https://launchpad.net/ubuntu/+source/berkeley-express/1.5.3+dfsg-3build3/+build/27576181 RUN: /usr/share/launchpad-buildd/bin/builder-prep Kernel version: Linux lcy02-amd64-104 5.4.0-169-generic #187-Ubuntu SMP Thu Nov 23 14:52:28 UTC 2023 x86_64 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 15:09:23 ntpdate[1858]: adjust time server 10.131.248.1 offset 0.000117 sec RUN: /usr/share/launchpad-buildd/bin/in-target unpack-chroot --backend=chroot --series=noble --arch=amd64 PACKAGEBUILD-27576181 --image-type chroot /home/buildd/filecache-default/1fe94ca8758119221c8de2550665a1bb335bd6a9 Creating target for build PACKAGEBUILD-27576181 RUN: /usr/share/launchpad-buildd/bin/in-target mount-chroot --backend=chroot --series=noble --arch=amd64 PACKAGEBUILD-27576181 Starting target for build PACKAGEBUILD-27576181 RUN: /usr/share/launchpad-buildd/bin/in-target override-sources-list --backend=chroot --series=noble --arch=amd64 PACKAGEBUILD-27576181 '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-27576181 RUN: /usr/share/launchpad-buildd/bin/in-target update-debian-chroot --backend=chroot --series=noble --arch=amd64 PACKAGEBUILD-27576181 Updating target for build PACKAGEBUILD-27576181 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 amd64 Packages [1406 kB] Get:6 http://ftpmaster.internal/ubuntu noble/main Translation-en [515 kB] Get:7 http://ftpmaster.internal/ubuntu noble/universe amd64 Packages [15.0 MB] Get:8 http://ftpmaster.internal/ubuntu noble/universe Translation-en [6031 kB] Get:9 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 Packages [160 kB] Get:10 http://ftpmaster.internal/ubuntu noble-proposed/main Translation-en [44.9 kB] Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe amd64 Packages [1070 kB] Get:12 http://ftpmaster.internal/ubuntu noble-proposed/universe Translation-en [325 kB] Fetched 25.1 MB in 3s (7467 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-x86-64-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 libgprofng0 libgssapi-krb5-2 libhwasan0 libidn2-0 libitm1 libk5crypto3 libkmod2 libkrb5-3 libkrb5support0 liblsan0 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 libquadmath0 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 libtsan2 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 135 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 111 MB of archives. After this operation, 6093 kB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu noble/main amd64 libnsl-dev amd64 1.3.0-3 [71.2 kB] Get:2 http://ftpmaster.internal/ubuntu noble/main amd64 libc6-dev amd64 2.38-3ubuntu1 [2114 kB] Get:3 http://ftpmaster.internal/ubuntu noble/main amd64 libc-dev-bin amd64 2.38-3ubuntu1 [20.3 kB] Get:4 http://ftpmaster.internal/ubuntu noble/main amd64 libtirpc-common all 1.3.4+ds-1 [7920 B] Get:5 http://ftpmaster.internal/ubuntu noble/main amd64 libtirpc-dev amd64 1.3.4+ds-1 [193 kB] Get:6 http://ftpmaster.internal/ubuntu noble/main amd64 libgssapi-krb5-2 amd64 1.20.1-5build1 [142 kB] Get:7 http://ftpmaster.internal/ubuntu noble/main amd64 libkrb5-3 amd64 1.20.1-5build1 [346 kB] Get:8 http://ftpmaster.internal/ubuntu noble/main amd64 libk5crypto3 amd64 1.20.1-5build1 [81.3 kB] Get:9 http://ftpmaster.internal/ubuntu noble/main amd64 libkrb5support0 amd64 1.20.1-5build1 [33.2 kB] Get:10 http://ftpmaster.internal/ubuntu noble/main amd64 libssl3 amd64 3.0.10-1ubuntu3 [1910 kB] Get:11 http://ftpmaster.internal/ubuntu noble/main amd64 libtirpc3 amd64 1.3.4+ds-1 [81.4 kB] Get:12 http://ftpmaster.internal/ubuntu noble/main amd64 libnsl2 amd64 1.3.0-3 [41.3 kB] Get:13 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 linux-libc-dev amd64 6.6.0-14.14 [1580 kB] Get:14 http://ftpmaster.internal/ubuntu noble/main amd64 libcc1-0 amd64 13.2.0-9ubuntu1 [48.0 kB] Get:15 http://ftpmaster.internal/ubuntu noble/main amd64 libgprofng0 amd64 2.41.50.20231214-1ubuntu1 [858 kB] Get:16 http://ftpmaster.internal/ubuntu noble/main amd64 libctf0 amd64 2.41.50.20231214-1ubuntu1 [83.2 