https://launchpad.net/ubuntu/+source/murasaki/1.68.6-13build2/+build/23595945 RUN: /usr/share/launchpad-buildd/bin/builder-prep Kernel version: Linux riscv64-qemu-lcy01-012 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_212~550~ubuntu20.04.1 python3-lpbuildd_212~550~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... 1 May 08:03:20 ntpdate[2709188]: adjust time server 10.211.37.1 offset -0.002204 sec RUN: /usr/share/launchpad-buildd/bin/in-target unpack-chroot --backend=chroot --series=kinetic --arch=riscv64 PACKAGEBUILD-23595945 --image-type chroot /home/buildd/filecache-default/6534a4ff757521d8f8bbfb46d24688ecd71c00f8 Creating target for build PACKAGEBUILD-23595945 RUN: /usr/share/launchpad-buildd/bin/in-target mount-chroot --backend=chroot --series=kinetic --arch=riscv64 PACKAGEBUILD-23595945 Starting target for build PACKAGEBUILD-23595945 RUN: /usr/share/launchpad-buildd/bin/in-target override-sources-list --backend=chroot --series=kinetic --arch=riscv64 PACKAGEBUILD-23595945 '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-23595945 RUN: /usr/share/launchpad-buildd/bin/in-target update-debian-chroot --backend=chroot --series=kinetic --arch=riscv64 PACKAGEBUILD-23595945 Updating target for build PACKAGEBUILD-23595945 Get:1 http://ftpmaster.internal/ubuntu kinetic InRelease [224 kB] Get:2 http://ftpmaster.internal/ubuntu kinetic-security InRelease [74.9 kB] Get:3 http://ftpmaster.internal/ubuntu kinetic-updates InRelease [74.9 kB] Get:4 http://ftpmaster.internal/ubuntu kinetic-proposed InRelease [74.9 kB] Get:5 http://ftpmaster.internal/ubuntu kinetic/main riscv64 Packages [1289 kB] Get:6 http://ftpmaster.internal/ubuntu kinetic/main Translation-en [511 kB] Get:7 http://ftpmaster.internal/ubuntu kinetic/universe riscv64 Packages [12.9 MB] Get:8 http://ftpmaster.internal/ubuntu kinetic/universe Translation-en [5652 kB] Get:9 http://ftpmaster.internal/ubuntu kinetic-proposed/main riscv64 Packages [183 kB] Get:10 http://ftpmaster.internal/ubuntu kinetic-proposed/main Translation-en [83.8 kB] Get:11 http://ftpmaster.internal/ubuntu kinetic-proposed/universe riscv64 Packages [977 kB] Get:12 http://ftpmaster.internal/ubuntu kinetic-proposed/universe Translation-en [585 kB] Get:13 http://ftpmaster.internal/ubuntu kinetic-proposed/restricted riscv64 Packages [720 B] Get:14 http://ftpmaster.internal/ubuntu kinetic-proposed/restricted Translation-en [6720 B] Get:15 http://ftpmaster.internal/ubuntu kinetic-proposed/multiverse riscv64 Packages [9232 B] Get:16 http://ftpmaster.internal/ubuntu kinetic-proposed/multiverse Translation-en [14.7 kB] Fetched 22.7 MB in 31s (727 kB/s) Reading package lists... W: Target Packages (main/binary-riscv64/Packages) is configured multiple times in /etc/apt/sources.list:4 and /etc/apt/sources.list.d/proposed.list:1 W: Target Packages (main/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:4 and /etc/apt/sources.list.d/proposed.list:1 W: Target Translations (main/i18n/Translation-en) is configured multiple times in /etc/apt/sources.list:4 and /etc/apt/sources.list.d/proposed.list:1 W: Target Packages (universe/binary-riscv64/Packages) is configured multiple times in /etc/apt/sources.list:4 and /etc/apt/sources.list.d/proposed.list:1 W: Target Packages (universe/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:4 and /etc/apt/sources.list.d/proposed.list:1 W: Target Translations (universe/i18n/Translation-en) is configured multiple times in /etc/apt/sources.list:4 and /etc/apt/sources.list.d/proposed.list:1 W: Target Packages (main/binary-riscv64/Packages) is configured multiple times in /etc/apt/sources.list:4 and /etc/apt/sources.list.d/proposed.list:1 W: Target Packages (main/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:4 and /etc/apt/sources.list.d/proposed.list:1 W: Target Translations (main/i18n/Translation-en) is configured multiple times in /etc/apt/sources.list:4 and /etc/apt/sources.list.d/proposed.list:1 W: Target Packages (universe/binary-riscv64/Packages) is configured multiple times in /etc/apt/sources.list:4 and /etc/apt/sources.list.d/proposed.list:1 W: Target Packages (universe/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:4 and /etc/apt/sources.list.d/proposed.list:1 W: Target Translations (universe/i18n/Translation-en) is configured multiple times in /etc/apt/sources.list:4 and /etc/apt/sources.list.d/proposed.list:1 Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages have been kept back: dash The following packages will be upgraded: cpp-11 g++-11 gcc-11 gcc-11-base gcc-12-base libasan6 libatomic1 libcc1-0 libgcc-11-dev libgcc-s1 libgnutls30 libgomp1 libgpg-error0 libjson-c5 libncurses6 libncursesw6 libp11-kit0 libpam-modules libpam-modules-bin libpam-runtime libpam0g libpcre2-8-0 libpcre3 libpng16-16 libreadline8 libsqlite3-0 libstdc++-11-dev libstdc++6 libtinfo6 libzstd1 linux-libc-dev lto-disabled-list ncurses-base ncurses-bin pinentry-curses readline-common 36 upgraded, 0 newly installed, 0 to remove and 1 not upgraded. Need to get 48.4 MB of archives. After this operation, 78.8 kB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu kinetic-proposed/main riscv64 ncurses-bin riscv64 6.3+20220423-1 [176 kB] Get:2 http://ftpmaster.internal/ubuntu kinetic-proposed/main riscv64 ncurses-base all 6.3+20220423-1 [21.4 kB] Get:3 http://ftpmaster.internal/ubuntu kinetic-proposed/main riscv64 libpam0g riscv64 1.4.0-13ubuntu1 [55.6 kB] Get:4 http://ftpmaster.internal/ubuntu kinetic-proposed/main riscv64 libpam-modules-bin riscv64 1.4.0-13ubuntu1 [36.9 kB] Get:5 http://ftpmaster.internal/ubuntu kinetic-proposed/main riscv64 libpam-modules riscv64 1.4.0-13ubuntu1 [263 kB] Get:6 http://ftpmaster.internal/ubuntu kinetic/main riscv64 libatomic1 riscv64 12-20220428-1ubuntu1 [7870 B] Get:7 http://ftpmaster.internal/ubuntu kinetic/main riscv64 gcc-12-base riscv64 12-20220428-1ubuntu1 [19.0 kB] Get:8 http://ftpmaster.internal/ubuntu kinetic/main riscv64 libstdc++6 riscv64 12-20220428-1ubuntu1 [690 kB] Get:9 http://ftpmaster.internal/ubuntu kinetic/main riscv64 libgomp1 riscv64 12-20220428-1ubuntu1 [111 kB] Get:10 http://ftpmaster.internal/ubuntu kinetic/main riscv64 libcc1-0 riscv64 12-20220428-1ubuntu1 [43.6 kB] Get:11 http://ftpmaster.internal/ubuntu kinetic/main riscv64 libgcc-s1 riscv64 12-20220428-1ubuntu1 [44.2 kB] Get:12 http://ftpmaster.internal/ubuntu kinetic-proposed/main riscv64 libgpg-error0 riscv64 1.45-2 [62.7 kB] Get:13 http://ftpmaster.internal/ubuntu kinetic-proposed/main riscv64 libpam-runtime all 1.4.0-13ubuntu1 [40.2 kB] Get:14 http://ftpmaster.internal/ubuntu kinetic-proposed/main riscv64 libpcre2-8-0 riscv64 10.40-1 [141 kB] Get:15 http://ftpmaster.internal/ubuntu kinetic-proposed/main riscv64 libpcre3 riscv64 2:8.39-14 [171 kB] Get:16 http://ftpmaster.internal/ubuntu kinetic-proposed/main riscv64 libncursesw6 riscv64 6.3+20220423-1 [128 kB] Get:17 http://ftpmaster.internal/ubuntu kinetic-proposed/main riscv64 libncurses6 riscv64 6.3+20220423-1 [93.6 kB] Get:18 http://ftpmaster.internal/ubuntu kinetic-proposed/main riscv64 libtinfo6 riscv64 6.3+20220423-1 [95.0 kB] Get:19 http://ftpmaster.internal/ubuntu kinetic-proposed/main riscv64 libzstd1 riscv64 1.5.2+dfsg-1 [318 kB] Get:20 http://ftpmaster.internal/ubuntu kinetic-proposed/main riscv64 libp11-kit0 riscv64 0.24.1-1 [205 kB] Get:21 http://ftpmaster.internal/ubuntu kinetic-proposed/main riscv64 libgnutls30 riscv64 3.7.4-2ubuntu1 [875 kB] Get:22 http://ftpmaster.internal/ubuntu kinetic/main riscv64 libjson-c5 riscv64 0.16-1 [29.3 kB] Get:23 http://ftpmaster.internal/ubuntu kinetic-proposed/main riscv64 readline-common all 8.1.2-1.2 [53.6 kB] Get:24 http://ftpmaster.internal/ubuntu kinetic-proposed/main riscv64 libreadline8 riscv64 8.1.2-1.2 [130 kB] Get:25 http://ftpmaster.internal/ubuntu kinetic-proposed/main riscv64 libsqlite3-0 riscv64 3.38.3-1 [572 kB] Get:26 http://ftpmaster.internal/ubuntu kinetic-proposed/main riscv64 libpng16-16 riscv64 1.6.37-5 [174 kB] Get:27 http://ftpmaster.internal/ubuntu kinetic/main riscv64 libasan6 riscv64 11.3.0-1ubuntu1 [2107 kB] Get:28 http://ftpmaster.internal/ubuntu kinetic/main riscv64 g++-11 riscv64 11.3.0-1ubuntu1 [9302 kB] Get:29 http://ftpmaster.internal/ubuntu kinetic/main riscv64 gcc-11 riscv64 11.3.0-1ubuntu1 [15.9 MB] Get:30 http://ftpmaster.internal/ubuntu kinetic/main riscv64 libstdc++-11-dev riscv64 11.3.0-1ubuntu1 [4775 kB] Get:31 http://ftpmaster.internal/ubuntu kinetic/main riscv64 libgcc-11-dev riscv64 11.3.0-1ubuntu1 [2396 kB] Get:32 http://ftpmaster.internal/ubuntu kinetic/main riscv64 cpp-11 riscv64 11.3.0-1ubuntu1 [7990 kB] Get:33 http://ftpmaster.internal/ubuntu kinetic/main riscv64 gcc-11-base riscv64 11.3.0-1ubuntu1 [21.1 kB] Get:34 http://ftpmaster.internal/ubuntu kinetic-proposed/main riscv64 linux-libc-dev riscv64 5.15.0-28.29 [1302 kB] Get:35 http://ftpmaster.internal/ubuntu kinetic/main riscv64 lto-disabled-list all 25 [12.6 kB] Get:36 http://ftpmaster.internal/ubuntu kinetic-proposed/main riscv64 pinentry-curses riscv64 1.2.0-1 [37.0 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 48.4 MB in 9s (5179 kB/s) (Reading database ... 13361 files and directories currently installed.) Preparing to unpack .../ncurses-bin_6.3+20220423-1_riscv64.deb ... Unpacking ncurses-bin (6.3+20220423-1) over (6.3-2) ... Setting up ncurses-bin (6.3+20220423-1) ... (Reading database ... 13361 files and directories currently installed.) Preparing to unpack .../ncurses-base_6.3+20220423-1_all.deb ... Unpacking ncurses-base (6.3+20220423-1) over (6.3-2) ... Setting up ncurses-base (6.3+20220423-1) ... (Reading database ... 13362 files and directories currently installed.) Preparing to unpack .../libpam0g_1.4.0-13ubuntu1_riscv64.deb ... Unpacking libpam0g:riscv64 (1.4.0-13ubuntu1) over (1.4.0-11ubuntu2) ... Setting up libpam0g:riscv64 (1.4.0-13ubuntu1) ... (Reading database ... 13362 files and directories currently installed.) Preparing to unpack .../libpam-modules-bin_1.4.0-13ubuntu1_riscv64.deb ... Unpacking libpam-modules-bin (1.4.0-13ubuntu1) over (1.4.0-11ubuntu2) ... Setting up libpam-modules-bin (1.4.0-13ubuntu1) ... 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Unpacking lto-disabled-list (25) over (24) ... Preparing to unpack .../14-pinentry-curses_1.2.0-1_riscv64.deb ... Unpacking pinentry-curses (1.2.0-1) over (1.1.1-1build2) ... Setting up gcc-11-base:riscv64 (11.3.0-1ubuntu1) ... Setting up lto-disabled-list (25) ... Setting up libsqlite3-0:riscv64 (3.38.3-1) ... Setting up linux-libc-dev:riscv64 (5.15.0-28.29) ... Setting up libgomp1:riscv64 (12-20220428-1ubuntu1) ... Setting up libasan6:riscv64 (11.3.0-1ubuntu1) ... Setting up libncurses6:riscv64 (6.3+20220423-1) ... Setting up libpng16-16:riscv64 (1.6.37-5) ... Setting up libatomic1:riscv64 (12-20220428-1ubuntu1) ... Setting up libncursesw6:riscv64 (6.3+20220423-1) ... Setting up libgcc-11-dev:riscv64 (11.3.0-1ubuntu1) ... Setting up libjson-c5:riscv64 (0.16-1) ... Setting up readline-common (8.1.2-1.2) ... Setting up libcc1-0:riscv64 (12-20220428-1ubuntu1) ... Setting up pinentry-curses (1.2.0-1) ... Setting up cpp-11 (11.3.0-1ubuntu1) ... Setting up libreadline8:riscv64 (8.1.2-1.2) ... Setting up libstdc++-11-dev:riscv64 (11.3.0-1ubuntu1) ... Setting up gcc-11 (11.3.0-1ubuntu1) ... Setting up g++-11 (11.3.0-1ubuntu1) ... Processing triggers for libc-bin (2.35-0ubuntu3) ... RUN: /usr/share/launchpad-buildd/bin/sbuild-package PACKAGEBUILD-23595945 riscv64 kinetic-proposed -c chroot:build-PACKAGEBUILD-23595945 --arch=riscv64 --dist=kinetic-proposed --nolog murasaki_1.68.6-13build2.dsc Initiating build PACKAGEBUILD-23595945 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-lcy01-012.buildd +==============================================================================+ | murasaki 1.68.6-13build2 (riscv64) Sun, 01 May 2022 08:08:14 +0000 | +==============================================================================+ Package: murasaki Version: 1.68.6-13build2 Source Version: 1.68.6-13build2 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-23595945/chroot-autobuild' with '<>' I: NOTICE: Log filtering will replace 'build/murasaki-8ehenC/resolver-IhTz0O' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- murasaki_1.68.6-13build2.dsc exists in .; copying to chroot I: NOTICE: Log filtering will replace 'build/murasaki-8ehenC/murasaki-1.68.6' with '<>' I: NOTICE: Log filtering will replace 'build/murasaki-8ehenC' with '<>' +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper-compat (= 13), libboost-regex-dev, libboost-iostreams-dev, libboost-filesystem-dev, libterm-readkey-perl, libtext-wrapper-perl, libcrypto++-dev, libpstreams-dev, libopenmpi-dev, build-essential, fakeroot Filtered Build-Depends: debhelper-compat (= 13), libboost-regex-dev, libboost-iostreams-dev, libboost-filesystem-dev, libterm-readkey-perl, libtext-wrapper-perl, libcrypto++-dev, libpstreams-dev, libopenmpi-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 [439 B] Get:5 copy:/<>/apt_archive ./ Packages [522 B] Fetched 1918 B in 1s (3076 B/s) Reading package lists... Reading package lists... W: Target Packages (main/binary-riscv64/Packages) is configured multiple times in /etc/apt/sources.list:4 and /etc/apt/sources.list.d/proposed.list:1 W: Target Packages (main/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:4 and /etc/apt/sources.list.d/proposed.list:1 W: Target Packages (universe/binary-riscv64/Packages) is configured multiple times in /etc/apt/sources.list:4 and /etc/apt/sources.list.d/proposed.list:1 W: Target Packages (universe/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:4 and /etc/apt/sources.list.d/proposed.list:1 Install main build dependencies (apt-based resolver) ---------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... 