https://launchpad.net/ubuntu/+source/lagan/2.0-9/+build/24257979 RUN: /usr/share/launchpad-buildd/bin/builder-prep Kernel version: Linux riscv64-qemu-lgw01-005 5.13.0-1019-generic #21~20.04.1-Ubuntu SMP Thu Mar 24 22:36:01 UTC 2022 riscv64 Buildd toolchain package versions: launchpad-buildd_218~581~ubuntu20.04.1 python3-lpbuildd_218~581~ubuntu20.04.1 sbuild_0.79.0-1ubuntu1 git_1:2.25.1-1ubuntu3.2 dpkg-dev_1.19.7ubuntu3 python3-debian_0.1.36ubuntu1. Syncing the system clock with the buildd NTP service... 7 Aug 17:14:13 ntpdate[75334]: adjust time server 10.211.37.1 offset -0.000497 sec RUN: /usr/share/launchpad-buildd/bin/in-target unpack-chroot --backend=chroot --series=kinetic --arch=riscv64 PACKAGEBUILD-24257979 --image-type chroot /home/buildd/filecache-default/71606a5f218d7969dca11cc1a0a8ecfd02d5af78 Creating target for build PACKAGEBUILD-24257979 RUN: /usr/share/launchpad-buildd/bin/in-target mount-chroot --backend=chroot --series=kinetic --arch=riscv64 PACKAGEBUILD-24257979 Starting target for build PACKAGEBUILD-24257979 RUN: /usr/share/launchpad-buildd/bin/in-target override-sources-list --backend=chroot --series=kinetic --arch=riscv64 PACKAGEBUILD-24257979 'deb http://ftpmaster.internal/ubuntu kinetic main universe' 'deb http://ftpmaster.internal/ubuntu kinetic-security main universe' 'deb http://ftpmaster.internal/ubuntu kinetic-updates main universe' 'deb http://ftpmaster.internal/ubuntu kinetic-proposed main universe' Overriding sources.list in build-PACKAGEBUILD-24257979 RUN: /usr/share/launchpad-buildd/bin/in-target update-debian-chroot --backend=chroot --series=kinetic --arch=riscv64 PACKAGEBUILD-24257979 Updating target for build PACKAGEBUILD-24257979 Get:1 http://ftpmaster.internal/ubuntu kinetic InRelease [267 kB] Get:2 http://ftpmaster.internal/ubuntu kinetic-security InRelease [90.7 kB] Get:3 http://ftpmaster.internal/ubuntu kinetic-updates InRelease [90.7 kB] Get:4 http://ftpmaster.internal/ubuntu kinetic-proposed InRelease [118 kB] Get:5 http://ftpmaster.internal/ubuntu kinetic/main riscv64 Packages [1300 kB] Get:6 http://ftpmaster.internal/ubuntu kinetic/main Translation-en [511 kB] Get:7 http://ftpmaster.internal/ubuntu kinetic/universe riscv64 Packages [13.3 MB] Get:8 http://ftpmaster.internal/ubuntu kinetic/universe Translation-en [5782 kB] Get:9 http://ftpmaster.internal/ubuntu kinetic-proposed/main riscv64 Packages [117 kB] Get:10 http://ftpmaster.internal/ubuntu kinetic-proposed/main Translation-en [53.1 kB] Get:11 http://ftpmaster.internal/ubuntu kinetic-proposed/universe riscv64 Packages [620 kB] Get:12 http://ftpmaster.internal/ubuntu kinetic-proposed/universe Translation-en [244 kB] Fetched 22.5 MB in 30s (745 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages were automatically installed and are no longer required: g++-11 libstdc++-11-dev Use 'sudo apt autoremove' to remove them. The following NEW packages will be installed: cpp-12 g++-12 gcc-12 libasan8 libfdisk1 libgcc-12-dev libstdc++-12-dev sgml-base util-linux-extra The following packages will be upgraded: adduser apt base-files binutils binutils-common binutils-riscv64-linux-gnu bsdutils cpp cpp-11 dash debianutils dpkg dpkg-dev e2fsprogs fakeroot g++ g++-11 gcc gcc-11 gcc-11-base gcc-12-base gpg gpg-agent gpgconf gpgv init init-system-helpers libapparmor1 libapt-pkg6.0 libasan6 libassuan0 libatomic1 libbinutils libblkid1 libcap-ng0 libcc1-0 libcom-err2 libcrypt-dev libcrypt1 libctf-nobfd0 libctf0 libdb5.3 libdpkg-perl libext2fs2 libfakeroot libgcc-11-dev libgcc-s1 libgcrypt20 libgnutls30 libgomp1 libgpg-error0 libgssapi-krb5-2 libidn2-0 libip4tc2 libisl23 libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblzma5 libmount1 libncurses6 libncursesw6 libperl5.34 libpng16-16 libreadline8 libselinux1 libsemanage-common libsemanage2 libsepol2 libsmartcols1 libsqlite3-0 libss2 libssl3 libstdc++-11-dev libstdc++6 libsystemd0 libtinfo6 libtirpc-common libtirpc-dev libtirpc3 libudev1 libuuid1 libzstd1 linux-libc-dev login logsave lto-disabled-list mawk mount ncurses-base ncurses-bin openssl passwd perl perl-base perl-modules-5.34 pinentry-curses policyrcd-script-zg2 readline-common systemd systemd-sysv util-linux xz-utils zlib1g 105 upgraded, 9 newly installed, 0 to remove and 0 not upgraded. Need to get 123 MB of archives. After this operation, 157 MB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu kinetic/main riscv64 libcrypt-dev riscv64 1:4.4.28-2 [240 kB] Get:2 http://ftpmaster.internal/ubuntu kinetic/main riscv64 libcrypt1 riscv64 1:4.4.28-2 [95.9 kB] Get:3 http://ftpmaster.internal/ubuntu kinetic/main riscv64 base-files riscv64 12.2ubuntu2 [72.9 kB] Get:4 http://ftpmaster.internal/ubuntu kinetic/main riscv64 bsdutils riscv64 1:2.38-4ubuntu1 [91.0 kB] Get:5 http://ftpmaster.internal/ubuntu kinetic/main riscv64 debianutils riscv64 5.7-0.3 [102 kB] Get:6 http://ftpmaster.internal/ubuntu kinetic/main riscv64 libzstd1 riscv64 1.5.2+dfsg-1 [318 kB] Get:7 http://ftpmaster.internal/ubuntu kinetic/main riscv64 libgpg-error0 riscv64 1.45-2 [62.7 kB] Get:8 http://ftpmaster.internal/ubuntu kinetic/main riscv64 libgcrypt20 riscv64 1.10.1-2ubuntu1 [508 kB] Get:9 http://ftpmaster.internal/ubuntu kinetic-proposed/main riscv64 libatomic1 riscv64 12.1.0-7ubuntu1 [7846 B] Get:10 http://ftpmaster.internal/ubuntu kinetic-proposed/main riscv64 libgomp1 riscv64 12.1.0-7ubuntu1 [111 kB] Get:11 http://ftpmaster.internal/ubuntu kinetic-proposed/main riscv64 gcc-12-base riscv64 12.1.0-7ubuntu1 [19.3 kB] Get:12 http://ftpmaster.internal/ubuntu kinetic-proposed/main riscv64 libgcc-s1 riscv64 12.1.0-7ubuntu1 [44.0 kB] Get:13 http://ftpmaster.internal/ubuntu kinetic-proposed/main riscv64 libcc1-0 riscv64 12.1.0-7ubuntu1 [43.0 kB] Get:14 http://ftpmaster.internal/ubuntu kinetic-proposed/main riscv64 libstdc++6 riscv64 12.1.0-7ubuntu1 [675 kB] Get:15 http://ftpmaster.internal/ubuntu kinetic/main riscv64 liblzma5 riscv64 5.2.5-2.1 [93.5 kB] Get:16 http://ftpmaster.internal/ubuntu kinetic/main riscv64 libblkid1 riscv64 2.38-4ubuntu1 [149 kB] Get:17 http://ftpmaster.internal/ubuntu kinetic/main riscv64 libuuid1 riscv64 2.38-4ubuntu1 [26.2 kB] Get:18 http://ftpmaster.internal/ubuntu kinetic/main riscv64 libfdisk1 riscv64 2.38-4ubuntu1 [194 kB] Get:19 http://ftpmaster.internal/ubuntu kinetic/main riscv64 systemd-sysv riscv64 251.2-2ubuntu2 [11.2 kB] Get:20 http://ftpmaster.internal/ubuntu kinetic/main riscv64 libapparmor1 riscv64 3.0.4-3ubuntu1 [33.7 kB] Get:21 http://ftpmaster.internal/ubuntu kinetic/main riscv64 libip4tc2 riscv64 1.8.7-1ubuntu6 [18.0 kB] Get:22 http://ftpmaster.internal/ubuntu kinetic/main riscv64 libselinux1 riscv64 3.4-1 [73.1 kB] Get:23 http://ftpmaster.internal/ubuntu kinetic/main riscv64 libmount1 riscv64 2.38-4ubuntu1 [157 kB] Get:24 http://ftpmaster.internal/ubuntu kinetic/main riscv64 libssl3 riscv64 3.0.4-1ubuntu1 [1448 kB] Get:25 http://ftpmaster.internal/ubuntu kinetic/main riscv64 mount riscv64 2.38-4ubuntu1 [130 kB] Get:26 http://ftpmaster.internal/ubuntu kinetic/main riscv64 libsemanage-common all 3.4-1 [9828 B] Get:27 http://ftpmaster.internal/ubuntu kinetic/main riscv64 libsepol2 riscv64 3.4-2 [256 kB] Get:28 http://ftpmaster.internal/ubuntu kinetic/main riscv64 libsemanage2 riscv64 3.4-1 [83.9 kB] Get:29 http://ftpmaster.internal/ubuntu kinetic/main riscv64 passwd riscv64 1:4.11.1+dfsg1-2ubuntu1 [735 kB] Get:30 http://ftpmaster.internal/ubuntu kinetic/main riscv64 adduser all 3.121ubuntu1 [150 kB] Get:31 http://ftpmaster.internal/ubuntu kinetic/main riscv64 systemd riscv64 251.2-2ubuntu2 [4235 kB] Get:32 http://ftpmaster.internal/ubuntu kinetic/main riscv64 libsystemd0 riscv64 251.2-2ubuntu2 [298 kB] Get:33 http://ftpmaster.internal/ubuntu kinetic/main riscv64 libudev1 riscv64 251.2-2ubuntu2 [74.5 kB] Get:34 http://ftpmaster.internal/ubuntu kinetic-proposed/main riscv64 zlib1g riscv64 1:1.2.11.dfsg-2ubuntu10 [55.6 kB] Get:35 http://ftpmaster.internal/ubuntu kinetic/main riscv64 libapt-pkg6.0 riscv64 2.5.2 [918 kB] Get:36 http://ftpmaster.internal/ubuntu kinetic/main riscv64 dpkg riscv64 1.21.9ubuntu1 [1290 kB] Get:37 http://ftpmaster.internal/ubuntu kinetic/main riscv64 dash riscv64 0.5.11+git20210903+057cd650a4ed-8ubuntu1 [82.2 kB] Get:38 http://ftpmaster.internal/ubuntu kinetic/main riscv64 login riscv64 1:4.11.1+dfsg1-2ubuntu1 [180 kB] Get:39 http://ftpmaster.internal/ubuntu kinetic/main riscv64 ncurses-bin riscv64 6.3+20220423-2 [176 kB] Get:40 http://ftpmaster.internal/ubuntu kinetic/main riscv64 libperl5.34 riscv64 5.34.0-5ubuntu1 [4110 kB] Get:41 http://ftpmaster.internal/ubuntu kinetic/main riscv64 perl riscv64 5.34.0-5ubuntu1 [231 kB] Get:42 http://ftpmaster.internal/ubuntu kinetic/main riscv64 perl-base riscv64 5.34.0-5ubuntu1 [1615 kB] Get:43 http://ftpmaster.internal/ubuntu kinetic/main riscv64 perl-modules-5.34 all 5.34.0-5ubuntu1 [2952 kB] Get:44 http://ftpmaster.internal/ubuntu kinetic/main riscv64 libdb5.3 riscv64 5.3.28+dfsg1-0.10 [664 kB] Get:45 http://ftpmaster.internal/ubuntu kinetic/main riscv64 libsmartcols1 riscv64 2.38-4ubuntu1 [102 kB] Get:46 http://ftpmaster.internal/ubuntu kinetic/main riscv64 util-linux-extra riscv64 2.38-4ubuntu1 [103 kB] Get:47 http://ftpmaster.internal/ubuntu kinetic/main riscv64 util-linux riscv64 2.38-4ubuntu1 [1142 kB] Get:48 http://ftpmaster.internal/ubuntu kinetic/main riscv64 init-system-helpers all 1.64 [38.7 kB] Get:49 http://ftpmaster.internal/ubuntu kinetic/main riscv64 ncurses-base all 6.3+20220423-2 [21.2 kB] Get:50 http://ftpmaster.internal/ubuntu kinetic/main riscv64 sgml-base all 1.30 [12.5 kB] Get:51 http://ftpmaster.internal/ubuntu kinetic/main riscv64 libidn2-0 riscv64 2.3.3-1 [94.0 kB] Get:52 http://ftpmaster.internal/ubuntu kinetic-proposed/main riscv64 libgnutls30 