https://launchpad.net/ubuntu/+source/pdb2pqr/2.1.1+dfsg-8/+build/23155576 RUN: /usr/share/launchpad-buildd/bin/builder-prep Kernel version: Linux riscv64-qemu-lcy01-007 5.11.0-1026-generic #28~20.04.1-Ubuntu SMP Fri Jan 7 12:35:22 UTC 2022 riscv64 Buildd toolchain package versions: launchpad-buildd_206~519~ubuntu18.04.1 python3-lpbuildd_206~519~ubuntu18.04.1 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... 11 Feb 02:04:28 ntpdate[206396]: adjust time server 10.211.37.1 offset 0.000662 sec RUN: /usr/share/launchpad-buildd/bin/in-target unpack-chroot --backend=chroot --series=jammy --arch=riscv64 PACKAGEBUILD-23155576 --image-type chroot /home/buildd/filecache-default/03bec7884d85d5bd8bcd177f093129b6620b2195 Creating target for build PACKAGEBUILD-23155576 RUN: /usr/share/launchpad-buildd/bin/in-target mount-chroot --backend=chroot --series=jammy --arch=riscv64 PACKAGEBUILD-23155576 Starting target for build PACKAGEBUILD-23155576 RUN: /usr/share/launchpad-buildd/bin/in-target override-sources-list --backend=chroot --series=jammy --arch=riscv64 PACKAGEBUILD-23155576 'deb http://ftpmaster.internal/ubuntu jammy main universe' 'deb http://ftpmaster.internal/ubuntu jammy-security main universe' 'deb http://ftpmaster.internal/ubuntu jammy-updates main universe' 'deb http://ftpmaster.internal/ubuntu jammy-proposed main universe' Overriding sources.list in build-PACKAGEBUILD-23155576 RUN: /usr/share/launchpad-buildd/bin/in-target update-debian-chroot --backend=chroot --series=jammy --arch=riscv64 PACKAGEBUILD-23155576 Updating target for build PACKAGEBUILD-23155576 Get:1 http://ftpmaster.internal/ubuntu jammy InRelease [270 kB] Get:2 http://ftpmaster.internal/ubuntu jammy-security InRelease [90.7 kB] Get:3 http://ftpmaster.internal/ubuntu jammy-updates InRelease [90.7 kB] Get:4 http://ftpmaster.internal/ubuntu jammy-proposed InRelease [121 kB] Get:5 http://ftpmaster.internal/ubuntu jammy/main riscv64 Packages [1296 kB] Get:6 http://ftpmaster.internal/ubuntu jammy/main Translation-en [513 kB] Get:7 http://ftpmaster.internal/ubuntu jammy/universe riscv64 Packages [12.7 MB] Get:8 http://ftpmaster.internal/ubuntu jammy/universe Translation-en [5609 kB] Get:9 http://ftpmaster.internal/ubuntu jammy-proposed/main riscv64 Packages [246 kB] Get:10 http://ftpmaster.internal/ubuntu jammy-proposed/main Translation-en [101 kB] Get:11 http://ftpmaster.internal/ubuntu jammy-proposed/universe riscv64 Packages [1186 kB] Get:12 http://ftpmaster.internal/ubuntu jammy-proposed/universe Translation-en [558 kB] Fetched 22.8 MB in 34s (673 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: libperl5.32 libssl1.1 perl-modules-5.32 Use 'sudo apt autoremove' to remove them. The following packages will be REMOVED: libsemanage1* The following NEW packages will be installed: libperl5.34 libsemanage2 libsepol2 libssl3 perl-modules-5.34 The following packages will be upgraded: apt base-files bash binutils binutils-common binutils-riscv64-linux-gnu bsdutils bzip2 ca-certificates coreutils cpp-11 dash debconf debianutils dpkg dpkg-dev e2fsprogs fakeroot g++-11 gcc-11 gcc-11-base gpg gpg-agent gpgconf gpgv grep init init-system-helpers libacl1 libapparmor1 libapt-pkg6.0 libasan6 libatomic1 libattr1 libbinutils libblkid1 libbz2-1.0 libc-bin libc-dev-bin libc6 libc6-dev libcap-ng0 libcc1-0 libcom-err2 libcrypt-dev libcrypt1 libcryptsetup12 libctf-nobfd0 libctf0 libdebconfclient0 libdpkg-perl libext2fs2 libfakeroot libffi8 libgcc-11-dev libgcc-s1 libgcrypt20 libgdbm-compat4 libgdbm6 libgmp10 libgnutls30 libgomp1 libgpg-error0 libgssapi-krb5-2 libidn2-0 libip4tc2 libisl23 libk5crypto3 libkmod2 libkrb5-3 libkrb5support0 libmount1 libmpc3 libncurses6 libncursesw6 libp11-kit0 libpam-modules libpam-modules-bin libpam-runtime libpam0g libpcre2-8-0 libreadline8 libseccomp2 libselinux1 libsemanage-common libsmartcols1 libsqlite3-0 libss2 libstdc++-11-dev libstdc++6 libsystemd0 libtasn1-6 libtinfo6 libudev1 libunistring2 libuuid1 libxxhash0 libzstd1 linux-libc-dev lockfile-progs login logsave lto-disabled-list make mawk mount ncurses-base ncurses-bin openssl passwd perl perl-base pkgbinarymangler readline-common sed sensible-utils systemd systemd-sysv systemd-timesyncd sysvinit-utils tzdata usrmerge util-linux 123 upgraded, 5 newly installed, 1 to remove and 0 not upgraded. Need to get 89.0 MB of archives. After this operation, 55.0 MB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu jammy/main riscv64 libcrypt-dev riscv64 1:4.4.27-1 [249 kB] Get:2 http://ftpmaster.internal/ubuntu jammy-proposed/main riscv64 libc6-dev riscv64 2.35-0ubuntu1 [3235 kB] Get:3 http://ftpmaster.internal/ubuntu jammy-proposed/main riscv64 libc-dev-bin riscv64 2.35-0ubuntu1 [18.9 kB] Get:4 http://ftpmaster.internal/ubuntu jammy-proposed/main riscv64 perl-modules-5.34 all 5.34.0-3ubuntu1 [2975 kB] Get:5 http://ftpmaster.internal/ubuntu jammy-proposed/main riscv64 libperl5.34 riscv64 5.34.0-3ubuntu1 [4206 kB] Get:6 http://ftpmaster.internal/ubuntu jammy-proposed/main riscv64 perl riscv64 5.34.0-3ubuntu1 [232 kB] Get:7 http://ftpmaster.internal/ubuntu jammy-proposed/main riscv64 perl-base riscv64 5.34.0-3ubuntu1 [1639 kB] Get:8 http://ftpmaster.internal/ubuntu jammy/main riscv64 bzip2 riscv64 1.0.8-5 [33.9 kB] Get:9 http://ftpmaster.internal/ubuntu jammy/main riscv64 libbz2-1.0 riscv64 1.0.8-5 [36.2 kB] Get:10 http://ftpmaster.internal/ubuntu jammy/main riscv64 libgdbm6 riscv64 1.23-1 [29.9 kB] Get:11 http://ftpmaster.internal/ubuntu jammy/main riscv64 libgdbm-compat4 riscv64 1.23-1 [5860 B] Get:12 http://ftpmaster.internal/ubuntu jammy/main riscv64 debconf all 1.5.79 [126 kB] Get:13 http://ftpmaster.internal/ubuntu jammy-proposed/main riscv64 libpam0g riscv64 1.4.0-11ubuntu1 [56.4 kB] Get:14 http://ftpmaster.internal/ubuntu jammy/main riscv64 libcrypt1 riscv64 1:4.4.27-1 [97.4 kB] Get:15 http://ftpmaster.internal/ubuntu jammy-proposed/main riscv64 linux-libc-dev riscv64 5.15.0-22.22 [1223 kB] Get:16 http://ftpmaster.internal/ubuntu jammy-proposed/main riscv64 libc6 riscv64 2.35-0ubuntu1 [2635 kB] Get:17 http://ftpmaster.internal/ubuntu jammy-proposed/main riscv64 libc-bin riscv64 2.35-0ubuntu1 [561 kB] Get:18 http://ftpmaster.internal/ubuntu jammy/main riscv64 libcc1-0 riscv64 11.2.0-16ubuntu1 [42.0 kB] Get:19 