https://launchpad.net/ubuntu/+source/berkeley-express/1.5.3+dfsg-3build3/+build/27576183 RUN: /usr/share/launchpad-buildd/bin/builder-prep Kernel version: Linux bos02-arm64-019 5.4.0-169-generic #187-Ubuntu SMP Thu Nov 23 14:53:38 UTC 2023 aarch64 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 15:17:54 ntpdate[1844]: adjust time server 10.211.37.1 offset -0.000790 sec RUN: /usr/share/launchpad-buildd/bin/in-target unpack-chroot --backend=chroot --series=noble --arch=armhf PACKAGEBUILD-27576183 --image-type chroot /home/buildd/filecache-default/59612f0fc5bae33f6226b6e60c2e882b82c04bd0 Creating target for build PACKAGEBUILD-27576183 RUN: /usr/share/launchpad-buildd/bin/in-target mount-chroot --backend=chroot --series=noble --arch=armhf PACKAGEBUILD-27576183 Starting target for build PACKAGEBUILD-27576183 RUN: /usr/share/launchpad-buildd/bin/in-target override-sources-list --backend=chroot --series=noble --arch=armhf PACKAGEBUILD-27576183 '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-27576183 RUN: /usr/share/launchpad-buildd/bin/in-target update-debian-chroot --backend=chroot --series=noble --arch=armhf PACKAGEBUILD-27576183 Updating target for build PACKAGEBUILD-27576183 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 armhf Packages [1335 kB] Get:6 http://ftpmaster.internal/ubuntu noble/main Translation-en [515 kB] Get:7 http://ftpmaster.internal/ubuntu noble/universe armhf Packages [14.5 MB] Get:8 http://ftpmaster.internal/ubuntu noble/universe Translation-en [6031 kB] Get:9 http://ftpmaster.internal/ubuntu noble-proposed/main armhf Packages [88.3 kB] Get:10 http://ftpmaster.internal/ubuntu noble-proposed/main Translation-en [44.9 kB] Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe armhf Packages [1034 kB] Get:12 http://ftpmaster.internal/ubuntu noble-proposed/universe Translation-en [325 kB] Fetched 24.4 MB in 10s (2438 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-arm-linux-gnueabihf binutils-common 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 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 129 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 89.8 MB of archives. After this operation, 751 kB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu noble/main armhf libnsl-dev armhf 1.3.0-3 [65.8 kB] Get:2 http://ftpmaster.internal/ubuntu noble/main armhf libc6-dev armhf 2.38-3ubuntu1 [1347 kB] Get:3 http://ftpmaster.internal/ubuntu noble/main armhf libc-dev-bin armhf 2.38-3ubuntu1 [18.9 kB] Get:4 http://ftpmaster.internal/ubuntu noble/main armhf libtirpc-common all 1.3.4+ds-1 [7920 B] Get:5 http://ftpmaster.internal/ubuntu noble/main armhf libtirpc-dev armhf 1.3.4+ds-1 [184 kB] Get:6 http://ftpmaster.internal/ubuntu noble/main armhf libgssapi-krb5-2 armhf 1.20.1-5build1 [118 kB] Get:7 http://ftpmaster.internal/ubuntu noble/main armhf libkrb5-3 armhf 1.20.1-5build1 [320 kB] Get:8 http://ftpmaster.internal/ubuntu noble/main armhf libk5crypto3 armhf 1.20.1-5build1 [78.6 kB] Get:9 http://ftpmaster.internal/ubuntu noble/main armhf libkrb5support0 armhf 1.20.1-5build1 [31.3 kB] Get:10 http://ftpmaster.internal/ubuntu noble/main armhf libssl3 armhf 3.0.10-1ubuntu3 [1560 kB] Get:11 http://ftpmaster.internal/ubuntu noble/main armhf libtirpc3 armhf 1.3.4+ds-1 [72.0 kB] Get:12 http://ftpmaster.internal/ubuntu noble/main armhf libnsl2 armhf 1.3.0-3 [35.9 kB] Get:13 http://ftpmaster.internal/ubuntu noble-proposed/main armhf linux-libc-dev armhf 6.6.0-14.14 [1539 kB] Get:14 http://ftpmaster.internal/ubuntu noble/main armhf libcc1-0 armhf 13.2.0-9ubuntu1 [43.8 kB] Get:15 http://ftpmaster.internal/ubuntu noble/main armhf libctf0 armhf 2.41.50.20231214-1ubuntu1 [72.5 kB] Get:16 http://ftpmaster.internal/ubuntu noble/main armhf libctf-nobfd0 armhf 2.41.50.20231214-1ubuntu1 [75.1 kB] Get:17 http://ftpmaster.internal/ubuntu noble/main armhf binutils-arm-linux-gnueabihf armhf 2.41.50.20231214-1ubuntu1 [2871 kB] Get:18 http://ftpmaster.internal/ubuntu noble/main armhf libbinutils armhf 2.41.50.20231214-1ubuntu1 [403 kB] Get:19 http://ftpmaster.internal/ubuntu noble/main armhf binutils-common armhf 2.41.50.20231214-1ubuntu1 [230 kB] Get:20 http://ftpmaster.internal/ubuntu noble/main armhf binutils armhf 2.41.50.20231214-1ubuntu1 [3092 B] Get:21 