https://launchpad.net/ubuntu/+source/amap-align/2.2+git20080214.600fc29+dfsg-2/+build/20306384 RUN: /usr/share/launchpad-buildd/bin/builder-prep Kernel version: Linux riscv64-qemu-lcy01-089 5.4.0-36-generic #41-Ubuntu SMP Thu Oct 1 14:51:42 UTC 2020 riscv64 Buildd toolchain package versions: launchpad-buildd_193~468~ubuntu18.04.1 python3-lpbuildd_193~468~ubuntu18.04.1 sbuild_0.79.0-1ubuntu1 git_1:2.25.1-1ubuntu3 dpkg-dev_1.19.7ubuntu3 python3-debian_0.1.36ubuntu1. Syncing the system clock with the buildd NTP service... 16 Nov 17:18:20 ntpdate[150462]: adjust time server 10.211.37.1 offset -0.000172 sec RUN: /usr/share/launchpad-buildd/bin/in-target unpack-chroot --backend=chroot --series=hirsute --arch=riscv64 PACKAGEBUILD-20306384 --image-type chroot /home/buildd/filecache-default/455112eaccac6437d04b3f98755ef0ead6caaf02 Creating target for build PACKAGEBUILD-20306384 RUN: /usr/share/launchpad-buildd/bin/in-target mount-chroot --backend=chroot --series=hirsute --arch=riscv64 PACKAGEBUILD-20306384 Starting target for build PACKAGEBUILD-20306384 RUN: /usr/share/launchpad-buildd/bin/in-target override-sources-list --backend=chroot --series=hirsute --arch=riscv64 PACKAGEBUILD-20306384 'deb http://ftpmaster.internal/ubuntu hirsute main universe' 'deb http://ftpmaster.internal/ubuntu hirsute-security main universe' 'deb http://ftpmaster.internal/ubuntu hirsute-updates main universe' 'deb http://ftpmaster.internal/ubuntu hirsute-proposed main universe' Overriding sources.list in build-PACKAGEBUILD-20306384 RUN: /usr/share/launchpad-buildd/bin/in-target update-debian-chroot --backend=chroot --series=hirsute --arch=riscv64 PACKAGEBUILD-20306384 Updating target for build PACKAGEBUILD-20306384 Get:1 http://ftpmaster.internal/ubuntu hirsute InRelease [267 kB] Get:2 http://ftpmaster.internal/ubuntu hirsute-security InRelease [88.4 kB] Get:3 http://ftpmaster.internal/ubuntu hirsute-updates InRelease [88.4 kB] Get:4 http://ftpmaster.internal/ubuntu hirsute-proposed InRelease [118 kB] Get:5 http://ftpmaster.internal/ubuntu hirsute/main riscv64 Packages [1273 kB] Get:6 http://ftpmaster.internal/ubuntu hirsute/main Translation-en [509 kB] Get:7 http://ftpmaster.internal/ubuntu hirsute/universe riscv64 Packages [12.1 MB] Get:8 http://ftpmaster.internal/ubuntu hirsute/universe Translation-en [5332 kB] Get:9 http://ftpmaster.internal/ubuntu hirsute-proposed/main riscv64 Packages [157 kB] Get:10 http://ftpmaster.internal/ubuntu hirsute-proposed/main Translation-en [75.2 kB] Get:11 http://ftpmaster.internal/ubuntu hirsute-proposed/universe riscv64 Packages [1638 kB] Get:12 http://ftpmaster.internal/ubuntu hirsute-proposed/universe Translation-en [596 kB] Fetched 22.2 MB in 33s (680 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following NEW packages will be installed: libperl5.32 perl-modules-5.32 The following packages will be upgraded: apt base-files base-passwd bash binutils binutils-common binutils-riscv64-linux-gnu coreutils cpp-10 dash dpkg dpkg-dev fakeroot g++-10 gcc-10 gcc-10-base grep libapparmor1 libapt-pkg6.0 libatomic1 libaudit-common libaudit1 libbinutils libc-bin libc-dev-bin libc6 libc6-dev libcap2 libcc1-0 libcrypt-dev libcrypt1 libcryptsetup12 libctf-nobfd0 libctf0 libdebconfclient0 libdpkg-perl libfakeroot libgcc-10-dev libgcc-s1 libgcrypt20 libgomp1 libidn2-0 libip4tc2 liblocale-gettext-perl libmpc3 libncursesw6 libnpth0 libreadline8 libseccomp2 libselinux1 libsemanage-common libsemanage1 libstdc++-10-dev libstdc++6 libsystemd0 libtext-charwidth-perl libtext-iconv-perl libtinfo6 libtirpc-common libtirpc-dev libtirpc3 libudev1 linux-libc-dev ncurses-base ncurses-bin perl perl-base readline-common systemd systemd-sysv systemd-timesyncd sysvinit-utils 72 upgraded, 2 newly installed, 0 to remove and 0 not upgraded. Need to get 61.0 MB of archives. After this operation, 42.6 MB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu hirsute/main riscv64 libcrypt-dev riscv64 1:4.4.17-1ubuntu1 [199 kB] Get:2 http://ftpmaster.internal/ubuntu hirsute/main riscv64 libcrypt1 riscv64 1:4.4.17-1ubuntu1 [89.8 kB] Get:3 http://ftpmaster.internal/ubuntu hirsute-proposed/main riscv64 libc6-dev riscv64 2.32-0ubuntu5 [3192 kB] Get:4 http://ftpmaster.internal/ubuntu hirsute-proposed/main riscv64 libc-dev-bin riscv64 2.32-0ubuntu5 [28.8 kB] Get:5 