RUN: /usr/share/launchpad-buildd/slavebin/slave-prep ['slave-prep'] Forking launchpad-buildd slave process... Kernel version: Linux z13-017 4.4.0-43-generic #63-Ubuntu SMP Wed Oct 12 13:54:32 UTC 2016 s390x Buildd toolchain package versions: launchpad-buildd_140 python-lpbuildd_140 sbuild_0.67.0-2ubuntu7 dpkg-dev_1.18.4ubuntu1.1 python-debian_0.1.27ubuntu2 qemu-user-static_1:2.5+dfsg-5ubuntu10.5. Syncing the system clock with the buildd NTP service... 9 Nov 05:28:23 ntpdate[30380]: adjust time server 10.211.37.1 offset 0.000206 sec RUN: /usr/share/launchpad-buildd/slavebin/unpack-chroot ['unpack-chroot', 'PACKAGEBUILD-11168025', '/home/buildd/filecache-default/309330829b4f61930f4191d7be733906953ac6c4'] Unpacking chroot for build PACKAGEBUILD-11168025 RUN: /usr/share/launchpad-buildd/slavebin/mount-chroot ['mount-chroot', 'PACKAGEBUILD-11168025'] Mounting chroot for build PACKAGEBUILD-11168025 RUN: /usr/share/launchpad-buildd/slavebin/override-sources-list ['override-sources-list', 'PACKAGEBUILD-11168025', 'deb http://ftpmaster.internal/ubuntu zesty main universe', 'deb http://ftpmaster.internal/ubuntu zesty-security main universe', 'deb http://ftpmaster.internal/ubuntu zesty-updates main universe', 'deb http://ftpmaster.internal/ubuntu zesty-proposed main universe'] Overriding sources.list in build-PACKAGEBUILD-11168025 RUN: /usr/share/launchpad-buildd/slavebin/update-debian-chroot ['update-debian-chroot', 'PACKAGEBUILD-11168025', 's390x'] Updating debian chroot for build PACKAGEBUILD-11168025 Get:1 http://ftpmaster.internal/ubuntu zesty InRelease [247 kB] Get:2 http://ftpmaster.internal/ubuntu zesty-security InRelease [92.2 kB] Get:3 http://ftpmaster.internal/ubuntu zesty-updates InRelease [92.1 kB] Get:4 http://ftpmaster.internal/ubuntu zesty-proposed InRelease [95.6 kB] Get:5 http://ftpmaster.internal/ubuntu zesty/main s390x Packages [1156 kB] Get:6 http://ftpmaster.internal/ubuntu zesty/main Translation-en [588 kB] Get:7 http://ftpmaster.internal/ubuntu zesty/universe s390x Packages [7548 kB] Get:8 http://ftpmaster.internal/ubuntu zesty/universe Translation-en [4566 kB] Get:9 http://ftpmaster.internal/ubuntu zesty-proposed/main s390x Packages [110 kB] Get:10 http://ftpmaster.internal/ubuntu zesty-proposed/main Translation-en [59.9 kB] Get:11 http://ftpmaster.internal/ubuntu zesty-proposed/universe s390x Packages [358 kB] Get:12 http://ftpmaster.internal/ubuntu zesty-proposed/universe Translation-en [221 kB] Fetched 15.1 MB in 17s (865 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages were automatically installed and are no longer required: libperl5.22 perl-modules-5.22 Use 'sudo apt autoremove' to remove them. The following NEW packages will be installed: libperl5.24 perl-modules-5.24 The following packages will be upgraded: adduser base-files bash binutils cpp-6 diffutils dmsetup g++-6 gcc-6 gcc-6-base grep init init-system-helpers libapparmor1 libasn1-8-heimdal libatomic1 libcc1-0 libcurl3-gnutls libdevmapper1.02.1 libgcc-6-dev libgcc1 libgomp1 libgssapi-krb5-2 libgssapi3-heimdal