http://ftpmaster.internal/ubuntu noble/main armhf gcc-13-base armhf 13.2.0-9ubuntu1 [45.2 kB] Get:22 http://ftpmaster.internal/ubuntu noble/main armhf libgcc-s1 armhf 13.2.0-9ubuntu1 [41.4 kB] Get:23 http://ftpmaster.internal/ubuntu noble/main armhf libgomp1 armhf 13.2.0-9ubuntu1 [120 kB] Get:24 http://ftpmaster.internal/ubuntu noble/main armhf libatomic1 armhf 13.2.0-9ubuntu1 [7794 B] Get:25 http://ftpmaster.internal/ubuntu noble/main armhf libasan8 armhf 13.2.0-9ubuntu1 [2749 kB] Get:26 http://ftpmaster.internal/ubuntu noble/main armhf libubsan1 armhf 13.2.0-9ubuntu1 [1072 kB] Get:27 http://ftpmaster.internal/ubuntu noble/main armhf g++-13 armhf 13.2.0-9ubuntu1 [9442 kB] Get:28 http://ftpmaster.internal/ubuntu noble/main armhf libstdc++-13-dev armhf 13.2.0-9ubuntu1 [2398 kB] Get:29 http://ftpmaster.internal/ubuntu noble/main armhf libgcc-13-dev armhf 13.2.0-9ubuntu1 [901 kB] Get:30 http://ftpmaster.internal/ubuntu noble/main armhf gcc-13 armhf 13.2.0-9ubuntu1 [16.5 MB] Get:31 http://ftpmaster.internal/ubuntu noble/main armhf cpp-13 armhf 13.2.0-9ubuntu1 [8249 kB] Get:32 http://ftpmaster.internal/ubuntu noble/main armhf libstdc++6 armhf 13.2.0-9ubuntu1 [698 kB] Get:33 http://ftpmaster.internal/ubuntu noble-proposed/main armhf zlib1g armhf 1:1.3.dfsg-3ubuntu1 [50.6 kB] Get:34 http://ftpmaster.internal/ubuntu noble/main armhf libsframe1 armhf 2.41.50.20231214-1ubuntu1 [11.8 kB] Get:35 http://ftpmaster.internal/ubuntu noble/main armhf libzstd1 armhf 1.5.5+dfsg2-2 [265 kB] Get:36 http://ftpmaster.internal/ubuntu noble/main armhf libc6 armhf 2.38-3ubuntu1 [2818 kB] Get:37 http://ftpmaster.internal/ubuntu noble/main armhf base-files armhf 13ubuntu5 [73.3 kB] Get:38 http://ftpmaster.internal/ubuntu noble/main armhf debianutils armhf 5.14 [88.0 kB] Get:39 http://ftpmaster.internal/ubuntu noble/main armhf bash armhf 5.2.21-2ubuntu1 [673 kB] Get:40 http://ftpmaster.internal/ubuntu noble/main armhf bsdutils armhf 1:2.39.2-6ubuntu1 [99.5 kB] Get:41 http://ftpmaster.internal/ubuntu noble/main armhf coreutils armhf 9.4-2ubuntu1 [1309 kB] Get:42 http://ftpmaster.internal/ubuntu noble/main armhf diffutils armhf 1:3.10-1 [167 kB] Get:43 http://ftpmaster.internal/ubuntu noble/main armhf liblzma5 armhf 5.4.5-0.1 [111 kB] Get:44 http://ftpmaster.internal/ubuntu noble/main armhf libapparmor1 armhf 4.0.0~alpha2-0ubuntu7 [43.8 kB] Get:45 http://ftpmaster.internal/ubuntu noble/main armhf libaudit-common all 1:3.1.2-1 [5512 B] Get:46 http://ftpmaster.internal/ubuntu noble/main armhf libcap-ng0 armhf 0.8.3-3 [13.6 kB] Get:47 http://ftpmaster.internal/ubuntu noble/main armhf libaudit1 armhf 1:3.1.2-1 [44.2 kB] Get:48 http://ftpmaster.internal/ubuntu noble/main armhf libblkid1 armhf 2.39.2-6ubuntu1 [159 kB] Get:49 http://ftpmaster.internal/ubuntu noble/main armhf libkmod2 armhf 30+20230601-2ubuntu1 [43.9 kB] Get:50 http://ftpmaster.internal/ubuntu noble/main armhf libpcre2-8-0 armhf 10.42-4ubuntu1 [198 kB] Get:51 http://ftpmaster.internal/ubuntu noble/main armhf libselinux1 armhf 3.5-1build2 [69.6 kB] Get:52 http://ftpmaster.internal/ubuntu noble/main armhf libmount1 armhf 2.39.2-6ubuntu1 [171 kB] Get:53 http://ftpmaster.internal/ubuntu noble/main armhf libpam0g armhf 1.5.2-9.1ubuntu1 [59.9 kB] Get:54 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libseccomp2 armhf 2.5.4-2ubuntu1 [48.9 kB] Get:55 http://ftpmaster.internal/ubuntu noble-proposed/main armhf systemd-sysv armhf 255-1ubuntu1 [11.7 kB] Get:56 http://ftpmaster.internal/ubuntu noble-proposed/main armhf systemd-dev all 255-1ubuntu1 [98.5 kB] Get:57 http://ftpmaster.internal/ubuntu noble-proposed/main armhf systemd armhf 255-1ubuntu1 [3513 kB] Get:58 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libsystemd-shared armhf 255-1ubuntu1 [2003 kB] Get:59 http://ftpmaster.internal/ubuntu noble/main armhf libargon2-1 armhf 0~20190702+dfsg-4 [22.3 kB] Get:60 http://ftpmaster.internal/ubuntu noble/main armhf libuuid1 armhf 2.39.2-6ubuntu1 [33.4 kB] Get:61 http://ftpmaster.internal/ubuntu noble/main armhf libcryptsetup12 armhf 2:2.6.1-5ubuntu1 [217 kB] Get:62 http://ftpmaster.internal/ubuntu noble/main armhf libfdisk1 armhf 2.39.2-6ubuntu1 [195 kB] Get:63 http://ftpmaster.internal/ubuntu noble/main armhf mount armhf 2.39.2-6ubuntu1 [132 kB] Get:64 