http://ftpmaster.internal/ubuntu jammy-proposed/main riscv64 libctf0 riscv64 2.38-1ubuntu1 [97.9 kB] Get:20 http://ftpmaster.internal/ubuntu jammy-proposed/main riscv64 libctf-nobfd0 riscv64 2.38-1ubuntu1 [99.6 kB] Get:21 http://ftpmaster.internal/ubuntu jammy-proposed/main riscv64 binutils-riscv64-linux-gnu riscv64 2.38-1ubuntu1 [927 kB] Get:22 http://ftpmaster.internal/ubuntu jammy-proposed/main riscv64 libbinutils riscv64 2.38-1ubuntu1 [492 kB] Get:23 http://ftpmaster.internal/ubuntu jammy-proposed/main riscv64 binutils-common riscv64 2.38-1ubuntu1 [213 kB] Get:24 http://ftpmaster.internal/ubuntu jammy-proposed/main riscv64 binutils riscv64 2.38-1ubuntu1 [3092 B] Get:25 http://ftpmaster.internal/ubuntu jammy/main riscv64 gcc-11-base riscv64 11.2.0-16ubuntu1 [20.9 kB] Get:26 http://ftpmaster.internal/ubuntu jammy/main riscv64 libgcc-s1 riscv64 11.2.0-16ubuntu1 [43.6 kB] Get:27 http://ftpmaster.internal/ubuntu jammy/main riscv64 libgomp1 riscv64 11.2.0-16ubuntu1 [103 kB] Get:28 http://ftpmaster.internal/ubuntu jammy/main riscv64 libatomic1 riscv64 11.2.0-16ubuntu1 [7866 B] Get:29 http://ftpmaster.internal/ubuntu jammy/main riscv64 libasan6 riscv64 11.2.0-16ubuntu1 [2107 kB] Get:30 http://ftpmaster.internal/ubuntu jammy/main riscv64 g++-11 riscv64 11.2.0-16ubuntu1 [9289 kB] Get:31 http://ftpmaster.internal/ubuntu jammy/main riscv64 libstdc++-11-dev riscv64 11.2.0-16ubuntu1 [4748 kB] Get:32 http://ftpmaster.internal/ubuntu jammy/main riscv64 libgcc-11-dev riscv64 11.2.0-16ubuntu1 [2399 kB] Get:33 http://ftpmaster.internal/ubuntu jammy/main riscv64 gcc-11 riscv64 11.2.0-16ubuntu1 [15.8 MB] Get:34 http://ftpmaster.internal/ubuntu jammy/main riscv64 cpp-11 riscv64 11.2.0-16ubuntu1 [7984 kB] Get:35 http://ftpmaster.internal/ubuntu jammy/main riscv64 libstdc++6 riscv64 11.2.0-16ubuntu1 [647 kB] Get:36 http://ftpmaster.internal/ubuntu jammy/main riscv64 libgmp10 riscv64 2:6.2.1+dfsg-3ubuntu1 [245 kB] Get:37 http://ftpmaster.internal/ubuntu jammy/main riscv64 libisl23 riscv64 0.24-2 [593 kB] Get:38 http://ftpmaster.internal/ubuntu jammy/main riscv64 libmpc3 riscv64 1.2.1-1 [44.4 kB] Get:39 http://ftpmaster.internal/ubuntu jammy/main riscv64 libzstd1 riscv64 1.4.8+dfsg-3 [370 kB] Get:40 http://ftpmaster.internal/ubuntu jammy/main riscv64 base-files riscv64 12ubuntu2 [62.9 kB] Get:41 http://ftpmaster.internal/ubuntu jammy/main riscv64 debianutils riscv64 5.5-1ubuntu1 [105 kB] Get:42 http://ftpmaster.internal/ubuntu jammy/main riscv64 bash riscv64 5.1-6ubuntu1 [647 kB] Get:43 http://ftpmaster.internal/ubuntu jammy/main riscv64 bsdutils riscv64 1:2.37.2-4ubuntu1 [91.2 kB] Get:44 http://ftpmaster.internal/ubuntu jammy-proposed/main riscv64 coreutils riscv64 8.32-4.1ubuntu1 [1318 kB] Get:45 http://ftpmaster.internal/ubuntu jammy/main riscv64 libgpg-error0 riscv64 1.43-3 [63.8 kB] Get:46 http://ftpmaster.internal/ubuntu jammy/main riscv64 libgcrypt20 riscv64 1.9.4-3ubuntu2 [498 kB] Get:47 http://ftpmaster.internal/ubuntu jammy/main riscv64 libssl3 riscv64 3.0.1-0ubuntu1 [1449 kB] Get:48 http://ftpmaster.internal/ubuntu jammy/main riscv64 libblkid1 riscv64 2.37.2-4ubuntu1 [148 kB] Get:49 http://ftpmaster.internal/ubuntu jammy/main riscv64 libuuid1 riscv64 2.37.2-4ubuntu1 [27.0 kB] Get:50 http://ftpmaster.internal/ubuntu jammy/main riscv64 libcryptsetup12 riscv64 2:2.4.3-1ubuntu1 [184 kB] Get:51 http://ftpmaster.internal/ubuntu jammy/main riscv64 libunistring2 riscv64 1.0-1 [540 kB] Get:52 http://ftpmaster.internal/ubuntu jammy/main riscv64 libidn2-0 riscv64 2.3.2-2 [67.5 kB] Get:53 http://ftpmaster.internal/ubuntu jammy/main riscv64 libffi8 riscv64 3.4.2-4 [20.4 kB] Get:54 http://ftpmaster.internal/ubuntu jammy/main riscv64 libp11-kit0 riscv64 0.24.0-6 [203 kB] Get:55 http://ftpmaster.internal/ubuntu jammy/main riscv64 libtasn1-6 riscv64 4.18.0-4 [38.9 kB] Get:56 http://ftpmaster.internal/ubuntu jammy/main riscv64 libgnutls30 riscv64 3.7.3-4ubuntu1 [870 kB] Get:57 http://ftpmaster.internal/ubuntu jammy/main riscv64 systemd-sysv riscv64 249.9-0ubuntu2 [10.5 kB] Get:58 http://ftpmaster.internal/ubuntu jammy/main riscv64 systemd-timesyncd riscv64 249.9-0ubuntu2 [28.8 kB] Get:59 http://ftpmaster.internal/ubuntu jammy/main riscv64 libacl1 riscv64 2.3.1-1 [15.3 kB] Get:60 http://ftpmaster.internal/ubuntu jammy-proposed/main riscv64 libapparmor1 riscv64 3.0.3-0ubuntu6 [33.6 kB] Get:61 http://ftpmaster.internal/ubuntu jammy/main riscv64 libip4tc2 riscv64 1.8.7-1ubuntu4 [18.1 kB] Get:62 http://ftpmaster.internal/ubuntu jammy/main riscv64 libkmod2 riscv64 29-1ubuntu1 [42.1 kB] Get:63 http://ftpmaster.internal/ubuntu jammy/main riscv64 libpcre2-8-0 riscv64 10.39-3 [136 kB] Get:64 http://ftpmaster.internal/ubuntu jammy-proposed/main riscv64 libselinux1 riscv64 3.3-1build1 [71.0 kB] Get:65 http://ftpmaster.internal/ubuntu jammy/main riscv64 libmount1 riscv64 2.37.2-4ubuntu1 [156 kB] Get:66 http://ftpmaster.internal/ubuntu jammy/main riscv64 libseccomp2 riscv64 2.5.2-2ubuntu3 [46.2 kB] Get:67 http://ftpmaster.internal/ubuntu jammy/main riscv64 login riscv64 1:4.8.1-2ubuntu1 [184 kB] Get:68 http://ftpmaster.internal/ubuntu jammy/main riscv64 util-linux riscv64 2.37.2-4ubuntu1 [1122 kB] Get:69 http://ftpmaster.internal/ubuntu jammy/main riscv64 mount riscv64 2.37.2-4ubuntu1 [129 kB] Get:70 http://ftpmaster.internal/ubuntu jammy/main riscv64 systemd riscv64 249.9-0ubuntu2 [4138 kB] Get:71 http://ftpmaster.internal/ubuntu jammy/main riscv64 libsystemd0 riscv64 249.9-0ubuntu2 [294 kB] Get:72 http://ftpmaster.internal/ubuntu jammy/main riscv64 libudev1 riscv64 249.9-0ubuntu2 [73.1 kB] Get:73 http://ftpmaster.internal/ubuntu jammy/main riscv64 libxxhash0 riscv64 0.8.1-1 [31.9 kB] Get:74 http://ftpmaster.internal/ubuntu jammy/main riscv64 libapt-pkg6.0 riscv64 2.3.15 [917 kB] Get:75 http://ftpmaster.internal/ubuntu jammy/main riscv64 dpkg riscv64 1.21.1ubuntu1 [1214 kB] Get:76 http://ftpmaster.internal/ubuntu jammy/main riscv64 dash riscv64 0.5.11+git20210903+057cd650a4ed-3 [86.3 kB] Get:77 http://ftpmaster.internal/ubuntu jammy/main riscv64 grep riscv64 3.7-1 [151 kB] Get:78 http://ftpmaster.internal/ubuntu jammy/main riscv64 libncurses6 riscv64 6.3-2 [93.6 kB] Get:79 http://ftpmaster.internal/ubuntu jammy/main riscv64 libncursesw6 riscv64 6.3-2 [128 kB] Get:80 http://ftpmaster.internal/ubuntu jammy/main