riscv64 3.7.7-2ubuntu1 [891 kB] Get:53 http://ftpmaster.internal/ubuntu kinetic/main riscv64 gpgv riscv64 2.2.27-3ubuntu3 [193 kB] Get:54 http://ftpmaster.internal/ubuntu kinetic/main riscv64 apt riscv64 2.5.2 [1337 kB] Get:55 http://ftpmaster.internal/ubuntu kinetic/main riscv64 logsave riscv64 1.46.5-2ubuntu2 [9366 B] Get:56 http://ftpmaster.internal/ubuntu kinetic/main riscv64 libext2fs2 riscv64 1.46.5-2ubuntu2 [192 kB] Get:57 http://ftpmaster.internal/ubuntu kinetic/main riscv64 e2fsprogs riscv64 1.46.5-2ubuntu2 [545 kB] Get:58 http://ftpmaster.internal/ubuntu kinetic/main riscv64 init riscv64 1.64 [5538 B] Get:59 http://ftpmaster.internal/ubuntu kinetic/main riscv64 libcap-ng0 riscv64 0.8.3-1 [13.8 kB] Get:60 http://ftpmaster.internal/ubuntu kinetic/main riscv64 libncurses6 riscv64 6.3+20220423-2 [92.7 kB] Get:61 http://ftpmaster.internal/ubuntu kinetic/main riscv64 libncursesw6 riscv64 6.3+20220423-2 [127 kB] Get:62 http://ftpmaster.internal/ubuntu kinetic/main riscv64 libtinfo6 riscv64 6.3+20220423-2 [89.8 kB] Get:63 http://ftpmaster.internal/ubuntu kinetic/main riscv64 libcom-err2 riscv64 1.46.5-2ubuntu2 [8028 B] Get:64 http://ftpmaster.internal/ubuntu kinetic/main riscv64 libss2 riscv64 1.46.5-2ubuntu2 [10.7 kB] Get:65 http://ftpmaster.internal/ubuntu kinetic/main riscv64 mawk riscv64 1.3.4.20200120-3.1 [100 kB] Get:66 http://ftpmaster.internal/ubuntu kinetic/main riscv64 libgssapi-krb5-2 riscv64 1.20-1 [125 kB] Get:67 http://ftpmaster.internal/ubuntu kinetic/main riscv64 libkrb5-3 riscv64 1.20-1 [328 kB] Get:68 http://ftpmaster.internal/ubuntu kinetic/main riscv64 libkrb5support0 riscv64 1.20-1 [29.8 kB] Get:69 http://ftpmaster.internal/ubuntu kinetic/main riscv64 libk5crypto3 riscv64 1.20-1 [96.6 kB] Get:70 http://ftpmaster.internal/ubuntu kinetic/main riscv64 libkeyutils1 riscv64 1.6.1-3ubuntu1 [8992 B] Get:71 http://ftpmaster.internal/ubuntu kinetic/main riscv64 readline-common all 8.1.2-1.2 [53.6 kB] Get:72 http://ftpmaster.internal/ubuntu kinetic/main riscv64 libreadline8 riscv64 8.1.2-1.2 [130 kB] Get:73 http://ftpmaster.internal/ubuntu kinetic/main riscv64 libsqlite3-0 riscv64 3.39.2-1 [579 kB] Get:74 http://ftpmaster.internal/ubuntu kinetic-proposed/main riscv64 libtirpc-common all 1.3.2-2.1 [7602 B] Get:75 http://ftpmaster.internal/ubuntu kinetic-proposed/main riscv64 libtirpc-dev riscv64 1.3.2-2.1 [310 kB] Get:76 http://ftpmaster.internal/ubuntu kinetic-proposed/main riscv64 libtirpc3 riscv64 1.3.2-2.1 [73.3 kB] Get:77 http://ftpmaster.internal/ubuntu kinetic/main riscv64 openssl riscv64 3.0.4-1ubuntu1 [1139 kB] Get:78 http://ftpmaster.internal/ubuntu kinetic/main riscv64 libpng16-16 riscv64 1.6.37-5 [174 kB] Get:79 http://ftpmaster.internal/ubuntu kinetic/main riscv64 xz-utils riscv64 5.2.5-2.1 [80.4 kB] Get:80 http://ftpmaster.internal/ubuntu kinetic/main riscv64 libctf0 riscv64 2.38.90.20220713-2ubuntu1 [98.8 kB] Get:81 http://ftpmaster.internal/ubuntu kinetic/main riscv64 libctf-nobfd0 riscv64 2.38.90.20220713-2ubuntu1 [101 kB] Get:82 http://ftpmaster.internal/ubuntu kinetic/main riscv64 libbinutils riscv64 2.38.90.20220713-2ubuntu1 [494 kB] Get:83 http://ftpmaster.internal/ubuntu kinetic/main riscv64 binutils riscv64 2.38.90.20220713-2ubuntu1 [3088 B] Get:84 http://ftpmaster.internal/ubuntu kinetic/main riscv64 binutils-common riscv64 2.38.90.20220713-2ubuntu1 [216 kB] Get:85 http://ftpmaster.internal/ubuntu kinetic/main riscv64 binutils-riscv64-linux-gnu riscv64 2.38.90.20220713-2ubuntu1 [931 kB] Get:86 http://ftpmaster.internal/ubuntu kinetic/main riscv64 libisl23 riscv64 0.25-1 [590 kB] Get:87 http://ftpmaster.internal/ubuntu kinetic-proposed/main riscv64 cpp-12 riscv64 12.1.0-7ubuntu1 [8281 kB] Get:88 http://ftpmaster.internal/ubuntu kinetic-proposed/main riscv64 libasan8 riscv64 12.1.0-7ubuntu1 [2308 kB] Get:89 http://ftpmaster.internal/ubuntu kinetic-proposed/main riscv64 libgcc-12-dev riscv64 12.1.0-7ubuntu1 [2595 kB] Get:90 http://ftpmaster.internal/ubuntu kinetic-proposed/main riscv64 gcc-12 riscv64 12.1.0-7ubuntu1 [16.3 MB] Get:91 http://ftpmaster.internal/ubuntu kinetic-proposed/main riscv64 libstdc++-12-dev riscv64 12.1.0-7ubuntu1 [4852 kB] Get:92 http://ftpmaster.internal/ubuntu kinetic-proposed/main riscv64 g++-12 riscv64 12.1.0-7ubuntu1 [9551 kB] Get:93 http://ftpmaster.internal/ubuntu kinetic-proposed/main riscv64 g++ riscv64 4:12.1.0-3ubuntu1 [1398 B] Get:94 http://ftpmaster.internal/ubuntu kinetic-proposed/main riscv64 gcc riscv64 4:12.1.0-3ubuntu1 [5132 B] Get:95 http://ftpmaster.internal/ubuntu kinetic-proposed/main riscv64 cpp riscv64 4:12.1.0-3ubuntu1 [27.4 kB] Get:96 http://ftpmaster.internal/ubuntu kinetic/main riscv64 libasan6 riscv64 11.3.0-5ubuntu1 [2092 kB] Get:97 http://ftpmaster.internal/ubuntu kinetic/main riscv64 g++-11 riscv64 11.3.0-5ubuntu1 [9260 kB] Get:98 http://ftpmaster.internal/ubuntu kinetic/main riscv64 gcc-11 riscv64 11.3.0-5ubuntu1 [15.8 MB] Get:99 http://ftpmaster.internal/ubuntu kinetic/main riscv64 libstdc++-11-dev riscv64 11.3.0-5ubuntu1 [4588 kB] Get:100 http://ftpmaster.internal/ubuntu kinetic/main riscv64 libgcc-11-dev riscv64 11.3.0-5ubuntu1 [2280 kB] Get:101 http://ftpmaster.internal/ubuntu kinetic/main riscv64 cpp-11 riscv64 11.3.0-5ubuntu1 [7949 kB] Get:102 http://ftpmaster.internal/ubuntu kinetic/main riscv64 gcc-11-base riscv64 11.3.0-5ubuntu1 [20.4 kB] Get:103 http://ftpmaster.internal/ubuntu kinetic/main riscv64 dpkg-dev all 1.21.9ubuntu1 [1070 kB] Get:104 http://ftpmaster.internal/ubuntu kinetic/main riscv64 libdpkg-perl all 1.21.9ubuntu1 [237 kB] Get:105 http://ftpmaster.internal/ubuntu kinetic/main riscv64 lto-disabled-list all 32 [12.2 kB] Get:106 http://ftpmaster.internal/ubuntu kinetic/main riscv64 libfakeroot riscv64 1.29-1ubuntu1 [26.6 kB] Get:107 http://ftpmaster.internal/ubuntu kinetic/main riscv64 fakeroot riscv64 1.29-1ubuntu1 [67.6 kB] Get:108 http://ftpmaster.internal/ubuntu kinetic/main riscv64 libassuan0 riscv64 2.5.5-4 [31.8 kB] Get:109 http://ftpmaster.internal/ubuntu kinetic/main riscv64 pinentry-curses riscv64 1.2.0-2ubuntu1 [36.1 kB] Get:110 http://ftpmaster.internal/ubuntu kinetic/main riscv64 gpg riscv64 2.2.27-3ubuntu3 [483 kB] Get:111 http://ftpmaster.internal/ubuntu kinetic/main riscv64 gpgconf riscv64 2.2.27-3ubuntu3 [113 kB] Get:112 http://ftpmaster.internal/ubuntu kinetic/main riscv64 gpg-agent riscv64 2.2.27-3ubuntu3 [226 kB] Get:113 http://ftpmaster.internal/ubuntu kinetic-proposed/main riscv64 linux-libc-dev riscv64 5.19.0-15.15 [1264 kB] Get:114 http://ftpmaster.internal/ubuntu kinetic/main riscv64 policyrcd-script-zg2 all 0.1-3.1 [5730 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 123 MB in 24s (5194 kB/s) (Reading database ... 13360 files and directories currently installed.) Preparing to unpack .../libcrypt-dev_1%3a4.4.28-2_riscv64.deb ... Unpacking libcrypt-dev:riscv64 (1:4.4.28-2) over (1:4.4.27-1) ... Preparing to unpack .../libcrypt1_1%3a4.4.28-2_riscv64.deb ... Unpacking libcrypt1:riscv64 (1:4.4.28-2) over (1:4.4.27-1) ... Setting up libcrypt1:riscv64 (1:4.4.28-2) ... (Reading database ... 13362 files and directories currently installed.) Preparing to unpack .../base-files_12.2ubuntu2_riscv64.deb ... Unpacking base-files (12.2ubuntu2) over (12ubuntu5) ... Setting up base-files (12.2ubuntu2) ... (Reading database ... 13374 files and directories currently installed.) Preparing to unpack .../bsdutils_1%3a2.38-4ubuntu1_riscv64.deb ... Unpacking bsdutils (1:2.38-4ubuntu1) over (1:2.37.2-4ubuntu3) ... Setting up bsdutils (1:2.38-4ubuntu1) ... (Reading database ... 13374 files and directories currently installed.) Preparing to unpack .../debianutils_5.7-0.3_riscv64.deb ... Unpacking debianutils (5.7-0.3) over (5.7-0.2) ... 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Setting up libtirpc-dev:riscv64 (1.3.2-2.1) ... Setting up gcc-12 (12.1.0-7ubuntu1) ... Setting up g++-12 (12.1.0-7ubuntu1) ... Setting up gcc (4:12.1.0-3ubuntu1) ... Setting up g++ (4:12.1.0-3ubuntu1) ... Processing triggers for libc-bin (2.35-0ubuntu3) ... Processing triggers for debianutils (5.7-0.3) ... RUN: /usr/share/launchpad-buildd/bin/sbuild-package PACKAGEBUILD-24257979 riscv64 kinetic-proposed -c chroot:build-PACKAGEBUILD-24257979 --arch=riscv64 --dist=kinetic-proposed --nolog lagan_2.0-9.dsc Initiating build PACKAGEBUILD-24257979 with 8 jobs across 8 processor cores. Kernel reported to sbuild: 5.13.0-1019-generic #21~20.04.1-Ubuntu SMP Thu Mar 24 22:36:01 UTC 2022 riscv64 sbuild (Debian sbuild) 0.79.0 (05 February 2020) on riscv64-qemu-lgw01-005.buildd +==============================================================================+ | lagan 2.0-9 (riscv64) Sun, 07 Aug 2022 17:24:28 +0000 | +==============================================================================+ Package: lagan Version: 2.0-9 Source Version: 2.0-9 Distribution: kinetic-proposed Machine Architecture: riscv64 Host Architecture: riscv64 Build Architecture: riscv64 Build Type: any I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-24257979/chroot-autobuild' with '<>' I: NOTICE: Log filtering will replace 'build/lagan-EyUBxJ/resolver-2ShayK' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- lagan_2.0-9.dsc exists in .; copying to chroot I: NOTICE: Log filtering will replace 'build/lagan-EyUBxJ/lagan-2.0' with '<>' I: NOTICE: Log filtering will replace 'build/lagan-EyUBxJ' with '<>' +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper-compat (= 13), libboost-dev, build-essential, fakeroot Filtered Build-Depends: debhelper-compat (= 13), libboost-dev, build-essential, fakeroot dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/<>/apt_archive/sbuild-build-depends-main-dummy.deb'. Ign:1 copy:/<>/apt_archive ./ InRelease Get:2 copy:/<>/apt_archive ./ Release [957 B] Ign:3 copy:/<>/apt_archive ./ Release.gpg Get:4 copy:/<>/apt_archive ./ Sources [378 B] Get:5 copy:/<>/apt_archive ./ Packages [462 B] Fetched 1797 B in 1s (2519 B/s) Reading package lists... Reading package lists... Install main build dependencies (apt-based resolver) ---------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following package was automatically installed and is no longer required: g++-11 Use 'apt autoremove' to remove it. The following additional packages will be installed: autoconf automake autopoint autotools-dev bsdextrautils debhelper debugedit dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base groff-base intltool-debian libarchive-zip-perl libboost-dev libboost1.74-dev libdebhelper-perl libdw1 libelf1 libfile-stripnondeterminism-perl libicu71 libmagic-mgc libmagic1 libpipeline1 libsigsegv2 libsub-override-perl libtool libuchardet0 libxml2 m4 man-db po-debconf Suggested packages: autoconf-archive gnu-standards autoconf-doc dh-make gettext-doc libasprintf-dev libgettextpo-dev groff libboost-doc libboost1.74-doc libboost-atomic1.74-dev libboost-chrono1.74-dev libboost-container1.74-dev libboost-context1.74-dev libboost-contract1.74-dev libboost-coroutine1.74-dev libboost-date-time1.74-dev libboost-exception1.74-dev libboost-fiber1.74-dev libboost-filesystem1.74-dev libboost-graph1.74-dev libboost-graph-parallel1.74-dev libboost-iostreams1.74-dev libboost-locale1.74-dev libboost-log1.74-dev libboost-math1.74-dev libboost-mpi1.74-dev libboost-mpi-python1.74-dev libboost-numpy1.74-dev libboost-program-options1.74-dev libboost-python1.74-dev libboost-random1.74-dev libboost-regex1.74-dev libboost-serialization1.74-dev libboost-stacktrace1.74-dev libboost-system1.74-dev libboost-test1.74-dev libboost-thread1.74-dev libboost-timer1.74-dev libboost-type-erasure1.74-dev libboost-wave1.74-dev libboost1.74-tools-dev libmpfrc++-dev libntl-dev libboost-nowide1.74-dev libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc apparmor less www-browser libmail-box-perl Recommended packages: curl | wget | lynx libarchive-cpio-perl libltdl-dev libmail-sendmail-perl The following NEW packages will be installed: autoconf automake autopoint autotools-dev bsdextrautils debhelper debugedit dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base groff-base intltool-debian libarchive-zip-perl libboost-dev libboost1.74-dev libdebhelper-perl libdw1 libelf1 libfile-stripnondeterminism-perl libicu71 libmagic-mgc libmagic1 libpipeline1 libsigsegv2 libsub-override-perl libtool libuchardet0 libxml2 m4 man-db po-debconf sbuild-build-depends-main-dummy 0 upgraded, 35 newly installed, 0 to remove and 0 not upgraded. Need to get 27.7 MB of archives. After this operation, 205 MB of additional disk space will be used. Get:1 copy:/<>/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [678 B] Get:2 http://ftpmaster.internal/ubuntu kinetic/main riscv64 libelf1 riscv64 0.187-1 [46.4 kB] Get:3 http://ftpmaster.internal/ubuntu kinetic/main riscv64 libicu71 riscv64 71.1-3 [10.5 MB] Get:4 http://ftpmaster.internal/ubuntu kinetic/main riscv64 libxml2 riscv64 2.9.14+dfsg-1 [597 kB] Get:5 http://ftpmaster.internal/ubuntu kinetic/main riscv64 bsdextrautils riscv64 2.38-4ubuntu1 [81.5 kB] Get:6 http://ftpmaster.internal/ubuntu kinetic/main riscv64 libmagic-mgc riscv64 1:5.41-4 [257 kB] Get:7 http://ftpmaster.internal/ubuntu kinetic/main riscv64 libmagic1 riscv64 1:5.41-4 [88.7 kB] Get:8 http://ftpmaster.internal/ubuntu kinetic/main riscv64 file riscv64 1:5.41-4 [20.6 kB] Get:9 http://ftpmaster.internal/ubuntu kinetic/main riscv64 gettext-base riscv64 0.21-6 [38.5 kB] Get:10 http://ftpmaster.internal/ubuntu kinetic/main riscv64 libuchardet0 riscv64 0.0.7-1build2 [78.9 kB] Get:11 http://ftpmaster.internal/ubuntu kinetic/main riscv64 groff-base riscv64 1.22.4-8build1 [925 kB] Get:12 http://ftpmaster.internal/ubuntu kinetic/main riscv64 libpipeline1 riscv64 1.5.6-1 [26.1 kB] Get:13 http://ftpmaster.internal/ubuntu kinetic/main riscv64 man-db riscv64 2.10.2-1 [1144 kB] Get:14 http://ftpmaster.internal/ubuntu kinetic/main riscv64 libsigsegv2 riscv64 2.13-1ubuntu3 [13.6 kB] Get:15 http://ftpmaster.internal/ubuntu kinetic/main riscv64 m4 riscv64 1.4.18-5ubuntu2 [193 kB] Get:16 http://ftpmaster.internal/ubuntu kinetic/main riscv64 autoconf all 2.71-2 [338 kB] Get:17 http://ftpmaster.internal/ubuntu kinetic/main riscv64 autotools-dev all 20220109.1 [44.9 kB] Get:18 http://ftpmaster.internal/ubuntu kinetic/main riscv64 automake all 1:1.16.5-1.3 [558 kB] Get:19 http://ftpmaster.internal/ubuntu kinetic/main riscv64 autopoint all 0.21-6 [421 kB] Get:20 http://ftpmaster.internal/ubuntu kinetic/main riscv64 libdebhelper-perl all 13.8ubuntu1 [66.8 kB] Get:21 http://ftpmaster.internal/ubuntu kinetic/main riscv64 libtool all 2.4.7-4 [166 kB] Get:22 http://ftpmaster.internal/ubuntu kinetic/main riscv64 dh-autoreconf all 20 [16.1 kB] Get:23 http://ftpmaster.internal/ubuntu kinetic/main riscv64 libarchive-zip-perl all 1.68-1 [90.2 kB] Get:24 http://ftpmaster.internal/ubuntu kinetic/main riscv64 libsub-override-perl all 0.09-3 [9756 B] Get:25 http://ftpmaster.internal/ubuntu kinetic/main riscv64 libfile-stripnondeterminism-perl all 1.13.0-1 [18.1 kB] Get:26 http://ftpmaster.internal/ubuntu kinetic/main riscv64 dh-strip-nondeterminism all 1.13.0-1 [5344 B] Get:27 http://ftpmaster.internal/ubuntu kinetic/main riscv64 libdw1 riscv64 0.187-1 [227 kB] Get:28 http://ftpmaster.internal/ubuntu kinetic/main riscv64 debugedit riscv64 1:5.0-5 [48.8 kB] Get:29 http://ftpmaster.internal/ubuntu kinetic/main riscv64 dwz riscv64 0.14-1build2 [105 kB] Get:30 http://ftpmaster.internal/ubuntu kinetic/main riscv64 gettext riscv64 0.21-6 [808 kB] Get:31 http://ftpmaster.internal/ubuntu kinetic/main riscv64 intltool-debian all 0.35.0+20060710.5 [24.9 kB] Get:32 http://ftpmaster.internal/ubuntu kinetic/main riscv64 po-debconf all 1.0.21+nmu1 [233 kB] Get:33 http://ftpmaster.internal/ubuntu kinetic/main riscv64 debhelper all 13.8ubuntu1 [938 kB] Get:34 http://ftpmaster.internal/ubuntu kinetic/main riscv64 libboost1.74-dev riscv64 1.74.0-16.1ubuntu1 [9589 kB] Get:35 http://ftpmaster.internal/ubuntu kinetic/main riscv64 libboost-dev riscv64 1.74.0.3ubuntu7 [3492 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 27.7 MB in 7s (4097 kB/s) Selecting previously unselected package libelf1:riscv64. 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Setting up libboost1.74-dev:riscv64 (1.74.0-16.1ubuntu1) ... Setting up bsdextrautils (2.38-4ubuntu1) ... Setting up libmagic-mgc (1:5.41-4) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.8ubuntu1) ... Setting up libmagic1:riscv64 (1:5.41-4) ... Setting up gettext-base (0.21-6) ... Setting up file (1:5.41-4) ... Setting up autotools-dev (20220109.1) ... Setting up libsigsegv2:riscv64 (2.13-1ubuntu3) ... Setting up autopoint (0.21-6) ... Setting up libuchardet0:riscv64 (0.0.7-1build2) ... Setting up libsub-override-perl (0.09-3) ... Setting up libboost-dev:riscv64 (1.74.0.3ubuntu7) ... Setting up libelf1:riscv64 (0.187-1) ... Setting up libxml2:riscv64 (2.9.14+dfsg-1) ... Setting up libfile-stripnondeterminism-perl (1.13.0-1) ... Setting up libdw1:riscv64 (0.187-1) ... Setting up gettext (0.21-6) ... Setting up libtool (2.4.7-4) ... Setting up m4 (1.4.18-5ubuntu2) ... Setting up intltool-debian (0.35.0+20060710.5) ... Setting up autoconf (2.71-2) ... Setting up dh-strip-nondeterminism (1.13.0-1) ... Setting up dwz (0.14-1build2) ... Setting up groff-base (1.22.4-8build1) ... Setting up debugedit (1:5.0-5) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up po-debconf (1.0.21+nmu1) ... Setting up man-db (2.10.2-1) ... Not building database; man-db/auto-update is not 'true'. Created symlink /etc/systemd/system/timers.target.wants/man-db.timer → /lib/systemd/system/man-db.timer. Setting up dh-autoreconf (20) ... Setting up debhelper (13.8ubuntu1) ... Setting up sbuild-build-depends-main-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.35-0ubuntu3) ... +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (riscv64 included in any) +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 5.13.0-1019-generic #21~20.04.1-Ubuntu SMP Thu Mar 24 22:36:01 UTC 2022 riscv64 (riscv64) Toolchain package versions: binutils_2.38.90.20220713-2ubuntu1 dpkg-dev_1.21.9ubuntu1 g++-11_11.3.0-5ubuntu1 g++-12_12.1.0-7ubuntu1 gcc-11_11.3.0-5ubuntu1 gcc-12_12.1.0-7ubuntu1 libc6-dev_2.35-0ubuntu3 libstdc++-11-dev_11.3.0-5ubuntu1 libstdc++-12-dev_12.1.0-7ubuntu1 libstdc++6_12.1.0-7ubuntu1 linux-libc-dev_5.19.0-15.15 Package versions: adduser_3.121ubuntu1 advancecomp_2.1-2.1ubuntu2 apt_2.5.2 autoconf_2.71-2 automake_1:1.16.5-1.3 autopoint_0.21-6 autotools-dev_20220109.1 base-files_12.2ubuntu2 base-passwd_3.5.52build1 bash_5.1-6ubuntu1 binutils_2.38.90.20220713-2ubuntu1 binutils-common_2.38.90.20220713-2ubuntu1 binutils-riscv64-linux-gnu_2.38.90.20220713-2ubuntu1 bsdextrautils_2.38-4ubuntu1 bsdutils_1:2.38-4ubuntu1 build-essential_12.9ubuntu3 bzip2_1.0.8-5build1 ca-certificates_20211016 coreutils_8.32-4.1ubuntu1 cpp_4:12.1.0-3ubuntu1 cpp-11_11.3.0-5ubuntu1 cpp-12_12.1.0-7ubuntu1 dash_0.5.11+git20210903+057cd650a4ed-8ubuntu1 debconf_1.5.79ubuntu1 debhelper_13.8ubuntu1 debianutils_5.7-0.3 debugedit_1:5.0-5 dh-autoreconf_20 dh-strip-nondeterminism_1.13.0-1 diffutils_1:3.8-0ubuntu2 dpkg_1.21.9ubuntu1 dpkg-dev_1.21.9ubuntu1 dwz_0.14-1build2 e2fsprogs_1.46.5-2ubuntu2 fakeroot_1.29-1ubuntu1 file_1:5.41-4 findutils_4.8.0-1ubuntu3 g++_4:12.1.0-3ubuntu1 g++-11_11.3.0-5ubuntu1 g++-12_12.1.0-7ubuntu1 gcc_4:12.1.0-3ubuntu1 gcc-11_11.3.0-5ubuntu1 gcc-11-base_11.3.0-5ubuntu1 gcc-12_12.1.0-7ubuntu1 gcc-12-base_12.1.0-7ubuntu1 gettext_0.21-6 gettext-base_0.21-6 