http://ftpmaster.internal/ubuntu hirsute-proposed/main riscv64 linux-libc-dev riscv64 5.8.0-26.27 [1130 kB] Get:6 http://ftpmaster.internal/ubuntu hirsute-proposed/main riscv64 libtirpc-common all 1.2.6-3 [7444 B] Get:7 http://ftpmaster.internal/ubuntu hirsute-proposed/main riscv64 libtirpc-dev riscv64 1.2.6-3 [270 kB] Get:8 http://ftpmaster.internal/ubuntu hirsute-proposed/main riscv64 libtirpc3 riscv64 1.2.6-3 [68.4 kB] Get:9 http://ftpmaster.internal/ubuntu hirsute/main riscv64 libcc1-0 riscv64 10.2.0-17ubuntu1 [38.2 kB] Get:10 http://ftpmaster.internal/ubuntu hirsute/main riscv64 gcc-10-base riscv64 10.2.0-17ubuntu1 [19.6 kB] Get:11 http://ftpmaster.internal/ubuntu hirsute/main riscv64 libgcc-s1 riscv64 10.2.0-17ubuntu1 [40.5 kB] Get:12 http://ftpmaster.internal/ubuntu hirsute/main riscv64 libgomp1 riscv64 10.2.0-17ubuntu1 [83.8 kB] Get:13 http://ftpmaster.internal/ubuntu hirsute/main riscv64 libatomic1 riscv64 10.2.0-17ubuntu1 [7492 B] Get:14 http://ftpmaster.internal/ubuntu hirsute/main riscv64 g++-10 riscv64 10.2.0-17ubuntu1 [7493 kB] Get:15 http://ftpmaster.internal/ubuntu hirsute/main riscv64 libstdc++-10-dev riscv64 10.2.0-17ubuntu1 [3605 kB] Get:16 http://ftpmaster.internal/ubuntu hirsute/main riscv64 libgcc-10-dev riscv64 10.2.0-17ubuntu1 [473 kB] Get:17 http://ftpmaster.internal/ubuntu hirsute/main riscv64 gcc-10 riscv64 10.2.0-17ubuntu1 [13.1 MB] Get:18 http://ftpmaster.internal/ubuntu hirsute/main riscv64 cpp-10 riscv64 10.2.0-17ubuntu1 [6522 kB] Get:19 http://ftpmaster.internal/ubuntu hirsute/main riscv64 libstdc++6 riscv64 10.2.0-17ubuntu1 [509 kB] Get:20 http://ftpmaster.internal/ubuntu hirsute-proposed/main riscv64 libmpc3 riscv64 1.2.0-1 [41.6 kB] Get:21 http://ftpmaster.internal/ubuntu hirsute-proposed/main riscv64 libctf-nobfd0 riscv64 2.35.1-2ubuntu1 [41.5 kB] Get:22 http://ftpmaster.internal/ubuntu hirsute-proposed/main riscv64 libctf0 riscv64 2.35.1-2ubuntu1 [40.4 kB] Get:23 http://ftpmaster.internal/ubuntu hirsute-proposed/main riscv64 libbinutils riscv64 2.35.1-2ubuntu1 [289 kB] Get:24 http://ftpmaster.internal/ubuntu hirsute-proposed/main riscv64 binutils-common riscv64 2.35.1-2ubuntu1 [205 kB] Get:25 http://ftpmaster.internal/ubuntu hirsute-proposed/main riscv64 binutils riscv64 2.35.1-2ubuntu1 [3292 B] Get:26 http://ftpmaster.internal/ubuntu hirsute-proposed/main riscv64 binutils-riscv64-linux-gnu riscv64 2.35.1-2ubuntu1 [676 kB] Get:27 http://ftpmaster.internal/ubuntu hirsute-proposed/main riscv64 libc6 riscv64 2.32-0ubuntu5 [2258 kB] Get:28 http://ftpmaster.internal/ubuntu hirsute/main riscv64 base-files riscv64 11ubuntu16 [60.1 kB] Get:29 http://ftpmaster.internal/ubuntu hirsute/main riscv64 bash riscv64 5.1~rc2-1ubuntu1 [617 kB] Get:30 http://ftpmaster.internal/ubuntu hirsute-proposed/main riscv64 coreutils riscv64 8.32-4ubuntu1 [1252 kB] Get:31 http://ftpmaster.internal/ubuntu hirsute-proposed/main riscv64 dpkg riscv64 1.20.5ubuntu3 [1136 kB] Get:32 http://ftpmaster.internal/ubuntu hirsute/main riscv64 dash riscv64 0.5.11+git20200708+dd9ef66-2 [81.7 kB] Get:33 http://ftpmaster.internal/ubuntu hirsute/main riscv64 grep riscv64 3.6-1 [145 kB] Get:34 http://ftpmaster.internal/ubuntu hirsute-proposed/main riscv64 libncursesw6 riscv64 6.2+20200918-1 [115 kB] Get:35 http://ftpmaster.internal/ubuntu hirsute-proposed/main riscv64 libtinfo6 riscv64 6.2+20200918-1 [79.1 kB] Get:36 http://ftpmaster.internal/ubuntu hirsute-proposed/main riscv64 ncurses-bin riscv64 6.2+20200918-1 [167 kB] Get:37 http://ftpmaster.internal/ubuntu hirsute-proposed/main riscv64 libtext-iconv-perl riscv64 1.7-7build1 [13.1 kB] Get:38 http://ftpmaster.internal/ubuntu hirsute-proposed/main riscv64 libtext-charwidth-perl riscv64 0.04-10build1 [9480 B] Get:39 http://ftpmaster.internal/ubuntu hirsute-proposed/main riscv64 perl-modules-5.32 all 5.32.0-5 [2754 kB] Get:40 http://ftpmaster.internal/ubuntu hirsute-proposed/main riscv64 libperl5.32 riscv64 5.32.0-5 [3545 kB] Get:41 http://ftpmaster.internal/ubuntu hirsute-proposed/main riscv64 perl riscv64 5.32.0-5 [225 kB] Get:42 http://ftpmaster.internal/ubuntu hirsute-proposed/main riscv64 perl-base riscv64 5.32.0-5 [1469 kB] Get:43 http://ftpmaster.internal/ubuntu hirsute-proposed/main riscv64 liblocale-gettext-perl riscv64 1.07-4build1 [16.3 kB] Get:44 http://ftpmaster.internal/ubuntu hirsute-proposed/main