libhcrypto4-heimdal libheimbase1-heimdal libheimntlm0-heimdal libhogweed4 libhx509-5-heimdal libitm1 libk5crypto3 libkrb5-26-heimdal libkrb5-3 libkrb5support0 libksba8 libldap-2.4-2 liblzma5 libnettle6 libpng16-16 libroken18-heimdal libsasl2-2 libsasl2-modules-db libselinux1 libsemanage-common libsemanage1 libsepol1 libslang2 libsqlite3-0 libstdc++-6-dev libstdc++6 libsystemd0 libudev1 libwind0-heimdal linux-libc-dev perl perl-base pinentry-curses systemd systemd-sysv tar tzdata ubuntu-keyring xz-utils 63 upgraded, 2 newly installed, 0 to remove and 0 not upgraded. Need to get 36.0 MB of archives. After this operation, 40.0 MB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu zesty/main s390x base-files s390x 9.6ubuntu6 [55.8 kB] Get:2 http://ftpmaster.internal/ubuntu zesty-proposed/main s390x bash s390x 4.4-1ubuntu1 [595 kB] Get:3 http://ftpmaster.internal/ubuntu zesty/main s390x diffutils s390x 1:3.5-1 [164 kB] Get:4 http://ftpmaster.internal/ubuntu zesty/main s390x grep s390x 2.26-1 [148 kB] Get:5 http://ftpmaster.internal/ubuntu zesty/main s390x perl-modules-5.24 all 5.24.1~rc3-3 [2661 kB] Get:6 http://ftpmaster.internal/ubuntu zesty/main s390x libperl5.24 s390x 5.24.1~rc3-3 [3314 kB] Get:7 http://ftpmaster.internal/ubuntu zesty/main s390x perl s390x 5.24.1~rc3-3 [237 kB] Get:8 http://ftpmaster.internal/ubuntu zesty/main s390x perl-base s390x 5.24.1~rc3-3 [1271 kB] Get:9 http://ftpmaster.internal/ubuntu zesty-proposed/main s390x tar s390x 1.29b-1.1 [222 kB] Get:10 http://ftpmaster.internal/ubuntu zesty/main s390x init-system-helpers all 1.46 [37.3 kB] Get:11 http://ftpmaster.internal/ubuntu zesty/main s390x libapparmor1 s390x 2.10.95-4ubuntu5.2 [29.5 kB] Get:12 http://ftpmaster.internal/ubuntu zesty/main s390x liblzma5 s390x 5.2.2-1.2 [90.8 kB] Get:13 http://ftpmaster.internal/ubuntu zesty/main s390x libselinux1 s390x 2.6-3 [64.5 kB] Get:14 http://ftpmaster.internal/ubuntu zesty/main s390x adduser all 3.113+nmu3ubuntu5 [161 kB] Get:15 http://ftpmaster.internal/ubuntu zesty/main s390x systemd s390x 232-2git1 [2250 kB] Get:16 http://ftpmaster.internal/ubuntu zesty/main s390x libsystemd0 s390x 232-2git1 [193 kB] Get:17 http://ftpmaster.internal/ubuntu zesty/main s390x init s390x 1.46 [5320 B] Get:18 http://ftpmaster.internal/ubuntu zesty/main s390x systemd-sysv s390x 232-2git1 [13.2 kB] Get:19 http://ftpmaster.internal/ubuntu zesty/main s390x libgomp1 s390x 6.2.0-11ubuntu1 [71.1 kB] Get:20 http://ftpmaster.internal/ubuntu zesty/main s390x libitm1 s390x 6.2.0-11ubuntu1 [27.3 kB] Get:21 http://ftpmaster.internal/ubuntu zesty/main s390x libcc1-0 s390x 6.2.0-11ubuntu1 [31.0 kB] Get:22 http://ftpmaster.internal/ubuntu zesty/main s390x libatomic1 s390x 6.2.0-11ubuntu1 [8154 B] Get:23 http://ftpmaster.internal/ubuntu zesty/main s390x gcc-6-base s390x 6.2.0-11ubuntu1 [17.5 kB] Get:24 http://ftpmaster.internal/ubuntu zesty/main s390x libstdc++6 s390x 6.2.0-11ubuntu1 [403 kB] Get:25 http://ftpmaster.internal/ubuntu zesty/main s390x g++-6 s390x 6.2.0-11ubuntu1 [5821 kB] Get:26 