https://launchpad.net/ubuntu/+source/berkeley-express/1.5.3+dfsg-3build3/+build/27576186 RUN: /usr/share/launchpad-buildd/bin/builder-prep Kernel version: Linux bos02-s390x-013 5.4.0-169-generic #187-Ubuntu SMP Thu Nov 23 14:52:16 UTC 2023 s390x Buildd toolchain package versions: launchpad-buildd_235~645~ubuntu20.04.1 python3-lpbuildd_235~645~ubuntu20.04.1 sbuild_0.79.0-1ubuntu1 git-build-recipe_0.3.6 git_1:2.25.1-1ubuntu3.11 dpkg-dev_1.19.7ubuntu3.2 python3-debian_0.1.36ubuntu1.1. Syncing the system clock with the buildd NTP service... 19 Dec 16:49:01 ntpdate[1874]: adjust time server 10.211.37.1 offset 0.000559 sec RUN: /usr/share/launchpad-buildd/bin/in-target unpack-chroot --backend=chroot --series=noble --arch=s390x PACKAGEBUILD-27576186 --image-type chroot /home/buildd/filecache-default/c23f799bb684944311373fdcead5a58221fa6ef7 Creating target for build PACKAGEBUILD-27576186 RUN: /usr/share/launchpad-buildd/bin/in-target mount-chroot --backend=chroot --series=noble --arch=s390x PACKAGEBUILD-27576186 Starting target for build PACKAGEBUILD-27576186 RUN: /usr/share/launchpad-buildd/bin/in-target override-sources-list --backend=chroot --series=noble --arch=s390x PACKAGEBUILD-27576186 'deb http://ftpmaster.internal/ubuntu noble main universe' 'deb http://ftpmaster.internal/ubuntu noble-security main universe' 'deb http://ftpmaster.internal/ubuntu noble-updates main universe' 'deb http://ftpmaster.internal/ubuntu noble-proposed main universe' Overriding sources.list in build-PACKAGEBUILD-27576186 RUN: /usr/share/launchpad-buildd/bin/in-target update-debian-chroot --backend=chroot --series=noble --arch=s390x PACKAGEBUILD-27576186 Updating target for build PACKAGEBUILD-27576186 Get:1 http://ftpmaster.internal/ubuntu noble InRelease [240 kB] Get:2 http://ftpmaster.internal/ubuntu noble-security InRelease [74.9 kB] Get:3 http://ftpmaster.internal/ubuntu noble-updates InRelease [74.9 kB] Get:4 http://ftpmaster.internal/ubuntu noble-proposed InRelease [102 kB] Get:5 http://ftpmaster.internal/ubuntu noble/main s390x Packages [1337 kB] Get:6 http://ftpmaster.internal/ubuntu noble/main Translation-en [515 kB] Get:7 http://ftpmaster.internal/ubuntu noble/universe s390x Packages [14.6 MB] Get:8 http://ftpmaster.internal/ubuntu noble/universe Translation-en [6031 kB] Get:9 http://ftpmaster.internal/ubuntu noble-proposed/main s390x Packages [95.5 kB] Get:10 http://ftpmaster.internal/ubuntu noble-proposed/main Translation-en [47.1 kB] Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe s390x Packages [1049 kB] Get:12 http://ftpmaster.internal/ubuntu noble-proposed/universe Translation-en [326 kB] Fetched 24.5 MB in 4s (6371 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following package was automatically installed and is no longer required: libunistring2 Use 'sudo apt autoremove' to remove it. The following NEW packages will be installed: libunistring5 The following packages will be upgraded: apt apt-utils base-files base-passwd bash bash-completion binutils binutils-common binutils-s390x-linux-gnu bsdextrautils bsdutils coreutils cpp cpp-13 debianutils diffutils dpkg dpkg-dev fakeroot g++ g++-13 gcc gcc-13 gcc-13-base grep init init-system-helpers krb5-locales libapparmor1 libapt-pkg6.0 libargon2-1 libasan8 libatomic1 libaudit-common libaudit1 libbinutils libblkid1 libc-bin libc-dev-bin libc6 libc6-dev libcap-ng0 libcc1-0 libcryptsetup12 libctf-nobfd0 libctf0 libdb5.3 libdebconfclient0 libdpkg-perl libfakeroot libfdisk1 libffi8 libgcc-13-dev libgcc-s1 libgdbm-compat4 libgdbm6 libgnutls30 libgomp1 libgpg-error-l10n libgpg-error0 libgssapi-krb5-2 libidn2-0 libitm1 libk5crypto3 libkmod2 libkrb5-3 libkrb5support0 liblzma5 libmount1 libncursesw6 libnsl-dev libnsl2 libp11-kit0 libpam-modules libpam-modules-bin libpam-runtime libpam0g libpcre2-8-0 libperl5.36 libpng16-16 libproc2-0 libreadline8 libseccomp2 libselinux1 libsemanage-common libsemanage2 libsepol2 libsframe1 libsmartcols1 libsqlite3-0 libssl3 libstdc++-13-dev libstdc++6 libsystemd-shared libsystemd0 libtinfo6 libtirpc-common libtirpc-dev libtirpc3 libubsan1 libudev1 libuuid1 libxxhash0 libzstd1 linux-libc-dev login lto-disabled-list mawk mount ncurses-base ncurses-bin openssl optipng passwd perl perl-base perl-modules-5.36 pinentry-curses procps readline-common systemd systemd-dev systemd-sysv sysvinit-utils tar ubuntu-keyring util-linux uuid-runtime xz-utils zlib1g 130 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 95.5 MB of archives. After this operation, 7503 kB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu noble/main s390x libnsl-dev s390x 1.3.0-3 [73.5 kB] Get:2 http://ftpmaster.internal/ubuntu noble/main s390x libc6-dev s390x 2.38-3ubuntu1 [1626 kB] Get:3 http://ftpmaster.internal/ubuntu noble/main s390x libc-dev-bin s390x 2.38-3ubuntu1 [20.0 kB] Get:4 http://ftpmaster.internal/ubuntu noble/main s390x libtirpc-common all 1.3.4+ds-1 [7920 B] Get:5 http://ftpmaster.internal/ubuntu noble/main s390x libtirpc-dev s390x 1.3.4+ds-1 [196 kB] Get:6 http://ftpmaster.internal/ubuntu noble/main s390x libgssapi-krb5-2 s390x 1.20.1-5build1 [146 kB] Get:7 http://ftpmaster.internal/ubuntu noble/main s390x libkrb5-3 s390x 1.20.1-5build1 [354 kB] Get:8 http://ftpmaster.internal/ubuntu noble/main s390x libk5crypto3 s390x 1.20.1-5build1 [89.1 kB] Get:9 http://ftpmaster.internal/ubuntu noble/main s390x libkrb5support0 s390x 1.20.1-5build1 [34.1 kB] Get:10 http://ftpmaster.internal/ubuntu noble/main s390x libssl3 s390x 3.0.10-1ubuntu3 [1625 kB] Get:11 http://ftpmaster.internal/ubuntu noble/main s390x libtirpc3 s390x 1.3.4+ds-1 [84.8 kB] Get:12 http://ftpmaster.internal/ubuntu noble/main s390x libnsl2 s390x 1.3.0-3 [44.4 kB] Get:13 http://ftpmaster.internal/ubuntu noble-proposed/main s390x linux-libc-dev s390x 6.6.0-14.14 [1576 kB] Get:14 http://ftpmaster.internal/ubuntu noble/main s390x libcc1-0 s390x 13.2.0-9ubuntu1 [50.1 kB] Get:15 http://ftpmaster.internal/ubuntu noble/main s390x libctf0 s390x 2.41.50.20231214-1ubuntu1 [84.0 kB] Get:16 http://ftpmaster.internal/ubuntu noble/main s390x libctf-nobfd0 s390x 2.41.50.20231214-1ubuntu1 [88.1 kB] Get:17 http://ftpmaster.internal/ubuntu noble/main s390x binutils-s390x-linux-gnu s390x 2.41.50.20231214-1ubuntu1 [2387 kB] Get:18 http://ftpmaster.internal/ubuntu noble/main s390x libbinutils s390x 2.41.50.20231214-1ubuntu1 [421 kB] Get:19 http://ftpmaster.internal/ubuntu noble/main s390x binutils-common s390x 2.41.50.20231214-1ubuntu1 [230 kB] Get:20 http://ftpmaster.internal/ubuntu noble/main s390x binutils s390x 2.41.50.20231214-1ubuntu1 [3062 B] Get:21 http://ftpmaster.internal/ubuntu noble/main s390x gcc-13-base s390x 13.2.0-9ubuntu1 [45.2 kB] Get:22 http://ftpmaster.internal/ubuntu noble/main s390x libgcc-s1 s390x 13.2.0-9ubuntu1 [35.9 kB] Get:23 http://ftpmaster.internal/ubuntu noble/main s390x libgomp1 s390x 13.2.0-9ubuntu1 [146 kB] Get:24 http://ftpmaster.internal/ubuntu noble/main s390x libitm1 s390x 13.2.0-9ubuntu1 [31.3 kB] Get:25 http://ftpmaster.internal/ubuntu noble/main s390x libatomic1 s390x 13.2.0-9ubuntu1 [9382 B] Get:26 http://ftpmaster.internal/ubuntu noble/main s390x libasan8 s390x 13.2.0-9ubuntu1 [2852 kB] Get:27 http://ftpmaster.internal/ubuntu noble/main s390x libubsan1 s390x 13.2.0-9ubuntu1 [1112 kB] Get:28 http://ftpmaster.internal/ubuntu noble/main s390x g++-13 s390x 13.2.0-9ubuntu1 [10.2 MB] Get:29 http://ftpmaster.internal/ubuntu noble/main s390x libstdc++-13-dev s390x 13.2.0-9ubuntu1 [2426 kB] Get:30 http://ftpmaster.internal/ubuntu noble/main s390x libgcc-13-dev s390x 13.2.0-9ubuntu1 [1003 kB] Get:31 http://ftpmaster.internal/ubuntu noble/main s390x gcc-13 s390x 13.2.0-9ubuntu1 [17.6 MB] Get:32 http://ftpmaster.internal/ubuntu noble/main s390x cpp-13 s390x 13.2.0-9ubuntu1 [8794 kB] Get:33 http://ftpmaster.internal/ubuntu noble/main s390x libstdc++6 s390x 