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 gfortran-11 groff-base ibverbs-providers icu-devtools intltool-debian libarchive-zip-perl libboost-filesystem-dev libboost-filesystem1.74-dev libboost-filesystem1.74.0 libboost-iostreams-dev libboost-iostreams1.74-dev libboost-iostreams1.74.0 libboost-regex-dev libboost-regex1.74-dev libboost-regex1.74.0 libboost-system1.74-dev libboost-system1.74.0 libboost1.74-dev libbrotli1 libbsd0 libcbor0.8 libcrypto++-dev libcrypto++8 libcurl3-gnutls libdebhelper-perl libdw1 libedit2 libelf1 libevent-2.1-7 libevent-core-2.1-7 libevent-dev libevent-extra-2.1-7 libevent-openssl-2.1-7 libevent-pthreads-2.1-7 libfabric1 libfido2-1 libfile-stripnondeterminism-perl libgfortran-11-dev libgfortran5 libhwloc-dev libhwloc-plugins libhwloc15 libibverbs-dev libibverbs1 libicu-dev libicu71 libjs-jquery libjs-jquery-ui libldap-2.5-0 libltdl-dev libltdl7 libmagic-mgc libmagic1 libmd0 libnghttp2-14 libnl-3-200 libnl-3-dev libnl-route-3-200 libnl-route-3-dev libnuma-dev libnuma1 libopenmpi-dev libopenmpi3 libpciaccess0 libpipeline1 libpmix-dev libpmix2 libpsl5 libpstreams-dev librdmacm1 librtmp1 libsasl2-2 libsasl2-modules-db libsigsegv2 libssh-4 libsub-override-perl libterm-readkey-perl libtext-wrapper-perl libtool libuchardet0 libx11-6 libx11-data libxau6 libxcb1 libxdmcp6 libxext6 libxml2 libxnvctrl0 m4 man-db ocl-icd-libopencl1 openmpi-bin openmpi-common openssh-client po-debconf zlib1g-dev Suggested packages: autoconf-archive gnu-standards autoconf-doc dh-make gettext-doc libasprintf-dev libgettextpo-dev gfortran-11-doc libcoarrays-dev groff 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-graph1.74-dev libboost-graph-parallel1.74-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-serialization1.74-dev libboost-stacktrace1.74-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 icu-doc libjs-jquery-ui-docs libtool-doc openmpi-doc pciutils gcj-jdk m4-doc apparmor less www-browser opencl-icd gfortran | fortran-compiler keychain libpam-ssh monkeysphere ssh-askpass libmail-box-perl Recommended packages: curl | wget | lynx libarchive-cpio-perl javascript-common libldap-common libcoarrays-openmpi-dev publicsuffix libsasl2-modules xauth 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 gfortran-11 groff-base ibverbs-providers icu-devtools intltool-debian libarchive-zip-perl libboost-filesystem-dev libboost-filesystem1.74-dev libboost-filesystem1.74.0 libboost-iostreams-dev libboost-iostreams1.74-dev libboost-iostreams1.74.0 libboost-regex-dev libboost-regex1.74-dev libboost-regex1.74.0 libboost-system1.74-dev libboost-system1.74.0 libboost1.74-dev libbrotli1 libbsd0 libcbor0.8 libcrypto++-dev libcrypto++8 libcurl3-gnutls libdebhelper-perl libdw1 libedit2 libelf1 libevent-2.1-7 libevent-core-2.1-7 libevent-dev libevent-extra-2.1-7 libevent-openssl-2.1-7 libevent-pthreads-2.1-7 libfabric1 libfido2-1 libfile-stripnondeterminism-perl libgfortran-11-dev libgfortran5 libhwloc-dev libhwloc-plugins libhwloc15 libibverbs-dev libibverbs1 libicu-dev libicu71 libjs-jquery libjs-jquery-ui libldap-2.5-0 libltdl-dev libltdl7 libmagic-mgc libmagic1 libmd0 libnghttp2-14 libnl-3-200 libnl-3-dev libnl-route-3-200 libnl-route-3-dev libnuma-dev libnuma1 libopenmpi-dev libopenmpi3 libpciaccess0 libpipeline1 libpmix-dev libpmix2 libpsl5 libpstreams-dev librdmacm1 librtmp1 libsasl2-2 libsasl2-modules-db libsigsegv2 libssh-4 libsub-override-perl libterm-readkey-perl libtext-wrapper-perl libtool libuchardet0 libx11-6 libx11-data libxau6 libxcb1 libxdmcp6 libxext6 libxml2 libxnvctrl0 m4 man-db ocl-icd-libopencl1 openmpi-bin openmpi-common openssh-client po-debconf sbuild-build-depends-main-dummy zlib1g-dev 0 upgraded, 110 newly installed, 0 to remove and 1 not upgraded. Need to get 81.4 MB of archives. After this operation, 508 MB of additional disk space will be used. Get:1 copy:/<>/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [742 B] Get:2 http://ftpmaster.internal/ubuntu kinetic/main riscv64 libmd0 riscv64 1.0.4-1build1 [30.1 kB] Get:3 http://ftpmaster.internal/ubuntu kinetic-proposed/main riscv64 libbsd0 riscv64 0.11.6-1 [40.7 kB] Get:4 http://ftpmaster.internal/ubuntu kinetic/main riscv64 libelf1 riscv64 0.186-1build1 [46.2 kB] Get:5 http://ftpmaster.internal/ubuntu kinetic/main riscv64 libicu71 riscv64 71.1-2 [10.6 MB] Get:6 http://ftpmaster.internal/ubuntu kinetic-proposed/main riscv64 libxml2 riscv64 2.9.13+dfsg-1build2 [605 kB] Get:7 http://ftpmaster.internal/ubuntu kinetic/main riscv64 bsdextrautils riscv64 2.37.2-4ubuntu3 [81.5 kB] Get:8 http://ftpmaster.internal/ubuntu kinetic-proposed/main riscv64 libmagic-mgc riscv64 1:5.41-4 [257 kB] Get:9 http://ftpmaster.internal/ubuntu kinetic-proposed/main riscv64 libmagic1 riscv64 1:5.41-4 [88.7 kB] Get:10 http://ftpmaster.internal/ubuntu kinetic-proposed/main riscv64 file riscv64 1:5.41-4 [20.6 kB] Get:11 http://ftpmaster.internal/ubuntu kinetic/main riscv64 gettext-base riscv64 0.21-4ubuntu4 [38.7 kB] Get:12 http://ftpmaster.internal/ubuntu kinetic/main riscv64 libuchardet0 riscv64 0.0.7-1build2 [78.9 kB] Get:13 http://ftpmaster.internal/ubuntu kinetic/main riscv64 groff-base riscv64 1.22.4-8build1 [925 kB] Get:14 http://ftpmaster.internal/ubuntu kinetic/main riscv64 libcbor0.8 riscv64 0.8.0-2ubuntu1 [20.7 kB] Get:15 http://ftpmaster.internal/ubuntu kinetic/main riscv64 libedit2 riscv64 3.1-20210910-1build1 [82.3 kB] Get:16 http://ftpmaster.internal/ubuntu kinetic/main riscv64 libfido2-1 riscv64 1.10.0-1 [72.6 kB] Get:17 http://ftpmaster.internal/ubuntu kinetic-proposed/main riscv64 libnghttp2-14 riscv64 1.47.0-1 [66.4 kB] Get:18 http://ftpmaster.internal/ubuntu kinetic/main riscv64 libnuma1 riscv64 2.0.14-3ubuntu2 [20.0 kB] Get:19 http://ftpmaster.internal/ubuntu kinetic-proposed/main riscv64 libpipeline1 riscv64 1.5.6-1 [26.1 kB] Get:20 http://ftpmaster.internal/ubuntu kinetic/main riscv64 libpsl5 riscv64 0.21.0-1.2build2 [57.3 kB] Get:21 http://ftpmaster.internal/ubuntu kinetic/main riscv64 libxau6 riscv64 1:1.0.9-1build5 [6836 B] Get:22 http://ftpmaster.internal/ubuntu kinetic/main riscv64 libxdmcp6 riscv64 1:1.1.3-0ubuntu5 [10.3 kB] Get:23 http://ftpmaster.internal/ubuntu kinetic/main riscv64 libxcb1 riscv64 1.14-3ubuntu3 [42.6 kB] Get:24 http://ftpmaster.internal/ubuntu kinetic/main riscv64 libx11-data all 2:1.7.5-1 [119 kB] Get:25 http://ftpmaster.internal/ubuntu kinetic/main riscv64 libx11-6 riscv64 2:1.7.5-1 [621 kB] Get:26 http://ftpmaster.internal/ubuntu kinetic/main riscv64 libxext6 riscv64 2:1.3.4-1build1 [27.8 kB] Get:27 http://ftpmaster.internal/ubuntu kinetic/main riscv64 man-db riscv64 2.10.2-1 [1144 kB] Get:28 http://ftpmaster.internal/ubuntu kinetic-proposed/main riscv64 openssh-client riscv64 1:9.0p1-1 [804 kB] Get:29 http://ftpmaster.internal/ubuntu kinetic/main riscv64 libsigsegv2 riscv64 2.13-1ubuntu3 [13.6 kB] Get:30 http://ftpmaster.internal/ubuntu kinetic/main riscv64 m4 riscv64 1.4.18-5ubuntu2 [193 kB] Get:31 http://ftpmaster.internal/ubuntu kinetic/main riscv64 autoconf all 2.71-2 [338 kB] Get:32 http://ftpmaster.internal/ubuntu kinetic/main riscv64 autotools-dev all 20220109.1 [44.9 kB] Get:33 http://ftpmaster.internal/ubuntu kinetic/main riscv64 automake all 1:1.16.5-1.3 [558 kB] Get:34 http://ftpmaster.internal/ubuntu kinetic/main riscv64 autopoint all 0.21-4ubuntu4 [422 kB] Get:35 http://ftpmaster.internal/ubuntu kinetic/main riscv64 libdebhelper-perl all 13.6ubuntu1 [67.2 kB] Get:36 http://ftpmaster.internal/ubuntu kinetic-proposed/main riscv64 libtool all 2.4.7-3 [166 kB] Get:37 http://ftpmaster.internal/ubuntu kinetic/main riscv64 dh-autoreconf all 20 [16.1 kB] Get:38 http://ftpmaster.internal/ubuntu kinetic/main riscv64 libarchive-zip-perl all 1.68-1 [90.2 kB] Get:39 http://ftpmaster.internal/ubuntu kinetic/main riscv64 libsub-override-perl all 0.09-2 [9532 B] Get:40 http://ftpmaster.internal/ubuntu kinetic/main riscv64 libfile-stripnondeterminism-perl all 1.13.0-1 [18.1 kB] Get:41 http://ftpmaster.internal/ubuntu kinetic/main riscv64 dh-strip-nondeterminism all 1.13.0-1 [5344 B] Get:42 http://ftpmaster.internal/ubuntu kinetic/main riscv64 libdw1 riscv64 0.186-1build1 [229 kB] Get:43 http://ftpmaster.internal/ubuntu kinetic/main riscv64 debugedit riscv64 1:5.0-4build1 [50.0 kB] Get:44 http://ftpmaster.internal/ubuntu kinetic/main riscv64 dwz riscv64 0.14-1build2 [105 kB] Get:45 http://ftpmaster.internal/ubuntu kinetic/main riscv64 gettext riscv64 0.21-4ubuntu4 [817 kB] Get:46 http://ftpmaster.internal/ubuntu kinetic/main riscv64 intltool-debian all 0.35.0+20060710.5 [24.9 kB] Get:47 http://ftpmaster.internal/ubuntu kinetic/main riscv64 po-debconf all 1.0.21+nmu1 [233 kB] Get:48 http://ftpmaster.internal/ubuntu kinetic/main riscv64 debhelper all 13.6ubuntu1 [923 kB] Get:49 http://ftpmaster.internal/ubuntu kinetic/main riscv64 libgfortran5 riscv64 12-20220428-1ubuntu1 [376 kB] Get:50 http://ftpmaster.internal/ubuntu kinetic/main riscv64 libgfortran-11-dev riscv64 11.3.0-1ubuntu1 [1157 kB] Get:51 http://ftpmaster.internal/ubuntu kinetic/main riscv64 gfortran-11 riscv64 11.3.0-1ubuntu1 [8495 kB] Get:52 http://ftpmaster.internal/ubuntu kinetic/main riscv64 libnl-3-200 riscv64 3.5.0-0.1 [50.4 kB] Get:53 http://ftpmaster.internal/ubuntu kinetic/main riscv64 libnl-route-3-200 riscv64 3.5.0-0.1 [158 kB] Get:54 http://ftpmaster.internal/ubuntu kinetic/main riscv64 libibverbs1 riscv64 39.0-1 [58.7 kB] Get:55 http://ftpmaster.internal/ubuntu kinetic/main riscv64 ibverbs-providers riscv64 39.0-1 [27.6 kB] Get:56 http://ftpmaster.internal/ubuntu kinetic/main riscv64 icu-devtools riscv64 71.1-2 [201 kB] Get:57 http://ftpmaster.internal/ubuntu kinetic-proposed/main riscv64 libboost1.74-dev riscv64 1.74.0-14ubuntu4 [9617 kB] Get:58 http://ftpmaster.internal/ubuntu kinetic-proposed/main riscv64 libboost-filesystem1.74.0 riscv64 1.74.0-14ubuntu4 [263 kB] Get:59 http://ftpmaster.internal/ubuntu kinetic-proposed/main riscv64 libboost-system1.74.0 riscv64 1.74.0-14ubuntu4 [220 kB] Get:60 http://ftpmaster.internal/ubuntu kinetic-proposed/main riscv64 libboost-system1.74-dev riscv64 1.74.0-14ubuntu4 [218 kB] Get:61 http://ftpmaster.internal/ubuntu kinetic-proposed/main riscv64 libboost-filesystem1.74-dev riscv64 1.74.0-14ubuntu4 [560 kB] Get:62 http://ftpmaster.internal/ubuntu kinetic/main riscv64 libboost-filesystem-dev riscv64 1.74.0.3ubuntu7 [3280 B] Get:63 http://ftpmaster.internal/ubuntu kinetic-proposed/main riscv64 libboost-regex1.74.0 riscv64 1.74.0-14ubuntu4 [497 kB] Get:64 http://ftpmaster.internal/ubuntu kinetic/main riscv64 libicu-dev riscv64 71.1-2 [16.8 MB] Get:65 http://ftpmaster.internal/ubuntu kinetic-proposed/main riscv64 libboost-regex1.74-dev riscv64 1.74.0-14ubuntu4 [2193 kB] Get:66 http://ftpmaster.internal/ubuntu kinetic-proposed/main riscv64 libboost-iostreams1.74.0 riscv64 1.74.0-14ubuntu4 [244 kB] Get:67 http://ftpmaster.internal/ubuntu kinetic-proposed/universe riscv64 libboost-iostreams1.74-dev riscv64 1.74.0-14ubuntu4 [345 kB] Get:68 http://ftpmaster.internal/ubuntu kinetic/universe riscv64 libboost-iostreams-dev riscv64 1.74.0.3ubuntu7 [3242 B] Get:69 http://ftpmaster.internal/ubuntu kinetic/main riscv64 libboost-regex-dev riscv64 1.74.0.3ubuntu7 [3508 B] Get:70 http://ftpmaster.internal/ubuntu kinetic/main riscv64 libbrotli1 riscv64 1.0.9-2build6 [330 kB] Get:71 http://ftpmaster.internal/ubuntu kinetic/universe riscv64 libcrypto++8 riscv64 8.6.0-2ubuntu1 [1365 kB] Get:72 http://ftpmaster.internal/ubuntu kinetic/universe riscv64 libcrypto++-dev riscv64 8.6.0-2ubuntu1 [6760 kB] Get:73 http://ftpmaster.internal/ubuntu kinetic/main riscv64 libsasl2-modules-db riscv64 2.1.27+dfsg2-3ubuntu1 [19.5 kB] Get:74 http://ftpmaster.internal/ubuntu