riscv64 libdebconfclient0 riscv64 0.255ubuntu1 [5648 B] Get:45 http://ftpmaster.internal/ubuntu hirsute/main riscv64 base-passwd riscv64 3.5.48 [45.9 kB] Get:46 http://ftpmaster.internal/ubuntu hirsute-proposed/main riscv64 libc-bin riscv64 2.32-0ubuntu5 [514 kB] Get:47 http://ftpmaster.internal/ubuntu hirsute-proposed/main riscv64 ncurses-base all 6.2+20200918-1 [18.7 kB] Get:48 http://ftpmaster.internal/ubuntu hirsute/main riscv64 sysvinit-utils riscv64 2.96-5ubuntu1 [19.5 kB] Get:49 http://ftpmaster.internal/ubuntu hirsute-proposed/main riscv64 libgcrypt20 riscv64 1.8.7-2ubuntu1 [390 kB] Get:50 http://ftpmaster.internal/ubuntu hirsute/main riscv64 systemd-sysv riscv64 246.6-2ubuntu1 [10.3 kB] Get:51 http://ftpmaster.internal/ubuntu hirsute/main riscv64 systemd-timesyncd riscv64 246.6-2ubuntu1 [25.7 kB] Get:52 http://ftpmaster.internal/ubuntu hirsute-proposed/main riscv64 libapparmor1 riscv64 3.0.0-0ubuntu4 [32.1 kB] Get:53 http://ftpmaster.internal/ubuntu hirsute/main riscv64 libaudit-common all 1:2.8.5-3ubuntu2 [4092 B] Get:54 http://ftpmaster.internal/ubuntu hirsute/main riscv64 libaudit1 riscv64 1:2.8.5-3ubuntu2 [37.6 kB] Get:55 http://ftpmaster.internal/ubuntu hirsute/main riscv64 libcap2 riscv64 1:2.44-1 [15.5 kB] Get:56 http://ftpmaster.internal/ubuntu hirsute/main riscv64 libcryptsetup12 riscv64 2:2.3.4-1ubuntu1 [167 kB] Get:57 http://ftpmaster.internal/ubuntu hirsute/main riscv64 libidn2-0 riscv64 2.3.0-3 [50.3 kB] Get:58 http://ftpmaster.internal/ubuntu hirsute/main riscv64 libip4tc2 riscv64 1.8.5-3ubuntu3 [17.2 kB] Get:59 http://ftpmaster.internal/ubuntu hirsute/main riscv64 libseccomp2 riscv64 2.4.3-1ubuntu5 [37.9 kB] Get:60 http://ftpmaster.internal/ubuntu hirsute/main riscv64 systemd riscv64 246.6-2ubuntu1 [3724 kB] Get:61 http://ftpmaster.internal/ubuntu hirsute/main riscv64 libsystemd0 riscv64 246.6-2ubuntu1 [246 kB] Get:62 http://ftpmaster.internal/ubuntu hirsute/main riscv64 libudev1 riscv64 246.6-2ubuntu1 [60.5 kB] Get:63 http://ftpmaster.internal/ubuntu hirsute/main riscv64 libapt-pkg6.0 riscv64 2.1.11 [805 kB] Get:64 http://ftpmaster.internal/ubuntu hirsute/main riscv64 apt riscv64 2.1.11 [1239 kB] Get:65 http://ftpmaster.internal/ubuntu hirsute/main riscv64 libselinux1 riscv64 3.1-2build1 [64.9 kB] Get:66 http://ftpmaster.internal/ubuntu hirsute/main riscv64 libsemanage-common all 3.1-1build1 [10.1 kB] Get:67 http://ftpmaster.internal/ubuntu hirsute/main riscv64 libsemanage1 riscv64 3.1-1build1 [75.6 kB] Get:68 http://ftpmaster.internal/ubuntu hirsute-proposed/main riscv64 readline-common all 8.1~rc2-2 [54.1 kB] Get:69 http://ftpmaster.internal/ubuntu hirsute-proposed/main riscv64 libreadline8 riscv64 8.1~rc2-2 [119 kB] Get:70 http://ftpmaster.internal/ubuntu hirsute-proposed/main riscv64 dpkg-dev all 1.20.5ubuntu3 [758 kB] Get:71 http://ftpmaster.internal/ubuntu hirsute-proposed/main riscv64 libdpkg-perl all 1.20.5ubuntu3 [232 kB] Get:72 http://ftpmaster.internal/ubuntu hirsute-proposed/main riscv64 libfakeroot riscv64 1.25.3-1 [24.3 kB] Get:73 http://ftpmaster.internal/ubuntu hirsute-proposed/main riscv64 fakeroot riscv64 1.25.3-1 [66.6 kB] Get:74 http://ftpmaster.internal/ubuntu hirsute/main riscv64 libnpth0 riscv64 1.6-3 [7052 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 61.0 MB in 14s (4284 kB/s) (Reading database ... 10910 files and directories currently installed.) 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Kernel reported to sbuild: 5.4.0-36-generic #41-Ubuntu SMP Thu Oct 1 14:51:42 UTC 2020 riscv64 sbuild (Debian sbuild) 0.79.0 (05 February 2020) on riscv64-qemu-lcy01-089.buildd +=====================================================================================+ | amap-align 2.2+git20080214.600fc29+dfsg-2 (riscv64) Mon, 16 Nov 2020 17:24:28 +0000 | +=====================================================================================+ Package: amap-align Version: 2.2+git20080214.600fc29+dfsg-2 Source Version: 2.2+git20080214.600fc29+dfsg-2 Distribution: hirsute-proposed Machine Architecture: riscv64 Host Architecture: riscv64 Build Architecture: riscv64 Build Type: any I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-20306384/chroot-autobuild' with '<>' I: NOTICE: Log filtering will replace 'build/amap-align-qAKbrq/resolver-kf79Id' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- amap-align_2.2+git20080214.600fc29+dfsg-2.dsc