riscv64 libtinfo6 riscv64 6.3-2 [96.1 kB] Get:81 http://ftpmaster.internal/ubuntu jammy/main riscv64 ncurses-bin riscv64 6.3-2 [176 kB] Get:82 http://ftpmaster.internal/ubuntu jammy/main riscv64 sed riscv64 4.8-1ubuntu1 [187 kB] Get:83 http://ftpmaster.internal/ubuntu jammy/main riscv64 init-system-helpers all 1.61 [39.3 kB] Get:84 http://ftpmaster.internal/ubuntu jammy/main riscv64 ncurses-base all 6.3-2 [20.1 kB] Get:85 http://ftpmaster.internal/ubuntu jammy/main riscv64 sysvinit-utils riscv64 3.01-1ubuntu1 [20.8 kB] Get:86 http://ftpmaster.internal/ubuntu jammy/main riscv64 gpgv riscv64 2.2.27-3ubuntu1 [195 kB] Get:87 http://ftpmaster.internal/ubuntu jammy/main riscv64 apt riscv64 2.3.15 [1348 kB] Get:88 http://ftpmaster.internal/ubuntu jammy/main riscv64 libsepol2 riscv64 3.3-1 [254 kB] Get:89 http://ftpmaster.internal/ubuntu jammy-proposed/main riscv64 libsemanage-common all 3.3-1build1 [10.0 kB] Get:90 http://ftpmaster.internal/ubuntu jammy-proposed/main riscv64 libsemanage2 riscv64 3.3-1build1 [83.9 kB] Get:91 http://ftpmaster.internal/ubuntu jammy/main riscv64 passwd riscv64 1:4.8.1-2ubuntu1 [736 kB] Get:92 http://ftpmaster.internal/ubuntu jammy-proposed/main riscv64 libpam-modules-bin riscv64 1.4.0-11ubuntu1 [36.9 kB] Get:93 http://ftpmaster.internal/ubuntu jammy-proposed/main riscv64 libpam-modules riscv64 1.4.0-11ubuntu1 [265 kB] Get:94 http://ftpmaster.internal/ubuntu jammy/main riscv64 logsave riscv64 1.46.5-2ubuntu1 [10.1 kB] Get:95 http://ftpmaster.internal/ubuntu jammy/main riscv64 libext2fs2 riscv64 1.46.5-2ubuntu1 [196 kB] Get:96 http://ftpmaster.internal/ubuntu jammy/main riscv64 e2fsprogs riscv64 1.46.5-2ubuntu1 [554 kB] Get:97 http://ftpmaster.internal/ubuntu jammy/main riscv64 init riscv64 1.61 [6106 B] Get:98 http://ftpmaster.internal/ubuntu jammy/main riscv64 libattr1 riscv64 1:2.5.1-1 [12.7 kB] Get:99 http://ftpmaster.internal/ubuntu jammy-proposed/main riscv64 libcap-ng0 riscv64 0.7.9-2.2build3 [10.3 kB] Get:100 http://ftpmaster.internal/ubuntu jammy/main riscv64 libcom-err2 riscv64 1.46.5-2ubuntu1 [8838 B] Get:101 http://ftpmaster.internal/ubuntu jammy-proposed/main riscv64 libdebconfclient0 riscv64 0.261ubuntu1 [6560 B] Get:102 http://ftpmaster.internal/ubuntu jammy/main riscv64 libk5crypto3 riscv64 1.19.2-1 [102 kB] Get:103 http://ftpmaster.internal/ubuntu jammy/main riscv64 libkrb5support0 riscv64 1.19.2-1 [30.7 kB] Get:104 http://ftpmaster.internal/ubuntu jammy/main riscv64 libkrb5-3 riscv64 1.19.2-1 [337 kB] Get:105 http://ftpmaster.internal/ubuntu jammy/main riscv64 libgssapi-krb5-2 riscv64 1.19.2-1 [127 kB] Get:106 http://ftpmaster.internal/ubuntu jammy-proposed/main riscv64 libpam-runtime all 1.4.0-11ubuntu1 [40.2 kB] Get:107 http://ftpmaster.internal/ubuntu jammy/main riscv64 libsmartcols1 riscv64 2.37.2-4ubuntu1 [102 kB] Get:108 http://ftpmaster.internal/ubuntu jammy/main riscv64 libss2 riscv64 1.46.5-2ubuntu1 [10.7 kB] Get:109 http://ftpmaster.internal/ubuntu jammy/main riscv64 mawk riscv64 1.3.4.20200120-3 [95.0 kB] Get:110 http://ftpmaster.internal/ubuntu jammy/main riscv64 sensible-utils all 0.0.17 [20.1 kB] Get:111 http://ftpmaster.internal/ubuntu jammy/main riscv64 usrmerge all 25ubuntu2 [54.7 kB] Get:112 http://ftpmaster.internal/ubuntu jammy/main riscv64 openssl riscv64 3.0.1-0ubuntu1 [1141 kB] Get:113 http://ftpmaster.internal/ubuntu jammy/main riscv64 ca-certificates all 20211016 [148 kB] Get:114 http://ftpmaster.internal/ubuntu jammy/main riscv64 readline-common all 8.1.2-1 [53.5 kB] Get:115 http://ftpmaster.internal/ubuntu jammy/main riscv64 libreadline8 riscv64 8.1.2-1 [130 kB] Get:116 http://ftpmaster.internal/ubuntu jammy/main riscv64 libsqlite3-0 riscv64 3.37.2-2 [559 kB] Get:117 http://ftpmaster.internal/ubuntu jammy/main riscv64 tzdata all 2021e-1ubuntu1 [343 kB] Get:118 http://ftpmaster.internal/ubuntu jammy/main riscv64 dpkg-dev all 1.21.1ubuntu1 [922 kB] Get:119 http://ftpmaster.internal/ubuntu jammy/main riscv64 libdpkg-perl all 1.21.1ubuntu1 [236 kB] Get:120 http://ftpmaster.internal/ubuntu jammy/main riscv64 make riscv64 4.3-4ubuntu2 [164 kB] Get:121 http://ftpmaster.internal/ubuntu jammy/main riscv64 lto-disabled-list all 19 [12.2 kB] Get:122 http://ftpmaster.internal/ubuntu jammy/main riscv64 libfakeroot riscv64 1.27-1ubuntu1 [28.2 kB] Get:123 http://ftpmaster.internal/ubuntu jammy/main riscv64 fakeroot riscv64 1.27-1ubuntu1 [68.1 kB] Get:124 http://ftpmaster.internal/ubuntu jammy/main riscv64 gpg riscv64 2.2.27-3ubuntu1 [488 kB] Get:125 http://ftpmaster.internal/ubuntu jammy/main riscv64 gpgconf riscv64 2.2.27-3ubuntu1 [115 kB] Get:126 http://ftpmaster.internal/ubuntu jammy/main riscv64 gpg-agent riscv64 2.2.27-3ubuntu1 [231 kB] Get:127 http://ftpmaster.internal/ubuntu jammy/main riscv64 lockfile-progs riscv64 0.1.19 [9330 B] Get:128 http://ftpmaster.internal/ubuntu jammy/main riscv64 pkgbinarymangler all 149 [32.4 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 89.0 MB in 20s (4355 kB/s) (Reading database ... 13170 files and directories currently installed.) 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Processing triggers for ca-certificates (20211016) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. RUN: /usr/share/launchpad-buildd/bin/sbuild-package PACKAGEBUILD-23155576 riscv64 jammy-proposed -c chroot:build-PACKAGEBUILD-23155576 --arch=riscv64 --dist=jammy-proposed --nolog pdb2pqr_2.1.1+dfsg-8.dsc Initiating build PACKAGEBUILD-23155576 with 8 jobs across 8 processor cores. Kernel reported to sbuild: 5.11.0-1026-generic #28~20.04.1-Ubuntu SMP Fri Jan 7 12:35:22 UTC 2022 riscv64 sbuild (Debian sbuild) 0.79.0 (05 February 2020) on riscv64-qemu-lcy01-007.buildd +==============================================================================+ | pdb2pqr 2.1.1+dfsg-8 (riscv64) Fri, 11 Feb 2022 02:15:11 +0000 | +==============================================================================+ Package: pdb2pqr Version: 2.1.1+dfsg-8 Source Version: 2.1.1+dfsg-8 Distribution: jammy-proposed Machine Architecture: riscv64 Host Architecture: riscv64 Build Architecture: riscv64 Build Type: any I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-23155576/chroot-autobuild' with '<>' I: NOTICE: Log filtering will replace 'build/pdb2pqr-C0ivtq/resolver-ah7fKd' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- pdb2pqr_2.1.1+dfsg-8.dsc