kB] Get:17 http://ftpmaster.internal/ubuntu noble/main amd64 libctf-nobfd0 amd64 2.41.50.20231214-1ubuntu1 [86.3 kB] Get:18 http://ftpmaster.internal/ubuntu noble/main amd64 binutils-x86-64-linux-gnu amd64 2.41.50.20231214-1ubuntu1 [2510 kB] Get:19 http://ftpmaster.internal/ubuntu noble/main amd64 libbinutils amd64 2.41.50.20231214-1ubuntu1 [539 kB] Get:20 http://ftpmaster.internal/ubuntu noble/main amd64 binutils-common amd64 2.41.50.20231214-1ubuntu1 [258 kB] Get:21 http://ftpmaster.internal/ubuntu noble/main amd64 binutils amd64 2.41.50.20231214-1ubuntu1 [7696 B] Get:22 http://ftpmaster.internal/ubuntu noble/main amd64 gcc-13-base amd64 13.2.0-9ubuntu1 [45.2 kB] Get:23 http://ftpmaster.internal/ubuntu noble/main amd64 libgcc-s1 amd64 13.2.0-9ubuntu1 [63.1 kB] Get:24 http://ftpmaster.internal/ubuntu noble/main amd64 libgomp1 amd64 13.2.0-9ubuntu1 [142 kB] Get:25 http://ftpmaster.internal/ubuntu noble/main amd64 libitm1 amd64 13.2.0-9ubuntu1 [29.5 kB] Get:26 http://ftpmaster.internal/ubuntu noble/main amd64 libatomic1 amd64 13.2.0-9ubuntu1 [10.5 kB] Get:27 http://ftpmaster.internal/ubuntu noble/main amd64 libasan8 amd64 13.2.0-9ubuntu1 [2835 kB] Get:28 http://ftpmaster.internal/ubuntu noble/main amd64 liblsan0 amd64 13.2.0-9ubuntu1 [1203 kB] Get:29 http://ftpmaster.internal/ubuntu noble/main amd64 libtsan2 amd64 13.2.0-9ubuntu1 [2606 kB] Get:30 http://ftpmaster.internal/ubuntu noble/main amd64 libubsan1 amd64 13.2.0-9ubuntu1 [1105 kB] Get:31 http://ftpmaster.internal/ubuntu noble/main amd64 libhwasan0 amd64 13.2.0-9ubuntu1 [1262 kB] Get:32 http://ftpmaster.internal/ubuntu noble/main amd64 libquadmath0 amd64 13.2.0-9ubuntu1 [153 kB] Get:33 http://ftpmaster.internal/ubuntu noble/main amd64 g++-13 amd64 13.2.0-9ubuntu1 [12.2 MB] Get:34 http://ftpmaster.internal/ubuntu noble/main amd64 libstdc++-13-dev amd64 13.2.0-9ubuntu1 [2336 kB] Get:35 http://ftpmaster.internal/ubuntu noble/main amd64 libgcc-13-dev amd64 13.2.0-9ubuntu1 [2687 kB] Get:36 http://ftpmaster.internal/ubuntu noble/main amd64 gcc-13 amd64 13.2.0-9ubuntu1 [21.5 MB] Get:37 http://ftpmaster.internal/ubuntu noble/main amd64 cpp-13 amd64 13.2.0-9ubuntu1 [10.7 MB] Get:38 http://ftpmaster.internal/ubuntu noble/main amd64 libstdc++6 amd64 13.2.0-9ubuntu1 [771 kB] Get:39 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 zlib1g amd64 1:1.3.dfsg-3ubuntu1 [63.3 kB] Get:40 http://ftpmaster.internal/ubuntu noble/main amd64 libsframe1 amd64 2.41.50.20231214-1ubuntu1 [13.8 kB] Get:41 http://ftpmaster.internal/ubuntu noble/main amd64 libzstd1 amd64 1.5.5+dfsg2-2 [297 kB] Get:42 http://ftpmaster.internal/ubuntu noble/main amd64 libc6 amd64 2.38-3ubuntu1 [3248 kB] Get:43 http://ftpmaster.internal/ubuntu noble/main amd64 base-files amd64 13ubuntu5 [73.6 kB] Get:44 http://ftpmaster.internal/ubuntu noble/main amd64 debianutils amd64 5.14 [89.0 kB] Get:45 http://ftpmaster.internal/ubuntu noble/main amd64 bash amd64 5.2.21-2ubuntu1 [795 kB] Get:46 http://ftpmaster.internal/ubuntu noble/main amd64 bsdutils amd64 1:2.39.2-6ubuntu1 [93.9 kB] Get:47 http://ftpmaster.internal/ubuntu noble/main amd64 coreutils amd64 9.4-2ubuntu1 [1395 kB] Get:48 http://ftpmaster.internal/ubuntu noble/main amd64 diffutils amd64 1:3.10-1 [176 kB] Get:49 http://ftpmaster.internal/ubuntu noble/main amd64 liblzma5 amd64 5.4.5-0.1 [128 kB] Get:50 http://ftpmaster.internal/ubuntu noble/main amd64 libapparmor1 amd64 4.0.0~alpha2-0ubuntu7 [48.2 kB] Get:51 http://ftpmaster.internal/ubuntu noble/main amd64 libaudit-common all 1:3.1.2-1 [5512 B] Get:52 http://ftpmaster.internal/ubuntu noble/main amd64 libcap-ng0 amd64 0.8.3-3 [15.3 kB] Get:53 http://ftpmaster.internal/ubuntu noble/main amd64 libaudit1 amd64 1:3.1.2-1 [46.7 kB] Get:54 http://ftpmaster.internal/ubuntu noble/main amd64 libblkid1 amd64 2.39.2-6ubuntu1 [122 kB] Get:55 http://ftpmaster.internal/ubuntu noble/main amd64 libkmod2 amd64 30+20230601-2ubuntu1 [51.4 kB] Get:56 http://ftpmaster.internal/ubuntu noble/main amd64 libpcre2-8-0 amd64 10.42-4ubuntu1 [228 kB] Get:57 http://ftpmaster.internal/ubuntu noble/main amd64 libselinux1 amd64 3.5-1build2 [78.5 kB] Get:58 http://ftpmaster.internal/ubuntu noble/main amd64 libmount1 amd64 2.39.2-6ubuntu1 [132 kB] Get:59 http://ftpmaster.internal/ubuntu noble/main amd64 libpam0g amd64 1.5.2-9.1ubuntu1 [65.1 kB] Get:60 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libseccomp2 amd64 2.5.4-2ubuntu1 [49.3 kB] Get:61 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 systemd-sysv amd64 255-1ubuntu1 [11.7 kB] Get:62 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 systemd-dev all 255-1ubuntu1 [98.5 kB] Get:63 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 systemd amd64 255-1ubuntu1 [3484 kB] Get:64 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libsystemd-shared amd64 255-1ubuntu1 [2062 kB] Get:65 http://ftpmaster.internal/ubuntu noble/main amd64 libargon2-1 amd64 0~20190702+dfsg-4 [21.4 kB] Get:66 http://ftpmaster.internal/ubuntu noble/main amd64 libuuid1 amd64 2.39.2-6ubuntu1 [34.1 kB] Get:67 http://ftpmaster.internal/ubuntu noble/main amd64 libcryptsetup12 amd64 2:2.6.1-5ubuntu1 [242 kB] Get:68 http://ftpmaster.internal/ubuntu noble/main amd64 libfdisk1 amd64 2.39.2-6ubuntu1 [145 kB] Get:69 http://ftpmaster.internal/ubuntu noble/main amd64 mount amd64 2.39.2-6ubuntu1 [118 kB] Get:70 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libsystemd0 amd64 255-1ubuntu1 [427 kB] Get:71 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libudev1 amd64 255-1ubuntu1 [169 kB] Get:72 http://ftpmaster.internal/ubuntu noble/main amd64 libxxhash0 amd64 0.8.2-2 [25.5 kB] Get:73 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libapt-pkg6.0 amd64 2.7.7 [945 kB] Get:74 http://ftpmaster.internal/ubuntu noble/main amd64 tar amd64 1.34+dfsg-1.2ubuntu2 [293 kB] Get:75 http://ftpmaster.internal/ubuntu noble/main amd64 dpkg amd64 1.22.1ubuntu5 [1387 kB] Get:76 http://ftpmaster.internal/ubuntu noble/main amd64 grep amd64 3.11-3 [161 kB] Get:77 http://ftpmaster.internal/ubuntu noble/main amd64 login amd64 1:4.13+dfsg1-3ubuntu1 [201 kB] Get:78 http://ftpmaster.internal/ubuntu noble/main amd64 ncurses-bin amd64 6.4+20231209-1 [187 kB] Get:79 http://ftpmaster.internal/ubuntu noble/main amd64 libperl5.36 amd64 5.36.0-10ubuntu1 [4782 kB] Get:80 http://ftpmaster.internal/ubuntu noble/main amd64 perl amd64 5.36.0-10ubuntu1 [235 kB] Get:81 http://ftpmaster.internal/ubuntu noble/main amd64 perl-base amd64 5.36.0-10ubuntu1 [1770 kB] Get:82 http://ftpmaster.internal/ubuntu noble/main amd64 perl-modules-5.36 all 5.36.0-10ubuntu1 [2984 kB] Get:83 http://ftpmaster.internal/ubuntu noble/main amd64 libdb5.3 amd64 5.3.28+dfsg2-4 [736 kB] Get:84 http://ftpmaster.internal/ubuntu noble/main amd64 libgdbm6 amd64 1.23-5 [33.3 kB] Get:85 http://ftpmaster.internal/ubuntu noble/main amd64 libgdbm-compat4 amd64 1.23-5 [6498 B] Get:86 http://ftpmaster.internal/ubuntu noble/main amd64 util-linux amd64 2.39.2-6ubuntu1 [1120 kB] Get:87 http://ftpmaster.internal/ubuntu noble/main amd64 libdebconfclient0 amd64 0.271ubuntu1 [11.3 kB] Get:88 http://ftpmaster.internal/ubuntu noble/main amd64 base-passwd amd64 3.6.3 [51.2 kB] Get:89 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 init-system-helpers all 1.66ubuntu1 [39.4 kB] Get:90 http://ftpmaster.internal/ubuntu noble/main amd64 libc-bin amd64 2.38-3ubuntu1 [680 kB] Get:91 http://ftpmaster.internal/ubuntu noble/main amd64 ncurses-base all 6.4+20231209-1 [25.2 kB] Get:92 http://ftpmaster.internal/ubuntu noble/main amd64 sysvinit-utils amd64 3.08-3ubuntu1 [33.7 kB] Get:93 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 apt amd64 2.7.7 [1376 kB] Get:94 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 apt-utils amd64 2.7.7 [216 kB] Get:95 http://ftpmaster.internal/ubuntu noble/main amd64 ubuntu-keyring all 2023.11.28.1 [11.1 kB] Get:96 http://ftpmaster.internal/ubuntu noble/main amd64 libunistring5 amd64 1.1-2 [537 kB] Get:97 http://ftpmaster.internal/ubuntu noble/main amd64 