kinetic/main riscv64 libsasl2-2 riscv64 2.1.27+dfsg2-3ubuntu1 [53.3 kB] Get:75 http://ftpmaster.internal/ubuntu kinetic/main riscv64 libldap-2.5-0 riscv64 2.5.11+dfsg-1~exp1ubuntu3 [163 kB] Get:76 http://ftpmaster.internal/ubuntu kinetic/main riscv64 librtmp1 riscv64 2.4+20151223.gitfa8646d.1-2build4 [54.6 kB] Get:77 http://ftpmaster.internal/ubuntu kinetic/main riscv64 libssh-4 riscv64 0.9.6-2build1 [162 kB] Get:78 http://ftpmaster.internal/ubuntu kinetic-proposed/main riscv64 libcurl3-gnutls riscv64 7.83.0-1 [250 kB] Get:79 http://ftpmaster.internal/ubuntu kinetic-proposed/main riscv64 libevent-2.1-7 riscv64 2.1.12-stable-5 [126 kB] Get:80 http://ftpmaster.internal/ubuntu kinetic-proposed/main riscv64 libevent-core-2.1-7 riscv64 2.1.12-stable-5 [80.0 kB] Get:81 http://ftpmaster.internal/ubuntu kinetic-proposed/main riscv64 libevent-extra-2.1-7 riscv64 2.1.12-stable-5 [56.5 kB] Get:82 http://ftpmaster.internal/ubuntu kinetic-proposed/main riscv64 libevent-pthreads-2.1-7 riscv64 2.1.12-stable-5 [7274 B] Get:83 http://ftpmaster.internal/ubuntu kinetic-proposed/main riscv64 libevent-openssl-2.1-7 riscv64 2.1.12-stable-5 [13.4 kB] Get:84 http://ftpmaster.internal/ubuntu kinetic-proposed/main riscv64 libevent-dev riscv64 2.1.12-stable-5 [528 kB] Get:85 http://ftpmaster.internal/ubuntu kinetic/main riscv64 librdmacm1 riscv64 39.0-1 [65.2 kB] Get:86 http://ftpmaster.internal/ubuntu kinetic/universe riscv64 libfabric1 riscv64 1.11.0-3 [333 kB] Get:87 http://ftpmaster.internal/ubuntu kinetic-proposed/universe riscv64 libhwloc15 riscv64 2.7.1-1 [135 kB] Get:88 http://ftpmaster.internal/ubuntu kinetic/main riscv64 libjs-jquery all 3.6.0+dfsg+~3.5.13-1 [321 kB] Get:89 http://ftpmaster.internal/ubuntu kinetic/universe riscv64 libjs-jquery-ui all 1.13.1+dfsg-1 [253 kB] Get:90 http://ftpmaster.internal/ubuntu kinetic-proposed/main riscv64 libltdl7 riscv64 2.4.7-3 [37.5 kB] Get:91 http://ftpmaster.internal/ubuntu kinetic-proposed/main riscv64 libltdl-dev riscv64 2.4.7-3 [193 kB] Get:92 http://ftpmaster.internal/ubuntu kinetic/main riscv64 libnl-3-dev riscv64 3.5.0-0.1 [188 kB] Get:93 http://ftpmaster.internal/ubuntu kinetic/main riscv64 libnl-route-3-dev riscv64 3.5.0-0.1 [549 kB] Get:94 http://ftpmaster.internal/ubuntu kinetic/main riscv64 libpciaccess0 riscv64 0.16-3 [16.8 kB] Get:95 http://ftpmaster.internal/ubuntu kinetic/main riscv64 libxnvctrl0 riscv64 510.47.03-0ubuntu1 [10.9 kB] Get:96 http://ftpmaster.internal/ubuntu kinetic/universe riscv64 ocl-icd-libopencl1 riscv64 2.2.14-3 [34.3 kB] Get:97 http://ftpmaster.internal/ubuntu kinetic-proposed/universe riscv64 libhwloc-plugins riscv64 2.7.1-1 [13.7 kB] Get:98 http://ftpmaster.internal/ubuntu kinetic/universe riscv64 libpmix2 riscv64 4.1.2-2ubuntu1 [565 kB] Get:99 http://ftpmaster.internal/ubuntu kinetic-proposed/universe riscv64 libopenmpi3 riscv64 4.1.3-2ubuntu1 [2016 kB] Get:100 http://ftpmaster.internal/ubuntu kinetic/main riscv64 libnuma-dev riscv64 2.0.14-3ubuntu2 [67.0 kB] Get:101 http://ftpmaster.internal/ubuntu kinetic-proposed/universe riscv64 libhwloc-dev riscv64 2.7.1-1 [521 kB] Get:102 http://ftpmaster.internal/ubuntu kinetic/main riscv64 zlib1g-dev riscv64 1:1.2.11.dfsg-2ubuntu9 [241 kB] Get:103 http://ftpmaster.internal/ubuntu kinetic/universe riscv64 libpmix-dev riscv64 4.1.2-2ubuntu1 [2465 kB] Get:104 http://ftpmaster.internal/ubuntu kinetic/universe riscv64 libpstreams-dev all 1.0.3-1 [115 kB] Get:105 http://ftpmaster.internal/ubuntu kinetic/main riscv64 libterm-readkey-perl riscv64 2.38-1build4 [24.1 kB] Get:106 http://ftpmaster.internal/ubuntu kinetic/universe riscv64 libtext-wrapper-perl all 1.05-2 [10.3 kB] Get:107 http://ftpmaster.internal/ubuntu kinetic-proposed/universe riscv64 openmpi-common all 4.1.3-2ubuntu1 [163 kB] Get:108 http://ftpmaster.internal/ubuntu kinetic-proposed/universe riscv64 openmpi-bin riscv64 4.1.3-2ubuntu1 [82.1 kB] Get:109 http://ftpmaster.internal/ubuntu kinetic/main riscv64 libibverbs-dev riscv64 39.0-1 [388 kB] Get:110 http://ftpmaster.internal/ubuntu kinetic-proposed/universe riscv64 libopenmpi-dev riscv64 4.1.3-2ubuntu1 [828 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 81.4 MB in 14s (5938 kB/s) Selecting previously unselected package libmd0:riscv64. (Reading database ... 13363 files and directories currently installed.) Preparing to unpack .../000-libmd0_1.0.4-1build1_riscv64.deb ... Unpacking libmd0:riscv64 (1.0.4-1build1) ... Selecting previously unselected package libbsd0:riscv64. Preparing to unpack .../001-libbsd0_0.11.6-1_riscv64.deb ... Unpacking libbsd0:riscv64 (0.11.6-1) ... Selecting previously unselected package libelf1:riscv64. Preparing to unpack .../002-libelf1_0.186-1build1_riscv64.deb ... Unpacking libelf1:riscv64 (0.186-1build1) ... Selecting previously unselected package libicu71:riscv64. Preparing to unpack .../003-libicu71_71.1-2_riscv64.deb ... Unpacking libicu71:riscv64 (71.1-2) ... Selecting previously unselected package libxml2:riscv64. Preparing to unpack .../004-libxml2_2.9.13+dfsg-1build2_riscv64.deb ... Unpacking libxml2:riscv64 (2.9.13+dfsg-1build2) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../005-bsdextrautils_2.37.2-4ubuntu3_riscv64.deb ... 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Selecting previously unselected package libopenmpi-dev:riscv64. Preparing to unpack .../108-libopenmpi-dev_4.1.3-2ubuntu1_riscv64.deb ... Unpacking libopenmpi-dev:riscv64 (4.1.3-2ubuntu1) ... Selecting previously unselected package sbuild-build-depends-main-dummy. Preparing to unpack .../109-sbuild-build-depends-main-dummy_0.invalid.0_riscv64.deb ... Unpacking sbuild-build-depends-main-dummy (0.invalid.0) ... Setting up libpipeline1:riscv64 (1.5.6-1) ... Setting up libboost-system1.74.0:riscv64 (1.74.0-14ubuntu4) ... Setting up libicu71:riscv64 (71.1-2) ... Setting up libpciaccess0:riscv64 (0.16-3) ... Setting up libxau6:riscv64 (1:1.0.9-1build5) ... Setting up libpsl5:riscv64 (0.21.0-1.2build2) ... Setting up libboost1.74-dev:riscv64 (1.74.0-14ubuntu4) ... Setting up bsdextrautils (2.37.2-4ubuntu3) ... update-alternatives: using /usr/bin/write.ul to provide /usr/bin/write (write) in auto mode Setting up libmagic-mgc (1:5.41-4) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libboost-iostreams1.74.0:riscv64 (1.74.0-14ubuntu4) ... Setting up libcbor0.8:riscv64 (0.8.0-2ubuntu1) ... Setting up libdebhelper-perl (13.6ubuntu1) ... Setting up libbrotli1:riscv64 (1.0.9-2build6) ... Setting up libnghttp2-14:riscv64 (1.47.0-1) ... Setting up libmagic1:riscv64 (1:5.41-4) ... Setting up gettext-base (0.21-4ubuntu4) ... Setting up libboost-filesystem1.74.0:riscv64 (1.74.0-14ubuntu4) ... Setting up libcrypto++8:riscv64 (8.6.0-2ubuntu1) ... Setting up file (1:5.41-4) ... Setting up libtext-wrapper-perl (1.05-2) ... Setting up libsasl2-modules-db:riscv64 (2.1.27+dfsg2-3ubuntu1) ... Setting up autotools-dev (20220109.1) ... Setting up libx11-data (2:1.7.5-1) ... Setting up librtmp1:riscv64 (2.4+20151223.gitfa8646d.1-2build4) ... Setting up libboost-system1.74-dev:riscv64 (1.74.0-14ubuntu4) ... Setting up libsigsegv2:riscv64 (2.13-1ubuntu3) ... Setting up libboost-regex1.74.0:riscv64 (1.74.0-14ubuntu4) ... Setting up libhwloc15:riscv64 (2.7.1-1) ... Setting up libevent-core-2.1-7:riscv64 (2.1.12-stable-5) ... Setting up libevent-2.1-7:riscv64 (2.1.12-stable-5) ... Setting up autopoint (0.21-4ubuntu4) ... Setting up icu-devtools (71.1-2) ... Setting up libltdl7:riscv64 (2.4.7-3) ... Setting up libsasl2-2:riscv64 (2.1.27+dfsg2-3ubuntu1) ... Setting up libssh-4:riscv64 (0.9.6-2build1) ... Setting up libgfortran5:riscv64 (12-20220428-1ubuntu1) ... Setting up zlib1g-dev:riscv64 (1:1.2.11.dfsg-2ubuntu9) ... Setting up libnuma1:riscv64 (2.0.14-3ubuntu2) ... Setting up libmd0:riscv64 (1.0.4-1build1) ... Setting up ocl-icd-libopencl1:riscv64 (2.2.14-3) ... Setting up libuchardet0:riscv64 (0.0.7-1build2) ... Setting up libnl-3-200:riscv64 (3.5.0-0.1) ... Setting up openmpi-common (4.1.3-2ubuntu1) ... Setting up libsub-override-perl (0.09-2) ... Setting up libboost-filesystem1.74-dev:riscv64 (1.74.0-14ubuntu4) ... Setting up libjs-jquery (3.6.0+dfsg+~3.5.13-1) ... Setting up libterm-readkey-perl (2.38-1build4) ... Setting up libfido2-1:riscv64 (1.10.0-1) ... Setting up libbsd0:riscv64 (0.11.6-1) ... Setting up libelf1:riscv64 (0.186-1build1) ... Setting up libicu-dev:riscv64 (71.1-2) ... Setting up libxml2:riscv64 (2.9.13+dfsg-1build2) ... Setting up libboost-filesystem-dev:riscv64 (1.74.0.3ubuntu7) ... Setting up libevent-pthreads-2.1-7:riscv64 (2.1.12-stable-5) ... Setting up libfile-stripnondeterminism-perl (1.13.0-1) ... Setting up libdw1:riscv64 (0.186-1build1) ... Setting up libxdmcp6:riscv64 (1:1.1.3-0ubuntu5) ... Setting up libevent-extra-2.1-7:riscv64 (2.1.12-stable-5) ... Setting up libxcb1:riscv64 (1.14-3ubuntu3) ... Setting up gettext (0.21-4ubuntu4) ... Setting up libtool (2.4.7-3) ... Setting up libgfortran-11-dev:riscv64 (11.3.0-1ubuntu1) ... Setting up libedit2:riscv64 (3.1-20210910-1build1) ... Setting up libcrypto++-dev:riscv64 (8.6.0-2ubuntu1) ... Setting up libevent-openssl-2.1-7:riscv64 (2.1.12-stable-5) ... Setting up m4 (1.4.18-5ubuntu2) ... Setting up libldap-2.5-0:riscv64 (2.5.11+dfsg-1~exp1ubuntu3) ... Setting up intltool-debian (0.35.0+20060710.5) ... Setting up libnuma-dev:riscv64 (2.0.14-3ubuntu2) ... Setting up libnl-route-3-200:riscv64 (3.5.0-0.1) ... Setting up libjs-jquery-ui (1.13.1+dfsg-1) ... Setting up libevent-dev (2.1.12-stable-5) ... Setting up libpstreams-dev (1.0.3-1) ... Setting up gfortran-11 (11.3.0-1ubuntu1) ... Setting up autoconf (2.71-2) ... Setting up dh-strip-nondeterminism (1.13.0-1) ... Setting up dwz (0.14-1build2) ... Setting up libboost-regex1.74-dev:riscv64 (1.74.0-14ubuntu4) ... Setting up libnl-3-dev:riscv64 (3.5.0-0.1) ... Setting up groff-base (1.22.4-8build1) ... Setting up debugedit (1:5.0-4build1) ... Setting up libx11-6:riscv64 (2:1.7.5-1) ... Setting up libboost-regex-dev:riscv64 (1.74.0.3ubuntu7) ... 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 libibverbs1:riscv64 (39.0-1) ... Setting up ibverbs-providers:riscv64 (39.0-1) ... Setting up openssh-client (1:9.0p1-1) ... update-alternatives: using /usr/bin/ssh to provide /usr/bin/rsh (rsh) in auto mode update-alternatives: using /usr/bin/slogin to provide /usr/bin/rlogin (rlogin) in auto mode update-alternatives: using /usr/bin/scp to provide /usr/bin/rcp (rcp) in auto mode Setting up po-debconf (1.0.21+nmu1) ... Setting up libxext6:riscv64 (2:1.3.4-1build1) ... Setting up libcurl3-gnutls:riscv64 (7.83.0-1) ... 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 libxnvctrl0:riscv64 (510.47.03-0ubuntu1) ... Setting up libboost-iostreams1.74-dev:riscv64 (1.74.0-14ubuntu4) ... Setting up dh-autoreconf (20) ... Setting up libnl-route-3-dev:riscv64 (3.5.0-0.1) ... Setting up libltdl-dev:riscv64 (2.4.7-3) ... Setting up libhwloc-dev:riscv64 (2.7.1-1) ... Setting up librdmacm1:riscv64 (39.0-1) ... Setting up debhelper (13.6ubuntu1) ... Setting up libboost-iostreams-dev:riscv64 (1.74.0.3ubuntu7) ... Setting up libibverbs-dev:riscv64 (39.0-1) ... Setting up libhwloc-plugins:riscv64 (2.7.1-1) ... Setting up libfabric1:riscv64 (1.11.0-3) ... Setting up libpmix2:riscv64 (4.1.2-2ubuntu1) ... Setting up libopenmpi3:riscv64 (4.1.3-2ubuntu1) ... Setting up libpmix-dev:riscv64 (4.1.2-2ubuntu1) ... Setting up openmpi-bin (4.1.3-2ubuntu1) ... update-alternatives: using /usr/bin/mpirun.openmpi to provide /usr/bin/mpirun (mpirun) in auto mode update-alternatives: using /usr/bin/mpicc.openmpi to provide /usr/bin/mpicc (mpi) in auto mode Setting up libopenmpi-dev:riscv64 (4.1.3-2ubuntu1) ... update-alternatives: using /usr/lib/riscv64-linux-gnu/openmpi/include to provide /usr/include/riscv64-linux-gnu/mpi (mpi-riscv64-linux-gnu) in auto mode 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 all) +------------------------------------------------------------------------------+ | 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_2.38-3ubuntu1 dpkg-dev_1.21.1ubuntu2 g++-11_11.3.0-1ubuntu1 gcc-11_11.3.0-1ubuntu1 libc6-dev_2.35-0ubuntu3 libstdc++-11-dev_11.3.0-1ubuntu1 libstdc++6_12-20220428-1ubuntu1 linux-libc-dev_5.15.0-28.29 Package versions: adduser_3.118ubuntu5 advancecomp_2.1-2.1ubuntu2 apt_2.4.5 autoconf_2.71-2 automake_1:1.16.5-1.3 autopoint_0.21-4ubuntu4 autotools-dev_20220109.1 base-files_12ubuntu5 base-passwd_3.5.52build1 bash_5.1-6ubuntu1 binutils_2.38-3ubuntu1 binutils-common_2.38-3ubuntu1 binutils-riscv64-linux-gnu_2.38-3ubuntu1 bsdextrautils_2.37.2-4ubuntu3 bsdutils_1:2.37.2-4ubuntu3 build-essential_12.9ubuntu3 bzip2_1.0.8-5build1 ca-certificates_20211016 coreutils_8.32-4.1ubuntu1 cpp_4:11.2.0-1ubuntu1 cpp-11_11.3.0-1ubuntu1 dash_0.5.11+git20210903+057cd650a4ed-3build1 