https://launchpad.net/~ginggs/+archive/ubuntu/testing/+build/27942511 RUN: /usr/share/launchpad-buildd/bin/builder-prep Kernel version: Linux bos03-amd64-049 5.4.0-173-generic #191-Ubuntu SMP Fri Feb 2 13:55:07 UTC 2024 x86_64 Buildd toolchain package versions: launchpad-buildd_236~650~ubuntu20.04.1 python3-lpbuildd_236~650~ubuntu20.04.1 sbuild_0.79.0-1ubuntu1 git-build-recipe_0.3.6 git_1:2.25.1-1ubuntu3.11 dpkg-dev_1.19.7ubuntu3.2 python3-debian_0.1.36ubuntu1.1. Syncing the system clock with the buildd NTP service... 19 Mar 21:26:04 ntpdate[1863]: adjust time server 10.211.37.1 offset -0.004834 sec RUN: /usr/share/launchpad-buildd/bin/in-target unpack-chroot --backend=chroot --series=noble --arch=amd64 PACKAGEBUILD-27942511 --image-type chroot /home/buildd/filecache-default/1fe94ca8758119221c8de2550665a1bb335bd6a9 Creating target for build PACKAGEBUILD-27942511 RUN: /usr/share/launchpad-buildd/bin/in-target mount-chroot --backend=chroot --series=noble --arch=amd64 PACKAGEBUILD-27942511 Starting target for build PACKAGEBUILD-27942511 RUN: /usr/share/launchpad-buildd/bin/in-target override-sources-list --backend=chroot --series=noble --arch=amd64 PACKAGEBUILD-27942511 'deb http://ppa.launchpadcontent.net/ginggs/testing/ubuntu noble main' 'deb http://ftpmaster.internal/ubuntu noble main restricted universe multiverse' 'deb http://ftpmaster.internal/ubuntu noble-security main restricted universe multiverse' 'deb http://ftpmaster.internal/ubuntu noble-updates main restricted universe multiverse' 'deb http://ftpmaster.internal/ubuntu noble-proposed main restricted universe multiverse' Overriding sources.list in build-PACKAGEBUILD-27942511 RUN: /usr/share/launchpad-buildd/bin/in-target add-trusted-keys --backend=chroot --series=noble --arch=amd64 PACKAGEBUILD-27942511 Adding trusted keys to build-PACKAGEBUILD-27942511 pub rsa1024/B5F195D208CC41D2 2012-04-29 [SC] Key fingerprint = F749 99B3 5A9F 07F1 E13C 0C78 B5F1 95D2 08CC 41D2 uid Launchpad PPA for Graham Inggs RUN: /usr/share/launchpad-buildd/bin/in-target update-debian-chroot --backend=chroot --series=noble --arch=amd64 PACKAGEBUILD-27942511 Updating target for build PACKAGEBUILD-27942511 Get:1 http://ftpmaster.internal/ubuntu noble InRelease [255 kB] Get:2 http://ppa.launchpadcontent.net/ginggs/testing/ubuntu noble InRelease [17.3 kB] Get:3 http://ppa.launchpadcontent.net/ginggs/testing/ubuntu noble/main amd64 Packages [8980 B] Get:4 http://ppa.launchpadcontent.net/ginggs/testing/ubuntu noble/main Translation-en [5524 B] Get:5 http://ftpmaster.internal/ubuntu noble-security InRelease [90.7 kB] Get:6 http://ftpmaster.internal/ubuntu noble-updates InRelease [90.7 kB] Get:7 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] Get:8 http://ftpmaster.internal/ubuntu noble/main amd64 Packages [1435 kB] Get:9 http://ftpmaster.internal/ubuntu noble/main Translation-en [518 kB] Get:10 http://ftpmaster.internal/ubuntu noble/restricted amd64 Packages [94.2 kB] Get:11 http://ftpmaster.internal/ubuntu noble/restricted Translation-en [15.5 kB] Get:12 http://ftpmaster.internal/ubuntu noble/universe amd64 Packages [15.2 MB] Get:13 http://ftpmaster.internal/ubuntu noble/universe Translation-en [6039 kB] Get:14 http://ftpmaster.internal/ubuntu noble/multiverse amd64 Packages [241 kB] Get:15 http://ftpmaster.internal/ubuntu noble/multiverse Translation-en [115 kB] Get:16 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 Packages [684 kB] Get:17 http://ftpmaster.internal/ubuntu noble-proposed/main Translation-en [234 kB] Get:18 http://ftpmaster.internal/ubuntu noble-proposed/restricted amd64 Packages [36.6 kB] Get:19 http://ftpmaster.internal/ubuntu noble-proposed/restricted Translation-en [8120 B] Get:20 http://ftpmaster.internal/ubuntu noble-proposed/universe amd64 Packages [4221 kB] Get:21 http://ftpmaster.internal/ubuntu noble-proposed/universe Translation-en [1539 kB] Get:22 http://ftpmaster.internal/ubuntu noble-proposed/multiverse amd64 Packages [67.2 kB] Get:23 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Translation-en [30.8 kB] Fetched 31.1 MB in 4s (8523 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* libnettle8* libnpth0* libreadline8* libssl3* libtirpc3* usrmerge* The following NEW packages will be installed: cpp-13-x86-64-linux-gnu cpp-x86-64-linux-gnu g++-13-x86-64-linux-gnu g++-x86-64-linux-gnu gcc-13-x86-64-linux-gnu gcc-14-base gcc-x86-64-linux-gnu libapt-pkg6.0t64 libdb5.3t64 libext2fs2t64 libgdbm-compat4t64 libgdbm6t64 libnettle8t64 libnpth0t64 libperl5.38t64 libreadline8t64 libssl3t64 libtirpc3t64 libunistring5 perl-modules-5.38 The following packages have been kept back: apt apt-utils optipng The following packages will be upgraded: base-files base-passwd bash bash-completion binutils binutils-common binutils-x86-64-linux-gnu bsdextrautils bsdutils bzip2 ca-certificates coreutils cpp cpp-13 dash debconf debconf-i18n debianutils diffutils dpkg dpkg-dev e2fsprogs fakeroot g++ g++-13 gcc gcc-13 gcc-13-base gpg gpg-agent gpgconf gpgv grep gzip hostname init init-system-helpers krb5-locales libacl1 libapparmor1 libargon2-1 libasan8 libatomic1 libattr1 libaudit-common libaudit1 libbinutils libblkid1 libbz2-1.0 libc-bin libc-dev-bin libc6 libc6-dev libcap-ng0 libcap2 libcc1-0 libcom-err2 libcrypt-dev libcrypt1 libcryptsetup12 libctf-nobfd0 libctf0 libdebconfclient0 libdevmapper1.02.1 libdpkg-perl libfakeroot libfdisk1 libffi8 libgcc-13-dev libgcc-s1 libgcrypt20 libgnutls30 libgomp1 libgpg-error-l10n libgpg-error0 libgprofng0 libgssapi-krb5-2 libhwasan0 libidn2-0 libip4tc2 libitm1 libk5crypto3 libkeyutils1 libkmod2 libkrb5-3 libkrb5support0 liblocale-gettext-perl liblsan0 liblzma5 libmd0 libmount1 libncursesw6 libnsl-dev libnsl2 libnss-nisplus libp11-kit0 libpam-modules libpam-modules-bin libpam-runtime libpam0g libpcre2-8-0 libpng16-16 libproc2-0 libquadmath0 libseccomp2 libselinux1 libsemanage-common libsemanage2 libsepol2 libsframe1 libsmartcols1 libsqlite3-0 libss2 libstdc++-13-dev libstdc++6 libsystemd-shared libsystemd0 libtext-charwidth-perl libtext-iconv-perl libtinfo6 libtirpc-common libtirpc-dev libtsan2 libubsan1 libudev1 libuuid1 libxxhash0 libzstd1 linux-libc-dev login logsave lto-disabled-list mawk mount ncurses-base ncurses-bin openssl passwd perl perl-base pinentry-curses procps psmisc readline-common sed sensible-utils systemd systemd-dev systemd-sysv sysvinit-utils tar tzdata ubuntu-keyring util-linux uuid-runtime xz-utils zlib1g 157 upgraded, 20 newly installed, 11 to remove and 3 not upgraded. Need to get 117 MB of archives. After this operation, 78.0 MB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libnsl-dev amd64 1.3.0-3build2 [70.5 kB] Get:2 http://ftpmaster.internal/ubuntu noble/main amd64 libcrypt-dev amd64 1:4.4.36-4 [128 kB] Get:3 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libc6-dev amd64 2.39-0ubuntu6 [2126 kB] Get:4 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libc-dev-bin amd64 2.39-0ubuntu6 [20.4 kB] Get:5 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libtirpc-common all 1.3.4+ds-1.1 [8018 B] Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libtirpc-dev amd64 1.3.4+ds-1.1 [193 kB] Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libnss-nisplus amd64 1.3-5 [22.3 kB] Get:8 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libtirpc3t64 amd64 1.3.4+ds-1.1 [82.5 kB] Get:9 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libgssapi-krb5-2 amd64 1.20.1-5.1build3 [142 kB] Get:10 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libkrb5-3 amd64 1.20.1-5.1build3 [347 kB] Get:11 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libk5crypto3 amd64 1.20.1-5.1build3 [81.8 kB] Get:12 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libkrb5support0 amd64 1.20.1-5.1build3 [33.5 kB] Get:13 http://ftpmaster.internal/ubuntu noble/main amd64 libacl1 amd64 2.3.2-1 [16.7 kB] Get:14 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libapparmor1 amd64 4.0.0-beta3-0ubuntu2 [49.4 kB] Get:15 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libaudit-common all 1:3.1.2-2.1 [5674 B] Get:16 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libcap-ng0 amd64 0.8.4-2build1 [15.1 kB] Get:17 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libaudit1 amd64 1:3.1.2-2.1 [46.8 kB] Get:18 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libblkid1 amd64 2.39.3-9ubuntu2 [122 kB] Get:19 http://ftpmaster.internal/ubuntu noble/main amd64 libcap2 amd64 1:2.66-5ubuntu1 [29.9 kB] Get:20 http://ftpmaster.internal/ubuntu noble/main amd64 libcrypt1 amd64 1:4.4.36-4 [95.3 kB] Get:21 http://ftpmaster.internal/ubuntu noble/main amd64 libgpg-error-l10n all 1.47-3build1 [8024 B] Get:22 http://ftpmaster.internal/ubuntu noble/main amd64 libgpg-error0 amd64 1.47-3build1 [70.0 kB] Get:23 http://ftpmaster.internal/ubuntu noble/main amd64 libgcrypt20 amd64 1.10.3-2 [532 kB] Get:24 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 liblzma5 amd64 5.6.0-0.2 [157 kB] Get:25 http://ftpmaster.internal/ubuntu noble/main amd64 libzstd1 amd64 1.5.5+dfsg2-2 [297 kB] Get:26 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libkmod2 amd64 31+20240202-2ubuntu4 [51.5 kB] Get:27 http://ftpmaster.internal/ubuntu noble/main amd64 libpcre2-8-0 amd64 10.42-4ubuntu1 [228 kB] Get:28 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libselinux1 amd64 3.5-2build3 [79.3 kB] Get:29 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libmount1 amd64 2.39.3-9ubuntu2 [134 kB] Get:30 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 perl-modules-5.38 all 5.38.2-3.2 [3110 kB] Get:31 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libdb5.3t64 amd64 5.3.28+dfsg2-5build1 [734 kB] Get:32 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libgdbm6t64 amd64 1.23-5.1 [34.4 kB] Get:33 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libgdbm-compat4t64 amd64 1.23-5.1 [6700 B] Get:34 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libperl5.38t64 amd64 5.38.2-3.2 [4871 kB] Get:35 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 perl amd64 5.38.2-3.2 [231 kB] Get:36 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 perl-base amd64 5.38.2-3.2 [1823 kB] Get:37 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 liblocale-gettext-perl amd64 1.07-6ubuntu3 [15.7 kB] Get:38 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libtext-iconv-perl amd64 1.7-8build2 [13.5 kB] Get:39 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libtext-charwidth-perl amd64 0.04-11build2 [9322 B] Get:40 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libc6 amd64 2.39-0ubuntu6 [3262 kB] Get:41 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libc-bin amd64 2.39-0ubuntu6 [682 kB] Get:42 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 openssl amd64 3.0.13-0ubuntu2 [1002 kB] Get:43 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libsystemd-shared amd64 255.4-1ubuntu5 [2067 kB] Get:44 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libcryptsetup12 amd64 2:2.7.0-1ubuntu2 [266 kB] Get:45 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libssl3t64 amd64 3.0.13-0ubuntu2 [1936 kB] Get:46 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 systemd-dev all 255.4-1ubuntu5 [103 kB] Get:47 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 systemd-sysv amd64 255.4-1ubuntu5 [11.9 kB] Get:48 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 systemd amd64 255.4-1ubuntu5 [3470 kB] Get:49 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libsystemd0 amd64 255.4-1ubuntu5 [428 kB] Get:50 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libpam-modules-bin amd64 1.5.3-5ubuntu3 [51.9 kB] Get:51 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libpam-modules amd64 1.5.3-5ubuntu3 [279 kB] Get:52 http://ftpmaster.internal/ubuntu noble/main amd64 bzip2 amd64 1.0.8-5ubuntu1 [34.6 kB] Get:53 http://ftpmaster.internal/ubuntu noble/main amd64 libbz2-1.0 amd64 1.0.8-5ubuntu1 [34.4 kB] Get:54 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 zlib1g amd64 1:1.3.dfsg-3.1ubuntu1 [62.7 kB] Get:55 http://ftpmaster.internal/ubuntu noble/main amd64 debconf-i18n all 1.5.86 [205 kB] Get:56 http://ftpmaster.internal/ubuntu noble/main amd64 debconf all 1.5.86 [124 kB] Get:57 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libpam0g amd64 1.5.3-5ubuntu3 [67.5 kB] Get:58 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libseccomp2 amd64 2.5.5-1ubuntu2 [50.3 kB] Get:59 http://ftpmaster.internal/ubuntu noble/main amd64 libargon2-1 amd64 0~20190702+dfsg-4 [21.4 kB] Get:60 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libudev1 amd64 255.4-1ubuntu5 [174 kB] Get:61 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libdevmapper1.02.1 amd64 2:1.02.185-3ubuntu2 [139 kB] Get:62 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libuuid1 amd64 2.39.3-9ubuntu2 [35.0 kB] Get:63 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libfdisk1 amd64 2.39.3-9ubuntu2 [146 kB] Get:64 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 mount amd64 2.39.3-9ubuntu2 [118 kB] Get:65 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libcom-err2 amd64 1.47.0-2.4~exp1ubuntu2 [22.7 kB] Get:66 http://ftpmaster.internal/ubuntu noble/main amd64 libkeyutils1 amd64 1.6.3-3 [9386 B] Get:67 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libnsl2 amd64 1.3.0-3build2 [41.3 kB] Get:68 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 linux-libc-dev amd64 6.8.0-20.20 [1597 kB] Get:69 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 gcc-14-base amd64 14-20240315-1ubuntu1 [47.0 kB] Get:70 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libgcc-s1 amd64 14-20240315-1ubuntu1 [78.1 kB] Get:71 http://ftpmaster.internal/ubuntu noble/main amd64 base-files amd64 13ubuntu7 [74.2 kB] Get:72 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 debianutils amd64 5.17 [89.8 kB] Get:73 http://ftpmaster.internal/ubuntu noble/main amd64 bash amd64 5.2.21-2ubuntu2 [794 kB] Get:74 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 bsdutils amd64 1:2.39.3-9ubuntu2 [94.9 kB] Get:75 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 coreutils amd64 9.4-3ubuntu3 [1411 kB] Get:76 http://ftpmaster.internal/ubuntu noble/main amd64 libp11-kit0 amd64 0.25.3-4ubuntu1 [299 kB] Get:77 http://ftpmaster.internal/ubuntu noble/main amd64 libunistring5 amd64 1.1-2 [537 kB] Get:78 http://ftpmaster.internal/ubuntu noble/main amd64 libgnutls30 amd64 3.8.3-1ubuntu1 [996 kB] Get:79 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libnettle8t64 amd64 3.9.1-2.2 [181 kB] Get:80 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libstdc++6 amd64 14-20240315-1ubuntu1 [795 kB] Get:81 http://ftpmaster.internal/ubuntu noble/main amd64 libxxhash0 amd64 0.8.2-2 [25.5 kB] Get:82 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libapt-pkg6.0t64 amd64 2.7.13ubuntu1 [985 kB] Get:83 http://ftpmaster.internal/ubuntu noble/main amd64 tar amd64 1.35+dfsg-3 [253 kB] Get:84 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 dpkg amd64 1.22.6ubuntu4 [1283 kB] Get:85 http://ftpmaster.internal/ubuntu noble/main amd64 dash amd64 0.5.12-6ubuntu4 [89.8 kB] Get:86 http://ftpmaster.internal/ubuntu noble/main amd64 diffutils amd64 1:3.10-1 [176 kB] Get:87 http://ftpmaster.internal/ubuntu noble/main amd64 grep amd64 3.11-4 [176 kB] Get:88 http://ftpmaster.internal/ubuntu noble/main amd64 gzip amd64 1.12-1ubuntu2 [98.8 kB] Get:89 http://ftpmaster.internal/ubuntu noble/main amd64 hostname amd64 3.23+nmu2ubuntu1 [11.0 kB] Get:90 http://ftpmaster.internal/ubuntu noble/main amd64 login amd64 1:4.13+dfsg1-4ubuntu1 [201 kB] Get:91 http://ftpmaster.internal/ubuntu noble/main amd64 ncurses-bin amd64 6.4+20240113-1ubuntu1 [188 kB] Get:92 http://ftpmaster.internal/ubuntu noble/main amd64 sed amd64 4.9-2 [204 kB] Get:93 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 util-linux amd64 2.39.3-9ubuntu2 [1127 kB] Get:94 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libdebconfclient0 amd64 0.271ubuntu2 [11.3 kB] Get:95 http://ftpmaster.internal/ubuntu noble/main amd64 base-passwd amd64 3.6.3 [51.2 kB] Get:96 http://ftpmaster.internal/ubuntu noble/main amd64 init-system-helpers all 1.66ubuntu1 [39.4 kB] Get:97 http://ftpmaster.internal/ubuntu noble/main amd64 ncurses-base all 6.4+20240113-1ubuntu1 [25.4 kB] Get:98 http://ftpmaster.internal/ubuntu noble/main amd64 sysvinit-utils amd64 3.08-6ubuntu2 [34.1 kB] Get:99 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 logsave amd64 1.47.0-2.4~exp1ubuntu2 [22.4 kB] Get:100 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libext2fs2t64 amd64 1.47.0-2.4~exp1ubuntu2 [221 kB] Get:101 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 e2fsprogs amd64 1.47.0-2.4~exp1ubuntu2 [601 kB] Get:102 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 gpg amd64 2.4.4-2ubuntu15 [565 kB] Get:103 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libreadline8t64 amd64 8.2-3.1 [153 kB] Get:104 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 gpgconf amd64 2.4.4-2ubuntu15 [103 kB] Get:105 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 gpg-agent amd64 2.4.4-2ubuntu15 [227 kB] Get:106 http://ftpmaster.internal/ubuntu noble/main amd64 libnpth0t64 amd64 1.6-3.1 [8316 B] Get:107 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 readline-common all 8.2-3.1 [56.4 kB] Get:108 http://ftpmaster.internal/ubuntu noble/main amd64 libncursesw6 amd64 6.4+20240113-1ubuntu1 [148 kB] Get:109 http://ftpmaster.internal/ubuntu noble/main amd64 libtinfo6 amd64 6.4+20240113-1ubuntu1 [108 kB] Get:110 http://ftpmaster.internal/ubuntu noble/main amd64 init amd64 1.66ubuntu1 [6186 B] Get:111 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libsmartcols1 amd64 2.39.3-9ubuntu2 [64.4 kB] Get:112 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 uuid-runtime amd64 2.39.3-9ubuntu2 [33.0 kB] Get:113 http://ftpmaster.internal/ubuntu noble/main amd64 libattr1 amd64 1:2.5.2-1 [11.4 kB] Get:114 http://ftpmaster.internal/ubuntu noble/main amd64 libmd0 amd64 1.1.0-2 [27.1 kB] Get:115 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libpam-runtime all 1.5.3-5ubuntu3 [40.8 kB] Get:116 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libsemanage-common all 3.5-1build4 [10.1 kB] Get:117 http://ftpmaster.internal/ubuntu noble/main amd64 libsepol2 amd64 3.5-2 [300 kB] Get:118 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libsemanage2 amd64 3.5-1build4 [93.1 kB] Get:119 http://ftpmaster.internal/ubuntu noble/main amd64 passwd amd64 1:4.13+dfsg1-4ubuntu1 [844 kB] Get:120 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 gpgv amd64 2.4.4-2ubuntu15 [157 kB] Get:121 http://ftpmaster.internal/ubuntu noble/main amd64 libffi8 amd64 3.4.6-1 [24.7 kB] Get:122 http://ftpmaster.internal/ubuntu noble/main amd64 libidn2-0 amd64 2.3.7-2 [66.0 kB] Get:123 http://ftpmaster.internal/ubuntu noble/main amd64 ubuntu-keyring all 2023.11.28.1 [11.1 kB] Get:124 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 g++-13 amd64 13.2.0-19ubuntu1 [14.5 kB] Get:125 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 gcc-13 amd64 13.2.0-19ubuntu1 [477 kB] Get:126 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 cpp-13 amd64 13.2.0-19ubuntu1 [1032 B] Get:127 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 