exists in .; copying to chroot I: NOTICE: Log filtering will replace 'build/pdb2pqr-C0ivtq/pdb2pqr-2.1.1+dfsg' with '<>' I: NOTICE: Log filtering will replace 'build/pdb2pqr-C0ivtq' with '<>' +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper-compat (= 12), dh-python, gfortran, swig, xmlto, openbabel, python3-dev, python3-numpy, scons (>= 3.1.1-4), dos2unix, pkg-config, build-essential, fakeroot Filtered Build-Depends: debhelper-compat (= 12), dh-python, gfortran, swig, xmlto, openbabel, python3-dev, python3-numpy, scons (>= 3.1.1-4), dos2unix, pkg-config, 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 [439 B] Get:5 copy:/<>/apt_archive ./ Packages [522 B] Fetched 1918 B in 1s (3145 B/s) Reading package lists... Reading package lists... Install main build dependencies (apt-based resolver) ---------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following packages were automatically installed and are no longer required: libperl5.32 libssl1.1 perl-modules-5.32 systemd-timesyncd Use 'apt autoremove' to remove them. The following additional packages will be installed: autoconf automake autopoint autotools-dev bsdextrautils debhelper debugedit dh-autoreconf dh-python dh-strip-nondeterminism docbook-xml docbook-xsl dos2unix dwz file fontconfig-config fonts-dejavu-core gettext gettext-base gfortran gfortran-11 groff-base intltool-debian libarchive-zip-perl libblas3 libboost-iostreams1.74.0 libbrotli1 libbsd0 libcairo2 libdebhelper-perl libdw1 libedit2 libelf1 libexpat1 libexpat1-dev libfile-stripnondeterminism-perl libfontconfig1 libfreetype6 libgfortran-11-dev libgfortran5 libglib2.0-0 libicu70 libinchi1 libjs-jquery libjs-sphinxdoc libjs-underscore liblapack3 libmaeparser1 libmagic-mgc libmagic1 libmd0 libmpdec3 libopenbabel7 libpipeline1 libpixman-1-0 libpython3-dev libpython3-stdlib libpython3.10 libpython3.10-dev libpython3.10-minimal libpython3.10-stdlib libpython3.9-minimal libpython3.9-stdlib libsigsegv2 libsub-override-perl libtool libuchardet0 libx11-6 libx11-data libxau6 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxml2 libxml2-utils libxrender1 libxslt1.1 m4 man-db media-types openbabel pkg-config po-debconf python3 python3-dev python3-distutils python3-lib2to3 python3-minimal python3-numpy python3-pkg-resources python3.10 python3.10-dev python3.10-minimal python3.9 python3.9-minimal scons sgml-base sgml-data swig swig4.0 ucf xml-core xmlto xsltproc zlib1g-dev Suggested packages: autoconf-archive gnu-standards autoconf-doc dh-make flit python3-build python3-tomli python3-installer docbook docbook-dsssl docbook-defguide dbtoepub docbook-xsl-doc-html | docbook-xsl-doc-pdf | docbook-xsl-doc-text | docbook-xsl-doc docbook-xsl-saxon fop libsaxon-java libxalan2-java libxslthl-java xalan gettext-doc libasprintf-dev libgettextpo-dev gfortran-doc gfortran-11-doc libcoarrays-dev groff libtool-doc gcj-jdk m4-doc apparmor less www-browser libmail-box-perl python3-doc python3-tk python3-venv python-numpy-doc python3-pytest python3-setuptools python3.10-venv python3.10-doc binfmt-support python3.9-venv python3.9-doc sgml-base-doc perlsgml w3-recs opensp swig-doc swig-examples swig4.0-examples swig4.0-doc w3m | lynx-cur | links texlive-htmlxml Recommended packages: curl | wget | lynx libarchive-cpio-perl libglib2.0-data shared-mime-info xdg-user-dirs javascript-common libltdl-dev libmail-sendmail-perl dblatex | fop libpaper-utils zip The following NEW packages will be installed: autoconf automake autopoint autotools-dev bsdextrautils debhelper debugedit dh-autoreconf dh-python dh-strip-nondeterminism docbook-xml docbook-xsl dos2unix dwz file fontconfig-config fonts-dejavu-core gettext gettext-base gfortran gfortran-11 groff-base intltool-debian libarchive-zip-perl libblas3 libboost-iostreams1.74.0 libbrotli1 libbsd0 libcairo2 libdebhelper-perl libdw1 libedit2 libelf1 libexpat1 libexpat1-dev libfile-stripnondeterminism-perl libfontconfig1 libfreetype6 libgfortran-11-dev libgfortran5 libglib2.0-0 libicu70 libinchi1 libjs-jquery libjs-sphinxdoc libjs-underscore liblapack3 libmaeparser1 libmagic-mgc libmagic1 libmd0 libmpdec3 libopenbabel7 libpipeline1 libpixman-1-0 libpython3-dev libpython3-stdlib libpython3.10 libpython3.10-dev libpython3.10-minimal libpython3.10-stdlib libpython3.9-minimal libpython3.9-stdlib libsigsegv2 libsub-override-perl libtool libuchardet0 libx11-6 libx11-data libxau6 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxml2 libxml2-utils libxrender1 libxslt1.1 m4 man-db media-types openbabel pkg-config po-debconf python3 python3-dev python3-distutils python3-lib2to3 python3-minimal python3-numpy python3-pkg-resources python3.10 python3.10-dev python3.10-minimal python3.9 python3.9-minimal sbuild-build-depends-main-dummy scons sgml-base sgml-data swig swig4.0 ucf xml-core xmlto xsltproc zlib1g-dev 0 upgraded, 108 newly installed, 0 to remove and 0 not upgraded. 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riscv64 7.4.2-2 [385 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 72.7 MB in 14s (5088 kB/s) Selecting previously unselected package libpython3.10-minimal:riscv64. 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Setting up gettext (0.21-4ubuntu3) ... Setting up python3.10 (3.10.2-1) ... Setting up libxrender1:riscv64 (1:0.9.10-1build3) ... Setting up libxext6:riscv64 (2:1.3.4-1) ... Setting up python3 (3.10.1-0ubuntu1) ... Setting up man-db (2.10.1-1) ... 