gpg_2.2.27-3ubuntu3 gpg-agent_2.2.27-3ubuntu3 gpgconf_2.2.27-3ubuntu3 gpgv_2.2.27-3ubuntu3 grep_3.7-1build1 groff-base_1.22.4-8build1 gzip_1.10-4ubuntu4 hostname_3.23ubuntu2 init_1.64 init-system-helpers_1.64 intltool-debian_0.35.0+20060710.5 libacl1_2.3.1-1 libapparmor1_3.0.4-3ubuntu1 libapt-pkg6.0_2.5.2 libarchive-zip-perl_1.68-1 libargon2-1_0~20171227-0.3 libasan6_11.3.0-5ubuntu1 libasan8_12.1.0-7ubuntu1 libassuan0_2.5.5-4 libatomic1_12.1.0-7ubuntu1 libattr1_1:2.5.1-1build1 libaudit-common_1:3.0.7-1build1 libaudit1_1:3.0.7-1build1 libbinutils_2.38.90.20220713-2ubuntu1 libblkid1_2.38-4ubuntu1 libboost-dev_1.74.0.3ubuntu7 libboost1.74-dev_1.74.0-16.1ubuntu1 libbz2-1.0_1.0.8-5build1 libc-bin_2.35-0ubuntu3 libc-dev-bin_2.35-0ubuntu3 libc6_2.35-0ubuntu3 libc6-dev_2.35-0ubuntu3 libcap-ng0_0.8.3-1 libcap2_1:2.44-1build3 libcc1-0_12.1.0-7ubuntu1 libcom-err2_1.46.5-2ubuntu2 libcrypt-dev_1:4.4.28-2 libcrypt1_1:4.4.28-2 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libtasn1-6_4.18.0-4build1 libtinfo6_6.3+20220423-2 libtirpc-common_1.3.2-2.1 libtirpc-dev_1.3.2-2.1 libtirpc3_1.3.2-2.1 libtool_2.4.7-4 libuchardet0_0.0.7-1build2 libudev1_251.2-2ubuntu2 libunistring2_1.0-1 libuuid1_2.38-4ubuntu1 libxml2_2.9.14+dfsg-1 libxxhash0_0.8.1-1 libzstd1_1.5.2+dfsg-1 linux-libc-dev_5.19.0-15.15 lockfile-progs_0.1.19build1 login_1:4.11.1+dfsg1-2ubuntu1 logsave_1.46.5-2ubuntu2 lsb-base_11.1.0ubuntu4 lto-disabled-list_32 m4_1.4.18-5ubuntu2 make_4.3-4.1build1 man-db_2.10.2-1 mawk_1.3.4.20200120-3.1 mount_2.38-4ubuntu1 ncurses-base_6.3+20220423-2 ncurses-bin_6.3+20220423-2 openssl_3.0.4-1ubuntu1 optipng_0.7.7-2build1 passwd_1:4.11.1+dfsg1-2ubuntu1 patch_2.7.6-7build2 perl_5.34.0-5ubuntu1 perl-base_5.34.0-5ubuntu1 perl-modules-5.34_5.34.0-5ubuntu1 pinentry-curses_1.2.0-2ubuntu1 pkgbinarymangler_149 po-debconf_1.0.21+nmu1 policyrcd-script-zg2_0.1-3.1 procps_2:3.3.17-6ubuntu2 readline-common_8.1.2-1.2 rpcsvc-proto_1.4.2-0ubuntu6 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.8-1ubuntu2 sensible-utils_0.0.17 sgml-base_1.30 systemd_251.2-2ubuntu2 systemd-sysv_251.2-2ubuntu2 sysvinit-utils_3.01-1ubuntu1 tar_1.34+dfsg-1build3 tzdata_2022a-0ubuntu1 ubuntu-keyring_2021.03.26 usrmerge_25ubuntu2 util-linux_2.38-4ubuntu1 util-linux-extra_2.38-4ubuntu1 xz-utils_5.2.5-2.1 zlib1g_1:1.2.11.dfsg-2ubuntu10 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: lagan Binary: lagan Architecture: any Version: 2.0-9 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille , Steffen Moeller Homepage: http://lagan.stanford.edu/lagan_web/index.shtml Standards-Version: 4.6.0 Vcs-Browser: https://salsa.debian.org/med-team/lagan Vcs-Git: https://salsa.debian.org/med-team/lagan.git Testsuite: autopkgtest Build-Depends: debhelper-compat (= 13), libboost-dev Package-List: lagan deb science optional arch=any Checksums-Sha1: 2417bec99ff59541287ad56fdfe3abb609323949 192945 lagan_2.0.orig.tar.gz aeceaa32ae0dd28bc38de25e11c6d94cc05a1808 9892 lagan_2.0-9.debian.tar.xz Checksums-Sha256: 9e3c27d0fd7a3f3448035ea51996a50e314b139942d9313858c3e4678aae1281 192945 lagan_2.0.orig.tar.gz d43a2b919a33f636a4f3a399c42d60a0b93bfec578e05331836a87a39eb30910 9892 lagan_2.0-9.debian.tar.xz Files: 7027ba63a2a5115871b85e205aa36bb7 192945 lagan_2.0.orig.tar.gz 44eca9fb7f6b27c1c2f48d61fc481594 9892 lagan_2.0-9.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJGBAEBCgAwFiEEPpmlJvXcwMu/HO6mALrnSzQzafEFAmLveTwSHG5pbGVzaEBk ZWJpYW4ub3JnAAoJEAC650s0M2nxoV4P/i4si9cGhO3UHrtjqUdRFZOqIPKvleO4 OqWCaKb4wgV6fegJWIUWBu0S0vap6zJMOioH4gRPwCysjjnriGe+NXoeA2Jws7qd K2+mSDeVv49dfjUOAlMu8lHhIxE3QxlbTyNVaQXDA0uuvvm9SruZzKcF3LNlfAdp i7SuMQICYnX2WicG4dKBpz1wbZYkiR64z02sqtlNmQgTocdCy/29gbrSA1iPnnqt 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do_not_define_conflicting_getline.patch dpkg-source: info: applying gcc-4.8.patch dpkg-source: info: applying ambiuousEnd.patch dpkg-source: info: applying addTest.patch dpkg-source: info: applying adjustPerlPaths.patch dpkg-source: info: applying hardening.patch dpkg-source: info: applying cross.patch dpkg-source: info: applying gcc9.patch dpkg-source: info: applying gcc10.patch dpkg-source: info: applying gcc-lto.patch Check disk space ---------------- Sufficient free space for build User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf DEB_BUILD_OPTIONS=parallel=8 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-24257979 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-24257979 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-24257979 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 lagan dpkg-buildpackage: info: source version 2.0-9 dpkg-buildpackage: info: source distribution unstable dpkg-source --before-build . dpkg-buildpackage: info: host architecture riscv64 debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/<>' dh_auto_clean make -j8 clean make[2]: Entering directory '/<>' rm -f chaos anchors order glocal utils/bin2bl mlagan utils/cstat utils/bin2mf utils/rc *~ utils/contigorder utils/getbounds utils/cextract utils/seqmerge utils/getlength utils/getoverlap utils/*~ utils/scorealign utils/scorecontigs mlagan.purify utils/getcontigpos utils/fa2xfa utils/Glue utils/dotplot utils/overlay make -C src clean make[3]: Entering directory '/<>/src' rm -f *.o *~ utils/*~ mlagan.purify core (cd glocal; make clean) make[4]: Entering directory '/<>/src/glocal' rm -f *.o ./*~ *~ core make[4]: Leaving directory '/<>/src/glocal' make[3]: Leaving directory '/<>/src' make[2]: Leaving directory '/<>' rm -f prolagan make[1]: Leaving directory '/<>' dh_clean debian/rules binary-arch dh binary-arch dh_update_autotools_config -a dh_autoreconf -a dh_auto_configure -a debian/rules override_dh_auto_build make[1]: Entering directory '/<>' dh_auto_build --sourcedirectory=src cd src && make -j8 "INSTALL=install --strip-program=true" make[2]: Entering directory '/<>/src' gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -o ../anchors anchors.c skiplist.c -Wl,-Bsymbolic-functions -Wl,-z,relro gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -o ../chaos fchaos.c thrtrie.c skiplist.c global.c translate.c filebuffer.c -lm -DCHAOS__FLAG -Wl,-Bsymbolic-functions -Wl,-z,relro gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -o ../order order.c diagmatrix.c filebuffer.c -Wl,-Bsymbolic-functions -Wl,-z,relro gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -o ../mlagan mlagan.c multial.c diagmatrix.c skiplist.c filebuffer.c -lm -DMULTIAL__FLAG -Wl,-Bsymbolic-functions -Wl,-z,relro gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -o ../prolagan prolagan.c multial.c diagmatrix.c skiplist.c filebuffer.c -lm -DMULTIAL__FLAG -Wl,-Bsymbolic-functions -Wl,-z,relro gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -o ../utils/bin2mf utils/bin2mf.c -Wl,-Bsymbolic-functions -Wl,-z,relro gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -o ../utils/bin2bl utils/bin2bl.c -Wl,-Bsymbolic-functions -Wl,-z,relro gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -o ../utils/cextract utils/cextract.c -Wl,-Bsymbolic-functions -Wl,-z,relro utils/cextract.c: In function ‘getLength’: utils/cextract.c:16:3: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 16 | fgets (buffer, 1024, file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ utils/cextract.c: In function ‘readfile’: utils/cextract.c:41:5: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 41 | fgets (buffer, 1024, file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ anchors.c: In function ‘anchors_getline’: anchors.c:232:3: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 232 | fgets(temp, 1024, infile); | ^~~~~~~~~~~~~~~~~~~~~~~~~ order.c: In function ‘doAlign’: order.c:409:5: warning: implicit declaration of function ‘printMFAAlign’; did you mean ‘printBinAlign’? [-Wimplicit-function-declaration] 409 | printMFAAlign(seq1->lets, seq2->lets, a, seq1->name, seq2->name); | ^~~~~~~~~~~~~ | printBinAlign fchaos.c: In function ‘readfile’: fchaos.c:357:25: warning: too many arguments for format [-Wformat-extra-args] 357 | fprintf(stderr, "WARNING %c converted to N\n", currchar, alpha); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ order.c:411:5: warning: implicit declaration of function ‘printXMFAAlign’; did you mean ‘printTextAlign’? [-Wimplicit-function-declaration] 411 | printXMFAAlign(seq1->lets, seq2->lets, a, seq1->name, seq2->name); | ^~~~~~~~~~~~~~ | printTextAlign order.c: In function ‘readfile’: order.c:61:3: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 61 | fgets(temp, 255, input); | ^~~~~~~~~~~~~~~~~~~~~~~ order.c: In function ‘readSubstMatrix’: order.c:145:7: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 145 | fscanf (file, "%d", &(substmatrix[(unsigned char) symbs[i]][(unsigned char) symbs[j]])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ order.c:149:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 149 | fscanf (file, "%d", &gapstart); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ order.c:150:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 150 | fscanf (file, "%d", &gapcont); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fchaos.c:344:3: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 344 | fgets(temp, 255, input); | ^~~~~~~~~~~~~~~~~~~~~~~ fchaos.c: In function ‘readSubstMatrix’: prolagan.c: In function ‘readfile’: fchaos.c:622:7: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 622 | fscanf (file, "%d", &(substmatrix[(unsigned char) symbs[i]][(unsigned char) symbs[j]])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ prolagan.c:93:25: warning: too many arguments for format [-Wformat-extra-args] 93 | fprintf(stderr, "Warning: %c converted to 