libidn2-0 amd64 2.3.4-1build1 [64.3 kB] Get:98 http://ftpmaster.internal/ubuntu noble/main amd64 libffi8 amd64 3.4.4-2 [24.4 kB] Get:99 http://ftpmaster.internal/ubuntu noble/main amd64 libp11-kit0 amd64 0.25.3-2ubuntu2 [298 kB] Get:100 http://ftpmaster.internal/ubuntu noble/main amd64 libgnutls30 amd64 3.8.1-4ubuntu6 [988 kB] Get:101 http://ftpmaster.internal/ubuntu noble/main amd64 libpam-modules-bin amd64 1.5.2-9.1ubuntu1 [47.6 kB] Get:102 http://ftpmaster.internal/ubuntu noble/main amd64 libpam-modules amd64 1.5.2-9.1ubuntu1 [284 kB] Get:103 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 init amd64 1.66ubuntu1 [6186 B] Get:104 http://ftpmaster.internal/ubuntu noble/main amd64 libsmartcols1 amd64 2.39.2-6ubuntu1 [63.3 kB] Get:105 http://ftpmaster.internal/ubuntu noble/main amd64 uuid-runtime amd64 2.39.2-6ubuntu1 [32.9 kB] Get:106 http://ftpmaster.internal/ubuntu noble/main amd64 libgpg-error-l10n all 1.47-3build1 [8024 B] Get:107 http://ftpmaster.internal/ubuntu noble/main amd64 libgpg-error0 amd64 1.47-3build1 [70.0 kB] Get:108 http://ftpmaster.internal/ubuntu noble/main amd64 libpam-runtime all 1.5.2-9.1ubuntu1 [41.5 kB] Get:109 http://ftpmaster.internal/ubuntu noble/main amd64 libsemanage-common all 3.5-1build1 [9982 B] Get:110 http://ftpmaster.internal/ubuntu noble/main amd64 libsepol2 amd64 3.5-2 [300 kB] Get:111 http://ftpmaster.internal/ubuntu noble/main amd64 libsemanage2 amd64 3.5-1build1 [92.9 kB] Get:112 http://ftpmaster.internal/ubuntu noble/main amd64 libncursesw6 amd64 6.4+20231209-1 [147 kB] Get:113 http://ftpmaster.internal/ubuntu noble/main amd64 libtinfo6 amd64 6.4+20231209-1 [107 kB] Get:114 http://ftpmaster.internal/ubuntu noble/main amd64 passwd amd64 1:4.13+dfsg1-3ubuntu1 [844 kB] Get:115 http://ftpmaster.internal/ubuntu noble/main amd64 libproc2-0 amd64 2:4.0.4-2ubuntu1 [59.0 kB] Get:116 http://ftpmaster.internal/ubuntu noble/main amd64 mawk amd64 1.3.4.20231126-1 [126 kB] Get:117 http://ftpmaster.internal/ubuntu noble/main amd64 procps amd64 2:4.0.4-2ubuntu1 [708 kB] Get:118 http://ftpmaster.internal/ubuntu noble/main amd64 krb5-locales all 1.20.1-5build1 [13.7 kB] Get:119 http://ftpmaster.internal/ubuntu noble/main amd64 readline-common all 8.2-3 [56.2 kB] Get:120 http://ftpmaster.internal/ubuntu noble/main amd64 libreadline8 amd64 8.2-3 [152 kB] Get:121 http://ftpmaster.internal/ubuntu noble/main amd64 libsqlite3-0 amd64 3.44.2-1 [685 kB] Get:122 http://ftpmaster.internal/ubuntu noble/main amd64 openssl amd64 3.0.10-1ubuntu3 [1188 kB] Get:123 http://ftpmaster.internal/ubuntu noble/main amd64 bash-completion all 1:2.11-8 [180 kB] Get:124 http://ftpmaster.internal/ubuntu noble/main amd64 bsdextrautils amd64 2.39.2-6ubuntu1 [73.5 kB] Get:125 http://ftpmaster.internal/ubuntu noble/main amd64 libpng16-16 amd64 1.6.40-2 [186 kB] Get:126 http://ftpmaster.internal/ubuntu noble/main amd64 xz-utils amd64 5.4.5-0.1 [268 kB] Get:127 http://ftpmaster.internal/ubuntu noble/main amd64 g++ amd64 4:13.2.0-2ubuntu1 [1122 B] Get:128 http://ftpmaster.internal/ubuntu noble/main amd64 gcc amd64 4:13.2.0-2ubuntu1 [5166 B] Get:129 http://ftpmaster.internal/ubuntu noble/main amd64 cpp amd64 4:13.2.0-2ubuntu1 [29.0 kB] Get:130 http://ftpmaster.internal/ubuntu noble/main amd64 dpkg-dev all 1.22.1ubuntu5 [1147 kB] Get:131 http://ftpmaster.internal/ubuntu noble/main amd64 libdpkg-perl all 1.22.1ubuntu5 [286 kB] Get:132 http://ftpmaster.internal/ubuntu noble/main amd64 lto-disabled-list all 44 [12.4 kB] Get:133 http://ftpmaster.internal/ubuntu noble/main amd64 libfakeroot amd64 1.32.2-1 [32.1 kB] Get:134 http://ftpmaster.internal/ubuntu noble/main amd64 fakeroot amd64 1.32.2-1 [67.1 kB] Get:135 http://ftpmaster.internal/ubuntu noble/main amd64 optipng amd64 0.7.7-3 [83.3 kB] Get:136 http://ftpmaster.internal/ubuntu noble/main amd64 pinentry-curses amd64 1.2.1-3ubuntu1 [34.9 kB] Preconfiguring packages ... 