debconf_1.5.79ubuntu1 debhelper_13.6ubuntu1 debianutils_5.5-1ubuntu2 debugedit_1:5.0-4build1 dh-autoreconf_20 dh-strip-nondeterminism_1.13.0-1 diffutils_1:3.8-0ubuntu2 dpkg_1.21.1ubuntu2 dpkg-dev_1.21.1ubuntu2 dwz_0.14-1build2 e2fsprogs_1.46.5-2ubuntu1 fakeroot_1.28-1ubuntu1 file_1:5.41-4 findutils_4.8.0-1ubuntu3 g++_4:11.2.0-1ubuntu1 g++-11_11.3.0-1ubuntu1 gcc_4:11.2.0-1ubuntu1 gcc-11_11.3.0-1ubuntu1 gcc-11-base_11.3.0-1ubuntu1 gcc-12-base_12-20220428-1ubuntu1 gettext_0.21-4ubuntu4 gettext-base_0.21-4ubuntu4 gfortran-11_11.3.0-1ubuntu1 gpg_2.2.27-3ubuntu2 gpg-agent_2.2.27-3ubuntu2 gpgconf_2.2.27-3ubuntu2 gpgv_2.2.27-3ubuntu2 grep_3.7-1build1 groff-base_1.22.4-8build1 gzip_1.10-4ubuntu4 hostname_3.23ubuntu2 ibverbs-providers_39.0-1 icu-devtools_71.1-2 init_1.62 init-system-helpers_1.62 intltool-debian_0.35.0+20060710.5 libacl1_2.3.1-1 libapparmor1_3.0.4-2ubuntu2 libapt-pkg6.0_2.4.5 libarchive-zip-perl_1.68-1 libargon2-1_0~20171227-0.3 libasan6_11.3.0-1ubuntu1 libassuan0_2.5.5-1build1 libatomic1_12-20220428-1ubuntu1 libattr1_1:2.5.1-1build1 libaudit-common_1:3.0.7-1build1 libaudit1_1:3.0.7-1build1 libbinutils_2.38-3ubuntu1 libblkid1_2.37.2-4ubuntu3 libboost-filesystem-dev_1.74.0.3ubuntu7 libboost-filesystem1.74-dev_1.74.0-14ubuntu4 libboost-filesystem1.74.0_1.74.0-14ubuntu4 libboost-iostreams-dev_1.74.0.3ubuntu7 libboost-iostreams1.74-dev_1.74.0-14ubuntu4 libboost-iostreams1.74.0_1.74.0-14ubuntu4 libboost-regex-dev_1.74.0.3ubuntu7 libboost-regex1.74-dev_1.74.0-14ubuntu4 libboost-regex1.74.0_1.74.0-14ubuntu4 libboost-system1.74-dev_1.74.0-14ubuntu4 libboost-system1.74.0_1.74.0-14ubuntu4 libboost1.74-dev_1.74.0-14ubuntu4 libbrotli1_1.0.9-2build6 libbsd0_0.11.6-1 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_0.7.9-2.2build3 libcap2_1:2.44-1build3 libcbor0.8_0.8.0-2ubuntu1 libcc1-0_12-20220428-1ubuntu1 libcom-err2_1.46.5-2ubuntu1 libcrypt-dev_1:4.4.27-1 libcrypt1_1:4.4.27-1 libcrypto++-dev_8.6.0-2ubuntu1 libcrypto++8_8.6.0-2ubuntu1 libcryptsetup12_2:2.4.3-1ubuntu1 libctf-nobfd0_2.38-3ubuntu1 libctf0_2.38-3ubuntu1 libcurl3-gnutls_7.83.0-1 libdb5.3_5.3.28+dfsg1-0.8ubuntu3 libdebconfclient0_0.261ubuntu1 libdebhelper-perl_13.6ubuntu1 libdevmapper1.02.1_2:1.02.175-2.1ubuntu4 libdpkg-perl_1.21.1ubuntu2 libdw1_0.186-1build1 libedit2_3.1-20210910-1build1 libelf1_0.186-1build1 libevent-2.1-7_2.1.12-stable-5 libevent-core-2.1-7_2.1.12-stable-5 libevent-dev_2.1.12-stable-5 libevent-extra-2.1-7_2.1.12-stable-5 libevent-openssl-2.1-7_2.1.12-stable-5 libevent-pthreads-2.1-7_2.1.12-stable-5 libext2fs2_1.46.5-2ubuntu1 libfabric1_1.11.0-3 libfakeroot_1.28-1ubuntu1 libffi8_3.4.2-4 libfido2-1_1.10.0-1 libfile-stripnondeterminism-perl_1.13.0-1 libgcc-11-dev_11.3.0-1ubuntu1 libgcc-s1_12-20220428-1ubuntu1 libgcrypt20_1.9.4-3ubuntu3 libgdbm-compat4_1.23-1 libgdbm6_1.23-1 libgfortran-11-dev_11.3.0-1ubuntu1 libgfortran5_12-20220428-1ubuntu1 libgmp10_2:6.2.1+dfsg-3ubuntu1 libgnutls30_3.7.4-2ubuntu1 libgomp1_12-20220428-1ubuntu1 libgpg-error0_1.45-2 libgssapi-krb5-2_1.19.2-2 libhogweed6_3.7.3-1build2 libhwloc-dev_2.7.1-1 libhwloc-plugins_2.7.1-1 libhwloc15_2.7.1-1 libibverbs-dev_39.0-1 libibverbs1_39.0-1 libicu-dev_71.1-2 libicu71_71.1-2 libidn2-0_2.3.2-2build1 libip4tc2_1.8.7-1ubuntu5 libisl23_0.24-2build1 libjs-jquery_3.6.0+dfsg+~3.5.13-1 libjs-jquery-ui_1.13.1+dfsg-1 libjson-c5_0.16-1 libk5crypto3_1.19.2-2 libkeyutils1_1.6.1-2ubuntu3 libkmod2_29-1ubuntu1 libkrb5-3_1.19.2-2 libkrb5support0_1.19.2-2 libldap-2.5-0_2.5.11+dfsg-1~exp1ubuntu3 liblockfile-bin_1.17-1build2 liblockfile1_1.17-1build2 libltdl-dev_2.4.7-3 libltdl7_2.4.7-3 liblz4-1_1.9.3-2build2 liblzma5_5.2.5-2ubuntu1 libmagic-mgc_1:5.41-4 libmagic1_1:5.41-4 libmd0_1.0.4-1build1 libmount1_2.37.2-4ubuntu3 libmpc3_1.2.1-2build1 libmpfr6_4.1.0-3build3 libncurses6_6.3+20220423-1 libncursesw6_6.3+20220423-1 libnettle8_3.7.3-1build2 libnghttp2-14_1.47.0-1 libnl-3-200_3.5.0-0.1 libnl-3-dev_3.5.0-0.1 libnl-route-3-200_3.5.0-0.1 libnl-route-3-dev_3.5.0-0.1 libnpth0_1.6-3build2 libnsl-dev_1.3.0-2build2 libnsl2_1.3.0-2build2 libnuma-dev_2.0.14-3ubuntu2 libnuma1_2.0.14-3ubuntu2 libopenmpi-dev_4.1.3-2ubuntu1 libopenmpi3_4.1.3-2ubuntu1 libp11-kit0_0.24.1-1 libpam-modules_1.4.0-13ubuntu1 libpam-modules-bin_1.4.0-13ubuntu1 libpam-runtime_1.4.0-13ubuntu1 libpam0g_1.4.0-13ubuntu1 libpciaccess0_0.16-3 libpcre2-8-0_10.40-1 libpcre3_2:8.39-14 libperl5.34_5.34.0-3ubuntu1 libpipeline1_1.5.6-1 libpmix-dev_4.1.2-2ubuntu1 libpmix2_4.1.2-2ubuntu1 libpng16-16_1.6.37-5 libprocps8_2:3.3.17-6ubuntu2 libpsl5_0.21.0-1.2build2 libpstreams-dev_1.0.3-1 librdmacm1_39.0-1 libreadline8_8.1.2-1.2 librtmp1_2.4+20151223.gitfa8646d.1-2build4 libsasl2-2_2.1.27+dfsg2-3ubuntu1 libsasl2-modules-db_2.1.27+dfsg2-3ubuntu1 libseccomp2_2.5.3-2ubuntu2 libselinux1_3.3-1build2 libsemanage-common_3.3-1build2 libsemanage2_3.3-1build2 libsepol2_3.3-1build1 libsigsegv2_2.13-1ubuntu3 libsmartcols1_2.37.2-4ubuntu3 libsqlite3-0_3.38.3-1 libss2_1.46.5-2ubuntu1 libssh-4_0.9.6-2build1 libssl3_3.0.2-0ubuntu1 libstdc++-11-dev_11.3.0-1ubuntu1 libstdc++6_12-20220428-1ubuntu1 libsub-override-perl_0.09-2 libsystemd0_249.11-0ubuntu3.1 libtasn1-6_4.18.0-4build1 libterm-readkey-perl_2.38-1build4 libtext-wrapper-perl_1.05-2 libtinfo6_6.3+20220423-1 libtirpc-common_1.3.2-2build1 libtirpc-dev_1.3.2-2build1 libtirpc3_1.3.2-2build1 libtool_2.4.7-3 libuchardet0_0.0.7-1build2 libudev1_249.11-0ubuntu3.1 libunistring2_1.0-1 libuuid1_2.37.2-4ubuntu3 libx11-6_2:1.7.5-1 libx11-data_2:1.7.5-1 libxau6_1:1.0.9-1build5 libxcb1_1.14-3ubuntu3 libxdmcp6_1:1.1.3-0ubuntu5 libxext6_2:1.3.4-1build1 libxml2_2.9.13+dfsg-1build2 libxnvctrl0_510.47.03-0ubuntu1 libxxhash0_0.8.1-1 libzstd1_1.5.2+dfsg-1 linux-libc-dev_5.15.0-28.29 lockfile-progs_0.1.19build1 login_1:4.8.1-2ubuntu2 logsave_1.46.5-2ubuntu1 lsb-base_11.1.0ubuntu4 lto-disabled-list_25 m4_1.4.18-5ubuntu2 make_4.3-4.1build1 man-db_2.10.2-1 mawk_1.3.4.20200120-3 mount_2.37.2-4ubuntu3 ncurses-base_6.3+20220423-1 ncurses-bin_6.3+20220423-1 ocl-icd-libopencl1_2.2.14-3 openmpi-bin_4.1.3-2ubuntu1 openmpi-common_4.1.3-2ubuntu1 openssh-client_1:9.0p1-1 openssl_3.0.2-0ubuntu1 optipng_0.7.7-2build1 passwd_1:4.8.1-2ubuntu2 patch_2.7.6-7build2 perl_5.34.0-3ubuntu1 perl-base_5.34.0-3ubuntu1 perl-modules-5.34_5.34.0-3ubuntu1 pinentry-curses_1.2.0-1 pkgbinarymangler_149 po-debconf_1.0.21+nmu1 policyrcd-script-zg2_0.1-3 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 systemd_249.11-0ubuntu3.1 systemd-sysv_249.11-0ubuntu3.1 sysvinit-utils_3.01-1ubuntu1 tar_1.34+dfsg-1build3 tzdata_2022a-0ubuntu1 ubuntu-keyring_2021.03.26 usrmerge_25ubuntu2 util-linux_2.37.2-4ubuntu3 xz-utils_5.2.5-2ubuntu1 zlib1g_1:1.2.11.dfsg-2ubuntu9 zlib1g-dev_1:1.2.11.dfsg-2ubuntu9 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: murasaki Binary: murasaki, murasaki-mpi, murasaki-common Architecture: any all Version: 1.68.6-13build2 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille , Nilesh Patra Homepage: http://murasaki.dna.bio.keio.ac.jp/wiki/ Standards-Version: 4.5.1 Vcs-Browser: https://salsa.debian.org/med-team/murasaki Vcs-Git: https://salsa.debian.org/med-team/murasaki.git Testsuite: autopkgtest Testsuite-Triggers: libboost-filesystem-dev, libboost-iostreams-dev, libboost-regex-dev, libcrypto++-dev, libopenmpi-dev, libpstreams-dev, libterm-readkey-perl, libtext-wrapper-perl Build-Depends: debhelper-compat (= 13), libboost-regex-dev, libboost-iostreams-dev, libboost-filesystem-dev, libterm-readkey-perl, libtext-wrapper-perl, libcrypto++-dev, libpstreams-dev, libopenmpi-dev Package-List: murasaki deb science optional arch=any murasaki-common deb science optional arch=all murasaki-mpi deb science optional arch=any Checksums-Sha1: 039363a4ee16888adc629ebbf658ccf2805370bd 3944341 murasaki_1.68.6.orig-debian-tests-data.tar.gz 398a53fe76476ec3c756754d13541dd25d98a58a 307745 murasaki_1.68.6.orig.tar.gz d0e6f067514095f97baab74eab5144777c9729eb 11308 murasaki_1.68.6-13build2.debian.tar.xz Checksums-Sha256: bb3fee13bdf2ee9184667c9a3535dcd54525d9d98782e67c8c8713393cbb7862 3944341 murasaki_1.68.6.orig-debian-tests-data.tar.gz ebb3f3df2c0b3dc9f43977685f6c5e37ea483fb4189f7d965acc634bd10aaefe 307745 murasaki_1.68.6.orig.tar.gz 19ce7a59fb6c1f921bbe6c7984c24900bf3867d0d470ab444aa31837eb2a60e8 11308 murasaki_1.68.6-13build2.debian.tar.xz Files: f7c0e6bdc9dea8bc893e806db571d228 3944341 murasaki_1.68.6.orig-debian-tests-data.tar.gz 25477c77aa21246d4a639527836e6c77 307745 murasaki_1.68.6.orig.tar.gz 61781af018e2151e8cf36fe8def3d061 11308 murasaki_1.68.6-13build2.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQIzBAEBCgAdFiEETQvhLw5HdtiqzpaW5mx3Wuv+bH0FAmJtW54ACgkQ5mx3Wuv+ bH2eNw/+MxB7VE4lpo2zbsfKJpZPQWzhmOJ3JVBdQQjqEOALXHL0FOAvI3oUk5GR Ep0/pF+t5GU791vh4EUFtmbCz8p5WfPtypF6fL7rdEqqtdUINag1g3rrwyjvGkBX 1zYmaIO0TEujx3/utk6oIs9xMOPTCW8I2RSGii+zDo+UBdR8fCAR0ygtPbRCB+1X vSlGPfAnJTSZkQdOtBaeJ3R5kxZ5rA0PtmLEtHiKJkfux3dKDW28sqmz3EcNKPPh MTS0+qLjkIXukMpSbAJTi7ZsnqrfyX6OybBK1XeAmqY76GHR8l8G0T3NoSwuGl3P MgQTXVnCGcknw9c0DZSod6Re+nkAbjQcXkJXct72CZJKDddXNNgTwVX8G0ixQJCW Zv94KMuR/HN2OoIpZnQp2Yvpyj3EOZeFa7vj2d3mKa0q1VrVT2r/ksSEcE+VrMTb l0FzNwvu8yKy6yHXQRkePbPOXJ/PdK8HuiOxO5ab8MGd3e4GfPm8l5J3dWBWYzV8 gMQfEscpGw/vdU8W1jxbjkEssh2NYGbA/gOfBtepdBE36UGQGqAni5tQDWoboGA3 65IkyeHYqG2X/Mp/tVLxa+AwqNOop21/t3oFV3S867xcfjMIs8VsLxkxs+TAbI8Q EKJFDRdgbBJl1I8lFSWeF7D7ijkIaeQx31xWBd8LbxD/SBXFydA= =BqN8 -----END PGP SIGNATURE----- gpgv: Signature made Sat Apr 30 15:54:06 2022 UTC gpgv: using RSA key 4D0BE12F0E4776D8AACE9696E66C775AEBFE6C7D gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify signature ./murasaki_1.68.6-13build2.dsc dpkg-source: info: extracting murasaki in /<> dpkg-source: info: unpacking murasaki_1.68.6.orig.tar.gz dpkg-source: info: unpacking murasaki_1.68.6.orig-debian-tests-data.tar.gz dpkg-source: info: unpacking murasaki_1.68.6-13build2.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying gcc11.patch dpkg-source: info: applying use_proper_libboost_names.patch dpkg-source: info: applying include_libpstream.patch dpkg-source: info: applying hardening.patch dpkg-source: info: applying spelling.patch dpkg-source: info: applying man_syntax.patch dpkg-source: info: applying freebsd.patch dpkg-source: info: applying gcc-6.patch dpkg-source: info: applying fix_mpi.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-23595945 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-23595945 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-23595945 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 murasaki dpkg-buildpackage: info: source version 1.68.6-13build2 dpkg-buildpackage: info: source distribution kinetic dpkg-source --before-build . dpkg-buildpackage: info: host architecture riscv64 debian/rules clean dh clean dh_auto_clean make -j8 clean make[1]: Entering directory '/<>' rm -rf *.o *~ .*~ core make -C src clean make[2]: Entering directory '/<>/src' rm -rf *.o *~ .