13.2.0-9ubuntu1 [875 kB] Get:34 http://ftpmaster.internal/ubuntu noble-proposed/main s390x zlib1g s390x 1:1.3.dfsg-3ubuntu1 [75.3 kB] Get:35 http://ftpmaster.internal/ubuntu noble/main s390x libsframe1 s390x 2.41.50.20231214-1ubuntu1 [13.1 kB] Get:36 http://ftpmaster.internal/ubuntu noble/main s390x libzstd1 s390x 1.5.5+dfsg2-2 [336 kB] Get:37 http://ftpmaster.internal/ubuntu noble/main s390x libc6 s390x 2.38-3ubuntu1 [2839 kB] Get:38 http://ftpmaster.internal/ubuntu noble/main s390x base-files s390x 13ubuntu5 [73.6 kB] Get:39 http://ftpmaster.internal/ubuntu noble/main s390x debianutils s390x 5.14 [89.3 kB] Get:40 http://ftpmaster.internal/ubuntu noble/main s390x bash s390x 5.2.21-2ubuntu1 [855 kB] Get:41 http://ftpmaster.internal/ubuntu noble/main s390x bsdutils s390x 1:2.39.2-6ubuntu1 [95.2 kB] Get:42 http://ftpmaster.internal/ubuntu noble/main s390x coreutils s390x 9.4-2ubuntu1 [1501 kB] Get:43 http://ftpmaster.internal/ubuntu noble/main s390x diffutils s390x 1:3.10-1 [187 kB] Get:44 http://ftpmaster.internal/ubuntu noble/main s390x liblzma5 s390x 5.4.5-0.1 [133 kB] Get:45 http://ftpmaster.internal/ubuntu noble/main s390x libapparmor1 s390x 4.0.0~alpha2-0ubuntu7 [49.6 kB] Get:46 http://ftpmaster.internal/ubuntu noble/main s390x libaudit-common all 1:3.1.2-1 [5512 B] Get:47 http://ftpmaster.internal/ubuntu noble/main s390x libcap-ng0 s390x 0.8.3-3 [15.7 kB] Get:48 http://ftpmaster.internal/ubuntu noble/main s390x libaudit1 s390x 1:3.1.2-1 [48.7 kB] Get:49 http://ftpmaster.internal/ubuntu noble/main s390x libblkid1 s390x 2.39.2-6ubuntu1 [126 kB] Get:50 http://ftpmaster.internal/ubuntu noble/main s390x libkmod2 s390x 30+20230601-2ubuntu1 [54.5 kB] Get:51 http://ftpmaster.internal/ubuntu noble/main s390x libpcre2-8-0 s390x 10.42-4ubuntu1 [243 kB] Get:52 http://ftpmaster.internal/ubuntu noble/main s390x libselinux1 s390x 3.5-1build2 [83.5 kB] Get:53 http://ftpmaster.internal/ubuntu noble/main s390x libmount1 s390x 2.39.2-6ubuntu1 [137 kB] Get:54 http://ftpmaster.internal/ubuntu noble/main s390x libpam0g s390x 1.5.2-9.1ubuntu1 [66.0 kB] Get:55 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libseccomp2 s390x 2.5.4-2ubuntu1 [52.2 kB] Get:56 http://ftpmaster.internal/ubuntu noble-proposed/main s390x systemd-sysv s390x 255-1ubuntu1 [11.7 kB] Get:57 http://ftpmaster.internal/ubuntu noble-proposed/main s390x systemd-dev all 255-1ubuntu1 [98.5 kB] Get:58 http://ftpmaster.internal/ubuntu noble-proposed/main s390x systemd s390x 255-1ubuntu1 [3581 kB] Get:59 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libsystemd-shared s390x 255-1ubuntu1 [2129 kB] Get:60 http://ftpmaster.internal/ubuntu noble/main s390x libargon2-1 s390x 0~20190702+dfsg-4 [53.1 kB] Get:61 http://ftpmaster.internal/ubuntu noble/main s390x libuuid1 s390x 2.39.2-6ubuntu1 [34.4 kB] Get:62 http://ftpmaster.internal/ubuntu noble/main s390x libcryptsetup12 s390x 2:2.6.1-5ubuntu1 [239 kB] Get:63 http://ftpmaster.internal/ubuntu noble/main s390x libfdisk1 s390x 2.39.2-6ubuntu1 [149 kB] Get:64 http://ftpmaster.internal/ubuntu noble/main s390x mount s390x 2.39.2-6ubuntu1 [118 kB] Get:65 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libsystemd0 s390x 255-1ubuntu1 [440 kB] Get:66 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libudev1 s390x 255-1ubuntu1 [174 kB] Get:67 http://ftpmaster.internal/ubuntu noble/main s390x libxxhash0 s390x 0.8.2-2 [23.6 kB] Get:68 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libapt-pkg6.0 s390x 2.7.7 [962 kB] Get:69 http://ftpmaster.internal/ubuntu noble/main s390x tar s390x 1.34+dfsg-1.2ubuntu2 [315 kB] Get:70 http://ftpmaster.internal/ubuntu noble/main s390x dpkg s390x 1.22.1ubuntu5 [1391 kB] Get:71 http://ftpmaster.internal/ubuntu noble/main s390x grep s390x 3.11-3 [172 kB] Get:72 http://ftpmaster.internal/ubuntu noble/main s390x login s390x 1:4.13+dfsg1-3ubuntu1 [202 kB] Get:73 http://ftpmaster.internal/ubuntu noble/main s390x ncurses-bin s390x 6.4+20231209-1 [196 kB] Get:74 http://ftpmaster.internal/ubuntu noble/main s390x libperl5.36 s390x 5.36.0-10ubuntu1 [4899 kB] Get:75 http://ftpmaster.internal/ubuntu noble/main s390x perl s390x 5.36.0-10ubuntu1 [235 kB] Get:76 http://ftpmaster.internal/ubuntu noble/main s390x perl-base s390x 5.36.0-10ubuntu1 [1881 kB] Get:77 http://ftpmaster.internal/ubuntu noble/main s390x perl-modules-5.36 all 5.36.0-10ubuntu1 [2984 kB] Get:78 http://ftpmaster.internal/ubuntu noble/main s390x libdb5.3 s390x 5.3.28+dfsg2-4 [752 kB] Get:79 http://ftpmaster.internal/ubuntu noble/main s390x libgdbm6 s390x 1.23-5 [35.5 kB] Get:80 http://ftpmaster.internal/ubuntu noble/main s390x libgdbm-compat4 s390x 1.23-5 [6538 B] Get:81 http://ftpmaster.internal/ubuntu noble/main s390x util-linux s390x 2.39.2-6ubuntu1 [1137 kB] Get:82 http://ftpmaster.internal/ubuntu noble/main s390x libdebconfclient0 s390x 0.271ubuntu1 [11.3 kB] Get:83 http://ftpmaster.internal/ubuntu noble/main s390x base-passwd s390x 3.6.3 [51.1 kB] Get:84 http://ftpmaster.internal/ubuntu noble-proposed/main s390x init-system-helpers all 1.66ubuntu1 [39.4 kB] Get:85 http://ftpmaster.internal/ubuntu noble/main s390x libc-bin s390x 2.38-3ubuntu1 [659 kB] Get:86 http://ftpmaster.internal/ubuntu noble/main s390x ncurses-base all 6.4+20231209-1 [25.2 kB] Get:87 http://ftpmaster.internal/ubuntu noble/main s390x sysvinit-utils s390x 3.08-3ubuntu1 [34.3 kB] Get:88 http://ftpmaster.internal/ubuntu noble-proposed/main s390x apt s390x 2.7.7 [1377 kB] Get:89 http://ftpmaster.internal/ubuntu noble-proposed/main s390x apt-utils s390x 2.7.7 [213 kB] Get:90 http://ftpmaster.internal/ubuntu noble/main s390x ubuntu-keyring all 2023.11.28.1 [11.1 kB] Get:91 http://ftpmaster.internal/ubuntu noble/main s390x libunistring5 s390x 1.1-2 [544 kB] Get:92 http://ftpmaster.internal/ubuntu noble/main s390x libidn2-0 s390x 2.3.4-1build1 [65.1 kB] Get:93 http://ftpmaster.internal/ubuntu noble/main s390x libffi8 s390x 3.4.4-2 [22.6 kB] Get:94 http://ftpmaster.internal/ubuntu noble/main s390x libp11-kit0 s390x 0.25.3-2ubuntu2 [313 kB] Get:95 http://ftpmaster.internal/ubuntu noble/main s390x libgnutls30 s390x 3.8.1-4ubuntu6 [937 kB] Get:96 http://ftpmaster.internal/ubuntu noble/main s390x libpam-modules-bin s390x 1.5.2-9.1ubuntu1 [51.9 kB] Get:97 http://ftpmaster.internal/ubuntu noble/main s390x libpam-modules s390x 1.5.2-9.1ubuntu1 [291 kB] Get:98 http://ftpmaster.internal/ubuntu noble-proposed/main s390x init s390x 1.66ubuntu1 [6188 B] Get:99 http://ftpmaster.internal/ubuntu noble/main s390x libsmartcols1 s390x 2.39.2-6ubuntu1 [66.3 kB] Get:100 http://ftpmaster.internal/ubuntu noble/main s390x uuid-runtime s390x 2.39.2-6ubuntu1 [33.2 kB] Get:101 http://ftpmaster.internal/ubuntu noble/main s390x libgpg-error-l10n all 1.47-3build1 [8024 B] Get:102 http://ftpmaster.internal/ubuntu noble/main s390x libgpg-error0 s390x 1.47-3build1 [75.6 kB] Get:103 http://ftpmaster.internal/ubuntu noble/main s390x libpam-runtime all 1.5.2-9.1ubuntu1 [41.5 kB] Get:104 http://ftpmaster.internal/ubuntu noble/main s390x libsemanage-common all 3.5-1build1 [9982 B] Get:105 http://ftpmaster.internal/ubuntu noble/main s390x libsepol2 s390x 3.5-2 [308 kB] Get:106 http://ftpmaster.internal/ubuntu noble/main s390x libsemanage2 s390x 3.5-1build1 [95.1 kB] Get:107 http://ftpmaster.internal/ubuntu noble/main s390x libncursesw6 s390x 6.4+20231209-1 [158 kB] Get:108 http://ftpmaster.internal/ubuntu noble/main s390x libtinfo6 s390x 6.4+20231209-1 [115 kB] Get:109 http://ftpmaster.internal/ubuntu noble/main s390x passwd s390x 1:4.13+dfsg1-3ubuntu1 [855 kB] Get:110 http://ftpmaster.internal/ubuntu noble/main s390x libproc2-0 s390x 2:4.0.4-2ubuntu1 [58.6 kB] Get:111 http://ftpmaster.internal/ubuntu noble/main s390x mawk s390x 1.3.4.20231126-1 [132 kB] Get:112 http://ftpmaster.internal/ubuntu noble/main s390x procps s390x 2:4.0.4-2ubuntu1 [722 kB] Get:113 http://ftpmaster.internal/ubuntu