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Setting up libtirpc-dev:amd64 (1.3.4+ds-1) ... Setting up gcc-13 (13.2.0-9ubuntu1) ... Setting up libdpkg-perl (1.22.1ubuntu5) ... Setting up libnsl2:amd64 (1.3.0-3) ... Setting up gcc (4:13.2.0-2ubuntu1) ... Setting up dpkg-dev (1.22.1ubuntu5) ... Setting up libnsl-dev:amd64 (1.3.0-3) ... Setting up libc6-dev:amd64 (2.38-3ubuntu1) ... Setting up libstdc++-13-dev:amd64 (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-27576181 amd64 noble-proposed -c chroot:build-PACKAGEBUILD-27576181 --arch=amd64 --dist=noble-proposed --nolog -A berkeley-express_1.5.3+dfsg-3build3.dsc Initiating build PACKAGEBUILD-27576181 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 5.4.0-169-generic #187-Ubuntu SMP Thu Nov 23 14:52:28 UTC 2023 x86_64 sbuild (Debian sbuild) 0.79.0 (05 February 2020) on lcy02-amd64-104.buildd +==============================================================================+ | berkeley-express 1.5.3+dfsg-3build3 (amd64) Tue, 19 Dec 2023 15:09:53 +0000 | +==============================================================================+ Package: berkeley-express Version: 1.5.3+dfsg-3build3 Source Version: 1.5.3+dfsg-3build3 Distribution: noble-proposed Machine Architecture: amd64 Host Architecture: amd64 Build Architecture: amd64 Build Type: binary I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-27576181/chroot-autobuild' with '<>' I: NOTICE: Log filtering will replace 'build/berkeley-express-GGasYL/resolver-XeeCuZ' 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-GGasYL/berkeley-express-1.5.3+dfsg' with '<>' I: NOTICE: Log filtering will replace 'build/berkeley-express-GGasYL' 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, libgoogle-perftools-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, libgoogle-perftools-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 [532 B] Fetched 1976 B in 0s (90.4 kB/s) Reading package lists... Reading package lists... Install main build dependencies (apt-based resolver) ---------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following packages were automatically installed and are no longer required: apt-utils bash-completion ca-certificates debconf-i18n krb5-locales libgpg-error-l10n libgpm2 libip4tc2 liblocale-gettext-perl 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 libgoogle-perftools-dev libgoogle-perftools4 libicu74 libjsoncpp25 libldap2 liblzma-dev 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 libtcmalloc-minimal4 libtool libuchardet0 libunwind-dev libunwind8 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 liblzma-doc 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 libgoogle-perftools-dev libgoogle-perftools4 libicu74 libjsoncpp25 libldap2 liblzma-dev 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 libtcmalloc-minimal4 libtool libuchardet0 libunwind-dev libunwind8 libuv1 libxml2 m4 man-db po-debconf protobuf-compiler sbuild-build-depends-main-dummy zlib1g-dev 0 upgraded, 85 newly installed, 0 to remove and 0 not upgraded. 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libarchive13 amd64 3.7.2-1ubuntu2 [378 kB] Get:23 http://ftpmaster.internal/ubuntu noble/main amd64 libbrotli1 amd64 1.1.0-2 [332 kB] Get:24 http://ftpmaster.internal/ubuntu noble/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-4 [20.1 kB] Get:25 http://ftpmaster.internal/ubuntu noble/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-4 [53.3 kB] Get:26 http://ftpmaster.internal/ubuntu noble/main amd64 libldap2 amd64 2.6.6+dfsg-1~exp1ubuntu1 [193 kB] Get:27 http://ftpmaster.internal/ubuntu noble/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2build4 [58.2 kB] Get:28 http://ftpmaster.internal/ubuntu noble/main amd64 libssh-4 amd64 0.10.5-3ubuntu1 [187 kB] Get:29 http://ftpmaster.internal/ubuntu noble/main amd64 libcurl4 amd64 8.4.0-2ubuntu1 [335 kB] Get:30 http://ftpmaster.internal/ubuntu noble/main amd64 libjsoncpp25 amd64 1.9.5-6 [82.3 kB] Get:31 http://ftpmaster.internal/ubuntu noble/main amd64 librhash0 amd64 1.4.3-3 [128 kB] Get:32 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 