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libsystemd0 armhf 255-1ubuntu1 [401 kB] Get:65 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libudev1 armhf 255-1ubuntu1 [161 kB] Get:66 http://ftpmaster.internal/ubuntu noble/main armhf libxxhash0 armhf 0.8.2-2 [31.3 kB] Get:67 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libapt-pkg6.0 armhf 2.7.7 [962 kB] Get:68 http://ftpmaster.internal/ubuntu noble/main armhf tar armhf 1.34+dfsg-1.2ubuntu2 [269 kB] Get:69 http://ftpmaster.internal/ubuntu noble/main armhf dpkg armhf 1.22.1ubuntu5 [1342 kB] Get:70 http://ftpmaster.internal/ubuntu noble/main armhf grep armhf 3.11-3 [157 kB] Get:71 http://ftpmaster.internal/ubuntu noble/main armhf login armhf 1:4.13+dfsg1-3ubuntu1 [200 kB] Get:72 http://ftpmaster.internal/ubuntu noble/main armhf ncurses-bin armhf 6.4+20231209-1 [177 kB] Get:73 http://ftpmaster.internal/ubuntu noble/main armhf libperl5.36 armhf 5.36.0-10ubuntu1 [4019 kB] Get:74 http://ftpmaster.internal/ubuntu noble/main armhf perl armhf 5.36.0-10ubuntu1 [235 kB] Get:75 http://ftpmaster.internal/ubuntu noble/main armhf perl-base armhf 5.36.0-10ubuntu1 [1617 kB] Get:76 http://ftpmaster.internal/ubuntu noble/main armhf perl-modules-5.36 all 5.36.0-10ubuntu1 [2984 kB] Get:77 http://ftpmaster.internal/ubuntu noble/main armhf libdb5.3 armhf 5.3.28+dfsg2-4 [652 kB] Get:78 http://ftpmaster.internal/ubuntu noble/main armhf libgdbm6 armhf 1.23-5 [29.8 kB] Get:79 http://ftpmaster.internal/ubuntu noble/main armhf libgdbm-compat4 armhf 1.23-5 [5970 B] Get:80 http://ftpmaster.internal/ubuntu noble/main armhf util-linux armhf 2.39.2-6ubuntu1 [1211 kB] Get:81 http://ftpmaster.internal/ubuntu noble/main armhf libdebconfclient0 armhf 0.271ubuntu1 [10.8 kB] Get:82 http://ftpmaster.internal/ubuntu noble/main armhf base-passwd armhf 3.6.3 [51.0 kB] Get:83 http://ftpmaster.internal/ubuntu noble-proposed/main armhf init-system-helpers all 1.66ubuntu1 [39.4 kB] Get:84 http://ftpmaster.internal/ubuntu noble/main armhf libc-bin armhf 2.38-3ubuntu1 [532 kB] Get:85 http://ftpmaster.internal/ubuntu noble/main armhf ncurses-base all 6.4+20231209-1 [25.2 kB] Get:86 http://ftpmaster.internal/ubuntu noble/main armhf sysvinit-utils armhf 3.08-3ubuntu1 [33.4 kB] Get:87 http://ftpmaster.internal/ubuntu noble-proposed/main armhf apt armhf 2.7.7 [1364 kB] Get:88 http://ftpmaster.internal/ubuntu noble-proposed/main armhf apt-utils armhf 2.7.7 [212 kB] Get:89 http://ftpmaster.internal/ubuntu noble/main armhf ubuntu-keyring all 2023.11.28.1 [11.1 kB] Get:90 http://ftpmaster.internal/ubuntu noble/main armhf libunistring5 armhf 1.1-2 [512 kB] Get:91 http://ftpmaster.internal/ubuntu noble/main armhf libidn2-0 armhf 2.3.4-1build1 [94.2 kB] Get:92 http://ftpmaster.internal/ubuntu noble/main armhf libffi8 armhf 3.4.4-2 [20.8 kB] Get:93 http://ftpmaster.internal/ubuntu noble/main armhf libp11-kit0 armhf 0.25.3-2ubuntu2 [261 kB] Get:94 http://ftpmaster.internal/ubuntu noble/main armhf libgnutls30 armhf 3.8.1-4ubuntu6 [941 kB] Get:95 http://ftpmaster.internal/ubuntu noble/main armhf libpam-modules-bin armhf 1.5.2-9.1ubuntu1 [43.6 kB] Get:96 http://ftpmaster.internal/ubuntu noble/main armhf libpam-modules armhf 1.5.2-9.1ubuntu1 [265 kB] Get:97 http://ftpmaster.internal/ubuntu noble-proposed/main armhf init armhf 1.66ubuntu1 [6186 B] Get:98 http://ftpmaster.internal/ubuntu noble/main armhf libsmartcols1 armhf 2.39.2-6ubuntu1 [116 kB] Get:99 http://ftpmaster.internal/ubuntu noble/main armhf uuid-runtime armhf 2.39.2-6ubuntu1 [40.7 kB] Get:100 http://ftpmaster.internal/ubuntu noble/main armhf libgpg-error-l10n all 1.47-3build1 [8024 B] Get:101 http://ftpmaster.internal/ubuntu noble/main armhf libgpg-error0 armhf 1.47-3build1 [61.6 kB] Get:102 http://ftpmaster.internal/ubuntu noble/main armhf libpam-runtime all 1.5.2-9.1ubuntu1 [41.5 kB] Get:103 http://ftpmaster.internal/ubuntu noble/main armhf libsemanage-common all 3.5-1build1 [9982 B] Get:104 http://ftpmaster.internal/ubuntu noble/main armhf libsepol2 armhf 3.5-2 [262 kB] Get:105 http://ftpmaster.internal/ubuntu noble/main armhf libsemanage2 armhf 3.5-1build1 [84.1 kB] Get:106 http://ftpmaster.internal/ubuntu noble/main armhf libncursesw6 armhf 6.4+20231209-1 [118 kB] Get:107 http://ftpmaster.internal/ubuntu noble/main armhf