noble/main s390x krb5-locales all 1.20.1-5build1 [13.7 kB] Get:114 http://ftpmaster.internal/ubuntu noble/main s390x readline-common all 8.2-3 [56.2 kB] Get:115 http://ftpmaster.internal/ubuntu noble/main s390x libreadline8 s390x 8.2-3 [167 kB] Get:116 http://ftpmaster.internal/ubuntu noble/main s390x libsqlite3-0 s390x 3.44.2-1 [727 kB] Get:117 http://ftpmaster.internal/ubuntu noble/main s390x openssl s390x 3.0.10-1ubuntu3 [1189 kB] Get:118 http://ftpmaster.internal/ubuntu noble/main s390x bash-completion all 1:2.11-8 [180 kB] Get:119 http://ftpmaster.internal/ubuntu noble/main s390x bsdextrautils s390x 2.39.2-6ubuntu1 [75.7 kB] Get:120 http://ftpmaster.internal/ubuntu noble/main s390x libpng16-16 s390x 1.6.40-2 [197 kB] Get:121 http://ftpmaster.internal/ubuntu noble/main s390x xz-utils s390x 5.4.5-0.1 [269 kB] Get:122 http://ftpmaster.internal/ubuntu noble/main s390x g++ s390x 4:13.2.0-2ubuntu1 [1118 B] Get:123 http://ftpmaster.internal/ubuntu noble/main s390x gcc s390x 4:13.2.0-2ubuntu1 [5172 B] Get:124 http://ftpmaster.internal/ubuntu noble/main s390x cpp s390x 4:13.2.0-2ubuntu1 [29.0 kB] Get:125 http://ftpmaster.internal/ubuntu noble/main s390x dpkg-dev all 1.22.1ubuntu5 [1147 kB] Get:126 http://ftpmaster.internal/ubuntu noble/main s390x libdpkg-perl all 1.22.1ubuntu5 [286 kB] Get:127 http://ftpmaster.internal/ubuntu noble/main s390x lto-disabled-list all 44 [12.4 kB] Get:128 http://ftpmaster.internal/ubuntu noble/main s390x libfakeroot s390x 1.32.2-1 [31.5 kB] Get:129 http://ftpmaster.internal/ubuntu noble/main s390x fakeroot s390x 1.32.2-1 [67.3 kB] Get:130 http://ftpmaster.internal/ubuntu noble/main s390x optipng s390x 0.7.7-3 [87.0 kB] Get:131 http://ftpmaster.internal/ubuntu noble/main s390x pinentry-curses s390x 1.2.1-3ubuntu1 [37.1 kB] Preconfiguring packages ... 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Setting up libstdc++-13-dev:s390x (13.2.0-9ubuntu1) ... Setting up g++-13 (13.2.0-9ubuntu1) ... Setting up g++ (4:13.2.0-2ubuntu1) ... Processing triggers for libc-bin (2.38-3ubuntu1) ... Processing triggers for debianutils (5.14) ... RUN: /usr/share/launchpad-buildd/bin/sbuild-package PACKAGEBUILD-27576186 s390x noble-proposed -c chroot:build-PACKAGEBUILD-27576186 --arch=s390x --dist=noble-proposed --nolog berkeley-express_1.5.3+dfsg-3build3.dsc Initiating build PACKAGEBUILD-27576186 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 5.4.0-169-generic #187-Ubuntu SMP Thu Nov 23 14:52:16 UTC 2023 s390x sbuild (Debian sbuild) 0.79.0 (05 February 2020) on bos02-s390x-013.buildd +==============================================================================+ | berkeley-express 1.5.3+dfsg-3build3 (s390x) Tue, 19 Dec 2023 16:49:25 +0000 | +==============================================================================+ Package: berkeley-express Version: 1.5.3+dfsg-3build3 Source Version: 1.5.3+dfsg-3build3 Distribution: noble-proposed Machine Architecture: s390x Host Architecture: s390x Build Architecture: s390x Build Type: any I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-27576186/chroot-autobuild' with '<>' I: NOTICE: Log filtering will replace 'build/berkeley-express-3mgRU7/resolver-bPwA3x' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- berkeley-express_1.5.3+dfsg-3build3.dsc exists in .; copying to chroot I: NOTICE: Log filtering will replace 'build/berkeley-express-3mgRU7/berkeley-express-1.5.3+dfsg' with '<>' I: NOTICE: Log filtering will replace 'build/berkeley-express-3mgRU7' with '<>' +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper-compat (= 13), libboost-thread-dev, libboost-system-dev, libboost-filesystem-dev, libboost-program-options-dev, libboost-date-time-dev, libbamtools-dev, libboost-tools-dev, cmake, libprotobuf-dev, protobuf-compiler, build-essential, fakeroot Filtered Build-Depends: debhelper-compat (= 13), libboost-thread-dev, libboost-system-dev, libboost-filesystem-dev, libboost-program-options-dev, libboost-date-time-dev, libbamtools-dev, libboost-tools-dev, cmake, libprotobuf-dev, protobuf-compiler, 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 [487 B] Get:5 copy:/<>/apt_archive ./ Packages [523 B] Fetched 1967 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 ca-certificates debconf-i18n krb5-locales libgpg-error-l10n libgpm2 libip4tc2 liblocale-gettext-perl libnss-nis libnss-nisplus libtext-charwidth-perl libtext-iconv-perl libtext-wrapi18n-perl libunistring2 openssl psmisc uuid-runtime Use 'apt autoremove' to remove them. The following additional packages will be installed: autoconf automake autopoint autotools-dev cmake cmake-data debhelper debugedit dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base groff-base intltool-debian libarchive-zip-perl libarchive13 libbamtools-dev libbamtools2.5.2 libboost-atomic1.83-dev libboost-atomic1.83.0 libboost-chrono1.83-dev libboost-chrono1.83.0 libboost-date-time-dev libboost-date-time1.83-dev libboost-date-time1.83.0 libboost-filesystem-dev libboost-filesystem1.83-dev libboost-filesystem1.83.0 libboost-program-options-dev libboost-program-options1.83-dev libboost-program-options1.83.0 libboost-serialization1.83-dev libboost-serialization1.83.0 libboost-system-dev libboost-system1.83-dev libboost-system1.83.0 libboost-thread-dev libboost-thread1.83-dev libboost-thread1.83.0 libboost-tools-dev libboost1.83-dev libboost1.83-tools-dev libbrotli1 libcurl4 libdebhelper-perl libdw1 libelf1 libexpat1 libfile-stripnondeterminism-perl libicu74 libjsoncpp25 libldap2 libmagic-mgc libmagic1 libnghttp2-14 libpipeline1 libprotobuf-dev libprotobuf-lite32 libprotobuf32 libprotoc32 libpsl5 librhash0 librtmp1 libsasl2-2 libsasl2-modules-db libssh-4 libsub-override-perl libtool libuchardet0 libuv1 libxml2 m4 man-db po-debconf protobuf-compiler zlib1g-dev Suggested packages: autoconf-archive gnu-standards autoconf-doc cmake-doc cmake-format elpa-cmake-mode ninja-build dh-make gettext-doc libasprintf-dev libgettextpo-dev groff lrzip libbamtools-doc libboost1.83-doc libboost-container1.83-dev libboost-context1.83-dev libboost-contract1.83-dev libboost-coroutine1.83-dev libboost-exception1.83-dev libboost-fiber1.83-dev libboost-graph1.83-dev libboost-graph-parallel1.83-dev libboost-iostreams1.83-dev libboost-locale1.83-dev libboost-log1.83-dev libboost-math1.83-dev libboost-mpi1.83-dev libboost-mpi-python1.83-dev libboost-numpy1.83-dev libboost-python1.83-dev libboost-random1.83-dev libboost-regex1.83-dev libboost-stacktrace1.83-dev libboost-test1.83-dev libboost-timer1.83-dev libboost-type-erasure1.83-dev libboost-wave1.83-dev libmpfrc++-dev libntl-dev libboost-nowide1.83-dev xsltproc doxygen docbook-xml docbook-xsl default-jdk fop libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc apparmor less www-browser libmail-box-perl protobuf-mode-el Recommended packages: curl | wget | lynx libarchive-cpio-perl libldap-common publicsuffix libsasl2-modules libltdl-dev libmail-sendmail-perl The following NEW packages will be installed: autoconf automake autopoint autotools-dev cmake cmake-data debhelper debugedit dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base groff-base intltool-debian libarchive-zip-perl libarchive13 libbamtools-dev libbamtools2.5.2 libboost-atomic1.83-dev libboost-atomic1.83.0 libboost-chrono1.83-dev libboost-chrono1.83.0 libboost-date-time-dev libboost-date-time1.83-dev libboost-date-time1.83.0 libboost-filesystem-dev libboost-filesystem1.83-dev libboost-filesystem1.83.0 libboost-program-options-dev libboost-program-options1.83-dev libboost-program-options1.83.0 libboost-serialization1.83-dev libboost-serialization1.83.0 libboost-system-dev libboost-system1.83-dev libboost-system1.83.0 libboost-thread-dev libboost-thread1.83-dev libboost-thread1.83.0 libboost-tools-dev libboost1.83-dev libboost1.83-tools-dev libbrotli1 libcurl4 libdebhelper-perl libdw1 libelf1 libexpat1 libfile-stripnondeterminism-perl libicu74 libjsoncpp25 libldap2 libmagic-mgc libmagic1 libnghttp2-14 libpipeline1 libprotobuf-dev libprotobuf-lite32 libprotobuf32 libprotoc32 libpsl5 librhash0 librtmp1 libsasl2-2 libsasl2-modules-db libssh-4 libsub-override-perl libtool libuchardet0 libuv1 libxml2 m4 man-db po-debconf protobuf-compiler sbuild-build-depends-main-dummy zlib1g-dev 0 upgraded, 79 newly installed, 0 to remove and 0 not upgraded. 