cmake-data all 3.28.0-1 [2154 kB] Get:33 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 cmake amd64 3.28.0-1 [11.3 MB] Get:34 http://ftpmaster.internal/ubuntu noble/main amd64 libdebhelper-perl all 13.11.8ubuntu1 [85.9 kB] Get:35 http://ftpmaster.internal/ubuntu noble/main amd64 libtool all 2.4.7-7 [166 kB] Get:36 http://ftpmaster.internal/ubuntu noble/main amd64 dh-autoreconf all 20 [16.1 kB] Get:37 http://ftpmaster.internal/ubuntu noble/main amd64 libarchive-zip-perl all 1.68-1 [90.2 kB] Get:38 http://ftpmaster.internal/ubuntu noble/main amd64 libsub-override-perl all 0.10-1 [10.0 kB] Get:39 http://ftpmaster.internal/ubuntu noble/main amd64 libfile-stripnondeterminism-perl all 1.13.1-1 [18.1 kB] Get:40 http://ftpmaster.internal/ubuntu noble/main amd64 dh-strip-nondeterminism all 1.13.1-1 [5362 B] Get:41 http://ftpmaster.internal/ubuntu noble/main amd64 libdw1 amd64 0.190-1 [260 kB] Get:42 http://ftpmaster.internal/ubuntu noble/main amd64 debugedit amd64 1:5.0-5 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libboost-date-time-dev amd64 1.83.0.1ubuntu2 [4058 B] Get:61 http://ftpmaster.internal/ubuntu noble-proposed/universe amd64 libboost-filesystem1.83.0 amd64 1.83.0-1ubuntu3 [283 kB] Get:62 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libboost-system1.83.0 amd64 1.83.0-1ubuntu3 [236 kB] Get:63 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libboost-system1.83-dev amd64 1.83.0-1ubuntu3 [231 kB] Get:64 http://ftpmaster.internal/ubuntu noble-proposed/universe amd64 libboost-filesystem1.83-dev amd64 1.83.0-1ubuntu3 [301 kB] Get:65 http://ftpmaster.internal/ubuntu noble-proposed/universe amd64 libboost-filesystem-dev amd64 1.83.0.1ubuntu2 [4096 B] Get:66 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libboost-program-options1.83.0 amd64 1.83.0-1ubuntu3 [320 kB] Get:67 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libboost-program-options1.83-dev amd64 1.83.0-1ubuntu3 [388 kB] Get:68 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libboost-program-options-dev amd64 1.83.0.1ubuntu2 [4086 B] Get:69 http://ftpmaster.internal/ubuntu noble-proposed/universe amd64 libboost-system-dev amd64 1.83.0.1ubuntu2 [4206 B] Get:70 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libboost-thread1.83.0 amd64 1.83.0-1ubuntu3 [275 kB] Get:71 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libboost-thread1.83-dev amd64 1.83.0-1ubuntu3 [282 kB] Get:72 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libboost-thread-dev amd64 1.83.0.1ubuntu2 [4088 B] Get:73 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libboost1.83-tools-dev amd64 1.83.0-1ubuntu3 [1402 kB] Get:74 http://ftpmaster.internal/ubuntu noble-proposed/universe amd64 libboost-tools-dev amd64 1.83.0.1ubuntu2 [4238 B] Get:75 http://ftpmaster.internal/ubuntu noble/main amd64 libtcmalloc-minimal4 amd64 2.13-1ubuntu1 [90.3 kB] Get:76 http://ftpmaster.internal/ubuntu noble/main amd64 libunwind8 amd64 1.6.2-3 [55.7 kB] Get:77 http://ftpmaster.internal/ubuntu noble/main amd64 libgoogle-perftools4 amd64 2.13-1ubuntu1 [206 kB] Get:78 http://ftpmaster.internal/ubuntu noble/main amd64 liblzma-dev amd64 5.4.5-0.1 [178 kB] Get:79 http://ftpmaster.internal/ubuntu noble/main amd64 libunwind-dev amd64 1.6.2-3 [1959 kB] Get:80 http://ftpmaster.internal/ubuntu noble/main amd64 libgoogle-perftools-dev amd64 2.13-1ubuntu1 [469 kB] Get:81 http://ftpmaster.internal/ubuntu noble/main amd64 libprotobuf-lite32 amd64 3.21.12-8ubuntu1 [242 kB] Get:82 http://ftpmaster.internal/ubuntu noble/main amd64 libprotobuf32 amd64 3.21.12-8ubuntu1 [930 kB] Get:83 http://ftpmaster.internal/ubuntu noble/main amd64 libprotoc32 amd64 3.21.12-8ubuntu1 [688 kB] Get:84 http://ftpmaster.internal/ubuntu noble/main amd64 libprotobuf-dev amd64 3.21.12-8ubuntu1 [1421 kB] Get:85 http://ftpmaster.internal/ubuntu noble/universe amd64 protobuf-compiler amd64 3.21.12-8ubuntu1 [29.0 kB] Preconfiguring packages ... 