exists in .; copying to chroot I: NOTICE: Log filtering will replace 'build/amap-align-qAKbrq/amap-align-2.2+git20080214.600fc29+dfsg' with '<>' I: NOTICE: Log filtering will replace 'build/amap-align-qAKbrq' with '<>' +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper-compat (= 13), build-essential, fakeroot Filtered Build-Depends: debhelper-compat (= 13), 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 [370 B] Get:5 copy:/<>/apt_archive ./ Packages [455 B] Fetched 1782 B in 1s (2811 B/s) Reading package lists... Reading package lists... Install main build dependencies (apt-based resolver) ---------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following packages were automatically installed and are no longer required: krb5-locales libgpm2 Use 'apt autoremove' to remove them. The following additional packages will be installed: autoconf automake autopoint autotools-dev debhelper dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base groff-base intltool-debian libarchive-zip-perl libcroco3 libdebhelper-perl libelf1 libfile-stripnondeterminism-perl libglib2.0-0 libicu67 libmagic-mgc libmagic1 libpipeline1 libsigsegv2 libsub-override-perl libtool libuchardet0 libxml2 m4 man-db po-debconf Suggested packages: autoconf-archive gnu-standards autoconf-doc dh-make gettext-doc libasprintf-dev libgettextpo-dev groff libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc apparmor less www-browser libmail-box-perl Recommended packages: curl | wget | lynx libarchive-cpio-perl libglib2.0-data shared-mime-info xdg-user-dirs libltdl-dev libmail-sendmail-perl The following NEW packages will be installed: autoconf automake autopoint autotools-dev debhelper dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base groff-base intltool-debian libarchive-zip-perl libcroco3 libdebhelper-perl libelf1 libfile-stripnondeterminism-perl libglib2.0-0 libicu67 libmagic-mgc libmagic1 libpipeline1 libsigsegv2 libsub-override-perl libtool libuchardet0 libxml2 m4 man-db po-debconf sbuild-build-depends-main-dummy 0 upgraded, 32 newly installed, 0 to remove and 0 not upgraded. Need to get 16.7 MB of archives. After this operation, 63.4 MB of additional disk space will be used. 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Processing triggers for libc-bin (2.32-0ubuntu5) ... +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (riscv64 included in any) +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 5.4.0-36-generic #41-Ubuntu SMP Thu Oct 1 14:51:42 UTC 2020 riscv64 (riscv64) Toolchain package versions: binutils_2.35.1-2ubuntu1 dpkg-dev_1.20.5ubuntu3 g++-10_10.2.0-17ubuntu1 gcc-10_10.2.0-17ubuntu1 libc6-dev_2.32-0ubuntu5 libstdc++-10-dev_10.2.0-17ubuntu1 libstdc++6_10.2.0-17ubuntu1 linux-libc-dev_5.8.0-26.27 Package versions: adduser_3.118ubuntu2 advancecomp_2.1-2.1build1 apt_2.1.11 autoconf_2.69-11.1 automake_1:1.16.2-4ubuntu1 autopoint_0.19.8.1-10build1 autotools-dev_20180224.1 base-files_11ubuntu16 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xz-utils_5.2.4-1ubuntu1 zlib1g_1:1.2.11.dfsg-2ubuntu4 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: amap-align Binary: amap-align Architecture: any Version: 2.2+git20080214.600fc29+dfsg-2 Maintainer: Debian Med Packaging Team Uploaders: Charles Plessy , Andreas Tille Homepage: https://github.com/mes5k/amap-align Standards-Version: 4.5.0 Vcs-Browser: https://salsa.debian.org/med-team/amap-align Vcs-Git: https://salsa.debian.org/med-team/amap-align.git Testsuite: autopkgtest Build-Depends: debhelper-compat (= 13) Package-List: amap-align deb science optional arch=any Checksums-Sha1: 685963f5b938e285cc938d8ab6a4a8084e18458a 65472 amap-align_2.2+git20080214.600fc29+dfsg.orig.tar.xz 72ab5ac9cd5ae3ef8cb19b370e9f84ec1735dd13 8816 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applying fix-gcc-4.6.diff dpkg-source: info: applying hardening.patch dpkg-source: info: applying mayhem.