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Get:1 copy:/<>/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [738 B] Get:2 http://ftpmaster.internal/ubuntu noble/main s390x libelf1 s390x 0.190-1 [68.7 kB] Get:3 http://ftpmaster.internal/ubuntu noble/main s390x libexpat1 s390x 2.5.0-2 [82.5 kB] Get:4 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libicu74 s390x 74.2-1ubuntu1 [10.9 MB] Get:5 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libxml2 s390x 2.9.14+dfsg-1.3build3 [819 kB] Get:6 http://ftpmaster.internal/ubuntu noble/main s390x libmagic-mgc s390x 1:5.45-2 [305 kB] Get:7 http://ftpmaster.internal/ubuntu noble/main s390x libmagic1 s390x 1:5.45-2 [91.6 kB] Get:8 http://ftpmaster.internal/ubuntu noble/main s390x file s390x 1:5.45-2 [22.2 kB] Get:9 http://ftpmaster.internal/ubuntu noble/main s390x gettext-base s390x 0.21-14 [39.1 kB] Get:10 http://ftpmaster.internal/ubuntu noble/main s390x libuchardet0 s390x 0.0.8-1 [76.1 kB] Get:11 http://ftpmaster.internal/ubuntu noble/main s390x groff-base 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libarchive13 s390x 3.7.2-1ubuntu2 [413 kB] Get:23 http://ftpmaster.internal/ubuntu noble/main s390x libbrotli1 s390x 1.1.0-2 [374 kB] Get:24 http://ftpmaster.internal/ubuntu noble/main s390x libsasl2-modules-db s390x 2.1.28+dfsg1-4 [20.8 kB] Get:25 http://ftpmaster.internal/ubuntu noble/main s390x libsasl2-2 s390x 2.1.28+dfsg1-4 [58.7 kB] Get:26 http://ftpmaster.internal/ubuntu noble/main s390x libldap2 s390x 2.6.6+dfsg-1~exp1ubuntu1 [199 kB] Get:27 http://ftpmaster.internal/ubuntu noble/main s390x librtmp1 s390x 2.4+20151223.gitfa8646d.1-2build4 [56.4 kB] Get:28 http://ftpmaster.internal/ubuntu noble/main s390x libssh-4 s390x 0.10.5-3ubuntu1 [183 kB] Get:29 http://ftpmaster.internal/ubuntu noble/main s390x libcurl4 s390x 8.4.0-2ubuntu1 [354 kB] Get:30 http://ftpmaster.internal/ubuntu noble/main s390x libjsoncpp25 s390x 1.9.5-6 [75.5 kB] Get:31 http://ftpmaster.internal/ubuntu noble/main s390x librhash0 s390x 1.4.3-3 [128 kB] Get:32 http://ftpmaster.internal/ubuntu noble-proposed/main 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[47.5 kB] Get:43 http://ftpmaster.internal/ubuntu noble/main s390x dwz s390x 0.15-1 [108 kB] Get:44 http://ftpmaster.internal/ubuntu noble/main s390x gettext s390x 0.21-14 [911 kB] Get:45 http://ftpmaster.internal/ubuntu noble/main s390x intltool-debian all 0.35.0+20060710.6 [23.2 kB] Get:46 http://ftpmaster.internal/ubuntu noble/main s390x po-debconf all 1.0.21+nmu1 [233 kB] Get:47 http://ftpmaster.internal/ubuntu noble/main s390x debhelper all 13.11.8ubuntu1 [940 kB] Get:48 http://ftpmaster.internal/ubuntu noble-proposed/universe s390x libbamtools2.5.2 s390x 2.5.2+dfsg-5 [142 kB] Get:49 http://ftpmaster.internal/ubuntu noble-proposed/main s390x zlib1g-dev s390x 1:1.3.dfsg-3ubuntu1 [905 kB] Get:50 http://ftpmaster.internal/ubuntu noble-proposed/universe s390x libbamtools-dev s390x 2.5.2+dfsg-5 [242 kB] Get:51 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libboost1.83-dev s390x 1.83.0-1ubuntu3 [10.7 MB] Get:52 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libboost-atomic1.83.0 s390x 1.83.0-1ubuntu3 [239 kB] Get:53 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libboost-atomic1.83-dev s390x 1.83.0-1ubuntu3 [235 kB] Get:54 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libboost-chrono1.83.0 s390x 1.83.0-1ubuntu3 [244 kB] Get:55 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libboost-chrono1.83-dev s390x 1.83.0-1ubuntu3 [247 kB] Get:56 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libboost-date-time1.83.0 s390x 1.83.0-1ubuntu3 [236 kB] Get:57 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libboost-serialization1.83.0 s390x 1.83.0-1ubuntu3 [349 kB] Get:58 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libboost-serialization1.83-dev s390x 1.83.0-1ubuntu3 [408 kB] Get:59 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libboost-date-time1.83-dev s390x 1.83.0-1ubuntu3 [239 kB] Get:60 http://ftpmaster.internal/ubuntu noble-proposed/universe s390x libboost-date-time-dev s390x 1.83.0.1ubuntu2 [4062 B] Get:61 http://ftpmaster.internal/ubuntu noble-proposed/universe s390x libboost-filesystem1.83.0 s390x 1.83.0-1ubuntu3 [286 kB] Get:62 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libboost-system1.83.0 s390x 1.83.0-1ubuntu3 [236 kB] Get:63 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libboost-system1.83-dev s390x 1.83.0-1ubuntu3 [231 kB] Get:64 http://ftpmaster.internal/ubuntu noble-proposed/universe s390x libboost-filesystem1.83-dev s390x 1.83.0-1ubuntu3 [305 kB] Get:65 http://ftpmaster.internal/ubuntu noble-proposed/universe s390x libboost-filesystem-dev s390x 1.83.0.1ubuntu2 [4096 B] Get:66 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libboost-program-options1.83.0 s390x 1.83.0-1ubuntu3 [325 kB] Get:67 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libboost-program-options1.83-dev s390x 1.83.0-1ubuntu3 [396 kB] Get:68 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libboost-program-options-dev s390x 1.83.0.1ubuntu2 [4088 B] Get:69 http://ftpmaster.internal/ubuntu noble-proposed/universe s390x libboost-system-dev s390x 1.83.0.1ubuntu2 [4206 B] Get:70 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libboost-thread1.83.0 s390x 1.83.0-1ubuntu3 [278 kB] Get:71 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libboost-thread1.83-dev s390x 1.83.0-1ubuntu3 [283 kB] Get:72 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libboost-thread-dev s390x 1.83.0.1ubuntu2 [4086 B] Get:73 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libboost1.83-tools-dev s390x 1.83.0-1ubuntu3 [1475 kB] Get:74 http://ftpmaster.internal/ubuntu noble-proposed/universe s390x libboost-tools-dev s390x 1.83.0.1ubuntu2 [4240 B] Get:75 http://ftpmaster.internal/ubuntu noble/main s390x libprotobuf-lite32 s390x 3.21.12-8ubuntu1 [241 kB] Get:76 http://ftpmaster.internal/ubuntu noble/main s390x libprotobuf32 s390x 3.21.12-8ubuntu1 [940 kB] Get:77 http://ftpmaster.internal/ubuntu noble/main s390x libprotoc32 s390x 3.21.12-8ubuntu1 [686 kB] Get:78 http://ftpmaster.internal/ubuntu noble/main s390x libprotobuf-dev s390x 3.21.12-8ubuntu1 [1429 kB] Get:79 http://ftpmaster.internal/ubuntu noble/universe s390x protobuf-compiler s390x 3.21.12-8ubuntu1 [28.9 kB] Preconfiguring packages ... Fetched 56.5 MB in 3s (21.0 MB/s) Selecting previously unselected package libelf1:s390x. (Reading database ... 13567 files and directories currently installed.) Preparing to unpack .../00-libelf1_0.190-1_s390x.deb ... Unpacking libelf1:s390x (0.190-1) ... Selecting previously unselected package libexpat1:s390x. Preparing to unpack .../01-libexpat1_2.5.0-2_s390x.deb ... Unpacking libexpat1:s390x (2.5.0-2) ... Selecting previously unselected package libicu74:s390x. Preparing to unpack .../02-libicu74_74.2-1ubuntu1_s390x.deb ... Unpacking libicu74:s390x (74.2-1ubuntu1) ... Selecting previously unselected package libxml2:s390x. Preparing to unpack .../03-libxml2_2.9.14+dfsg-1.3build3_s390x.deb ... Unpacking libxml2:s390x (2.9.14+dfsg-1.3build3) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../04-libmagic-mgc_1%3a5.45-2_s390x.deb ... Unpacking libmagic-mgc (1:5.45-2) ... Selecting previously unselected package libmagic1:s390x. 