cpp-13-x86-64-linux-gnu amd64 13.2.0-19ubuntu1 [11.2 MB] Get:128 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libcc1-0 amd64 14-20240315-1ubuntu1 [47.7 kB] Get:129 http://ftpmaster.internal/ubuntu noble/main amd64 libgprofng0 amd64 2.42-3ubuntu1 [851 kB] Get:130 http://ftpmaster.internal/ubuntu noble/main amd64 libctf0 amd64 2.42-3ubuntu1 [94.5 kB] Get:131 http://ftpmaster.internal/ubuntu noble/main amd64 libctf-nobfd0 amd64 2.42-3ubuntu1 [97.1 kB] Get:132 http://ftpmaster.internal/ubuntu noble/main amd64 libsframe1 amd64 2.42-3ubuntu1 [14.9 kB] Get:133 http://ftpmaster.internal/ubuntu noble/main amd64 binutils-x86-64-linux-gnu amd64 2.42-3ubuntu1 [2469 kB] Get:134 http://ftpmaster.internal/ubuntu noble/main amd64 libbinutils amd64 2.42-3ubuntu1 [573 kB] Get:135 http://ftpmaster.internal/ubuntu noble/main amd64 binutils amd64 2.42-3ubuntu1 [18.0 kB] Get:136 http://ftpmaster.internal/ubuntu noble/main amd64 binutils-common amd64 2.42-3ubuntu1 [239 kB] Get:137 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libstdc++-13-dev amd64 13.2.0-19ubuntu1 [2342 kB] Get:138 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libgomp1 amd64 14-20240315-1ubuntu1 [147 kB] Get:139 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libitm1 amd64 14-20240315-1ubuntu1 [28.9 kB] Get:140 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libatomic1 amd64 14-20240315-1ubuntu1 [10.4 kB] Get:141 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libasan8 amd64 14-20240315-1ubuntu1 [3026 kB] Get:142 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 liblsan0 amd64 14-20240315-1ubuntu1 [1310 kB] Get:143 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libgcc-13-dev amd64 13.2.0-19ubuntu1 [2687 kB] Get:144 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libtsan2 amd64 14-20240315-1ubuntu1 [2732 kB] Get:145 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libubsan1 amd64 14-20240315-1ubuntu1 [1172 kB] Get:146 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libhwasan0 amd64 14-20240315-1ubuntu1 [1629 kB] Get:147 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libquadmath0 amd64 14-20240315-1ubuntu1 [155 kB] Get:148 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 gcc-13-x86-64-linux-gnu amd64 13.2.0-19ubuntu1 [21.8 MB] Get:149 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 g++-13-x86-64-linux-gnu amd64 13.2.0-19ubuntu1 [12.5 MB] Get:150 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 gcc-13-base amd64 13.2.0-19ubuntu1 [47.7 kB] Get:151 http://ftpmaster.internal/ubuntu noble/main amd64 libproc2-0 amd64 2:4.0.4-4ubuntu1 [59.2 kB] Get:152 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libss2 amd64 1.47.0-2.4~exp1ubuntu2 [17.0 kB] Get:153 http://ftpmaster.internal/ubuntu noble/main amd64 mawk amd64 1.3.4.20240123-1 [127 kB] Get:154 http://ftpmaster.internal/ubuntu noble/main amd64 procps amd64 2:4.0.4-4ubuntu1 [708 kB] Get:155 http://ftpmaster.internal/ubuntu noble/main amd64 sensible-utils all 0.0.22 [22.5 kB] Get:156 http://ftpmaster.internal/ubuntu noble/main amd64 ca-certificates all 20240203 [159 kB] Get:157 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 krb5-locales all 1.20.1-5.1build3 [13.8 kB] Get:158 http://ftpmaster.internal/ubuntu noble/main amd64 libip4tc2 amd64 1.8.10-3ubuntu1 [23.3 kB] Get:159 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libsqlite3-0 amd64 3.45.1-1ubuntu1 [701 kB] Get:160 http://ftpmaster.internal/ubuntu noble/main amd64 tzdata all 2024a-1ubuntu1 [273 kB] Get:161 http://ftpmaster.internal/ubuntu noble/main amd64 bash-completion all 1:2.11-8 [180 kB] Get:162 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 bsdextrautils amd64 2.39.3-9ubuntu2 [73.6 kB] Get:163 http://ftpmaster.internal/ubuntu noble/main amd64 libpng16-16 amd64 1.6.43-1 [186 kB] Get:164 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 psmisc amd64 23.7-1 [179 kB] Get:165 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 xz-utils amd64 5.6.0-0.2 [272 kB] Get:166 http://ftpmaster.internal/ubuntu noble/main amd64 g++ amd64 4:13.2.0-7ubuntu1 [1100 B] Get:167 http://ftpmaster.internal/ubuntu noble/main amd64 gcc amd64 4:13.2.0-7ubuntu1 [5018 B] Get:168 http://ftpmaster.internal/ubuntu noble/main amd64 cpp amd64 4:13.2.0-7ubuntu1 [22.4 kB] Get:169 http://ftpmaster.internal/ubuntu noble/main amd64 cpp-x86-64-linux-gnu amd64 4:13.2.0-7ubuntu1 [5326 B] Get:170 http://ftpmaster.internal/ubuntu noble/main amd64 gcc-x86-64-linux-gnu amd64 4:13.2.0-7ubuntu1 [1212 B] Get:171 http://ftpmaster.internal/ubuntu noble/main amd64 g++-x86-64-linux-gnu amd64 4:13.2.0-7ubuntu1 [964 B] Get:172 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 dpkg-dev all 1.22.6ubuntu4 [1074 kB] Get:173 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libdpkg-perl all 1.22.6ubuntu4 [268 kB] Get:174 http://ftpmaster.internal/ubuntu noble/main amd64 lto-disabled-list all 47 [12.4 kB] Get:175 http://ftpmaster.internal/ubuntu noble/main amd64 libfakeroot amd64 1.33-1 [32.4 kB] Get:176 http://ftpmaster.internal/ubuntu noble/main amd64 fakeroot amd64 1.33-1 [67.2 kB] Get:177 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 pinentry-curses amd64 1.2.1-3ubuntu4 [35.2 kB] Preconfiguring packages ... 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Unpacking systemd (255.4-1ubuntu5) over (253.5-1ubuntu6) ... dpkg: warning: unable to delete old directory '/lib/systemd/system-preset': Directory not empty dpkg: warning: unable to delete old directory '/lib/systemd/system-generators': Directory not empty dpkg: warning: unable to delete old directory '/lib/systemd/system/user@0.service.d': Directory not empty dpkg: warning: unable to delete old directory '/lib/systemd/system/user@.service.d': Directory not empty dpkg: warning: unable to delete old directory '/lib/systemd/system/user-.slice.d': Directory not empty dpkg: warning: unable to delete old directory '/lib/systemd/system/timers.target.wants': Directory not empty dpkg: warning: unable to delete old directory '/lib/systemd/system/systemd-localed.service.d': Directory not empty dpkg: warning: unable to delete old directory '/lib/systemd/system/sysinit.target.wants': Directory not empty dpkg: warning: unable to delete old directory '/lib/systemd/system/sockets.target.wants': Directory not empty dpkg: warning: unable to delete old directory '/lib/systemd/system/rescue.target.wants': Directory not empty dpkg: warning: unable to delete old directory '/lib/systemd/system/rc-local.service.d': Directory not empty dpkg: warning: unable to delete old directory '/lib/systemd/system/multi-user.target.wants': Directory not empty dpkg: warning: unable to delete old directory '/lib/systemd/system/initrd.target.wants': Directory not empty dpkg: warning: unable to delete old directory '/lib/systemd/system/initrd-root-fs.target.wants': Directory not empty dpkg: warning: unable to delete old directory '/lib/systemd/system/initrd-root-device.target.wants': Directory not empty dpkg: warning: unable to delete old directory '/lib/systemd/system/graphical.target.wants': Directory not empty dpkg: warning: unable to delete old directory '/lib/systemd/system/getty.target.wants': Directory not empty dpkg: warning: unable to delete old directory '/lib/systemd/network': Directory not empty dpkg: warning: unable to delete old directory '/lib/systemd/journald.conf.d': Directory not empty dpkg: warning: unable to delete old directory '/lib/modprobe.d': Directory not empty Preparing to unpack .../libsystemd0_255.4-1ubuntu5_amd64.deb ... 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Setting up gpgconf (2.4.4-2ubuntu15) ... Setting up libc6-dev:amd64 (2.39-0ubuntu6) ... Setting up gpg (2.4.4-2ubuntu15) ... Setting up libstdc++-13-dev:amd64 (13.2.0-19ubuntu1) ... Setting up binutils-x86-64-linux-gnu (2.42-3ubuntu1) ... Setting up cpp-x86-64-linux-gnu (4:13.2.0-7ubuntu1) ... Setting up gpg-agent (2.4.4-2ubuntu15) ... Setting up cpp-13 (13.2.0-19ubuntu1) ... Setting up libtirpc3t64:amd64 (1.3.4+ds-1.1) ... Setting up gcc-13-x86-64-linux-gnu (13.2.0-19ubuntu1) ... Setting up binutils (2.42-3ubuntu1) ... Setting up dpkg-dev (1.22.6ubuntu4) ... Setting up libtirpc-dev:amd64 (1.3.4+ds-1.1) ... Setting up gcc-13 (13.2.0-19ubuntu1) ... Setting up cpp (4:13.2.0-7ubuntu1) ... Setting up libnsl2:amd64 (1.3.0-3build2) ... Setting up g++-13-x86-64-linux-gnu (13.2.0-19ubuntu1) ... Setting up gcc-x86-64-linux-gnu (4:13.2.0-7ubuntu1) ... Setting up libnss-nisplus:amd64 (1.3-5) ... Setting up gcc (4:13.2.0-7ubuntu1) ... Setting up libnsl-dev:amd64 (1.3.0-3build2) ... Setting up g++-x86-64-linux-gnu (4:13.2.0-7ubuntu1) ... Setting up g++-13 (13.2.0-19ubuntu1) ... Setting up g++ (4:13.2.0-7ubuntu1) ... Processing triggers for libc-bin (2.39-0ubuntu6) ... Processing triggers for debianutils (5.17) ... (Reading database ... 15762 files and directories currently installed.) Purging configuration files for libssl3:amd64 (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-27942511 amd64 noble -c chroot:build-PACKAGEBUILD-27942511 --arch=amd64 --dist=noble --nolog -A 'jellyfish_2.3.1-3~ppa1.dsc' Initiating build PACKAGEBUILD-27942511 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 5.4.0-173-generic #191-Ubuntu SMP Fri Feb 2 13:55:07 UTC 2024 x86_64 sbuild (Debian sbuild) 0.79.0 (05 February 2020) on bos03-amd64-049.buildd +==============================================================================+ | jellyfish 2.3.1-3~ppa1 (amd64) Tue, 19 Mar 2024 21:26:37 +0000 | +==============================================================================+ Package: jellyfish Version: 2.3.1-3~ppa1 Source Version: 2.3.1-3~ppa1 Distribution: noble Machine Architecture: amd64 Host Architecture: amd64 Build Architecture: amd64 Build Type: binary I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-27942511/chroot-autobuild' with '<>' I: NOTICE: Log filtering will replace 'build/jellyfish-O6eEHg/resolver-BVX7Hx' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- jellyfish_2.3.1-3~ppa1.dsc exists in .; copying to chroot I: NOTICE: Log filtering will replace 'build/jellyfish-O6eEHg/jellyfish-2.3.1' with '<>' I: NOTICE: Log filtering will replace 'build/jellyfish-O6eEHg' with '<>' +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper-compat (= 13), architecture-is-little-endian, architecture-is-64-bit, d-shlibs, autoconf-archive, yaggo, pkgconf, bc, time, procps, swig, python3-all-dev, dh-sequence-python3, python3-setuptools, perl, chrpath, libhts-dev, dos2unix, samtools, build-essential, fakeroot Filtered Build-Depends: debhelper-compat (= 13), architecture-is-little-endian, architecture-is-64-bit, d-shlibs, autoconf-archive, yaggo, pkgconf, bc, time, procps, swig, python3-all-dev, dh-sequence-python3, python3-setuptools, perl, chrpath, libhts-dev, dos2unix, samtools, 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 [486 B] Get:5 copy:/<>/apt_archive ./ Packages [572 B] Fetched 2015 B in 0s (0 B/s) Reading package lists... Reading package lists... Install main build dependencies (apt-based resolver) ---------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following packages were automatically installed and are no longer required: apt-utils bash-completion debconf-i18n krb5-locales libgpg-error-l10n libgpm2 libip4tc2 liblocale-gettext-perl libnsl-dev libnsl2 libnss-nis libnss-nisplus libperl5.36 libtext-charwidth-perl libtext-iconv-perl libtext-wrapi18n-perl libtirpc-common libtirpc-dev libtirpc3t64 libunistring2 perl-modules-5.36 psmisc uuid-runtime Use 'apt autoremove' to remove them. The following additional packages will be installed: architecture-properties autoconf autoconf-archive automake autopoint autotools-dev bc chrpath d-shlibs debhelper debugedit dh-autoreconf dh-python dh-strip-nondeterminism dos2unix dwz file gettext gettext-base groff-base intltool-debian libarchive-zip-perl libbrotli1 libbsd0 libcurl3t64-gnutls libcurl4-gnutls-dev libdebhelper-perl libdeflate-dev libdeflate0 libdw1t64 libedit2 libelf1t64 libexpat1 libexpat1-dev libfile-stripnondeterminism-perl libgnutls30t64 libhogweed6t64 libhts-dev libhts3t64 libhtscodecs2 libicu74 libjs-jquery libjs-sphinxdoc libjs-underscore libldap2 liblzma-dev libmagic-mgc libmagic1t64 libncurses6 libnghttp2-14 libpipeline1 libpkgconf3 libpsl5t64 libpython3-all-dev libpython3-dev libpython3-stdlib libpython3.12-dev libpython3.12-minimal libpython3.12-stdlib libpython3.12t64 librtmp1 libruby libruby3.2 libsasl2-2 libsasl2-modules-db libssh-4 libsub-override-perl libtool libuchardet0 libxml2 libyaml-0-2 m4 man-db media-types netbase pkgconf pkgconf-bin po-debconf python3 python3-all python3-all-dev python3-dev python3-minimal python3-pkg-resources python3-setuptools python3.12 python3.12-dev python3.12-minimal rake ruby ruby-net-telnet ruby-rubygems ruby-sdbm ruby-webrick ruby-xmlrpc ruby3.2 rubygems-integration samtools swig time yaggo zlib1g-dev Suggested packages: gnu-standards autoconf-doc dh-make flit python3-build python3-installer python3-wheel gettext-doc libasprintf-dev libgettextpo-dev groff libcurl4-doc libgnutls28-dev libidn-dev libkrb5-dev libldap2-dev librtmp-dev libssh2-1-dev gnutls-bin liblzma-doc libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc apparmor less www-browser libmail-box-perl python3-doc python3-tk python3-venv python-setuptools-doc python3.12-venv python3.12-doc binfmt-support ri ruby-dev bundler cwltool swig-doc swig-examples Recommended packages: curl | wget | lynx libarchive-cpio-perl javascript-common libldap-common publicsuffix libsasl2-modules libltdl-dev libmail-sendmail-perl zip fonts-lato The following packages will be REMOVED: libgnutls30* libhogweed6* The following NEW packages will be installed: architecture-properties autoconf autoconf-archive automake autopoint autotools-dev bc chrpath d-shlibs debhelper debugedit dh-autoreconf dh-python dh-strip-nondeterminism dos2unix dwz file gettext gettext-base groff-base intltool-debian libarchive-zip-perl libbrotli1 libbsd0 libcurl3t64-gnutls libcurl4-gnutls-dev libdebhelper-perl libdeflate-dev libdeflate0 libdw1t64 libedit2 libelf1t64 libexpat1 libexpat1-dev libfile-stripnondeterminism-perl libgnutls30t64 libhogweed6t64 libhts-dev libhts3t64 libhtscodecs2 libicu74 libjs-jquery libjs-sphinxdoc libjs-underscore libldap2 liblzma-dev libmagic-mgc libmagic1t64 libncurses6 libnghttp2-14 libpipeline1 libpkgconf3 libpsl5t64 libpython3-all-dev libpython3-dev libpython3-stdlib libpython3.12-dev libpython3.12-minimal libpython3.12-stdlib libpython3.12t64 librtmp1 libruby libruby3.2 libsasl2-2 libsasl2-modules-db libssh-4 libsub-override-perl libtool libuchardet0 libxml2 libyaml-0-2 m4 man-db media-types netbase pkgconf pkgconf-bin po-debconf python3 python3-all python3-all-dev python3-dev python3-minimal python3-pkg-resources python3-setuptools python3.12 python3.12-dev python3.12-minimal rake ruby ruby-net-telnet ruby-rubygems ruby-sdbm ruby-webrick ruby-xmlrpc ruby3.2 rubygems-integration samtools sbuild-build-depends-main-dummy swig time yaggo zlib1g-dev 0 upgraded, 103 newly installed, 2 to remove and 3 not upgraded. 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3.12.2-4build3 [498 kB] Get:98 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 python3-dev amd64 3.12.2-0ubuntu1 [26.7 kB] Get:99 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 python3-all-dev amd64 3.12.2-0ubuntu1 [910 B] Get:100 http://ftpmaster.internal/ubuntu noble/universe amd64 samtools amd64 1.19.2-1 [593 kB] Get:101 http://ftpmaster.internal/ubuntu noble/universe amd64 swig amd64 4.2.0-2ubuntu1 [1187 kB] Get:102 http://ftpmaster.internal/ubuntu noble/universe amd64 yaggo all 1.5.11-1 [21.7 kB] Get:103 http://ftpmaster.internal/ubuntu noble/universe amd64 dos2unix amd64 7.5.1-1 [501 kB] Preconfiguring packages ... Fetched 54.5 MB in 3s (17.5 MB/s) dpkg: libhogweed6:amd64: dependency problems, but removing anyway as you requested: libgnutls30:amd64 depends on libhogweed6 (>= 3.6). (Reading database ... 15762 files and directories currently installed.) Removing libhogweed6:amd64 (3.9.1-2) ... Selecting previously unselected package libhogweed6t64:amd64. (Reading database ... 15757 files and directories currently installed.) Preparing to unpack .../libhogweed6t64_3.9.1-2.2_amd64.deb ... Unpacking libhogweed6t64:amd64 (3.9.1-2.2) ... dpkg: libgnutls30:amd64: dependency problems, but removing anyway as you requested: apt depends on libgnutls30 (>= 3.7.5). (Reading database ... 15763 files and directories currently installed.) Removing libgnutls30:amd64 (3.8.3-1ubuntu1) ... Selecting previously unselected package libgnutls30t64:amd64. (Reading database ... 15754 files and directories currently installed.) Preparing to unpack .../libgnutls30t64_3.8.3-1.1ubuntu2_amd64.deb ... 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Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up groff-base (1.23.0-3build1) ... Setting up libhts3t64:amd64 (1.19+ds-1.1build2) ... Setting up libpython3-stdlib:amd64 (3.12.2-0ubuntu1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libhts-dev:amd64 (1.19+ds-1.1build2) ... Setting up python3 (3.12.2-0ubuntu1) ... Setting up libpython3.12-dev:amd64 (3.12.2-4build3) ... Setting up man-db (2.12.0-3build4) ... Not building database; man-db/auto-update is not 'true'. Created symlink /etc/systemd/system/timers.target.wants/man-db.timer → /usr/lib/systemd/system/man-db.timer. Setting up samtools (1.19.2-1) ... Setting up python3.12-dev (3.12.2-4build3) ... Setting up python3-pkg-resources (68.1.2-2ubuntu1) ... Setting up libpython3-dev:amd64 (3.12.2-0ubuntu1) ... Setting up python3-setuptools (68.1.2-2ubuntu1) ... Setting up python3-all (3.12.2-0ubuntu1) ... Setting up debhelper (13.14.1ubuntu5) ... Setting up libpython3-all-dev:amd64 (3.12.2-0ubuntu1) ... Setting up python3-dev (3.12.2-0ubuntu1) ... Setting up dh-python (6.20231223ubuntu2) ... Setting up python3-all-dev (3.12.2-0ubuntu1) ... Setting up rake (13.0.6-3) ... Setting up ruby3.2 (3.2.3-1build2) ... Setting up libruby3.2:amd64 (3.2.3-1build2) ... Setting up libruby:amd64 (1:3.2~ubuntu1) ... Setting up ruby (1:3.2~ubuntu1) ... Setting up yaggo (1.5.11-1) ... Setting up sbuild-build-depends-main-dummy (0.invalid.0) ... Setting up ruby-sdbm:amd64 (1.0.0-5build4) ... Setting up ruby-rubygems (3.4.20-1) ... Processing triggers for libc-bin (2.39-0ubuntu6) ... Processing triggers for systemd (255.4-1ubuntu5) ... (Reading database ... 