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-20306384 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-20306384 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-20306384 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 amap-align dpkg-buildpackage: info: source version 2.2+git20080214.600fc29+dfsg-2 dpkg-buildpackage: info: source distribution unstable dpkg-source --before-build . dpkg-buildpackage: info: host architecture riscv64 debian/rules clean dh clean --sourcedirectory=align dh_auto_clean -O--sourcedirectory=align cd align && make -j8 clean make[1]: Entering directory '/<>/align' rm -f amap make[1]: Leaving directory '/<>/align' dh_autoreconf_clean -O--sourcedirectory=align dh_clean -O--sourcedirectory=align debian/rules binary-arch dh binary-arch --sourcedirectory=align dh_update_autotools_config -a -O--sourcedirectory=align dh_autoreconf -a -O--sourcedirectory=align dh_auto_configure -a -O--sourcedirectory=align debian/rules override_dh_auto_build make[1]: Entering directory '/<>' dh_auto_build cd align && make -j8 "INSTALL=install --strip-program=true" make[2]: Entering directory '/<>/align' g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -W -Wall -pedantic -DNDEBUG -DNumInsertStates=1 -DVERSION='"AMAP.2.2"' -funroll-loops -lm -o amap Amap.cc -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now In file included from MultiSequence.h:18, from Amap.cc:8: Sequence.h: In member function ‘Sequence* Sequence::Clone() const’: Sequence.h:293:21: warning: implicitly-declared ‘SafeVector& SafeVector::operator=(const SafeVector&)’ is deprecated [-Wdeprecated-copy] 293 | *(ret->data) = *data; | ^~~~ In file included from Amap.cc:7: SafeVector.h:29:3: note: because ‘SafeVector’ has user-provided ‘SafeVector::SafeVector(const SafeVector&) [with TYPE = char]’ 29 | SafeVector (const SafeVector &source) : std::vector(source) {} | ^~~~~~~~~~ In file included from Amap.cc:9: MultiSequenceDag.h: In member function ‘std::string MultiSequenceDag::GetSequences()’: MultiSequenceDag.h:749:92: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses] 749 | else if (pepGroup[(int) oldPtrs[j][colPos[j]] - 'A'] == consensus || consensus >= 'A' && pepSim[(int) consensus - 'A'][(int) oldPtrs[j][colPos[j]] - 'A']) | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ MultiSequenceDag.h: In member function ‘MultiSequence* MultiSequenceDag::AlignDag(const SafeVector >&, float, bool, bool, bool, float)’: MultiSequenceDag.h:849:67: warning: operation on ‘guiFrame’ may be undefined [-Wsequence-point] 849 | if (outputForGUI && guiStartWeight >= edge->weight && !(guiFrame = ++guiFrame % guiStepSize)) { | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ MultiSequenceDag.h:849:67: warning: operation on ‘guiFrame’ may be undefined [-Wsequence-point] In file included from Amap.cc:12: ProbabilisticModel.h: In member function ‘void ProbabilisticModel::ComputeNewParameters(Sequence*, Sequence*, const VF&, const VF&, VF&, VF&, VF&, VVF&, VF&, bool) const’: ProbabilisticModel.h:504:31: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses] 504 | if (enableTrainEmissions && i != 1 || j != 1){ | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~ Amap.cc: In function ‘void PrintParameters(const char*, const VF&, const VF&, const VF&, const VVF&, const VF&, const char*)’: Amap.cc:323:5: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 323 | for (int i = 0; i < NumMatrixTypes; i++) fprintf (file, "%.10f ", initDistrib[i]); fprintf (file, "\n"); | ^~~ Amap.cc:323:88: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 323 | for (int i = 0; i < NumMatrixTypes; i++) fprintf (file, "%.10f ", initDistrib[i]); fprintf (file, "\n"); | ^~~~~~~ Amap.cc:324:5: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 324 | for (int i = 0; i < 2*NumInsertStates; i++) fprintf (file, "%.10f ", gapOpen[i]); fprintf (file, "\n"); | ^~~ Amap.cc:324:87: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 324 | for (int i = 0; i < 2*NumInsertStates; i++) fprintf (file, "%.10f ", gapOpen[i]); fprintf (file, "\n"); | ^~~~~~~ Amap.cc:325:5: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 325 | for (int i = 0; i < 2*NumInsertStates; i++) fprintf (file, "%.10f ", gapExtend[i]); fprintf (file, "\n"); | ^~~ Amap.cc:325:89: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 325 | for (int i = 0; i < 2*NumInsertStates; i++) fprintf (file, "%.10f ", gapExtend[i]); fprintf (file, "\n"); | ^~~~~~~ Amap.cc: In function ‘MultiSequence* DoAlign(MultiSequence*, const ProbabilisticModel&, VF&, VF&, VF&, VVF&, VF&)’: Amap.cc:482:24: warning: implicitly-declared ‘SafeVector >& SafeVector >::operator=(const