*~ core ../murasaki ../cgr-image ../cgr-compare ../cgr-random ../cgr-sample ../testeco ../align-compare ../align-or ../geneparse ../align-and ../align-best ../align-coverage ../getsegments ../mbfa make[2]: Leaving directory '/<>/src' 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 -- USE_MPI=YES make -j8 "INSTALL=install --strip-program=true" USE_MPI=YES make[2]: Entering directory '/<>' make -C src all make[3]: Entering directory '/<>/src' mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c murasaki.cc mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c timing.cc mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c dinkymath.cc mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c sequence.cc mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c msethash.cc mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c options.cc mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c ecohash.cc mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c ecolist.cc mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c murasaki_mpi.cc sequence.cc: In destructor ‘Sequence::~Sequence()’: sequence.cc:377:9: warning: ‘throw’ will always call ‘terminate’ [-Wterminate] 377 | throw MurasakiException("Couldn't mark System V IPC shared memory region for deletion for sequence "+name+strerror(errno)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ sequence.cc:377:9: note: in C++11 destructors default to ‘noexcept’ dinkymath.cc: In function ‘std::string littleEndianStr(unsigned int, int)’: dinkymath.cc:40:7: warning: variable ‘last’ set but not used [-Wunused-but-set-variable] 40 | int last=0; | ^~~~ dinkymath.cc: In function ‘std::string littleEndianPat(unsigned int, int)’: dinkymath.cc:53:7: warning: variable ‘last’ set but not used [-Wunused-but-set-variable] 53 | int last=0; | ^~~~ sequence.cc: In member function ‘void BitSequence::loadBinary(const SequenceBinary&)’: sequence.cc:1113:9: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of type ‘ShmVector >::val_type’ {aka ‘struct std::pair’} with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 1113 | memcpy(&matchRegions.front(),binseq.regions[srcMatchRegionsIdx],sizeof(SequenceBinary::Region)*binseq.regionSizes[srcMatchRegionsIdx]); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/bits/stl_algobase.h:64, from /usr/include/c++/11/bits/stl_tree.h:63, from /usr/include/c++/11/set:60, from cmultiset.h:33, from sequence.h:30, from murasaki.h:24, from sequence.cc:28: /usr/include/c++/11/bits/stl_pair.h:211:12: note: ‘ShmVector >::val_type’ {aka ‘struct std::pair’} declared here 211 | struct pair | ^~~~ sequence.cc:1114:9: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of type ‘ShmVector >::val_type’ {aka ‘struct std::pair’} with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 1114 | memcpy(&subSeqs.front(),binseq.regions[0],sizeof(SequenceBinary::Region)*binseq.regionSizes[0]); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/bits/stl_algobase.h:64, from /usr/include/c++/11/bits/stl_tree.h:63, from /usr/include/c++/11/set:60, from cmultiset.h:33, from sequence.h:30, from murasaki.h:24, from sequence.cc:28: /usr/include/c++/11/bits/stl_pair.h:211:12: note: ‘ShmVector >::val_type’ {aka ‘struct std::pair’} declared here 211 | struct pair | ^~~~ sequence.cc: In destructor ‘BitSequence::~BitSequence()’: sequence.cc:1394:9: warning: ‘throw’ will always call ‘terminate’ [-Wterminate] 1394 | throw MurasakiException("Couldn't detach System V shared memory region for "+(seq ? seq->filename:string("(anon)"))+strerror(errno)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ sequence.cc:1394:9: note: in C++11 destructors default to ‘noexcept’ sequence.cc: In member function ‘std::pair IntervalSet::entropy() const’: sequence.cc:3332:10: warning: variable ‘shortest’ set but not used [-Wunused-but-set-variable] 3332 | SeqPos shortest=0,shortlen=length(spaces[0]); | ^~~~~~~~ In file included from sequence.h:44, from murasaki.h:24, from sequence.cc:28: shmvector.hh: In instantiation of ‘void ShmVector::shmRealloc(size_t) [with T = std::pair; size_t = long unsigned int]’: shmvector.hh:282:5: required from ‘void ShmVector::resize(size_t) [with T = std::pair; size_t = long unsigned int]’ sequence.cc:1110:17: required from here shmvector.hh:225:13: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of type ‘struct std::pair’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 225 | memcpy(_data,old_data,(oldByteCapacity<_byteCapacity ? oldByteCapacity:_byteCapacity)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/bits/stl_algobase.h:64, from /usr/include/c++/11/bits/stl_tree.h:63, from /usr/include/c++/11/set:60, from cmultiset.h:33, from sequence.h:30, from murasaki.h:24, from sequence.cc:28: /usr/include/c++/11/bits/stl_pair.h:211:12: note: ‘struct std::pair’ declared here 211 | struct pair | ^~~~ murasaki.cc: In function ‘void procLocs(LocList&, std::__cxx11::list&, int, int)’: murasaki.cc:1008:8: warning: variable ‘revZero’ set but not used [-Wunused-but-set-variable] 1008 | bool revZero=false; | ^~~~~~~ murasaki_mpi.cc: In function ‘void mpi_hasher_client_mode(BitSequence*)’: murasaki_mpi.cc:561:9: warning: variable ‘send_done’ set but not used [-Wunused-but-set-variable] 561 | int send_done; | ^~~~~~~~~ mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c arrayhash.cc mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c seqread.cc mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c scoring.cc mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c openhash.cc murasaki_mpi.cc: In function ‘void mpi_types_init()’: murasaki_mpi.cc:107:18: warning: ‘msg’ may be used uninitialized [-Wmaybe-uninitialized] 107 | MPI_Get_address(&msg.key,disp); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ In file included from murasaki_mpi.cc:29: /usr/lib/riscv64-linux-gnu/openmpi/include/mpi.h:1565:20: note: by argument 1 of type ‘const void*’ to ‘int MPI_Get_address(const void*, MPI_Aint*)’ declared here 1565 | OMPI_DECLSPEC int MPI_Get_address(const void *location, MPI_Aint *address); | ^~~~~~~~~~~~~~~ murasaki_mpi.cc:102:19: note: ‘msg’ declared here 102 | MPI_HashMessage msg; | ^~~ mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c genopts.cc mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c binseq.cc mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c cgr-image.cc mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c cgr.cc mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c cgr-compare.cc mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c cgr-random.cc mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c cgr-sample.cc binseq.cc: In member function ‘bool SequenceBinary::save(std::string)’: binseq.cc:70:28: warning: catching polymorphic type ‘class std::ios_base::failure’ by value [-Wcatch-value=] 70 | }catch(ofstream::failure e){ | ^ binseq.cc: In member function ‘void SequenceBinary::fillCopyVectors()’: binseq.cc:158:9: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of type ‘__gnu_cxx::__alloc_traits >, std::pair >::value_type’ {aka ‘struct std::pair’} with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 158 | memcpy(&subSeqs.front(),regions[0],regionSizes[0]*sizeof(Region)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/bits/stl_algobase.h:64, from /usr/include/c++/11/bits/char_traits.h:39, from /usr/include/c++/11/ios:40, from /usr/include/c++/11/istream:38, from /usr/include/c++/11/fstream:38, from seqread.h:30, from binseq.hh:31, from binseq.cc:21: /usr/include/c++/11/bits/stl_pair.h:211:12: note: ‘__gnu_cxx::__alloc_traits >, std::pair >::value_type’ {aka ‘struct std::pair’} declared here 211 | struct pair | ^~~~ binseq.cc:160:9: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of type ‘__gnu_cxx::__alloc_traits >, std::pair >::value_type’ {aka ‘struct std::pair’} with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 160 | memcpy(&readableRegions.front(),regions[1],regionSizes[1]*sizeof(Region)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/bits/stl_algobase.h:64, from /usr/include/c++/11/bits/char_traits.h:39, from /usr/include/c++/11/ios:40, from /usr/include/c++/11/istream:38, from /usr/include/c++/11/fstream:38, from seqread.h:30, from binseq.hh:31, from binseq.cc:21: /usr/include/c++/11/bits/stl_pair.h:211:12: note: ‘__gnu_cxx::__alloc_traits >, std::pair >::value_type’ {aka ‘struct std::pair’} declared here 211 | struct pair | ^~~~ binseq.cc:162:9: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of type ‘__gnu_cxx::__alloc_traits >, std::pair >::value_type’ {aka ‘struct std::pair’} with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 162 | memcpy(&unmaskedRegions.front(),regions[2],regionSizes[2]*sizeof(Region)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/bits/stl_algobase.h:64, from /usr/include/c++/11/bits/char_traits.h:39, from /usr/include/c++/11/ios:40, from /usr/include/c++/11/istream:38, from /usr/include/c++/11/fstream:38, from seqread.h:30, from binseq.hh:31, from binseq.cc:21: /usr/include/c++/11/bits/stl_pair.h:211:12: note: ‘__gnu_cxx::__alloc_traits >, std::pair >::value_type’ {aka ‘struct std::pair’} declared here 211 | struct pair | ^~~~ cgr.cc: In member function ‘void Cgr::merge(Cgr&)’: cgr.cc:140:7: warning: variable ‘redist’ set but not used [-Wunused-but-set-variable] 140 | int redist=(unsigned long)(rez*rez)<=seedcount; | ^~~~~~ cgr.cc: In member function ‘bool Cgr::savePNG(std::string)’: cgr.cc:288:7: warning: variable ‘res’ set but not used [-Wunused-but-set-variable] 288 | int res; | ^~~ cgr.cc: In member function ‘int PgmBuffer::loadPGM(std::string)’: cgr.cc:435:7: warning: variable ‘wordwidth’ set but not used [-Wunused-but-set-variable] 435 | int wordwidth=1; | ^~~~~~~~~ mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c testeco.cc mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c align-compare.cc mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c alignments.cc cgr.cc: In member function ‘int PgmBuffer::loadBinaryPGM(std::string)’: cgr.cc:557:31: warning: ‘height’ may be used uninitialized in this function [-Wmaybe-uninitialized] 557 | if(data.size()<(uint)(height*width)) | ~~~~~~~^~~~~~~ cgr.cc:557:31: warning: ‘width’ may be used uninitialized in this function [-Wmaybe-uninitialized] cgr.cc: In member function ‘int PgmBuffer::loadPGM(std::string)’: cgr.cc:485:31: warning: ‘height’ may be used uninitialized in this function [-Wmaybe-uninitialized] 485 | if(data.size()<(uint)(height*width)) | ~~~~~~~^~~~~~~ cgr.cc:485:31: warning: ‘width’ may be used uninitialized in this function [-Wmaybe-uninitialized] mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c align-or.cc mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c geneparse.cc mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c align-and.cc cgr-sample.cc: In function ‘int main(int, char**)’: cgr-sample.cc:54:8: warning: variable ‘repeatmask’ set but not used [-Wunused-but-set-variable] 54 | bool repeatmask=false,save=false; | ^~~~~~~~~~ mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c align-best.cc mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c align-coverage.cc mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c getsegments.cc mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -c mbfa.cc mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -o ../murasaki murasaki.o timing.o dinkymath.o sequence.o msethash.o options.o ecohash.o ecolist.o murasaki_mpi.o arrayhash.o seqread.o scoring.o openhash.o genopts.o binseq.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -o ../cgr-image cgr-image.o cgr.o dinkymath.o timing.o seqread.o genopts.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -o ../cgr-compare cgr-compare.o cgr.o dinkymath.o timing.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -o ../cgr-random cgr-random.o cgr.o dinkymath.o timing.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -o ../cgr-sample cgr.o cgr-sample.o seqread.o genopts.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -o ../testeco testeco.o ecolist.o dinkymath.o timing.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -o ../geneparse geneparse.o seqread.o genopts.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now align-coverage.cc: In function ‘int main(int, char**)’: align-coverage.cc:148:10: warning: variable ‘seqStats’ set but not used [-Wunused-but-set-variable] 148 | bool seqStats=true; | ^~~~~~~~ getsegments.cc: In function ‘size_t getSubSeqs(SequenceFileReader&, std::__cxx11::list > >&, std::string)’: getsegments.cc:153:29: warning: catching polymorphic type ‘class boost::bad_lexical_cast’ by value [-Wcatch-value=] 153 | }catch(bad_lexical_cast e){ | ^ mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -o ../mbfa mbfa.o dinkymath.o timing.o seqread.o binseq.o genopts.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -o ../align-compare align-compare.o dinkymath.o alignments.o timing.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -o ../align-or align-or.o alignments.o dinkymath.o timing.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -o ../align-and align-and.o alignments.o dinkymath.o timing.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -o ../align-best align-best.o alignments.o dinkymath.o timing.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -o ../align-coverage align-coverage.o alignments.o dinkymath.o timing.o seqread.o genopts.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now mpicxx -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DMURASAKI_MPI -DUSE_SHM_SYSV -DLARGESEQ_SUPPORT -o ../getsegments getsegments.o seqread.o genopts.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now make[3]: Leaving directory '/<>/src' make[2]: Leaving directory '/<>' for bin in geneparse mbfa murasaki cgr-* testeco align-* ; do \ mv ${bin} ${bin}-mpi ; \ done make clean make[2]: Entering directory '/<>' rm -rf *.o *~ .*~ core make -C src clean make[3]: Entering directory '/<>/src' rm -rf *.o *~ .*~ core ../murasaki ../cgr-image ../cgr-compare ../cgr-random ../cgr-sample ../testeco ../align-compare ../align-or ../geneparse ../align-and ../align-best ../align-coverage ../getsegments ../mbfa make[3]: Leaving directory '/<>/src' make[2]: Leaving directory '/<>' dh_auto_build -- USE_MPI=NO make -j8 "INSTALL=install --strip-program=true" USE_MPI=NO make[2]: Entering directory '/<>' make -C src all make[3]: Entering directory '/<>/src' g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c murasaki.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c timing.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c dinkymath.