24561 files and directories currently installed.) Purging configuration files for libgnutls30:amd64 (3.8.3-1ubuntu1) ... +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (amd64 included in any all) +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 5.4.0-173-generic #191-Ubuntu SMP Fri Feb 2 13:55:07 UTC 2024 amd64 (x86_64) Toolchain package versions: binutils_2.42-3ubuntu1 dpkg-dev_1.22.6ubuntu4 g++-13_13.2.0-19ubuntu1 gcc-13_13.2.0-19ubuntu1 libc6-dev_2.39-0ubuntu6 libstdc++-13-dev_13.2.0-19ubuntu1 libstdc++6_14-20240315-1ubuntu1 linux-libc-dev_6.8.0-20.20 Package versions: adduser_3.137ubuntu1 advancecomp_2.5-1 apt_2.7.3 apt-utils_2.7.3 architecture-properties_0.1.1 autoconf_2.71-3 autoconf-archive_20220903-3 automake_1:1.16.5-1.3ubuntu1 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+------------------------------------------------------------------------------+ Unpack source ------------- -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: jellyfish Binary: jellyfish, libjellyfish-2.0-2, libjellyfish-2.0-dev, python3-dna-jellyfish, libjellyfish-perl, jellyfish-examples Architecture: any all Version: 2.3.1-3~ppa1 Maintainer: Debian Med Packaging Team Uploaders: Shaun Jackman , Andreas Tille , Michael R. Crusoe , Étienne Mollier Homepage: https://www.genome.umd.edu/jellyfish.html Standards-Version: 4.6.2 Vcs-Browser: https://salsa.debian.org/med-team/jellyfish Vcs-Git: https://salsa.debian.org/med-team/jellyfish.git Testsuite: autopkgtest Testsuite-Triggers: @builddeps@ Build-Depends: debhelper-compat (= 13), architecture-is-little-endian, architecture-is-64-bit, d-shlibs, autoconf-archive, yaggo, pkgconf, bc, time, procps, swig, python3-all-dev, dh-sequence-python3, python3-setuptools, perl, chrpath, libhts-dev, dos2unix, samtools Package-List: jellyfish deb science optional arch=any jellyfish-examples deb science optional arch=all libjellyfish-2.0-2 deb libs optional arch=any libjellyfish-2.0-dev deb libdevel optional arch=any libjellyfish-perl deb perl optional arch=any python3-dna-jellyfish deb python optional arch=any Checksums-Sha1: 9aaf5f07cecf638544d27ca3de7cb7057184c92c 681990 jellyfish_2.3.1.orig.tar.gz 4da01f3097fda46a12c135d2f4d0dbdc5c5bf8b7 13388 jellyfish_2.3.1-3~ppa1.debian.tar.xz Checksums-Sha256: 540d09457fb4e14b98c7f1428cf885c333e2d6ef4f6a3735aa06be13eb523d69 681990 jellyfish_2.3.1.orig.tar.gz 2e87bc42c540005a7d0256071ec45d58a7d4293ac6e744eb08b1a8109473e7c8 13388 jellyfish_2.3.1-3~ppa1.debian.tar.xz Files: 27fb29ad3edfe25d776cfbf98dcc8c0e 681990 jellyfish_2.3.1.orig.tar.gz 502f33bba26b218e1f635214234a9610 13388 jellyfish_2.3.1-3~ppa1.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQIzBAEBCgAdFiEEJeP/LX9Gnb59DU5Qr8/sjmac4cIFAmX6AmsACgkQr8/sjmac 4cLHCQ/6AyVB0wSyzFYELA4soyPQ7PA35nIt4PehaqZgxT1PAm2TXu8IVoG+DiqZ JmgDnWOg9qmwa4uPDOjkVrmOdGY34cVAw6FBmLig/ha9FMY4tE2o/vBNqc+NVdHE dTCOY7FObiyKuIoo4TBqC5b/TQILN/Lo3ksXBw1EqNC2ROBQZBO4PB0Esxmo3E38 FvYme6gIStzGlxy0ZQ0quVe3j6e3N17EHHMoCa+oHLlAIPyM8bWF0JeHa5hTv5qF +jVuiplLNcupRiHKUcgLC9MugX1SeMMIktGcMz5BnEcksoU9azD/8XMZq+DNjtB1 x+TDQC6ox+Dl7yVOe/0a/9YVejFPV7He8tue5Bf9WAxOoo7dR2/RLU44x7lDDX/h mzIOVsXXW5dWsXGvmOgeYYtSge+c4Oq29yujo1Il6eXE6pOqjO6eGVmhlEj4wXml ikMQCsduPatSGcYnJix2lNonuAXv+/jS4uID5/yJgIQJvqiPoJj2xrcA1ydGc2uE fxc1p2rtTG1lM12h5pOf8/8nbh/oPOgUtFO3lTNXHb2O40L3L5Pudy6xlpkEqkgA 3DqvlWxrWunDyPbk+UweW4WFNYXOF6u9XQet303monZsIDcM9nx2Jrl7/ctbtS9e 4xmVJbU++irGBPUpWX0P3+mZcjnDgwAmt4j47hquj6rjlbpszAM= =76Q3 -----END PGP SIGNATURE----- gpgv: Signature made Tue Mar 19 21:23:55 2024 UTC gpgv: using RSA key 25E3FF2D7F469DBE7D0D4E50AFCFEC8E669CE1C2 gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./jellyfish_2.3.1-3~ppa1.dsc: no acceptable signature found dpkg-source: info: extracting jellyfish in /<> dpkg-source: info: unpacking jellyfish_2.3.1.orig.tar.gz dpkg-source: info: unpacking jellyfish_2.3.1-3~ppa1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying drop_distutils dpkg-source: info: applying manpage_whatis_entry.patch dpkg-source: info: applying portability.patch dpkg-source: info: applying test_needs_bash dpkg-source: info: applying python3 Check disk space ---------------- Sufficient free space for build User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf DEB_BUILD_OPTIONS=noautodbgsym 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-27942511 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-27942511 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-27942511 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 jellyfish dpkg-buildpackage: info: source version 2.3.1-3~ppa1 dpkg-buildpackage: info: source distribution noble dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean dh_clean debian/rules execute_after_dh_clean make[1]: Entering directory '/<>' if [ -d debian/tmp_save_tests ] ; then \ mv debian/tmp_save_tests/* tests ; \ rmdir debian/tmp_save_tests ; \ fi make[1]: Leaving directory '/<>' debian/rules binary dh binary debian/rules override_dh_update_autotools_config make[1]: Entering directory '/<>' # use python configuration from autoconf-archive mv m4/m4-ax_python_devel.m4 /tmp dh_update_autotools_config make[1]: Leaving directory '/<>' dh_autoreconf libtoolize: putting auxiliary files in '.'. libtoolize: copying file './ltmain.sh' libtoolize: putting macros in AC_CONFIG_MACRO_DIRS, 'm4'. libtoolize: copying file 'm4/libtool.m4' libtoolize: copying file 'm4/ltoptions.m4' libtoolize: copying file 'm4/ltsugar.m4' libtoolize: copying file 'm4/ltversion.m4' libtoolize: copying file 'm4/lt~obsolete.m4' configure.ac:8: installing './compile' configure.ac:2: installing './config.guess' configure.ac:2: installing './config.sub' configure.ac:4: installing './install-sh' configure.ac:4: installing './missing' Makefile.am: installing './depcomp' parallel-tests: installing './test-driver' debian/rules override_dh_auto_configure make[1]: Entering directory '/<>' dh_auto_configure -- --enable-swig --enable-perl-binding --enable-htslib --enable-python-binding PYTHON=/usr/bin/python3 ./configure --build=x86_64-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/x86_64-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking --enable-swig --enable-perl-binding --enable-htslib --enable-python-binding PYTHON=/usr/bin/python3 checking build system type... x86_64-pc-linux-gnu checking host system type... x86_64-pc-linux-gnu checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a race-free mkdir -p... /usr/bin/mkdir -p checking for gawk... no checking for mawk... mawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking whether make supports nested variables... (cached) yes checking how to print strings... printf checking whether make supports the include directive... yes (GNU style) checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether the compiler supports GNU C... yes checking whether gcc accepts -g... yes checking for gcc option to enable C11 features... none needed checking whether gcc understands -c and -o together... yes checking dependency style of gcc... none checking for a sed that does not truncate output... /usr/bin/sed checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... /usr/bin/grep -E checking for fgrep... /usr/bin/grep -F checking for ld used by gcc... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B checking the name lister (/usr/bin/nm -B) interface... BSD nm checking whether ln -s works... yes checking the maximum length of command line arguments... 1572864 checking how to convert x86_64-pc-linux-gnu file names to x86_64-pc-linux-gnu format... func_convert_file_noop checking how to convert x86_64-pc-linux-gnu file names to toolchain format... func_convert_file_noop checking for /usr/bin/ld option to reload object files... -r checking for file... file checking for objdump... objdump checking how to recognize dependent libraries... pass_all checking for dlltool... no checking how to associate runtime and link libraries... printf %s\n checking for ar... ar checking for archiver @FILE support... @ checking for strip... strip checking for ranlib... ranlib checking command to parse /usr/bin/nm -B output from gcc object... ok checking for sysroot... no checking for a working dd... /usr/bin/dd checking how to truncate binary pipes... /usr/bin/dd bs=4096 count=1 checking for mt... no checking if : is a manifest tool... no checking for stdio.h... yes checking for stdlib.h... yes checking for string.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for strings.h... yes checking for sys/stat.h... yes checking for sys/types.h... yes checking for unistd.h... yes checking for dlfcn.h... yes checking for objdir... .libs checking if gcc supports -fno-rtti -fno-exceptions... no checking for gcc option to produce PIC... -fPIC -DPIC checking if gcc PIC flag -fPIC -DPIC works... yes checking if gcc static flag -static works... yes checking if gcc supports -c -o file.o... yes checking if gcc supports -c -o file.o... (cached) yes checking whether the gcc linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking whether -lc should be explicitly linked in... no checking dynamic linker characteristics... GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... yes checking whether to build static libraries... yes checking for ld... /usr/bin/ld -m elf_x86_64 checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld... yes checking for shared library run path origin... done checking for pkg-config... /usr/bin/pkg-config checking pkg-config is at least version 0.9.0... yes checking for g++... g++ checking whether the compiler supports GNU C++... yes checking whether g++ accepts -g... yes checking for g++ option to enable C++11 features... none needed checking dependency style of g++... none checking how to run the C++ preprocessor... g++ -E checking for ld used by g++... /usr/bin/ld -m elf_x86_64 checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld... yes checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking for g++ option to produce PIC... -fPIC -DPIC checking if g++ PIC flag -fPIC -DPIC works... yes checking if g++ static flag -static works... yes checking if g++ supports -c -o file.o... yes checking if g++ supports -c -o file.o... (cached) yes checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking dynamic linker characteristics... (cached) GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking 32-bit host C ABI... no checking for ELF binary format... yes checking for the common suffixes of directories in the library search path... lib,lib,lib64 checking for htslib... yes checking for samtools... /usr/bin/samtools checking for unix2dos... /usr/bin/unix2dos checking for md5sum... md5sum checking for yaggo... /usr/bin/yaggo checking for x86 cpuid output... unknown checking for x86-AVX xgetbv output... unknown checking for x86 cpuid 0x00000000 output... d:68747541:444d4163:69746e65 checking for x86 cpuid 0x80000000 output... 8000001e:68747541:444d4163:69746e65 checking for x86 cpuid 0x00000001 output... 830f10:800:fef83203:78bfbff checking for x86 cpuid 0x00000007 output... 0:219c01a9:400004:0 checking for x86 cpuid 0x80000001 output... 830f10:0:c003f5:2fd3fbff checking for x86-AVX xgetbv 0x00000000 output... 7:0 checking whether RDRND is supported by the processor... yes checking whether RDRND is supported by the processor and OS... yes checking whether C++ compiler accepts -mrdrnd... yes checking whether BMI1 is supported by the processor... yes checking whether BMI1 is supported by the processor and OS... yes checking whether C++ compiler accepts -mbmi... yes checking whether BMI2 is supported by the processor... yes checking whether BMI2 is supported by the processor and OS... yes checking whether C++ compiler accepts -mbmi2... yes checking whether ADX is supported by the processor... yes checking whether ADX is supported by the processor and OS... yes checking whether C++ compiler accepts -madx... yes checking whether MPX is supported by the processor... no checking whether PREFETCHWT1 is supported by the processor... no checking whether ABM is supported by the processor... yes checking whether ABM is supported by the processor and OS... yes checking whether C++ compiler accepts -mabm... yes checking whether MMX is supported by the processor... yes checking whether MMX is supported by the processor and OS... yes checking whether C++ compiler accepts -mmmx... yes checking whether SSE is supported by the processor... yes checking whether SSE is supported by the processor and OS... yes checking whether C++ compiler accepts -msse... yes checking whether SSE2 is supported by the processor... yes checking whether SSE2 is supported by the processor and OS... yes checking whether C++ compiler accepts -msse2... yes checking whether SSE3 is supported by the processor... yes checking whether SSE3 is supported by the processor and OS... yes checking whether C++ compiler accepts -msse3... yes checking whether SSSE3 is supported by the processor... yes checking whether SSSE3 is supported by the processor and OS... yes checking whether C++ compiler accepts -mssse3... yes checking whether SSE4.1 is supported by the processor... yes checking whether SSE4.1 is supported by the processor and OS... yes checking whether C++ compiler accepts -msse4.1... yes checking whether SSE4.2 is supported by the processor... yes checking whether SSE4.2 is supported by the processor and OS... yes checking whether C++ compiler accepts -msse4.2... yes checking whether SSE4a is supported by the processor... yes checking whether SSE4a is supported by the processor and OS... yes checking whether C++ compiler accepts -msse4a... yes checking whether SHA is supported by the processor... yes checking whether SHA is supported by the processor and OS... yes checking whether C++ compiler accepts -msha... yes checking whether AES is supported by the processor... yes checking whether AES is supported by the processor and OS... yes checking whether C++ compiler accepts -maes... yes checking whether AVX is supported by the processor... yes checking whether AVX is supported by the processor and OS... yes checking whether C++ compiler accepts -mavx... yes checking whether FMA3 is supported by the processor... yes checking whether FMA3 is supported by the processor and OS... yes checking whether C++ compiler accepts -mfma... yes checking whether FMA4 is supported by the processor... no checking whether XOP is supported by the processor... no checking whether AVX2 is supported by the processor... yes checking whether AVX2 is supported by the processor and OS... yes checking whether C++ compiler accepts -mavx2... yes checking whether AVX512-F is supported by the processor... no checking whether AVX512-CD is supported by the processor... no checking whether AVX512-PF is supported by the processor... no checking whether AVX512-ER is supported by the processor... no checking whether AVX512-VL is supported by the processor... no checking whether AVX512-BW is supported by the processor... no checking whether AVX512-DQ is supported by the processor... no checking whether AVX512-IFMA is supported by the processor... no checking whether AVX512-VBMI is supported by the processor... no checking for __int128... yes checking for std::numeric_limits<__int128>... yes checking for _NSGetExecutablePath... no checking for execinfo.h... yes checking for ext/stdio_filebuf.h... yes checking for sys/syscall.h... yes checking for sys/prctl.h... yes checking for siginfo_t.si_int... yes checking for swig... /usr/bin/swig checking SWIG version... 4.2.0 checking for SWIG library... /usr/share/swig4.0 checking for python... /usr/bin/python3 checking for a version of Python >= '2.1.0'... yes checking for the sysconfig Python package... yes checking for Python include path... -I/usr/include/python3.12 checking for Python library path... -L/usr/lib/x86_64-linux-gnu -lpython3.12 checking for Python site-packages path... /usr/lib/python3.12/site-packages checking for Python platform specific site-packages path... /usr/lib/python3.12/site-packages checking python extra libraries... -ldl -lm checking python extra linking flags... -Xlinker -export-dynamic -Wl,-O1 -Wl,-Bsymbolic-functions checking consistency of all components of python development environment... yes checking for perl... /usr/bin/perl checking for Perl prefix... /usr checking for Perl extension include path... /usr/lib/x86_64-linux-gnu/perl/5.38/CORE checking for Perl extension target directory... /usr/lib/perl/5.38.0 checking for Perl extensions C preprocessor flags... -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fwrapv -fno-strict-aliasing -pipe -I/usr/local/include checking for Perl extensions linker flags... -shared -L/usr/local/lib -fstack-protector-strong checking for posix_memalign... yes checking for aligned_alloc... yes checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating compat.sh config.status: creating jellyfish-2.0.pc config.status: creating config.h config.status: executing depfiles commands config.status: executing libtool commands dh_auto_configure --sourcedirectory=swig/perl5 cd swig/perl5 && /usr/bin/perl Makefile.PL INSTALLDIRS=vendor "OPTIMIZE=-g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/jellyfish-2.3.1-3~ppa1 -Wdate-time -D_FORTIFY_SOURCE=3" "LD=x86_64-linux-gnu-gcc -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/jellyfish-2.3.1-3~ppa1 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -lpthread" -I/<>/debian/tmp/usr/include/jellyfish-2.3.1 -L/<>/debian/tmp/usr/lib/x86_64-linux-gnu -ljellyfish-2.0 -lpthread -L/<>/debian/tmp/usr/lib/x86_64-linux-gnu Warning (mostly harmless): No library found for -ljellyfish-2.0 Generating a Unix-style Makefile Writing Makefile for jellyfish Writing MYMETA.yml and MYMETA.json dh_auto_configure --sourcedirectory=swig/python --buildsystem=pybuild I: pybuild base:305: python3.12 setup.py config running config mv /tmp/m4-ax_python_devel.m4 m4 make[1]: Leaving directory '/<>' debian/rules override_dh_auto_build make[1]: Entering directory '/<>' mkdir -p debian/tmp_save_tests cp -a tests/* debian/tmp_save_tests dh_auto_build --no-parallel -- all bin/generate_sequence bin/test_all bin/fastq2sam make -j1 all bin/generate_sequence bin/test_all bin/fastq2sam make[2]: Entering directory '/<>' /usr/bin/yaggo --license ./header-license -o sub_commands/count_main_cmdline.hpp sub_commands/count_main_cmdline.yaggo /usr/bin/yaggo --license ./header-license -o sub_commands/info_main_cmdline.hpp sub_commands/info_main_cmdline.yaggo /usr/bin/yaggo --license ./header-license -o sub_commands/dump_main_cmdline.hpp sub_commands/dump_main_cmdline.yaggo /usr/bin/yaggo --license ./header-license -o sub_commands/histo_main_cmdline.hpp sub_commands/histo_main_cmdline.yaggo /usr/bin/yaggo --license ./header-license -o sub_commands/stats_main_cmdline.hpp sub_commands/stats_main_cmdline.yaggo /usr/bin/yaggo --license ./header-license -o sub_commands/merge_main_cmdline.hpp sub_commands/merge_main_cmdline.yaggo /usr/bin/yaggo --license ./header-license -o sub_commands/bc_main_cmdline.hpp sub_commands/bc_main_cmdline.yaggo /usr/bin/yaggo --license ./header-license -o sub_commands/query_main_cmdline.hpp sub_commands/query_main_cmdline.yaggo /usr/bin/yaggo --license ./header-license -o sub_commands/cite_main_cmdline.hpp sub_commands/cite_main_cmdline.yaggo /usr/bin/yaggo --license ./header-license -o sub_commands/mem_main_cmdline.hpp sub_commands/mem_main_cmdline.yaggo /usr/bin/yaggo --license ./header-license -o jellyfish/generate_sequence_cmdline.hpp jellyfish/generate_sequence_cmdline.yaggo /usr/bin/yaggo --license ./header-license -o jellyfish/fastq2sam_cmdline.hpp jellyfish/fastq2sam_cmdline.yaggo /usr/bin/yaggo --license ./header-license -o unit_tests/test_main_cmdline.hpp unit_tests/test_main_cmdline.yaggo /usr/bin/swig -c++ -python -I./../include -o swig/python/swig_wrap.cpp swig/jellyfish.i /usr/bin/swig -c++ -perl5 -I./../include -o swig/perl5/swig_wrap.cpp swig/jellyfish.i make all-am make[3]: Entering directory '/<>' g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=3 -I/<>/debian/tmp/usr/include -Werror -std=c++11 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/jellyfish-2.3.1-3~ppa1 -Wno-nonnull -c -o sub_commands/jellyfish.o sub_commands/jellyfish.cc g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=3 -I/<>/debian/tmp/usr/include -Werror -std=c++11 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/jellyfish-2.3.1-3~ppa1 -Wno-nonnull -c -o sub_commands/count_main.o sub_commands/count_main.cc g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=3 -I/<>/debian/tmp/usr/include -Werror -std=c++11 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/jellyfish-2.3.1-3~ppa1 -Wno-nonnull -c -o sub_commands/info_main.o sub_commands/info_main.cc g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=3 -I/<>/debian/tmp/usr/include -Werror -std=c++11 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/jellyfish-2.3.1-3~ppa1 -Wno-nonnull -c -o sub_commands/dump_main.o sub_commands/dump_main.cc g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=3 -I/<>/debian/tmp/usr/include -Werror -std=c++11 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/jellyfish-2.3.1-3~ppa1 -Wno-nonnull -c -o sub_commands/histo_main.o sub_commands/histo_main.cc g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=3 -I/<>/debian/tmp/usr/include -Werror -std=c++11 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/jellyfish-2.3.1-3~ppa1 -Wno-nonnull -c -o sub_commands/stats_main.o sub_commands/stats_main.cc g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=3 -I/<>/debian/tmp/usr/include -Werror -std=c++11 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/jellyfish-2.3.1-3~ppa1 -Wno-nonnull -c -o sub_commands/merge_main.o sub_commands/merge_main.cc g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=3 -I/<>/debian/tmp/usr/include -Werror -std=c++11 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/jellyfish-2.3.1-3~ppa1 -Wno-nonnull -c -o sub_commands/bc_main.o sub_commands/bc_main.cc g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=3 -I/<>/debian/tmp/usr/include -Werror -std=c++11 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/jellyfish-2.3.1-3~ppa1 -Wno-nonnull -c -o sub_commands/query_main.o sub_commands/query_main.cc g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=3 -I/<>/debian/tmp/usr/include -Werror -std=c++11 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/jellyfish-2.3.1-3~ppa1 -Wno-nonnull -c -o sub_commands/cite_main.o sub_commands/cite_main.cc g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=3 -I/<>/debian/tmp/usr/include -Werror -std=c++11 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/jellyfish-2.3.1-3~ppa1 -Wno-nonnull -c -o sub_commands/mem_main.o sub_commands/mem_main.cc g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=3 -I/<>/debian/tmp/usr/include -Werror -std=c++11 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/jellyfish-2.3.1-3~ppa1 -Wno-nonnull -c -o jellyfish/merge_files.o jellyfish/merge_files.cc /bin/bash ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=3 -I/<>/debian/tmp/usr/include -Werror -std=c++11 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/jellyfish-2.3.1-3~ppa1 -Wno-nonnull -c -o lib/rectangular_binary_matrix.lo lib/rectangular_binary_matrix.cc libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=3 -I/<>/debian/tmp/usr/include -Werror -std=c++11 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection "-fdebug-prefix-map=/<>=/usr/src/jellyfish-2.3.1-3~ppa1" -Wno-nonnull -c lib/rectangular_binary_matrix.cc -fPIC -DPIC -o lib/.libs/rectangular_binary_matrix.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=3 -I/<>/debian/tmp/usr/include -Werror -std=c++11 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection "-fdebug-prefix-map=/<>=/usr/src/jellyfish-2.3.1-3~ppa1" -Wno-nonnull -c lib/rectangular_binary_matrix.cc -o lib/rectangular_binary_matrix.o >/dev/null 2>&1 /bin/bash ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=3 -I/<>/debian/tmp/usr/include -Werror -std=c++11 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer 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unit_tests/bin_test_all-test_generator_manager.o unit_tests/bin_test_all-test_atomic_bits_array.o unit_tests/bin_test_all-test_stdio_filebuf.o jellyfish/bin_test_all-backtrace.o libgtest.la libjellyfish-2.0.la libtool: link: g++ -I/<>/debian/tmp/usr/include -Werror -I./unit_tests/gtest/include -I./unit_tests -I./include -Wno-unused-variable -std=c++11 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection "-fdebug-prefix-map=/<>=/usr/src/jellyfish-2.3.1-3~ppa1" -Wno-nonnull -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z -Wl,relro -Wl,-z -Wl,now -o bin/.libs/test_all unit_tests/bin_test_all-test_main.o unit_tests/bin_test_all-test_misc.o unit_tests/bin_test_all-test_offsets_key_value.o unit_tests/bin_test_all-test_simple_circular_buffer.o unit_tests/bin_test_all-test_rectangular_binary_matrix.o unit_tests/bin_test_all-test_mer_dna.o unit_tests/bin_test_all-test_large_hash_array.o unit_tests/bin_test_all-test_mer_overlap_sequence_parser.o unit_tests/bin_test_all-test_file_header.o unit_tests/bin_test_all-test_mer_iterator.o unit_tests/bin_test_all-test_hash_counter.o unit_tests/bin_test_all-test_mer_heap.o unit_tests/bin_test_all-test_stream_iterator.o unit_tests/bin_test_all-test_token_ring.o unit_tests/bin_test_all-test_text_dumper.o unit_tests/bin_test_all-test_dumpers.o unit_tests/bin_test_all-test_mapped_file.o unit_tests/bin_test_all-test_int128.o unit_tests/bin_test_all-test_mer_dna_bloom_counter.o unit_tests/bin_test_all-test_whole_sequence_parser.o unit_tests/bin_test_all-test_allocators_mmap.o unit_tests/bin_test_all-test_cooperative_pool2.o unit_tests/bin_test_all-test_generator_manager.o unit_tests/bin_test_all-test_atomic_bits_array.o unit_tests/bin_test_all-test_stdio_filebuf.o jellyfish/bin_test_all-backtrace.o -L/<>/debian/tmp/usr/lib/x86_64-linux-gnu ./.libs/libgtest.a -lhts -lpthread ./.libs/libjellyfish-2.0.so -pthread -Wl,-rpath -Wl,/<>/debian/tmp/usr/lib/x86_64-linux-gnu g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=3 -I/<>/debian/tmp/usr/include -Werror -std=c++11 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/jellyfish-2.3.1-3~ppa1 -Wno-nonnull -c -o jellyfish/fastq2sam.o jellyfish/fastq2sam.cc /bin/bash ./libtool --tag=CXX --mode=link g++ -I/<>/debian/tmp/usr/include -Werror -std=c++11 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/jellyfish-2.3.1-3~ppa1 -Wno-nonnull -pthread -L/<>/debian/tmp/usr/lib/x86_64-linux-gnu -lhts -R/<>/debian/tmp/usr/lib/x86_64-linux-gnu -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -lpthread -o bin/fastq2sam jellyfish/fastq2sam.o libjellyfish-2.0.la libtool: link: g++ -I/<>/debian/tmp/usr/include -Werror -std=c++11 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection "-fdebug-prefix-map=/<>=/usr/src/jellyfish-2.3.1-3~ppa1" -Wno-nonnull -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z -Wl,relro -Wl,-z -Wl,now -o bin/.libs/fastq2sam jellyfish/fastq2sam.o -L/<>/debian/tmp/usr/lib/x86_64-linux-gnu -lhts -lpthread ./.libs/libjellyfish-2.0.so -pthread -Wl,-rpath -Wl,/<>/debian/tmp/usr/lib/x86_64-linux-gnu make[2]: Leaving directory '/<>' dh_auto_install -- install-data make -j1 install DESTDIR=/<>/debian/tmp AM_UPDATE_INFO_DIR=no install-data make[2]: Entering directory '/<>' make install-am make[3]: Entering directory '/<>' make[4]: Entering directory '/<>' /usr/bin/mkdir -p '/<>/debian/tmp/usr/lib/x86_64-linux-gnu' /bin/bash ./libtool --mode=install /usr/bin/install -c libjellyfish-2.0.la '/<>/debian/tmp/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c .libs/libjellyfish-2.0.so.2.0.0 /<>/debian/tmp/usr/lib/x86_64-linux-gnu/libjellyfish-2.0.so.2.0.0 libtool: install: (cd /<>/debian/tmp/usr/lib/x86_64-linux-gnu && { ln -s -f libjellyfish-2.0.so.2.0.0 libjellyfish-2.0.so.2 || { rm -f libjellyfish-2.0.so.2 && ln -s libjellyfish-2.0.so.2.0.0 libjellyfish-2.0.so.2; }; }) libtool: install: (cd /<>/debian/tmp/usr/lib/x86_64-linux-gnu && { ln -s -f libjellyfish-2.0.so.2.0.0 libjellyfish-2.0.so || { rm -f libjellyfish-2.0.so && ln -s libjellyfish-2.0.so.2.0.0 libjellyfish-2.0.so; }; }) libtool: install: /usr/bin/install -c .libs/libjellyfish-2.0.lai /<>/debian/tmp/usr/lib/x86_64-linux-gnu/libjellyfish-2.0.la libtool: install: /usr/bin/install -c .libs/libjellyfish-2.0.a /<>/debian/tmp/usr/lib/x86_64-linux-gnu/libjellyfish-2.0.a libtool: install: chmod 644 /<>/debian/tmp/usr/lib/x86_64-linux-gnu/libjellyfish-2.0.a libtool: install: ranlib /<>/debian/tmp/usr/lib/x86_64-linux-gnu/libjellyfish-2.0.a libtool: warning: remember to run 'libtool --finish /usr/lib/x86_64-linux-gnu' /usr/bin/mkdir -p '/<>/debian/tmp/usr/bin' /bin/bash ./libtool --mode=install /usr/bin/install -c bin/jellyfish '/<>/debian/tmp/usr/bin' libtool: warning: 'libjellyfish-2.0.la' has not been installed in '/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c bin/.libs/jellyfish /<>/debian/tmp/usr/bin/jellyfish /usr/bin/mkdir -p '/<>/debian/tmp/usr/include/jellyfish-2.3.1/jellyfish' /usr/bin/install -c -m 644 include/jellyfish/allocators_mmap.hpp include/jellyfish/backtrace.hpp include/jellyfish/atomic_gcc.hpp include/jellyfish/large_hash_array.hpp include/jellyfish/err.hpp include/jellyfish/misc.hpp include/jellyfish/offsets_key_value.hpp include/jellyfish/int128.hpp include/jellyfish/rectangular_binary_matrix.hpp include/jellyfish/mer_dna.hpp include/jellyfish/storage.hpp include/jellyfish/simple_circular_buffer.hpp include/jellyfish/circular_buffer.hpp include/jellyfish/atomic_field.hpp include/jellyfish/compare_and_swap.hpp include/jellyfish/divisor.hpp include/jellyfish/large_hash_iterator.hpp include/jellyfish/jellyfish.hpp include/jellyfish/thread_exec.hpp include/jellyfish/stream_iterator.hpp include/jellyfish/mer_overlap_sequence_parser.hpp include/jellyfish/whole_sequence_parser.hpp include/jellyfish/parser_common.hpp include/jellyfish/sam_format.hpp include/jellyfish/binary_dumper.hpp include/jellyfish/sorted_dumper.hpp include/jellyfish/text_dumper.hpp include/jellyfish/dumper.hpp include/jellyfish/time.hpp include/jellyfish/mer_heap.hpp include/jellyfish/token_ring.hpp include/jellyfish/locks_pthread.hpp include/jellyfish/file_header.hpp include/jellyfish/generic_file_header.hpp include/jellyfish/json.h include/jellyfish/hash_counter.hpp include/jellyfish/mapped_file.hpp include/jellyfish/mer_dna_bloom_counter.hpp include/jellyfish/bloom_common.hpp include/jellyfish/bloom_counter2.hpp '/<>/debian/tmp/usr/include/jellyfish-2.3.1/jellyfish' /usr/bin/install -c -m 644 include/jellyfish/bloom_filter.hpp include/jellyfish/cooperative_pool.hpp include/jellyfish/cooperative_pool2.hpp include/jellyfish/stream_manager.hpp include/jellyfish/generator_manager.hpp include/jellyfish/cpp_array.hpp include/jellyfish/mer_iterator.hpp include/jellyfish/atomic_bits_array.hpp include/jellyfish/stdio_filebuf.hpp include/jellyfish/mer_qual_iterator.hpp '/<>/debian/tmp/usr/include/jellyfish-2.3.1/jellyfish' /usr/bin/mkdir -p '/<>/debian/tmp/usr/share/man/man1' /usr/bin/install -c -m 644 'doc/jellyfish.man' '/<>/debian/tmp/usr/share/man/man1/jellyfish.1' /usr/bin/mkdir -p '/<>/debian/tmp/usr/lib/perl/5.38.0' /bin/bash ./libtool --mode=install /usr/bin/install -c swig/perl5/jellyfish.la '/<>/debian/tmp/usr/lib/perl/5.38.0' libtool: warning: relinking 'swig/perl5/jellyfish.la' libtool: install: (cd /<>; /bin/bash "/<>/libtool" --tag CXX --mode=relink g++ -I/<>/debian/tmp/usr/include -Werror -Wno-error -std=c++11 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection "-fdebug-prefix-map=/<>=/usr/src/jellyfish-2.3.1-3~ppa1" -Wno-nonnull -module -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -lpthread -o swig/perl5/jellyfish.la -rpath /usr/lib/perl/5.38.0 swig/perl5/swig_perl5_jellyfish_la-swig_wrap.lo libjellyfish-2.0.la -inst-prefix-dir /<>/debian/tmp) libtool: relink: g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/x86_64-linux-gnu/13/../../../x86_64-linux-gnu/crti.o /usr/lib/gcc/x86_64-linux-gnu/13/crtbeginS.o swig/perl5/.libs/swig_perl5_jellyfish_la-swig_wrap.o -lpthread -L/<>/debian/tmp/usr/lib/x86_64-linux-gnu -L/usr/lib/x86_64-linux-gnu -ljellyfish-2.0 -L/usr/lib/gcc/x86_64-linux-gnu/13 -L/usr/lib/gcc/x86_64-linux-gnu/13/../../../x86_64-linux-gnu -L/usr/lib/gcc/x86_64-linux-gnu/13/../../../../lib -L/lib/x86_64-linux-gnu -L/lib/../lib -L/usr/lib/../lib -L/usr/lib/gcc/x86_64-linux-gnu/13/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/x86_64-linux-gnu/13/crtendS.o /usr/lib/gcc/x86_64-linux-gnu/13/../../../x86_64-linux-gnu/crtn.o -g -O2 -mno-omit-leaf-frame-pointer -flto=auto -fstack-protector-strong -Wl,-Bsymbolic-functions -flto=auto -Wl,-z -Wl,relro -Wl,-z -Wl,now -Wl,-soname -Wl,jellyfish.so.0 -o swig/perl5/.libs/jellyfish.so.0.0.0 libtool: install: /usr/bin/install -c swig/perl5/.libs/jellyfish.so.0.0.0T /<>/debian/tmp/usr/lib/perl/5.38.0/jellyfish.so.0.0.0 libtool: install: (cd /<>/debian/tmp/usr/lib/perl/5.38.0 && { ln -s -f jellyfish.so.0.0.0 jellyfish.so.0 || { rm -f jellyfish.so.0 && ln -s jellyfish.so.0.0.0 jellyfish.so.0; }; }) libtool: install: (cd /<>/debian/tmp/usr/lib/perl/5.38.0 && { ln -s -f jellyfish.so.0.0.0 jellyfish.so || { rm -f jellyfish.so && ln -s jellyfish.so.0.0.0 jellyfish.so; }; }) libtool: install: /usr/bin/install -c swig/perl5/.libs/jellyfish.lai /<>/debian/tmp/usr/lib/perl/5.38.0/jellyfish.la libtool: install: /usr/bin/install -c swig/perl5/.libs/jellyfish.a /<>/debian/tmp/usr/lib/perl/5.38.0/jellyfish.a libtool: install: chmod 644 /<>/debian/tmp/usr/lib/perl/5.38.0/jellyfish.a libtool: install: ranlib /<>/debian/tmp/usr/lib/perl/5.38.0/jellyfish.a libtool: warning: remember to run 'libtool --finish /usr/lib/perl/5.38.0' /usr/bin/mkdir -p '/<>/debian/tmp/usr/lib/perl/5.38.0' /usr/bin/install -c swig/perl5/jellyfish.pm '/<>/debian/tmp/usr/lib/perl/5.38.0' /usr/bin/mkdir -p '/<>/debian/tmp/usr/lib/x86_64-linux-gnu/pkgconfig' /usr/bin/install -c -m 644 jellyfish-2.0.pc '/<>/debian/tmp/usr/lib/x86_64-linux-gnu/pkgconfig' /usr/bin/mkdir -p '/<>/debian/tmp/usr/lib/python3.12/site-packages/dna_jellyfish' /bin/bash ./libtool --mode=install /usr/bin/install -c swig/python/_dna_jellyfish.la '/<>/debian/tmp/usr/lib/python3.12/site-packages/dna_jellyfish' libtool: warning: relinking 'swig/python/_dna_jellyfish.la' libtool: install: (cd /<>; /bin/bash "/<>/libtool" --tag CXX --mode=relink g++ -I/<>/debian/tmp/usr/include -Werror -std=c++11 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection "-fdebug-prefix-map=/<>=/usr/src/jellyfish-2.3.1-3~ppa1" -Wno-nonnull -module -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -lpthread -o swig/python/_dna_jellyfish.la -rpath /usr/lib/python3.12/site-packages/dna_jellyfish swig/python/swig_python__dna_jellyfish_la-swig_wrap.lo libjellyfish-2.0.la -inst-prefix-dir /<>/debian/tmp) libtool: relink: g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/x86_64-linux-gnu/13/../../../x86_64-linux-gnu/crti.o /usr/lib/gcc/x86_64-linux-gnu/13/crtbeginS.o swig/python/.libs/swig_python__dna_jellyfish_la-swig_wrap.o -lpthread -L/<>/debian/tmp/usr/lib/x86_64-linux-gnu -L/usr/lib/x86_64-linux-gnu -ljellyfish-2.0 -L/usr/lib/gcc/x86_64-linux-gnu/13 -L/usr/lib/gcc/x86_64-linux-gnu/13/../../../x86_64-linux-gnu -L/usr/lib/gcc/x86_64-linux-gnu/13/../../../../lib -L/lib/x86_64-linux-gnu -L/lib/../lib -L/usr/lib/../lib -L/usr/lib/gcc/x86_64-linux-gnu/13/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/x86_64-linux-gnu/13/crtendS.o /usr/lib/gcc/x86_64-linux-gnu/13/../../../x86_64-linux-gnu/crtn.o -g -O2 -mno-omit-leaf-frame-pointer -flto=auto -fstack-protector-strong -Wl,-Bsymbolic-functions -flto=auto -Wl,-z -Wl,relro -Wl,-z -Wl,now -Wl,-soname -Wl,_dna_jellyfish.so.0 -o swig/python/.libs/_dna_jellyfish.so.0.0.0 libtool: install: /usr/bin/install -c swig/python/.libs/_dna_jellyfish.so.0.0.0T /<>/debian/tmp/usr/lib/python3.12/site-packages/dna_jellyfish/_dna_jellyfish.so.0.0.0 libtool: install: (cd /<>/debian/tmp/usr/lib/python3.12/site-packages/dna_jellyfish && { ln -s -f _dna_jellyfish.so.0.0.0 _dna_jellyfish.so.0 || { rm -f _dna_jellyfish.so.0 && ln -s _dna_jellyfish.so.0.0.0 _dna_jellyfish.so.0; }; }) libtool: install: (cd /<>/debian/tmp/usr/lib/python3.12/site-packages/dna_jellyfish && { ln -s -f _dna_jellyfish.so.0.0.0 _dna_jellyfish.so || { rm -f _dna_jellyfish.so && ln -s _dna_jellyfish.so.0.0.0 _dna_jellyfish.so; }; }) libtool: install: /usr/bin/install -c swig/python/.libs/_dna_jellyfish.lai /<>/debian/tmp/usr/lib/python3.12/site-packages/dna_jellyfish/_dna_jellyfish.la libtool: install: /usr/bin/install -c swig/python/.libs/_dna_jellyfish.a /<>/debian/tmp/usr/lib/python3.12/site-packages/dna_jellyfish/_dna_jellyfish.a libtool: install: chmod 644 /<>/debian/tmp/usr/lib/python3.12/site-packages/dna_jellyfish/_dna_jellyfish.a libtool: install: ranlib /<>/debian/tmp/usr/lib/python3.12/site-packages/dna_jellyfish/_dna_jellyfish.a libtool: warning: remember to run 'libtool --finish /usr/lib/python3.12/site-packages/dna_jellyfish' /usr/bin/mkdir -p '/<>/debian/tmp/usr/lib/python3.12/site-packages/dna_jellyfish' /usr/bin/install -c swig/python/__init__.pyc '/<>/debian/tmp/usr/lib/python3.12/site-packages/dna_jellyfish' make[4]: Leaving directory '/<>' make[3]: Leaving directory '/<>' /usr/bin/mkdir -p '/<>/debian/tmp/usr/include/jellyfish-2.3.1/jellyfish' /usr/bin/install -c -m 644 include/jellyfish/allocators_mmap.hpp include/jellyfish/backtrace.hpp include/jellyfish/atomic_gcc.hpp include/jellyfish/large_hash_array.hpp include/jellyfish/err.hpp include/jellyfish/misc.hpp include/jellyfish/offsets_key_value.hpp include/jellyfish/int128.hpp include/jellyfish/rectangular_binary_matrix.hpp include/jellyfish/mer_dna.hpp include/jellyfish/storage.hpp include/jellyfish/simple_circular_buffer.hpp include/jellyfish/circular_buffer.hpp include/jellyfish/atomic_field.hpp include/jellyfish/compare_and_swap.hpp include/jellyfish/divisor.hpp include/jellyfish/large_hash_iterator.hpp include/jellyfish/jellyfish.hpp include/jellyfish/thread_exec.hpp include/jellyfish/stream_iterator.hpp include/jellyfish/mer_overlap_sequence_parser.hpp include/jellyfish/whole_sequence_parser.hpp include/jellyfish/parser_common.hpp include/jellyfish/sam_format.hpp include/jellyfish/binary_dumper.hpp include/jellyfish/sorted_dumper.hpp include/jellyfish/text_dumper.hpp include/jellyfish/dumper.hpp include/jellyfish/time.hpp include/jellyfish/mer_heap.hpp include/jellyfish/token_ring.hpp include/jellyfish/locks_pthread.hpp include/jellyfish/file_header.hpp include/jellyfish/generic_file_header.hpp include/jellyfish/json.h include/jellyfish/hash_counter.hpp include/jellyfish/mapped_file.hpp include/jellyfish/mer_dna_bloom_counter.hpp include/jellyfish/bloom_common.hpp include/jellyfish/bloom_counter2.hpp '/<>/debian/tmp/usr/include/jellyfish-2.3.1/jellyfish' /usr/bin/install -c -m 644 include/jellyfish/bloom_filter.hpp include/jellyfish/cooperative_pool.hpp include/jellyfish/cooperative_pool2.hpp include/jellyfish/stream_manager.hpp include/jellyfish/generator_manager.hpp include/jellyfish/cpp_array.hpp include/jellyfish/mer_iterator.hpp include/jellyfish/atomic_bits_array.hpp