SafeVector >&)’ is deprecated [-Wdeprecated-copy] 482 | sparseMatrices = originalSparseMatrices; | ^~~~~~~~~~~~~~~~~~~~~~ In file included from Amap.cc:7: SafeVector.h:29:3: note: because ‘SafeVector >’ has user-provided ‘SafeVector::SafeVector(const SafeVector&) [with TYPE = SafeVector]’ 29 | SafeVector (const SafeVector &source) : std::vector(source) {} | ^~~~~~~~~~ Amap.cc: In function ‘void ReadParameters()’: Amap.cc:1081:40: warning: implicitly-declared ‘SafeVector >& SafeVector >::operator=(const SafeVector >&)’ is deprecated [-Wdeprecated-copy] 1081 | emitPairs = VVF (256, VF (256, 1e-10)); | ^ In file included from Amap.cc:7: SafeVector.h:29:3: note: because ‘SafeVector >’ has user-provided ‘SafeVector::SafeVector(const SafeVector&) [with TYPE = SafeVector]’ 29 | SafeVector (const SafeVector &source) : std::vector(source) {} | ^~~~~~~~~~ Amap.cc:1082:29: warning: implicitly-declared ‘SafeVector& SafeVector::operator=(const SafeVector&)’ is deprecated [-Wdeprecated-copy] 1082 | emitSingle = VF (256, 1e-5); | ^ In file included from Amap.cc:7: SafeVector.h:29:3: note: because ‘SafeVector’ has user-provided ‘SafeVector::SafeVector(const SafeVector&) [with TYPE = float]’ 29 | SafeVector (const SafeVector &source) : std::vector(source) {} | ^~~~~~~~~~ make[2]: Leaving directory '/<>/align' #### This is how the *.jar can be recreated # cd display && mkdir -p lib && ant jar #### Unfortunately the command suggested in readme ## java -jar display/AmapDisplay.jar examples/BB12020.tfa.out #### segfaults. So currently this display function is not supported make[1]: Leaving directory '/<>' dh: command-omitted: The call to "dh_auto_test -a -O--sourcedirectory=align" was omitted due to "DEB_BUILD_OPTIONS=nocheck" create-stamp debian/debhelper-build-stamp dh_testroot -a -O--sourcedirectory=align dh_prep -a -O--sourcedirectory=align dh_auto_install -a -O--sourcedirectory=align dh_install -a -O--sourcedirectory=align dh_installdocs -a -O--sourcedirectory=align dh_installchangelogs -a -O--sourcedirectory=align debian/rules override_dh_installexamples make[1]: Entering directory '/<>' dh_installexamples chmod 644 debian/amap-align/usr/share/doc/amap-align/examples/BB12020.tfa make[1]: Leaving directory '/<>' dh_installman -a -O--sourcedirectory=align dh_installsystemduser -a -O--sourcedirectory=align dh_perl -a -O--sourcedirectory=align dh_link -a -O--sourcedirectory=align dh_strip_nondeterminism -a -O--sourcedirectory=align dh_compress -a -O--sourcedirectory=align dh_fixperms -a -O--sourcedirectory=align dh_missing -a -O--sourcedirectory=align dh_dwz -a -a -O--sourcedirectory=align dh_strip -a -a -O--sourcedirectory=align dh_makeshlibs -a -a -O--sourcedirectory=align dh_shlibdeps -a -a -O--sourcedirectory=align dh_installdeb -a -O--sourcedirectory=align dh_gencontrol -a -O--sourcedirectory=align dh_md5sums -a -O--sourcedirectory=align dh_builddeb -a -O--sourcedirectory=align INFO: pkgstriptranslations version 146 INFO: pkgstriptranslations version 146 pkgstriptranslations: processing amap-align (in debian/amap-align); do_strip: , oemstrip: pkgstriptranslations: processing amap-align-dbgsym (in debian/.debhelper/amap-align/dbgsym-root); do_strip: , oemstrip: pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/amap-align/DEBIAN/control, package amap-align, directory debian/amap-align pkgstripfiles: Truncating usr/share/doc/amap-align/changelog.Debian.gz to topmost ten records pkgstripfiles: Running PNG optimization (using 8 cpus) for package amap-align ... pkgstripfiles: No PNG files. dpkg-deb: building package 'amap-align' in '../amap-align_2.2+git20080214.600fc29+dfsg-2_riscv64.deb'. pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/.debhelper/amap-align/dbgsym-root/DEBIAN/control, package amap-align-dbgsym, directory debian/.debhelper/amap-align/dbgsym-root dpkg-deb: building package 'amap-align-dbgsym' in 'debian/.debhelper/scratch-space/build-amap-align/amap-align-dbgsym_2.2+git20080214.600fc29+dfsg-2_riscv64.deb'. Renaming amap-align-dbgsym_2.2+git20080214.600fc29+dfsg-2_riscv64.deb to amap-align-dbgsym_2.2+git20080214.600fc29+dfsg-2_riscv64.ddeb dpkg-genbuildinfo --build=any dpkg-genchanges --build=any -mLaunchpad Build Daemon >../amap-align_2.2+git20080214.600fc29+dfsg-2_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 