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Processing triggers for libc-bin (2.38-3ubuntu1) ... +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (s390x included in any all) +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 5.4.0-169-generic #187-Ubuntu SMP Thu Nov 23 14:52:16 UTC 2023 s390x (s390x) Toolchain package versions: binutils_2.41.50.20231214-1ubuntu1 dpkg-dev_1.22.1ubuntu5 g++-13_13.2.0-9ubuntu1 gcc-13_13.2.0-9ubuntu1 libc6-dev_2.38-3ubuntu1 libstdc++-13-dev_13.2.0-9ubuntu1 libstdc++6_13.2.0-9ubuntu1 linux-libc-dev_6.6.0-14.14 Package versions: adduser_3.137ubuntu1 advancecomp_2.5-1 apt_2.7.7 apt-utils_2.7.7 autoconf_2.71-3 automake_1:1.16.5-1.3 autopoint_0.21-14 autotools-dev_20220109.1 base-files_13ubuntu5 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zlib1g-dev_1:1.3.dfsg-3ubuntu1 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: berkeley-express Binary: berkeley-express, berkeley-express-doc Architecture: any all Version: 1.5.3+dfsg-3build3 Maintainer: Ubuntu Developers Uploaders: Michael R. Crusoe Homepage: http://bio.math.berkeley.edu/eXpress/index.html Standards-Version: 4.6.1 Vcs-Browser: https://salsa.debian.org/med-team/berkeley-express Vcs-Git: https://salsa.debian.org/med-team/berkeley-express.git Testsuite: autopkgtest Testsuite-Triggers: bowtie, gzip, samtools Build-Depends: debhelper-compat (= 13), libboost-thread-dev, libboost-system-dev, libboost-filesystem-dev, libboost-program-options-dev, libboost-date-time-dev, libbamtools-dev, libboost-tools-dev, libgoogle-perftools-dev [amd64 arm64 armel armhf i386 powerpc ppc64el], cmake, libprotobuf-dev, protobuf-compiler Package-List: berkeley-express deb science optional arch=any berkeley-express-doc deb doc optional arch=all Checksums-Sha1: a24eee0a32da390f2f75be7526bf6a9a971bd3a3 365872 berkeley-express_1.5.3+dfsg.orig.tar.xz 5a9428231dac726adbeee8eee48dcdf8def3cfd2 10936 berkeley-express_1.5.3+dfsg-3build3.debian.tar.xz Checksums-Sha256: f26e2f6e4e04671a64619f014ab2195f42d53fbac8b8b84f46082c5cdc6d845b 365872 berkeley-express_1.5.3+dfsg.orig.tar.xz 0ac83674ca984c5b85d272b6cc5078c83028d1d33b6d84257ba28cda1b62349c 10936 berkeley-express_1.5.3+dfsg-3build3.debian.tar.xz Files: cdb0c73b54ec20a662c14e6bfee0e384 365872 berkeley-express_1.5.3+dfsg.orig.tar.xz db23453ce46ca00e357c18648a0d4ab9 10936 berkeley-express_1.5.3+dfsg-3build3.debian.tar.xz Original-Maintainer: Debian Med Packaging Team -----BEGIN PGP SIGNATURE----- iQIzBAEBCgAdFiEEVovyKmYzfL/Jprm3LIPbyOm9DjcFAmWBsBwACgkQLIPbyOm9 DjfdVg/+LGpD6pPrt9bLJG4qXNeIfgpHWzqUoKVHaFf35b0b8rxkVmbfItVzTW74 NyE+bwt7WXaCRRMkv63T+daRmhO1DTEtCheNbk8TQ8BYAWQzsAWq8Lx2t/IiQN0p jpbOuipe1Un8/D519W4JXs4Q+JV9BJToBso8JKc3HuOf797xRiJV8weyqnBfOxc2 gcpTjOaNPUpEoQFi4bhi93qj3choLRFq7eKJy6BHTV32sxJx7No8LbT4bvYaXa3D lg+xyaJsfcX/4n4RPxwIRmKD0A5SnUWhTcIFtRW1HOM3+tSlNcWOulaGCy5ZjHkd y7QbHMfwCue3b+OtQeOYoNCmgcpJcwPlP7SUb8W6wOFPLjqw9Qc23eQ3C0E/HLOZ 2WedjBOhbUH1+9OWKiwQjUtm+0JmON0yxG0ibQPkOq5h9PNkuKinJSuzMIz9vcQM dK6GzrVgSZodErVyWlwVvbCDyNOPeOaih70Cz3CBaWvxGGPWv2IUHsK9jBb5JCqi QDSXVadwJrJUorNSAmeE5tKTkauUUBdyZ+OvvgbTqdPF0zYlBjN3xEhevw++TYE0 DcstkQHOpujqe6ELRZqj5qHjG2RbU9JY3GaSOhIC4zmeCSCF1ZbQ4uYPUiA/sgnv gHlijxS2wPqaYF+VU1MECeWzsN4IdO+Fl4XuI89G2LJsWf2KFYI= =Od3O -----END PGP SIGNATURE----- gpgv: Signature made Tue Dec 19 15:00:44 2023 UTC gpgv: using RSA key 568BF22A66337CBFC9A6B9B72C83DBC8E9BD0E37 gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./berkeley-express_1.5.3+dfsg-3build3.dsc: no acceptable signature found dpkg-source: info: extracting berkeley-express in /<> dpkg-source: info: unpacking berkeley-express_1.5.3+dfsg.orig.tar.xz dpkg-source: info: unpacking berkeley-express_1.5.3+dfsg-3build3.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying spelling-fixes dpkg-source: info: applying fix-bamtools-path dpkg-source: info: applying drop-zlib dpkg-source: info: applying correct-debug-flags.patch dpkg-source: info: applying privacy-breach.patch Check disk space ---------------- Sufficient free space for build User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf DEB_BUILD_OPTIONS=parallel=4 HOME=/sbuild-nonexistent LANG=C.UTF-8 LC_ALL=C.UTF-8 LOGNAME=buildd PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games SCHROOT_ALIAS_NAME=build-PACKAGEBUILD-27576186 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-27576186 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-27576186 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 berkeley-express dpkg-buildpackage: info: source version 1.5.3+dfsg-3build3 dpkg-buildpackage: info: source distribution noble dpkg-source --before-build . dpkg-buildpackage: info: host architecture s390x debian/rules clean dh clean debian/rules override_dh_clean make[1]: Entering directory '/<>' dh_clean src/config.h make[1]: Leaving directory '/<>' debian/rules binary-arch dh binary-arch dh_update_autotools_config -a dh_autoreconf -a dh_auto_configure -a cd obj-s390x-linux-gnu && DEB_PYTHON_INSTALL_LAYOUT=deb cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=None -DCMAKE_INSTALL_SYSCONFDIR=/etc -DCMAKE_INSTALL_LOCALSTATEDIR=/var -DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON -DCMAKE_FIND_USE_PACKAGE_REGISTRY=OFF -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON -DFETCHCONTENT_FULLY_DISCONNECTED=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run -DCMAKE_SKIP_INSTALL_ALL_DEPENDENCY=ON "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/s390x-linux-gnu .. CMake Deprecation Warning at CMakeLists.txt:1 (cmake_minimum_required): Compatibility with CMake < 3.5 will be removed from a future version of CMake. Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions. -- The C compiler identification is GNU 13.2.0 -- The CXX compiler identification is GNU 13.2.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/cc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Found Boost: /usr/lib/s390x-linux-gnu/cmake/Boost-1.83.0/BoostConfig.cmake (found suitable version "1.83.0", minimum required is "1.39") found components: thread system filesystem program_options date_time -- Could NOT find GPERFTOOLS_TCMALLOC: Install to improve speed. -- Found Protobuf: /usr/lib/s390x-linux-gnu/libprotobuf.so (found version "3.21.12") -- Do not try to find libbamtools.a -- Configuring done (0.7s) -- Generating done (0.0s) CMake Warning: Manually-specified variables were not used by the project: CMAKE_EXPORT_NO_PACKAGE_REGISTRY CMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY CMAKE_INSTALL_LIBDIR CMAKE_INSTALL_LOCALSTATEDIR CMAKE_INSTALL_RUNSTATEDIR CMAKE_INSTALL_SYSCONFDIR FETCHCONTENT_FULLY_DISCONNECTED -- Build files have been written to: /<>/obj-s390x-linux-gnu dh_auto_build -a cd obj-s390x-linux-gnu && make -j4 "INSTALL=install --strip-program=true" VERBOSE=1 make[1]: Entering directory '/<>/obj-s390x-linux-gnu' /usr/bin/cmake -S/<> -B/<>/obj-s390x-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /<>/obj-s390x-linux-gnu/CMakeFiles /<>/obj-s390x-linux-gnu//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/<>/obj-s390x-linux-gnu' make -f src/CMakeFiles/express.dir/build.make src/CMakeFiles/express.dir/depend make[3]: Entering directory '/<>/obj-s390x-linux-gnu' [ 5%] Running cpp protocol buffer compiler on /<>/src/targets.proto [ 11%] Running cpp protocol buffer compiler on /<>/src/alignments.proto cd /<>/obj-s390x-linux-gnu/src && /usr/bin/protoc --cpp_out :/<>/obj-s390x-linux-gnu/src -I /<>/src /<>/src/targets.proto cd /<>/obj-s390x-linux-gnu/src && /usr/bin/protoc --cpp_out :/<>/obj-s390x-linux-gnu/src -I /<>/src /<>/src/alignments.proto [libprotobuf WARNING google/protobuf/compiler/parser.cc:646] No syntax specified for the proto file: targets.proto. Please use 'syntax = "proto2";' or 'syntax = "proto3";' to specify a syntax version. (Defaulted to proto2 syntax.) [libprotobuf WARNING google/protobuf/compiler/parser.cc:646] No syntax specified for the proto file: alignments.proto. Please use 'syntax = "proto2";' or 'syntax = "proto3";' to specify a syntax version. (Defaulted to proto2 syntax.) cd /<>/obj-s390x-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/src /<>/obj-s390x-linux-gnu /<>/obj-s390x-linux-gnu/src /<>/obj-s390x-linux-gnu/src/CMakeFiles/express.