster.internal/ubuntu oracular/main arm64 libtexlua53-5 arm64 2023.20230311.66589-9build3 [121 kB] Get:144 http://ftpmaster.internal/ubuntu oracular/main arm64 libxmu6 arm64 2:1.1.3-3build2 [47.5 kB] Get:145 http://ftpmaster.internal/ubuntu oracular/main arm64 libxaw7 arm64 2:1.0.14-1build2 [183 kB] Get:146 http://ftpmaster.internal/ubuntu oracular/main arm64 libxi6 arm64 2:1.8.1-1build1 [31.9 kB] Get:147 http://ftpmaster.internal/ubuntu oracular/universe arm64 libzzip-0-13t64 arm64 0.13.72+dfsg.1-1.2build1 [29.2 kB] Get:148 http://ftpmaster.internal/ubuntu oracular/universe arm64 tex-common all 6.18 [32.8 kB] Get:149 http://ftpmaster.internal/ubuntu oracular/universe arm64 preview-latex-style all 13.2-1 [347 kB] Get:150 http://ftpmaster.internal/ubuntu oracular/main arm64 python3-all arm64 3.12.3-0ubuntu1 [888 B] Get:151 http://ftpmaster.internal/ubuntu oracular/main arm64 python3.12-dev arm64 3.12.3-1 [498 kB] Get:152 http://ftpmaster.internal/ubuntu oracular/main arm64 python3-dev arm64 3.12.3-0ubuntu1 [26.7 kB] Get:153 http://ftpmaster.internal/ubuntu oracular/main arm64 python3-all-dev arm64 3.12.3-0ubuntu1 [910 B] Get:154 http://ftpmaster.internal/ubuntu oracular/main arm64 t1utils arm64 1.41-4build3 [61.0 kB] Get:155 http://ftpmaster.internal/ubuntu oracular/universe arm64 texlive-binaries arm64 2023.20230311.66589-9build3 [8364 kB] Get:156 http://ftpmaster.internal/ubuntu oracular/main arm64 xdg-utils all 1.1.3-4.1ubuntu3 [62.0 kB] Get:157 http://ftpmaster.internal/ubuntu oracular/universe arm64 texlive-base all 2023.20240207-1 [21.7 MB] Get:158 http://ftpmaster.internal/ubuntu oracular/universe arm64 texlive-font-utils all 2023.20240207-1 [7035 kB] Get:159 http://ftpmaster.internal/ubuntu oracular/universe arm64 texlive-fonts-recommended all 2023.20240207-1 [4973 kB] Get:160 http://ftpmaster.internal/ubuntu oracular/universe arm64 texlive-lang-greek all 2023.20240207-1 [79.2 MB] Get:161 http://ftpmaster.internal/ubuntu oracular/universe arm64 texlive-latex-base all 2023.20240207-1 [1238 kB] Get:162 http://ftpmaster.internal/ubuntu oracular/universe arm64 libfontbox-java all 1:1.8.16-5 [208 kB] Get:163 http://ftpmaster.internal/ubuntu oracular/universe arm64 libpdfbox-java all 1:1.8.16-5 [5521 kB] Get:164 http://ftpmaster.internal/ubuntu oracular/universe arm64 texlive-latex-recommended all 2023.20240207-1 [8826 kB] Get:165 http://ftpmaster.internal/ubuntu oracular/universe arm64 texlive-pictures all 2023.20240207-1 [16.7 MB] Get:166 http://ftpmaster.internal/ubuntu oracular/universe arm64 texlive-latex-extra all 2023.20240207-1 [19.2 MB] Get:167 http://ftpmaster.internal/ubuntu oracular/universe arm64 texlive-science all 2023.20240207-1 [3779 kB] Preconfiguring packages ... Fetched 253 MB in 16s (16.1 MB/s) Selecting previously unselected package libpython3.12-minimal:arm64. (Reading database ... 16019 files and directories currently installed.) Preparing to unpack .../libpython3.12-minimal_3.12.3-1_arm64.deb ... Unpacking libpython3.12-minimal:arm64 (3.12.3-1) ... Selecting previously unselected package libexpat1:arm64. Preparing to unpack .../libexpat1_2.6.2-1_arm64.deb ... Unpacking libexpat1:arm64 (2.6.2-1) ... Selecting previously unselected package python3.12-minimal. Preparing to unpack .../python3.12-minimal_3.12.3-1_arm64.deb ... Unpacking python3.12-minimal (3.12.3-1) ... Setting up libpython3.12-minimal:arm64 (3.12.3-1) ... Setting up libexpat1:arm64 (2.6.2-1) ... Setting up python3.12-minimal (3.12.3-1) ... Selecting previously unselected package python3-minimal. (Reading database ... 16337 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.12.3-0ubuntu1_arm64.deb ... 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Setting up libdatrie1:arm64 (0.2.13-3build1) ... Setting up libmagic-mgc (1:5.45-3build1) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libijs-0.35:arm64 (0.35-15.1build1) ... Setting up libdebhelper-perl (13.14.1ubuntu5) ... Setting up libgs-common (10.02.1~dfsg1-0ubuntu7) ... Setting up libbrotli1:arm64 (1.1.0-2build2) ... Setting up libfontbox-java (1:1.8.16-5) ... Setting up libmagic1t64:arm64 (1:5.45-3build1) ... Setting up x11-common (1:7.7+23ubuntu3) ... Running in chroot, ignoring request. invoke-rc.d: policy-rc.d denied execution of start. Setting up libdeflate0:arm64 (1.20-1) ... Setting up gettext-base (0.21-14ubuntu2) ... Setting up m4 (1.4.19-4build1) ... Setting up file (1:5.45-3build1) ... Setting up libjbig0:arm64 (2.1-6.1ubuntu2) ... Setting up libelf1t64:arm64 (0.191-1) ... Setting up poppler-data (0.4.12-1) ... Setting up libdw1t64:arm64 (0.191-1) ... Setting up libfontenc1:arm64 (1:1.1.8-1build1) ... Setting up autotools-dev (20220109.1) ... Setting up libglib2.0-0t64:arm64 (2.80.0-6ubuntu1) ... No schema files found: doing nothing. Setting up libexpat1-dev:arm64 (2.6.2-1) ... Setting up libzzip-0-13t64:arm64 (0.13.72+dfsg.1-1.2build1) ... Setting up libfreetype6:arm64 (2.13.2+dfsg-1build3) ... Setting up libx11-data (2:1.8.7-1build1) ... Setting up libjbig2dec0:arm64 (0.20-1build3) ... Setting up libteckit0:arm64 (2.5.12+ds1-1) ... Setting up aglfn (1.7+git20191031.4036a9c-2) ... Setting up libapache-pom-java (29-2) ... Setting up libavahi-common-data:arm64 (0.8-13ubuntu6) ... Setting up libdbus-1-3:arm64 (1.14.10-4ubuntu4) ... Setting up xfonts-encodings (1:1.0.5-0ubuntu2) ... Setting up libfribidi0:arm64 (1.0.13-3build1) ... Setting up t1utils (1.41-4build3) ... Setting up libtexlua53-5:arm64 (2023.20230311.66589-9build3) ... Setting up fonts-dejavu-mono (2.37-8) ... Setting up libidn12:arm64 (1.42-2) ... Setting up autopoint (0.21-14ubuntu2) ... Setting up fonts-dejavu-core (2.37-8) ... Setting up d-shlibs (0.106) ... Setting up ucf (3.0043+nmu1) ... Setting up libjpeg-turbo8:arm64 (2.1.5-2ubuntu2) ... Setting up libkpathsea6:arm64 (2023.20230311.66589-9build3) ... Setting up autoconf (2.71-3) ... Setting up libwebp7:arm64 (1.3.2-0.4build3) ... Setting up libicu74:arm64 (74.2-1ubuntu3) ... Setting up zlib1g-dev:arm64 (1:1.3.dfsg-3.1ubuntu2) ... Setting up dwz (0.15-1build6) ... Setting up fonts-gfs-baskerville (1.1-6) ... Setting up libuchardet0:arm64 (0.0.8-1build1) ... Setting up debugedit (1:5.0-5build2) ... Setting up fonts-lmodern (2.005-1) ... Setting up liblua5.4-0:arm64 (5.4.6-3build2) ... Setting up libopenjp2-7:arm64 (2.5.0-2build3) ... Setting up libsub-override-perl (0.10-1) ... Setting up libharfbuzz0b:arm64 (8.3.0-2build2) ... Setting up libthai-data (0.1.29-2build1) ... Setting up netbase (6.4) ... Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Setting up libde265-0:arm64 (1.0.15-1build3) ... Setting up libwebpmux3:arm64 (1.3.2-0.4build3) ... Setting up libbsd0:arm64 (0.12.2-1) ... Setting up libxml2:arm64 (2.9.14+dfsg-1.3ubuntu3) ... Setting up xdg-utils (1.1.3-4.1ubuntu3) ... update-alternatives: using /usr/bin/xdg-open to provide /usr/bin/open (open) in auto mode Setting up libsynctex2:arm64 (2023.20230311.66589-9build3) ... Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... Setting up libpotrace0:arm64 (1.16-2build1) ... Setting up libjpeg8:arm64 (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 gnuplot-data (6.0.0+dfsg1-1ubuntu3) ... Setting up libpaper1:arm64 (1.1.29build1) ... Creating config file /etc/papersize with new version Setting up libice6:arm64 (2:1.0.10-1build3) ... Setting up libxdmcp6:arm64 (1:1.1.3-0ubuntu6) ... Setting up libxcb1:arm64 (1.15-1ubuntu2) ... Setting up gettext (0.21-14ubuntu2) ... Setting up libpdfbox-java (1:1.8.16-5) ... Setting up libpython3.12-stdlib:arm64 (3.12.3-1) ... Setting up libtool (2.4.7-7build1) ... Setting up libxcb-render0:arm64 (1.15-1ubuntu2) ... Setting up fontconfig-config (2.15.0-1.1ubuntu2) ... Setting up python3.12 (3.12.3-1) ... Setting up libedit2:arm64 (3.1-20230828-1build1) ... Setting up libcommons-parent-java (56-1) ... Setting up libavahi-common3:arm64 (0.8-13ubuntu6) ... Setting up libcommons-logging-java (1.3.0-1ubuntu1) ... Setting up libxcb-shm0:arm64 (1.15-1ubuntu2) ... Setting up libpaper-utils (1.1.29build1) ... Setting up xfonts-utils (1:7.7+6build3) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up libpython3.12t64:arm64 (3.12.3-1) ... Setting up dh-autoreconf (20) ... Setting up tex-common (6.18) ... update-language: texlive-base not installed and configured, doing nothing! Setting up libthai0:arm64 (0.1.29-2build1) ... Setting up libptexenc1:arm64 (2023.20230311.66589-9build3) ... Setting up libjs-sphinxdoc (7.2.6-6) ... Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up groff-base (1.23.0-4) ... Setting up libtiff6:arm64 (4.5.1+git230720-4ubuntu2) ... Setting up libx11-6:arm64 (2:1.8.7-1build1) ... Setting up libfontconfig1:arm64 (2.15.0-1.1ubuntu2) ... Setting up libsm6:arm64 (2:1.2.3-1build3) ... Setting up libavahi-client3:arm64 (0.8-13ubuntu6) ... Setting up libpython3-stdlib:arm64 (3.12.3-0ubuntu1) ... Setting up fontconfig (2.15.0-1.1ubuntu2) ... Regenerating fonts cache... done. Setting up libxpm4:arm64 (1:3.5.17-1build2) ... Setting up libxrender1:arm64 (1:0.9.10-1.1build1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up preview-latex-style (13.2-1) ... Setting up libpango-1.0-0:arm64 (1.52.1+ds-1build1) ... Setting up libxext6:arm64 (2:1.3.4-1build2) ... Setting up python3 (3.12.3-0ubuntu1) ... Setting up libpython3.12-dev:arm64 (3.12.3-1) ... Setting up fonts-urw-base35 (20200910-8) ... Setting up man-db (2.12.1-1) ... Not building database; man-db/auto-update is not 'true'. Created symlink /etc/systemd/system/timers.target.wants/man-db.timer → /usr/lib/systemd/system/man-db.timer. Setting up libcairo2:arm64 (1.18.0-3build1) ... Setting up libxt6t64:arm64 (1:1.2.1-1.2build1) ... Setting up python3.12-dev (3.12.3-1) ... Setting up cython3 (3.0.8-1ubuntu3) ... Setting up libpangoft2-1.0-0:arm64 (1.52.1+ds-1build1) ... Setting up libcups2t64:arm64 (2.4.7-1.2ubuntu7) ... Setting up libpangocairo-1.0-0:arm64 (1.52.1+ds-1build1) ... Setting up python3-pkg-resources (68.1.2-2ubuntu1) ... Setting up libgs10-common (10.02.1~dfsg1-0ubuntu7) ... Setting up libxmu6:arm64 (2:1.1.3-3build2) ... Setting up libpython3-dev:arm64 (3.12.3-0ubuntu1) ... Setting up python3-setuptools (68.1.2-2ubuntu1) ... Setting up libxi6:arm64 (2:1.8.1-1build1) ... Setting up python3-all (3.12.3-0ubuntu1) ... Setting up debhelper (13.14.1ubuntu5) ... Setting up libxaw7:arm64 (2:1.0.14-1build2) ... Setting up libpython3-all-dev:arm64 (3.12.3-0ubuntu1) ... Setting up python3-dev (3.12.3-0ubuntu1) ... Setting up texlive-binaries (2023.20230311.66589-9build3) ... update-alternatives: using /usr/bin/xdvi-xaw to provide /usr/bin/xdvi.bin (xdvi.bin) in auto mode update-alternatives: using /usr/bin/bibtex.original to provide /usr/bin/bibtex (bibtex) in auto mode Setting up texlive-base (2023.20240207-1) ... tl-paper: setting paper size for dvips to a4: /var/lib/texmf/dvips/config/config-paper.ps tl-paper: setting paper size for dvipdfmx to a4: /var/lib/texmf/dvipdfmx/dvipdfmx-paper.cfg tl-paper: setting paper size for xdvi to a4: /var/lib/texmf/xdvi/XDvi-paper tl-paper: setting paper size for pdftex to a4: /var/lib/texmf/tex/generic/tex-ini-files/pdftexconfig.tex Setting up libgs10:arm64 (10.02.1~dfsg1-0ubuntu7) ... Setting up dh-python (6.20240422) ... Setting up python3-all-dev (3.12.3-0ubuntu1) ... Setting up texlive-lang-greek (2023.20240207-1) ... Setting up texlive-font-utils (2023.20240207-1) ... Setting up ghostscript (10.02.1~dfsg1-0ubuntu7) ... Setting up texlive-latex-base (2023.20240207-1) ... Setting up texlive-latex-recommended (2023.20240207-1) ... Setting up texlive-pictures (2023.20240207-1) ... Setting up texlive-fonts-recommended (2023.20240207-1) ... Setting up texlive-science (2023.20240207-1) ... Setting up texlive-latex-extra (2023.20240207-1) ... Setting up libheif-plugin-aomdec:arm64 (1.17.6-1ubuntu4) ... Setting up libheif1:arm64 (1.17.6-1ubuntu4) ... Setting up libgd3:arm64 (2.3.3-9ubuntu5) ... Setting up gnuplot-nox (6.0.0+dfsg1-1ubuntu3) ... update-alternatives: using /usr/bin/gnuplot-nox to provide /usr/bin/gnuplot (gnuplot) in auto mode Setting up sbuild-build-depends-main-dummy (0.invalid.0) ... Setting up libheif-plugin-libde265:arm64 (1.17.6-1ubuntu4) ... Processing triggers for libc-bin (2.39-0ubuntu8.1) ... Processing triggers for systemd (255.4-1ubuntu8) ... Processing triggers for tex-common (6.18) ... Running updmap-sys. This may take some time... done. Running mktexlsr /var/lib/texmf ... done. Building format(s) --all. This may take some time... done. +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (arm64 included in any) +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 5.4.0-177-generic #197-Ubuntu SMP Thu Mar 28 22:51:24 UTC 2024 arm64 (aarch64) Toolchain package versions: binutils_2.42-4ubuntu2 dpkg-dev_1.22.6ubuntu10 g++-13_13.2.0-23ubuntu4 gcc-13_13.2.0-23ubuntu4 libc6-dev_2.39-0ubuntu8.1 libstdc++-13-dev_13.2.0-23ubuntu4 libstdc++6_14-20240412-0ubuntu1 linux-libc-dev_6.8.0-31.31 Package versions: adduser_3.137ubuntu1 advancecomp_2.5-1build1 aglfn_1.7+git20191031.4036a9c-2 apt_2.9.2 apt-utils_2.9.2 autoconf_2.71-3 automake_1:1.16.5-1.3ubuntu1 autopoint_0.21-14ubuntu2 autotools-dev_20220109.1 base-files_13.1ubuntu1 base-passwd_3.6.3build1 bash_5.2.21-2ubuntu4 bash-completion_1:2.13.0-1 binutils_2.42-4ubuntu2 binutils-aarch64-linux-gnu_2.42-4ubuntu2 binutils-common_2.42-4ubuntu2 bsdextrautils_2.39.3-9ubuntu6 bsdutils_1:2.39.3-9ubuntu6 build-essential_12.10ubuntu1 bzip2_1.0.8-5.1 ca-certificates_20240203 coreutils_9.4-3ubuntu6 cpp_4:13.2.0-7ubuntu1 cpp-13_13.2.0-23ubuntu4 cpp-13-aarch64-linux-gnu_13.2.0-23ubuntu4 cpp-aarch64-linux-gnu_4:13.2.0-7ubuntu1 cython3_3.0.8-1ubuntu3 d-shlibs_0.106 dash_0.5.12-6ubuntu5 debconf_1.5.86ubuntu1 debconf-i18n_1.5.86ubuntu1 debhelper_13.14.1ubuntu5 debianutils_5.17build1 debugedit_1:5.0-5build2 dh-autoreconf_20 dh-python_6.20240422 dh-strip-nondeterminism_1.13.1-1 diffutils_1:3.10-1build1 dpkg_1.22.6ubuntu10 dpkg-dev_1.22.6ubuntu10 dwz_0.15-1build6 e2fsprogs_1.47.0-2.4~exp1ubuntu4 fakeroot_1.34-1 file_1:5.45-3build1 findutils_4.9.0-5build1 fontconfig_2.15.0-1.1ubuntu2 fontconfig-config_2.15.0-1.1ubuntu2 fonts-dejavu-core_2.37-8 fonts-dejavu-mono_2.37-8 fonts-gfs-baskerville_1.1-6 fonts-gfs-porson_1.1-7 fonts-lmodern_2.005-1 fonts-urw-base35_20200910-8 g++_4:13.2.0-7ubuntu1 g++-13_13.2.0-23ubuntu4 g++-13-aarch64-linux-gnu_13.2.0-23ubuntu4 g++-aarch64-linux-gnu_4:13.2.0-7ubuntu1 gcc_4:13.2.0-7ubuntu1 gcc-13_13.2.0-23ubuntu4 gcc-13-aarch64-linux-gnu_13.2.0-23ubuntu4 gcc-13-base_13.2.0-23ubuntu4 gcc-14-base_14-20240412-0ubuntu1 gcc-aarch64-linux-gnu_4:13.2.0-7ubuntu1 gettext_0.21-14ubuntu2 gettext-base_0.21-14ubuntu2 ghostscript_10.02.1~dfsg1-0ubuntu7 gnuplot-data_6.0.0+dfsg1-1ubuntu3 gnuplot-nox_6.0.0+dfsg1-1ubuntu3 gpg_2.4.4-2ubuntu17 gpg-agent_2.4.4-2ubuntu17 gpgconf_2.4.4-2ubuntu17 gpgv_2.4.4-2ubuntu17 grep_3.11-4build1 groff-base_1.23.0-4 gzip_1.12-1ubuntu3 hostname_3.23+nmu2ubuntu2 init_1.66ubuntu1 init-system-helpers_1.66ubuntu1 intltool-debian_0.35.0+20060710.6 krb5-locales_1.20.1-6ubuntu2 libacl1_2.3.2-2 libaom3_3.8.2-2build1 libapache-pom-java_29-2 libapparmor1_4.0.0-beta3-0ubuntu3 libapt-pkg6.0t64_2.9.2 libarchive-zip-perl_1.68-1 libargon2-1_0~20190702+dfsg-4build1 libasan8_14-20240412-0ubuntu1 libassuan0_2.5.6-1build1 libatomic1_14-20240412-0ubuntu1 libattr1_1:2.5.2-1build1 libaudit-common_1:3.1.2-2.1build1 libaudit1_1:3.1.2-2.1build1 libavahi-client3_0.8-13ubuntu6 libavahi-common-data_0.8-13ubuntu6 libavahi-common3_0.8-13ubuntu6 libbinutils_2.42-4ubuntu2 libblkid1_2.39.3-9ubuntu6 libbrotli1_1.1.0-2build2 libbsd0_0.12.2-1 libbz2-1.0_1.0.8-5.1 libc-bin_2.39-0ubuntu8.1 libc-dev-bin_2.39-0ubuntu8.1 libc6_2.39-0ubuntu8.1 libc6-dev_2.39-0ubuntu8.1 libcairo2_1.18.0-3build1 libcap-ng0_0.8.5-1 libcap2_1:2.66-5ubuntu2 libcc1-0_14-20240412-0ubuntu1 libcom-err2_1.47.0-2.4~exp1ubuntu4 libcommons-logging-java_1.3.0-1ubuntu1 libcommons-parent-java_56-1 libcrypt-dev_1:4.4.36-4build1 libcrypt1_1:4.4.36-4build1 libcryptsetup12_2:2.7.0-1ubuntu4 libctf-nobfd0_2.42-4ubuntu2 libctf0_2.42-4ubuntu2 libcups2t64_2.4.7-1.2ubuntu7 libdatrie1_0.2.13-3build1 libdb5.3t64_5.3.28+dfsg2-7 libdbus-1-3_1.14.10-4ubuntu4 libde265-0_1.0.15-1build3 libdebconfclient0_0.271ubuntu3 libdebhelper-perl_13.14.1ubuntu5 libdeflate0_1.20-1 libdevmapper1.02.1_2:1.02.185-3ubuntu3 libdpkg-perl_1.22.6ubuntu10 libdw1t64_0.191-1 libedit2_3.1-20230828-1build1 libelf1t64_0.191-1 libexpat1_2.6.2-1 libexpat1-dev_2.6.2-1 libext2fs2t64_1.47.0-2.4~exp1ubuntu4 libfakeroot_1.34-1 libfdisk1_2.39.3-9ubuntu6 libffi8_3.4.6-1build1 libfile-stripnondeterminism-perl_1.13.1-1 libfontbox-java_1:1.8.16-5 libfontconfig1_2.15.0-1.1ubuntu2 libfontenc1_1:1.1.8-1build1 libfreetype6_2.13.2+dfsg-1build3 libfribidi0_1.0.13-3build1 libgcc-13-dev_13.2.0-23ubuntu4 libgcc-s1_14-20240412-0ubuntu1 libgcrypt20_1.10.3-2build1 libgd3_2.3.3-9ubuntu5 libgdbm-compat4t64_1.23-5.1build1 libgdbm6t64_1.23-5.1build1 libglib2.0-0t64_2.80.0-6ubuntu1 libgmp10_2:6.3.0+dfsg-2ubuntu6 libgnutls30t64_3.8.3-1.1ubuntu3.1 libgomp1_14-20240412-0ubuntu1 libgpg-error-l10n_1.47-3build2 libgpg-error0_1.47-3build2 libgpm2_1.20.7-11 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libkrb5support0_1.20.1-6ubuntu2 liblerc4_4.0.0+ds-4ubuntu2 liblocale-gettext-perl_1.07-6ubuntu5 liblockfile-bin_1.17-1build3 liblockfile1_1.17-1build3 liblsan0_14-20240412-0ubuntu1 liblua5.4-0_5.4.6-3build2 liblz4-1_1.9.4-2 liblzma5_5.6.1+really5.4.5-1 libmagic-mgc_1:5.45-3build1 libmagic1t64_1:5.45-3build1 libmd0_1.1.0-2build1 libmount1_2.39.3-9ubuntu6 libmpc3_1.3.1-1build1 libmpfr6_4.2.1-1build1 libncursesw6_6.4+20240113-1ubuntu2 libnettle8t64_3.9.1-2.2build1 libnpth0t64_1.6-3.1build1 libnsl-dev_1.3.0-3build3 libnsl2_1.3.0-3build3 libnss-nis_3.1-0ubuntu7 libnss-nisplus_1.3-5build1 libopenjp2-7_2.5.0-2build3 libp11-kit0_0.25.3-4ubuntu2 libpam-modules_1.5.3-7ubuntu1 libpam-modules-bin_1.5.3-7ubuntu1 libpam-runtime_1.5.3-7ubuntu1 libpam0g_1.5.3-7ubuntu1 libpango-1.0-0_1.52.1+ds-1build1 libpangocairo-1.0-0_1.52.1+ds-1build1 libpangoft2-1.0-0_1.52.1+ds-1build1 libpaper-utils_1.1.29build1 libpaper1_1.1.29build1 libpcre2-8-0_10.42-4ubuntu2 libpdfbox-java_1:1.8.16-5 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python3-minimal_3.12.3-0ubuntu1 python3-pkg-resources_68.1.2-2ubuntu1 python3-setuptools_68.1.2-2ubuntu1 python3.12_3.12.3-1 python3.12-dev_3.12.3-1 python3.12-minimal_3.12.3-1 readline-common_8.2-4build1 rpcsvc-proto_1.4.2-0ubuntu7 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.9-2build1 sensible-utils_0.0.22 systemd_255.4-1ubuntu8 systemd-dev_255.4-1ubuntu8 systemd-sysv_255.4-1ubuntu8 sysvinit-utils_3.08-6ubuntu3 t1utils_1.41-4build3 tar_1.35+dfsg-3build1 tex-common_6.18 texlive-base_2023.20240207-1 texlive-binaries_2023.20230311.66589-9build3 texlive-font-utils_2023.20240207-1 texlive-fonts-recommended_2023.20240207-1 texlive-lang-greek_2023.20240207-1 texlive-latex-base_2023.20240207-1 texlive-latex-extra_2023.20240207-1 texlive-latex-recommended_2023.20240207-1 texlive-pictures_2023.20240207-1 texlive-science_2023.20240207-1 tzdata_2024a-4ubuntu1 ubuntu-keyring_2023.11.28.1 ucf_3.0043+nmu1 util-linux_2.39.3-9ubuntu6 uuid-runtime_2.39.3-9ubuntu6 x11-common_1:7.7+23ubuntu3 xdg-utils_1.1.3-4.1ubuntu3 xfonts-encodings_1:1.0.5-0ubuntu2 xfonts-utils_1:7.7+6build3 xz-utils_5.6.1+really5.4.5-1 zlib1g_1:1.3.dfsg-3.1ubuntu2 zlib1g-dev_1:1.3.dfsg-3.1ubuntu2 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: minimap2 Binary: minimap2, libminimap2-dev, python3-mappy Architecture: any Version: 2.27+dfsg-1 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille Homepage: https://github.com/lh3/minimap2 Standards-Version: 4.6.2 Vcs-Browser: https://salsa.debian.org/med-team/minimap2 Vcs-Git: https://salsa.debian.org/med-team/minimap2.git Testsuite: autopkgtest Testsuite-Triggers: python3-all Build-Depends: debhelper-compat (= 13), python3-setuptools, dh-sequence-python3, cython3, python3-all-dev, d-shlibs, zlib1g-dev, texlive-latex-extra, texlive-science, texlive-font-utils, ghostscript, gnuplot-nox | gnuplot, libsimde-dev Package-List: libminimap2-dev deb libdevel optional arch=any minimap2 deb science optional arch=any python3-mappy deb python optional arch=any Checksums-Sha1: 5b1fc195a089c03049c1da7e1130fbeea929c3b3 200448 minimap2_2.27+dfsg.orig.tar.xz a7aa130e9464843d8736dc295f5628441895c4e7 11544 minimap2_2.27+dfsg-1.debian.tar.xz Checksums-Sha256: 3ee11256b940a750072baa0f70e32187f61613f83d3936eb0a5eaedff1cf16df 200448 minimap2_2.27+dfsg.orig.tar.xz 45d509d32766d87c4ca3c8ed7310e2758794418e0c53918fda09f45f8cac5826 11544 minimap2_2.27+dfsg-1.debian.tar.xz Files: 2f98c85235a8086e03367622ae70aef0 200448 minimap2_2.27+dfsg.orig.tar.xz 2b0538bcbffb92d0d127c6a47728340b 11544 minimap2_2.27+dfsg-1.