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Processing triggers for libc-bin (2.38-3ubuntu1) ... +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (amd64 included in any all) +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 5.4.0-169-generic #187-Ubuntu SMP Thu Nov 23 14:52:28 UTC 2023 amd64 (x86_64) 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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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-27576181 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-27576181 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-27576181 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 amd64 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 dh binary dh_update_autotools_config dh_autoreconf dh_auto_configure cd obj-x86_64-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/x86_64-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/x86_64-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 -- Found GPERFTOOLS_TCMALLOC: /usr/lib/x86_64-linux-gnu/libtcmalloc.so -- Found Protobuf: /usr/lib/x86_64-linux-gnu/libprotobuf.so (found version "3.21.12") -- Do not try to find libbamtools.a -- Configuring done (0.8s) -- 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-x86_64-linux-gnu dh_auto_build cd obj-x86_64-linux-gnu && make -j4 "INSTALL=install --strip-program=true" VERBOSE=1 make[1]: Entering directory '/<>/obj-x86_64-linux-gnu' /usr/bin/cmake -S/<> -B/<>/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /<>/obj-x86_64-linux-gnu/CMakeFiles /<>/obj-x86_64-linux-gnu//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/<>/obj-x86_64-linux-gnu' make -f src/CMakeFiles/express.dir/build.make src/CMakeFiles/express.dir/depend make[3]: Entering directory '/<>/obj-x86_64-linux-gnu' [ 5%] Running cpp protocol buffer compiler on /<>/src/targets.proto cd /<>/obj-x86_64-linux-gnu/src && /usr/bin/protoc --cpp_out :/<>/obj-x86_64-linux-gnu/src -I /<>/src /<>/src/targets.proto [ 11%] Running cpp protocol buffer compiler on /<>/src/alignments.proto cd /<>/obj-x86_64-linux-gnu/src && /usr/bin/protoc --cpp_out :/<>/obj-x86_64-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-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/src /<>/obj-x86_64-linux-gnu /<>/obj-x86_64-linux-gnu/src /<>/obj-x86_64-linux-gnu/src/CMakeFiles/express.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/<>/obj-x86_64-linux-gnu' make -f src/CMakeFiles/express.dir/build.make src/CMakeFiles/express.dir/build make[3]: Entering directory '/<>/obj-x86_64-linux-gnu' [ 22%] Building CXX object src/CMakeFiles/express.dir/biascorrection.cpp.o [ 22%] Building CXX object src/CMakeFiles/express.dir/bundles.cpp.o cd /<>/obj-x86_64-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 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-fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 [ 33%] Building CXX object src/CMakeFiles/express.dir/fragments.cpp.o cd /<>/obj-x86_64-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 -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/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 cd /<>/obj-x86_64-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 -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/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 : warning: "__FILE__" redefined [-Wbuiltin-macro-redefined] : warning: "__FILE__" redefined [-Wbuiltin-macro-redefined] : 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-x86_64-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 -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/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-x86_64-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 -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/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-x86_64-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 -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/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-x86_64-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 -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/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-x86_64-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 -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/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-x86_64-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 -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/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-x86_64-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 -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/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] 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 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dh_strip_nondeterminism debian/rules override_dh_compress make[1]: Entering directory '/<>' dh_compress --exclude=express-doc.pdf make[1]: Leaving directory '/<>' dh_fixperms dh_missing dh_dwz -a dh_strip -a 831ae380a5a47e192a229649874f68bff0c4805c dh_makeshlibs -a dh_shlibdeps -a dh_installdeb dh_gencontrol dh_md5sums dh_builddeb INFO: pkgstriptranslations version 154 INFO: pkgstriptranslations version 154 INFO: pkgstriptranslations version 154 pkgstriptranslations: processing berkeley-express (in debian/berkeley-express); do_strip: , oemstrip: pkgstriptranslations: processing berkeley-express-doc (in debian/berkeley-express-doc); 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 pkgmaintainermangler: Not overriding Maintainer for 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for -doc package berkeley-express-doc (to save build time) dpkg-deb: building package 'berkeley-express-doc' in '../berkeley-express-doc_1.5.3+dfsg-3build3_all.deb'. 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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-doc_1.5.3+dfsg-3build3_all.deb ----------------------------------------------- new Debian package, version 2.0. size 723620 bytes: control archive=2782 bytes. 3013 bytes, 53 lines control 3829 bytes, 40 lines md5sums Package: berkeley-express-doc Source: berkeley-express Version: 1.5.3+dfsg-3build3 Architecture: all Maintainer: Ubuntu Developers Installed-Size: 3248 Section: doc Priority: optional Multi-Arch: foreign Homepage: http://bio.math.berkeley.edu/eXpress/index.html Description: Documentation for RNA-Seq tool eXpress This package provides a PDF with the documentation for eXpress. . 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. 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./usr/share/doc/berkeley-express/sample_data/reads_1.fastq.gz -rw-r--r-- root/root 200283 2019-11-14 16:14 ./usr/share/doc/berkeley-express/sample_data/reads_2.fastq.gz -rw-r--r-- root/root 7000 2019-11-14 16:14 ./usr/share/doc/berkeley-express/sample_data/transcripts.fasta.gz berkeley-express_1.5.3+dfsg-3build3_amd64.deb --------------------------------------------- new Debian package, version 2.0. size 209952 bytes: control archive=1852 bytes. 3190 bytes, 51 lines control 454 bytes, 6 lines md5sums Package: berkeley-express Version: 1.5.3+dfsg-3build3 Architecture: amd64 Maintainer: Ubuntu Developers Installed-Size: 578 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 569112 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: amd64 Build Type: binary Build-Space: 111088 Build-Time: 42 Distribution: noble-proposed Host Architecture: amd64 Install-Time: 12 Job: berkeley-express_1.5.3+dfsg-3build3.dsc Machine Architecture: amd64 Package: berkeley-express Package-Time: 55 Source-Version: 1.5.3+dfsg-3build3 Space: 111088 Status: successful Version: 1.5.3+dfsg-3build3 -------------------------------------------------------------------------------- Finished at 2023-12-19T15:10:48Z Build needed 00:00:55, 111088k disk space RUN: /usr/share/launchpad-buildd/bin/in-target scan-for-processes --backend=chroot --series=noble --arch=amd64 PACKAGEBUILD-27576181 Scanning for processes to kill in build PACKAGEBUILD-27576181