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/<>/obj-s390x-linux-gnu' make -f src/CMakeFiles/express.dir/build.make src/CMakeFiles/express.dir/build make[3]: Entering directory '/<>/obj-s390x-linux-gnu' [ 16%] Building CXX object src/CMakeFiles/express.dir/biascorrection.cpp.o [ 22%] Building CXX object src/CMakeFiles/express.dir/bundles.cpp.o cd /<>/obj-s390x-linux-gnu/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_DATE_TIME_DYN_LINK -DBOOST_DATE_TIME_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -I/usr/include/bamtools -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/berkeley-express-1.5.3+dfsg-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -D__FILE__=\"\" -std=gnu++11 -MD -MT src/CMakeFiles/express.dir/biascorrection.cpp.o -MF CMakeFiles/express.dir/biascorrection.cpp.o.d -o CMakeFiles/express.dir/biascorrection.cpp.o -c /<>/src/biascorrection.cpp cd /<>/obj-s390x-linux-gnu/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_DATE_TIME_DYN_LINK -DBOOST_DATE_TIME_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -I/usr/include/bamtools -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/berkeley-express-1.5.3+dfsg-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -D__FILE__=\"\" -std=gnu++11 -MD -MT src/CMakeFiles/express.dir/bundles.cpp.o -MF CMakeFiles/express.dir/bundles.cpp.o.d -o CMakeFiles/express.dir/bundles.cpp.o -c /<>/src/bundles.cpp [ 27%] Building CXX object src/CMakeFiles/express.dir/directiondetector.cpp.o cd /<>/obj-s390x-linux-gnu/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_DATE_TIME_DYN_LINK -DBOOST_DATE_TIME_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -I/usr/include/bamtools -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/berkeley-express-1.5.3+dfsg-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -D__FILE__=\"\" -std=gnu++11 -MD -MT src/CMakeFiles/express.dir/directiondetector.cpp.o -MF CMakeFiles/express.dir/directiondetector.cpp.o.d -o CMakeFiles/express.dir/directiondetector.cpp.o -c /<>/src/directiondetector.cpp [ 33%] Building CXX object src/CMakeFiles/express.dir/fragments.cpp.o : warning: "__FILE__" redefined [-Wbuiltin-macro-redefined] : warning: "__FILE__" redefined [-Wbuiltin-macro-redefined] cd /<>/obj-s390x-linux-gnu/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_DATE_TIME_DYN_LINK -DBOOST_DATE_TIME_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -I/usr/include/bamtools -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/berkeley-express-1.5.3+dfsg-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -D__FILE__=\"\" -std=gnu++11 -MD -MT src/CMakeFiles/express.dir/fragments.cpp.o -MF CMakeFiles/express.dir/fragments.cpp.o.d -o CMakeFiles/express.dir/fragments.cpp.o -c /<>/src/fragments.cpp : warning: "__FILE__" redefined [-Wbuiltin-macro-redefined] : warning: "__FILE__" redefined [-Wbuiltin-macro-redefined] [ 38%] Building CXX object src/CMakeFiles/express.dir/lengthdistribution.cpp.o cd /<>/obj-s390x-linux-gnu/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_DATE_TIME_DYN_LINK -DBOOST_DATE_TIME_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -I/usr/include/bamtools -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/berkeley-express-1.5.3+dfsg-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -D__FILE__=\"\" -std=gnu++11 -MD -MT src/CMakeFiles/express.dir/lengthdistribution.cpp.o -MF CMakeFiles/express.dir/lengthdistribution.cpp.o.d -o CMakeFiles/express.dir/lengthdistribution.cpp.o -c /<>/src/lengthdistribution.cpp : warning: "__FILE__" redefined [-Wbuiltin-macro-redefined] [ 44%] Building CXX object src/CMakeFiles/express.dir/main.cpp.o cd /<>/obj-s390x-linux-gnu/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_DATE_TIME_DYN_LINK -DBOOST_DATE_TIME_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -I/usr/include/bamtools -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/berkeley-express-1.5.3+dfsg-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -D__FILE__=\"\" -std=gnu++11 -MD -MT src/CMakeFiles/express.dir/main.cpp.o -MF CMakeFiles/express.dir/main.cpp.o.d -o CMakeFiles/express.dir/main.cpp.o -c /<>/src/main.cpp : warning: "__FILE__" redefined [-Wbuiltin-macro-redefined] In file included from /usr/include/boost/math/special_functions/detail/round_fwd.hpp:11, from /usr/include/boost/math/special_functions/math_fwd.hpp:29, from /usr/include/boost/math/special_functions/beta.hpp:13, from /usr/include/boost/math/distributions/binomial.hpp:83, from /<>/src/lengthdistribution.cpp:15: /usr/include/boost/math/tools/config.hpp:23:6: warning: #warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)" [-Wcpp] 23 | # warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)" | ^~~~~~~ [ 50%] Building CXX object src/CMakeFiles/express.dir/mapparser.cpp.o cd /<>/obj-s390x-linux-gnu/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_DATE_TIME_DYN_LINK -DBOOST_DATE_TIME_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -I/usr/include/bamtools -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/berkeley-express-1.5.3+dfsg-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -D__FILE__=\"\" -std=gnu++11 -MD -MT src/CMakeFiles/express.dir/mapparser.cpp.o -MF CMakeFiles/express.dir/mapparser.cpp.o.d -o CMakeFiles/express.dir/mapparser.cpp.o -c /<>/src/mapparser.cpp : warning: "__FILE__" redefined [-Wbuiltin-macro-redefined] [ 55%] Building CXX object src/CMakeFiles/express.dir/markovmodel.cpp.o cd /<>/obj-s390x-linux-gnu/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_DATE_TIME_DYN_LINK -DBOOST_DATE_TIME_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -I/usr/include/bamtools -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/berkeley-express-1.5.3+dfsg-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -D__FILE__=\"\" -std=gnu++11 -MD -MT src/CMakeFiles/express.dir/markovmodel.cpp.o -MF CMakeFiles/express.dir/markovmodel.cpp.o.d -o CMakeFiles/express.dir/markovmodel.cpp.o -c /<>/src/markovmodel.cpp : warning: "__FILE__" redefined [-Wbuiltin-macro-redefined] [ 61%] Building CXX object src/CMakeFiles/express.dir/mismatchmodel.cpp.o cd /<>/obj-s390x-linux-gnu/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_DATE_TIME_DYN_LINK -DBOOST_DATE_TIME_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -I/usr/include/bamtools -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/berkeley-express-1.5.3+dfsg-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -D__FILE__=\"\" -std=gnu++11 -MD -MT src/CMakeFiles/express.dir/mismatchmodel.cpp.o -MF CMakeFiles/express.dir/mismatchmodel.cpp.o.d -o CMakeFiles/express.dir/mismatchmodel.cpp.o -c /<>/src/mismatchmodel.cpp : warning: "__FILE__" redefined [-Wbuiltin-macro-redefined] [ 66%] Building CXX object src/CMakeFiles/express.dir/robertsfilter.cpp.o cd /<>/obj-s390x-linux-gnu/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_DATE_TIME_DYN_LINK -DBOOST_DATE_TIME_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -I/usr/include/bamtools -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/berkeley-express-1.5.3+dfsg-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -D__FILE__=\"\" -std=gnu++11 -MD -MT src/CMakeFiles/express.dir/robertsfilter.cpp.o -MF CMakeFiles/express.dir/robertsfilter.cpp.o.d -o CMakeFiles/express.dir/robertsfilter.cpp.o -c /<>/src/robertsfilter.cpp : warning: "__FILE__" redefined [-Wbuiltin-macro-redefined] [ 72%] Building CXX object src/CMakeFiles/express.dir/sequence.cpp.o cd /<>/obj-s390x-linux-gnu/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_DATE_TIME_DYN_LINK -DBOOST_DATE_TIME_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -I/usr/include/bamtools -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/berkeley-express-1.5.3+dfsg-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -D__FILE__=\"\" -std=gnu++11 -MD -MT src/CMakeFiles/express.dir/sequence.cpp.o -MF CMakeFiles/express.dir/sequence.cpp.o.d -o CMakeFiles/express.dir/sequence.cpp.o -c /<>/src/sequence.cpp : warning: "__FILE__" redefined [-Wbuiltin-macro-redefined] [ 77%] Building CXX object src/CMakeFiles/express.dir/targets.cpp.o cd /<>/obj-s390x-linux-gnu/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_DATE_TIME_DYN_LINK -DBOOST_DATE_TIME_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -I/usr/include/bamtools -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/berkeley-express-1.5.3+dfsg-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -D__FILE__=\"\" -std=gnu++11 -MD -MT src/CMakeFiles/express.dir/targets.cpp.o -MF CMakeFiles/express.dir/targets.cpp.o.d -o CMakeFiles/express.dir/targets.cpp.o -c /<>/src/targets.cpp : warning: "__FILE__" redefined [-Wbuiltin-macro-redefined] In file included from /usr/include/boost/math/special_functions/detail/round_fwd.hpp:11, from /usr/include/boost/math/special_functions/math_fwd.hpp:29, from /usr/include/boost/math/special_functions/beta.hpp:13, from /usr/include/boost/math/distributions/binomial.hpp:83, from /<>/src/sequence.cpp:11: /usr/include/boost/math/tools/config.hpp:23:6: warning: #warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)" [-Wcpp] 23 | # warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)" | ^~~~~~~ [ 83%] Building CXX object src/CMakeFiles/express.dir/threadsafety.cpp.o cd /<>/obj-s390x-linux-gnu/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_DATE_TIME_DYN_LINK -DBOOST_DATE_TIME_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -I/usr/include/bamtools -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/berkeley-express-1.5.3+dfsg-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -D__FILE__=\"\" -std=gnu++11 -MD -MT src/CMakeFiles/express.dir/threadsafety.cpp.o -MF CMakeFiles/express.dir/threadsafety.cpp.o.d -o CMakeFiles/express.dir/threadsafety.cpp.o -c /<>/src/threadsafety.cpp : warning: "__FILE__" redefined [-Wbuiltin-macro-redefined] [ 88%] Building CXX object src/CMakeFiles/express.dir/alignments.pb.cc.o cd /<>/obj-s390x-linux-gnu/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_DATE_TIME_DYN_LINK -DBOOST_DATE_TIME_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -I/usr/include/bamtools -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/berkeley-express-1.5.3+dfsg-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -D__FILE__=\"\" -std=gnu++11 -MD -MT src/CMakeFiles/express.dir/alignments.pb.cc.o -MF CMakeFiles/express.dir/alignments.pb.cc.o.d -o CMakeFiles/express.dir/alignments.pb.cc.o -c /<>/obj-s390x-linux-gnu/src/alignments.pb.cc : warning: "__FILE__" redefined [-Wbuiltin-macro-redefined] [ 94%] Building CXX object src/CMakeFiles/express.dir/targets.pb.cc.o cd /<>/obj-s390x-linux-gnu/src && /usr/bin/c++ -DBOOST_ATOMIC_DYN_LINK -DBOOST_ATOMIC_NO_LIB -DBOOST_DATE_TIME_DYN_LINK -DBOOST_DATE_TIME_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_FILESYSTEM_NO_LIB -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_NO_LIB -DBOOST_SYSTEM_DYN_LINK -DBOOST_SYSTEM_NO_LIB -DBOOST_THREAD_DYN_LINK -DBOOST_THREAD_NO_LIB -I/usr/include/bamtools -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/berkeley-express-1.5.3+dfsg-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -D__FILE__=\"\" -std=gnu++11 -MD -MT src/CMakeFiles/express.dir/targets.pb.cc.o -MF CMakeFiles/express.dir/targets.pb.cc.o.d -o CMakeFiles/express.dir/targets.pb.cc.o -c /<>/obj-s390x-linux-gnu/src/targets.pb.cc : warning: "__FILE__" redefined [-Wbuiltin-macro-redefined] [100%] Linking CXX executable express cd /<>/obj-s390x-linux-gnu/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/express.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fno-omit-frame-pointer -mbackchain -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -fdebug-prefix-map=/<>=/usr/src/berkeley-express-1.5.3+dfsg-3build3 -Wdate-time -D_FORTIFY_SOURCE=3 -D__FILE__=\"\" -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/express.dir/biascorrection.cpp.o CMakeFiles/express.dir/bundles.cpp.o CMakeFiles/express.dir/directiondetector.cpp.o CMakeFiles/express.dir/fragments.cpp.o CMakeFiles/express.dir/lengthdistribution.cpp.o CMakeFiles/express.dir/main.cpp.o CMakeFiles/express.dir/mapparser.cpp.o CMakeFiles/express.dir/markovmodel.cpp.o CMakeFiles/express.dir/mismatchmodel.cpp.o CMakeFiles/express.dir/robertsfilter.cpp.o CMakeFiles/express.dir/sequence.cpp.o CMakeFiles/express.dir/targets.cpp.o CMakeFiles/express.dir/threadsafety.cpp.o CMakeFiles/express.dir/alignments.pb.cc.o CMakeFiles/express.dir/targets.pb.cc.o -o express /usr/lib/s390x-linux-gnu/libboost_thread.so.1.83.0 /usr/lib/s390x-linux-gnu/libboost_system.so.1.83.0 /usr/lib/s390x-linux-gnu/libboost_filesystem.so.1.83.0 /usr/lib/s390x-linux-gnu/libboost_program_options.so.1.83.0 /usr/lib/s390x-linux-gnu/libboost_date_time.so.1.83.0 -lbamtools -lprotobuf -lpthread -lrt /usr/lib/s390x-linux-gnu/libboost_atomic.so.1.83.0 make[3]: Leaving directory '/<>/obj-s390x-linux-gnu' [100%] Built target express make[2]: Leaving directory '/<>/obj-s390x-linux-gnu' /usr/bin/cmake -E cmake_progress_start /<>/obj-s390x-linux-gnu/CMakeFiles 0 make[1]: Leaving directory '/<>/obj-s390x-linux-gnu' dh_auto_test -a create-stamp debian/debhelper-build-stamp dh_prep -a dh_installdirs -a dh_auto_install -a cd obj-s390x-linux-gnu && make -j4 install DESTDIR=/<>/berkeley-express-1.5.3\+dfsg/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[1]: Entering directory '/<>/obj-s390x-linux-gnu' /usr/bin/cmake -S/<> -B/<>/obj-s390x-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 preinstall make[2]: Entering directory '/<>/obj-s390x-linux-gnu' make[2]: Nothing to be done for 'preinstall'. make[2]: Leaving directory '/<>/obj-s390x-linux-gnu' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "None" -- Installing: /<>/debian/tmp/usr/bin/express make[1]: Leaving directory '/<>/obj-s390x-linux-gnu' dh_install -a dh_installdocs -a dh_installchangelogs -a dh_installexamples -a dh_installman -a dh_perl -a dh_link -a dh_strip_nondeterminism -a debian/rules override_dh_compress make[1]: Entering directory '/<>' dh_compress --exclude=express-doc.pdf make[1]: Leaving directory '/<>' dh_fixperms -a dh_missing -a dh_dwz -a dh_strip -a 9c31ec2b7068352b7bed19baa41be5bf9e19c609 dh_makeshlibs -a dh_shlibdeps -a dh_installdeb -a dh_gencontrol -a dh_md5sums -a dh_builddeb -a INFO: pkgstriptranslations version 154 INFO: pkgstriptranslations version 154 pkgstriptranslations: processing berkeley-express (in debian/berkeley-express); do_strip: , oemstrip: pkgstriptranslations: processing berkeley-express-dbgsym (in debian/.debhelper/berkeley-express/dbgsym-root); do_strip: , oemstrip: pkgmaintainermangler: Not overriding Maintainer for domain lists.ubuntu.com pkgmaintainermangler: Not overriding Maintainer for domain lists.ubuntu.com pkgstripfiles: processing control file: debian/berkeley-express/DEBIAN/control, package berkeley-express, directory debian/berkeley-express pkgstripfiles: Running PNG optimization (using 4 cpus) for package berkeley-express ... pkgstripfiles: No PNG files. dpkg-deb: building package 'berkeley-express' in '../berkeley-express_1.5.3+dfsg-3build3_s390x.deb'. pkgstripfiles: processing control file: debian/.debhelper/berkeley-express/dbgsym-root/DEBIAN/control, package berkeley-express-dbgsym, directory debian/.debhelper/berkeley-express/dbgsym-root dpkg-deb: building package 'berkeley-express-dbgsym' in 'debian/.debhelper/scratch-space/build-berkeley-express/berkeley-express-dbgsym_1.5.3+dfsg-3build3_s390x.deb'. 