'N'\n", currchar, alpha); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fchaos.c:627:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 627 | fscanf (file, "%d", &gappenstart); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fchaos.c:628:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 628 | fscanf (file, "%d", &gappenext); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mlagan.c: In function ‘readfile’: mlagan.c:93:25: warning: too many arguments for format [-Wformat-extra-args] 93 | fprintf(stderr, "Warning: %c converted to 'N'\n", currchar, alpha); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ prolagan.c: In function ‘main’: prolagan.c:1091:5: warning: implicit declaration of function ‘printXMFAAlign’; did you mean ‘printFASTAAlign’? [-Wimplicit-function-declaration] 1091 | printXMFAAlign(outfile, final); | ^~~~~~~~~~~~~~ | printFASTAAlign prolagan.c: In function ‘readfile’: prolagan.c:79:3: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 79 | fgets(temp, 255, input); | ^~~~~~~~~~~~~~~~~~~~~~~ mlagan.c: In function ‘main’: mlagan.c:1071:5: warning: implicit declaration of function ‘printXMFAAlign’; did you mean ‘printFASTAAlign’? [-Wimplicit-function-declaration] 1071 | printXMFAAlign(outfile, final); | ^~~~~~~~~~~~~~ | printFASTAAlign mlagan.c: In function ‘readfile’: mlagan.c:79:3: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 79 | fgets(temp, 255, input); | ^~~~~~~~~~~~~~~~~~~~~~~ gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -o ../utils/cstat utils/cstat.c -Wl,-Bsymbolic-functions -Wl,-z,relro gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -o ../utils/contigorder utils/contigorder.c -Wl,-Bsymbolic-functions -Wl,-z,relro utils/cstat.c: In function ‘cntlets’: utils/cstat.c:51:10: warning: implicit declaration of function ‘isspace’ [-Wimplicit-function-declaration] 51 | if (!isspace(currchar)) { | ^~~~~~~ utils/cstat.c:6:1: note: include ‘’ or provide a declaration of ‘isspace’ 5 | #include +++ |+#include 6 | utils/cstat.c:52:18: warning: implicit declaration of function ‘toupper’ [-Wimplicit-function-declaration] 52 | currchar = toupper(currchar); | ^~~~~~~ utils/cstat.c:52:18: note: include ‘’ or provide a declaration of ‘toupper’ utils/cstat.c:44:3: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 44 | fgets(temp, 255, input); | ^~~~~~~~~~~~~~~~~~~~~~~ utils/cstat.c: In function ‘readseq’: utils/cstat.c:67:3: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 67 | fgets(temp, 255, input); | ^~~~~~~~~~~~~~~~~~~~~~~ skiplist.c: In function ‘printSLE’: skiplist.c:12:19: warning: format ‘%x’ expects argument of type ‘unsigned int’, but argument 3 has type ‘void *’ [-Wformat=] 12 | printf(" %d %x\n", tbp->index, tbp->myelem); | ~^ ~~~~~~~~~~~ | | | | unsigned int void * | %p utils/contigorder.c: In function ‘getFileInfo’: utils/contigorder.c:15:57: warning: format ‘%s’ expects a matching ‘char *’ argument [-Wformat=] 15 | fprintf (stderr, "contigorder: Error opening file: %s\n"); | ~^ | | | char * gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -o ../utils/getbounds utils/getbounds.c -Wl,-Bsymbolic-functions -Wl,-z,relro utils/contigorder.c:26:25: warning: unknown conversion type character ‘&’ in format [-Wformat=] 26 | fscanf (file, "%&d", &dummy); | ^ utils/contigorder.c:26:23: warning: too many arguments for format [-Wformat-extra-args] 26 | fscanf (file, "%&d", &dummy); | ^~~~~ utils/contigorder.c: In function ‘getScores’: utils/contigorder.c:52:57: warning: format ‘%s’ expects a matching ‘char *’ argument [-Wformat=] 52 | fprintf (stderr, "contigorder: Error opening file: %s\n"); | ~^ | | | char * utils/contigorder.c: In function ‘getFileInfo’: utils/contigorder.c:19:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 19 | fscanf (file, "numContigs = %d\n", numContigs); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ utils/contigorder.c:20:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 20 | fscanf (file, "seqLen = %d\n", seqLen); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ utils/contigorder.c:26:9: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 26 | fscanf (file, "%&d", &dummy); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ utils/contigorder.c: In function ‘getScores’: utils/contigorder.c:56:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 56 | fscanf (file, "numContigs = %*d\n"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ utils/contigorder.c:57:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 57 | fscanf (file, "seqLen = %*d\n"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ utils/contigorder.c:63:9: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 63 | fscanf (file, "%d", &((*score)[i][j])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ utils/getbounds.c: In function ‘getLength’: utils/getbounds.c:18:3: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 18 | fgets (buffer, 1024, file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -o ../utils/getlength utils/getlength.c -Wl,-Bsymbolic-functions -Wl,-z,relro utils/getlength.c: In function ‘main’: utils/getlength.c:20:3: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 20 | fgets (buffer, BUF_SIZE, file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -o ../utils/getoverlap utils/getoverlap.c -Wl,-Bsymbolic-functions -Wl,-z,relro gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -o ../utils/rc utils/rc.c -Wl,-Bsymbolic-functions -Wl,-z,relro gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -o ../utils/seqmerge utils/seqmerge.c -Wl,-Bsymbolic-functions -Wl,-z,relro gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -o ../utils/scorealign utils/scorealign.c -lm -Wl,-Bsymbolic-functions -Wl,-z,relro utils/rc.c: In function ‘main’: utils/rc.c:39:3: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 39 | fgets(temp, 255, stdin); | ^~~~~~~~~~~~~~~~~~~~~~~ utils/seqmerge.c: In function ‘main’: utils/seqmerge.c:19:5: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 19 | fgets (buffer, 1024, file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ utils/scorealign.c: In function ‘getSequence’: utils/scorealign.c:266:3: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 266 | fgets (line, 1024, file); | ^~~~~~~~~~~~~~~~~~~~~~~~ utils/scorealign.c: In function ‘readScoreMatrix’: utils/scorealign.c:415:3: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 415 | fgets (line, 1024, file); | ^~~~~~~~~~~~~~~~~~~~~~~~ utils/scorealign.c:423:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 423 | fscanf (file, "%1s", &(line[0])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ utils/scorealign.c:425:7: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 425 | fscanf (file, "%d", &k); | ^~~~~~~~~~~~~~~~~~~~~~~ utils/scorealign.c:430:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 430 | fscanf (file, "%d%d", &gapopen, &gapcont); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -o ../utils/scorecontigs utils/scorecontigs.c -lm -Wl,-Bsymbolic-functions -Wl,-z,relro gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -o ../utils/getcontigpos utils/getcontigpos.c -Wl,-Bsymbolic-functions -Wl,-z,relro utils/scorecontigs.c: In function ‘cntlets’: utils/scorecontigs.c:63:10: warning: implicit declaration of function ‘isspace’ [-Wimplicit-function-declaration] 63 | if (!isspace(currchar)) { | ^~~~~~~ utils/scorecontigs.c:6:1: note: include ‘’ or provide a declaration of ‘isspace’ 5 | #include +++ |+#include 6 | utils/scorecontigs.c:64:18: warning: implicit declaration of function ‘toupper’ [-Wimplicit-function-declaration] 64 | currchar = toupper(currchar); | ^~~~~~~ utils/scorecontigs.c:64:18: note: include ‘’ or provide a declaration of ‘toupper’ utils/scorecontigs.c:65:27: warning: implicit declaration of function ‘isalpha’ [-Wimplicit-function-declaration] 65 | if (!lettersonly || isalpha (currchar)){ | ^~~~~~~ utils/scorecontigs.c:65:27: note: include ‘’ or provide a declaration of ‘isalpha’ utils/scorecontigs.c: In function ‘main’: utils/scorecontigs.c:384:38: warning: format ‘%s’ expects argument of type ‘char *’, but argument 6 has type ‘char (*)[1024]’ [-Wformat=] 384 | if (fscanf (filelist, "%d %d %d %s\n", &(num[numseqs]), &(offs1[numseqs]), &(offs2[numseqs]), &(contignames[numseqs])) == 4){ | ~^ ~~~~~~~~~~~~~~~~~~~~~~~ | | | | char * char (*)[1024] utils/scorecontigs.c: In function ‘cntlets’: utils/scorecontigs.c:55:3: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 55 | fgets(temp, 1024, input); | ^~~~~~~~~~~~~~~~~~~~~~~~ utils/scorecontigs.c: In function ‘readseq’: utils/scorecontigs.c:81:3: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 81 | fgets (temp, 1024, input); | ^~~~~~~~~~~~~~~~~~~~~~~~~ utils/getcontigpos.c: In function ‘getLength’: utils/getcontigpos.c:16:3: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 16 | fgets (buffer, 1024, file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ utils/getcontigpos.c: In function ‘readfile’: utils/getcontigpos.c:41:5: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 41 | fgets (buffer, 1024, file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -o ../utils/fa2xfa utils/fa2xfa.c -Wl,-Bsymbolic-functions -Wl,-z,relro utils/fa2xfa.c: In function ‘getLength’: utils/fa2xfa.c:30:3: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 30 | fgets (buffer, 1024, file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ utils/fa2xfa.c: In function ‘readfile’: utils/fa2xfa.c:55:5: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 55 | fgets (buffer, 1024, file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -o ../utils/Glue utils/Glue.cpp -Wl,-Bsymbolic-functions -Wl,-z,relro multial.c:603:9: warning: ‘gapcache’ is static but used in inline function ‘openGap’ which is not static 603 | sav = gapcache[(v(ali->numseq - (alopen + ali->cnts[CNTS_CB][w]) + other->cnts[CNTS_GS][ow])) | | ^~~~~~~~ multial.c:586:10: warning: ‘gapcache’ is static but used in inline function ‘contGap’ which is not static 586 | return gapcache[(v(other->cnts[CNTS_GS][ow])) | | ^~~~~~~~ multial.c:581:10: warning: ‘gapcache’ is static but used in inline function ‘endGap2’ which is not static 581 | return gapcache[(v((a->numseq - a->cnts[CNTS_GS][ai] - a->cnts[CNTS_GC][ai]) + b->cnts[CNTS_GE][bi])<<12) | | ^~~~~~~~ multial.c:576:10: warning: ‘gapcache’ is static but used in inline function ‘endGap1’ which is not static 576 | return gapcache[(v((b->numseq - b->cnts[CNTS_GS][bi] - b->cnts[CNTS_GC][bi]) + a->cnts[CNTS_GE][ai]) << 12) | | ^~~~~~~~ multial.c:570:10: warning: ‘gapcache’ is static but used in inline function ‘endGap0’ which is not static 570 | return gapcache[(v(a->cnts[CNTS_GE][ai]+b->cnts[CNTS_GE][bi])<<12) | | ^~~~~~~~ multial.c:563:10: warning: ‘matchcache’ is static but used in inline function ‘scoreOpp’ which is not static 563 | return matchcache[v(other->cnts[0][ow]) | | ^~~~~~~~~~ multial.c:556:5: warning: ‘gapcache’ is static but used in inline function ‘matchscore’ which is not static 556 | gapcache[v(a->cnts[CNTS_GS][ai] + b->cnts[CNTS_GS][bi]) | | ^~~~~~~~ multial.c:552:5: warning: ‘matchcache’ is static but used in inline function ‘matchscore’ which is not static 552 | matchcache[v(a->cnts[0][ai] + b->cnts[0][bi]) | | ^~~~~~~~~~ multial.c: In function ‘readSubstMatrix’: multial.c:478:7: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 478 | fscanf (file, "%d", &k); | ^~~~~~~~~~~~~~~~~~~~~~~ multial.c:486:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 486 | fscanf (file, "%d", &gapstart); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ multial.c:487:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 487 | fscanf (file, "%d", &gapcont); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ multial.c:603:9: warning: ‘gapcache’ is static but used in inline function ‘openGap’ which is not static 603 | sav = gapcache[(v(ali->numseq - (alopen + ali->cnts[CNTS_CB][w]) + other->cnts[CNTS_GS][ow])) | | ^~~~~~~~ multial.c:586:10: warning: ‘gapcache’ is static but used in inline function ‘contGap’ which is not static 586 | return gapcache[(v(other->cnts[CNTS_GS][ow])) | | ^~~~~~~~ multial.c:581:10: warning: ‘gapcache’ is static but used in inline function ‘endGap2’ which is not static 581 | return gapcache[(v((a->numseq - a->cnts[CNTS_GS][ai] - a->cnts[CNTS_GC][ai]) + b->cnts[CNTS_GE][bi])<<12) | | ^~~~~~~~ multial.c:576:10: warning: ‘gapcache’ is static but used in inline function ‘endGap1’ which is not static 576 | return gapcache[(v((b->numseq - b->cnts[CNTS_GS][bi] - b->cnts[CNTS_GC][bi]) + a->cnts[CNTS_GE][ai]) << 12) | | ^~~~~~~~ multial.c:570:10: warning: ‘gapcache’ is static but used in inline function ‘endGap0’ which is not static 570 | return gapcache[(v(a->cnts[CNTS_GE][ai]+b->cnts[CNTS_GE][bi])<<12) | | ^~~~~~~~ multial.c:563:10: warning: ‘matchcache’ is static but used in inline function ‘scoreOpp’ which is not static 563 | return matchcache[v(other->cnts[0][ow]) | | ^~~~~~~~~~ multial.c:556:5: warning: ‘gapcache’ is static but used in inline function ‘matchscore’ which is not static 556 | gapcache[v(a->cnts[CNTS_GS][ai] + b->cnts[CNTS_GS][bi]) | | ^~~~~~~~ multial.c:552:5: warning: ‘matchcache’ is static but used in inline function ‘matchscore’ which is not static 552 | matchcache[v(a->cnts[0][ai] + b->cnts[0][bi]) | | ^~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -o ../utils/dotplot utils/dotplot.cpp -Wl,-Bsymbolic-functions -Wl,-z,relro multial.c: In function ‘readSubstMatrix’: multial.c:478:7: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 478 | fscanf (file, "%d", &k); | ^~~~~~~~~~~~~~~~~~~~~~~ multial.c:486:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 486 | fscanf (file, "%d", &gapstart); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ multial.c:487:3: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 487 | fscanf (file, "%d", &gapcont); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ utils/dotplot.cpp: In function ‘int main(int, char**)’: utils/dotplot.cpp:37:11: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37 | fgets (buffer, 105, file); | ~~~~~~^~~~~~~~~~~~~~~~~~~ utils/dotplot.cpp:74:11: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 74 | fgets (buffer, 105, file); | ~~~~~~^~~~~~~~~~~~~~~~~~~ utils/dotplot.cpp:97:11: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 97 | fgets (buffer, 105, file); | ~~~~~~^~~~~~~~~~~~~~~~~~~ gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -o ../utils/overlay utils/overlay.c -Wl,-Bsymbolic-functions -Wl,-z,relro utils/overlay.c: In function ‘read_align’: utils/overlay.c:119:10: warning: implicit declaration of function ‘isspace’ [-Wimplicit-function-declaration] 119 | if (!isspace(currchar)) { | ^~~~~~~ utils/overlay.c:5:1: note: include ‘’ or provide a declaration of ‘isspace’ 4 | #include +++ |+#include 5 | utils/overlay.c:120:19: warning: implicit declaration of function ‘toupper’ [-Wimplicit-function-declaration] 120 | checkchar = toupper(currchar); | ^~~~~~~ utils/overlay.c:120:19: note: include ‘’ or provide a declaration of ‘toupper’ utils/overlay.c:109:3: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 109 | fgets(temp, 255, input); | ^~~~~~~~~~~~~~~~~~~~~~~ skiplist.c: In function ‘printSLE’: skiplist.c:12:19: warning: format ‘%x’ expects argument of type ‘unsigned int’, but argument 3 has type ‘void *’ [-Wformat=] 12 | printf(" %d %x\n", tbp->index, tbp->myelem); | ~^ ~~~~~~~~~~~ | | | | unsigned int void * | %p utils/Glue.cpp: In function ‘void calculateScoreMatrix(int)’: utils/Glue.cpp:64:17: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 64 | char *alpha = "ATCG"; | ^~~~~~ utils/Glue.cpp:11:32: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] 11 | #define NUCLEOTIDE_MATRIX_FILE "nucmatrix.txt" | ^~~~~~~~~~~~~~~ utils/Glue.cpp:72:22: note: in expansion of macro ‘NUCLEOTIDE_MATRIX_FILE’ 72 | readScoreMatrix (NUCLEOTIDE_MATRIX_FILE); | ^~~~~~~~~~~~~~~~~~~~~~ utils/Glue.cpp: In function ‘void readScoreMatrix(char*)’: utils/Glue.cpp:44:9: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 44 | fgets (line, 1024, file); | ~~~~~~^~~~~~~~~~~~~~~~~~ utils/Glue.cpp:52:12: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 52 | fscanf (file, "%1s", &(line[0])); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ utils/Glue.cpp:54:14: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 54 | fscanf (file, "%d", &k); | ~~~~~~~^~~~~~~~~~~~~~~~ utils/Glue.cpp:59:10: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 59 | fscanf (file, "%d%d", &gapopen, &gapcont); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ skiplist.c: In function ‘printSLE’: skiplist.c:12:19: warning: format ‘%x’ expects argument of type ‘unsigned int’, but argument 3 has type ‘void *’ [-Wformat=] 12 | printf(" %d %x\n", tbp->index, tbp->myelem); | ~^ ~~~~~~~~~~~ | | | | unsigned int void * | %p skiplist.c: In function ‘printSLE’: skiplist.c:12:19: warning: format ‘%x’ expects argument of type ‘unsigned int’, but argument 3 has type ‘void *’ [-Wformat=] 12 | printf(" %d %x\n", tbp->index, tbp->myelem); | ~^ ~~~~~~~~~~~ | | | | unsigned int void * | %p (cd glocal; make LDFLAGS="-Wl,-Bsymbolic-functions -Wl,-z,relro") make[3]: Entering directory '/<>/src/glocal' g++ -Wno-deprecated -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -O3 -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I./ -c glocal.cpp -Wl,-Bsymbolic-functions -Wl,-z,relro g++ -Wno-deprecated -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -O3 -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I./ -c io.cpp -Wl,-Bsymbolic-functions -Wl,-z,relro g++ -Wno-deprecated -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -O3 -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I./ -c rightinfluence.cpp -Wl,-Bsymbolic-functions -Wl,-z,relro g++ -Wno-deprecated -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -O3 -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I./ -c leftinfluence.cpp -Wl,-Bsymbolic-functions -Wl,-z,relro g++ -Wno-deprecated -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fsigned-char -O3 -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I./ -c score.cpp -Wl,-Bsymbolic-functions -Wl,-z,relro io.cpp: In function ‘long long int getline(FILE*, hll*)’: io.cpp:60:14: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 60 | fgets(temp, 1024, infile); | ~~~~~^~~~~~~~~~~~~~~~~~~~ g++ glocal.o io.o rightinfluence.o leftinfluence.o score.o -o ../../glocal -lm -Wl,-Bsymbolic-functions -Wl,-z,relro make[3]: Leaving directory '/<>/src/glocal' make[2]: Leaving directory '/<>/src' make[1]: Leaving directory '/<>' dh: command-omitted: The call to "dh_auto_test -a" was omitted due to "DEB_BUILD_OPTIONS=nocheck" create-stamp debian/debhelper-build-stamp dh_prep -a dh_auto_install --destdir=debian/lagan/ -a dh_install -a dh_installdocs -a dh_installchangelogs -a dh_installexamples -a dh_installman -a dh_lintian -a dh_perl -a dh_link -a dh_strip_nondeterminism -a dh_compress -a debian/rules override_dh_fixperms make[1]: Entering directory '/<>' dh_fixperms find debian -name flipchaos.pl -exec chmod +x \{\} \; make[1]: Leaving directory '/<>' dh_missing -a dh_dwz -a dh_strip -a debugedit: debian/lagan/usr/bin/anchors: Unknown DWARF DW_FORM_0x1f21 063d5f62500aaf1fc9a8821f03f3b5d7fd1aec10 debugedit: debian/lagan/usr/bin/order: Unknown DWARF DW_FORM_0x1f21 404513c6783d3d9d5d2c1fef5d7233f1ee5f5f8d debugedit: debian/lagan/usr/bin/mlagan: Unknown DWARF DW_FORM_0x1f21 89bb58f384a60151870cc8724e70ac028e22c07a debugedit: debian/lagan/usr/bin/prolagan: Unknown DWARF DW_FORM_0x1f21 821bc2787c0777fb121434141e9f124d4f2ab188 debugedit: debian/lagan/usr/bin/glocal: Unknown DWARF DW_FORM_0x1f20 274f29c270df55919df506b3d0b0e2dbab2df221 debugedit: debian/lagan/usr/lib/lagan/bin/chaos: Unknown DWARF DW_FORM_0x1f20 e3d9682bf626c86999763106ed32a1171e53dbc6 debugedit: debian/lagan/usr/lib/lagan/utils/cstat: Unknown DWARF DW_FORM_0x1f20 b049b891a9faad13b2b273d8d42eb9edc7afc1f1 debugedit: debian/lagan/usr/lib/lagan/utils/getbounds: Unknown DWARF DW_FORM_0x1f21 4f2f1c642ee1c04d2e55be96c8b024ba5143e9c2 debugedit: debian/lagan/usr/lib/lagan/utils/cextract: Unknown DWARF DW_FORM_0x1f20 286cfc93efadd8b2bff67f7212d7945eb1398c3c debugedit: debian/lagan/usr/lib/lagan/utils/scorealign: Unknown DWARF DW_FORM_0x1f21 669a3377850b4663de13f2aefd136d8ec9b0696f debugedit: debian/lagan/usr/lib/lagan/utils/rc: Unknown DWARF DW_FORM_0x1f21 3e203c34fab19ec7ae1cab90bbc8a276edad4828 debugedit: debian/lagan/usr/lib/lagan/utils/dotplot: Unknown DWARF DW_FORM_0x1f20 7e7aeaebbd78649af6a0d82d3fabb05a549f5251 debugedit: debian/lagan/usr/lib/lagan/utils/overlay: Unknown DWARF DW_FORM_0x1f20 2a7c526cec8214c958aa5127500827d470668ce1 debugedit: debian/lagan/usr/lib/lagan/utils/bin2mf: Unknown DWARF DW_FORM_0x1f21 aaf53068fb5a139aef513e3a56a7393b953dac98 debugedit: debian/lagan/usr/lib/lagan/utils/fa2xfa: Unknown DWARF DW_FORM_0x1f21 1f3a68a73fc205289a13568776df389cbf09f2df debugedit: debian/lagan/usr/lib/lagan/utils/getlength: Unknown DWARF DW_FORM_0x1f21 9dc220f3c2d43804386c932e17aa976eb8b4bf0a debugedit: debian/lagan/usr/lib/lagan/utils/contigorder: Unknown DWARF DW_FORM_0x1f21 7679b3a4b52c921a945c0e0555e2a6f20a17915f debugedit: debian/lagan/usr/lib/lagan/utils/Glue: Unknown DWARF DW_FORM_0x1f21 a0055070efbe3377867faa38faca6a2c4586b323 debugedit: debian/lagan/usr/lib/lagan/utils/getoverlap: Unknown DWARF DW_FORM_0x1f21 c301739790dd8043bdaf33cb90a90ee2f58177d0 debugedit: debian/lagan/usr/lib/lagan/utils/seqmerge: Unknown DWARF DW_FORM_0x1f21 17f3bce4895327093100ecd8e57a0a13cd623f24 debugedit: debian/lagan/usr/lib/lagan/utils/bin2bl: Unknown DWARF DW_FORM_0x1f20 efdd6cc08548746a02d95dbfcaf34217ee9d0c52 debugedit: debian/lagan/usr/lib/lagan/utils/getcontigpos: Unknown DWARF DW_FORM_0x1f21 b3cf3cbec9c348d3286b9d88b5ecf9f1187b3acb debugedit: debian/lagan/usr/lib/lagan/utils/scorecontigs: Unknown DWARF DW_FORM_0x1f21 6d776050b15fb511df779e6110656f4e66702499 dh_makeshlibs -a dh_shlibdeps -a dh_installdeb -a dh_gencontrol -a dpkg-gencontrol: warning: package lagan: substitution variable ${perl:Depends} unused, but is defined dpkg-gencontrol: warning: package lagan: substitution variable ${perl:Depends} unused, but is defined dh_md5sums -a dh_builddeb -a INFO: pkgstriptranslations version 149 INFO: pkgstriptranslations version 149 pkgstriptranslations: processing lagan (in debian/lagan); do_strip: , oemstrip: pkgstriptranslations: processing lagan-dbgsym (in debian/.debhelper/lagan/dbgsym-root); do_strip: , oemstrip: pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/lagan/DEBIAN/control, package lagan, directory debian/lagan pkgstripfiles: Running PNG optimization (using 8 cpus) for package lagan ... pkgstripfiles: No PNG files. pkgstripfiles: processing control file: debian/.debhelper/lagan/dbgsym-root/DEBIAN/control, package lagan-dbgsym, directory debian/.debhelper/lagan/dbgsym-root dpkg-deb: building package 'lagan-dbgsym' in 'debian/.debhelper/scratch-space/build-lagan/lagan-dbgsym_2.0-9_riscv64.deb'. dpkg-deb: building package 'lagan' in '../lagan_2.0-9_riscv64.deb'. Renaming lagan-dbgsym_2.0-9_riscv64.deb to lagan-dbgsym_2.0-9_riscv64.ddeb dpkg-genbuildinfo --build=any -O../lagan_2.0-9_riscv64.buildinfo dpkg-genchanges --build=any -mLaunchpad Build Daemon -O../lagan_2.0-9_riscv64.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 2022-08-07T17:34:32Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ lagan_2.0-9_riscv64.changes: ---------------------------- Format: 1.8 Date: Sun, 07 Aug 2022 13:59:54 +0530 Source: lagan Binary: lagan Built-For-Profiles: noudeb Architecture: riscv64 Version: 2.0-9 Distribution: kinetic-proposed Urgency: medium Maintainer: Launchpad Build Daemon Changed-By: Nilesh Patra Description: lagan - highly parametrizable pairwise global genome sequence aligner Closes: 1015467 Changes: lagan (2.0-9) unstable; urgency=medium . * Team upload. * Propagate hardening flags in src/glocal * Add patch to fix FTBFS with lto (Closes: #1015467) * d/p/hardening.patch: quote LDFLAGS so as to pass all relevant flags in makefile w/o confusing make Checksums-Sha1: 2fa69374169d469fe5efabec6975e90b2516d087 744348 lagan-dbgsym_2.0-9_riscv64.ddeb a64fd0bd21c5df0d3e9ef3dfbf55af25fbf22723 5768 lagan_2.0-9_riscv64.buildinfo c6a60fd7c2f884c59e9d83b5cbfe1765abb43d26 183120 lagan_2.0-9_riscv64.deb Checksums-Sha256: 9d090b2c2d25da9f77459b089617e428a115b00485c8eb3c7531cca100460858 744348 lagan-dbgsym_2.0-9_riscv64.ddeb a79746bc4bc0cba4f7394bf2c8b4cae0ced39923a977127ec4af6dbeb0eafb36 5768 lagan_2.0-9_riscv64.buildinfo 308339720738625a8e6caa2ef06ee391a3ec3b26c2ad4ea94af11459d65150d7 183120 lagan_2.0-9_riscv64.deb Files: 6cd2540a2005f65a17e948b562ee148f 744348 debug optional lagan-dbgsym_2.0-9_riscv64.ddeb cf0a11f449a38782d2f04f9bec1a10d3 5768 science optional lagan_2.0-9_riscv64.buildinfo 01a3e15be65b3df313d5db91e19e23be 183120 science optional lagan_2.0-9_riscv64.deb /<>/lagan_2.0-9_riscv64.changes.new could not be renamed to /<>/lagan_2.0-9_riscv64.changes: Illegal seek Distribution field may be wrong!!! +------------------------------------------------------------------------------+ | Buildinfo | +------------------------------------------------------------------------------+ Format: 1.0 Source: lagan Binary: lagan lagan-dbgsym Architecture: riscv64 Version: 2.0-9 Checksums-Md5: 6cd2540a2005f65a17e948b562ee148f 744348 lagan-dbgsym_2.0-9_riscv64.ddeb 01a3e15be65b3df313d5db91e19e23be 183120 lagan_2.0-9_riscv64.deb Checksums-Sha1: 2fa69374169d469fe5efabec6975e90b2516d087 744348 lagan-dbgsym_2.0-9_riscv64.ddeb c6a60fd7c2f884c59e9d83b5cbfe1765abb43d26 183120 lagan_2.0-9_riscv64.deb Checksums-Sha256: 9d090b2c2d25da9f77459b089617e428a115b00485c8eb3c7531cca100460858 744348 lagan-dbgsym_2.0-9_riscv64.ddeb 308339720738625a8e6caa2ef06ee391a3ec3b26c2ad4ea94af11459d65150d7 183120 lagan_2.0-9_riscv64.deb Build-Origin: Ubuntu Build-Architecture: riscv64 Build-Date: Sun, 07 Aug 2022 17:34:26 +0000 Build-Path: /<> Build-Tainted-By: merged-usr-via-aliased-dirs usr-local-has-programs Installed-Build-Depends: autoconf (= 2.71-2), automake (= 1:1.16.5-1.3), autopoint (= 0.21-6), autotools-dev (= 20220109.1), base-files (= 12.2ubuntu2), base-passwd (= 3.5.52build1), bash (= 5.1-6ubuntu1), binutils (= 2.38.90.20220713-2ubuntu1), binutils-common (= 2.38.90.20220713-2ubuntu1), binutils-riscv64-linux-gnu (= 2.38.90.20220713-2ubuntu1), bsdextrautils (= 2.38-4ubuntu1), bsdutils (= 1:2.38-4ubuntu1), build-essential (= 12.9ubuntu3), bzip2 (= 1.0.8-5build1), coreutils (= 8.32-4.1ubuntu1), cpp (= 4:12.1.0-3ubuntu1), cpp-11 (= 11.3.0-5ubuntu1), cpp-12 (= 12.1.0-7ubuntu1), dash (= 0.5.11+git20210903+057cd650a4ed-8ubuntu1), debconf (= 1.5.79ubuntu1), debhelper (= 13.8ubuntu1), debianutils (= 5.7-0.3), debugedit (= 1:5.0-5), dh-autoreconf (= 20), dh-strip-nondeterminism (= 1.13.0-1), diffutils (= 1:3.8-0ubuntu2), dpkg (= 1.21.9ubuntu1), dpkg-dev (= 1.21.9ubuntu1), dwz (= 0.14-1build2), file (= 1:5.41-4), findutils (= 4.8.0-1ubuntu3), g++ (= 4:12.1.0-3ubuntu1), g++-12 (= 12.1.0-7ubuntu1), gcc (= 4:12.1.0-3ubuntu1), gcc-11 (= 11.3.0-5ubuntu1), gcc-11-base (= 11.3.0-5ubuntu1), gcc-12 (= 12.1.0-7ubuntu1), gcc-12-base (= 12.1.0-7ubuntu1), gettext (= 0.21-6), gettext-base (= 0.21-6), grep (= 3.7-1build1), groff-base (= 1.22.4-8build1), gzip (= 1.10-4ubuntu4), hostname (= 3.23ubuntu2), init-system-helpers (= 1.64), intltool-debian (= 0.35.0+20060710.5), libacl1 (= 2.3.1-1), libarchive-zip-perl (= 1.68-1), libasan6 (= 11.3.0-5ubuntu1), libasan8 (= 12.1.0-7ubuntu1), libatomic1 (= 12.1.0-7ubuntu1), libattr1 (= 1:2.5.1-1build1), libaudit-common (= 1:3.0.7-1build1), libaudit1 (= 1:3.0.7-1build1), libbinutils (= 2.38.90.20220713-2ubuntu1), libblkid1 (= 2.38-4ubuntu1), libboost-dev (= 1.74.0.3ubuntu7), libboost1.74-dev (= 1.74.0-16.1ubuntu1), libbz2-1.0 (= 1.0.8-5build1), libc-bin (= 2.35-0ubuntu3), libc-dev-bin (= 2.35-0ubuntu3), libc6 (= 2.35-0ubuntu3), libc6-dev (= 2.35-0ubuntu3), libcap-ng0 (= 0.8.3-1), libcap2 (= 1:2.44-1build3), libcc1-0 (= 12.1.0-7ubuntu1), libcom-err2 (= 1.46.5-2ubuntu2), libcrypt-dev (= 1:4.4.28-2), libcrypt1 (= 1:4.4.28-2), libctf-nobfd0 (= 2.38.90.20220713-2ubuntu1), libctf0 (= 2.38.90.20220713-2ubuntu1), libdb5.3 (= 5.3.28+dfsg1-0.10), libdebconfclient0 (= 0.261ubuntu1), libdebhelper-perl (= 13.8ubuntu1), libdpkg-perl (= 1.21.9ubuntu1), libdw1 (= 0.187-1), libelf1 (= 0.187-1), libfile-stripnondeterminism-perl (= 1.13.0-1), libgcc-11-dev (= 11.3.0-5ubuntu1), libgcc-12-dev (= 12.1.0-7ubuntu1), libgcc-s1 (= 12.1.0-7ubuntu1), libgcrypt20 (= 1.10.1-2ubuntu1), libgdbm-compat4 (= 1.23-1), libgdbm6 (= 1.23-1), libgmp10 (= 2:6.2.1+dfsg-3ubuntu1), libgomp1 (= 12.1.0-7ubuntu1), libgpg-error0 (= 1.45-2), libgssapi-krb5-2 (= 1.20-1), libicu71 (= 71.1-3), libisl23 (= 0.25-1), libk5crypto3 (= 1.20-1), libkeyutils1 (= 1.6.1-3ubuntu1), libkrb5-3 (= 1.20-1), libkrb5support0 (= 1.20-1), liblz4-1 (= 1.9.3-2build2), liblzma5 (= 5.2.5-2.1), libmagic-mgc (= 1:5.41-4), libmagic1 (= 1:5.41-4), libmount1 (= 2.38-4ubuntu1), libmpc3 (= 1.2.1-2build1), libmpfr6 (= 4.1.0-3build3), libnsl-dev (= 1.3.0-2build2), libnsl2 (= 1.3.0-2build2), libpam-modules (= 1.4.0-13ubuntu1), libpam-modules-bin (= 1.4.0-13ubuntu1), libpam-runtime (= 1.4.0-13ubuntu1), libpam0g (= 1.4.0-13ubuntu1), libpcre2-8-0 (= 10.40-1), libpcre3 (= 2:8.39-14), libperl5.34 (= 5.34.0-5ubuntu1), libpipeline1 (= 1.5.6-1), libselinux1 (= 3.4-1), libsigsegv2 (= 2.13-1ubuntu3), libsmartcols1 (= 2.38-4ubuntu1), libssl3 (= 3.0.4-1ubuntu1), libstdc++-11-dev (= 11.3.0-5ubuntu1), libstdc++-12-dev (= 12.1.0-7ubuntu1), libstdc++6 (= 12.1.0-7ubuntu1), libsub-override-perl (= 0.09-3), libsystemd0 (= 251.2-2ubuntu2), libtinfo6 (= 6.3+20220423-2), libtirpc-common (= 1.3.2-2.1), libtirpc-dev (= 1.3.2-2.1), libtirpc3 (= 1.3.2-2.1), libtool (= 2.4.7-4), libuchardet0 (= 0.0.7-1build2), libudev1 (= 251.2-2ubuntu2), libunistring2 (= 1.0-1), libuuid1 (= 2.38-4ubuntu1), libxml2 (= 2.9.14+dfsg-1), libzstd1 (= 1.5.2+dfsg-1), linux-libc-dev (= 5.19.0-15.15), login (= 1:4.11.1+dfsg1-2ubuntu1), lsb-base (= 11.1.0ubuntu4), lto-disabled-list (= 32), m4 (= 1.4.18-5ubuntu2), make (= 4.3-4.1build1), man-db (= 2.10.2-1), mawk (= 1.3.4.20200120-3.1), ncurses-base (= 6.3+20220423-2), ncurses-bin (= 6.3+20220423-2), patch (= 2.7.6-7build2), perl (= 5.34.0-5ubuntu1), perl-base (= 5.34.0-5ubuntu1), perl-modules-5.34 (= 5.34.0-5ubuntu1), po-debconf (= 1.0.21+nmu1), rpcsvc-proto (= 1.4.2-0ubuntu6), sed (= 4.8-1ubuntu2), sensible-utils (= 0.0.17), sysvinit-utils (= 3.01-1ubuntu1), tar (= 1.34+dfsg-1build3), util-linux (= 2.38-4ubuntu1), util-linux-extra (= 2.38-4ubuntu1), xz-utils (= 5.2.5-2.1), zlib1g (= 1:1.2.11.dfsg-2ubuntu10) Environment: DEB_BUILD_OPTIONS="nocheck parallel=8" DEB_BUILD_PROFILES="noudeb" LANG="C.UTF-8" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1659860994" +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ lagan_2.0-9_riscv64.deb ----------------------- new Debian package, version 2.0. size 183120 bytes: control archive=2400 bytes. 883 bytes, 18 lines control 3953 bytes, 63 lines md5sums Package: lagan Version: 2.0-9 Architecture: riscv64 Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 647 Depends: libc6 (>= 2.34), libgcc-s1 (>= 3.4), libstdc++6 (>= 11) Section: science Priority: optional Homepage: http://lagan.stanford.edu/lagan_web/index.shtml Description: highly parametrizable pairwise global genome sequence aligner Lagan takes local alignments generated by CHAOS as anchors, and limits the search area of the Needleman-Wunsch algorithm around these anchors. . Multi-LAGAN is a generalization of the pairwise algorithm to multiple sequence alignment. M-LAGAN performs progressive pairwise alignments, guided by a user-specified phylogenetic tree. Alignments are aligned to other alignments using the sum-of-pairs metric. drwxr-xr-x root/root 0 2022-08-07 08:29 ./ drwxr-xr-x root/root 0 2022-08-07 08:29 ./usr/ drwxr-xr-x root/root 0 2022-08-07 08:29 ./usr/bin/ -rwxr-xr-x root/root 3110 2022-08-07 08:29 ./usr/bin/anal_gloc.pl -rwxr-xr-x root/root 10672 2022-08-07 08:29 ./usr/bin/anchors -rwxr-xr-x root/root 43840 2022-08-07 08:29 ./usr/bin/glocal -rwxr-xr-x root/root 6255 2022-08-07 08:29 ./usr/bin/lagan.pl lrwxrwxrwx root/root 0 2022-08-07 08:29 ./usr/bin/lagan_chaos -> ../lib/lagan/bin/chaos -rwxr-xr-x root/root 47816 2022-08-07 08:29 ./usr/bin/mlagan -rwxr-xr-x root/root 23080 2022-08-07 08:29 ./usr/bin/order -rwxr-xr-x root/root 47800 2022-08-07 08:29 ./usr/bin/prolagan -rwxr-xr-x root/root 9417 2022-08-07 08:29 ./usr/bin/rechaos.pl -rwxr-xr-x root/root 1146 2006-09-14 20:40 ./usr/bin/slagan-mfa.pl -rwxr-xr-x root/root 5266 2006-09-14 20:40 ./usr/bin/slagan.pl -rwxr-xr-x root/root 72331 2006-09-14 20:40 ./usr/bin/supermap.pl -rwxr-xr-x root/root 1642 2006-09-14 20:40 ./usr/bin/xmfa2mfa.pl drwxr-xr-x root/root 0 2022-08-07 08:29 ./usr/lib/ drwxr-xr-x root/root 0 2022-08-07 08:29 ./usr/lib/lagan/ lrwxrwxrwx root/root 0 2022-08-07 08:29 ./usr/lib/lagan/anchors -> ../../bin/anchors drwxr-xr-x root/root 0 2022-08-07 08:29 ./usr/lib/lagan/bin/ -rwxr-xr-x root/root 39552 2022-08-07 08:29 ./usr/lib/lagan/bin/chaos -rw-r--r-- root/root 1899 2006-09-14 20:40 ./usr/lib/lagan/blosum62.txt -rw-r--r-- root/root 3003 2006-09-14 20:40 ./usr/lib/lagan/blosum62s.txt lrwxrwxrwx root/root 0 2022-08-07 08:29 ./usr/lib/lagan/chaos -> bin/chaos -rw-r--r-- root/root 234 2006-09-14 20:40 ./usr/lib/lagan/nucmatrix.txt lrwxrwxrwx root/root 0 2022-08-07 08:29 ./usr/lib/lagan/rechaos.pl -> ../../bin/rechaos.pl drwxr-xr-x root/root 0 2022-08-07 08:29 ./usr/lib/lagan/utils/ -rwxr-xr-x root/root 35560 2022-08-07 08:29 ./usr/lib/lagan/utils/Glue -rw-r--r-- root/root 12736 2022-08-07 08:29 ./usr/lib/lagan/utils/Utils.pm -rwxr-xr-x root/root 10680 2022-08-07 08:29 ./usr/lib/lagan/utils/bin2bl -rwxr-xr-x root/root 6472 2022-08-07 08:29 ./usr/lib/lagan/utils/bin2mf -rwxr-xr-x root/root 10648 2022-08-07 08:29 ./usr/lib/lagan/utils/cextract -rwxr-xr-x root/root 7056 2022-08-07 08:29 ./usr/lib/lagan/utils/cmerge2.pl -rwxr-xr-x root/root 14720 2022-08-07 08:29 ./usr/lib/lagan/utils/contigorder -rwxr-xr-x root/root 10672 2022-08-07 08:29 ./usr/lib/lagan/utils/cstat -rwxr-xr-x root/root 10568 2022-08-07 08:29 ./usr/lib/lagan/utils/dotplot -rwxr-xr-x root/root 7749 2022-08-07 08:29 ./usr/lib/lagan/utils/draft.pl -rwxr-xr-x root/root 10656 2022-08-07 08:29 ./usr/lib/lagan/utils/fa2xfa -rwxr-xr-x root/root 326 2006-09-14 20:40 ./usr/lib/lagan/utils/flipchaos.pl -rwxr-xr-x root/root 10584 2022-08-07 08:29 ./usr/lib/lagan/utils/getbounds -rwxr-xr-x root/root 10632 2022-08-07 08:29 ./usr/lib/lagan/utils/getcontigpos -rwxr-xr-x root/root 6472 2022-08-07 08:29 ./usr/lib/lagan/utils/getlength -rwxr-xr-x root/root 6448 2022-08-07 08:29 ./usr/lib/lagan/utils/getoverlap -rwxr-xr-x root/root 1839 2022-08-07 08:29 ./usr/lib/lagan/utils/mextract.pl -rwxr-xr-x root/root 1617 2022-08-07 08:29 ./usr/lib/lagan/utils/mf2bin.pl -rwxr-xr-x root/root 4887 2022-08-07 08:29 ./usr/lib/lagan/utils/mpretty.pl -rwxr-xr-x root/root 1319 2022-08-07 08:29 ./usr/lib/lagan/utils/mproject.pl -rwxr-xr-x root/root 6224 2022-08-07 08:29 ./usr/lib/lagan/utils/mrun.pl -rwxr-xr-x root/root 1783 2022-08-07 08:29 ./usr/lib/lagan/utils/mrunfile.pl -rwxr-xr-x root/root 6038 2022-08-07 08:29 ./usr/lib/lagan/utils/mrunpairs.pl -rwxr-xr-x root/root 1825 2022-08-07 08:29 ./usr/lib/lagan/utils/msplit.pl -rwxr-xr-x root/root 5067 2022-08-07 08:29 ./usr/lib/lagan/utils/mviz.pl -rwxr-xr-x root/root 10664 2022-08-07 08:29 ./usr/lib/lagan/utils/overlay -rwxr-xr-x root/root 10616 2022-08-07 08:29 ./usr/lib/lagan/utils/rc -rwxr-xr-x root/root 14816 2022-08-07 08:29 ./usr/lib/lagan/utils/scorealign -rwxr-xr-x root/root 14824 2022-08-07 08:29 ./usr/lib/lagan/utils/scorecontigs -rwxr-xr-x root/root 6488 2022-08-07 08:29 ./usr/lib/lagan/utils/seqmerge drwxr-xr-x root/root 0 2022-08-07 08:29 ./usr/share/ drwxr-xr-x root/root 0 2022-08-07 08:29 ./usr/share/doc/ drwxr-xr-x root/root 0 2022-08-07 08:29 ./usr/share/doc/lagan/ -rw-r--r-- root/root 812 2022-03-10 05:30 ./usr/share/doc/lagan/README.Debian -rw-r--r-- root/root 3832 2006-09-14 21:23 ./usr/share/doc/lagan/README.FIRST -rw-r--r-- root/root 3569 2006-09-14 20:40 ./usr/share/doc/lagan/README.chaos.gz -rw-r--r-- root/root 2929 2006-09-14 23:12 ./usr/share/doc/lagan/README.lagan -rw-r--r-- root/root 2982 2006-09-14 21:29 ./usr/share/doc/lagan/README.mlagan -rw-r--r-- root/root 2681 2006-09-14 23:14 ./usr/share/doc/lagan/README.shuffle -rw-r--r-- root/root 305 2022-03-10 05:30 ./usr/share/doc/lagan/README.test -rw-r--r-- root/root 2858 2006-09-14 20:40 ./usr/share/doc/lagan/README.tools.gz -rw-r--r-- root/root 1412 2022-08-07 08:29 ./usr/share/doc/lagan/changelog.Debian.gz -rw-r--r-- root/root 1203 2022-03-10 05:30 ./usr/share/doc/lagan/copyright drwxr-xr-x root/root 0 2022-08-07 08:29 ./usr/share/doc/lagan/examples/ -rw-r--r-- root/root 1218 2006-09-14 20:40 ./usr/share/doc/lagan/examples/sample.fasta -rw-r--r-- root/root 961 2006-09-14 20:40 ./usr/share/doc/lagan/examples/sample.params -rw-r--r-- root/root 177 2006-09-14 20:40 ./usr/share/doc/lagan/examples/test.score -rw-r--r-- root/root 3291 2022-03-10 05:51 ./usr/share/doc/lagan/run-mlagan-test -rw-r--r-- root/root 3295 2022-03-10 05:30 ./usr/share/doc/lagan/run-unit-test drwxr-xr-x root/root 0 2022-08-07 08:29 ./usr/share/lintian/ drwxr-xr-x root/root 0 2022-08-07 08:29 ./usr/share/lintian/overrides/ -rw-r--r-- root/root 1012 2022-03-10 05:30 ./usr/share/lintian/overrides/lagan drwxr-xr-x root/root 0 2022-08-07 08:29 ./usr/share/man/ drwxr-xr-x root/root 0 2022-08-07 08:29 ./usr/share/man/man1/ -rw-r--r-- root/root 752 2022-08-07 08:29 ./usr/share/man/man1/mlagan.1.gz +------------------------------------------------------------------------------+ | Post Build | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not removing build depends: as requested +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: riscv64 Build Type: any Build-Space: 11228 Build-Time: 266 Distribution: kinetic-proposed Host Architecture: riscv64 Install-Time: 310 Job: lagan_2.0-9.dsc Machine Architecture: riscv64 Package: lagan Package-Time: 604 Source-Version: 2.0-9 Space: 11228 Status: successful Version: 2.0-9 -------------------------------------------------------------------------------- Finished at 2022-08-07T17:34:32Z Build needed 00:10:04, 11228k disk space Adding user buildd to group lxd RUN: /usr/share/launchpad-buildd/bin/in-target scan-for-processes --backend=chroot --series=kinetic --arch=riscv64 PACKAGEBUILD-24257979 Scanning for processes to kill in build PACKAGEBUILD-24257979 RUN: /usr/share/launchpad-buildd/bin/in-target umount-chroot --backend=chroot --series=kinetic --arch=riscv64 PACKAGEBUILD-24257979 Stopping target for build PACKAGEBUILD-24257979 RUN: /usr/share/launchpad-buildd/bin/in-target remove-build --backend=chroot --series=kinetic --arch=riscv64 PACKAGEBUILD-24257979 Removing build PACKAGEBUILD-24257979