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 gfortran (4:11.2.0-1ubuntu1) ... update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f95 (f95) in auto mode update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f77 (f77) in auto mode Setting up libcairo2:riscv64 (1.16.0-5ubuntu2) ... Setting up intltool-debian (0.35.0+20060710.5) ... Setting up dh-autoreconf (20) ... Setting up libpython3.10-dev:riscv64 (3.10.2-1) ... Setting up python3.10-dev (3.10.2-1) ... Setting up libxslt1.1:riscv64 (1.1.34-4build1) ... Setting up libxml2-utils (2.9.12+dfsg-5build1) ... Setting up python3-lib2to3 (3.9.10-1) ... Setting up python3-pkg-resources (59.6.0-1.2) ... Setting up python3-distutils (3.9.10-1) ... Setting up dh-python (5.20220119) ... Setting up libpython3-dev:riscv64 (3.10.1-0ubuntu1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up xsltproc (1.1.34-4build1) ... Setting up libopenbabel7 (3.1.1+dfsg-6ubuntu5) ... Setting up debhelper (13.5.2ubuntu1) ... Setting up python3-dev (3.10.1-0ubuntu1) ... Setting up scons (4.0.1+dfsg-2) ... Setting up python3-numpy (1:1.21.5-1) ... Setting up openbabel (3.1.1+dfsg-6ubuntu5) ... Processing triggers for libc-bin (2.35-0ubuntu1) ... Processing triggers for sgml-base (1.30) ... Setting up docbook-xsl (1.79.2+dfsg-1) ... Setting up sgml-data (2.0.11+nmu1) ... Processing triggers for sgml-base (1.30) ... Setting up docbook-xml (4.5-11) ... Processing triggers for sgml-base (1.30) ... Setting up xmlto (0.0.28-2.1) ... Setting up sbuild-build-depends-main-dummy (0.invalid.0) ... +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (riscv64 included in any all) +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 5.11.0-1026-generic #28~20.04.1-Ubuntu SMP Fri Jan 7 12:35:22 UTC 2022 riscv64 (riscv64) Toolchain package versions: binutils_2.38-1ubuntu1 dpkg-dev_1.21.1ubuntu1 g++-11_11.2.0-16ubuntu1 gcc-11_11.2.0-16ubuntu1 libc6-dev_2.35-0ubuntu1 libstdc++-11-dev_11.2.0-16ubuntu1 libstdc++6_11.2.0-16ubuntu1 linux-libc-dev_5.15.0-22.22 Package versions: adduser_3.118ubuntu5 advancecomp_2.1-2.1ubuntu1 apt_2.3.15 autoconf_2.71-2 automake_1:1.16.5-1.1 autopoint_0.21-4ubuntu3 autotools-dev_20220109.1 base-files_12ubuntu2 base-passwd_3.5.52 bash_5.1-6ubuntu1 binutils_2.38-1ubuntu1 binutils-common_2.38-1ubuntu1 binutils-riscv64-linux-gnu_2.38-1ubuntu1 bsdextrautils_2.37.2-4ubuntu1 bsdutils_1:2.37.2-4ubuntu1 build-essential_12.9ubuntu2 bzip2_1.0.8-5 ca-certificates_20211016 coreutils_8.32-4.1ubuntu1 cpp_4:11.2.0-1ubuntu1 cpp-11_11.2.0-16ubuntu1 dash_0.5.11+git20210903+057cd650a4ed-3 debconf_1.5.79 debhelper_13.5.2ubuntu1 debianutils_5.5-1ubuntu1 debugedit_1:5.0-4 dh-autoreconf_20 dh-python_5.20220119 dh-strip-nondeterminism_1.13.0-1 diffutils_1:3.8-0ubuntu1 docbook-xml_4.5-11 docbook-xsl_1.79.2+dfsg-1 dos2unix_7.4.2-2 dpkg_1.21.1ubuntu1 dpkg-dev_1.21.1ubuntu1 dwz_0.14-1build1 e2fsprogs_1.46.5-2ubuntu1 fakeroot_1.27-1ubuntu1 file_1:5.41-2 findutils_4.8.0-1ubuntu2 fontconfig-config_2.13.1-4.2ubuntu4 fonts-dejavu-core_2.37-2build1 g++_4:11.2.0-1ubuntu1 g++-11_11.2.0-16ubuntu1 gcc_4:11.2.0-1ubuntu1 gcc-11_11.2.0-16ubuntu1 gcc-11-base_11.2.0-16ubuntu1 gettext_0.21-4ubuntu3 gettext-base_0.21-4ubuntu3 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+------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: pdb2pqr Binary: pdb2pqr, pdb2pqr-doc Architecture: any all Version: 2.1.1+dfsg-8 Maintainer: Debian Med Packaging Team Uploaders: Steffen Moeller , Manuel Prinz , Andreas Tille Homepage: https://www.poissonboltzmann.org Standards-Version: 4.5.0 Vcs-Browser: https://salsa.debian.org/med-team/pdb2pqr Vcs-Git: https://salsa.debian.org/med-team/pdb2pqr.git Testsuite: autopkgtest Testsuite-Triggers: python3-networkx Build-Depends: debhelper-compat (= 12), dh-python, gfortran, swig, xmlto, openbabel, python3-dev, python3-numpy, scons (>= 3.1.1-4), dos2unix, pkg-config Package-List: pdb2pqr deb science optional arch=any pdb2pqr-doc deb doc optional arch=all Checksums-Sha1: f32a6fdea111872ca6b3467f742f98dfdac91c7e 5191276 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do_not_try_to_build_removed_js_target.patch dpkg-source: info: applying fix_hardening_no_relro dpkg-source: info: applying fix_no_debug_symbols_warning dpkg-source: info: applying spelling.patch dpkg-source: info: applying python3_PR516.patch dpkg-source: info: applying python3_scons.patch dpkg-source: info: applying python3_sundry.patch dpkg-source: info: applying python3_scriptbang.patch dpkg-source: info: applying use_pkg-config.patch dpkg-source: info: applying reproducible-build.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-23155576 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-23155576 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-23155576 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 pdb2pqr dpkg-buildpackage: info: source version 2.1.1+dfsg-8 dpkg-buildpackage: info: source distribution unstable dpkg-source --before-build . dpkg-buildpackage: info: host architecture riscv64 debian/rules clean dh clean --with python3 debian/rules override_dh_auto_clean make[1]: Entering directory '/<>' ( cd pdb2pka && \ if [ -e pMC_mult_wrap.cpp.saved ]; then mv pMC_mult_wrap.cpp.saved pMC_mult_wrap.cpp; fi && \ if [ -e pMC_mult.py.saved ]; then mv pMC_mult.py.saved pMC_mult.py; fi ) find . -name *.pyc -delete find . -name *.so -delete find . -name *.os -delete rm -f *.cgi .sconsign.dblite .variables.cache pdb2pqr.py html/server.html src/aconf.py dh_auto_clean make[1]: Leaving directory '/<>' dh_clean debian/rules binary-arch dh binary-arch --with python3 dh_update_autotools_config -a dh_autoreconf -a debian/rules override_dh_auto_configure make[1]: Entering directory '/<>' dh_auto_configure ( cd pdb2pka && \ cp -a pMC_mult_wrap.cpp pMC_mult_wrap.cpp.saved && \ cp -a pMC_mult.py pMC_mult.py.saved && \ swig -c++ -python -o pMC_mult_wrap.cpp pMC_mult.i ) scons \ URL="http://localhost/pdb2pqr/" \ PREFIX="/usr/share/pdb2pqr" No entry for terminal type "unknown"; using dumb terminal settings. scons: Reading SConscript files ... not using opal scons: done reading SConscript files. scons: Building targets ... CopySubAction("pdb2pqr.py", "pdb2pqr.py.in") Chmod("pdb2pqr.py", 0755) CopySubAction("apbs_cgi.cgi", "apbs_cgi.py") Chmod("apbs_cgi.cgi", 0755) CopySubAction("visualize.cgi", "visualize.py") Chmod("visualize.cgi", 0755) CopySubAction("querystatus.cgi", "querystatus.py") Chmod("querystatus.cgi", 0755) CopySubAction("src/aconf.py", "src/aconf.py.in") CopySubAction("html/server.html", "html/server.html.in") Copy("pdb2pqr.cgi", "pdb2pqr.py") g++ -o pdb2pka/substruct/Algorithms.os -c -g -fPIC -I/usr/include/python3.10 -I/usr/include/riscv64-linux-gnu/python3.10 -I/usr/include/python3.10 -I/usr/lib/python3/dist-packages/numpy/core/include pdb2pka/substruct/Algorithms.cpp In file included from /usr/include/python3.10/numpy/ndarraytypes.h:1969, from /usr/include/python3.10/numpy/ndarrayobject.h:12, from /usr/include/python3.10/numpy/arrayobject.h:4, from pdb2pka/substruct/Algorithms.cpp:43: /usr/include/python3.10/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 17 | #warning "Using deprecated NumPy API, disable it with " \ | ^~~~~~~ pdb2pka/substruct/Algorithms.cpp: In function 'PyObject* initAlgorithms()': pdb2pka/substruct/Algorithms.cpp:333:1: warning: control reaches end of non-void function [-Wreturn-type] 333 | }; | ^ g++ -o pdb2pka/substruct/Algorithms.cpython-310-riscv64-linux-gnu.so -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -shared pdb2pka/substruct/Algorithms.os -L/usr/lib/riscv64-linux-gnu g++ -o pdb2pka/pMC_mult.os -c -g -fPIC -I/usr/include/python3.10 -I/usr/include/riscv64-linux-gnu/python3.10 -I/usr/include/python3.10 -I/usr/lib/python3/dist-packages/numpy/core/include pdb2pka/pMC_mult.cpp g++ -o pdb2pka/pMC_mult_wrap.os -c -g -fPIC -I/usr/include/python3.10 -I/usr/include/riscv64-linux-gnu/python3.10 -I/usr/include/python3.10 -I/usr/lib/python3/dist-packages/numpy/core/include pdb2pka/pMC_mult_wrap.cpp g++ -o pdb2pka/_pMC_mult.cpython-310-riscv64-linux-gnu.so -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -shared pdb2pka/pMC_mult.os pdb2pka/pMC_mult_wrap.os -L/usr/lib/riscv64-linux-gnu scons: done building targets. TARGETS: ['pdb2pqr.py', 'apbs_cgi.cgi', 'visualize.cgi', 'querystatus.cgi', 'src/aconf.py', 'html/server.html', 'pdb2pqr.cgi', 'pdb2pka/substruct/Algorithms.cpython-310-riscv64-linux-gnu.so', 'pdb2pka/_pMC_mult.cpython-310-riscv64-linux-gnu.so'] ======================== Configuration Parameters ======================== Version: 2.1.1 Install directory: /usr/share/pdb2pqr/ pdb2pka and ligand support: True Path to the website directory: http://localhost/pdb2pqr/ PDB2PQR jobs run via the web interface will be forked on the server. The preferred way to configure the build is by editing the file build_config.py Run scons with the python3 that you intend to use with pdb2pqr. For example: "scons" will setup pdb2pqr to be run with Debian default Python3 interpreter Run "scons install" to install pdb2pqr in /usr/share/pdb2pqr/ Run "scons basic-test" for a basic functionality test Run "scons advanced-test" for a single test of ligand and PROPKA support. Requires numpy and PDB2PKA support compiled. Run "scons complete-test" for a complete test of all functionality EXCEPT PDB2PKA. Requires numpy and PDB2PKA support compiled. Run "scons pdb2pka-test" for a test of PDB2PKA functionality. Requires numpy, PDB2PKA support compiled AND the APBS python3 libraries compiled and installed in the pdb2pka directory. To setup a web service create a symbolic link to /usr/share/pdb2pqr/ that enables you to view http://localhost/pdb2pqr/ after running "scons install" Run "scons msvs" to build Visual Studio projects for the Algorithms and pMC_mult modules. VS project generation is not well supported in scons. Resulting projects should build using NMAKE but cannot be used for debugging. The resulting projects will need to modified to use VS natively to compile the code or debug. Build succeeded. make[1]: Leaving directory '/<>' create-stamp debian/debhelper-build-stamp dh_prep -a dh_installdirs -a debian/rules override_dh_install-arch make[1]: Entering directory '/<>' dh_install -a dos2unix debian/pdb2pqr/usr/share/pdb2pqr/propka30/propka.py dos2unix: converting file debian/pdb2pqr/usr/share/pdb2pqr/propka30/propka.py to Unix format... dos2unix debian/pdb2pqr/usr/share/pdb2pqr/src/psize.py dos2unix: converting file debian/pdb2pqr/usr/share/pdb2pqr/src/psize.py to Unix format... make[1]: Leaving directory '/<>' dh_installdocs -a debian/rules override_dh_installchangelogs make[1]: Entering directory '/<>' dh_installchangelogs ChangeLog.md make[1]: Leaving directory '/<>' debian/rules override_dh_installexamples make[1]: Entering directory '/<>' dh_installexamples for bakerdoc in $( grep -l "http://agave.wustl.edu/css/baker.css" -R debian/pdb2pqr-doc/usr/share/doc/pdb2pqr/* ); do \ sed "s|href=\"http://agave.wustl.edu/css/baker.css\"|href=\"baker.css\"|g" -i $bakerdoc; done grep: debian/pdb2pqr-doc/usr/share/doc/pdb2pqr/*: No such file or directory make[1]: Leaving directory '/<>' debian/rules override_dh_installman-arch make[1]: Entering directory '/<>' dh_installman -a xmlto -o debian/pdb2pqr/usr/share/man/man1/ man debian/pdb2pqr.1.xml Note: Writing pdb2pqr.1 xmlto -o debian/pdb2pqr/usr/share/man/man1/ man debian/psize.1.xml Note: Writing psize.1 xmlto -o debian/pdb2pqr/usr/share/man/man1/ man debian/propka.1.xml Note: Writing propka.1 make[1]: Leaving directory '/<>' dh_python3 -a dh_perl -a debian/rules override_dh_link-arch make[1]: Entering directory '/<>' dh_link -a dh_link -a usr/lib/pdb2pqr/pdb2pka/_pMC_mult.cpython-310-riscv64-linux-gnu.so usr/share/pdb2pqr/pdb2pka/_pMC_mult.so dh_link -a usr/lib/pdb2pqr/pdb2pka/substruct/Algorithms.cpython-310-riscv64-linux-gnu.so usr/share/pdb2pqr/pdb2pka/substruct/Algorithms.so make[1]: Leaving directory '/<>' dh_strip_nondeterminism -a dh_compress -a debian/rules override_dh_fixperms-arch make[1]: Entering directory '/<>' dh_fixperms -a chmod 0644 debian/pdb2pqr/usr/share/pdb2pqr/main.py chmod 0644 debian/pdb2pqr/usr/share/pdb2pqr/main_cgi.py chmod 0644 debian/pdb2pqr/usr/share/pdb2pqr/pdb2pka/ligandclean/__init__.py chmod 0644 debian/pdb2pqr/usr/share/pdb2pqr/pdb2pka/pka_routines.py chmod 0644 debian/pdb2pqr/usr/share/pdb2pqr/pdb2pka/pKaIO_compat.py chmod 0644 debian/pdb2pqr/usr/share/pdb2pqr/pdb2pka/pKa_utility_functions_compat.py chmod 0644 debian/pdb2pqr/usr/share/pdb2pqr/src/errors.py chmod +x debian/pdb2pqr/usr/share/pdb2pqr/propka30/propka.py chmod +x debian/pdb2pqr/usr/share/pdb2pqr/src/psize.py make[1]: Leaving directory '/<>' dh_missing -a dh_dwz -a dh_strip -a debugedit: debian/pdb2pqr/usr/lib/pdb2pqr/pdb2pka/_pMC_mult.cpython-310-riscv64-linux-gnu.so: Unknown DWARF DW_FORM_0x1f20 5671750ae64835c4187aee793673d190b1ad22d9 debugedit: debian/pdb2pqr/usr/lib/pdb2pqr/pdb2pka/substruct/Algorithms.cpython-310-riscv64-linux-gnu.so: Unknown DWARF DW_FORM_0x1f21 e5390abe75c89d2ad8f65a92cc1db0b3e78a0753 dh_makeshlibs -a dh_shlibdeps -a dh_installdeb -a dh_gencontrol -a dh_md5sums -a dh_builddeb -a INFO: pkgstriptranslations version 149 INFO: pkgstriptranslations version 149 pkgstriptranslations: processing pdb2pqr (in debian/pdb2pqr); do_strip: , oemstrip: pkgstriptranslations: processing pdb2pqr-dbgsym (in