libtinfo6 armhf 6.4+20231209-1 [90.4 kB] Get:108 http://ftpmaster.internal/ubuntu noble/main armhf passwd armhf 1:4.13+dfsg1-3ubuntu1 [817 kB] Get:109 http://ftpmaster.internal/ubuntu noble/main armhf libproc2-0 armhf 2:4.0.4-2ubuntu1 [49.6 kB] Get:110 http://ftpmaster.internal/ubuntu noble/main armhf mawk armhf 1.3.4.20231126-1 [115 kB] Get:111 http://ftpmaster.internal/ubuntu noble/main armhf procps armhf 2:4.0.4-2ubuntu1 [699 kB] Get:112 http://ftpmaster.internal/ubuntu noble/main armhf krb5-locales all 1.20.1-5build1 [13.7 kB] Get:113 http://ftpmaster.internal/ubuntu noble/main armhf readline-common all 8.2-3 [56.2 kB] Get:114 http://ftpmaster.internal/ubuntu noble/main armhf libreadline8 armhf 8.2-3 [129 kB] Get:115 http://ftpmaster.internal/ubuntu noble/main armhf libsqlite3-0 armhf 3.44.2-1 [593 kB] Get:116 http://ftpmaster.internal/ubuntu noble/main armhf openssl armhf 3.0.10-1ubuntu3 [1158 kB] Get:117 http://ftpmaster.internal/ubuntu noble/main armhf bash-completion all 1:2.11-8 [180 kB] Get:118 http://ftpmaster.internal/ubuntu noble/main armhf bsdextrautils armhf 2.39.2-6ubuntu1 [77.7 kB] Get:119 http://ftpmaster.internal/ubuntu noble/main armhf libpng16-16 armhf 1.6.40-2 [166 kB] Get:120 http://ftpmaster.internal/ubuntu noble/main armhf xz-utils armhf 5.4.5-0.1 [266 kB] Get:121 http://ftpmaster.internal/ubuntu noble/main armhf g++ armhf 4:13.2.0-2ubuntu1 [1108 B] Get:122 http://ftpmaster.internal/ubuntu noble/main armhf gcc armhf 4:13.2.0-2ubuntu1 [5196 B] Get:123 http://ftpmaster.internal/ubuntu noble/main armhf cpp armhf 4:13.2.0-2ubuntu1 [29.0 kB] Get:124 http://ftpmaster.internal/ubuntu noble/main armhf dpkg-dev all 1.22.1ubuntu5 [1147 kB] Get:125 http://ftpmaster.internal/ubuntu noble/main armhf libdpkg-perl all 1.22.1ubuntu5 [286 kB] Get:126 http://ftpmaster.internal/ubuntu noble/main armhf lto-disabled-list all 44 [12.4 kB] Get:127 http://ftpmaster.internal/ubuntu noble/main armhf libfakeroot armhf 1.32.2-1 [28.0 kB] Get:128 http://ftpmaster.internal/ubuntu noble/main armhf fakeroot armhf 1.32.2-1 [68.8 kB] Get:129 http://ftpmaster.internal/ubuntu noble/main armhf optipng armhf 0.7.7-3 [82.2 kB] Get:130 http://ftpmaster.internal/ubuntu noble/main armhf pinentry-curses armhf 1.2.1-3ubuntu1 [36.4 kB] Preconfiguring packages ... Fetched 89.8 MB in 8s (11.7 MB/s) (Reading database ... 13362 files and directories currently installed.) Preparing to unpack .../00-libnsl-dev_1.3.0-3_armhf.deb ... Unpacking libnsl-dev:armhf (1.3.0-3) over (1.3.0-2build2) ... Preparing to unpack .../01-libc6-dev_2.38-3ubuntu1_armhf.deb ... Unpacking libc6-dev:armhf (2.38-3ubuntu1) over (2.38-1ubuntu6) ... Preparing to unpack .../02-libc-dev-bin_2.38-3ubuntu1_armhf.deb ... Unpacking libc-dev-bin (2.38-3ubuntu1) over (2.38-1ubuntu6) ... Preparing to unpack .../03-libtirpc-common_1.3.4+ds-1_all.deb ... Unpacking libtirpc-common (1.3.4+ds-1) over (1.3.3+ds-1) ... Preparing to unpack .../04-libtirpc-dev_1.3.4+ds-1_armhf.deb ... Unpacking libtirpc-dev:armhf (1.3.4+ds-1) over (1.3.3+ds-1) ... Preparing to unpack .../05-libgssapi-krb5-2_1.20.1-5build1_armhf.deb ... Unpacking libgssapi-krb5-2:armhf (1.20.1-5build1) over (1.20.1-3ubuntu1) ... Preparing to unpack .../06-libkrb5-3_1.20.1-5build1_armhf.deb ... 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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-27576183 armhf noble-proposed -c chroot:build-PACKAGEBUILD-27576183 --arch=armhf --dist=noble-proposed --nolog berkeley-express_1.5.3+dfsg-3build3.dsc Initiating build PACKAGEBUILD-27576183 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 5.4.0-169-generic #187-Ubuntu SMP Thu Nov 23 14:53:38 UTC 2023 armv7l sbuild (Debian sbuild) 0.79.0 (05 February 2020) on bos02-arm64-019.buildd +==============================================================================+ | berkeley-express 1.5.3+dfsg-3build3 (armhf) Tue, 19 Dec 2023 15:19:04 +0000 | +==============================================================================+ Package: berkeley-express Version: 1.5.3+dfsg-3build3 Source Version: 1.5.3+dfsg-3build3 Distribution: noble-proposed Machine Architecture: arm64 Host Architecture: armhf Build Architecture: armhf Build Type: any I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-27576183/chroot-autobuild' with '<>' I: NOTICE: Log filtering will replace 'build/berkeley-express-z9qt9E/resolver-jI2QTo' 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-z9qt9E/berkeley-express-1.5.3+dfsg' with '<>' I: NOTICE: Log filtering will replace 'build/berkeley-express-z9qt9E' 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 [528 B] Fetched 1972 B in 0s (63.9 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 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 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 libgoogle-perftools-dev libgoogle-perftools4 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 libtcmalloc-minimal4 libtool libuchardet0 libuv1 libxml2 m4 man-db po-debconf protobuf-compiler sbuild-build-depends-main-dummy zlib1g-dev 0 upgraded, 82 newly installed, 0 to remove and 0 not upgraded. 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libboost-atomic1.83.0 armhf 1.83.0-1ubuntu3 [238 kB] Get:53 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libboost-atomic1.83-dev armhf 1.83.0-1ubuntu3 [234 kB] Get:54 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libboost-chrono1.83.0 armhf 1.83.0-1ubuntu3 [244 kB] Get:55 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libboost-chrono1.83-dev armhf 1.83.0-1ubuntu3 [245 kB] Get:56 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libboost-date-time1.83.0 armhf 1.83.0-1ubuntu3 [236 kB] Get:57 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libboost-serialization1.83.0 armhf 1.83.0-1ubuntu3 [332 kB] Get:58 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libboost-serialization1.83-dev armhf 1.83.0-1ubuntu3 [403 kB] Get:59 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libboost-date-time1.83-dev armhf 1.83.0-1ubuntu3 [239 kB] Get:60 http://ftpmaster.internal/ubuntu noble-proposed/universe armhf libboost-date-time-dev armhf 1.83.0.1ubuntu2 [4058 B] Get:61 http://ftpmaster.internal/ubuntu noble-proposed/universe armhf libboost-filesystem1.83.0 armhf 1.83.0-1ubuntu3 [280 kB] Get:62 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libboost-system1.83.0 armhf 1.83.0-1ubuntu3 [236 kB] Get:63 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libboost-system1.83-dev armhf 1.83.0-1ubuntu3 [231 kB] Get:64 http://ftpmaster.internal/ubuntu noble-proposed/universe armhf libboost-filesystem1.83-dev armhf 1.83.0-1ubuntu3 [291 kB] Get:65 http://ftpmaster.internal/ubuntu noble-proposed/universe armhf libboost-filesystem-dev armhf 1.83.0.1ubuntu2 [4094 B] Get:66 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libboost-program-options1.83.0 armhf 1.83.0-1ubuntu3 [344 kB] Get:67 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libboost-program-options1.83-dev armhf 1.83.0-1ubuntu3 [389 kB] Get:68 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libboost-program-options-dev armhf 1.83.0.1ubuntu2 [4084 B] Get:69 http://ftpmaster.internal/ubuntu noble-proposed/universe armhf libboost-system-dev armhf 1.83.0.1ubuntu2 [4204 B] Get:70 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libboost-thread1.83.0 armhf 1.83.0-1ubuntu3 [270 kB] Get:71 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libboost-thread1.83-dev armhf 1.83.0-1ubuntu3 [281 kB] Get:72 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libboost-thread-dev armhf 1.83.0.1ubuntu2 [4088 B] Get:73 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libboost1.83-tools-dev armhf 1.83.0-1ubuntu3 [1466 kB] Get:74 http://ftpmaster.internal/ubuntu noble-proposed/universe armhf libboost-tools-dev armhf 1.83.0.1ubuntu2 [4238 B] Get:75 http://ftpmaster.internal/ubuntu noble/main armhf libtcmalloc-minimal4 armhf 2.13-1ubuntu1 [81.0 kB] Get:76 http://ftpmaster.internal/ubuntu noble/main armhf libgoogle-perftools4 armhf 2.13-1ubuntu1 [182 kB] Get:77 http://ftpmaster.internal/ubuntu noble/main armhf libgoogle-perftools-dev armhf 2.13-1ubuntu1 [464 kB] Get:78 http://ftpmaster.internal/ubuntu noble/main armhf libprotobuf-lite32 armhf 3.21.12-8ubuntu1 [227 kB] Get:79 http://ftpmaster.internal/ubuntu noble/main armhf libprotobuf32 armhf 3.21.12-8ubuntu1 [911 kB] Get:80 http://ftpmaster.internal/ubuntu noble/main armhf libprotoc32 armhf 3.21.12-8ubuntu1 [822 kB] Get:81 http://ftpmaster.internal/ubuntu noble/main armhf libprotobuf-dev armhf 3.21.12-8ubuntu1 [1426 kB] Get:82 http://ftpmaster.internal/ubuntu noble/universe armhf protobuf-compiler armhf 3.21.12-8ubuntu1 [29.0 kB] Preconfiguring packages ... 