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQIzBAEBCgAdFiEEck1gkzcRPHEFUNdHPCZ2P2xn5uIFAmX4beEACgkQPCZ2P2xn 5uIp7g/+L/NnH0UhRPs5Y1qnjFBKgw65y0MB8QyW2WoSqf9qETpmdf83ZiFUfvFD 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info: unpacking minimap2_2.27+dfsg.orig.tar.xz dpkg-source: info: unpacking minimap2_2.27+dfsg-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying hardening.patch dpkg-source: info: applying do_not_use_natbib.bst.patch dpkg-source: info: applying ar.patch dpkg-source: info: applying link_mappy_to_libminimap.patch dpkg-source: info: applying python-sse4-arch.patch dpkg-source: info: applying simde dpkg-source: info: applying reenable-simde.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-28285771 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-28285771 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-28285771 SCHROOT_UID=2001 SCHROOT_USER=buildd SHELL=/bin/sh TERM=unknown USER=buildd V=1 dpkg-buildpackage ----------------- Command: dpkg-buildpackage -us -uc -mLaunchpad Build Daemon -B -rfakeroot dpkg-buildpackage: info: source package minimap2 dpkg-buildpackage: info: source version 2.27+dfsg-1 dpkg-buildpackage: info: source distribution unstable dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/<>' dh_auto_clean make -j4 clean make[2]: Entering directory '/<>' rm -fr gmon.out *.o a.out minimap2 sdust minimap2-lite *~ *.a *.dSYM build dist mappy*.so mappy.c python/mappy.c mappy.egg* make[2]: Leaving directory '/<>' dh_auto_clean --buildsystem=pybuild I: pybuild base:311: python3.12 setup.py clean /usr/lib/python3/dist-packages/setuptools/__init__.py:84: _DeprecatedInstaller: setuptools.installer and fetch_build_eggs are deprecated. !! ******************************************************************************** Requirements should be satisfied by a PEP 517 installer. If you are using pip, you can try `pip install --use-pep517`. ******************************************************************************** !! dist.fetch_build_eggs(dist.setup_requires) WARNING: The wheel package is not available. running clean removing '/<>/.pybuild/cpython3_3.12/build' (and everything under it) 'build/bdist.linux-aarch64' does not exist -- can't clean it 'build/scripts-3.12' does not exist -- can't clean it cd tex && make clean make[2]: Entering directory '/<>/tex' rm -fr *.toc *.aux *.bbl *.blg *.idx *.log *.out *~ minimap2.pdf make[2]: Leaving directory '/<>/tex' make[1]: Leaving directory '/<>' dh_clean debian/rules binary-arch dh binary-arch 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 -- -f Makefile.simde make -j4 "INSTALL=install --strip-program=true" -f Makefile.simde make[2]: Entering directory '/<>' cc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/minimap2-2.27+dfsg-1 -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -Wdate-time -D_FORTIFY_SOURCE=3 main.c -o main.o cc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/minimap2-2.27+dfsg-1 -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -Wdate-time -D_FORTIFY_SOURCE=3 kthread.c -o kthread.o cc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/minimap2-2.27+dfsg-1 -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -Wdate-time -D_FORTIFY_SOURCE=3 kalloc.c -o kalloc.o cc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/minimap2-2.27+dfsg-1 -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -Wdate-time -D_FORTIFY_SOURCE=3 misc.c -o misc.o cc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/minimap2-2.27+dfsg-1 -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -Wdate-time -D_FORTIFY_SOURCE=3 bseq.c -o bseq.o cc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/minimap2-2.27+dfsg-1 -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -Wdate-time -D_FORTIFY_SOURCE=3 sketch.c -o sketch.o cc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/minimap2-2.27+dfsg-1 -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -Wdate-time -D_FORTIFY_SOURCE=3 sdust.c -o sdust.o cc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/minimap2-2.27+dfsg-1 -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -Wdate-time -D_FORTIFY_SOURCE=3 options.c -o options.o cc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/minimap2-2.27+dfsg-1 -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -Wdate-time -D_FORTIFY_SOURCE=3 index.c -o index.o cc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/minimap2-2.27+dfsg-1 -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -Wdate-time -D_FORTIFY_SOURCE=3 lchain.c -o lchain.o cc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/minimap2-2.27+dfsg-1 -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -Wdate-time -D_FORTIFY_SOURCE=3 align.c -o align.o cc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/minimap2-2.27+dfsg-1 -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -Wdate-time -D_FORTIFY_SOURCE=3 hit.c -o hit.o index.c: In function ‘mm_idx_load’: index.c:520:17: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 520 | fread(&l, 1, 1, fp); | ^~~~~~~~~~~~~~~~~~~ index.c:523:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 523 | fread(s->name, 1, l, fp); | ^~~~~~~~~~~~~~~~~~~~~~~~ index.c:526:17: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 526 | fread(&s->len, 4, 1, fp); | ^~~~~~~~~~~~~~~~~~~~~~~~ index.c:536:17: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 536 | fread(&b->n, 4, 1, fp); | ^~~~~~~~~~~~~~~~~~~~~~ index.c:538:17: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 538 | fread(b->p, 8, b->n, fp); | ^~~~~~~~~~~~~~~~~~~~~~~~ index.c:539:17: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 539 | fread(&size, 4, 1, fp); | ^~~~~~~~~~~~~~~~~~~~~~ index.c:546:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 546 | fread(x, 8, 2, fp); | ^~~~~~~~~~~~~~~~~~ index.c:554:17: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 554 | fread(mi->S, 4, (sum_len + 7) / 8, fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/minimap2-2.27+dfsg-1 -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -Wdate-time -D_FORTIFY_SOURCE=3 seed.c -o seed.o cc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/minimap2-2.27+dfsg-1 -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -Wdate-time -D_FORTIFY_SOURCE=3 map.c -o map.o cc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/minimap2-2.27+dfsg-1 -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -Wdate-time -D_FORTIFY_SOURCE=3 format.c -o format.o cc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/minimap2-2.27+dfsg-1 -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -Wdate-time -D_FORTIFY_SOURCE=3 pe.c -o pe.o cc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/minimap2-2.27+dfsg-1 -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -Wdate-time -D_FORTIFY_SOURCE=3 esterr.c -o esterr.o cc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/minimap2-2.27+dfsg-1 -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -Wdate-time -D_FORTIFY_SOURCE=3 splitidx.c -o splitidx.o cc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/minimap2-2.27+dfsg-1 -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -Wdate-time -D_FORTIFY_SOURCE=3 ksw2_ll_sse.c -o ksw2_ll_sse.o cc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/minimap2-2.27+dfsg-1 -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -Wdate-time -D_FORTIFY_SOURCE=3 -DKSW_SSE2_ONLY -D__SSE2__ ksw2_extz2_sse.c -o ksw2_extz2.o ksw2_extz2_sse.c:5: warning: "SIMDE_ENABLE_NATIVE_ALIASES" redefined 5 | #define SIMDE_ENABLE_NATIVE_ALIASES | : note: this is the location of the previous definition cc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/minimap2-2.27+dfsg-1 -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -Wdate-time -D_FORTIFY_SOURCE=3 -DKSW_SSE2_ONLY -D__SSE2__ ksw2_extd2_sse.c -o ksw2_extd2.o ksw2_extd2_sse.c:6: warning: "SIMDE_ENABLE_NATIVE_ALIASES" redefined 6 | #define SIMDE_ENABLE_NATIVE_ALIASES | : note: this is the location of the previous definition cc -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/minimap2-2.27+dfsg-1 -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES -Wdate-time -D_FORTIFY_SOURCE=3 -DKSW_SSE2_ONLY -D__SSE2__ ksw2_exts2_sse.c -o ksw2_exts2.o ksw2_exts2_sse.c:6: warning: "SIMDE_ENABLE_NATIVE_ALIASES" redefined 6 | #define SIMDE_ENABLE_NATIVE_ALIASES | : note: this is the location of the previous definition rm -f libminimap2.a ar csrD libminimap2.a kthread.o kalloc.o misc.o bseq.o sketch.o sdust.o options.o index.o lchain.o align.o hit.o seed.o map.o format.o pe.o esterr.o splitidx.o ksw2_ll_sse.o ksw2_extz2.o ksw2_extd2.o ksw2_exts2.o cc -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/minimap2-2.27+dfsg-1 -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -g -Wall -O2 -Wc++-compat -DHAVE_KALLOC -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES main.o -o minimap2 -L. -lminimap2 -lm -lz -lpthread -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now make[2]: Leaving directory '/<>' cd tex && make make[2]: Entering 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(./minimap2.aux) LaTeX Font Warning: Size substitutions with differences (Font) up to 0.5pt have occurred. LaTeX Warning: There were undefined references. LaTeX Warning: Label(s) may have changed. Rerun to get cross-references right. Package rerunfilecheck Warning: File `minimap2.out' has changed. (rerunfilecheck) Rerun to get outlines right (rerunfilecheck) or use package `bookmark'. ) (see the transcript file for additional information) Output written on minimap2.pdf (5 pages, 254628 bytes). Transcript written on minimap2.log. This is BibTeX, Version 0.99d (TeX Live 2023/Debian) The top-level auxiliary file: minimap2.aux The style file: apalike.bst Database file #1: minimap2.bib This is pdfTeX, Version 3.141592653-2.6-1.40.25 (TeX Live 2023/Debian) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./minimap2.tex LaTeX2e <2023-11-01> patch level 1 L3 programming layer <2024-01-22> (./bioinfo.cls Document Class: bioinfo 2003/02/08 0.1 (/usr/share/texlive/texmf-dist/tex/latex/base/inputenc.sty) (/usr/share/texlive/texmf-dist/tex/latex/crop/crop.sty (/usr/share/texlive/texmf-dist/tex/generic/iftex/ifluatex.sty (/usr/share/texlive/texmf-dist/tex/generic/iftex/iftex.sty)) (/usr/share/texlive/texmf-dist/tex/latex/graphics/color.