debian/.debhelper/pdb2pqr/dbgsym-root); do_strip: , oemstrip: pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/pdb2pqr/DEBIAN/control, package pdb2pqr, directory debian/pdb2pqr .. removing usr/share/doc/pdb2pqr/changelog.gz pkgstripfiles: processing control file: debian/.debhelper/pdb2pqr/dbgsym-root/DEBIAN/control, package pdb2pqr-dbgsym, directory debian/.debhelper/pdb2pqr/dbgsym-root dpkg-deb: building package 'pdb2pqr-dbgsym' in 'debian/.debhelper/scratch-space/build-pdb2pqr/pdb2pqr-dbgsym_2.1.1+dfsg-8_riscv64.deb'. pkgstripfiles: Truncating usr/share/doc/pdb2pqr/changelog.Debian.gz to topmost ten records pkgstripfiles: Running PNG optimization (using 8 cpus) for package pdb2pqr ... pkgstripfiles: No PNG files. dpkg-deb: building package 'pdb2pqr' in '../pdb2pqr_2.1.1+dfsg-8_riscv64.deb'. Renaming pdb2pqr-dbgsym_2.1.1+dfsg-8_riscv64.deb to pdb2pqr-dbgsym_2.1.1+dfsg-8_riscv64.ddeb dpkg-genbuildinfo --build=any -O../pdb2pqr_2.1.1+dfsg-8_riscv64.buildinfo dpkg-genchanges --build=any -mLaunchpad Build Daemon -O../pdb2pqr_2.1.1+dfsg-8_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 2022-02-11T02:28:48Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ pdb2pqr_2.1.1+dfsg-8_riscv64.changes: ------------------------------------- Format: 1.8 Date: Thu, 10 Feb 2022 09:28:48 -0500 Source: pdb2pqr Binary: pdb2pqr Built-For-Profiles: noudeb Architecture: riscv64 Version: 2.1.1+dfsg-8 Distribution: jammy-proposed Urgency: medium Maintainer: Launchpad Build Daemon Changed-By: Andrius Merkys Description: pdb2pqr - Preparation of protein structures for electrostatics calculations Changes: pdb2pqr (2.1.1+dfsg-8) unstable; urgency=medium . * Team upload. * Add an autopkgtest for propka. * Fix Python problem causing crashes in propka. * Source moved to GitHub. 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/<>/pdb2pqr_2.1.1+dfsg-8_riscv64.changes: Illegal seek Distribution field may be wrong!!! +------------------------------------------------------------------------------+ | Buildinfo | +------------------------------------------------------------------------------+ Format: 1.0 Source: pdb2pqr Binary: pdb2pqr pdb2pqr-dbgsym Architecture: riscv64 Version: 2.1.1+dfsg-8 Checksums-Md5: d7de7635c73c00b58221387cc0de09a6 307788 pdb2pqr-dbgsym_2.1.1+dfsg-8_riscv64.ddeb 8410f96918fc2fe38e7ab68ff2142069 428004 pdb2pqr_2.1.1+dfsg-8_riscv64.deb Checksums-Sha1: 5ac442682dfbc65b965ddda98478dc1a697fb099 307788 pdb2pqr-dbgsym_2.1.1+dfsg-8_riscv64.ddeb 67a994cf7789969b122d0b6cfc4982a226000764 428004 pdb2pqr_2.1.1+dfsg-8_riscv64.deb Checksums-Sha256: 0fa1c1c7da7205dbc3d0a2612eef1ac4c63c4dbde6a7e285d428d66601a8322e 307788 pdb2pqr-dbgsym_2.1.1+dfsg-8_riscv64.ddeb 0fbf513f36049ff2f9971c3055cd3c620035bcc376030c443a501231d02fd386 428004 pdb2pqr_2.1.1+dfsg-8_riscv64.deb Build-Origin: Ubuntu Build-Architecture: riscv64 Build-Date: Fri, 11 Feb 2022 02:28:42 +0000 Build-Path: /<> Build-Tainted-By: merged-usr-via-aliased-dirs usr-local-has-programs Installed-Build-Depends: autoconf (= 2.71-2), automake (= 1:1.16.5-1.1), autopoint (= 0.21-4ubuntu3), autotools-dev (= 20220109.1), base-files (= 12ubuntu2), base-passwd (= 3.5.52), bash (= 5.1-6ubuntu1), binutils (= 2.38-1ubuntu1), binutils-common (= 2.38-1ubuntu1), binutils-riscv64-linux-gnu (= 2.38-1ubuntu1), bsdextrautils (= 2.37.2-4ubuntu1), bsdutils (= 1:2.37.2-4ubuntu1), build-essential (= 12.9ubuntu2), bzip2 (= 1.0.8-5), coreutils (= 8.32-4.1ubuntu1), cpp (= 4:11.2.0-1ubuntu1), cpp-11 (= 11.2.0-16ubuntu1), dash (= 0.5.11+git20210903+057cd650a4ed-3), debconf (= 1.5.79), debhelper (= 13.5.2ubuntu1), debianutils (= 5.5-1ubuntu1), debugedit (= 1:5.0-4), dh-autoreconf (= 20), dh-python (= 5.20220119), dh-strip-nondeterminism (= 1.13.0-1), diffutils (= 1:3.8-0ubuntu1), docbook-xml (= 4.5-11), docbook-xsl (= 1.79.2+dfsg-1), dos2unix (= 7.4.2-2), dpkg (= 1.21.1ubuntu1), dpkg-dev (= 1.21.1ubuntu1), dwz (= 0.14-1build1), file (= 1:5.41-2), findutils (= 4.8.0-1ubuntu2), fontconfig-config (= 2.13.1-4.2ubuntu4), fonts-dejavu-core (= 2.37-2build1), g++ (= 4:11.2.0-1ubuntu1), g++-11 (= 11.2.0-16ubuntu1), gcc (= 4:11.2.0-1ubuntu1), gcc-11 (= 11.2.0-16ubuntu1), gcc-11-base (= 11.2.0-16ubuntu1), gettext (= 0.21-4ubuntu3), gettext-base (= 0.21-4ubuntu3), gfortran (= 4:11.2.0-1ubuntu1), gfortran-11 (= 11.2.0-16ubuntu1), grep (= 3.7-1), groff-base (= 1.22.4-8), gzip (= 1.10-4ubuntu2), hostname (= 3.23ubuntu1), init-system-helpers (= 1.61), intltool-debian (= 0.35.0+20060710.5), libacl1 (= 2.3.1-1), libarchive-zip-perl (= 1.68-1), libasan6 (= 11.2.0-16ubuntu1), libatomic1 (= 11.2.0-16ubuntu1), libattr1 (= 1:2.5.1-1), libaudit-common (= 1:3.0-2ubuntu3), libaudit1 (= 1:3.0-2ubuntu3), libbinutils (= 2.38-1ubuntu1), libblas3 (= 3.10.0-2ubuntu1), libblkid1 (= 2.37.2-4ubuntu1), libboost-iostreams1.74.0 (= 1.74.0-14ubuntu2), libbrotli1 (= 1.0.9-2build4), libbsd0 (= 0.11.5-1), libbz2-1.0 (= 1.0.8-5), libc-bin (= 2.35-0ubuntu1), libc-dev-bin (= 2.35-0ubuntu1), libc6 (= 2.35-0ubuntu1), libc6-dev (= 2.35-0ubuntu1), libcairo2 (= 1.16.0-5ubuntu2), libcap-ng0 (= 0.7.9-2.2build3), libcap2 (= 1:2.44-1build2), libcc1-0 (= 11.2.0-16ubuntu1), libcom-err2 (= 1.46.5-2ubuntu1), libcrypt-dev (= 1:4.4.27-1), libcrypt1 (= 1:4.4.27-1), libctf-nobfd0 (= 2.38-1ubuntu1), libctf0 (= 2.38-1ubuntu1), libdb5.3 (= 5.3.28+dfsg1-0.8ubuntu2), libdebconfclient0 (= 0.261ubuntu1), libdebhelper-perl (= 13.5.2ubuntu1), libdpkg-perl (= 1.21.1ubuntu1), libdw1 (= 0.186-1), libedit2 (= 3.1-20210910-1), libelf1 (= 0.186-1), libexpat1 (= 2.4.4-1), libexpat1-dev (= 2.4.4-1), libffi8 (= 3.4.2-4), libfile-stripnondeterminism-perl (= 1.13.0-1), libfontconfig1 (= 2.13.1-4.2ubuntu4), libfreetype6 (= 2.11.1+dfsg-1), libgcc-11-dev (= 11.2.0-16ubuntu1), libgcc-s1 (= 11.2.0-16ubuntu1), libgcrypt20 (= 1.9.4-3ubuntu2), libgdbm-compat4 (= 1.23-1), libgdbm6 (= 1.23-1), libgfortran-11-dev (= 11.2.0-16ubuntu1), libgfortran5 (= 11.2.0-16ubuntu1), libglib2.0-0 (= 2.71.1-1), libgmp10 (= 2:6.2.1+dfsg-3ubuntu1), libgomp1 (= 11.2.0-16ubuntu1), libgpg-error0 (= 1.43-3), libgssapi-krb5-2 (= 1.19.2-1), libicu70 (= 70.1-2), libinchi1 (= 1.03+dfsg-4), libisl23 (= 0.24-2), libjs-jquery (= 3.5.1+dfsg+~3.5.5-8), libjs-sphinxdoc (= 4.3.2-1), libjs-underscore (= 1.13.2~dfsg-2), libk5crypto3 (= 1.19.2-1), libkeyutils1 (= 