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uuid-runtime_2.39.2-6ubuntu1 xz-utils_5.4.5-0.1 zlib1g_1:1.3.dfsg-3ubuntu1 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-27576183 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-27576183 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-27576183 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 armhf 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-arm-linux-gnueabihf && 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/arm-linux-gnueabihf .. 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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/libtcmalloc.so -- Found Protobuf: /usr/lib/arm-linux-gnueabihf/libprotobuf.so (found version "3.21.12") -- Do not try to find libbamtools.a -- Configuring done (1.9s) -- 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-arm-linux-gnueabihf dh_auto_build -a cd obj-arm-linux-gnueabihf && make -j4 "INSTALL=install --strip-program=true" VERBOSE=1 make[1]: Entering directory '/<>/obj-arm-linux-gnueabihf' /usr/bin/cmake -S/<> -B/<>/obj-arm-linux-gnueabihf --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /<>/obj-arm-linux-gnueabihf/CMakeFiles /<>/obj-arm-linux-gnueabihf//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/<>/obj-arm-linux-gnueabihf' make -f src/CMakeFiles/express.dir/build.make src/CMakeFiles/express.dir/depend make[3]: Entering directory '/<>/obj-arm-linux-gnueabihf' [ 11%] Running cpp protocol buffer compiler on /<>/src/alignments.proto [ 11%] Running cpp protocol buffer compiler on /<>/src/targets.proto cd /<>/obj-arm-linux-gnueabihf/src && /usr/bin/protoc --cpp_out :/<>/obj-arm-linux-gnueabihf/src -I /<>/src /<>/src/targets.proto cd /<>/obj-arm-linux-gnueabihf/src && /usr/bin/protoc --cpp_out :/<>/obj-arm-linux-gnueabihf/src -I /<>/src /<>/src/alignments.proto [libprotobuf WARNING google/protobuf/compiler/parser.cc:646] No syntax specified for the proto file: alignments.proto. Please us[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.) e 'syntax = "proto2";' or 'syntax = "proto3";' to specify a syntax version. (Defaulted to proto2 syntax.) cd /<>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/src /<>/obj-arm-linux-gnueabihf /<>/obj-arm-linux-gnueabihf/src /<>/obj-arm-linux-gnueabihf/src/CMakeFiles/express.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/<>/obj-arm-linux-gnueabihf' make -f src/CMakeFiles/express.dir/build.make src/CMakeFiles/express.dir/build make[3]: Entering directory '/<>/obj-arm-linux-gnueabihf' [ 16%] Building CXX object src/CMakeFiles/express.dir/biascorrection.cpp.o [ 27%] Building CXX object src/CMakeFiles/express.dir/bundles.cpp.o [ 27%] Building CXX object src/CMakeFiles/express.dir/directiondetector.cpp.o cd /<>/obj-arm-linux-gnueabihf/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 -ffile-prefix-map=/<>=. -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-arm-linux-gnueabihf/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 -ffile-prefix-map=/<>=. -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 cd /<>/obj-arm-linux-gnueabihf/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 -ffile-prefix-map=/<>=. -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 cd /<>/obj-arm-linux-gnueabihf/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 -ffile-prefix-map=/<>=. -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] : 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-arm-linux-gnueabihf/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 -ffile-prefix-map=/<>=. -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-arm-linux-gnueabihf/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 -ffile-prefix-map=/<>=. -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-arm-linux-gnueabihf/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 -ffile-prefix-map=/<>=. -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-arm-linux-gnueabihf/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 -ffile-prefix-map=/<>=. -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-arm-linux-gnueabihf/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 -ffile-prefix-map=/<>=. -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] In file included from /usr/include/c++/13/vector:72, from /<>/src/lengthdistribution.h:12, from /<>/src/lengthdistribution.cpp:9: /usr/include/c++/13/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’: /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’, inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]’ at /usr/include/c++/13/bits/stl_vector.h:1296:21, inlined from ‘LengthDistribution::LengthDistribution(std::string, std::string)’ at /<>/src/lengthdistribution.cpp:91:20: /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 66%] Building CXX object src/CMakeFiles/express.dir/robertsfilter.cpp.o cd /<>/obj-arm-linux-gnueabihf/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 -ffile-prefix-map=/<>=. -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-arm-linux-gnueabihf/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 -ffile-prefix-map=/<>=. -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-arm-linux-gnueabihf/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 -ffile-prefix-map=/<>=. -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-arm-linux-gnueabihf/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 -ffile-prefix-map=/<>=. -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-arm-linux-gnueabihf/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 -ffile-prefix-map=/<>=. -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-arm-linux-gnueabihf/src/alignments.pb.cc : warning: "__FILE__" redefined [-Wbuiltin-macro-redefined] [ 94%] Building CXX object src/CMakeFiles/express.dir/targets.pb.cc.o cd /<>/obj-arm-linux-gnueabihf/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 -ffile-prefix-map=/<>=. -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-arm-linux-gnueabihf/src/targets.pb.cc : warning: "__FILE__" redefined [-Wbuiltin-macro-redefined] [100%] Linking CXX executable express cd /<>/obj-arm-linux-gnueabihf/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/express.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/<>=. -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 -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/arm-linux-gnueabihf/libboost_thread.so.1.83.0 /usr/lib/arm-linux-gnueabihf/libboost_system.so.1.83.0 /usr/lib/arm-linux-gnueabihf/libboost_filesystem.so.1.83.0 /usr/lib/arm-linux-gnueabihf/libboost_program_options.so.1.83.0 /usr/lib/arm-linux-gnueabihf/libboost_date_time.so.1.83.0 -lbamtools -lprotobuf -lpthread -lrt /usr/lib/arm-linux-gnueabihf/libboost_atomic.so.1.83.0 make[3]: Leaving directory '/<>/obj-arm-linux-gnueabihf' [100%] Built target express make[2]: Leaving directory '/<>/obj-arm-linux-gnueabihf' /usr/bin/cmake -E cmake_progress_start /<>/obj-arm-linux-gnueabihf/CMakeFiles 0 make[1]: Leaving directory '/<>/obj-arm-linux-gnueabihf' dh_auto_test -a create-stamp debian/debhelper-build-stamp dh_prep -a dh_installdirs -a dh_auto_install -a cd obj-arm-linux-gnueabihf && 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-arm-linux-gnueabihf' /usr/bin/cmake -S/<> -B/<>/obj-arm-linux-gnueabihf --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 preinstall make[2]: Entering directory '/<>/obj-arm-linux-gnueabihf' make[2]: Nothing to be done for 'preinstall'. make[2]: Leaving directory '/<>/obj-arm-linux-gnueabihf' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "None" -- Installing: /<>/debian/tmp/usr/bin/express make[1]: Leaving directory '/<>/obj-arm-linux-gnueabihf' 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 f138e8bd36a9e1349adf35cedc3d22d2e885469e dh_makeshlibs -a dh_shlibdeps -a dpkg-shlibdeps: warning: debian/berkeley-express/usr/lib/debian-med/bin/express contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin 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_armhf.