2020-11-16T17:31:21Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ amap-align_2.2+git20080214.600fc29+dfsg-2_riscv64.changes: ---------------------------------------------------------- Format: 1.8 Date: Mon, 16 Nov 2020 09:45:41 +0100 Source: amap-align Binary: amap-align Architecture: riscv64 Version: 2.2+git20080214.600fc29+dfsg-2 Distribution: hirsute-proposed Urgency: medium Maintainer: Launchpad Build Daemon Changed-By: Andreas Tille Description: amap-align - Protein multiple alignment by sequence annealing Changes: amap-align (2.2+git20080214.600fc29+dfsg-2) unstable; urgency=medium . * Standards-Version: 4.5.0 (routine-update) * debhelper-compat 13 (routine-update) * Add salsa-ci file (routine-update) * Rules-Requires-Root: no (routine-update) * Trim trailing whitespace. * Set upstream metadata fields: Bug-Database, Bug-Submit. * Refer to specific version of license GPL-2+. 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132364 amap-align_2.2+git20080214.600fc29+dfsg-2_riscv64.deb Checksums-Sha256: 56764a7c6d30f10aaed944c687929149780bfc95fb607975688225980bfb0d56 620504 amap-align-dbgsym_2.2+git20080214.600fc29+dfsg-2_riscv64.ddeb 71bb3c32602c048780e15def9cbc285adbf9d8ae3e027f2e0cf8570d0c89ac81 132364 amap-align_2.2+git20080214.600fc29+dfsg-2_riscv64.deb Build-Origin: Ubuntu Build-Architecture: riscv64 Build-Date: Mon, 16 Nov 2020 17:31:17 +0000 Build-Path: /<> Build-Tainted-By: usr-local-has-programs Installed-Build-Depends: autoconf (= 2.69-11.1), automake (= 1:1.16.2-4ubuntu1), autopoint (= 0.19.8.1-10build1), autotools-dev (= 20180224.1), base-files (= 11ubuntu16), base-passwd (= 3.5.48), bash (= 5.1~rc2-1ubuntu1), binutils (= 2.35.1-2ubuntu1), binutils-common (= 2.35.1-2ubuntu1), binutils-riscv64-linux-gnu (= 2.35.1-2ubuntu1), bsdextrautils (= 2.36-3ubuntu1), bsdutils (= 1:2.36-3ubuntu1), build-essential (= 12.8ubuntu3), bzip2 (= 1.0.8-4ubuntu2), coreutils (= 8.32-4ubuntu1), cpp (= 4:10.2.0-1ubuntu1), cpp-10 (= 10.2.0-17ubuntu1), dash (= 0.5.11+git20200708+dd9ef66-2), debconf (= 1.5.74), debhelper (= 13.2.1ubuntu1), debianutils (= 4.11.2), dh-autoreconf (= 19), dh-strip-nondeterminism (= 1.9.0-1), diffutils (= 1:3.7-3ubuntu1), dpkg (= 1.20.5ubuntu3), dpkg-dev (= 1.20.5ubuntu3), dwz (= 0.13-5), file (= 1:5.38-5), findutils (= 4.7.0-1ubuntu2), g++ (= 4:10.2.0-1ubuntu1), g++-10 (= 10.2.0-17ubuntu1), gcc (= 4:10.2.0-1ubuntu1), gcc-10 (= 10.2.0-17ubuntu1), gcc-10-base (= 10.2.0-17ubuntu1), gettext (= 0.19.8.1-10build1), gettext-base (= 0.19.8.1-10build1), grep (= 3.6-1), groff-base (= 1.22.4-5), gzip (= 1.10-2ubuntu1), hostname (= 3.23), init-system-helpers (= 1.58), intltool-debian (= 0.35.0+20060710.5), libacl1 (= 2.2.53-8), libarchive-zip-perl (= 1.68-1), libatomic1 (= 10.2.0-17ubuntu1), libattr1 (= 1:2.4.48-5), libaudit-common (= 1:2.8.5-3ubuntu2), libaudit1 (= 1:2.8.5-3ubuntu2), libbinutils (= 2.35.1-2ubuntu1), libblkid1 (= 2.36-3ubuntu1), libbz2-1.0 (= 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libk5crypto3 (= 1.17-10), libkeyutils1 (= 1.6.1-2ubuntu1), libkrb5-3 (= 1.17-10), libkrb5support0 (= 1.17-10), liblz4-1 (= 1.9.2-2), liblzma5 (= 5.2.4-1ubuntu1), libmagic-mgc (= 1:5.38-5), libmagic1 (= 1:5.38-5), libmount1 (= 2.36-3ubuntu1), libmpc3 (= 1.2.0-1), libmpfr6 (= 4.1.0-3), libnsl-dev (= 1.3.0-0ubuntu3), libnsl2 (= 1.3.0-0ubuntu3), libpam-modules (= 1.3.1-5ubuntu6), libpam-modules-bin (= 1.3.1-5ubuntu6), libpam-runtime (= 1.3.1-5ubuntu6), libpam0g (= 1.3.1-5ubuntu6), libpcre2-8-0 (= 10.34-7), libpcre3 (= 2:8.39-13), libperl5.32 (= 5.32.0-5), libpipeline1 (= 1.5.3-1), libselinux1 (= 3.1-2build1), libsigsegv2 (= 2.12-2build1), libsmartcols1 (= 2.36-3ubuntu1), libssl1.1 (= 1.1.1f-1ubuntu4), libstdc++-10-dev (= 10.2.0-17ubuntu1), libstdc++6 (= 10.2.0-17ubuntu1), libsub-override-perl (= 0.09-2), libsystemd0 (= 246.6-2ubuntu1), libtinfo6 (= 6.2+20200918-1), libtirpc-common (= 1.2.6-3), libtirpc-dev (= 1.2.6-3), libtirpc3 (= 1.2.6-3), libtool (= 2.4.6-14), libuchardet0 (= 0.0.7-1), libudev1 (= 246.6-2ubuntu1), libunistring2 (= 0.9.10-4), libuuid1 (= 2.36-3ubuntu1), libxml2 (= 2.9.10+dfsg-6.2), libzstd1 (= 1.4.5+dfsg-4), linux-libc-dev (= 5.8.0-26.27), login (= 1:4.8.1-1ubuntu6), lsb-base (= 11.1.0ubuntu2), m4 (= 1.4.18-4), make (= 4.3-4ubuntu1), man-db (= 2.9.3-2), mawk (= 1.3.4.20200120-2), ncurses-base (= 