1.6.1-2ubuntu2), libkrb5-3 (= 1.19.2-1), libkrb5support0 (= 1.19.2-1), liblapack3 (= 3.10.0-2ubuntu1), liblz4-1 (= 1.9.3-2build1), liblzma5 (= 5.2.5-2build1), libmaeparser1 (= 1.2.4-1build1), libmagic-mgc (= 1:5.41-2), libmagic1 (= 1:5.41-2), libmd0 (= 1.0.4-1), libmount1 (= 2.37.2-4ubuntu1), libmpc3 (= 1.2.1-1), libmpdec3 (= 2.5.1-2build1), libmpfr6 (= 4.1.0-3build2), libncursesw6 (= 6.3-2), libnsl-dev (= 1.3.0-2build1), libnsl2 (= 1.3.0-2build1), libopenbabel7 (= 3.1.1+dfsg-6ubuntu5), libpam-modules (= 1.4.0-11ubuntu1), libpam-modules-bin (= 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3.10.1-0ubuntu1), python3-dev (= 3.10.1-0ubuntu1), python3-distutils (= 3.9.10-1), python3-lib2to3 (= 3.9.10-1), python3-minimal (= 3.10.1-0ubuntu1), python3-numpy (= 1:1.21.5-1), python3-pkg-resources (= 59.6.0-1.2), python3.10 (= 3.10.2-1), python3.10-dev (= 3.10.2-1), python3.10-minimal (= 3.10.2-1), python3.9 (= 3.9.10-1), python3.9-minimal (= 3.9.10-1), readline-common (= 8.1.2-1), rpcsvc-proto (= 1.4.2-0ubuntu5), scons (= 4.0.1+dfsg-2), sed (= 4.8-1ubuntu1), sensible-utils (= 0.0.17), sgml-base (= 1.30), sgml-data (= 2.0.11+nmu1), swig (= 4.0.2-1ubuntu1), swig4.0 (= 4.0.2-1ubuntu1), sysvinit-utils (= 3.01-1ubuntu1), tar (= 1.34+dfsg-1build2), tzdata (= 2021e-1ubuntu1), ucf (= 3.0043), util-linux (= 2.37.2-4ubuntu1), xml-core (= 0.18+nmu1), xmlto (= 0.0.28-2.1), xsltproc (= 1.1.34-4build1), xz-utils (= 5.2.5-2build1), zlib1g (= 1:1.2.11.dfsg-2ubuntu7), zlib1g-dev (= 1:1.2.11.dfsg-2ubuntu7) Environment: DEB_BUILD_OPTIONS="nocheck parallel=8" DEB_BUILD_PROFILES="noudeb" LANG="C.UTF-8" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1644503328" +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ pdb2pqr_2.1.1+dfsg-8_riscv64.deb -------------------------------- new Debian package, version 2.0. size 428004 bytes: control archive=4851 bytes. 1448 bytes, 29 lines control 9616 bytes, 129 lines md5sums 291 bytes, 12 lines * postinst #!/bin/sh 404 bytes, 12 lines * prerm #!/bin/sh Package: pdb2pqr Version: 2.1.1+dfsg-8 Architecture: riscv64 Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 2927 Depends: libc6 (>= 2.27), libgcc-s1 (>= 3.0), libstdc++6 (>= 11), python3 (<< 3.11), python3 (>= 3.10~), python3:any, python3-numpy, python3-networkx Suggests: apbs Enhances: autodocktools Replaces: propka Provides: propka Section: science Priority: optional Homepage: https://www.poissonboltzmann.org Description: Preparation of protein structures for electrostatics calculations PDB2PQR is a Python software package that automates many of the common tasks of preparing structures for continuum electrostatics calculations. It thus provides a platform-independent utility for converting protein files in PDB format to PQR format. These tasks include: * Adding a limited number of missing heavy atoms to biomolecular structures * Determining side-chain pKas * Placing missing hydrogens * Optimizing the protein for favorable hydrogen bonding * Assigning charge and radius parameters from a variety of force fields . This package also includes PropKa, a tool to modify the protonation state of protein structures in the Protein Data Bank (PDB) format to match a given pKa value. It can also be used to refine NMR structures, which often yield inaccurate pKa values for some residues. drwxr-xr-x root/root 0 2022-02-10 14:28 ./ drwxr-xr-x root/root 0 2022-02-10 14:28 ./usr/ drwxr-xr-x root/root 0 2022-02-10 14:28 ./usr/bin/ lrwxrwxrwx root/root 0 2022-02-10 14:28 ./usr/bin/pdb2pqr -> ../share/pdb2pqr/pdb2pqr.py lrwxrwxrwx root/root 0 2022-02-10 14:28 ./usr/bin/propka -> ../share/pdb2pqr/propka30/propka.py lrwxrwxrwx root/root 0 2022-02-10 14:28 ./usr/bin/psize -> ../share/pdb2pqr/src/psize.py drwxr-xr-x root/root 0 2022-02-10 14:28 ./usr/lib/ drwxr-xr-x root/root 0 2022-02-10 14:28 ./usr/lib/pdb2pqr/ drwxr-xr-x root/root 0 2022-02-10 14:28 ./usr/lib/pdb2pqr/pdb2pka/ -rw-r--r-- root/root 664744 2022-02-10 14:28 ./usr/lib/pdb2pqr/pdb2pka/_pMC_mult.cpython-310-riscv64-linux-gnu.so drwxr-xr-x root/root 0 2022-02-10 14:28 ./usr/lib/pdb2pqr/pdb2pka/substruct/ -rw-r--r-- root/root 15472 2022-02-10 14:28 ./usr/lib/pdb2pqr/pdb2pka/substruct/Algorithms.cpython-310-riscv64-linux-gnu.so drwxr-xr-x root/root 0 2022-02-10 14:28 ./usr/share/ drwxr-xr-x root/root 0 2022-02-10 14:28 ./usr/share/doc/ drwxr-xr-x root/root 0 2022-02-10 14:28 ./usr/share/doc/pdb2pqr/ -rw-r--r-- root/root 31 2016-02-18 19:56 ./usr/share/doc/pdb2pqr/AUTHORS -rw-r--r-- root/root 175 2016-02-18 19:56 ./usr/share/doc/pdb2pqr/NEWS.gz -rw-r--r-- root/root 783 2022-02-10 13:59 ./usr/share/doc/pdb2pqr/README.Debian -rw-r--r-- root/root 688 2016-02-18 19:56 ./usr/share/doc/pdb2pqr/README.md -rw-r--r-- root/root 1873 2022-02-10 14:28 ./usr/share/doc/pdb2pqr/changelog.Debian.gz -rw-r--r-- root/root 5186 2022-02-10 13:59 ./usr/share/doc/pdb2pqr/copyright drwxr-xr-x root/root 0 2022-02-10 14:28 ./usr/share/man/ drwxr-xr-x root/root 0 2022-02-10 14:28 ./usr/share/man/man1/ -rw-r--r-- root/root 2082 2022-02-10 14:28 ./usr/share/man/man1/pdb2pqr.1.gz -rw-r--r-- root/root 1044 2022-02-10 14:28 ./usr/share/man/man1/propka.1.gz 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+------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: riscv64 Build Type: any Build-Space: 61656 Build-Time: 284 Distribution: jammy-proposed Host Architecture: riscv64 Install-Time: 498 Job: pdb2pqr_2.1.1+dfsg-8.dsc Machine Architecture: riscv64 Package: pdb2pqr Package-Time: 817 Source-Version: 2.1.1+dfsg-8 Space: 61656 Status: successful Version: 2.1.1+dfsg-8 -------------------------------------------------------------------------------- Finished at 2022-02-11T02:28:48Z Build needed 00:13:37, 61656k disk space Adding user buildd to group lxd RUN: /usr/share/launchpad-buildd/bin/in-target scan-for-processes --backend=chroot --series=jammy --arch=riscv64 PACKAGEBUILD-23155576 Scanning for processes to kill in build PACKAGEBUILD-23155576 RUN: /usr/share/launchpad-buildd/bin/in-target umount-chroot --backend=chroot --series=jammy --arch=riscv64 PACKAGEBUILD-23155576 Stopping target for build PACKAGEBUILD-23155576 RUN: /usr/share/launchpad-buildd/bin/in-target remove-build --backend=chroot --series=jammy --arch=riscv64 PACKAGEBUILD-23155576 Removing build PACKAGEBUILD-23155576