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c sequence.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c msethash.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c options.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c ecohash.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c ecolist.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c murasaki_mpi.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c arrayhash.cc sequence.cc: In member function ‘void BitSequence::loadBinary(const SequenceBinary&)’: sequence.cc:1113:9: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of type ‘ShmVector >::val_type’ {aka ‘struct std::pair’} with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 1113 | memcpy(&matchRegions.front(),binseq.regions[srcMatchRegionsIdx],sizeof(SequenceBinary::Region)*binseq.regionSizes[srcMatchRegionsIdx]); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/bits/stl_algobase.h:64, from /usr/include/c++/11/bits/stl_tree.h:63, from /usr/include/c++/11/set:60, from cmultiset.h:33, from sequence.h:30, from murasaki.h:24, from sequence.cc:28: /usr/include/c++/11/bits/stl_pair.h:211:12: note: ‘ShmVector >::val_type’ {aka ‘struct std::pair’} declared here 211 | struct pair | ^~~~ sequence.cc:1114:9: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of type ‘ShmVector >::val_type’ {aka ‘struct std::pair’} with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 1114 | memcpy(&subSeqs.front(),binseq.regions[0],sizeof(SequenceBinary::Region)*binseq.regionSizes[0]); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/bits/stl_algobase.h:64, from /usr/include/c++/11/bits/stl_tree.h:63, from /usr/include/c++/11/set:60, from cmultiset.h:33, from sequence.h:30, from murasaki.h:24, from sequence.cc:28: /usr/include/c++/11/bits/stl_pair.h:211:12: note: ‘ShmVector >::val_type’ {aka ‘struct std::pair’} declared here 211 | struct pair | ^~~~ dinkymath.cc: In function ‘std::string littleEndianStr(unsigned int, int)’: dinkymath.cc:40:7: warning: variable ‘last’ set but not used [-Wunused-but-set-variable] 40 | int last=0; | ^~~~ dinkymath.cc: In function ‘std::string littleEndianPat(unsigned int, int)’: dinkymath.cc:53:7: warning: variable ‘last’ set but not used [-Wunused-but-set-variable] 53 | int last=0; | ^~~~ sequence.cc: In member function ‘std::pair IntervalSet::entropy() const’: sequence.cc:3332:10: warning: variable ‘shortest’ set but not used [-Wunused-but-set-variable] 3332 | SeqPos shortest=0,shortlen=length(spaces[0]); | ^~~~~~~~ In file included from sequence.h:44, from murasaki.h:24, from sequence.cc:28: shmvector.hh: In instantiation of ‘void ShmVector::shmRealloc(size_t) [with T = std::pair; size_t = long unsigned int]’: shmvector.hh:282:5: required from ‘void ShmVector::resize(size_t) [with T = std::pair; size_t = long unsigned int]’ sequence.cc:1110:17: required from here shmvector.hh:225:13: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of type ‘struct std::pair’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 225 | memcpy(_data,old_data,(oldByteCapacity<_byteCapacity ? oldByteCapacity:_byteCapacity)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/bits/stl_algobase.h:64, from /usr/include/c++/11/bits/stl_tree.h:63, from /usr/include/c++/11/set:60, from cmultiset.h:33, from sequence.h:30, from murasaki.h:24, from sequence.cc:28: /usr/include/c++/11/bits/stl_pair.h:211:12: note: ‘struct std::pair’ declared here 211 | struct pair | ^~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c seqread.cc murasaki.cc: In function ‘void procLocs(LocList&, std::__cxx11::list&, int, int)’: murasaki.cc:1008:8: warning: variable ‘revZero’ set but not used [-Wunused-but-set-variable] 1008 | bool revZero=false; | ^~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c scoring.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c openhash.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c genopts.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c binseq.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c cgr-image.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c cgr.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c cgr-compare.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c cgr-random.cc binseq.cc: In member function ‘bool SequenceBinary::save(std::string)’: binseq.cc:70:28: warning: catching polymorphic type ‘class std::ios_base::failure’ by value [-Wcatch-value=] 70 | }catch(ofstream::failure e){ | ^ binseq.cc: In member function ‘void SequenceBinary::fillCopyVectors()’: binseq.cc:158:9: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of type ‘__gnu_cxx::__alloc_traits >, std::pair >::value_type’ {aka ‘struct std::pair’} with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 158 | memcpy(&subSeqs.front(),regions[0],regionSizes[0]*sizeof(Region)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/bits/stl_algobase.h:64, from /usr/include/c++/11/bits/char_traits.h:39, from /usr/include/c++/11/ios:40, from /usr/include/c++/11/istream:38, from /usr/include/c++/11/fstream:38, from seqread.h:30, from binseq.hh:31, from binseq.cc:21: /usr/include/c++/11/bits/stl_pair.h:211:12: note: ‘__gnu_cxx::__alloc_traits >, std::pair >::value_type’ {aka ‘struct std::pair’} declared here 211 | struct pair | ^~~~ binseq.cc:160:9: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of type ‘__gnu_cxx::__alloc_traits >, std::pair >::value_type’ {aka ‘struct std::pair’} with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 160 | memcpy(&readableRegions.front(),regions[1],regionSizes[1]*sizeof(Region)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/bits/stl_algobase.h:64, from /usr/include/c++/11/bits/char_traits.h:39, from /usr/include/c++/11/ios:40, from /usr/include/c++/11/istream:38, from /usr/include/c++/11/fstream:38, from seqread.h:30, from binseq.hh:31, from binseq.cc:21: /usr/include/c++/11/bits/stl_pair.h:211:12: note: ‘__gnu_cxx::__alloc_traits >, std::pair >::value_type’ {aka ‘struct std::pair’} declared here 211 | struct pair | ^~~~ binseq.cc:162:9: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of type ‘__gnu_cxx::__alloc_traits >, std::pair >::value_type’ {aka ‘struct std::pair’} with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 162 | memcpy(&unmaskedRegions.front(),regions[2],regionSizes[2]*sizeof(Region)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/bits/stl_algobase.h:64, from /usr/include/c++/11/bits/char_traits.h:39, from /usr/include/c++/11/ios:40, from /usr/include/c++/11/istream:38, from /usr/include/c++/11/fstream:38, from seqread.h:30, from binseq.hh:31, from binseq.cc:21: /usr/include/c++/11/bits/stl_pair.h:211:12: note: ‘__gnu_cxx::__alloc_traits >, std::pair >::value_type’ {aka ‘struct std::pair’} declared here 211 | struct pair | ^~~~ cgr.cc: In member function ‘void Cgr::merge(Cgr&)’: cgr.cc:140:7: warning: variable ‘redist’ set but not used [-Wunused-but-set-variable] 140 | int redist=(unsigned long)(rez*rez)<=seedcount; | ^~~~~~ cgr.cc: In member function ‘bool Cgr::savePNG(std::string)’: cgr.cc:288:7: warning: variable ‘res’ set but not used [-Wunused-but-set-variable] 288 | int res; | ^~~ cgr.cc: In member function ‘int PgmBuffer::loadPGM(std::string)’: cgr.cc:435:7: warning: variable ‘wordwidth’ set but not used [-Wunused-but-set-variable] 435 | int wordwidth=1; | ^~~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c cgr-sample.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c testeco.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c align-compare.cc cgr.cc: In member function ‘int PgmBuffer::loadBinaryPGM(std::string)’: cgr.cc:557:31: warning: ‘height’ may be used uninitialized in this function [-Wmaybe-uninitialized] 557 | if(data.size()<(uint)(height*width)) | ~~~~~~~^~~~~~~ cgr.cc:557:31: warning: ‘width’ may be used uninitialized in this function [-Wmaybe-uninitialized] cgr.cc: In member function ‘int PgmBuffer::loadPGM(std::string)’: cgr.cc:485:31: warning: ‘height’ may be used uninitialized in this function [-Wmaybe-uninitialized] 485 | if(data.size()<(uint)(height*width)) | ~~~~~~~^~~~~~~ cgr.cc:485:31: warning: ‘width’ may be used uninitialized in this function [-Wmaybe-uninitialized] g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c alignments.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c align-or.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c geneparse.cc cgr-sample.cc: In function ‘int main(int, char**)’: cgr-sample.cc:54:8: warning: variable ‘repeatmask’ set but not used [-Wunused-but-set-variable] 54 | bool repeatmask=false,save=false; | ^~~~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c align-and.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c align-best.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c align-coverage.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c getsegments.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -c mbfa.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -o ../murasaki murasaki.o timing.o dinkymath.o sequence.o msethash.o options.o ecohash.o ecolist.o murasaki_mpi.o arrayhash.o seqread.o scoring.o openhash.o genopts.o binseq.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -o ../cgr-image cgr-image.o cgr.o dinkymath.o timing.o seqread.o genopts.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -o ../cgr-compare cgr-compare.o cgr.o dinkymath.o timing.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now align-coverage.cc: In function ‘int main(int, char**)’: align-coverage.cc:148:10: warning: variable ‘seqStats’ set but not used [-Wunused-but-set-variable] 148 | bool seqStats=true; | ^~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -o ../cgr-random cgr-random.o cgr.o dinkymath.o timing.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -o ../cgr-sample cgr.o cgr-sample.o seqread.o genopts.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -o ../testeco testeco.o ecolist.o dinkymath.o timing.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -o ../geneparse geneparse.o seqread.o genopts.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now getsegments.cc: In function ‘size_t getSubSeqs(SequenceFileReader&, std::__cxx11::list > >&, std::string)’: getsegments.cc:153:29: warning: catching polymorphic type ‘class boost::bad_lexical_cast’ by value [-Wcatch-value=] 153 | }catch(bad_lexical_cast e){ | ^ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -o ../mbfa mbfa.o dinkymath.o timing.o seqread.o binseq.o genopts.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -o ../align-compare align-compare.o dinkymath.o alignments.o timing.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -o ../align-or align-or.o alignments.o dinkymath.o timing.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -o ../align-and align-and.o alignments.o dinkymath.o timing.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -o ../align-best align-best.o alignments.o dinkymath.o timing.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -o ../align-coverage align-coverage.o alignments.o dinkymath.o timing.o seqread.o genopts.