include/jellyfish/stdio_filebuf.hpp include/jellyfish/mer_qual_iterator.hpp '/<>/debian/tmp/usr/include/jellyfish-2.3.1/jellyfish' /usr/bin/mkdir -p '/<>/debian/tmp/usr/share/man/man1' /usr/bin/install -c -m 644 'doc/jellyfish.man' '/<>/debian/tmp/usr/share/man/man1/jellyfish.1' /usr/bin/mkdir -p '/<>/debian/tmp/usr/lib/x86_64-linux-gnu' /bin/bash ./libtool --mode=install /usr/bin/install -c libjellyfish-2.0.la '/<>/debian/tmp/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c .libs/libjellyfish-2.0.so.2.0.0 /<>/debian/tmp/usr/lib/x86_64-linux-gnu/libjellyfish-2.0.so.2.0.0 libtool: install: (cd /<>/debian/tmp/usr/lib/x86_64-linux-gnu && { ln -s -f libjellyfish-2.0.so.2.0.0 libjellyfish-2.0.so.2 || { rm -f libjellyfish-2.0.so.2 && ln -s libjellyfish-2.0.so.2.0.0 libjellyfish-2.0.so.2; }; }) libtool: install: (cd /<>/debian/tmp/usr/lib/x86_64-linux-gnu && { ln -s -f libjellyfish-2.0.so.2.0.0 libjellyfish-2.0.so || { rm -f libjellyfish-2.0.so && ln -s libjellyfish-2.0.so.2.0.0 libjellyfish-2.0.so; }; }) libtool: install: /usr/bin/install -c .libs/libjellyfish-2.0.lai /<>/debian/tmp/usr/lib/x86_64-linux-gnu/libjellyfish-2.0.la libtool: install: /usr/bin/install -c .libs/libjellyfish-2.0.a /<>/debian/tmp/usr/lib/x86_64-linux-gnu/libjellyfish-2.0.a libtool: install: chmod 644 /<>/debian/tmp/usr/lib/x86_64-linux-gnu/libjellyfish-2.0.a libtool: install: ranlib /<>/debian/tmp/usr/lib/x86_64-linux-gnu/libjellyfish-2.0.a libtool: warning: remember to run 'libtool --finish /usr/lib/x86_64-linux-gnu' /usr/bin/mkdir -p '/<>/debian/tmp/usr/lib/perl/5.38.0' /bin/bash ./libtool --mode=install /usr/bin/install -c swig/perl5/jellyfish.la '/<>/debian/tmp/usr/lib/perl/5.38.0' libtool: warning: relinking 'swig/perl5/jellyfish.la' libtool: install: (cd /<>; /bin/bash "/<>/libtool" --tag CXX --mode=relink g++ -I/<>/debian/tmp/usr/include -Werror -Wno-error -std=c++11 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection "-fdebug-prefix-map=/<>=/usr/src/jellyfish-2.3.1-3~ppa1" -Wno-nonnull -module -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -lpthread -o swig/perl5/jellyfish.la -rpath /usr/lib/perl/5.38.0 swig/perl5/swig_perl5_jellyfish_la-swig_wrap.lo libjellyfish-2.0.la -inst-prefix-dir /<>/debian/tmp) libtool: relink: g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/x86_64-linux-gnu/13/../../../x86_64-linux-gnu/crti.o /usr/lib/gcc/x86_64-linux-gnu/13/crtbeginS.o swig/perl5/.libs/swig_perl5_jellyfish_la-swig_wrap.o -lpthread -L/<>/debian/tmp/usr/lib/x86_64-linux-gnu -L/usr/lib/x86_64-linux-gnu -ljellyfish-2.0 -L/usr/lib/gcc/x86_64-linux-gnu/13 -L/usr/lib/gcc/x86_64-linux-gnu/13/../../../x86_64-linux-gnu -L/usr/lib/gcc/x86_64-linux-gnu/13/../../../../lib -L/lib/x86_64-linux-gnu -L/lib/../lib -L/usr/lib/../lib -L/usr/lib/gcc/x86_64-linux-gnu/13/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/x86_64-linux-gnu/13/crtendS.o /usr/lib/gcc/x86_64-linux-gnu/13/../../../x86_64-linux-gnu/crtn.o -g -O2 -mno-omit-leaf-frame-pointer -flto=auto -fstack-protector-strong -Wl,-Bsymbolic-functions -flto=auto -Wl,-z -Wl,relro -Wl,-z -Wl,now -Wl,-soname -Wl,jellyfish.so.0 -o swig/perl5/.libs/jellyfish.so.0.0.0 libtool: install: /usr/bin/install -c swig/perl5/.libs/jellyfish.so.0.0.0T /<>/debian/tmp/usr/lib/perl/5.38.0/jellyfish.so.0.0.0 libtool: install: (cd /<>/debian/tmp/usr/lib/perl/5.38.0 && { ln -s -f jellyfish.so.0.0.0 jellyfish.so.0 || { rm -f jellyfish.so.0 && ln -s jellyfish.so.0.0.0 jellyfish.so.0; }; }) libtool: install: (cd /<>/debian/tmp/usr/lib/perl/5.38.0 && { ln -s -f jellyfish.so.0.0.0 jellyfish.so || { rm -f jellyfish.so && ln -s jellyfish.so.0.0.0 jellyfish.so; }; }) libtool: install: /usr/bin/install -c swig/perl5/.libs/jellyfish.lai /<>/debian/tmp/usr/lib/perl/5.38.0/jellyfish.la libtool: install: /usr/bin/install -c swig/perl5/.libs/jellyfish.a /<>/debian/tmp/usr/lib/perl/5.38.0/jellyfish.a libtool: install: chmod 644 /<>/debian/tmp/usr/lib/perl/5.38.0/jellyfish.a libtool: install: ranlib /<>/debian/tmp/usr/lib/perl/5.38.0/jellyfish.a libtool: warning: remember to run 'libtool --finish /usr/lib/perl/5.38.0' /usr/bin/mkdir -p '/<>/debian/tmp/usr/lib/perl/5.38.0' /usr/bin/install -c swig/perl5/jellyfish.pm '/<>/debian/tmp/usr/lib/perl/5.38.0' /usr/bin/mkdir -p '/<>/debian/tmp/usr/lib/x86_64-linux-gnu/pkgconfig' /usr/bin/install -c -m 644 jellyfish-2.0.pc '/<>/debian/tmp/usr/lib/x86_64-linux-gnu/pkgconfig' /usr/bin/mkdir -p '/<>/debian/tmp/usr/lib/python3.12/site-packages/dna_jellyfish' /bin/bash ./libtool --mode=install /usr/bin/install -c swig/python/_dna_jellyfish.la '/<>/debian/tmp/usr/lib/python3.12/site-packages/dna_jellyfish' libtool: warning: relinking 'swig/python/_dna_jellyfish.la' libtool: install: (cd /<>; /bin/bash "/<>/libtool" --tag CXX --mode=relink g++ -I/<>/debian/tmp/usr/include -Werror -std=c++11 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection "-fdebug-prefix-map=/<>=/usr/src/jellyfish-2.3.1-3~ppa1" -Wno-nonnull -module -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -lpthread -o swig/python/_dna_jellyfish.la -rpath /usr/lib/python3.12/site-packages/dna_jellyfish swig/python/swig_python__dna_jellyfish_la-swig_wrap.lo libjellyfish-2.0.la -inst-prefix-dir /<>/debian/tmp) libtool: relink: g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/x86_64-linux-gnu/13/../../../x86_64-linux-gnu/crti.o /usr/lib/gcc/x86_64-linux-gnu/13/crtbeginS.o swig/python/.libs/swig_python__dna_jellyfish_la-swig_wrap.o -lpthread -L/<>/debian/tmp/usr/lib/x86_64-linux-gnu -L/usr/lib/x86_64-linux-gnu -ljellyfish-2.0 -L/usr/lib/gcc/x86_64-linux-gnu/13 -L/usr/lib/gcc/x86_64-linux-gnu/13/../../../x86_64-linux-gnu -L/usr/lib/gcc/x86_64-linux-gnu/13/../../../../lib -L/lib/x86_64-linux-gnu -L/lib/../lib -L/usr/lib/../lib -L/usr/lib/gcc/x86_64-linux-gnu/13/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/x86_64-linux-gnu/13/crtendS.o /usr/lib/gcc/x86_64-linux-gnu/13/../../../x86_64-linux-gnu/crtn.o -g -O2 -mno-omit-leaf-frame-pointer -flto=auto -fstack-protector-strong -Wl,-Bsymbolic-functions -flto=auto -Wl,-z -Wl,relro -Wl,-z -Wl,now -Wl,-soname -Wl,_dna_jellyfish.so.0 -o swig/python/.libs/_dna_jellyfish.so.0.0.0 libtool: install: /usr/bin/install -c swig/python/.libs/_dna_jellyfish.so.0.0.0T /<>/debian/tmp/usr/lib/python3.12/site-packages/dna_jellyfish/_dna_jellyfish.so.0.0.0 libtool: install: (cd /<>/debian/tmp/usr/lib/python3.12/site-packages/dna_jellyfish && { ln -s -f _dna_jellyfish.so.0.0.0 _dna_jellyfish.so.0 || { rm -f _dna_jellyfish.so.0 && ln -s _dna_jellyfish.so.0.0.0 _dna_jellyfish.so.0; }; }) libtool: install: (cd /<>/debian/tmp/usr/lib/python3.12/site-packages/dna_jellyfish && { ln -s -f _dna_jellyfish.so.0.0.0 _dna_jellyfish.so || { rm -f _dna_jellyfish.so && ln -s _dna_jellyfish.so.0.0.0 _dna_jellyfish.so; }; }) libtool: install: /usr/bin/install -c swig/python/.libs/_dna_jellyfish.lai /<>/debian/tmp/usr/lib/python3.12/site-packages/dna_jellyfish/_dna_jellyfish.la libtool: install: /usr/bin/install -c swig/python/.libs/_dna_jellyfish.a /<>/debian/tmp/usr/lib/python3.12/site-packages/dna_jellyfish/_dna_jellyfish.a libtool: install: chmod 644 /<>/debian/tmp/usr/lib/python3.12/site-packages/dna_jellyfish/_dna_jellyfish.a libtool: install: ranlib /<>/debian/tmp/usr/lib/python3.12/site-packages/dna_jellyfish/_dna_jellyfish.a libtool: warning: remember to run 'libtool --finish /usr/lib/python3.12/site-packages/dna_jellyfish' /usr/bin/mkdir -p '/<>/debian/tmp/usr/lib/python3.12/site-packages/dna_jellyfish' /usr/bin/install -c swig/python/__init__.pyc '/<>/debian/tmp/usr/lib/python3.12/site-packages/dna_jellyfish' make[2]: Leaving directory '/<>' dh_auto_build --sourcedirectory=swig/perl5 cd swig/perl5 && make -j4 make[2]: Entering directory '/<>/swig/perl5' Running Mkbootstrap for jellyfish () g++ -c -std=c++0x -I/<>/debian/tmp/usr/include/jellyfish-2.3.1 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/jellyfish-2.3.1-3~ppa1 -Wdate-time -D_FORTIFY_SOURCE=3 -DVERSION=\"0.0.1\" -DXS_VERSION=\"0.0.1\" -fPIC "-I/usr/lib/x86_64-linux-gnu/perl/5.38/CORE" swig_wrap.cpp chmod 644 "jellyfish.bs" "/usr/bin/perl" -MExtUtils::Command::MM -e 'cp_nonempty' -- jellyfish.bs blib/arch/auto/jellyfish/jellyfish.bs 644 rm -f blib/arch/auto/jellyfish/jellyfish.so x86_64-linux-gnu-gcc -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/jellyfish-2.3.1-3~ppa1 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -lpthread -shared -L/usr/local/lib -fstack-protector-strong swig_wrap.o -o blib/arch/auto/jellyfish/jellyfish.so \ -lpthread \ chmod 755 blib/arch/auto/jellyfish/jellyfish.so make[2]: Leaving directory '/<>/swig/perl5' dh_auto_build --sourcedirectory=swig/python --buildsystem=pybuild I: pybuild base:305: /usr/bin/python3 setup.py build build_ext -L/<>/.libs running build running build_py copying dna_jellyfish.py -> /<>/.pybuild/cpython3_3.12_dna_jellyfish/build running build_ext building '_dna_jellyfish' extension creating build creating build/temp.linux-x86_64-cpython-312 x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/jellyfish-2.3.1-3~ppa1 -Wdate-time -D_FORTIFY_SOURCE=3 -fPIC -I/<>/debian/tmp/usr/include/jellyfish-2.3.1 -I/usr/include/python3.12 -c swig_wrap.cpp -o build/temp.linux-x86_64-cpython-312/swig_wrap.o -std=c++0x x86_64-linux-gnu-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -lpthread -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/jellyfish-2.3.1-3~ppa1 -Wdate-time -D_FORTIFY_SOURCE=3 build/temp.linux-x86_64-cpython-312/swig_wrap.o -L-L/<>/debian/tmp/usr/lib/x86_64-linux-gnu -L/<>/.libs -L/usr/lib/x86_64-linux-gnu -ljellyfish-2.0 -lpthread -o /<>/.pybuild/cpython3_3.12_dna_jellyfish/build/_dna_jellyfish.cpython-312-x86_64-linux-gnu.so -Wl,-rpath,-L/<>/debian/tmp/usr/lib/x86_64-linux-gnu make[1]: Leaving directory '/<>' debian/rules override_dh_auto_test make[1]: Entering directory '/<>' if ! dh_auto_test \ ; then echo "E: tests failed, ./test-suite.log follows:" \ ; cat ./test-suite.log \ ; echo "E: end of ./test-suite.log after test failure." \ ; exit 1 \ ; fi make -j4 check "TESTSUITEFLAGS=-j4 --verbose" VERBOSE=1 make[2]: Entering directory '/<>' make check-am make[3]: Entering directory '/<>' make bin/generate_sequence bin/fastq2sam bin/test_all libgtest.la libgtest_main.la make[4]: Entering directory '/<>' make[4]: 'bin/generate_sequence' is up to date. make[4]: 'bin/fastq2sam' is up to date. make[4]: 'bin/test_all' is up to date. make[4]: 'libgtest.la' is up to date. /bin/bash ./libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=3 -I./unit_tests -std=c++11 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/jellyfish-2.3.1-3~ppa1 -Wno-nonnull -c -o unit_tests/gtest/src/libgtest_main_la-gtest_main.lo `test -f 'unit_tests/gtest/src/gtest_main.cc' || echo './'`unit_tests/gtest/src/gtest_main.cc libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=3 -I./unit_tests -std=c++11 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection "-fdebug-prefix-map=/<>=/usr/src/jellyfish-2.3.1-3~ppa1" -Wno-nonnull -c unit_tests/gtest/src/gtest_main.cc -fPIC -DPIC -o unit_tests/gtest/src/.libs/libgtest_main_la-gtest_main.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=3 -I./unit_tests -std=c++11 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection "-fdebug-prefix-map=/<>=/usr/src/jellyfish-2.3.1-3~ppa1" -Wno-nonnull -c unit_tests/gtest/src/gtest_main.cc -o unit_tests/gtest/src/libgtest_main_la-gtest_main.o >/dev/null 2>&1 /bin/bash ./libtool --tag=CXX --mode=link g++ -I./unit_tests -std=c++11 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/jellyfish-2.3.1-3~ppa1 -Wno-nonnull -pthread -L/<>/debian/tmp/usr/lib/x86_64-linux-gnu -lhts -R/<>/debian/tmp/usr/lib/x86_64-linux-gnu -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -lpthread -o libgtest_main.la unit_tests/gtest/src/libgtest_main_la-gtest_main.lo libgtest.la libtool: link: (cd .libs/libgtest_main.lax/libgtest.a && ar x "/<>/./.libs/libgtest.a") libtool: link: ar cr .libs/libgtest_main.a unit_tests/gtest/src/.libs/libgtest_main_la-gtest_main.o .libs/libgtest_main.lax/libgtest.a/libgtest_la-gtest-all.o libtool: link: ranlib .libs/libgtest_main.a libtool: link: rm -fr .libs/libgtest_main.lax libtool: link: ( cd ".libs" && rm -f "libgtest_main.la" && ln -s "../libgtest_main.la" "libgtest_main.la" ) make[4]: Leaving directory '/<>' make check-TESTS make[4]: Entering directory '/<>' make[5]: Entering directory '/<>' SKIP: tests/big.sh PASS: tests/generate_sequence.sh PASS: tests/bloom_filter.sh PASS: tests/subset_hashing.sh PASS: tests/merge.sh PASS: tests/bloom_counter.sh PASS: tests/multi_file.sh PASS: tests/large_key.sh PASS: tests/parallel_hashing.sh PASS: tests/sam.sh SKIP: tests/swig_ruby.sh PASS: tests/swig_python.sh PASS: tests/swig_perl.sh PASS: tests/small_mers.sh PASS: unit_tests/unit_tests.sh ============================================================================ Testsuite summary for jellyfish 2.3.1 ============================================================================ # TOTAL: 15 # PASS: 13 # SKIP: 2 # XFAIL: 0 # FAIL: 0 # XPASS: 0 # ERROR: 0 ============================================================================ make[5]: Leaving directory '/<>' make[4]: Leaving directory '/<>' make[3]: Leaving directory '/<>' make[2]: Leaving directory '/<>' make[1]: Leaving directory '/<>' create-stamp debian/debhelper-build-stamp dh_prep debian/rules override_dh_auto_install make[1]: Entering directory '/<>' chrpath --delete bin/.libs/* dh_auto_install -- install-data make -j1 install DESTDIR=/<>/debian/tmp AM_UPDATE_INFO_DIR=no install-data make[2]: Entering directory '/<>' make install-am make[3]: Entering directory '/<>' make[4]: Entering directory '/<>' /usr/bin/mkdir -p '/<>/debian/tmp/usr/lib/x86_64-linux-gnu' /bin/bash ./libtool --mode=install /usr/bin/install -c libjellyfish-2.0.la '/<>/debian/tmp/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c .libs/libjellyfish-2.0.so.2.0.0 /<>/debian/tmp/usr/lib/x86_64-linux-gnu/libjellyfish-2.0.so.2.0.0 libtool: install: (cd /<>/debian/tmp/usr/lib/x86_64-linux-gnu && { ln -s -f libjellyfish-2.0.so.2.0.0 libjellyfish-2.0.so.2 || { rm -f libjellyfish-2.0.so.2 && ln -s libjellyfish-2.0.so.2.0.0 libjellyfish-2.0.so.2; }; }) libtool: install: (cd /<>/debian/tmp/usr/lib/x86_64-linux-gnu && { ln -s -f libjellyfish-2.0.so.2.0.0 libjellyfish-2.0.so || { rm -f libjellyfish-2.0.so && ln -s libjellyfish-2.0.so.2.0.0 libjellyfish-2.0.so; }; }) libtool: install: /usr/bin/install -c .libs/libjellyfish-2.0.lai /<>/debian/tmp/usr/lib/x86_64-linux-gnu/libjellyfish-2.0.la libtool: install: /usr/bin/install -c .libs/libjellyfish-2.0.a /<>/debian/tmp/usr/lib/x86_64-linux-gnu/libjellyfish-2.0.a libtool: install: chmod 644 /<>/debian/tmp/usr/lib/x86_64-linux-gnu/libjellyfish-2.0.a libtool: install: ranlib /<>/debian/tmp/usr/lib/x86_64-linux-gnu/libjellyfish-2.0.a libtool: warning: remember to run 'libtool --finish /usr/lib/x86_64-linux-gnu' /usr/bin/mkdir -p '/<>/debian/tmp/usr/bin' /bin/bash ./libtool --mode=install /usr/bin/install -c bin/jellyfish '/<>/debian/tmp/usr/bin' libtool: warning: 'libjellyfish-2.0.la' has not been installed in '/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c bin/.libs/jellyfish /<>/debian/tmp/usr/bin/jellyfish /usr/bin/mkdir -p '/<>/debian/tmp/usr/include/jellyfish-2.3.1/jellyfish' /usr/bin/install -c -m 644 include/jellyfish/allocators_mmap.hpp include/jellyfish/backtrace.hpp include/jellyfish/atomic_gcc.hpp include/jellyfish/large_hash_array.hpp include/jellyfish/err.hpp include/jellyfish/misc.hpp include/jellyfish/offsets_key_value.hpp include/jellyfish/int128.hpp include/jellyfish/rectangular_binary_matrix.hpp include/jellyfish/mer_dna.hpp include/jellyfish/storage.hpp include/jellyfish/simple_circular_buffer.hpp include/jellyfish/circular_buffer.hpp include/jellyfish/atomic_field.hpp include/jellyfish/compare_and_swap.hpp include/jellyfish/divisor.hpp include/jellyfish/large_hash_iterator.hpp include/jellyfish/jellyfish.hpp include/jellyfish/thread_exec.hpp include/jellyfish/stream_iterator.hpp include/jellyfish/mer_overlap_sequence_parser.hpp include/jellyfish/whole_sequence_parser.hpp include/jellyfish/parser_common.hpp include/jellyfish/sam_format.hpp include/jellyfish/binary_dumper.hpp include/jellyfish/sorted_dumper.hpp include/jellyfish/text_dumper.hpp include/jellyfish/dumper.hpp include/jellyfish/time.hpp include/jellyfish/mer_heap.hpp include/jellyfish/token_ring.hpp include/jellyfish/locks_pthread.hpp include/jellyfish/file_header.hpp include/jellyfish/generic_file_header.hpp include/jellyfish/json.h include/jellyfish/hash_counter.hpp include/jellyfish/mapped_file.hpp include/jellyfish/mer_dna_bloom_counter.hpp include/jellyfish/bloom_common.hpp include/jellyfish/bloom_counter2.hpp '/<>/debian/tmp/usr/include/jellyfish-2.3.1/jellyfish' /usr/bin/install -c -m 644 include/jellyfish/bloom_filter.hpp include/jellyfish/cooperative_pool.hpp include/jellyfish/cooperative_pool2.hpp include/jellyfish/stream_manager.hpp include/jellyfish/generator_manager.hpp include/jellyfish/cpp_array.hpp include/jellyfish/mer_iterator.hpp include/jellyfish/atomic_bits_array.hpp include/jellyfish/stdio_filebuf.hpp include/jellyfish/mer_qual_iterator.hpp '/<>/debian/tmp/usr/include/jellyfish-2.3.1/jellyfish' /usr/bin/mkdir -p '/<>/debian/tmp/usr/share/man/man1' /usr/bin/install -c -m 644 'doc/jellyfish.man' '/<>/debian/tmp/usr/share/man/man1/jellyfish.1' /usr/bin/mkdir -p '/<>/debian/tmp/usr/lib/perl/5.38.0' /bin/bash ./libtool --mode=install /usr/bin/install -c swig/perl5/jellyfish.la '/<>/debian/tmp/usr/lib/perl/5.38.0' libtool: warning: relinking 'swig/perl5/jellyfish.la' libtool: install: (cd /<>; /bin/bash "/<>/libtool" --tag CXX --mode=relink g++ -I/<>/debian/tmp/usr/include -Werror -Wno-error -std=c++11 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection "-fdebug-prefix-map=/<>=/usr/src/jellyfish-2.3.1-3~ppa1" -Wno-nonnull -module -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -lpthread -o swig/perl5/jellyfish.la -rpath /usr/lib/perl/5.38.0 swig/perl5/swig_perl5_jellyfish_la-swig_wrap.lo libjellyfish-2.0.la -inst-prefix-dir /<>/debian/tmp) libtool: relink: g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/x86_64-linux-gnu/13/../../../x86_64-linux-gnu/crti.o /usr/lib/gcc/x86_64-linux-gnu/13/crtbeginS.o swig/perl5/.libs/swig_perl5_jellyfish_la-swig_wrap.o -lpthread -L/<>/debian/tmp/usr/lib/x86_64-linux-gnu -L/usr/lib/x86_64-linux-gnu -ljellyfish-2.0 -L/usr/lib/gcc/x86_64-linux-gnu/13 -L/usr/lib/gcc/x86_64-linux-gnu/13/../../../x86_64-linux-gnu -L/usr/lib/gcc/x86_64-linux-gnu/13/../../../../lib -L/lib/x86_64-linux-gnu -L/lib/../lib -L/usr/lib/../lib -L/usr/lib/gcc/x86_64-linux-gnu/13/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/x86_64-linux-gnu/13/crtendS.o /usr/lib/gcc/x86_64-linux-gnu/13/../../../x86_64-linux-gnu/crtn.o -g -O2 -mno-omit-leaf-frame-pointer -flto=auto -fstack-protector-strong -Wl,-Bsymbolic-functions -flto=auto -Wl,-z -Wl,relro -Wl,-z -Wl,now -Wl,-soname -Wl,jellyfish.so.0 -o swig/perl5/.libs/jellyfish.so.0.0.0 libtool: install: /usr/bin/install -c swig/perl5/.libs/jellyfish.so.0.0.0T /<>/debian/tmp/usr/lib/perl/5.38.0/jellyfish.so.0.0.0 libtool: install: (cd /<>/debian/tmp/usr/lib/perl/5.38.0 && { ln -s -f jellyfish.so.0.0.0 jellyfish.so.0 || { rm -f jellyfish.so.0 && ln -s jellyfish.so.0.0.0 jellyfish.so.0; }; }) libtool: install: (cd /<>/debian/tmp/usr/lib/perl/5.38.0 && { ln -s -f jellyfish.so.0.0.0 jellyfish.so || { rm -f jellyfish.so && ln -s jellyfish.so.0.0.0 jellyfish.so; }; }) libtool: install: /usr/bin/install -c swig/perl5/.libs/jellyfish.lai /<>/debian/tmp/usr/lib/perl/5.38.0/jellyfish.la libtool: install: /usr/bin/install -c swig/perl5/.libs/jellyfish.a /<>/debian/tmp/usr/lib/perl/5.38.0/jellyfish.a libtool: install: chmod 644 /<>/debian/tmp/usr/lib/perl/5.38.0/jellyfish.a libtool: install: ranlib /<>/debian/tmp/usr/lib/perl/5.38.0/jellyfish.a libtool: warning: remember to run 'libtool --finish /usr/lib/perl/5.38.0' /usr/bin/mkdir -p '/<>/debian/tmp/usr/lib/perl/5.38.0' /usr/bin/install -c swig/perl5/jellyfish.pm '/<>/debian/tmp/usr/lib/perl/5.38.0' /usr/bin/mkdir -p '/<>/debian/tmp/usr/lib/x86_64-linux-gnu/pkgconfig' /usr/bin/install -c -m 644 jellyfish-2.0.pc '/<>/debian/tmp/usr/lib/x86_64-linux-gnu/pkgconfig' /usr/bin/mkdir -p '/<>/debian/tmp/usr/lib/python3.12/site-packages/dna_jellyfish' /bin/bash ./libtool --mode=install /usr/bin/install -c swig/python/_dna_jellyfish.la '/<>/debian/tmp/usr/lib/python3.12/site-packages/dna_jellyfish' libtool: warning: relinking 'swig/python/_dna_jellyfish.la' libtool: install: (cd /<>; /bin/bash "/<>/libtool" --tag CXX --mode=relink g++ -I/<>/debian/tmp/usr/include -Werror -std=c++11 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection "-fdebug-prefix-map=/<>=/usr/src/jellyfish-2.3.1-3~ppa1" -Wno-nonnull -module -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -lpthread -o swig/python/_dna_jellyfish.la -rpath /usr/lib/python3.12/site-packages/dna_jellyfish swig/python/swig_python__dna_jellyfish_la-swig_wrap.lo libjellyfish-2.0.la -inst-prefix-dir /<>/debian/tmp) libtool: relink: g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/x86_64-linux-gnu/13/../../../x86_64-linux-gnu/crti.o /usr/lib/gcc/x86_64-linux-gnu/13/crtbeginS.o swig/python/.libs/swig_python__dna_jellyfish_la-swig_wrap.o -lpthread -L/<>/debian/tmp/usr/lib/x86_64-linux-gnu -L/usr/lib/x86_64-linux-gnu -ljellyfish-2.0 -L/usr/lib/gcc/x86_64-linux-gnu/13 -L/usr/lib/gcc/x86_64-linux-gnu/13/../../../x86_64-linux-gnu -L/usr/lib/gcc/x86_64-linux-gnu/13/../../../../lib -L/lib/x86_64-linux-gnu -L/lib/../lib -L/usr/lib/../lib -L/usr/lib/gcc/x86_64-linux-gnu/13/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/x86_64-linux-gnu/13/crtendS.o /usr/lib/gcc/x86_64-linux-gnu/13/../../../x86_64-linux-gnu/crtn.o -g -O2 -mno-omit-leaf-frame-pointer -flto=auto -fstack-protector-strong -Wl,-Bsymbolic-functions -flto=auto -Wl,-z -Wl,relro -Wl,-z -Wl,now -Wl,-soname -Wl,_dna_jellyfish.so.0 -o swig/python/.libs/_dna_jellyfish.so.0.0.0 libtool: install: /usr/bin/install -c swig/python/.libs/_dna_jellyfish.so.0.0.0T /<>/debian/tmp/usr/lib/python3.12/site-packages/dna_jellyfish/_dna_jellyfish.so.0.0.0 libtool: install: (cd /<>/debian/tmp/usr/lib/python3.12/site-packages/dna_jellyfish && { ln -s -f _dna_jellyfish.so.0.0.0 _dna_jellyfish.so.0 || { rm -f _dna_jellyfish.so.0 && ln -s _dna_jellyfish.so.0.0.0 _dna_jellyfish.so.0; }; }) libtool: install: (cd /<>/debian/tmp/usr/lib/python3.12/site-packages/dna_jellyfish && { ln -s -f _dna_jellyfish.so.0.0.0 _dna_jellyfish.so || { rm -f _dna_jellyfish.so && ln -s _dna_jellyfish.so.0.0.0 _dna_jellyfish.so; }; }) libtool: install: /usr/bin/install -c swig/python/.libs/_dna_jellyfish.lai /<>/debian/tmp/usr/lib/python3.12/site-packages/dna_jellyfish/_dna_jellyfish.la libtool: install: /usr/bin/install -c swig/python/.libs/_dna_jellyfish.a /<>/debian/tmp/usr/lib/python3.12/site-packages/dna_jellyfish/_dna_jellyfish.a libtool: install: chmod 644 /<>/debian/tmp/usr/lib/python3.12/site-packages/dna_jellyfish/_dna_jellyfish.a libtool: install: ranlib /<>/debian/tmp/usr/lib/python3.12/site-packages/dna_jellyfish/_dna_jellyfish.a libtool: warning: remember to run 'libtool --finish /usr/lib/python3.12/site-packages/dna_jellyfish' /usr/bin/mkdir -p '/<>/debian/tmp/usr/lib/python3.12/site-packages/dna_jellyfish' /usr/bin/install -c swig/python/__init__.pyc '/<>/debian/tmp/usr/lib/python3.12/site-packages/dna_jellyfish' make[4]: Leaving directory '/<>' make[3]: Leaving directory '/<>' /usr/bin/mkdir -p '/<>/debian/tmp/usr/include/jellyfish-2.3.1/jellyfish' /usr/bin/install -c -m 644 include/jellyfish/allocators_mmap.hpp include/jellyfish/backtrace.hpp include/jellyfish/atomic_gcc.hpp include/jellyfish/large_hash_array.hpp include/jellyfish/err.hpp include/jellyfish/misc.hpp include/jellyfish/offsets_key_value.hpp include/jellyfish/int128.hpp include/jellyfish/rectangular_binary_matrix.hpp include/jellyfish/mer_dna.hpp include/jellyfish/storage.hpp include/jellyfish/simple_circular_buffer.hpp include/jellyfish/circular_buffer.hpp include/jellyfish/atomic_field.hpp include/jellyfish/compare_and_swap.hpp include/jellyfish/divisor.hpp include/jellyfish/large_hash_iterator.hpp include/jellyfish/jellyfish.hpp include/jellyfish/thread_exec.hpp include/jellyfish/stream_iterator.hpp include/jellyfish/mer_overlap_sequence_parser.hpp include/jellyfish/whole_sequence_parser.hpp include/jellyfish/parser_common.hpp include/jellyfish/sam_format.hpp include/jellyfish/binary_dumper.hpp include/jellyfish/sorted_dumper.hpp include/jellyfish/text_dumper.hpp include/jellyfish/dumper.hpp include/jellyfish/time.hpp include/jellyfish/mer_heap.hpp include/jellyfish/token_ring.hpp include/jellyfish/locks_pthread.hpp include/jellyfish/file_header.hpp include/jellyfish/generic_file_header.hpp include/jellyfish/json.h include/jellyfish/hash_counter.hpp include/jellyfish/mapped_file.hpp include/jellyfish/mer_dna_bloom_counter.hpp include/jellyfish/bloom_common.hpp include/jellyfish/bloom_counter2.hpp '/<>/debian/tmp/usr/include/jellyfish-2.3.1/jellyfish' /usr/bin/install -c -m 644 include/jellyfish/bloom_filter.hpp include/jellyfish/cooperative_pool.hpp include/jellyfish/cooperative_pool2.hpp include/jellyfish/stream_manager.hpp include/jellyfish/generator_manager.hpp include/jellyfish/cpp_array.hpp include/jellyfish/mer_iterator.hpp include/jellyfish/atomic_bits_array.hpp include/jellyfish/stdio_filebuf.hpp include/jellyfish/mer_qual_iterator.hpp '/<>/debian/tmp/usr/include/jellyfish-2.3.1/jellyfish' /usr/bin/mkdir -p '/<>/debian/tmp/usr/share/man/man1' /usr/bin/install -c -m 644 'doc/jellyfish.man' '/<>/debian/tmp/usr/share/man/man1/jellyfish.1' /usr/bin/mkdir -p '/<>/debian/tmp/usr/lib/x86_64-linux-gnu' /bin/bash ./libtool --mode=install /usr/bin/install -c libjellyfish-2.0.la '/<>/debian/tmp/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c .libs/libjellyfish-2.0.so.2.0.0 /<>/debian/tmp/usr/lib/x86_64-linux-gnu/libjellyfish-2.0.so.2.0.0 libtool: install: (cd /<>/debian/tmp/usr/lib/x86_64-linux-gnu && { ln -s -f libjellyfish-2.0.so.2.0.0 libjellyfish-2.0.so.2 || { rm -f libjellyfish-2.0.so.2 && ln -s libjellyfish-2.0.so.2.0.0 libjellyfish-2.0.so.2; }; }) libtool: install: (cd /<>/debian/tmp/usr/lib/x86_64-linux-gnu && { ln -s -f libjellyfish-2.0.so.2.0.0 libjellyfish-2.0.so || { rm -f libjellyfish-2.0.so && ln -s libjellyfish-2.0.so.2.0.0 libjellyfish-2.0.so; }; }) libtool: install: /usr/bin/install -c .libs/libjellyfish-2.0.lai /<>/debian/tmp/usr/lib/x86_64-linux-gnu/libjellyfish-2.0.la libtool: install: /usr/bin/install -c .libs/libjellyfish-2.0.a /<>/debian/tmp/usr/lib/x86_64-linux-gnu/libjellyfish-2.0.a libtool: install: chmod 644 /<>/debian/tmp/usr/lib/x86_64-linux-gnu/libjellyfish-2.0.a libtool: install: ranlib /<>/debian/tmp/usr/lib/x86_64-linux-gnu/libjellyfish-2.0.a libtool: warning: remember to run 'libtool --finish /usr/lib/x86_64-linux-gnu' /usr/bin/mkdir -p '/<>/debian/tmp/usr/lib/perl/5.38.0' /bin/bash ./libtool --mode=install /usr/bin/install -c swig/perl5/jellyfish.la '/<>/debian/tmp/usr/lib/perl/5.38.0' libtool: warning: relinking 'swig/perl5/jellyfish.la' libtool: install: (cd /<>; /bin/bash "/<>/libtool" --tag CXX --mode=relink g++ -I/<>/debian/tmp/usr/include -Werror -Wno-error -std=c++11 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection "-fdebug-prefix-map=/<>=/usr/src/jellyfish-2.3.1-3~ppa1" -Wno-nonnull -module -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -lpthread -o swig/perl5/jellyfish.la -rpath /usr/lib/perl/5.38.0 swig/perl5/swig_perl5_jellyfish_la-swig_wrap.lo libjellyfish-2.0.la -inst-prefix-dir /<>/debian/tmp) libtool: relink: g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/x86_64-linux-gnu/13/../../../x86_64-linux-gnu/crti.o /usr/lib/gcc/x86_64-linux-gnu/13/crtbeginS.o swig/perl5/.libs/swig_perl5_jellyfish_la-swig_wrap.o -lpthread -L/<>/debian/tmp/usr/lib/x86_64-linux-gnu -L/usr/lib/x86_64-linux-gnu -ljellyfish-2.0 -L/usr/lib/gcc/x86_64-linux-gnu/13 -L/usr/lib/gcc/x86_64-linux-gnu/13/../../../x86_64-linux-gnu -L/usr/lib/gcc/x86_64-linux-gnu/13/../../../../lib -L/lib/x86_64-linux-gnu -L/lib/../lib -L/usr/lib/../lib -L/usr/lib/gcc/x86_64-linux-gnu/13/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/x86_64-linux-gnu/13/crtendS.o /usr/lib/gcc/x86_64-linux-gnu/13/../../../x86_64-linux-gnu/crtn.o -g -O2 -mno-omit-leaf-frame-pointer -flto=auto -fstack-protector-strong -Wl,-Bsymbolic-functions -flto=auto -Wl,-z -Wl,relro -Wl,-z -Wl,now -Wl,-soname -Wl,jellyfish.so.0 -o swig/perl5/.libs/jellyfish.so.0.0.0 libtool: install: /usr/bin/install -c swig/perl5/.libs/jellyfish.so.0.0.0T /<>/debian/tmp/usr/lib/perl/5.38.0/jellyfish.so.0.0.0 libtool: install: (cd /<>/debian/tmp/usr/lib/perl/5.38.0 && { ln -s -f jellyfish.so.0.0.0 jellyfish.so.0 || { rm -f jellyfish.so.0 && ln -s jellyfish.so.0.0.0 jellyfish.so.0; }; }) libtool: install: (cd /<>/debian/tmp/usr/lib/perl/5.38.0 && { ln -s -f jellyfish.so.0.0.0 jellyfish.so || { rm -f jellyfish.so && ln -s jellyfish.so.0.0.0 jellyfish.so; }; }) libtool: install: /usr/bin/install -c swig/perl5/.libs/jellyfish.lai /<>/debian/tmp/usr/lib/perl/5.38.0/jellyfish.la libtool: install: /usr/bin/install -c swig/perl5/.libs/jellyfish.a /<>/debian/tmp/usr/lib/perl/5.38.0/jellyfish.a libtool: install: chmod 644 /<>/debian/tmp/usr/lib/perl/5.38.0/jellyfish.a libtool: install: ranlib /<>/debian/tmp/usr/lib/perl/5.38.0/jellyfish.a libtool: warning: remember to run 'libtool --finish /usr/lib/perl/5.38.0' /usr/bin/mkdir -p '/<>/debian/tmp/usr/lib/perl/5.38.0' /usr/bin/install -c swig/perl5/jellyfish.pm '/<>/debian/tmp/usr/lib/perl/5.38.0' /usr/bin/mkdir -p '/<>/debian/tmp/usr/lib/x86_64-linux-gnu/pkgconfig' /usr/bin/install -c -m 644 jellyfish-2.0.pc '/<>/debian/tmp/usr/lib/x86_64-linux-gnu/pkgconfig' /usr/bin/mkdir -p '/<>/debian/tmp/usr/lib/python3.12/site-packages/dna_jellyfish' /bin/bash ./libtool --mode=install /usr/bin/install -c swig/python/_dna_jellyfish.la '/<>/debian/tmp/usr/lib/python3.12/site-packages/dna_jellyfish' libtool: warning: relinking 'swig/python/_dna_jellyfish.la' libtool: install: (cd /<>; /bin/bash "/<>/libtool" --tag CXX --mode=relink g++ -I/<>/debian/tmp/usr/include -Werror -std=c++11 -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection "-fdebug-prefix-map=/<>=/usr/src/jellyfish-2.3.1-3~ppa1" -Wno-nonnull -module -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -lpthread -o swig/python/_dna_jellyfish.la -rpath /usr/lib/python3.12/site-packages/dna_jellyfish swig/python/swig_python__dna_jellyfish_la-swig_wrap.lo libjellyfish-2.0.la -inst-prefix-dir /<>/debian/tmp) libtool: relink: g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/x86_64-linux-gnu/13/../../../x86_64-linux-gnu/crti.o /usr/lib/gcc/x86_64-linux-gnu/13/crtbeginS.o swig/python/.libs/swig_python__dna_jellyfish_la-swig_wrap.o -lpthread -L/<>/debian/tmp/usr/lib/x86_64-linux-gnu -L/usr/lib/x86_64-linux-gnu -ljellyfish-2.0 -L/usr/lib/gcc/x86_64-linux-gnu/13 -L/usr/lib/gcc/x86_64-linux-gnu/13/../../../x86_64-linux-gnu -L/usr/lib/gcc/x86_64-linux-gnu/13/../../../../lib -L/lib/x86_64-linux-gnu -L/lib/../lib -L/usr/lib/../lib -L/usr/lib/gcc/x86_64-linux-gnu/13/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/x86_64-linux-gnu/13/crtendS.o /usr/lib/gcc/x86_64-linux-gnu/13/../../../x86_64-linux-gnu/crtn.o -g -O2 -mno-omit-leaf-frame-pointer -flto=auto -fstack-protector-strong -Wl,-Bsymbolic-functions -flto=auto -Wl,-z -Wl,relro -Wl,-z -Wl,now -Wl,-soname -Wl,_dna_jellyfish.so.0 -o swig/python/.libs/_dna_jellyfish.so.0.0.0 libtool: install: /usr/bin/install -c swig/python/.libs/_dna_jellyfish.so.0.0.0T /<>/debian/tmp/usr/lib/python3.12/site-packages/dna_jellyfish/_dna_jellyfish.so.0.0.0 libtool: install: (cd /<>/debian/tmp/usr/lib/python3.12/site-packages/dna_jellyfish && { ln -s -f _dna_jellyfish.so.0.0.0 _dna_jellyfish.so.0 || { rm -f _dna_jellyfish.so.0 && ln -s _dna_jellyfish.so.0.0.0 _dna_jellyfish.so.0; }; }) libtool: install: (cd /<>/debian/tmp/usr/lib/python3.12/site-packages/dna_jellyfish && { ln -s -f _dna_jellyfish.so.0.0.0 _dna_jellyfish.so || { rm -f _dna_jellyfish.so && ln -s _dna_jellyfish.so.0.0.0 _dna_jellyfish.so; }; }) libtool: install: /usr/bin/install -c swig/python/.libs/_dna_jellyfish.lai /<>/debian/tmp/usr/lib/python3.12/site-packages/dna_jellyfish/_dna_jellyfish.la libtool: install: /usr/bin/install -c swig/python/.libs/_dna_jellyfish.a /<>/debian/tmp/usr/lib/python3.12/site-packages/dna_jellyfish/_dna_jellyfish.a libtool: install: chmod 644 /<>/debian/tmp/usr/lib/python3.12/site-packages/dna_jellyfish/_dna_jellyfish.a libtool: install: ranlib /<>/debian/tmp/usr/lib/python3.12/site-packages/dna_jellyfish/_dna_jellyfish.a libtool: warning: remember to run 'libtool --finish /usr/lib/python3.12/site-packages/dna_jellyfish' /usr/bin/mkdir -p '/<>/debian/tmp/usr/lib/python3.12/site-packages/dna_jellyfish' /usr/bin/install -c swig/python/__init__.pyc '/<>/debian/tmp/usr/lib/python3.12/site-packages/dna_jellyfish' make[2]: Leaving directory '/<>' dh_auto_install --sourcedirectory=swig/python --buildsystem=pybuild I: pybuild base:305: /usr/bin/python3 setup.py install --root /<>/debian/python3-dna-jellyfish running install /usr/lib/python3/dist-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated. !! ******************************************************************************** Please avoid running ``setup.py`` directly. Instead, use pypa/build, pypa/installer or other standards-based tools. See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. ******************************************************************************** !! self.initialize_options() running build running build_py running build_ext running install_lib creating /<>/debian/python3-dna-jellyfish creating /<>/debian/python3-dna-jellyfish/usr creating /<>/debian/python3-dna-jellyfish/usr/lib creating /<>/debian/python3-dna-jellyfish/usr/lib/python3.12 creating /<>/debian/python3-dna-jellyfish/usr/lib/python3.12/dist-packages copying /<>/.pybuild/cpython3_3.12_dna_jellyfish/build/dna_jellyfish.py -> /<>/debian/python3-dna-jellyfish/usr/lib/python3.12/dist-packages copying /<>/.pybuild/cpython3_3.12_dna_jellyfish/build/_dna_jellyfish.cpython-312-x86_64-linux-gnu.so -> /<>/debian/python3-dna-jellyfish/usr/lib/python3.12/dist-packages byte-compiling /<>/debian/python3-dna-jellyfish/usr/lib/python3.12/dist-packages/dna_jellyfish.py to dna_jellyfish.cpython-312.pyc running install_egg_info running egg_info creating dna_jellyfish.egg-info writing dna_jellyfish.egg-info/PKG-INFO writing dependency_links to dna_jellyfish.egg-info/dependency_links.txt writing top-level names to dna_jellyfish.egg-info/top_level.txt writing manifest file 'dna_jellyfish.egg-info/SOURCES.txt' reading manifest file 'dna_jellyfish.egg-info/SOURCES.txt' writing manifest file 'dna_jellyfish.egg-info/SOURCES.txt' Copying dna_jellyfish.egg-info to /<>/debian/python3-dna-jellyfish/usr/lib/python3.12/dist-packages/dna_jellyfish-0.0.1.egg-info Skipping SOURCES.txt running install_scripts dh_auto_install --sourcedirectory=swig/perl5 cd swig/perl5 && make -j4 install DESTDIR=/<>/debian/tmp AM_UPDATE_INFO_DIR=no PREFIX=/usr make[2]: Entering directory '/<>/swig/perl5' "/usr/bin/perl" -MExtUtils::Command::MM -e 'cp_nonempty' -- jellyfish.bs blib/arch/auto/jellyfish/jellyfish.bs 644 Files found in blib/arch: installing files in blib/lib into architecture dependent library tree Installing /<>/debian/tmp/usr/lib/x86_64-linux-gnu/perl5/5.38/auto/jellyfish/jellyfish.so make[2]: Leaving directory '/<>/swig/perl5' ls -l debian/tmp/usr/lib/*/perl5/*/auto/jellyfish/jellyfish.so -r-xr-xr-x 1 buildd buildd 1117736 Mar 19 21:29 debian/tmp/usr/lib/x86_64-linux-gnu/perl5/5.38/auto/jellyfish/jellyfish.so if [ ! -e debian/tmp/usr/lib/*/perl5/*/auto/jellyfish/jellyfish.so ] ; then sleep 1; fi chmod +w debian/tmp/usr/lib/*/perl5/*/auto/jellyfish/jellyfish.so chrpath --delete debian/tmp/usr/lib/*/perl5/*/auto/jellyfish/jellyfish.so dh_install d-shlibmove --commit \ --multiarch \ --devunversioned \ --movedev "debian/tmp/usr/include/jellyfish*/jellyfish/*.hpp" usr/include/jellyfish \ --movedev "debian/tmp/usr/include/jellyfish*/jellyfish/*.h" usr/include/jellyfish \ --movedev config.h usr/include/jellyfish \ debian/tmp/usr/lib/*/libjellyfish-*.so Library package automatic movement utility set -e install -d -m 755 debian/libjellyfish-2.0-dev/usr/lib/x86_64-linux-gnu install -d -m 755 debian/libjellyfish-2.0-2/usr/lib/x86_64-linux-gnu mv debian/tmp/usr/lib/x86_64-linux-gnu/libjellyfish-2.0.a debian/libjellyfish-2.0-dev/usr/lib/x86_64-linux-gnu mv debian/tmp/usr/lib/x86_64-linux-gnu/libjellyfish-2.0.la debian/libjellyfish-2.0-dev/usr/lib/x86_64-linux-gnu || true mv debian/tmp/usr/lib/x86_64-linux-gnu/libjellyfish-2.0.so debian/libjellyfish-2.0-dev/usr/lib/x86_64-linux-gnu mv /<>/debian/tmp/usr/lib/x86_64-linux-gnu/libjellyfish-2.0.so.2 debian/libjellyfish-2.0-2/usr/lib/x86_64-linux-gnu mv /<>/debian/tmp/usr/lib/x86_64-linux-gnu/libjellyfish-2.0.so.2.0.0 debian/libjellyfish-2.0-2/usr/lib/x86_64-linux-gnu PKGDEV=libjellyfish-2.0-dev PKGSHL=libjellyfish-2.0-2 install -d -m 755 debian/libjellyfish-2.0-dev/usr/include/jellyfish mv debian/tmp/usr/include/jellyfish*/jellyfish/*.hpp debian/libjellyfish-2.0-dev/usr/include/jellyfish install -d -m 755 debian/libjellyfish-2.0-dev/usr/include/jellyfish mv debian/tmp/usr/include/jellyfish*/jellyfish/*.h debian/libjellyfish-2.0-dev/usr/include/jellyfish install -d -m 755 debian/libjellyfish-2.0-dev/usr/include/jellyfish mv config.h debian/libjellyfish-2.0-dev/usr/include/jellyfish sed -i "/dependency_libs/ s/'.*'/''/" ./debian/libjellyfish-2.0-dev/usr/lib/x86_64-linux-gnu/*.la chrpath --delete debian/*/usr/lib/python*/dist-packages/_dna_jellyfish*.so make[1]: Leaving directory '/<>' dh_install debian/rules execute_after_dh_install make[1]: Entering directory '/<>' # Fix PACKAGE_NAME defined in config.h colliding with potential reverse # dependencies autotools invocations, per lintian warning. rm -vf debian/libjellyfish-2.0-dev/usr/include/jellyfish/config.h removed 'debian/libjellyfish-2.0-dev/usr/include/jellyfish/config.h' make[1]: Leaving directory '/<>' dh_installdocs dh_installchangelogs dh_installexamples dh_installman dh_python3 dh_lintian dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms debian/rules override_dh_missing make[1]: Entering directory '/<>' # Python files are just installed rm -rf debian/tmp/usr/lib/python3/dist-packages # Necessary Perl files are just installed rm -rf debian/tmp/usr/lib/perl/5.