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/color.cfg) (/usr/share/texlive/texmf-dist/tex/latex/graphics-def/pdftex.def) (/usr/share/texlive/texmf-dist/tex/latex/graphics/mathcolor.ltx)) (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphics.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/trig.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/graphics.cfg))) (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphicx.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty)) (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsmath.sty For additional information on amsmath, use the `?' option. 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Package natbib Warning: Citation `Dobin:2013kx' on page 4 undefined on input li ne 592. Underfull \hbox (badness 4634) in paragraph at lines 598--610 \OT1/ptm/m/n/9 Direct RNA-seq dataset ([]http://bit.ly/na12878ont[]). Minimap2 Overfull \hbox (261.0pt too wide) has occurred while \output is active [][] Overfull \vbox (1.0pt too high) has occurred while \output is active Overfull \hbox (261.0pt too wide) has occurred while \output is active [][] [4 <./roc-color.pdf>] Package natbib Warning: Citation `Langmead:2012fk' on page 5 undefined on input line 637. Package natbib Warning: Citation `Zaharia:2011aa' on page 5 undefined on input line 638. Package natbib Warning: Citation `Depristo:2011vn' on page 5 undefined on input line 649. Package natbib Warning: Citation `Li223297' on page 5 undefined on input line 6 53. Package natbib Warning: Citation `Marcais:2018aa' on page 5 undefined on input line 664. Underfull \hbox (badness 2027) in paragraph at lines 687--700 []\OT1/ptm/m/n/9 The capability of minimap2 comes from a fast base-level Underfull \hbox (badness 1226) in paragraph at lines 714--719 \OT1/ptm/m/n/9 releasing their masterpiece and insightful notes before formal Package hyperref Warning: Difference (3) between bookmark levels is greater (hyperref) than one, level fixed on input line 720. (./minimap2.bbl Overfull \hbox (261.0pt too wide) has occurred while \output is active [][] Overfull \vbox (1.0pt too high) has occurred while \output is active [5] Underfull \hbox (badness 1953) in paragraph at lines 120--123 []\OT1/ptm/m/n/7 Li, H. et al. (2009). The Sequence Alignment/Map format and S AMtools. ) Overfull \hbox (261.0pt too wide) has occurred while \output is active [][] Overfull \hbox (261.0pt too wide) has occurred while \output is active [][] [6] Package natbib Warning: There were undefined citations. (./minimap2.aux Package natbib Warning: Citation(s) may have changed. (natbib) Rerun to get citations correct. ) LaTeX Font Warning: Size substitutions with differences (Font) up to 0.5pt have occurred. ) (see the transcript file for additional information) Output written on minimap2.pdf (6 pages, 265939 bytes). Transcript written on minimap2.log. This is pdfTeX, Version 3.141592653-2.6-1.40.25 (TeX Live 2023/Debian) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./minimap2.tex LaTeX2e <2023-11-01> patch level 1 L3 programming layer <2024-01-22> (./bioinfo.cls Document Class: bioinfo 2003/02/08 0.1 (/usr/share/texlive/texmf-dist/tex/latex/base/inputenc.sty) (/usr/share/texlive/texmf-dist/tex/latex/crop/crop.sty (/usr/share/texlive/texmf-dist/tex/generic/iftex/ifluatex.sty (/usr/share/texlive/texmf-dist/tex/generic/iftex/iftex.sty)) (/usr/share/texlive/texmf-dist/tex/latex/graphics/color.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/color.cfg) (/usr/share/texlive/texmf-dist/tex/latex/graphics-def/pdftex.def) (/usr/share/texlive/texmf-dist/tex/latex/graphics/mathcolor.ltx)) (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphics.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/trig.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/graphics.cfg))) (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphicx.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty)) (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsmath.sty For additional information on amsmath, use the `?' option. 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LaTeX Font Warning: Font shape `OML/cmm/m/it' in size <6.5> not available (Font) size <6> substituted on input line 58. LaTeX Font Warning: Font shape `OMS/cmsy/m/n' in size <6.5> not available (Font) size <6> substituted on input line 58. Underfull \hbox (badness 1478) in paragraph at lines 71--80 \OT1/ptm/m/n/9 minor modifications could enable the base algorithm to map Underfull \hbox (badness 1019) in paragraph at lines 71--80 \OT1/ptm/m/n/9 mRNAs as well. Minimap2 becomes a first RNA-seq aligner [1{/var/lib/texmf/fonts/map/pdftex/updmap/pdftex.map}{/usr/share/texlive/texmf- dist/fonts/enc/dvips/base/8r.enc}] Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `math shift' on input line 204. Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `math shift' on input line 204. Underfull \vbox (badness 10000) has occurred while \output is active Overfull \hbox (261.0pt too wide) has occurred while \output is active [][] Overfull \vbox (1.0pt too high) has occurred while \output is active Overfull \hbox (261.0pt too wide) has occurred while \output is active [][] [2] Underfull \hbox (badness 1769) in paragraph at lines 382--386 \OT1/ptm/m/n/8 performs local alignment between the two subsequences involved i n Overfull \hbox (261.0pt too wide) has occurred while \output is active [][] Overfull \vbox (1.0pt too high) has occurred while \output is active [3] LaTeX Font Warning: Font shape `OT1/cmtt/m/n' in size <6.5> not available (Font) size <6> substituted on input line 492. Overfull \hbox (9.0pt too wide) in paragraph at lines 496--515 [][] Underfull \hbox (badness 1248) in paragraph at lines 518--535 []\OT1/ptm/m/n/9 2016[]), Kart (v2.2.5; []Lin and Hsu[], []2017[]), minialign ( v0.5.3; Overfull \hbox (3.90332pt too wide) in paragraph at lines 518--535 []\OT1/ptm/m/n/9 https://github.com/ocxtal/minialign[]) and NGMLR (v0.2.5; []Se dlazeck Underfull \hbox (badness 2189) in paragraph at lines 590--597 \OT1/ptm/m/n/9 GMAP (v2017-06-20; []Wu and Watanabe[], []2005[]), minimap2, Underfull \hbox (badness 1424) in paragraph at lines 590--597 \OT1/ptm/m/n/9 et al.[], []2013[]). In general, minimap2 is more consistent wit h Overfull \hbox (261.0pt too wide) has occurred while \output is active [][] Overfull \vbox (1.0pt too high) has occurred while \output is active Overfull \hbox (261.0pt too wide) has occurred while \output is active [][] [4 <./roc-color.pdf>] Underfull \hbox (badness 4634) in paragraph at lines 598--610 \OT1/ptm/m/n/9 Direct RNA-seq dataset ([]http://bit.ly/na12878ont[]). Minimap2 Underfull \hbox (badness 2096) in paragraph at lines 647--659 \OT1/ptm/m/n/9 v3.5 ([]Depristo et al.[], []2011[]). This run was sequenced fro m Underfull \hbox (badness 1454) in paragraph at lines 662--671 \OT1/ptm/m/n/9 the paftools.js script from the minimap2 package, we called Underfull \hbox (badness 1137) in paragraph at lines 662--671 \OT1/ptm/m/n/9 regions. The transition-to-transversion ratio (ts/tv) is 2.01. I n Underfull \hbox (badness 2027) in paragraph at lines 687--700 []\OT1/ptm/m/n/9 The capability of minimap2 comes from a fast base-level Underfull \hbox (badness 1226) in paragraph at lines 714--719 \OT1/ptm/m/n/9 releasing their masterpiece and insightful notes before formal Package hyperref Warning: Difference (3) between bookmark levels is greater (hyperref) than one, level fixed on input line 720. (./minimap2.bbl Overfull \hbox (261.0pt too wide) has occurred while \output is active [][] Overfull \vbox (1.0pt too high) has occurred while \output is active [5] Underfull \hbox (badness 1953) in paragraph at lines 120--123 []\OT1/ptm/m/n/7 Li, H. et al. (2009). The Sequence Alignment/Map format and S AMtools. Underfull \vbox (badness 10000) has occurred while \output is active) Overfull \hbox (261.0pt too wide) has occurred while \output is active [][] Overfull \hbox (261.0pt too wide) has occurred while \output is active [][] [6] (./minimap2.aux) LaTeX Font Warning: Size substitutions with differences (Font) up to 0.5pt have occurred. ) (see the transcript file for additional information) Output written on minimap2.pdf (6 pages, 269462 bytes). Transcript written on minimap2.log. make[2]: Leaving directory '/<>/tex' dh_auto_build --buildsystem=pybuild I: pybuild base:311: /usr/bin/python3 setup.py build /usr/lib/python3/dist-packages/setuptools/__init__.py:84: _DeprecatedInstaller: setuptools.installer and fetch_build_eggs are deprecated. !! ******************************************************************************** Requirements should be satisfied by a PEP 517 installer. If you are using pip, you can try `pip install --use-pep517`. ******************************************************************************** !! dist.fetch_build_eggs(dist.setup_requires) WARNING: The wheel package is not available. running build running build_ext /usr/lib/python3/dist-packages/Cython/Compiler/Main.py:381: FutureWarning: Cython directive 'language_level' not set, using '3str' for now (Py3). This has changed from earlier releases! File: /<>/python/mappy.pyx tree = Parsing.p_module(s, pxd, full_module_name) Compiling python/mappy.pyx because it changed. [1/1] Cythonizing python/mappy.pyx building 'mappy' extension creating build creating build/temp.linux-aarch64-cpython-312 creating build/temp.linux-aarch64-cpython-312/python aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/minimap2-2.27+dfsg-1 -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -I. -I/usr/include/python3.12 -c align.c -o build/temp.linux-aarch64-cpython-312/align.o -DHAVE_KALLOC -ftree-vectorize -DKSW_SSE2_ONLY -DUSE_SIMDE -D__SSE2__ -DSIMDE_ENABLE_NATIVE_ALIASES -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP align.c: In function ‘mm_get_hplen_back’: align.c:365:43: warning: comparison of integer expressions of different signedness: ‘uint32_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 365 | if (mm_seq4_get(mi->S, i) != c) break; | ^~ align.c: In function ‘mm_seed_ext_score’: align.c:552:56: warning: operand of ‘?:’ changes signedness from ‘int’ to ‘uint32_t’ {aka ‘unsigned int’} due to unsignedness of other operand [-Wsign-compare] 552 | re = re + ext_len < (int32_t)mi->seq[rid].len? re + ext_len : mi->seq[rid].len; | ^~~~~~~~~~~~ align.c: In function ‘mm_align1’: align.c:646:59: warning: operand of ‘?:’ changes signedness from ‘int32_t’ {aka ‘int’} to ‘uint32_t’ {aka ‘unsigned int’} due to unsignedness of other operand [-Wsign-compare] 646 | re0 = re + l < (int32_t)mi->seq[rid].len? re + l : mi->seq[rid].len; | ^~~~~~ align.c:698:65: warning: operand of ‘?:’ changes signedness from ‘int32_t’ {aka ‘int’} to ‘uint32_t’ {aka ‘unsigned int’} due to unsignedness of other operand [-Wsign-compare] 698 | l = l < (int32_t)mi->seq[rid].len - re? l : mi->seq[rid].len - re; | ^ aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/minimap2-2.27+dfsg-1 -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -I. -I/usr/include/python3.12 -c bseq.c -o build/temp.linux-aarch64-cpython-312/bseq.o -DHAVE_KALLOC -ftree-vectorize -DKSW_SSE2_ONLY -DUSE_SIMDE -D__SSE2__ -DSIMDE_ENABLE_NATIVE_ALIASES -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/minimap2-2.27+dfsg-1 -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -I. -I/usr/include/python3.12 -c esterr.c -o build/temp.linux-aarch64-cpython-312/esterr.o -DHAVE_KALLOC -ftree-vectorize -DKSW_SSE2_ONLY -DUSE_SIMDE -D__SSE2__ -DSIMDE_ENABLE_NATIVE_ALIASES -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/minimap2-2.27+dfsg-1 -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -I. -I/usr/include/python3.12 -c format.c -o build/temp.linux-aarch64-cpython-312/format.o -DHAVE_KALLOC -ftree-vectorize -DKSW_SSE2_ONLY -DUSE_SIMDE -D__SSE2__ -DSIMDE_ENABLE_NATIVE_ALIASES -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/minimap2-2.27+dfsg-1 -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -I. -I/usr/include/python3.12 -c hit.c -o build/temp.linux-aarch64-cpython-312/hit.o -DHAVE_KALLOC -ftree-vectorize -DKSW_SSE2_ONLY -DUSE_SIMDE -D__SSE2__ -DSIMDE_ENABLE_NATIVE_ALIASES -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP hit.c: In function ‘mm_hit_sort’: hit.c:190:55: warning: variable ‘no_cigar’ set but not used [-Wunused-but-set-variable] 190 | int32_t i, n_aux, n = *n_regs, has_cigar = 0, no_cigar = 0; | ^~~~~~~~ hit.c:190:40: warning: variable ‘has_cigar’ set but not used [-Wunused-but-set-variable] 190 | int32_t i, n_aux, n = *n_regs, has_cigar = 0, no_cigar = 0; | ^~~~~~~~~ aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/minimap2-2.27+dfsg-1 -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -I. -I/usr/include/python3.12 -c index.c -o build/temp.linux-aarch64-cpython-312/index.o -DHAVE_KALLOC -ftree-vectorize -DKSW_SSE2_ONLY -DUSE_SIMDE -D__SSE2__ -DSIMDE_ENABLE_NATIVE_ALIASES -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP index.c: In function ‘mm_idx_name2id’: index.c:149:32: warning: operand of ‘?:’ changes signedness from ‘int’ to ‘uint32_t’ {aka ‘unsigned int’} due to unsignedness of other operand [-Wsign-compare] 149 | return k == kh_end(h)? -1 : kh_val(h, k); | ^~ index.c: In function ‘mm_idx_gen’: index.c:382:70: warning: operand of ‘?:’ changes signedness from ‘int’ to ‘uint64_t’ {aka ‘long unsigned int’} due to unsignedness of other operand [-Wsign-compare] 382 | pl.mini_batch_size = (uint64_t)mini_batch_size < batch_size? mini_batch_size : batch_size; | ^~~~~~~~~~~~~~~ index.c: In function ‘mm_idx_dump’: index.c:483:23: warning: comparison of integer expressions of different signedness: ‘uint32_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 483 | for (i = 0; i < 1<b; ++i) { | ^ index.c: In function ‘mm_idx_load’: index.c:531:23: warning: comparison of integer expressions of different signedness: ‘uint32_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 531 | for (i = 0; i < 1<b; ++i) { | ^ index.c: In function ‘mm_idx_bed_read’: index.c:748:23: warning: comparison of integer expressions of different signedness: ‘int32_t’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 748 | for (i = 0; i < mi->n_seq; ++i) // TODO: eliminate redundant intervals | ^ index.c: In function ‘mm_idx_bed_junc’: index.c:758:42: warning: comparison of integer expressions of different signedness: ‘int32_t’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 758 | if (mi->I == 0 || ctg < 0 || ctg >= mi->n_seq) return -1; | ^~ index.c: In function ‘mm_idx_load’: index.c:520:17: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 520 | fread(&l, 1, 1, fp); | ^~~~~~~~~~~~~~~~~~~ index.c:523:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 523 | fread(s->name, 1, l, fp); | ^~~~~~~~~~~~~~~~~~~~~~~~ index.c:526:17: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 526 | fread(&s->len, 4, 1, fp); | ^~~~~~~~~~~~~~~~~~~~~~~~ index.c:536:17: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 536 | fread(&b->n, 4, 1, fp); | ^~~~~~~~~~~~~~~~~~~~~~ index.c:538:17: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 538 | fread(b->p, 8, b->n, fp); | ^~~~~~~~~~~~~~~~~~~~~~~~ index.c:539:17: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 539 | fread(&size, 4, 1, fp); | ^~~~~~~~~~~~~~~~~~~~~~ index.c:546:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 546 | fread(x, 8, 2, fp); | ^~~~~~~~~~~~~~~~~~ index.c:554:17: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 554 | fread(mi->S, 4, (sum_len + 7) / 8, fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/minimap2-2.27+dfsg-1 -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -I. -I/usr/include/python3.12 -c kalloc.c -o build/temp.linux-aarch64-cpython-312/kalloc.o -DHAVE_KALLOC -ftree-vectorize -DKSW_SSE2_ONLY -DUSE_SIMDE -D__SSE2__ -DSIMDE_ENABLE_NATIVE_ALIASES -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/minimap2-2.27+dfsg-1 -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -I. -I/usr/include/python3.12 -c ksw2_extd2_sse.c -o build/temp.linux-aarch64-cpython-312/ksw2_extd2_sse.o -DHAVE_KALLOC -ftree-vectorize -DKSW_SSE2_ONLY -DUSE_SIMDE -D__SSE2__ -DSIMDE_ENABLE_NATIVE_ALIASES -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP ksw2_extd2_sse.c:6: warning: "SIMDE_ENABLE_NATIVE_ALIASES" redefined 6 | #define SIMDE_ENABLE_NATIVE_ALIASES | : note: this is the location of the previous definition aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/minimap2-2.27+dfsg-1 -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -I. -I/usr/include/python3.12 -c ksw2_exts2_sse.c -o build/temp.linux-aarch64-cpython-312/ksw2_exts2_sse.o -DHAVE_KALLOC -ftree-vectorize -DKSW_SSE2_ONLY -DUSE_SIMDE -D__SSE2__ -DSIMDE_ENABLE_NATIVE_ALIASES -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP ksw2_exts2_sse.c:6: warning: "SIMDE_ENABLE_NATIVE_ALIASES" redefined 6 | #define SIMDE_ENABLE_NATIVE_ALIASES | : note: this is the location of the previous definition aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/minimap2-2.27+dfsg-1 -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -I. -I/usr/include/python3.12 -c ksw2_extz2_sse.c -o build/temp.linux-aarch64-cpython-312/ksw2_extz2_sse.o -DHAVE_KALLOC -ftree-vectorize -DKSW_SSE2_ONLY -DUSE_SIMDE -D__SSE2__ -DSIMDE_ENABLE_NATIVE_ALIASES -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP ksw2_extz2_sse.c:5: warning: "SIMDE_ENABLE_NATIVE_ALIASES" redefined 5 | #define SIMDE_ENABLE_NATIVE_ALIASES | : note: this is the location of the previous definition aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/minimap2-2.27+dfsg-1 -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -I. -I/usr/include/python3.12 -c ksw2_ll_sse.c -o build/temp.linux-aarch64-cpython-312/ksw2_ll_sse.o -DHAVE_KALLOC -ftree-vectorize -DKSW_SSE2_ONLY -DUSE_SIMDE -D__SSE2__ -DSIMDE_ENABLE_NATIVE_ALIASES -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/minimap2-2.27+dfsg-1 -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -I. -I/usr/include/python3.12 -c kthread.c -o build/temp.linux-aarch64-cpython-312/kthread.o -DHAVE_KALLOC -ftree-vectorize -DKSW_SSE2_ONLY -DUSE_SIMDE -D__SSE2__ -DSIMDE_ENABLE_NATIVE_ALIASES -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/minimap2-2.27+dfsg-1 -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -I. -I/usr/include/python3.12 -c lchain.c -o build/temp.linux-aarch64-cpython-312/lchain.o -DHAVE_KALLOC -ftree-vectorize -DKSW_SSE2_ONLY -DUSE_SIMDE -D__SSE2__ -DSIMDE_ENABLE_NATIVE_ALIASES -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP lchain.c: In function ‘mg_chain_bk_end’: lchain.c:18:37: warning: operand of ‘?:’ changes signedness from ‘int32_t’ {aka ‘int’} to ‘uint64_t’ {aka ‘long unsigned int’} due to unsignedness of other operand [-Wsign-compare] 18 | s = i < 0? z[k].x : (int32_t)z[k].x - f[i]; | ^~~~~~~~~~~~~~~~~~~~~~ lchain.c: In function ‘mg_chain_backtrack’: lchain.c:51:46: warning: operand of ‘?:’ changes signedness from ‘int32_t’ {aka ‘int’} to ‘uint64_t’ {aka ‘long unsigned int’} due to unsignedness of other operand [-Wsign-compare] 51 | sc = i < 0? z[k].x : (int32_t)z[k].x - f[i]; | ^~~~~~~~~~~~~~~~~~~~~~ lchain.c:66:46: warning: operand of ‘?:’ changes signedness from ‘int32_t’ {aka ‘int’} to ‘uint64_t’ {aka ‘long unsigned int’} due to unsignedness of other operand [-Wsign-compare] 66 | sc = i < 0? z[k].x : (int32_t)z[k].x - f[i]; | ^~~~~~~~~~~~~~~~~~~~~~ lchain.c: In function ‘mg_lchain_dp’: lchain.c:190:56: warning: comparison of integer expressions of different signedness: ‘uint64_t’ {aka ‘long unsigned int’} and ‘long int’ [-Wsign-compare] 190 | if (max_ii < 0 || a[i].x - a[max_ii].x > (int64_t)max_dist_x) { | ^ lchain.c:204:57: warning: comparison of integer expressions of different signedness: ‘uint64_t’ {aka ‘long unsigned int’} and ‘long int’ [-Wsign-compare] 204 | if (max_ii < 0 || (a[i].x - a[max_ii].x <= (int64_t)max_dist_x && f[max_ii] < f[i])) | ^~ lchain.c: In function ‘mg_lchain_rmq’: lchain.c:295:117: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 295 | while (st < i && (a[i].x>>32 != a[st].x>>32 || a[i].x > a[st].x + max_dist || krmq_size(head, root) > cap_rmq_size)) { | ^ lchain.c:304:155: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 304 | while (st_inner < i && (a[i].x>>32 != a[st_inner].x>>32 || a[i].x > a[st_inner].x + max_dist_inner || krmq_size(head, root_inner) > cap_rmq_size)) { | ^ lchain.c:356:34: warning: comparison of integer expressions of different signedness: ‘int32_t’ {aka ‘int’} and ‘unsigned int’ [-Wsign-compare] 356 | if (max_rmq_size < krmq_size(head, root)) max_rmq_size = krmq_size(head, root); | ^ aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/minimap2-2.27+dfsg-1 -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -I. -I/usr/include/python3.12 -c map.c -o build/temp.linux-aarch64-cpython-312/map.o -DHAVE_KALLOC -ftree-vectorize -DKSW_SSE2_ONLY -DUSE_SIMDE -D__SSE2__ -DSIMDE_ENABLE_NATIVE_ALIASES -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP map.c: In function ‘mm_dust_minier’: map.c:48:70: warning: operand of ‘?:’ changes signedness from ‘int32_t’ {aka ‘int’} to ‘uint64_t’ {aka ‘long unsigned int’} due to unsignedness of other operand [-Wsign-compare] 48 | int ss = s > (int32_t)(dreg[v]>>32)? s : dreg[v]>>32; | ^ map.c:49:64: warning: operand of ‘?:’ changes signedness from ‘int32_t’ {aka ‘int’} to ‘unsigned int’ due to unsignedness of other operand [-Wsign-compare] 49 | int ee = e < (int32_t)dreg[v]? e : (uint32_t)dreg[v]; | ^ map.c: In function ‘mm_map_frag’: map.c:367:84: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int64_t’ {aka ‘long int’} [-Wsign-compare] 367 | if (kmst.largest > 1U<<28 || (opt->cap_kalloc > 0 && kmst.capacity > opt->cap_kalloc)) { | ^ aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/minimap2-2.27+dfsg-1 -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -I. -I/usr/include/python3.12 -c misc.c -o build/temp.linux-aarch64-cpython-312/misc.o -DHAVE_KALLOC -ftree-vectorize -DKSW_SSE2_ONLY -DUSE_SIMDE -D__SSE2__ -DSIMDE_ENABLE_NATIVE_ALIASES -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/minimap2-2.27+dfsg-1 -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -I. -I/usr/include/python3.12 -c options.c -o build/temp.linux-aarch64-cpython-312/options.o -DHAVE_KALLOC -ftree-vectorize -DKSW_SSE2_ONLY -DUSE_SIMDE -D__SSE2__ -DSIMDE_ENABLE_NATIVE_ALIASES -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/minimap2-2.27+dfsg-1 -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -I. -I/usr/include/python3.12 -c pe.c -o build/temp.linux-aarch64-cpython-312/pe.o -DHAVE_KALLOC -ftree-vectorize -DKSW_SSE2_ONLY -DUSE_SIMDE -D__SSE2__ -DSIMDE_ENABLE_NATIVE_ALIASES -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/minimap2-2.27+dfsg-1 -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -I. -I/usr/include/python3.12 -c python/mappy.c -o build/temp.linux-aarch64-cpython-312/python/mappy.o -DHAVE_KALLOC -ftree-vectorize -DKSW_SSE2_ONLY -DUSE_SIMDE -D__SSE2__ -DSIMDE_ENABLE_NATIVE_ALIASES -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/minimap2-2.27+dfsg-1 -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -I. -I/usr/include/python3.12 -c sdust.c -o build/temp.linux-aarch64-cpython-312/sdust.o -DHAVE_KALLOC -ftree-vectorize -DKSW_SSE2_ONLY -DUSE_SIMDE -D__SSE2__ -DSIMDE_ENABLE_NATIVE_ALIASES -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/minimap2-2.27+dfsg-1 -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -I. -I/usr/include/python3.12 -c seed.c -o build/temp.linux-aarch64-cpython-312/seed.o -DHAVE_KALLOC -ftree-vectorize -DKSW_SSE2_ONLY -DUSE_SIMDE -D__SSE2__ -DSIMDE_ENABLE_NATIVE_ALIASES -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP seed.c: In function ‘mm_seed_mz_flt’: seed.c:9:19: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int32_t’ {aka ‘int’} [-Wsign-compare] 9 | if (mv->n <= q_occ_max || q_occ_frac <= 0.0f || q_occ_max <= 0) return; | ^~ seed.c: In function ‘mm_seed_select’: seed.c:65:28: warning: comparison of integer expressions of different signedness: ‘uint32_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 65 | if (a[i].n > max_occ) ++m; | ^ seed.c:68:38: warning: comparison of integer expressions of different signedness: ‘uint32_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 68 | if (i == n || a[i].n <= max_occ) { | ^~ seed.c:71:54: warning: operand of ‘?:’ changes signedness from ‘int’ to ‘unsigned int’ due to unsignedness of other operand [-Wsign-compare] 71 | int32_t pe = i == n? len : (uint32_t)a[i].q_pos>>1; | ^~~ seed.c:81:60: warning: comparison of integer expressions of different signedness: ‘uint32_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 81 | if (a[j].n < (int32_t)(b[0]>>32)) { // then update the heap | ^ seed.c:90:52: warning: comparison of integer expressions of different signedness: ‘uint32_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 90 | if (a[j].n > max_max_occ) | ^ seed.c: In function ‘mm_collect_matches’: seed.c:109:31: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 109 | for (i = 0; i < n_m0; ++i) | ^ seed.c:110:36: warning: comparison of integer expressions of different signedness: ‘uint32_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 110 | if (m[i].n > max_occ) | ^ seed.c:113:56: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 113 | for (i = 0, n_m = 0, *rep_len = 0, *n_a = 0; i < n_m0; ++i) { | ^ aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/minimap2-2.27+dfsg-1 -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -I. -I/usr/include/python3.12 -c sketch.c -o build/temp.linux-aarch64-cpython-312/sketch.o -DHAVE_KALLOC -ftree-vectorize -DKSW_SSE2_ONLY -DUSE_SIMDE -D__SSE2__ -DSIMDE_ENABLE_NATIVE_ALIASES -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP aarch64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/minimap2-2.27+dfsg-1 -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -I. -I/usr/include/python3.12 -c splitidx.c -o build/temp.linux-aarch64-cpython-312/splitidx.o -DHAVE_KALLOC -ftree-vectorize -DKSW_SSE2_ONLY -DUSE_SIMDE -D__SSE2__ -DSIMDE_ENABLE_NATIVE_ALIASES -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP aarch64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fdebug-prefix-map=/<>=/usr/src/minimap2-2.27+dfsg-1 -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP -Wdate-time -D_FORTIFY_SOURCE=3 build/temp.linux-aarch64-cpython-312/align.o build/temp.linux-aarch64-cpython-312/bseq.o build/temp.linux-aarch64-cpython-312/esterr.o build/temp.linux-aarch64-cpython-312/format.o build/temp.linux-aarch64-cpython-312/hit.o build/temp.linux-aarch64-cpython-312/index.o build/temp.linux-aarch64-cpython-312/kalloc.o build/temp.linux-aarch64-cpython-312/ksw2_extd2_sse.o build/temp.linux-aarch64-cpython-312/ksw2_exts2_sse.o build/temp.linux-aarch64-cpython-312/ksw2_extz2_sse.o build/temp.linux-aarch64-cpython-312/ksw2_ll_sse.o build/temp.linux-aarch64-cpython-312/kthread.o build/temp.linux-aarch64-cpython-312/lchain.o build/temp.linux-aarch64-cpython-312/map.o build/temp.linux-aarch64-cpython-312/misc.o build/temp.linux-aarch64-cpython-312/options.o build/temp.linux-aarch64-cpython-312/pe.o build/temp.linux-aarch64-cpython-312/python/mappy.o build/temp.linux-aarch64-cpython-312/sdust.o build/temp.linux-aarch64-cpython-312/seed.o build/temp.linux-aarch64-cpython-312/sketch.o build/temp.linux-aarch64-cpython-312/splitidx.o -L/usr/lib/aarch64-linux-gnu -lz -lm -lpthread -o /<>/.pybuild/cpython3_3.12/build/mappy.cpython-312-aarch64-linux-gnu.so running build_scripts creating build/scripts-3.12 copying and adjusting python/minimap2.py -> build/scripts-3.12 changing mode of build/scripts-3.12/minimap2.py from 644 to 755 make[1]: Leaving directory '/<>' debian/rules override_dh_auto_test make[1]: Entering directory '/<>' debian/test_script [M::mm_idx_gen::0.006*2.13] collected minimizers [M::mm_idx_gen::0.009*2.28] sorted minimizers [M::main::0.009*2.26] loaded/built the index for 1 target sequence(s) [M::mm_mapopt_update::0.010*2.12] mid_occ = 10 [M::mm_idx_stat] kmer size: 15; skip: 10; is_hpc: 0; #seq: 1 [M::mm_idx_stat::0.011*2.05] distinct minimizers: 3111 (100.00% are singletons); average occurrences: 1.000; average spacing: 5.326; total length: 16569 [M::worker_pipeline::0.040*1.41] mapped 1 sequences [M::main] Version: 2.27-r1193 [M::main] CMD: minimap2 -a test/MT-human.fa test/MT-orang.fa [M::main] Real time: 0.044 sec; CPU: 0.060 sec; Peak RSS: 0.004 GB [M::mm_idx_gen::0.009*2.23] collected minimizers [M::mm_idx_gen::0.014*2.30] sorted minimizers [M::main::0.019*1.93] loaded/built the index for 1 target sequence(s) [M::mm_idx_stat] kmer size: 15; skip: 10; is_hpc: 0; #seq: 1 [M::mm_idx_stat::0.021*1.87] distinct minimizers: 3111 (100.00% are singletons); average occurrences: 1.000; average spacing: 5.326; total length: 16569 [M::main] Version: 2.27-r1193 [M::main] CMD: minimap2 -d MT-human.mmi test/MT-human.fa [M::main] Real time: 0.023 sec; CPU: 0.041 sec; Peak RSS: 0.003 GB [M::main::0.007*1.32] loaded/built the index for 1 target sequence(s) [M::mm_mapopt_update::0.009*1.27] mid_occ = 10 [M::mm_idx_stat] kmer size: 15; skip: 10; is_hpc: 0; #seq: 1 [M::mm_idx_stat::0.010*1.23] distinct minimizers: 3111 (100.00% are singletons); average occurrences: 1.000; average spacing: 5.326; total length: 16569 [M::worker_pipeline::0.048*1.00] mapped 1 sequences [M::main] Version: 2.27-r1193 [M::main] CMD: minimap2 -a MT-human.mmi test/MT-orang.fa [M::main] Real time: 0.053 sec; CPU: 0.056 sec; Peak RSS: 0.005 GB rm test.sam make[1]: Leaving directory '/<>' create-stamp debian/debhelper-build-stamp dh_prep -a dh_installdirs -a debian/rules override_dh_auto_install make[1]: Entering directory '/<>' dh_auto_install dh_auto_install --buildsystem=pybuild I: pybuild base:311: /usr/bin/python3 setup.py install --root /<>/debian/tmp /usr/lib/python3/dist-packages/setuptools/__init__.py:84: _DeprecatedInstaller: setuptools.installer and fetch_build_eggs are deprecated. !! ******************************************************************************** Requirements should be satisfied by a PEP 517 installer. If you are using pip, you can try `pip install --use-pep517`. ******************************************************************************** !! dist.fetch_build_eggs(dist.setup_requires) WARNING: The wheel package is not available. running install /usr/lib/python3/dist-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated. !! ******************************************************************************** Please avoid running ``setup.py`` directly. Instead, use pypa/build, pypa/installer or other standards-based tools. See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. ******************************************************************************** !! self.initialize_options() running build running build_ext running build_scripts running install_lib creating /<>/debian/tmp/usr creating /<>/debian/tmp/usr/lib creating /<>/debian/tmp/usr/lib/python3.12 creating /<>/debian/tmp/usr/lib/python3.12/dist-packages copying /<>/.pybuild/cpython3_3.12/build/mappy.cpython-312-aarch64-linux-gnu.so -> /<>/debian/tmp/usr/lib/python3.12/dist-packages running install_egg_info running egg_info creating mappy.egg-info writing mappy.egg-info/PKG-INFO writing dependency_links to mappy.egg-info/dependency_links.txt writing top-level names to mappy.egg-info/top_level.txt writing manifest file 'mappy.egg-info/SOURCES.txt' reading manifest file 'mappy.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no files found matching 'sse2neon/emmintrin.h' adding license file 'LICENSE.txt' writing manifest file 'mappy.egg-info/SOURCES.txt' Copying mappy.egg-info to /<>/debian/tmp/usr/lib/python3.12/dist-packages/mappy-2.27.egg-info Skipping SOURCES.txt running install_scripts creating /<>/debian/tmp/usr/bin copying build/scripts-3.12/minimap2.py -> /<>/debian/tmp/usr/bin changing mode of /<>/debian/tmp/usr/bin/minimap2.py to 755 make[1]: Leaving directory '/<>' dh_install -a dh_installdocs -a dh_installchangelogs -a debian/rules override_dh_installman make[1]: Entering directory '/<>' dh_installman --language=C make[1]: Leaving directory '/<>' dh_python3 -a dh_lintian -a dh_perl -a dh_link -a dh_strip_nondeterminism -a debian/rules override_dh_compress make[1]: Entering directory '/<>' dh_compress --exclude=.pdf make[1]: Leaving directory '/<>' dh_fixperms -a dh_missing -a dh_dwz -a debian/rules override_dh_strip make[1]: Entering directory '/<>' dh_strip a0f3a06980a2d379e0059ec4f456d7e0134a0fe8 74642669bf99ee2f98fee35543220ccd266af18d ranlib /<>/debian/libminimap2-dev/usr/lib/libminimap2.a make[1]: Leaving directory '/<>' dh_makeshlibs -a dh_shlibdeps -a dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 from: /lib/ld-linux-aarch64.so.1 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 to: /lib/ld-linux-aarch64.so.1.usr-is-merged dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 from: /lib/ld-linux-aarch64.so.1 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 to: /lib/ld-linux-aarch64.so.1.usr-is-merged dh_installdeb -a dh_gencontrol -a dpkg-gencontrol: warning: Depends field of package libminimap2-dev: substitution variable ${shlibs:Depends} used, but is not defined dh_md5sums -a dh_builddeb -a INFO: pkgstriptranslations version 154 INFO: pkgstriptranslations version 154 INFO: pkgstriptranslations version 154 pkgstriptranslations: processing libminimap2-dev (in debian/libminimap2-dev); do_strip: , oemstrip: pkgstriptranslations: processing minimap2 (in debian/minimap2); do_strip: , oemstrip: pkgstriptranslations: processing python3-mappy-dbgsym (in debian/.debhelper/python3-mappy/dbgsym-root); do_strip: , oemstrip: pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/libminimap2-dev/DEBIAN/control, package libminimap2-dev, directory debian/libminimap2-dev INFO: pkgstripfiles: waiting for lock (libminimap2-dev) ... pkgstripfiles: processing control file: debian/minimap2/DEBIAN/control, package minimap2, directory debian/minimap2 pkgstripfiles: Running PNG optimization (using 4 cpus) for package minimap2 ... pkgstripfiles: No PNG files. pkgstripfiles: processing control file: debian/.debhelper/python3-mappy/dbgsym-root/DEBIAN/control, package python3-mappy-dbgsym, directory debian/.debhelper/python3-mappy/dbgsym-root dpkg-deb: building package 'python3-mappy-dbgsym' in 'debian/.debhelper/scratch-space/build-python3-mappy/python3-mappy-dbgsym_2.27+dfsg-1_arm64.deb'. dpkg-deb: building package 'minimap2' in '../minimap2_2.27+dfsg-1_arm64.deb'. Renaming python3-mappy-dbgsym_2.27+dfsg-1_arm64.deb to python3-mappy-dbgsym_2.27+dfsg-1_arm64.ddeb pkgstripfiles: Running PNG optimization (using 4 cpus) for package libminimap2-dev ... pkgstripfiles: No PNG files. dpkg-deb: building package 'libminimap2-dev' in '../libminimap2-dev_2.27+dfsg-1_arm64.deb'. INFO: pkgstriptranslations version 154 pkgstriptranslations: processing minimap2-dbgsym (in debian/.debhelper/minimap2/dbgsym-root); do_strip: , oemstrip: INFO: pkgstriptranslations version 154 pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstriptranslations: processing python3-mappy (in debian/python3-mappy); do_strip: , oemstrip: pkgstripfiles: processing control file: debian/.debhelper/minimap2/dbgsym-root/DEBIAN/control, package minimap2-dbgsym, directory debian/.debhelper/minimap2/dbgsym-root dpkg-deb: building package 'minimap2-dbgsym' in 'debian/.debhelper/scratch-space/build-minimap2/minimap2-dbgsym_2.27+dfsg-1_arm64.deb'. Renaming minimap2-dbgsym_2.27+dfsg-1_arm64.deb to minimap2-dbgsym_2.27+dfsg-1_arm64.ddeb pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/python3-mappy/DEBIAN/control, package python3-mappy, directory debian/python3-mappy pkgstripfiles: Running PNG optimization (using 4 cpus) for package python3-mappy ... pkgstripfiles: No PNG files. dpkg-deb: building package 'python3-mappy' in '../python3-mappy_2.27+dfsg-1_arm64.deb'. dpkg-genbuildinfo --build=any -O../minimap2_2.27+dfsg-1_arm64.buildinfo dpkg-genchanges --build=any -mLaunchpad Build Daemon -O../minimap2_2.27+dfsg-1_arm64.changes dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) -------------------------------------------------------------------------------- Build finished at 2024-05-03T12:11:15Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ minimap2_2.27+dfsg-1_arm64.changes: ----------------------------------- Format: 1.8 Date: Mon, 18 Mar 2024 17:12:17 +0100 Source: minimap2 Binary: libminimap2-dev minimap2 python3-mappy Built-For-Profiles: noudeb Architecture: arm64 Version: 2.27+dfsg-1 Distribution: oracular-proposed Urgency: medium Maintainer: Launchpad Build Daemon Changed-By: Michael R. Crusoe Description: libminimap2-dev - development headers for libminimap minimap2 - versatile pairwise aligner for genomic and spliced nucleotide seq python3-mappy - Python3 interface minimap2 Closes: 1046060 Changes: minimap2 (2.27+dfsg-1) unstable; urgency=medium . * Team upload. * d/rules, d/clean: simply cleanup code. * d/rules: clean using pybuild. 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+------------------------------------------------------------------------------+ | Buildinfo | +------------------------------------------------------------------------------+ Format: 1.0 Source: minimap2 Binary: libminimap2-dev minimap2 minimap2-dbgsym python3-mappy python3-mappy-dbgsym Architecture: arm64 Version: 2.27+dfsg-1 Checksums-Md5: 764dc883ba4bb7eb2aac668ac9f083dc 127282 libminimap2-dev_2.27+dfsg-1_arm64.deb d443d4a95491eeb074d4527e9766fdd0 251786 minimap2-dbgsym_2.27+dfsg-1_arm64.ddeb d027186f4db36f4833ab8ff879c8fc13 381830 minimap2_2.27+dfsg-1_arm64.deb 31dd1337525908f4201db8674a2d2ee5 622292 python3-mappy-dbgsym_2.27+dfsg-1_arm64.ddeb 89d2995c1a578979bd0ff88196cf50f5 167196 python3-mappy_2.27+dfsg-1_arm64.deb Checksums-Sha1: f87320f817731e4004291e37b83bc47f1e182473 127282 libminimap2-dev_2.27+dfsg-1_arm64.deb d0975107d037cf5e8bfa982970e78f2317ceca23 251786 minimap2-dbgsym_2.27+dfsg-1_arm64.ddeb ee26f5f4662f5cb09a545a65d0eecf7a9ef0d0dd 381830 minimap2_2.27+dfsg-1_arm64.deb 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0.20-1build3), libjpeg-turbo8 (= 2.1.5-2ubuntu2), libjpeg8 (= 8c-2ubuntu11), libjs-jquery (= 3.6.1+dfsg+~3.5.14-1), libjs-sphinxdoc (= 7.2.6-6), libjs-underscore (= 1.13.4~dfsg+~1.11.4-3), libk5crypto3 (= 1.20.1-6ubuntu2), libkeyutils1 (= 1.6.3-3build1), libkpathsea6 (= 2023.20230311.66589-9build3), libkrb5-3 (= 1.20.1-6ubuntu2), libkrb5support0 (= 1.20.1-6ubuntu2), liblerc4 (= 4.0.0+ds-4ubuntu2), liblsan0 (= 14-20240412-0ubuntu1), liblua5.4-0 (= 5.4.6-3build2), liblz4-1 (= 1.9.4-2), liblzma5 (= 5.6.1+really5.4.5-1), libmagic-mgc (= 1:5.45-3build1), libmagic1t64 (= 1:5.45-3build1), libmd0 (= 1.1.0-2build1), libmount1 (= 2.39.3-9ubuntu6), libmpc3 (= 1.3.1-1build1), libmpfr6 (= 4.2.1-1build1), libncursesw6 (= 6.4+20240113-1ubuntu2), libnettle8t64 (= 3.9.1-2.2build1), libnpth0t64 (= 1.6-3.1build1), libopenjp2-7 (= 2.5.0-2build3), libp11-kit0 (= 0.25.3-4ubuntu2), libpam-modules (= 1.5.3-7ubuntu1), libpam-modules-bin (= 1.5.3-7ubuntu1), libpam-runtime (= 1.5.3-7ubuntu1), libpam0g (= 1.5.3-7ubuntu1), libpango-1.0-0 (= 1.52.1+ds-1build1), libpangocairo-1.0-0 (= 1.52.1+ds-1build1), libpangoft2-1.0-0 (= 1.52.1+ds-1build1), libpaper-utils (= 1.1.29build1), libpaper1 (= 1.1.29build1), libpcre2-8-0 (= 10.42-4ubuntu2), libpdfbox-java (= 1:1.8.16-5), libperl5.38t64 (= 5.38.2-4), libpipeline1 (= 1.5.7-2), libpixman-1-0 (= 0.42.2-1build1), libpng16-16t64 (= 1.6.43-5build1), libpotrace0 (= 1.16-2build1), libptexenc1 (= 2023.20230311.66589-9build3), libpython3-all-dev (= 3.12.3-0ubuntu1), libpython3-dev (= 3.12.3-0ubuntu1), libpython3-stdlib (= 3.12.3-0ubuntu1), libpython3.12-dev (= 3.12.3-1), libpython3.12-minimal (= 3.12.3-1), libpython3.12-stdlib (= 3.12.3-1), libpython3.12t64 (= 3.12.3-1), libreadline8t64 (= 8.2-4build1), libseccomp2 (= 2.5.5-1ubuntu3), libselinux1 (= 3.5-2ubuntu2), libsemanage-common (= 3.5-1build5), libsemanage2 (= 3.5-1build5), libsepol2 (= 3.5-2build1), libsframe1 (= 2.42-4ubuntu2), libsharpyuv0 (= 1.3.2-0.4build3), libsimde-dev (= 0.8.2-1), libsm6 (= 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1.15-1ubuntu2), libxcb1 (= 1.15-1ubuntu2), libxdmcp6 (= 1:1.1.3-0ubuntu6), libxext6 (= 2:1.3.4-1build2), libxi6 (= 2:1.8.1-1build1), libxml2 (= 2.9.14+dfsg-1.3ubuntu3), libxmu6 (= 2:1.1.3-3build2), libxpm4 (= 1:3.5.17-1build2), libxrender1 (= 1:0.9.10-1.1build1), libxt6t64 (= 1:1.2.1-1.2build1), libxxhash0 (= 0.8.2-2build1), libzstd1 (= 1.5.5+dfsg2-2build1), libzzip-0-13t64 (= 0.13.72+dfsg.1-1.2build1), linux-libc-dev (= 6.8.0-31.31), login (= 1:4.13+dfsg1-4ubuntu3), lto-disabled-list (= 47), m4 (= 1.4.19-4build1), make (= 4.3-4.1build2), man-db (= 2.12.1-1), mawk (= 1.3.4.20240123-1build1), media-types (= 10.1.0), ncurses-base (= 6.4+20240113-1ubuntu2), ncurses-bin (= 6.4+20240113-1ubuntu2), netbase (= 6.4), passwd (= 1:4.13+dfsg1-4ubuntu3), patch (= 2.7.6-7build3), perl (= 5.38.2-4), perl-base (= 5.38.2-4), perl-modules-5.38 (= 5.38.2-4), po-debconf (= 1.0.21+nmu1), poppler-data (= 0.4.12-1), preview-latex-style (= 13.2-1), python3 (= 3.12.3-0ubuntu1), python3-all (= 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3.0043+nmu1), util-linux (= 2.39.3-9ubuntu6), x11-common (= 1:7.7+23ubuntu3), xdg-utils (= 1.1.3-4.1ubuntu3), xfonts-encodings (= 1:1.0.5-0ubuntu2), xfonts-utils (= 1:7.7+6build3), xz-utils (= 5.6.1+really5.4.5-1), zlib1g (= 1:1.3.dfsg-3.1ubuntu2), zlib1g-dev (= 1:1.3.dfsg-3.1ubuntu2) Environment: DEB_BUILD_OPTIONS="parallel=4" DEB_BUILD_PROFILES="noudeb" LANG="C.UTF-8" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1710778337" +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ libminimap2-dev_2.27+dfsg-1_arm64.deb ------------------------------------- new Debian package, version 2.0. size 127282 bytes: control archive=1292 bytes. 1113 bytes, 24 lines control 970 bytes, 17 lines md5sums Package: libminimap2-dev Source: minimap2 Version: 2.27+dfsg-1 Architecture: arm64 Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 376 Depends: zlib1g-dev Section: libdevel Priority: optional Homepage: https://github.com/lh3/minimap2 Description: development headers for libminimap Minimap2 is a versatile sequence alignment program that aligns DNA or mRNA sequences against a large reference database. Typical use cases include: (1) mapping PacBio or Oxford Nanopore genomic reads to the human genome; (2) finding overlaps between long reads with error rate up to ~15%; (3) splice-aware alignment of PacBio Iso-Seq or Nanopore cDNA or Direct RNA reads against a reference genome; (4) aligning Illumina single- or paired-end reads; (5) assembly-to-assembly alignment; (6) full- genome alignment between two closely related species with divergence below ~15%. . This package contains the C library headers for using minimap in custom tools, along with a static library. drwxr-xr-x root/root 0 2024-03-18 16:12 ./ drwxr-xr-x root/root 0 2024-03-18 16:12 ./usr/ drwxr-xr-x root/root 0 2024-03-18 16:12 ./usr/include/ -rw-r--r-- root/root 1811 2024-03-12 17:20 ./usr/include/bseq.h -rw-r--r-- root/root 2630 2024-03-12 17:20 ./usr/include/kalloc.h -rw-r--r-- root/root 4400 2024-03-12 17:20 ./usr/include/kdq.h -rw-r--r-- root/root 3969 2024-03-12 17:20 ./usr/include/ketopt.h -rw-r--r-- root/root 21381 2024-03-12 17:20 ./usr/include/khash.h -rw-r--r-- root/root 16446 2024-03-12 17:20 ./usr/include/krmq.h -rw-r--r-- root/root 8780 2024-03-12 17:20 ./usr/include/kseq.h -rw-r--r-- root/root 5145 2024-03-12 17:20 ./usr/include/ksort.h -rw-r--r-- root/root 8620 2024-03-12 17:20 ./usr/include/ksw2.h -rw-r--r-- root/root 291 2024-03-12 17:20 ./usr/include/kthread.h -rw-r--r-- root/root 3029 2024-03-12 17:20 ./usr/include/kvec.h -rw-r--r-- root/root 14346 2024-03-12 17:20 ./usr/include/minimap.h -rw-r--r-- root/root 6507 2024-03-12 17:20 ./usr/include/mmpriv.h -rw-r--r-- root/root 574 2024-03-12 17:20 ./usr/include/sdust.h drwxr-xr-x root/root 0 2024-03-18 16:12 ./usr/lib/ -rw-r--r-- root/root 265170 2024-03-18 16:12 ./usr/lib/libminimap2.a drwxr-xr-x root/root 0 2024-03-18 16:12 ./usr/share/ drwxr-xr-x root/root 0 2024-03-18 16:12 ./usr/share/doc/ drwxr-xr-x root/root 0 2024-03-18 16:12 ./usr/share/doc/libminimap2-dev/ -rw-r--r-- root/root 1732 2024-03-18 16:12 ./usr/share/doc/libminimap2-dev/changelog.Debian.gz -rw-r--r-- root/root 3132 2024-03-18 16:12 ./usr/share/doc/libminimap2-dev/copyright minimap2_2.27+dfsg-1_arm64.deb ------------------------------ new Debian package, version 2.0. size 381830 bytes: control archive=1441 bytes. 1510 bytes, 28 lines control 981 bytes, 14 lines md5sums Package: minimap2 Version: 2.27+dfsg-1 Architecture: arm64 Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 510 Depends: libc6 (>= 2.34), zlib1g (>= 1:1.1.4) Section: science Priority: optional Homepage: https://github.com/lh3/minimap2 Description: versatile pairwise aligner for genomic and spliced nucleotide sequences Minimap2 is a versatile sequence alignment program that aligns DNA or mRNA sequences against a large reference database. Typical use cases include: (1) mapping PacBio or Oxford Nanopore genomic reads to the human genome; (2) finding overlaps between long reads with error rate up to ~15%; (3) splice-aware alignment of PacBio Iso-Seq or Nanopore cDNA or Direct RNA reads against a reference genome; (4) aligning Illumina single- or paired-end reads; (5) assembly-to-assembly alignment; (6) full- genome alignment between two closely related species with divergence below ~15%. . For ~10kb noisy reads sequences, minimap2 is tens of times faster than mainstream long-read mappers such as BLASR, BWA-MEM, NGMLR and GMAP. It is more accurate on simulated long reads and produces biologically meaningful alignment ready for downstream analyses. For >100bp Illumina short reads, minimap2 is three times as fast as BWA-MEM and Bowtie2, and as accurate on simulated data. Detailed evaluations are available from the minimap2 paper or the preprint. drwxr-xr-x root/root 0 2024-03-18 16:12 ./ drwxr-xr-x root/root 0 2024-03-18 16:12 ./usr/ drwxr-xr-x root/root 0 2024-03-18 16:12 ./usr/bin/ -rwxr-xr-x root/root 199632 2024-03-18 16:12 ./usr/bin/minimap2 drwxr-xr-x root/root 0 2024-03-18 16:12 ./usr/share/ drwxr-xr-x root/root 0 2024-03-18 16:12 ./usr/share/doc-base/ -rw-r--r-- root/root 553 2020-01-10 15:56 ./usr/share/doc-base/minimap2.minimap2 drwxr-xr-x root/root 0 2024-03-18 16:12 ./usr/share/doc/ drwxr-xr-x root/root 0 2024-03-18 16:12 ./usr/share/doc/minimap2/ -rw-r--r-- root/root 1728 2024-03-18 16:12 ./usr/share/doc/minimap2/changelog.Debian.gz -rw-r--r-- root/root 3132 2024-03-18 16:12 ./usr/share/doc/minimap2/copyright -rw-r--r-- root/root 269462 2024-03-18 16:12 ./usr/share/doc/minimap2/minimap2.pdf -rw-r--r-- root/root 347 2020-01-10 15:56 ./usr/share/doc/minimap2/run-unit-test drwxr-xr-x root/root 0 2024-03-18 16:12 ./usr/share/doc/minimap2/test/ -rw-r--r-- root/root 5354 2024-03-12 17:20 ./usr/share/doc/minimap2/test/MT-human.fa.gz -rw-r--r-- root/root 5367 2024-03-12 17:20 ./usr/share/doc/minimap2/test/MT-orang.fa.gz -rw-r--r-- root/root 3540 2024-03-12 17:20 ./usr/share/doc/minimap2/test/q-inv.fa.gz -rw-r--r-- root/root 44 2024-03-12 17:20 ./usr/share/doc/minimap2/test/q2.fa -rw-r--r-- root/root 2525 2024-03-12 17:20 ./usr/share/doc/minimap2/test/t-inv.fa.gz -rw-r--r-- root/root 79 2024-03-12 17:20 ./usr/share/doc/minimap2/test/t2.fa -rw-r--r-- root/root 1095 2020-01-10 15:56 ./usr/share/doc/minimap2/test_script drwxr-xr-x root/root 0 2024-03-18 16:12 ./usr/share/man/ drwxr-xr-x root/root 0 2024-03-18 16:12 ./usr/share/man/man1/ -rw-r--r-- root/root 8195 2024-03-18 16:12 ./usr/share/man/man1/minimap2.1.gz python3-mappy_2.27+dfsg-1_arm64.deb ----------------------------------- new Debian package, version 2.0. size 167196 bytes: control archive=1478 bytes. 1136 bytes, 23 lines control 753 bytes, 9 lines md5sums 273 bytes, 12 lines * postinst #!/bin/sh 386 bytes, 12 lines * prerm #!/bin/sh Package: python3-mappy Source: minimap2 Version: 2.27+dfsg-1 Architecture: arm64 Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 430 Depends: libc6 (>= 2.34), zlib1g (>= 1:1.2.3.3), python3 (<< 3.13), python3 (>= 3.12~), python3:any Section: python Priority: optional Homepage: https://github.com/lh3/minimap2 Description: Python3 interface minimap2 Minimap2 is a versatile sequence alignment program that aligns DNA or mRNA sequences against a large reference database. Typical use cases include: (1) mapping PacBio or Oxford Nanopore genomic reads to the human genome; (2) finding overlaps between long reads with error rate up to ~15%; (3) splice-aware alignment of PacBio Iso-Seq or Nanopore cDNA or Direct RNA reads against a reference genome; (4) aligning Illumina single- or paired-end reads; (5) assembly-to-assembly alignment; (6) full- genome alignment between two closely related species with divergence below ~15%. . 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