6.2+20200918-1), ncurses-bin (= 6.2+20200918-1), patch (= 2.7.6-6), perl (= 5.32.0-5), perl-base (= 5.32.0-5), perl-modules-5.32 (= 5.32.0-5), po-debconf (= 1.0.21), rpcsvc-proto (= 1.4.2-0ubuntu4), sed (= 4.7-1ubuntu1), sensible-utils (= 0.0.13), sysvinit-utils (= 2.96-5ubuntu1), tar (= 1.30+dfsg-7), util-linux (= 2.36-3ubuntu1), xz-utils (= 5.2.4-1ubuntu1), zlib1g (= 1:1.2.11.dfsg-2ubuntu4) Environment: DEB_BUILD_OPTIONS="nocheck parallel=8" LANG="C.UTF-8" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1605516341" +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ amap-align_2.2+git20080214.600fc29+dfsg-2_riscv64.deb ----------------------------------------------------- new Debian package, version 2.0. size 132364 bytes: control archive=1168 bytes. 987 bytes, 20 lines control 710 bytes, 10 lines md5sums Package: amap-align Version: 2.2+git20080214.600fc29+dfsg-2 Architecture: riscv64 Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 1151 Depends: libc6 (>= 2.27), libgcc-s1 (>= 3.0), libstdc++6 (>= 9) Section: science Priority: optional Homepage: https://github.com/mes5k/amap-align Description: Protein multiple alignment by sequence annealing AMAP is a command line tool to perform multiple alignment of peptidic sequences. It utilizes posterior decoding, and a sequence-annealing alignment, instead of the traditional progressive alignment method. It is the only alignment program that allows one to control the sensitivity / specificity tradeoff. It is based on the ProbCons source code, but uses alignment metric accuracy and eliminates the consistency transformation. . The Java visualisation tool of AMAP 2.2 is not yet packaged in Debian. drwxr-xr-x root/root 0 2020-11-16 08:45 ./ drwxr-xr-x root/root 0 2020-11-16 08:45 ./usr/ drwxr-xr-x root/root 0 2020-11-16 08:45 ./usr/bin/ -rwxr-xr-x root/root 184896 2020-11-16 08:45 ./usr/bin/amap drwxr-xr-x root/root 0 2020-11-16 08:45 ./usr/share/ drwxr-xr-x root/root 0 2020-11-16 08:45 ./usr/share/doc/ drwxr-xr-x root/root 0 2020-11-16 08:45 ./usr/share/doc/amap-align/ -rw-r--r-- root/root 382 2020-11-16 08:45 ./usr/share/doc/amap-align/NEWS.Debian.gz -rw-r--r-- root/root 3912 2008-02-14 00:36 ./usr/share/doc/amap-align/PROBCONS.README -rw-r--r-- root/root 1049 2008-02-14 00:36 ./usr/share/doc/amap-align/README -rw-r--r-- root/root 477 2020-11-16 08:45 ./usr/share/doc/amap-align/README.Debian -rw-r--r-- root/root 2165 2020-11-16 08:45 ./usr/share/doc/amap-align/changelog.Debian.gz -rw-r--r-- root/root 2548 2020-11-16 08:45 ./usr/share/doc/amap-align/copyright drwxr-xr-x root/root 0 2020-11-16 08:45 ./usr/share/doc/amap-align/examples/ -rw-r--r-- root/root 545 2008-02-14 00:36 ./usr/share/doc/amap-align/examples/BB12020.tfa -rwxr-xr-x root/root 963850 2008-02-14 00:36 ./usr/share/doc/amap-align/examples/BB12020.tfa.out drwxr-xr-x root/root 0 2020-11-16 08:45 ./usr/share/man/ drwxr-xr-x root/root 0 2020-11-16 08:45 ./usr/share/man/man1/ -rw-r--r-- root/root 2898 2020-11-16 08:45 ./usr/share/man/man1/amap.1.gz +------------------------------------------------------------------------------+ | Post Build | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not removing build depends: as requested +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: riscv64 Build Type: any Build-Space: 6896 Build-Time: 284 Distribution: hirsute-proposed Host Architecture: riscv64 Install-Time: 99 Job: amap-align_2.2+git20080214.600fc29+dfsg-2.dsc Machine Architecture: riscv64 Package: amap-align Package-Time: 413 Source-Version: 2.2+git20080214.600fc29+dfsg-2 Space: 6896 Status: successful Version: 2.2+git20080214.600fc29+dfsg-2 -------------------------------------------------------------------------------- Finished at 2020-11-16T17:31:21Z Build needed 00:06:53, 6896k disk space RUN: /usr/share/launchpad-buildd/bin/in-target scan-for-processes --backend=chroot --series=hirsute --arch=riscv64 PACKAGEBUILD-20306384 Scanning for processes to kill in build PACKAGEBUILD-20306384 RUN: /usr/share/launchpad-buildd/bin/in-target umount-chroot --backend=chroot --series=hirsute --arch=riscv64 PACKAGEBUILD-20306384 Stopping target for build PACKAGEBUILD-20306384 RUN: /usr/share/launchpad-buildd/bin/in-target remove-build --backend=chroot --series=hirsute --arch=riscv64 PACKAGEBUILD-20306384 Removing build PACKAGEBUILD-20306384