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now g++ -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -g -I/usr/include/pstreams -Wall -DLARGESEQ_SUPPORT -o ../getsegments getsegments.o seqread.o genopts.o -lboost_regex -lboost_filesystem -lboost_iostreams -lboost_system -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now make[3]: Leaving directory '/<>/src' make[2]: Leaving directory '/<>' 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 -a debian/rules override_dh_install-arch make[1]: Entering directory '/<>' dh_install -a # using wildcards in install files is practical but it duplicates some files find debian/murasaki/usr -name "*-mpi" -delete make[1]: Leaving directory '/<>' dh_installdocs -a dh_installchangelogs -a debian/rules override_dh_installman-arch make[1]: Entering directory '/<>' dh_installman -a mkdir -p debian/murasaki-mpi/usr/share/man/man1 for man in debian/murasaki/usr/share/man/man1/*.1 ; do \ cp -a ${man} debian/murasaki-mpi/usr/share/man/man1/`basename ${man} .1`-mpi.1 ; \ done make[1]: Leaving directory '/<>' dh_perl -a dh_link -a dh_strip_nondeterminism -a dh_compress -a dh_fixperms -a dh_missing -a dh_dwz -a dh_strip -a debugedit: debian/murasaki-mpi/usr/bin/mbfa-mpi: Unknown DWARF DW_FORM_0x1f20 debugedit: debian/murasaki/usr/bin/murasaki: Unknown DWARF DW_FORM_0x1f20 5d579777fef539dd24acf7ab195eb430d3c02b3f cbb0f28c27f0ea157e2c167675f6e9edced36bc4 debugedit: debian/murasaki-mpi/usr/bin/geneparse-mpi: Unknown DWARF DW_FORM_0x1f21 91b1c3979f61030d1141fad5690ea9887db77c2e debugedit: debian/murasaki/usr/bin/mbfa: Unknown DWARF DW_FORM_0x1f20 a7a352dd1ec91b5415eb3d104480a47ea9aa21d9 debugedit: debian/murasaki-mpi/usr/bin/murasaki-mpi: Unknown DWARF DW_FORM_0x1f21 b0406e416cf62e4bf390be4de1b2292c5f158666 debugedit: debian/murasaki/usr/bin/geneparse: Unknown DWARF DW_FORM_0x1f21 915b885c0fbcfc25e783745b95ef49b66144143f debugedit: debian/murasaki/usr/lib/murasaki/align-or: Unknown DWARF DW_FORM_0x1f20 3331b951e2df788e41ee043334e091c957b890d0 debugedit: debian/murasaki-mpi/usr/lib/murasaki/align-and-mpi: Unknown DWARF DW_FORM_0x1f20 7f92dcd9755b10f9123f1a3d9b28e67f3b20dd18 debugedit: debian/murasaki/usr/lib/murasaki/align-and: Unknown DWARF DW_FORM_0x1f20 4922dc4c78a409ad90fa9728faad7f3beeb96779 debugedit: debian/murasaki-mpi/usr/lib/murasaki/cgr-compare-mpi: Unknown DWARF DW_FORM_0x1f20 59a1249df434f9ae19d7d64d4f81d75a4b8fee37 debugedit: debian/murasaki/usr/lib/murasaki/cgr-compare: Unknown DWARF DW_FORM_0x1f20 615b9e8a0ad22b20fbcc6808e7ca1774855dba92 debugedit: debian/murasaki/usr/lib/murasaki/cgr-random: Unknown DWARF DW_FORM_0x1f20 baabedd48a699b5ff398f2e89b646f63eb748fcd debugedit: debian/murasaki-mpi/usr/lib/murasaki/cgr-random-mpi: Unknown DWARF DW_FORM_0x1f20 3e13be046c4e262a437f9aef05421d649201eed8 debugedit: debian/murasaki/usr/lib/murasaki/align-compare: Unknown DWARF DW_FORM_0x1f20 02a42d6527ea6eeb6270b4b00fe1d5b5bb8618e1 debugedit: debian/murasaki-mpi/usr/lib/murasaki/testeco-mpi: Unknown DWARF DW_FORM_0x1f20 11284a0fb23c2dda59bf08b22242db5088d54a71 debugedit: debian/murasaki-mpi/usr/lib/murasaki/align-best-mpi: Unknown DWARF DW_FORM_0x1f20 debugedit: debian/murasaki/usr/lib/murasaki/align-coverage: Unknown DWARF DW_FORM_0x1f20 f640f1ff740e88b21d3a5e23862b4cd4dc4cd2fd d3e7c482dfc388722b317804755fef7a7e09a4e1 debugedit: debian/murasaki-mpi/usr/lib/murasaki/align-compare-mpi: Unknown DWARF DW_FORM_0x1f20 f4b46371f72c5ecdbae4389369dc8f4b6e94fe61 debugedit: debian/murasaki/usr/lib/murasaki/align-best: Unknown DWARF DW_FORM_0x1f20 7134f69523c54b90f97d5c0158a0ac693dbdacb1 debugedit: debian/murasaki-mpi/usr/lib/murasaki/cgr-image-mpi: Unknown DWARF DW_FORM_0x1f20 d19202b3da4351f31dd958b814434ec68c290aec debugedit: debian/murasaki/usr/lib/murasaki/testeco: Unknown DWARF DW_FORM_0x1f20 cbd6203bac96fb1b0294dae4353dda95f3d7c8bc debugedit: debian/murasaki/usr/lib/murasaki/cgr-sample: Unknown DWARF DW_FORM_0x1f21 0685d355f589ba383f67c8cacd69af2081d6ab14 debugedit: debian/murasaki-mpi/usr/lib/murasaki/align-or-mpi: Unknown DWARF DW_FORM_0x1f20 8b023f1b0aa91a2e199fded4a9ad2896c481fa0b debugedit: debian/murasaki/usr/lib/murasaki/cgr-image: Unknown DWARF DW_FORM_0x1f20 debugedit: debian/murasaki-mpi/usr/lib/murasaki/cgr-sample-mpi: Unknown DWARF DW_FORM_0x1f21 fe5ded63612a864f60ad61fe6dc09712c0b9bb5c a03050278df1589c2038b870288a80897240bb00 debugedit: debian/murasaki-mpi/usr/lib/murasaki/align-coverage-mpi: Unknown DWARF DW_FORM_0x1f20 9a1f7ceb73b0dcddb483ccd835007ee46c0ae63b dh_makeshlibs -a dh_shlibdeps -a dh_installdeb -a dh_gencontrol -a dpkg-gencontrol: warning: package murasaki-mpi: substitution variable ${perl:Depends} unused, but is defined dpkg-gencontrol: warning: package murasaki-mpi: substitution variable ${perl:Depends} unused, but is defined dh_md5sums -a dh_builddeb -a INFO: pkgstriptranslations version 149 INFO: pkgstriptranslations version 149 INFO: pkgstriptranslations version 149 INFO: pkgstriptranslations version 149 pkgstriptranslations: processing murasaki-mpi (in debian/murasaki-mpi); do_strip: , oemstrip: pkgstriptranslations: processing murasaki-dbgsym (in debian/.debhelper/murasaki/dbgsym-root); do_strip: , oemstrip: pkgstriptranslations: processing murasaki (in debian/murasaki); do_strip: , oemstrip: pkgstriptranslations: processing murasaki-mpi-dbgsym (in debian/.debhelper/murasaki-mpi/dbgsym-root); do_strip: , oemstrip: pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/murasaki-mpi/DEBIAN/control, package murasaki-mpi, directory debian/murasaki-mpi INFO: pkgstripfiles: waiting for lock (murasaki-mpi) ... pkgstripfiles: processing control file: debian/murasaki/DEBIAN/control, package murasaki, directory debian/murasaki INFO: pkgstripfiles: waiting for lock (murasaki-mpi) ... pkgstripfiles: processing control file: debian/.debhelper/murasaki-mpi/dbgsym-root/DEBIAN/control, package murasaki-mpi-dbgsym, directory debian/.debhelper/murasaki-mpi/dbgsym-root dpkg-deb: building package 'murasaki-mpi-dbgsym' in 'debian/.debhelper/scratch-space/build-murasaki-mpi/murasaki-mpi-dbgsym_1.68.6-13build2_riscv64.deb'. pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: Truncating usr/share/doc/murasaki/changelog.Debian.gz to topmost ten records pkgstripfiles: Running PNG optimization (using 8 cpus) for package murasaki ... pkgstripfiles: No PNG files. dpkg-deb: building package 'murasaki' in '../murasaki_1.68.6-13build2_riscv64.deb'. pkgstripfiles: Truncating usr/share/doc/murasaki-mpi/changelog.Debian.gz to topmost ten records pkgstripfiles: Running PNG optimization (using 8 cpus) for package murasaki-mpi ... pkgstripfiles: No PNG files. dpkg-deb: building package 'murasaki-mpi' in '../murasaki-mpi_1.68.6-13build2_riscv64.deb'. pkgstripfiles: processing control file: debian/.debhelper/murasaki/dbgsym-root/DEBIAN/control, package murasaki-dbgsym, directory debian/.debhelper/murasaki/dbgsym-root dpkg-deb: building package 'murasaki-dbgsym' in 'debian/.debhelper/scratch-space/build-murasaki/murasaki-dbgsym_1.68.6-13build2_riscv64.deb'. Renaming murasaki-dbgsym_1.68.6-13build2_riscv64.deb to murasaki-dbgsym_1.68.6-13build2_riscv64.ddeb Renaming murasaki-mpi-dbgsym_1.68.6-13build2_riscv64.deb to murasaki-mpi-dbgsym_1.68.6-13build2_riscv64.ddeb dpkg-genbuildinfo --build=any -O../murasaki_1.68.6-13build2_riscv64.buildinfo dpkg-genchanges --build=any -mLaunchpad Build Daemon -O../murasaki_1.68.6-13build2_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 2022-05-01T08:34:55Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ murasaki_1.68.6-13build2_riscv64.changes: ----------------------------------------- Format: 1.8 Date: Sat, 30 Apr 2022 11:54:04 -0400 Source: murasaki Binary: murasaki murasaki-mpi Built-For-Profiles: noudeb Architecture: riscv64 Version: 1.68.6-13build2 Distribution: kinetic-proposed Urgency: medium Maintainer: Launchpad Build Daemon Changed-By: Jeremy Bicha Description: murasaki - homology detection tool across multiple large genomes murasaki-mpi - homology detection tool across multiple large genomes (MPI-versio Changes: murasaki (1.68.6-13build2) kinetic; urgency=medium . * No-change rebuild against latest icu Checksums-Sha1: 3a92ad933bdcafde0d785e1c1a031ccead08e49a 7703320 murasaki-dbgsym_1.68.6-13build2_riscv64.ddeb 5a677da6580cfd12dc705956cd993a0641949d42 8780920 murasaki-mpi-dbgsym_1.68.6-13build2_riscv64.ddeb de120f6903a357ddc0c5836b37840a6d9d154f46 681042 murasaki-mpi_1.68.6-13build2_riscv64.deb f5c37cad21399b8081a7fd8ac5bbd43052cdcee6 9354 murasaki_1.68.6-13build2_riscv64.buildinfo 9a63b097a65b976f9bb65f6834778cde299f504c 548286 murasaki_1.68.6-13build2_riscv64.deb Checksums-Sha256: 3f1c9f750519cf7bd0c9ac3872730c34a6ff8695e958d868572357cf7bde65cc 7703320 murasaki-dbgsym_1.68.6-13build2_riscv64.ddeb 5fb82d84b01977576522716279f6311566d60f680a8aec2d48dab1216419df3b 8780920 murasaki-mpi-dbgsym_1.68.6-13build2_riscv64.ddeb 48f046760ae133a0ef2617db0149bc164d0b1de25f53aee52f16da88339f01fe 681042 murasaki-mpi_1.68.6-13build2_riscv64.deb 0a66d4a329e58045569d6f3ced3bb14cfb006782eb8cd78d7110f2d805e66348 9354 murasaki_1.68.6-13build2_riscv64.buildinfo f7e47733c1b0b83a8c23dcc84c88d0224fde8bafd089f227b2548a299b746c73 548286 murasaki_1.68.6-13build2_riscv64.deb Files: 46d0364e5f458a67e61baaabca8e3e33 7703320 debug optional murasaki-dbgsym_1.68.6-13build2_riscv64.ddeb a26995bac357a9bbed1bf5ae81ddd571 8780920 debug optional murasaki-mpi-dbgsym_1.68.6-13build2_riscv64.ddeb 1e9819ecf7760c0eba1d318a416ac1a7 681042 science optional murasaki-mpi_1.68.6-13build2_riscv64.deb f9fd53a59c2667c5959019597b204981 9354 science optional murasaki_1.68.6-13build2_riscv64.buildinfo 2a92050883c7672e8af44d151788d716 548286 science optional murasaki_1.68.6-13build2_riscv64.deb /<>/murasaki_1.68.6-13build2_riscv64.changes.new could not be renamed to /<>/murasaki_1.68.6-13build2_riscv64.changes: Illegal seek Distribution field may be wrong!!! +------------------------------------------------------------------------------+ | Buildinfo | +------------------------------------------------------------------------------+ Format: 1.0 Source: murasaki Binary: murasaki murasaki-dbgsym murasaki-mpi murasaki-mpi-dbgsym Architecture: riscv64 Version: 1.68.6-13build2 Checksums-Md5: 46d0364e5f458a67e61baaabca8e3e33 7703320 murasaki-dbgsym_1.68.6-13build2_riscv64.ddeb a26995bac357a9bbed1bf5ae81ddd571 8780920 murasaki-mpi-dbgsym_1.68.6-13build2_riscv64.ddeb 1e9819ecf7760c0eba1d318a416ac1a7 681042 murasaki-mpi_1.68.6-13build2_riscv64.deb 2a92050883c7672e8af44d151788d716 548286 murasaki_1.68.6-13build2_riscv64.deb Checksums-Sha1: 3a92ad933bdcafde0d785e1c1a031ccead08e49a 7703320 murasaki-dbgsym_1.68.6-13build2_riscv64.ddeb 5a677da6580cfd12dc705956cd993a0641949d42 8780920 murasaki-mpi-dbgsym_1.68.6-13build2_riscv64.ddeb de120f6903a357ddc0c5836b37840a6d9d154f46 681042 murasaki-mpi_1.68.6-13build2_riscv64.deb 9a63b097a65b976f9bb65f6834778cde299f504c 548286 murasaki_1.68.6-13build2_riscv64.deb Checksums-Sha256: 3f1c9f750519cf7bd0c9ac3872730c34a6ff8695e958d868572357cf7bde65cc 7703320 murasaki-dbgsym_1.68.6-13build2_riscv64.ddeb 5fb82d84b01977576522716279f6311566d60f680a8aec2d48dab1216419df3b 8780920 murasaki-mpi-dbgsym_1.68.6-13build2_riscv64.ddeb 48f046760ae133a0ef2617db0149bc164d0b1de25f53aee52f16da88339f01fe 681042 murasaki-mpi_1.68.6-13build2_riscv64.deb f7e47733c1b0b83a8c23dcc84c88d0224fde8bafd089f227b2548a299b746c73 548286 murasaki_1.68.6-13build2_riscv64.deb Build-Origin: Ubuntu Build-Architecture: riscv64 Build-Date: Sun, 01 May 2022 08:34:45 +0000 Build-Path: /<> Build-Tainted-By: merged-usr-via-aliased-dirs usr-local-has-programs Installed-Build-Depends: adduser (= 3.118ubuntu5), autoconf (= 2.71-2), automake (= 1:1.16.5-1.3), autopoint (= 0.21-4ubuntu4), autotools-dev (= 20220109.1), base-files (= 12ubuntu5), base-passwd (= 3.5.52build1), bash (= 5.1-6ubuntu1), binutils (= 2.38-3ubuntu1), binutils-common (= 2.38-3ubuntu1), binutils-riscv64-linux-gnu (= 2.38-3ubuntu1), bsdextrautils (= 2.37.2-4ubuntu3), bsdutils (= 1:2.37.2-4ubuntu3), build-essential (= 12.9ubuntu3), bzip2 (= 1.0.8-5build1), coreutils (= 8.32-4.1ubuntu1), cpp (= 4:11.2.0-1ubuntu1), cpp-11 (= 11.3.0-1ubuntu1), dash (= 0.5.11+git20210903+057cd650a4ed-3build1), debconf (= 1.5.79ubuntu1), debhelper (= 13.6ubuntu1), debianutils (= 5.5-1ubuntu2), debugedit (= 1:5.0-4build1), dh-autoreconf (= 20), dh-strip-nondeterminism (= 1.13.0-1), diffutils (= 1:3.8-0ubuntu2), dpkg (= 1.21.1ubuntu2), dpkg-dev (= 1.21.1ubuntu2), dwz (= 0.14-1build2), file (= 1:5.41-4), findutils (= 4.8.0-1ubuntu3), g++ (= 4:11.2.0-1ubuntu1), g++-11 (= 11.3.0-1ubuntu1), gcc (= 4:11.2.0-1ubuntu1), gcc-11 (= 11.3.0-1ubuntu1), gcc-11-base (= 11.3.0-1ubuntu1), gcc-12-base (= 12-20220428-1ubuntu1), gettext (= 0.21-4ubuntu4), gettext-base (= 0.21-4ubuntu4), gfortran-11 (= 11.3.0-1ubuntu1), grep (= 3.7-1build1), groff-base (= 1.22.4-8build1), gzip (= 1.10-4ubuntu4), hostname (= 3.23ubuntu2), ibverbs-providers (= 39.0-1), icu-devtools (= 71.1-2), init-system-helpers (= 1.62), intltool-debian (= 0.35.0+20060710.5), libacl1 (= 2.3.1-1), libarchive-zip-perl (= 1.68-1), libasan6 (= 11.3.0-1ubuntu1), libatomic1 (= 12-20220428-1ubuntu1), libattr1 (= 1:2.5.1-1build1), libaudit-common (= 1:3.0.7-1build1), libaudit1 (= 1:3.0.7-1build1), libbinutils (= 2.38-3ubuntu1), libblkid1 (= 2.37.2-4ubuntu3), libboost-filesystem-dev (= 1.74.0.3ubuntu7), libboost-filesystem1.74-dev (= 1.74.0-14ubuntu4), libboost-filesystem1.74.0 (= 1.74.0-14ubuntu4), libboost-iostreams-dev (= 1.74.0.3ubuntu7), libboost-iostreams1.74-dev (= 1.74.0-14ubuntu4), libboost-iostreams1.74.0 (= 1.74.0-14ubuntu4), libboost-regex-dev (= 1.74.0.3ubuntu7), libboost-regex1.74-dev (= 1.74.0-14ubuntu4), libboost-regex1.74.0 (= 1.74.0-14ubuntu4), libboost-system1.74-dev (= 1.74.0-14ubuntu4), libboost-system1.74.0 (= 1.74.0-14ubuntu4), libboost1.74-dev (= 1.74.0-14ubuntu4), libbrotli1 (= 1.0.9-2build6), libbsd0 (= 0.11.6-1), 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 (= 0.7.9-2.2build3), libcap2 (= 1:2.44-1build3), libcbor0.8 (= 0.8.0-2ubuntu1), libcc1-0 (= 12-20220428-1ubuntu1), libcom-err2 (= 1.46.5-2ubuntu1), libcrypt-dev (= 1:4.4.27-1), libcrypt1 (= 1:4.4.27-1), libcrypto++-dev (= 8.6.0-2ubuntu1), libcrypto++8 (= 8.6.0-2ubuntu1), libctf-nobfd0 (= 2.38-3ubuntu1), libctf0 (= 2.38-3ubuntu1), libcurl3-gnutls (= 7.83.0-1), libdb5.3 (= 5.3.28+dfsg1-0.8ubuntu3), libdebconfclient0 (= 0.261ubuntu1), libdebhelper-perl (= 13.6ubuntu1), libdpkg-perl (= 1.21.1ubuntu2), libdw1 (= 0.186-1build1), libedit2 (= 3.1-20210910-1build1), libelf1 (= 0.186-1build1), libevent-2.1-7 (= 2.1.12-stable-5), libevent-core-2.1-7 (= 2.1.12-stable-5), libevent-dev (= 2.1.12-stable-5), libevent-extra-2.1-7 (= 2.1.12-stable-5), libevent-openssl-2.1-7 (= 2.1.12-stable-5), libevent-pthreads-2.1-7 (= 2.1.12-stable-5), libfabric1 (= 1.11.0-3), libffi8 (= 3.4.2-4), libfido2-1 (= 1.10.0-1), libfile-stripnondeterminism-perl (= 1.13.0-1), libgcc-11-dev (= 11.3.0-1ubuntu1), libgcc-s1 (= 12-20220428-1ubuntu1), libgcrypt20 (= 1.9.4-3ubuntu3), libgdbm-compat4 (= 1.23-1), libgdbm6 (= 1.23-1), libgfortran-11-dev (= 11.3.0-1ubuntu1), libgfortran5 (= 12-20220428-1ubuntu1), libgmp10 (= 2:6.2.1+dfsg-3ubuntu1), libgnutls30 (= 3.7.4-2ubuntu1), libgomp1 (= 12-20220428-1ubuntu1), libgpg-error0 (= 1.45-2), libgssapi-krb5-2 (= 1.19.2-2), libhogweed6 (= 3.7.3-1build2), libhwloc-dev (= 2.7.1-1), libhwloc-plugins (= 2.7.1-1), libhwloc15 (= 2.7.1-1), libibverbs-dev (= 39.0-1), libibverbs1 (= 39.0-1), libicu-dev (= 71.1-2), libicu71 (= 71.1-2), libidn2-0 (= 2.3.2-2build1), libisl23 (= 0.24-2build1), libjs-jquery (= 3.6.0+dfsg+~3.5.13-1), libjs-jquery-ui (= 1.13.1+dfsg-1), libk5crypto3 (= 1.19.2-2), libkeyutils1 (= 1.6.1-2ubuntu3), libkrb5-3 (= 1.19.2-2), libkrb5support0 (= 1.19.2-2), libldap-2.5-0 (= 2.5.11+dfsg-1~exp1ubuntu3), libltdl-dev (= 2.4.7-3), libltdl7 (= 2.4.7-3), liblz4-1 (= 1.9.3-2build2), liblzma5 (= 5.2.5-2ubuntu1), libmagic-mgc (= 1:5.41-4), libmagic1 (= 1:5.41-4), libmd0 (= 1.0.4-1build1), libmount1 (= 2.37.2-4ubuntu3), libmpc3 (= 1.2.1-2build1), libmpfr6 (= 4.1.0-3build3), libnettle8 (= 3.7.3-1build2), libnghttp2-14 (= 1.47.0-1), libnl-3-200 (= 3.5.0-0.1), libnl-3-dev (= 3.5.0-0.1), libnl-route-3-200 (= 3.5.0-0.1), libnl-route-3-dev (= 3.5.0-0.1), libnsl-dev (= 1.3.0-2build2), libnsl2 (= 1.3.0-2build2), libnuma-dev (= 2.0.14-3ubuntu2), libnuma1 (= 2.0.14-3ubuntu2), libopenmpi-dev (= 4.1.3-2ubuntu1), libopenmpi3 (= 4.1.3-2ubuntu1), libp11-kit0 (= 0.24.1-1), libpam-modules (= 1.4.0-13ubuntu1), libpam-modules-bin (= 1.4.0-13ubuntu1), libpam-runtime (= 1.4.0-13ubuntu1), libpam0g (= 1.4.0-13ubuntu1), libpciaccess0 (= 0.16-3), libpcre2-8-0 (= 10.40-1), libpcre3 (= 2:8.39-14), libperl5.34 (= 5.34.0-3ubuntu1), libpipeline1 (= 1.5.6-1), libpmix-dev (= 4.1.2-2ubuntu1), libpmix2 (= 4.1.2-2ubuntu1), libpsl5 (= 0.21.0-1.2build2), libpstreams-dev (= 1.0.3-1), librdmacm1 (= 39.0-1), librtmp1 (= 2.4+20151223.gitfa8646d.1-2build4), libsasl2-2 (= 2.1.27+dfsg2-3ubuntu1), libsasl2-modules-db (= 2.1.27+dfsg2-3ubuntu1), libselinux1 (= 3.3-1build2), libsemanage-common (= 3.3-1build2), libsemanage2 (= 3.3-1build2), libsepol2 (= 3.3-1build1), libsigsegv2 (= 2.13-1ubuntu3), libsmartcols1 (= 2.37.2-4ubuntu3), libssh-4 (= 0.9.6-2build1), libssl3 (= 3.0.2-0ubuntu1), libstdc++-11-dev (= 11.3.0-1ubuntu1), libstdc++6 (= 12-20220428-1ubuntu1), libsub-override-perl (= 0.09-2), libsystemd0 (= 249.11-0ubuntu3.1), libtasn1-6 (= 4.18.0-4build1), libterm-readkey-perl (= 2.38-1build4), libtext-wrapper-perl (= 1.05-2), libtinfo6 (= 6.3+20220423-1), libtirpc-common (= 1.3.2-2build1), libtirpc-dev (= 1.3.2-2build1), libtirpc3 (= 1.3.2-2build1), libtool (= 2.4.7-3), libuchardet0 (= 0.0.7-1build2), libudev1 (= 249.11-0ubuntu3.1), libunistring2 (= 1.0-1), libuuid1 (= 2.37.2-4ubuntu3), libx11-6 (= 2:1.7.5-1), libx11-data (= 2:1.7.5-1), libxau6 (= 1:1.0.9-1build5), libxcb1 (= 1.14-3ubuntu3), libxdmcp6 (= 1:1.1.3-0ubuntu5), libxext6 (= 2:1.3.4-1build1), libxml2 (= 2.9.13+dfsg-1build2), libxnvctrl0 (= 510.47.03-0ubuntu1), libzstd1 (= 1.5.2+dfsg-1), linux-libc-dev (= 5.15.0-28.29), login (= 1:4.8.1-2ubuntu2), lsb-base (= 11.1.0ubuntu4), lto-disabled-list (= 25), m4 (= 1.4.18-5ubuntu2), make (= 4.3-4.1build1), man-db (= 2.10.2-1), mawk (= 1.3.4.20200120-3), ncurses-base (= 6.3+20220423-1), ncurses-bin (= 6.3+20220423-1), ocl-icd-libopencl1 (= 2.2.14-3), openmpi-bin (= 4.1.3-2ubuntu1), openmpi-common (= 4.1.3-2ubuntu1), openssh-client (= 1:9.0p1-1), passwd (= 1:4.8.1-2ubuntu2), patch (= 2.7.6-7build2), perl (= 5.34.0-3ubuntu1), perl-base (= 5.34.0-3ubuntu1), perl-modules-5.34 (= 5.34.0-3ubuntu1), 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 (= 2.37.2-4ubuntu3), xz-utils (= 5.2.5-2ubuntu1), zlib1g (= 1:1.2.11.dfsg-2ubuntu9), zlib1g-dev (= 1:1.2.11.dfsg-2ubuntu9) Environment: DEB_BUILD_OPTIONS="nocheck parallel=8" DEB_BUILD_PROFILES="noudeb" LANG="C.UTF-8" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1651334044" +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ murasaki-mpi_1.68.6-13build2_riscv64.deb ---------------------------------------- new Debian package, version 2.0. size 681042 bytes: control archive=1563 bytes. 1468 bytes, 29 lines control 1326 bytes, 20 lines md5sums Package: murasaki-mpi Source: murasaki Version: 1.68.6-13build2 Architecture: riscv64 Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 3213 Depends: murasaki-common, libboost-filesystem1.74.0 (>= 1.74.0), libboost-iostreams1.74.0 (>= 1.74.0), libboost-regex1.74.0-icu71, libc6 (>= 2.34), libgcc-s1 (>= 3.4), libopenmpi3 (>= 4.1.3), libstdc++6 (>= 11) Section: science Priority: optional Homepage: http://murasaki.dna.bio.keio.ac.jp/wiki/ Description: homology detection tool across multiple large genomes (MPI-version) Murasaki is a scalable and fast, language theory-based homology detection tool across multiple large genomes. It enable whole-genome scale multiple genome global alignments. Supports unlimited length gapped-seed patterns and unique TF-IDF based filtering. . Murasaki is an anchor alignment software, which is * exteremely fast (17 CPU hours for whole Human x Mouse genome (with 40 nodes: 52 wall minutes)) * scalable (Arbitrarily parallelizable across multiple nodes using MPI. Even a single node with 16GB of ram can handle over 1Gbp of sequence.) * unlimited pattern length * repeat tolerant * intelligent noise reduction . This package provides the MPI-enabled binary for murasaki. While this will speed up operation on multi-processor machines it will slow down on a single processor. drwxr-xr-x root/root 0 2022-04-30 15:54 ./ drwxr-xr-x root/root 0 2022-04-30 15:54 ./usr/ drwxr-xr-x root/root 0 2022-04-30 15:54 ./usr/bin/ -rwxr-xr-x root/root 196680 2022-04-30 15:54 ./usr/bin/geneparse-mpi -rwxr-xr-x root/root 296320 2022-04-30 15:54 ./usr/bin/mbfa-mpi -rwxr-xr-x root/root 664304 2022-04-30 15:54 ./usr/bin/murasaki-mpi drwxr-xr-x root/root 0 2022-04-30 15:54 ./usr/lib/ drwxr-xr-x root/root 0 2022-04-30 15:54 ./usr/lib/murasaki/ -rwxr-xr-x root/root 201496 2022-04-30 15:54 ./usr/lib/murasaki/align-and-mpi -rwxr-xr-x root/root 205648 2022-04-30 15:54 ./usr/lib/murasaki/align-best-mpi -rwxr-xr-x root/root 222120 2022-04-30 15:54 ./usr/lib/murasaki/align-compare-mpi -rwxr-xr-x root/root 312720 2022-04-30 15:54 ./usr/lib/murasaki/align-coverage-mpi -rwxr-xr-x root/root 197368 2022-04-30 15:54 ./usr/lib/murasaki/align-or-mpi -rwxr-xr-x root/root 139832 2022-04-30 15:54 ./usr/lib/murasaki/cgr-compare-mpi -rwxr-xr-x root/root 308728 2022-04-30 15:54 ./usr/lib/murasaki/cgr-image-mpi -rwxr-xr-x root/root 7138 2010-08-24 14:18 ./usr/lib/murasaki/cgr-image.pl-mpi -rwxr-xr-x root/root 148144 2022-04-30 15:54 ./usr/lib/murasaki/cgr-random-mpi -rwxr-xr-x root/root 233648 2022-04-30 15:54 ./usr/lib/murasaki/cgr-sample-mpi -rwxr-xr-x root/root 114840 2022-04-30 15:54 ./usr/lib/murasaki/testeco-mpi drwxr-xr-x root/root 0 2022-04-30 15:54 ./usr/share/ drwxr-xr-x root/root 0 2022-04-30 15:54 ./usr/share/doc/ drwxr-xr-x root/root 0 2022-04-30 15:54 ./usr/share/doc/murasaki-mpi/ -rw-r--r-- root/root 249 2021-03-19 18:45 ./usr/share/doc/murasaki-mpi/README.test -rw-r--r-- root/root 1181 2022-04-30 15:54 ./usr/share/doc/murasaki-mpi/changelog.Debian.gz -rw-r--r-- root/root 2225 2021-03-19 18:45 ./usr/share/doc/murasaki-mpi/copyright drwxr-xr-x root/root 0 2022-04-30 15:54 ./usr/share/man/ drwxr-xr-x root/root 0 2022-04-30 15:54 ./usr/share/man/man1/ -rw-r--r-- root/root 2518 2022-04-30 15:54 ./usr/share/man/man1/geneparse-mpi.1.gz -rw-r--r-- root/root 2721 2022-04-30 15:54 ./usr/share/man/man1/mbfa-mpi.1.gz -rw-r--r-- root/root 10888 2022-04-30 15:54 ./usr/share/man/man1/murasaki-mpi.1.gz murasaki_1.68.6-13build2_riscv64.deb ------------------------------------ new Debian package, version 2.0. size 548286 bytes: control archive=1410 bytes. 1239 bytes, 24 lines control 1182 bytes, 19 lines md5sums Package: murasaki Version: 1.68.6-13build2 Architecture: riscv64 Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 2417 Depends: murasaki-common, libboost-filesystem1.74.0 (>= 1.74.0), libboost-iostreams1.74.0 (>= 1.74.0), libboost-regex1.74.0-icu71, libc6 (>= 2.34), libgcc-s1 (>= 3.4), libstdc++6 (>= 11) Section: science Priority: optional Homepage: http://murasaki.dna.bio.keio.ac.jp/wiki/ Description: homology detection tool across multiple large genomes Murasaki is a scalable and fast, language theory-based homology detection tool across multiple large genomes. It enable whole-genome scale multiple genome global alignments. Supports unlimited length gapped-seed patterns and unique TF-IDF based filtering. . Murasaki is an anchor alignment software, which is * exteremely fast (17 CPU hours for whole Human x Mouse genome (with 40 nodes: 52 wall minutes)) * scalable (Arbitrarily parallelizable across multiple nodes using MPI. Even a single node with 16GB of ram can handle over 1Gbp of sequence.) * unlimited pattern length * repeat tolerant * intelligent noise reduction drwxr-xr-x root/root 0 2022-04-30 15:54 ./ drwxr-xr-x root/root 0 2022-04-30 15:54 ./usr/ drwxr-xr-x root/root 0 2022-04-30 15:54 ./usr/bin/ -rwxr-xr-x root/root 196672 2022-04-30 15:54 ./usr/bin/geneparse -rwxr-xr-x root/root 229512 2022-04-30 15:54 ./usr/bin/mbfa -rwxr-xr-x root/root 510928 2022-04-30 15:54 ./usr/bin/murasaki drwxr-xr-x root/root 0 2022-04-30 15:54 ./usr/lib/ drwxr-xr-x root/root 0 2022-04-30 15:54 ./usr/lib/murasaki/ -rwxr-xr-x root/root 134664 2022-04-30 15:54 ./usr/lib/murasaki/align-and -rwxr-xr-x root/root 138816 2022-04-30 15:54 ./usr/lib/murasaki/align-best -rwxr-xr-x root/root 155288 2022-04-30 15:54 ./usr/lib/murasaki/align-compare -rwxr-xr-x root/root 245888 2022-04-30 15:54 ./usr/lib/murasaki/align-coverage -rwxr-xr-x root/root 134632 2022-04-30 15:54 ./usr/lib/murasaki/align-or -rwxr-xr-x root/root 77104 2022-04-30 15:54 ./usr/lib/murasaki/cgr-compare -rwxr-xr-x root/root 241904 2022-04-30 15:54 ./usr/lib/murasaki/cgr-image -rwxr-xr-x root/root 81336 2022-04-30 15:54 ./usr/lib/murasaki/cgr-random -rwxr-xr-x root/root 233640 2022-04-30 15:54 ./usr/lib/murasaki/cgr-sample -rwxr-xr-x root/root 52120 2022-04-30 15:54 ./usr/lib/murasaki/testeco drwxr-xr-x root/root 0 2022-04-30 15:54 ./usr/share/ drwxr-xr-x root/root 0 2022-04-30 15:54 ./usr/share/doc/ drwxr-xr-x root/root 0 2022-04-30 15:54 ./usr/share/doc/murasaki/ -rw-r--r-- root/root 249 2021-03-19 18:45 ./usr/share/doc/murasaki/README.test -rw-r--r-- root/root 1179 2022-04-30 15:54 ./usr/share/doc/murasaki/changelog.Debian.gz -rw-r--r-- root/root 2225 2021-03-19 18:45 ./usr/share/doc/murasaki/copyright drwxr-xr-x root/root 0 2022-04-30 15:54 ./usr/share/man/ drwxr-xr-x root/root 0 2022-04-30 15:54 ./usr/share/man/man1/ -rw-r--r-- root/root 2518 2022-04-30 15:54 ./usr/share/man/man1/geneparse.1.gz -rw-r--r-- root/root 2721 2022-04-30 15:54 ./usr/share/man/man1/mbfa.1.gz -rw-r--r-- root/root 10888 2022-04-30 15:54 ./usr/share/man/man1/murasaki.1.gz +------------------------------------------------------------------------------+ | Post Build | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not removing build depends: as requested +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: riscv64 Build Type: any Build-Space: 239004 Build-Time: 1182 Distribution: kinetic-proposed Host Architecture: riscv64 Install-Time: 387 Job: murasaki_1.68.6-13build2.dsc Machine Architecture: riscv64 Package: murasaki Package-Time: 1601 Source-Version: 1.68.6-13build2 Space: 239004 Status: successful Version: 1.68.6-13build2 -------------------------------------------------------------------------------- Finished at 2022-05-01T08:34:55Z Build needed 00:26:41, 239004k 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-23595945 Scanning for processes to kill in build PACKAGEBUILD-23595945 RUN: /usr/share/launchpad-buildd/bin/in-target umount-chroot --backend=chroot --series=kinetic --arch=riscv64 PACKAGEBUILD-23595945 Stopping target for build PACKAGEBUILD-23595945 RUN: /usr/share/launchpad-buildd/bin/in-target remove-build --backend=chroot --series=kinetic --arch=riscv64 PACKAGEBUILD-23595945 Removing build PACKAGEBUILD-23595945