* dh_missing make[1]: Leaving directory '/<>' dh_dwz -a dh_strip -a debugedit: debian/jellyfish/usr/lib/jellyfish/bin/fastq2sam: Unknown DWARF DW_FORM_0x1f20 0c0f98d8e691d009ebca74da1fde65c5b677d1aa 701e82b72f6d926a501df216babf0b9ccdf2d63e 375092ca1e4188a9888efaf00f4c0705577b7c12 debugedit: debian/jellyfish/usr/lib/jellyfish/bin/test_all: Unknown DWARF DW_FORM_0x1f20 f7145c561360b94a31bb590d0a79359af840ee2b debugedit: debian/jellyfish/usr/lib/jellyfish/bin/generate_sequence: Unknown DWARF DW_FORM_0x1f20 cb6608abac48ea956d5aa87e16726b14202f1deb debugedit: debian/jellyfish/usr/bin/jellyfish: Unknown DWARF DW_FORM_0x1f21 3017e0dc0858056d505396b104153897bec0905e 98992e34900480920d8ebabf7e31d5743506e382 dh_makeshlibs -a dh_shlibdeps -a dh_installdeb dh_gencontrol dpkg-gencontrol: warning: Depends field of package jellyfish-examples: substitution variable ${shlibs:Depends} used, but is not defined dh_md5sums dh_builddeb INFO: pkgstriptranslations version 154 INFO: pkgstriptranslations version 154 INFO: pkgstriptranslations version 154 pkgstriptranslations: processing libjellyfish-2.0-dev (in debian/libjellyfish-2.0-dev); do_strip: , oemstrip: pkgstriptranslations: processing jellyfish (in debian/jellyfish); do_strip: , oemstrip: pkgstriptranslations: processing libjellyfish-perl (in debian/libjellyfish-perl); 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/libjellyfish-2.0-dev/DEBIAN/control, package libjellyfish-2.0-dev, directory debian/libjellyfish-2.0-dev INFO: pkgstripfiles: waiting for lock (libjellyfish-2.0-dev) ... pkgstripfiles: processing control file: debian/jellyfish/DEBIAN/control, package jellyfish, directory debian/jellyfish Searching for duplicated docs in dependency libjellyfish-2.0-2... pkgstripfiles: processing control file: debian/libjellyfish-perl/DEBIAN/control, package libjellyfish-perl, directory debian/libjellyfish-perl symlinking changelog.Debian.gz in jellyfish to file in libjellyfish-2.0-2 INFO: pkgstripfiles: waiting for lock (libjellyfish-perl) ... pkgstripfiles: Running PNG optimization (using 4 cpus) for package jellyfish ... pkgstripfiles: No PNG files. dpkg-deb: building package 'jellyfish' in '../jellyfish_2.3.1-3~ppa1_amd64.deb'. INFO: pkgstripfiles: waiting for lock (libjellyfish-2.0-dev) ... INFO: pkgstripfiles: waiting for lock (libjellyfish-perl) ... INFO: pkgstriptranslations version 154 pkgstriptranslations: processing libjellyfish-2.0-2 (in debian/libjellyfish-2.0-2); do_strip: , oemstrip: pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/libjellyfish-2.0-2/DEBIAN/control, package libjellyfish-2.0-2, directory debian/libjellyfish-2.0-2 pkgstripfiles: Running PNG optimization (using 4 cpus) for package libjellyfish-2.0-2 ... pkgstripfiles: No PNG files. dpkg-deb: building package 'libjellyfish-2.0-2' in '../libjellyfish-2.0-2_2.3.1-3~ppa1_amd64.deb'. Searching for duplicated docs in dependency libjellyfish-2.0-2... symlinking changelog.Debian.gz in libjellyfish-2.0-dev to file in libjellyfish-2.0-2 pkgstripfiles: Running PNG optimization (using 4 cpus) for package libjellyfish-2.0-dev ... pkgstripfiles: No PNG files. dpkg-deb: building package 'libjellyfish-2.0-dev' in '../libjellyfish-2.0-dev_2.3.1-3~ppa1_amd64.deb'. INFO: pkgstripfiles: waiting for lock (libjellyfish-perl) ... INFO: pkgstriptranslations version 154 pkgstriptranslations: processing python3-dna-jellyfish (in debian/python3-dna-jellyfish); do_strip: , oemstrip: pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " INFO: pkgstripfiles: waiting for lock (libjellyfish-perl) ... pkgstripfiles: processing control file: debian/python3-dna-jellyfish/DEBIAN/control, package python3-dna-jellyfish, directory debian/python3-dna-jellyfish Searching for duplicated docs in dependency libjellyfish-2.0-2... symlinking changelog.Debian.gz in python3-dna-jellyfish to file in libjellyfish-2.0-2 pkgstripfiles: Running PNG optimization (using 4 cpus) for package python3-dna-jellyfish ... pkgstripfiles: No PNG files. dpkg-deb: building package 'python3-dna-jellyfish' in '../python3-dna-jellyfish_2.3.1-3~ppa1_amd64.deb'. pkgstripfiles: Running PNG optimization (using 4 cpus) for package libjellyfish-perl ... pkgstripfiles: No PNG files. dpkg-deb: building package 'libjellyfish-perl' in '../libjellyfish-perl_2.3.1-3~ppa1_amd64.deb'. INFO: pkgstriptranslations version 154 pkgstriptranslations: processing jellyfish-examples (in debian/jellyfish-examples); do_strip: , oemstrip: pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/jellyfish-examples/DEBIAN/control, package jellyfish-examples, directory debian/jellyfish-examples pkgstripfiles: Running PNG optimization (using 4 cpus) for package jellyfish-examples ... pkgstripfiles: No PNG files. dpkg-deb: building package 'jellyfish-examples' in '../jellyfish-examples_2.3.1-3~ppa1_all.deb'. dpkg-genbuildinfo --build=binary -O../jellyfish_2.3.1-3~ppa1_amd64.buildinfo dpkg-genchanges --build=binary -mLaunchpad Build Daemon -O../jellyfish_2.3.1-3~ppa1_amd64.changes dpkg-genchanges: warning: the current version (2.3.1-3~ppa1) is earlier than the previous one (2.3.1-3) dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) -------------------------------------------------------------------------------- Build finished at 2024-03-19T21:31:32Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ jellyfish_2.3.1-3~ppa1_amd64.changes: ------------------------------------- Format: 1.8 Date: Tue, 19 Mar 2024 21:23:13 +0000 Source: jellyfish Binary: jellyfish jellyfish-examples libjellyfish-2.0-2 libjellyfish-2.0-dev libjellyfish-perl python3-dna-jellyfish Built-For-Profiles: noudeb Architecture: all amd64 Version: 2.3.1-3~ppa1 Distribution: noble Urgency: medium Maintainer: Launchpad Build Daemon Changed-By: Graham Inggs Description: jellyfish - count k-mers in DNA sequences jellyfish-examples - count k-mers in DNA sequences (examples for testing) libjellyfish-2.0-2 - count k-mers in DNA sequences (dynamic library of jellyfish) libjellyfish-2.0-dev - count k-mers in DNA sequences (development files of jellyfish) libjellyfish-perl - count k-mers in DNA sequences (Perl bindings of jellyfish) python3-dna-jellyfish - count k-mers in DNA sequences (Python bindings of jellyfish) Changes: jellyfish (2.3.1-3~ppa1) noble; urgency=medium . * No-change backport to noble Checksums-Sha1: 958d882c6aa7f0cba9cc359e6c116e613de2f030 14032 jellyfish-examples_2.3.1-3~ppa1_all.deb a25bb314d05f6e9338858dcf9015751064533c4e 10336 jellyfish_2.3.1-3~ppa1_amd64.buildinfo f007c1194468401f110c60f9711ef2911408395b 757926 jellyfish_2.3.1-3~ppa1_amd64.deb 58eab7dc0953c89a77aa933c6fb3829e9df3541b 68762 libjellyfish-2.0-2_2.3.1-3~ppa1_amd64.deb c3f204d4da24b1603b7eea27d8ec665da5403af1 141984 libjellyfish-2.0-dev_2.3.1-3~ppa1_amd64.deb 867299cf368e0ee18d148e3b22524d0172e6e377 57596 libjellyfish-perl_2.3.1-3~ppa1_amd64.deb b9f3db7e1acc84330a5b2831e8d92b96401be94b 53310 python3-dna-jellyfish_2.3.1-3~ppa1_amd64.deb Checksums-Sha256: 66c4ae7917377041532881e5a4857858a6d51d0a3f018d1006266a63862e9833 14032 jellyfish-examples_2.3.1-3~ppa1_all.deb 27ff9eea484afb8dd7a396f8a93a7d4f42fc2878277c12945be1cffaaf40842b 10336 jellyfish_2.3.1-3~ppa1_amd64.buildinfo e857d47d17c9a7b091229258bc648d4569d6ec9f5f14a5c42a09b68837cae43f 757926 jellyfish_2.3.1-3~ppa1_amd64.deb e0886487c1aaf0f31ccfaf24698ea581b51fdfa5ab7b7f0228ed65579f1466d9 68762 libjellyfish-2.0-2_2.3.1-3~ppa1_amd64.deb 7e46ec500bbc7377ce414157d4722e4fb801e30db5e22d7d4c86cee0240eaae7 141984 libjellyfish-2.0-dev_2.3.1-3~ppa1_amd64.deb 474145535655e2971ee600c05b389b25de9015ba939becd2ff921e6c6b9b0f98 57596 libjellyfish-perl_2.3.1-3~ppa1_amd64.deb 23bb2aa44ff70a30fdb2308cfda0ee2458a0dc702b9fabb4ed7a6d84a3562705 53310 python3-dna-jellyfish_2.3.1-3~ppa1_amd64.deb Files: 45c601bd036b789806e8953a01c2836c 14032 science optional jellyfish-examples_2.3.1-3~ppa1_all.deb 677fe0dda41c6a8737422ad4b4a978fa 10336 science optional jellyfish_2.3.1-3~ppa1_amd64.buildinfo 2963f81e8061ce843cb6fd723a5fec71 757926 science optional jellyfish_2.3.1-3~ppa1_amd64.deb 50c7cc0519906abfaa776015e8efd61c 68762 libs optional libjellyfish-2.0-2_2.3.1-3~ppa1_amd64.deb c9cda63a659d87228d7fec084b917f1a 141984 libdevel optional libjellyfish-2.0-dev_2.3.1-3~ppa1_amd64.deb ac73a0ea258ebb606bf2c93ff6131963 57596 perl optional libjellyfish-perl_2.3.1-3~ppa1_amd64.deb 7070e5194d1b5805a4a73c82b9659c57 53310 python optional python3-dna-jellyfish_2.3.1-3~ppa1_amd64.deb /<>/jellyfish_2.3.1-3~ppa1_amd64.changes.new could not be renamed to /<>/jellyfish_2.3.1-3~ppa1_amd64.changes: Illegal seek Distribution field may be wrong!!! +------------------------------------------------------------------------------+ | Buildinfo | +------------------------------------------------------------------------------+ Format: 1.0 Source: jellyfish Binary: jellyfish jellyfish-examples libjellyfish-2.0-2 libjellyfish-2.0-dev libjellyfish-perl python3-dna-jellyfish Architecture: all amd64 Version: 2.3.1-3~ppa1 Checksums-Md5: 45c601bd036b789806e8953a01c2836c 14032 jellyfish-examples_2.3.1-3~ppa1_all.deb 2963f81e8061ce843cb6fd723a5fec71 757926 jellyfish_2.3.1-3~ppa1_amd64.deb 50c7cc0519906abfaa776015e8efd61c 68762 libjellyfish-2.0-2_2.3.1-3~ppa1_amd64.deb c9cda63a659d87228d7fec084b917f1a 141984 libjellyfish-2.0-dev_2.3.1-3~ppa1_amd64.deb ac73a0ea258ebb606bf2c93ff6131963 57596 libjellyfish-perl_2.3.1-3~ppa1_amd64.deb 7070e5194d1b5805a4a73c82b9659c57 53310 python3-dna-jellyfish_2.3.1-3~ppa1_amd64.deb Checksums-Sha1: 958d882c6aa7f0cba9cc359e6c116e613de2f030 14032 jellyfish-examples_2.3.1-3~ppa1_all.deb f007c1194468401f110c60f9711ef2911408395b 757926 jellyfish_2.3.1-3~ppa1_amd64.deb 58eab7dc0953c89a77aa933c6fb3829e9df3541b 68762 libjellyfish-2.0-2_2.3.1-3~ppa1_amd64.deb c3f204d4da24b1603b7eea27d8ec665da5403af1 141984 libjellyfish-2.0-dev_2.3.1-3~ppa1_amd64.deb 867299cf368e0ee18d148e3b22524d0172e6e377 57596 libjellyfish-perl_2.3.1-3~ppa1_amd64.deb b9f3db7e1acc84330a5b2831e8d92b96401be94b 53310 python3-dna-jellyfish_2.3.1-3~ppa1_amd64.deb Checksums-Sha256: 66c4ae7917377041532881e5a4857858a6d51d0a3f018d1006266a63862e9833 14032 jellyfish-examples_2.3.1-3~ppa1_all.deb e857d47d17c9a7b091229258bc648d4569d6ec9f5f14a5c42a09b68837cae43f 757926 jellyfish_2.3.1-3~ppa1_amd64.deb e0886487c1aaf0f31ccfaf24698ea581b51fdfa5ab7b7f0228ed65579f1466d9 68762 libjellyfish-2.0-2_2.3.1-3~ppa1_amd64.deb 7e46ec500bbc7377ce414157d4722e4fb801e30db5e22d7d4c86cee0240eaae7 141984 libjellyfish-2.0-dev_2.3.1-3~ppa1_amd64.deb 474145535655e2971ee600c05b389b25de9015ba939becd2ff921e6c6b9b0f98 57596 libjellyfish-perl_2.3.1-3~ppa1_amd64.deb 23bb2aa44ff70a30fdb2308cfda0ee2458a0dc702b9fabb4ed7a6d84a3562705 53310 python3-dna-jellyfish_2.3.1-3~ppa1_amd64.deb Build-Origin: Ubuntu Build-Architecture: amd64 Build-Date: Tue, 19 Mar 2024 21:31:32 +0000 Build-Path: /<> Build-Tainted-By: merged-usr-via-aliased-dirs usr-local-has-programs Installed-Build-Depends: adduser (= 3.137ubuntu1), apt (= 2.7.3), architecture-properties (= 0.1.1), autoconf (= 2.71-3), autoconf-archive (= 20220903-3), automake (= 1:1.16.5-1.3ubuntu1), autopoint (= 0.21-14ubuntu1), autotools-dev (= 20220109.1), base-files (= 13ubuntu7), base-passwd (= 3.6.3), bash (= 5.2.21-2ubuntu2), bc (= 1.07.1-3ubuntu2), binutils (= 2.42-3ubuntu1), binutils-common (= 2.42-3ubuntu1), binutils-x86-64-linux-gnu (= 2.42-3ubuntu1), bsdextrautils (= 2.39.3-9ubuntu2), bsdutils (= 1:2.39.3-9ubuntu2), build-essential (= 12.10ubuntu1), bzip2 (= 1.0.8-5ubuntu1), ca-certificates (= 20240203), chrpath (= 0.16-2build1), coreutils (= 9.4-3ubuntu3), cpp (= 4:13.2.0-7ubuntu1), cpp-13 (= 13.2.0-19ubuntu1), cpp-13-x86-64-linux-gnu (= 13.2.0-19ubuntu1), cpp-x86-64-linux-gnu (= 4:13.2.0-7ubuntu1), d-shlibs (= 0.106), dash (= 0.5.12-6ubuntu4), debconf (= 1.5.86), debhelper (= 13.14.1ubuntu5), debianutils (= 5.17), debugedit (= 1:5.0-5), dh-autoreconf (= 20), dh-python (= 6.20231223ubuntu2), dh-strip-nondeterminism (= 1.13.1-1), diffutils (= 1:3.10-1), dos2unix (= 7.5.1-1), dpkg (= 1.22.6ubuntu4), dpkg-dev (= 1.22.6ubuntu4), dwz (= 0.15-1build5), file (= 1:5.45-3), findutils (= 4.9.0-5), g++ (= 4:13.2.0-7ubuntu1), g++-13 (= 13.2.0-19ubuntu1), g++-13-x86-64-linux-gnu (= 13.2.0-19ubuntu1), g++-x86-64-linux-gnu (= 4:13.2.0-7ubuntu1), gcc (= 4:13.2.0-7ubuntu1), gcc-13 (= 13.2.0-19ubuntu1), gcc-13-base (= 13.2.0-19ubuntu1), gcc-13-x86-64-linux-gnu (= 13.2.0-19ubuntu1), gcc-14-base (= 14-20240315-1ubuntu1), gcc-x86-64-linux-gnu (= 4:13.2.0-7ubuntu1), gettext (= 0.21-14ubuntu1), gettext-base (= 0.21-14ubuntu1), gpgv (= 2.4.4-2ubuntu15), grep (= 3.11-4), groff-base (= 1.23.0-3build1), gzip (= 1.12-1ubuntu2), hostname (= 3.23+nmu2ubuntu1), init-system-helpers (= 1.66ubuntu1), intltool-debian (= 0.35.0+20060710.6), libacl1 (= 2.3.2-1), libapt-pkg6.0t64 (= 2.7.13ubuntu1), libarchive-zip-perl (= 1.68-1), libasan8 (= 14-20240315-1ubuntu1), libassuan0 (= 2.5.6-1), libatomic1 (= 14-20240315-1ubuntu1), libattr1 (= 1:2.5.2-1), libaudit-common (= 1:3.1.2-2.1), libaudit1 (= 1:3.1.2-2.1), libbinutils (= 2.42-3ubuntu1), libblkid1 (= 2.39.3-9ubuntu2), libbrotli1 (= 1.1.0-2build1), libbsd0 (= 0.12.1-1), libbz2-1.0 (= 1.0.8-5ubuntu1), libc-bin (= 2.39-0ubuntu6), libc-dev-bin (= 2.39-0ubuntu6), libc6 (= 2.39-0ubuntu6), libc6-dev (= 2.39-0ubuntu6), libcap-ng0 (= 0.8.4-2build1), libcap2 (= 1:2.66-5ubuntu1), libcc1-0 (= 14-20240315-1ubuntu1), libcom-err2 (= 1.47.0-2.4~exp1ubuntu2), libcrypt-dev (= 1:4.4.36-4), libcrypt1 (= 1:4.4.36-4), libctf-nobfd0 (= 2.42-3ubuntu1), libctf0 (= 2.42-3ubuntu1), libcurl3t64-gnutls (= 8.5.0-2ubuntu7), libcurl4-gnutls-dev (= 8.5.0-2ubuntu7), libdb5.3t64 (= 5.3.28+dfsg2-5build1), libdebconfclient0 (= 0.271ubuntu2), libdebhelper-perl (= 13.14.1ubuntu5), libdeflate-dev (= 1.19-1), libdeflate0 (= 1.19-1), libdpkg-perl (= 1.22.6ubuntu4), libdw1t64 (= 0.190-1.1build2), libedit2 (= 3.1-20230828-1), libelf1t64 (= 0.190-1.1build2), libexpat1 (= 2.6.1-2), libexpat1-dev (= 2.6.1-2), 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+------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ jellyfish-examples_2.3.1-3~ppa1_all.deb --------------------------------------- new Debian package, version 2.0. size 14032 bytes: control archive=1818 bytes. 1257 bytes, 28 lines control 3053 bytes, 33 lines md5sums Package: jellyfish-examples Source: jellyfish Version: 2.3.1-3~ppa1 Architecture: all Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 59 Recommends: jellyfish Section: science Priority: optional Multi-Arch: foreign Homepage: https://www.genome.umd.edu/jellyfish.html Description: count k-mers in DNA sequences (examples for testing) JELLYFISH is a tool for fast, memory-efficient counting of k-mers in DNA. A k-mer is a substring of length k, and counting the occurrences of all such substrings is a central step in many analyses of DNA sequence. JELLYFISH can count k-mers using an order of magnitude less memory and an order of magnitude faster than other k-mer counting packages by using an efficient encoding of a hash table and by exploiting the "compare-and-swap" CPU instruction to increase parallelism. . JELLYFISH is a command-line program that reads FASTA and multi-FASTA files containing DNA sequences. It outputs its k-mer counts in an binary format, which can be translated into a human-readable text format using the "jellyfish dump" command. . This package contains examples to test the package drwxr-xr-x root/root 0 2024-03-19 21:23 ./ drwxr-xr-x root/root 0 2024-03-19 21:23 ./usr/ drwxr-xr-x root/root 0 2024-03-19 21:23 ./usr/lib/ drwxr-xr-x root/root 0 2024-03-19 21:23 ./usr/lib/jellyfish/ drwxr-xr-x root/root 0 2024-03-19 21:23 ./usr/lib/jellyfish/bin/ lrwxrwxrwx root/root 0 2024-03-19 21:23 ./usr/lib/jellyfish/bin/jellyfish -> ../../../bin/jellyfish drwxr-xr-x root/root 0 2024-03-19 21:23 ./usr/share/ drwxr-xr-x root/root 0 2024-03-19 21:23 ./usr/share/doc/ drwxr-xr-x root/root 0 2024-03-19 21:23 ./usr/share/doc/jellyfish-examples/ -rw-r--r-- root/root 2834 2024-03-19 21:23 ./usr/share/doc/jellyfish-examples/changelog.Debian.gz -rw-r--r-- root/root 6395 2024-03-19 17:20 ./usr/share/doc/jellyfish-examples/copyright drwxr-xr-x root/root 0 2024-03-19 21:23 ./usr/share/doc/jellyfish-examples/examples/ -rw-r--r-- root/root 809 2023-12-06 21:50 ./usr/share/doc/jellyfish-examples/examples/big.sh -rw-r--r-- root/root 1535 2023-12-06 21:50 ./usr/share/doc/jellyfish-examples/examples/bloom_counter.sh -rw-r--r-- root/root 931 2023-12-06 21:50 ./usr/share/doc/jellyfish-examples/examples/bloom_filter.sh -rw-r--r-- root/root 695 2024-03-19 21:23 ./usr/share/doc/jellyfish-examples/examples/compat.sh -rw-r--r-- root/root 755 2023-12-06 21:50 ./usr/share/doc/jellyfish-examples/examples/from_stream.sh -rw-r--r-- root/root 567 2023-12-06 21:50 ./usr/share/doc/jellyfish-examples/examples/from_stream_fastq.sh -rw-r--r-- root/root 227 2023-12-06 21:50 ./usr/share/doc/jellyfish-examples/examples/generate_fastq_sequence.sh -rwxr-xr-x root/root 620 2023-12-06 21:50 ./usr/share/doc/jellyfish-examples/examples/generate_sequence.sh -rw-r--r-- root/root 837 2023-12-06 21:50 ./usr/share/doc/jellyfish-examples/examples/large_key.sh -rw-r--r-- root/root 1954 2023-12-06 21:50 ./usr/share/doc/jellyfish-examples/examples/merge.sh -rw-r--r-- root/root 454 2023-12-06 21:50 ./usr/share/doc/jellyfish-examples/examples/min_qual.sh -rw-r--r-- root/root 1286 2023-12-06 21:50 ./usr/share/doc/jellyfish-examples/examples/multi_file.sh -rw-r--r-- root/root 544 2023-12-06 21:50 ./usr/share/doc/jellyfish-examples/examples/multi_file_fastq.sh -rwxr-xr-x root/root 891 2023-12-06 21:50 ./usr/share/doc/jellyfish-examples/examples/parallel_direct_indexing.sh -rw-r--r-- root/root 798 2023-12-06 21:50 ./usr/share/doc/jellyfish-examples/examples/parallel_fastq_direct_indexing.sh -rw-r--r-- root/root 629 2023-12-06 21:50 ./usr/share/doc/jellyfish-examples/examples/parallel_fastq_hashing.sh -rw-r--r-- root/root 541 2023-12-06 21:50 ./usr/share/doc/jellyfish-examples/examples/parallel_fastq_sequence_hashing.sh -rwxr-xr-x root/root 3795 2023-12-06 21:50 ./usr/share/doc/jellyfish-examples/examples/parallel_hashing.sh -rw-r--r-- root/root 309 2023-12-06 21:50 ./usr/share/doc/jellyfish-examples/examples/parsers.sh -rw-r--r-- root/root 881 2023-12-06 21:50 ./usr/share/doc/jellyfish-examples/examples/quality_filter.sh -rw-r--r-- root/root 863 2023-12-06 21:50 ./usr/share/doc/jellyfish-examples/examples/raw_hash.sh -rw-r--r-- root/root 1242 2023-12-06 21:50 ./usr/share/doc/jellyfish-examples/examples/sam.sh -rwxr-xr-x root/root 427 2023-12-06 21:50 ./usr/share/doc/jellyfish-examples/examples/serial_direct_indexing.sh -rwxr-xr-x root/root 541 2023-12-06 21:50 ./usr/share/doc/jellyfish-examples/examples/serial_hashing.sh -rwxr-xr-x root/root 540 2023-12-06 21:50 ./usr/share/doc/jellyfish-examples/examples/small.sh -rw-r--r-- root/root 455 2024-03-19 21:23 ./usr/share/doc/jellyfish-examples/examples/small_mers.sh -rw-r--r-- root/root 696 2023-12-06 21:50 ./usr/share/doc/jellyfish-examples/examples/subset_hashing.sh -rw-r--r-- root/root 536 2023-12-06 21:50 ./usr/share/doc/jellyfish-examples/examples/swig_perl.sh -rw-r--r-- root/root 595 2023-12-06 21:50 ./usr/share/doc/jellyfish-examples/examples/swig_python.sh -rw-r--r-- root/root 490 2023-12-06 21:50 ./usr/share/doc/jellyfish-examples/examples/swig_ruby.sh -rw-r--r-- root/root 132 2023-12-06 21:50 ./usr/share/doc/jellyfish-examples/examples/unit_tests.sh jellyfish_2.3.1-3~ppa1_amd64.deb -------------------------------- new Debian package, version 2.0. size 757926 bytes: control archive=1217 bytes. 