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libpam-modules-bin (= 1.5.2-9.1ubuntu1), libpam-runtime (= 1.5.2-9.1ubuntu1), libpam0g (= 1.5.2-9.1ubuntu1), libpcre2-8-0 (= 10.42-4ubuntu1), libperl5.36 (= 5.36.0-10ubuntu1), libpipeline1 (= 1.5.7-1), libproc2-0 (= 2:4.0.4-2ubuntu1), libprotobuf-dev (= 3.21.12-8ubuntu1), libprotobuf-lite32 (= 3.21.12-8ubuntu1), libprotobuf32 (= 3.21.12-8ubuntu1), libprotoc32 (= 3.21.12-8ubuntu1), libpsl5 (= 0.21.2-1build1), librhash0 (= 1.4.3-3), librtmp1 (= 2.4+20151223.gitfa8646d.1-2build4), libsasl2-2 (= 2.1.28+dfsg1-4), libsasl2-modules-db (= 2.1.28+dfsg1-4), libseccomp2 (= 2.5.4-2ubuntu1), libselinux1 (= 3.5-1build2), libsframe1 (= 2.41.50.20231214-1ubuntu1), libsmartcols1 (= 2.39.2-6ubuntu1), libssh-4 (= 0.10.5-3ubuntu1), libssl3 (= 3.0.10-1ubuntu3), libstdc++-13-dev (= 13.2.0-9ubuntu1), libstdc++6 (= 13.2.0-9ubuntu1), libsub-override-perl (= 0.10-1), libsystemd0 (= 255-1ubuntu1), libtasn1-6 (= 4.19.0-3), libtinfo6 (= 6.4+20231209-1), libtirpc-common (= 1.3.4+ds-1), libtirpc-dev (= 1.3.4+ds-1), libtirpc3 (= 1.3.4+ds-1), libtool (= 2.4.7-7), libubsan1 (= 13.2.0-9ubuntu1), libuchardet0 (= 0.0.8-1), libudev1 (= 255-1ubuntu1), libunistring5 (= 1.1-2), libuuid1 (= 2.39.2-6ubuntu1), libuv1 (= 1.46.0-2ubuntu1), libxml2 (= 2.9.14+dfsg-1.3build3), libzstd1 (= 1.5.5+dfsg2-2), linux-libc-dev (= 6.6.0-14.14), login (= 1:4.13+dfsg1-3ubuntu1), lto-disabled-list (= 44), m4 (= 1.4.19-4), make (= 4.3-4.1build1), man-db (= 2.12.0-1), mawk (= 1.3.4.20231126-1), ncurses-base (= 6.4+20231209-1), ncurses-bin (= 6.4+20231209-1), patch (= 2.7.6-7build2), perl (= 5.36.0-10ubuntu1), perl-base (= 5.36.0-10ubuntu1), perl-modules-5.36 (= 5.36.0-10ubuntu1), po-debconf (= 1.0.21+nmu1), procps (= 2:4.0.4-2ubuntu1), protobuf-compiler (= 3.21.12-8ubuntu1), rpcsvc-proto (= 1.4.2-0ubuntu6), sed (= 4.9-1), sensible-utils (= 0.0.20), sysvinit-utils (= 3.08-3ubuntu1), tar (= 1.34+dfsg-1.2ubuntu2), util-linux (= 2.39.2-6ubuntu1), xz-utils (= 5.4.5-0.1), zlib1g (= 1:1.3.dfsg-3ubuntu1), zlib1g-dev (= 1:1.3.dfsg-3ubuntu1) Environment: DEB_BUILD_OPTIONS="parallel=4" DEB_BUILD_PROFILES="noudeb" LANG="C.UTF-8" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1702997189" +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ berkeley-express_1.5.3+dfsg-3build3_s390x.deb --------------------------------------------- new Debian package, version 2.0. size 231724 bytes: control archive=1853 bytes. 3190 bytes, 51 lines control 454 bytes, 6 lines md5sums Package: berkeley-express Version: 1.5.3+dfsg-3build3 Architecture: s390x Maintainer: Ubuntu Developers Installed-Size: 638 Depends: libbamtools2.5.2 (>= 2.5.2+dfsg), libboost-filesystem1.83.0 (>= 1.83.0), libboost-program-options1.83.0 (>= 1.83.0), libboost-thread1.83.0 (>= 1.83.0), libc6 (>= 2.38), libgcc-s1 (>= 3.3.1), libprotobuf32 (>= 3.21.12), libstdc++6 (>= 13.1) Recommends: med-config Section: science Priority: optional Homepage: http://bio.math.berkeley.edu/eXpress/index.html Description: Streaming quantification for high-throughput sequencing eXpress is a streaming tool for quantifying the abundances of a set of target sequences from sampled subsequences. Example applications include transcript-level RNA-Seq quantification, allele-specific/haplotype expression analysis (from RNA-Seq), transcription factor binding quantification in ChIP-Seq, and analysis of metagenomic data. It is based on an online-EM algorithm that results in space (memory) requirements proportional to the total size of the target sequences and time requirements that are proportional to the number of sampled fragments. Thus, in applications such as RNA-Seq, eXpress can accurately quantify much larger samples than other currently available tools greatly reducing computing infrastructure requirements. eXpress can be used to build lightweight high-throughput sequencing processing pipelines when coupled with a streaming aligner (such as Bowtie), as output can be piped directly into eXpress, effectively eliminating the need to store read alignments in memory or on disk. . In an analysis of the performance of eXpress for RNA-Seq data, it was observed that this efficiency does not come at a cost of accuracy. eXpress is more accurate than other available tools, even when limited to smaller datasets that do not require such efficiency. Moreover, like the Cufflinks program, eXpress can be used to estimate transcript abundances in multi-isoform genes. eXpress is also able to resolve multi-mappings of reads across gene families, and does not require a reference genome so that it can be used in conjunction with de novo assemblers such as Trinity, Oases, or Trans-ABySS. The underlying model is based on previously described probabilistic models developed for RNA-Seq but is applicable to other settings where target sequences are sampled, and includes parameters for fragment length distributions, errors in reads, and sequence-specific fragment bias. . eXpress can be used to resolve ambiguous mappings in other high-throughput sequencing based applications. The only required inputs to eXpress are a set of target sequences and a set of sequenced fragments multiply-aligned to them. While these target sequences will often be gene isoforms, they need not be. Haplotypes can be used as the reference for allele-specific expression analysis, binding regions for ChIP-Seq, or target genomes in metagenomics experiments. eXpress is useful in any analysis where reads multi-map to sequences that differ in abundance. Original-Maintainer: Debian Med Packaging Team drwxr-xr-x root/root 0 2023-12-19 14:46 ./ drwxr-xr-x root/root 0 2023-12-19 14:46 ./usr/ drwxr-xr-x root/root 0 2023-12-19 14:46 ./usr/bin/ lrwxrwxrwx root/root 0 2023-12-19 14:46 ./usr/bin/berkeley-express -> ../lib/debian-med/bin/express drwxr-xr-x root/root 0 2023-12-19 14:46 ./usr/lib/ drwxr-xr-x root/root 0 2023-12-19 14:46 ./usr/lib/debian-med/ drwxr-xr-x root/root 0 2023-12-19 14:46 ./usr/lib/debian-med/bin/ -rwxr-xr-x root/root 630216 2023-12-19 14:46 ./usr/lib/debian-med/bin/express drwxr-xr-x root/root 0 2023-12-19 14:46 ./usr/share/ drwxr-xr-x root/root 0 2023-12-19 14:46 ./usr/share/doc/ drwxr-xr-x root/root 0 2023-12-19 14:46 ./usr/share/doc/berkeley-express/ -rw-r--r-- root/root 987 2022-11-01 19:13 ./usr/share/doc/berkeley-express/README.Debian -rw-r--r-- root/root 1540 2019-11-14 16:14 ./usr/share/doc/berkeley-express/README.gz -rw-r--r-- root/root 855 2023-12-19 14:46 ./usr/share/doc/berkeley-express/changelog.Debian.gz -rw-r--r-- root/root 2869 2022-11-01 19:13 ./usr/share/doc/berkeley-express/copyright drwxr-xr-x root/root 0 2023-12-19 14:46 ./usr/share/man/ drwxr-xr-x root/root 0 2023-12-19 14:46 ./usr/share/man/man1/ -rw-r--r-- root/root 1192 2023-12-19 14:46 ./usr/share/man/man1/berkeley-express.1.gz +------------------------------------------------------------------------------+ | Post Build | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not removing build depends: as requested +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: s390x Build Type: any Build-Space: 109156 Build-Time: 32 Distribution: noble-proposed Host Architecture: s390x Install-Time: 10 Job: berkeley-express_1.5.3+dfsg-3build3.dsc Machine Architecture: s390x Package: berkeley-express Package-Time: 44 Source-Version: 1.5.3+dfsg-3build3 Space: 109156 Status: successful Version: 1.5.3+dfsg-3build3 -------------------------------------------------------------------------------- Finished at 2023-12-19T16:50:09Z Build needed 00:00:44, 109156k disk space RUN: /usr/share/launchpad-buildd/bin/in-target scan-for-processes --backend=chroot --series=noble --arch=s390x PACKAGEBUILD-27576186 Scanning for processes to kill in build PACKAGEBUILD-27576186