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_armhf.deb'. Renaming berkeley-express-dbgsym_1.5.3+dfsg-3build3_armhf.deb to berkeley-express-dbgsym_1.5.3+dfsg-3build3_armhf.ddeb dpkg-genbuildinfo --build=any -O../berkeley-express_1.5.3+dfsg-3build3_armhf.buildinfo dpkg-genchanges --build=any -mLaunchpad Build Daemon -O../berkeley-express_1.5.3+dfsg-3build3_armhf.changes dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) -------------------------------------------------------------------------------- Build finished at 2023-12-19T15:21:43Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ berkeley-express_1.5.3+dfsg-3build3_armhf.changes: -------------------------------------------------- Format: 1.8 Date: Tue, 19 Dec 2023 15:46:29 +0100 Source: berkeley-express Binary: berkeley-express Built-For-Profiles: noudeb Architecture: armhf Version: 1.5.3+dfsg-3build3 Distribution: noble-proposed Urgency: medium Maintainer: Launchpad Build Daemon Changed-By: Matthias Klose Description: berkeley-express - Streaming quantification for high-throughput sequencing Changes: berkeley-express (1.5.3+dfsg-3build3) noble; urgency=medium . * No-change rebuild for boost defaults change. 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libboost-thread1.83-dev (= 1.83.0-1ubuntu3), libboost-thread1.83.0 (= 1.83.0-1ubuntu3), libboost-tools-dev (= 1.83.0.1ubuntu2), libboost1.83-dev (= 1.83.0-1ubuntu3), libboost1.83-tools-dev (= 1.83.0-1ubuntu3), libbrotli1 (= 1.1.0-2), libbz2-1.0 (= 1.0.8-5build1), libc-bin (= 2.38-3ubuntu1), libc-dev-bin (= 2.38-3ubuntu1), libc6 (= 2.38-3ubuntu1), libc6-dev (= 2.38-3ubuntu1), libcap-ng0 (= 0.8.3-3), libcap2 (= 1:2.66-4ubuntu1), libcc1-0 (= 13.2.0-9ubuntu1), libcom-err2 (= 1.47.0-2ubuntu1), libcrypt-dev (= 1:4.4.36-2), libcrypt1 (= 1:4.4.36-2), libctf-nobfd0 (= 2.41.50.20231214-1ubuntu1), libctf0 (= 2.41.50.20231214-1ubuntu1), libcurl4 (= 8.4.0-2ubuntu1), libdb5.3 (= 5.3.28+dfsg2-4), libdebconfclient0 (= 0.271ubuntu1), libdebhelper-perl (= 13.11.8ubuntu1), libdpkg-perl (= 1.22.1ubuntu5), libdw1 (= 0.190-1), libelf1 (= 0.190-1), libexpat1 (= 2.5.0-2), libffi8 (= 3.4.4-2), libfile-stripnondeterminism-perl (= 1.13.1-1), libgcc-13-dev (= 13.2.0-9ubuntu1), libgcc-s1 (= 13.2.0-9ubuntu1), libgcrypt20 (= 1.10.2-3ubuntu1), libgdbm-compat4 (= 1.23-5), libgdbm6 (= 1.23-5), libgmp10 (= 2:6.3.0+dfsg-2ubuntu4), libgnutls30 (= 3.8.1-4ubuntu6), libgomp1 (= 13.2.0-9ubuntu1), libgoogle-perftools-dev (= 2.13-1ubuntu1), libgoogle-perftools4 (= 2.13-1ubuntu1), libgpg-error0 (= 1.47-3build1), libgssapi-krb5-2 (= 1.20.1-5build1), libhogweed6 (= 3.9.1-2), libicu74 (= 74.2-1ubuntu1), libidn2-0 (= 2.3.4-1build1), libisl23 (= 0.26-3), libjansson4 (= 2.14-2), libjsoncpp25 (= 1.9.5-6), libk5crypto3 (= 1.20.1-5build1), libkeyutils1 (= 1.6.3-2), libkrb5-3 (= 1.20.1-5build1), libkrb5support0 (= 1.20.1-5build1), libldap2 (= 2.6.6+dfsg-1~exp1ubuntu1), liblz4-1 (= 1.9.4-1), liblzma5 (= 5.4.5-0.1), libmagic-mgc (= 1:5.45-2), libmagic1 (= 1:5.45-2), libmd0 (= 1.1.0-1), libmount1 (= 2.39.2-6ubuntu1), libmpc3 (= 1.3.1-1), libmpfr6 (= 4.2.1-1), libncursesw6 (= 6.4+20231209-1), libnettle8 (= 3.9.1-2), libnghttp2-14 (= 1.58.0-1), libnsl-dev (= 1.3.0-3), libnsl2 (= 1.3.0-3), libp11-kit0 (= 0.25.3-2ubuntu2), libpam-modules (= 1.5.2-9.1ubuntu1), 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), libtcmalloc-minimal4 (= 2.13-1ubuntu1), 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_armhf.deb --------------------------------------------- new Debian package, version 2.0. size 216676 bytes: control archive=1852 bytes. 3188 bytes, 51 lines control 454 bytes, 6 lines md5sums Package: berkeley-express Version: 1.5.3+dfsg-3build3 Architecture: armhf Maintainer: Ubuntu Developers Installed-Size: 521 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 (>= 3.5), 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 510160 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: armhf Build Type: any Build-Space: 66976 Build-Time: 112 Distribution: noble-proposed Host Architecture: armhf Install-Time: 44 Job: berkeley-express_1.5.3+dfsg-3build3.dsc Machine Architecture: arm64 Package: berkeley-express Package-Time: 159 Source-Version: 1.5.3+dfsg-3build3 Space: 66976 Status: successful Version: 1.5.3+dfsg-3build3 -------------------------------------------------------------------------------- Finished at 2023-12-19T15:21:43Z Build needed 00:02:39, 66976k disk space RUN: /usr/share/launchpad-buildd/bin/in-target scan-for-processes --backend=chroot --series=noble --arch=armhf PACKAGEBUILD-27576183 Scanning for processes to kill in build PACKAGEBUILD-27576183