1242 bytes, 24 lines control 755 bytes, 11 lines md5sums Package: jellyfish Version: 2.3.1-3~ppa1 Architecture: amd64 Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 2149 Depends: libc6 (>= 2.38), libgcc-s1 (>= 3.3.1), libhts3t64 (>= 1.17), libjellyfish-2.0-2 (= 2.3.1-3~ppa1), libstdc++6 (>= 13.1) Section: science Priority: optional Homepage: https://www.genome.umd.edu/jellyfish.html Description: count k-mers in DNA sequences JELLYFISH is a tool for fast, memory-efficient counting of k-mers in DNA. A k-mer is a substring of length k, and counting the occurrences of all such substrings is a central step in many analyses of DNA sequence. JELLYFISH can count k-mers using an order of magnitude less memory and an order of magnitude faster than other k-mer counting packages by using an efficient encoding of a hash table and by exploiting the "compare-and-swap" CPU instruction to increase parallelism. . JELLYFISH is a command-line program that reads FASTA and multi-FASTA files containing DNA sequences. It outputs its k-mer counts in an binary format, which can be translated into a human-readable text format using the "jellyfish dump" command. drwxr-xr-x root/root 0 2024-03-19 21:23 ./ drwxr-xr-x root/root 0 2024-03-19 21:23 ./usr/ drwxr-xr-x root/root 0 2024-03-19 21:23 ./usr/bin/ -rwxr-xr-x root/root 281936 2024-03-19 21:23 ./usr/bin/jellyfish drwxr-xr-x root/root 0 2024-03-19 21:23 ./usr/lib/ drwxr-xr-x root/root 0 2024-03-19 21:23 ./usr/lib/jellyfish/ drwxr-xr-x root/root 0 2024-03-19 21:23 ./usr/lib/jellyfish/bin/ -rwxr-xr-x root/root 23072 2024-03-19 21:23 ./usr/lib/jellyfish/bin/fastq2sam -rwxr-xr-x root/root 31464 2024-03-19 21:23 ./usr/lib/jellyfish/bin/generate_sequence -rwxr-xr-x root/root 1604376 2024-03-19 21:23 ./usr/lib/jellyfish/bin/test_all drwxr-xr-x root/root 0 2024-03-19 21:23 ./usr/share/ drwxr-xr-x root/root 0 2024-03-19 21:23 ./usr/share/doc-base/ -rw-r--r-- root/root 987 2019-09-27 12:56 ./usr/share/doc-base/jellyfish.jellyfish drwxr-xr-x root/root 0 2024-03-19 21:23 ./usr/share/doc/ drwxr-xr-x root/root 0 2024-03-19 21:23 ./usr/share/doc/jellyfish/ -rw-r--r-- root/root 321 2019-09-27 12:56 ./usr/share/doc/jellyfish/README.test lrwxrwxrwx root/root 0 2024-03-19 21:23 ./usr/share/doc/jellyfish/changelog.Debian.gz -> ../libjellyfish-2.0-2/changelog.Debian.gz -rw-r--r-- root/root 6395 2024-03-19 17:20 ./usr/share/doc/jellyfish/copyright -rw-r--r-- root/root 221453 2023-12-06 21:50 ./usr/share/doc/jellyfish/jellyfish.pdf.gz -rw-r--r-- root/root 1665 2024-02-28 13:56 ./usr/share/doc/jellyfish/run-unit-test drwxr-xr-x root/root 0 2024-03-19 21:23 ./usr/share/lintian/ drwxr-xr-x root/root 0 2024-03-19 21:23 ./usr/share/lintian/overrides/ -rw-r--r-- root/root 144 2024-02-28 13:56 ./usr/share/lintian/overrides/jellyfish drwxr-xr-x root/root 0 2024-03-19 21:23 ./usr/share/man/ drwxr-xr-x root/root 0 2024-03-19 21:23 ./usr/share/man/man1/ -rw-r--r-- root/root 4554 2024-03-19 21:23 ./usr/share/man/man1/jellyfish.1.gz libjellyfish-2.0-2_2.3.1-3~ppa1_amd64.deb ----------------------------------------- new Debian package, version 2.0. size 68762 bytes: control archive=1199 bytes. 1461 bytes, 32 lines control 330 bytes, 4 lines md5sums 49 bytes, 1 lines shlibs 75 bytes, 2 lines triggers Package: libjellyfish-2.0-2 Source: jellyfish Version: 2.3.1-3~ppa1 Architecture: amd64 Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 187 Depends: libc6 (>= 2.38), libgcc-s1 (>= 3.3.1), libstdc++6 (>= 13.1) Conflicts: libjellyfish-2.0-2t64 Replaces: libjellyfish-2.0-2t64 Provides: libjellfish-2.0-2t64 (= 2.3.1-3~ppa1) Section: libs Priority: optional Multi-Arch: same Homepage: https://www.genome.umd.edu/jellyfish.html Description: count k-mers in DNA sequences (dynamic library of jellyfish) JELLYFISH is a tool for fast, memory-efficient counting of k-mers in DNA. A k-mer is a substring of length k, and counting the occurrences of all such substrings is a central step in many analyses of DNA sequence. JELLYFISH can count k-mers using an order of magnitude less memory and an order of magnitude faster than other k-mer counting packages by using an efficient encoding of a hash table and by exploiting the "compare-and-swap" CPU instruction to increase parallelism. . JELLYFISH is a command-line program that reads FASTA and multi-FASTA files containing DNA sequences. It outputs its k-mer counts in an binary format, which can be translated into a human-readable text format using the "jellyfish dump" command. . This package contains the dynamic library the main executable of jellyfish is linked to. drwxr-xr-x root/root 0 2024-03-19 21:23 ./ drwxr-xr-x root/root 0 2024-03-19 21:23 ./usr/ drwxr-xr-x root/root 0 2024-03-19 21:23 ./usr/lib/ drwxr-xr-x root/root 0 2024-03-19 21:23 ./usr/lib/x86_64-linux-gnu/ lrwxrwxrwx root/root 0 2024-03-19 21:23 ./usr/lib/x86_64-linux-gnu/libjellyfish-2.0.so.2 -> libjellyfish-2.0.so.2.0.0 -rw-r--r-- root/root 166072 2024-03-19 21:23 ./usr/lib/x86_64-linux-gnu/libjellyfish-2.0.so.2.0.0 drwxr-xr-x root/root 0 2024-03-19 21:23 ./usr/share/ drwxr-xr-x root/root 0 2024-03-19 21:23 ./usr/share/doc/ drwxr-xr-x root/root 0 2024-03-19 21:23 ./usr/share/doc/libjellyfish-2.0-2/ -rw-r--r-- root/root 2834 2024-03-19 21:23 ./usr/share/doc/libjellyfish-2.0-2/changelog.Debian.gz -rw-r--r-- root/root 6395 2024-03-19 17:20 ./usr/share/doc/libjellyfish-2.0-2/copyright drwxr-xr-x root/root 0 2024-03-19 21:23 ./usr/share/lintian/ drwxr-xr-x root/root 0 2024-03-19 21:23 ./usr/share/lintian/overrides/ -rw-r--r-- root/root 178 2024-03-19 17:17 ./usr/share/lintian/overrides/libjellyfish-2.0-2 libjellyfish-2.0-dev_2.3.1-3~ppa1_amd64.deb ------------------------------------------- new Debian package, version 2.0. size 141984 bytes: control archive=2463 bytes. 1304 bytes, 28 lines control 4012 bytes, 54 lines md5sums Package: libjellyfish-2.0-dev Source: jellyfish Version: 2.3.1-3~ppa1 Architecture: amd64 Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 688 Depends: libjellyfish-2.0-2 (= 2.3.1-3~ppa1) Section: libdevel Priority: optional Homepage: https://www.genome.umd.edu/jellyfish.html Description: count k-mers in DNA sequences (development files of jellyfish) JELLYFISH is a tool for fast, memory-efficient counting of k-mers in DNA. A k-mer is a substring of length k, and counting the occurrences of all such substrings is a central step in many analyses of DNA sequence. JELLYFISH can count k-mers using an order of magnitude less memory and an order of magnitude faster than other k-mer counting packages by using an efficient encoding of a hash table and by exploiting the "compare-and-swap" CPU instruction to increase parallelism. . JELLYFISH is a command-line program that reads FASTA and multi-FASTA files containing DNA sequences. It outputs its k-mer counts in an binary format, which can be translated into a human-readable text format using the "jellyfish dump" command. . This package contains the development files (static library and header files) drwxr-xr-x root/root 0 2024-03-19 21:23 ./ drwxr-xr-x root/root 0 2024-03-19 21:23 ./usr/ drwxr-xr-x root/root 0 2024-03-19 21:23 ./usr/include/ drwxr-xr-x root/root 0 2024-03-19 21:23 ./usr/include/jellyfish/ -rw-r--r-- root/root 1596 2024-03-19 21:23 ./usr/include/jellyfish/allocators_mmap.hpp -rw-r--r-- root/root 5898 2024-03-19 21:23 ./usr/include/jellyfish/atomic_bits_array.hpp -rw-r--r-- root/root 4770 2024-03-19 21:23 ./usr/include/jellyfish/atomic_field.hpp -rw-r--r-- root/root 1392 2024-03-19 21:23 ./usr/include/jellyfish/atomic_gcc.hpp -rw-r--r-- root/root 272 2024-03-19 21:23 ./usr/include/jellyfish/backtrace.hpp -rw-r--r-- root/root 6829 2024-03-19 21:23 ./usr/include/jellyfish/binary_dumper.hpp -rw-r--r-- root/root 3480 2024-03-19 21:23 ./usr/include/jellyfish/bloom_common.hpp -rw-r--r-- root/root 6778 2024-03-19 21:23 ./usr/include/jellyfish/bloom_counter2.hpp -rw-r--r-- root/root 5447 2024-03-19 21:23 ./usr/include/jellyfish/bloom_filter.hpp -rw-r--r-- root/root 5211 2024-03-19 21:23 ./usr/include/jellyfish/circular_buffer.hpp -rw-r--r-- root/root 2408 2024-03-19 21:23 ./usr/include/jellyfish/compare_and_swap.hpp -rw-r--r-- root/root 7472 2024-03-19 21:23 ./usr/include/jellyfish/cooperative_pool.hpp -rw-r--r-- root/root 8494 2024-03-19 21:23 ./usr/include/jellyfish/cooperative_pool2.hpp -rw-r--r-- root/root 4125 2024-03-19 21:23 ./usr/include/jellyfish/cpp_array.hpp -rw-r--r-- root/root 2742 2024-03-19 21:23 ./usr/include/jellyfish/divisor.hpp -rw-r--r-- root/root 2710 2024-03-19 21:23 ./usr/include/jellyfish/dumper.hpp -rw-r--r-- root/root 2257 2024-03-19 21:23 ./usr/include/jellyfish/err.hpp -rw-r--r-- root/root 4033 2024-03-19 21:23 ./usr/include/jellyfish/file_header.hpp -rw-r--r-- root/root 4637 2024-03-19 21:23 ./usr/include/jellyfish/generator_manager.hpp -rw-r--r-- root/root 6814 2024-03-19 21:23 ./usr/include/jellyfish/generic_file_header.hpp -rw-r--r-- root/root 8326 2024-03-19 21:23 ./usr/include/jellyfish/hash_counter.hpp -rw-r--r-- root/root 7025 2024-03-19 21:23 ./usr/include/jellyfish/int128.hpp -rw-r--r-- root/root 1118 2024-03-19 21:23 ./usr/include/jellyfish/jellyfish.hpp -rw-r--r-- root/root 61697 2024-03-19 21:23 ./usr/include/jellyfish/json.h -rw-r--r-- root/root 40578 2024-03-19 21:23 ./usr/include/jellyfish/large_hash_array.hpp -rw-r--r-- root/root 7564 2024-03-19 21:23 ./usr/include/jellyfish/large_hash_iterator.hpp -rw-r--r-- root/root 4328 2024-03-19 21:23 ./usr/include/jellyfish/locks_pthread.hpp -rw-r--r-- root/root 5181 2024-03-19 21:23 ./usr/include/jellyfish/mapped_file.hpp -rw-r--r-- root/root 23839 2024-03-19 21:23 ./usr/include/jellyfish/mer_dna.hpp -rw-r--r-- root/root 1296 2024-03-19 21:23 ./usr/include/jellyfish/mer_dna_bloom_counter.hpp -rw-r--r-- root/root 3076 2024-03-19 21:23 ./usr/include/jellyfish/mer_heap.hpp -rw-r--r-- root/root 2588 2024-03-19 21:23 ./usr/include/jellyfish/mer_iterator.hpp -rw-r--r-- root/root 9371 2024-03-19 21:23 ./usr/include/jellyfish/mer_overlap_sequence_parser.hpp -rw-r--r-- root/root 3247 2024-03-19 21:23 ./usr/include/jellyfish/mer_qual_iterator.hpp -rw-r--r-- root/root 8066 2024-03-19 21:23 ./usr/include/jellyfish/misc.hpp -rw-r--r-- root/root 10025 2024-03-19 21:23 ./usr/include/jellyfish/offsets_key_value.hpp -rw-r--r-- root/root 960 2024-03-19 21:23 ./usr/include/jellyfish/parser_common.hpp -rw-r--r-- root/root 12859 2024-03-19 21:23 ./usr/include/jellyfish/rectangular_binary_matrix.hpp -rw-r--r-- root/root 2311 2024-03-19 21:23 ./usr/include/jellyfish/sam_format.hpp -rw-r--r-- root/root 3504 2024-03-19 21:23 ./usr/include/jellyfish/simple_circular_buffer.hpp -rw-r--r-- root/root 3346 2024-03-19 21:23 ./usr/include/jellyfish/sorted_dumper.hpp -rw-r--r-- root/root 5069 2024-03-19 21:23 ./usr/include/jellyfish/stdio_filebuf.hpp -rw-r--r-- root/root 602 2024-03-19 21:23 ./usr/include/jellyfish/storage.hpp -rw-r--r-- root/root 2036 2024-03-19 21:23 ./usr/include/jellyfish/stream_iterator.hpp -rw-r--r-- root/root 6318 2024-03-19 21:23 ./usr/include/jellyfish/stream_manager.hpp -rw-r--r-- root/root 2063 2024-03-19 21:23 ./usr/include/jellyfish/text_dumper.hpp -rw-r--r-- root/root 994 2024-03-19 21:23 ./usr/include/jellyfish/thread_exec.hpp -rw-r--r-- root/root 1884 2024-03-19 21:23 ./usr/include/jellyfish/time.hpp -rw-r--r-- root/root 1599 2024-03-19 21:23 ./usr/include/jellyfish/token_ring.hpp -rw-r--r-- root/root 6761 2024-03-19 21:23 ./usr/include/jellyfish/whole_sequence_parser.hpp drwxr-xr-x root/root 0 2024-03-19 21:23 ./usr/lib/ drwxr-xr-x root/root 0 2024-03-19 21:23 ./usr/lib/x86_64-linux-gnu/ -rw-r--r-- root/root 316500 2024-03-19 21:23 ./usr/lib/x86_64-linux-gnu/libjellyfish-2.0.a -rw-r--r-- root/root 1005 2024-03-19 21:23 ./usr/lib/x86_64-linux-gnu/libjellyfish-2.0.la lrwxrwxrwx root/root 0 2024-03-19 21:23 ./usr/lib/x86_64-linux-gnu/libjellyfish-2.0.so -> libjellyfish-2.0.so.2.0.0 drwxr-xr-x root/root 0 2024-03-19 21:23 ./usr/lib/x86_64-linux-gnu/pkgconfig/ -rw-r--r-- root/root 273 2024-03-19 21:23 ./usr/lib/x86_64-linux-gnu/pkgconfig/jellyfish-2.0.pc drwxr-xr-x root/root 0 2024-03-19 21:23 ./usr/share/ drwxr-xr-x root/root 0 2024-03-19 21:23 ./usr/share/doc/ drwxr-xr-x root/root 0 2024-03-19 21:23 ./usr/share/doc/libjellyfish-2.0-dev/ lrwxrwxrwx root/root 0 2024-03-19 21:23 ./usr/share/doc/libjellyfish-2.0-dev/changelog.Debian.gz -> ../libjellyfish-2.0-2/changelog.Debian.gz -rw-r--r-- root/root 6395 2024-03-19 17:20 ./usr/share/doc/libjellyfish-2.0-dev/copyright libjellyfish-perl_2.3.1-3~ppa1_amd64.deb ---------------------------------------- new Debian package, version 2.0. size 57596 bytes: control archive=1046 bytes. 1325 bytes, 28 lines control 323 bytes, 4 lines md5sums Package: libjellyfish-perl Source: jellyfish Version: 2.3.1-3~ppa1 Architecture: amd64 Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 167 Depends: perl (>= 5.38.2-3.2), perlapi-5.38.2, libc6 (>= 2.38), libgcc-s1 (>= 3.3.1) Section: perl Priority: optional Multi-Arch: same Homepage: https://www.genome.umd.edu/jellyfish.html Description: count k-mers in DNA sequences (Perl bindings of jellyfish) JELLYFISH is a tool for fast, memory-efficient counting of k-mers in DNA. A k-mer is a substring of length k, and counting the occurrences of all such substrings is a central step in many analyses of DNA sequence. JELLYFISH can count k-mers using an order of magnitude less memory and an order of magnitude faster than other k-mer counting packages by using an efficient encoding of a hash table and by exploiting the "compare-and-swap" CPU instruction to increase parallelism. . JELLYFISH is a command-line program that reads FASTA and multi-FASTA files containing DNA sequences. It outputs its k-mer counts in an binary format, which can be translated into a human-readable text format using the "jellyfish dump" command. . This package contains the Perl bindings of jellyfish. drwxr-xr-x root/root 0 2024-03-19 21:23 ./ drwxr-xr-x root/root 0 2024-03-19 21:23 ./usr/ drwxr-xr-x root/root 0 2024-03-19 21:23 ./usr/lib/ drwxr-xr-x root/root 0 2024-03-19 21:23 ./usr/lib/x86_64-linux-gnu/ drwxr-xr-x root/root 0 2024-03-19 21:23 ./usr/lib/x86_64-linux-gnu/perl5/ drwxr-xr-x root/root 0 2024-03-19 21:23 ./usr/lib/x86_64-linux-gnu/perl5/5.38/ drwxr-xr-x root/root 0 2024-03-19 21:23 ./usr/lib/x86_64-linux-gnu/perl5/5.38/auto/ drwxr-xr-x root/root 0 2024-03-19 21:23 ./usr/lib/x86_64-linux-gnu/perl5/5.38/auto/jellyfish/ -rw-r--r-- root/root 138680 2024-03-19 21:23 ./usr/lib/x86_64-linux-gnu/perl5/5.38/auto/jellyfish/jellyfish.so drwxr-xr-x root/root 0 2024-03-19 21:23 ./usr/share/ drwxr-xr-x root/root 0 2024-03-19 21:23 ./usr/share/doc/ drwxr-xr-x root/root 0 2024-03-19 21:23 ./usr/share/doc/libjellyfish-perl/ -rw-r--r-- root/root 2837 2024-03-19 21:23 ./usr/share/doc/libjellyfish-perl/changelog.Debian.gz -rw-r--r-- root/root 6395 2024-03-19 17:20 ./usr/share/doc/libjellyfish-perl/copyright drwxr-xr-x root/root 0 2024-03-19 21:23 ./usr/share/perl5/ -rw-r--r-- root/root 7414 2024-03-19 21:23 ./usr/share/perl5/jellyfish.pm python3-dna-jellyfish_2.3.1-3~ppa1_amd64.deb -------------------------------------------- new Debian package, version 2.0. size 53310 bytes: control archive=1450 bytes. 1385 bytes, 27 lines control 595 bytes, 6 lines md5sums 289 bytes, 12 lines * postinst #!/bin/sh 402 bytes, 12 lines * prerm #!/bin/sh Package: python3-dna-jellyfish Source: jellyfish Version: 2.3.1-3~ppa1 Architecture: amd64 Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 173 Depends: python3 (<< 3.13), python3 (>= 3.12~), python3:any, libc6 (>= 2.38), libgcc-s1 (>= 3.3.1), libjellyfish-2.0-2 (>= 2.3.1), libstdc++6 (>= 13.1) Section: python Priority: optional Homepage: https://www.genome.umd.edu/jellyfish.html Description: count k-mers in DNA sequences (Python bindings of jellyfish) JELLYFISH is a tool for fast, memory-efficient counting of k-mers in DNA. A k-mer is a substring of length k, and counting the occurrences of all such substrings is a central step in many analyses of DNA sequence. JELLYFISH can count k-mers using an order of magnitude less memory and an order of magnitude faster than other k-mer counting packages by using an efficient encoding of a hash table and by exploiting the "compare-and-swap" CPU instruction to increase parallelism. . JELLYFISH is a command-line program that reads FASTA and multi-FASTA files containing DNA sequences. It outputs its k-mer counts in an binary format, which can be translated into a human-readable text format using the "jellyfish dump" command. . This package contains the Python bindings of jellyfish. drwxr-xr-x root/root 0 2024-03-19 21:23 ./ drwxr-xr-x root/root 0 2024-03-19 21:23 ./usr/ drwxr-xr-x root/root 0 2024-03-19 21:23 ./usr/lib/ drwxr-xr-x root/root 0 2024-03-19 21:23 ./usr/lib/python3/ drwxr-xr-x root/root 0 2024-03-19 21:23 ./usr/lib/python3/dist-packages/ -rw-r--r-- root/root 137720 2024-03-19 21:23 ./usr/lib/python3/dist-packages/_dna_jellyfish.cpython-312-x86_64-linux-gnu.so drwxr-xr-x root/root 0 2024-03-19 21:23 ./usr/lib/python3/dist-packages/dna_jellyfish-0.0.1.egg-info/ -rw-r--r-- root/root 127 2024-03-19 21:23 ./usr/lib/python3/dist-packages/dna_jellyfish-0.0.1.egg-info/PKG-INFO -rw-r--r-- root/root 1 2024-03-19 21:23 ./usr/lib/python3/dist-packages/dna_jellyfish-0.0.1.egg-info/dependency_links.txt -rw-r--r-- root/root 29 2024-03-19 21:23 ./usr/lib/python3/dist-packages/dna_jellyfish-0.0.1.egg-info/top_level.txt -rw-r--r-- root/root 12643 2024-03-19 21:23 ./usr/lib/python3/dist-packages/dna_jellyfish.py drwxr-xr-x root/root 0 2024-03-19 21:23 ./usr/share/ drwxr-xr-x root/root 0 2024-03-19 21:23 ./usr/share/doc/ drwxr-xr-x root/root 0 2024-03-19 21:23 ./usr/share/doc/python3-dna-jellyfish/ lrwxrwxrwx root/root 0 2024-03-19 21:23 ./usr/share/doc/python3-dna-jellyfish/changelog.Debian.gz -> ../libjellyfish-2.0-2/changelog.Debian.gz -rw-r--r-- root/root 6395 2024-03-19 17:20 ./usr/share/doc/python3-dna-jellyfish/copyright +------------------------------------------------------------------------------+ | Post Build | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not removing build depends: as requested +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: amd64 Build Type: binary Build-Space: 1853168 Build-Time: 281 Distribution: noble Host Architecture: amd64 Install-Time: 13 Job: jellyfish_2.3.1-3~ppa1.dsc Machine Architecture: amd64 Package: jellyfish Package-Time: 295 Source-Version: 2.3.1-3~ppa1 Space: 1853168 Status: successful Version: 2.3.1-3~ppa1 -------------------------------------------------------------------------------- Finished at 2024-03-19T21:31:32Z Build needed 00:04:55, 1853168k disk space RUN: /usr/share/launchpad-buildd/bin/in-target scan-for-processes --backend=chroot --series=noble --arch=amd64 PACKAGEBUILD-27942511 Scanning for processes to kill in build PACKAGEBUILD-27942511