http://ftpmaster.internal/ubuntu zesty/main s390x libstdc++-6-dev s390x 6.2.0-11ubuntu1 [1391 kB] Get:27 http://ftpmaster.internal/ubuntu zesty/main s390x libgcc-6-dev s390x 6.2.0-11ubuntu1 [267 kB] Get:28 http://ftpmaster.internal/ubuntu zesty/main s390x gcc-6 s390x 6.2.0-11ubuntu1 [5610 kB] Get:29 http://ftpmaster.internal/ubuntu zesty/main s390x cpp-6 s390x 6.2.0-11ubuntu1 [5068 kB] Get:30 http://ftpmaster.internal/ubuntu zesty/main s390x libgcc1 s390x 1:6.2.0-11ubuntu1 [24.5 kB] Get:31 http://ftpmaster.internal/ubuntu zesty-proposed/main s390x binutils s390x 2.27.51.20161108-1ubuntu1 [1063 kB] Get:32 http://ftpmaster.internal/ubuntu zesty/main s390x libsepol1 s390x 2.6-1 [200 kB] Get:33 http://ftpmaster.internal/ubuntu zesty/main s390x libsemanage-common all 2.6-1 [6832 B] Get:34 http://ftpmaster.internal/ubuntu zesty/main s390x libsemanage1 s390x 2.6-1 [76.6 kB] Get:35 http://ftpmaster.internal/ubuntu zesty/main s390x libudev1 s390x 232-2git1 [53.1 kB] Get:36 http://ftpmaster.internal/ubuntu zesty/main s390x ubuntu-keyring all 2016.10.27 [16.6 kB] Get:37 http://ftpmaster.internal/ubuntu zesty/main s390x tzdata all 2016i-1 [169 kB] Get:38 http://ftpmaster.internal/ubuntu zesty/main s390x libdevmapper1.02.1 s390x 2:1.02.133-1ubuntu1 [148 kB] Get:39 http://ftpmaster.internal/ubuntu zesty/main s390x dmsetup s390x 2:1.02.133-1ubuntu1 [75.4 kB] Get:40 http://ftpmaster.internal/ubuntu zesty-proposed/main s390x libroken18-heimdal s390x 1.7~git20160703+dfsg-1 [39.3 kB] Get:41 http://ftpmaster.internal/ubuntu zesty-proposed/main s390x libasn1-8-heimdal s390x 1.7~git20160703+dfsg-1 [147 kB] Get:42 http://ftpmaster.internal/ubuntu zesty-proposed/main s390x libheimbase1-heimdal s390x 1.7~git20160703+dfsg-1 [27.5 kB] Get:43 http://ftpmaster.internal/ubuntu zesty-proposed/main s390x libhcrypto4-heimdal s390x 1.7~git20160703+dfsg-1 [84.4 kB] Get:44 http://ftpmaster.internal/ubuntu zesty-proposed/main s390x libwind0-heimdal s390x 1.7~git20160703+dfsg-1 [48.2 kB] Get:45 http://ftpmaster.internal/ubuntu zesty-proposed/main s390x libhx509-5-heimdal s390x 1.7~git20160703+dfsg-1 [100.0 kB] Get:46 http://ftpmaster.internal/ubuntu zesty-proposed/main s390x libsqlite3-0 s390x 3.15.1-1 [456 kB] Get:47 http://ftpmaster.internal/ubuntu zesty-proposed/main s390x libkrb5-26-heimdal s390x 1.7~git20160703+dfsg-1 [188 kB] Get:48 http://ftpmaster.internal/ubuntu zesty-proposed/main s390x libheimntlm0-heimdal s390x 1.7~git20160703+dfsg-1 [14.7 kB] Get:49 http://ftpmaster.internal/ubuntu zesty-proposed/main s390x libgssapi3-heimdal s390x 1.7~git20160703+dfsg-1 [89.0 kB] Get:50 http://ftpmaster.internal/ubuntu zesty/main s390x libhogweed4 s390x 3.3-1 [134 kB] Get:51 http://ftpmaster.internal/ubuntu zesty/main s390x libnettle6 s390x 3.3-1 [104 kB] Get:52 http://ftpmaster.internal/ubuntu zesty/main s390x libksba8 s390x 1.3.5-2 [86.3 kB] Get:53 http://ftpmaster.internal/ubuntu zesty-proposed/main s390x libsasl2-modules-db s390x 2.1.27~72-g88d82a3+dfsg-1 [14.6 kB] Get:54 http://ftpmaster.internal/ubuntu zesty-proposed/main s390x libsasl2-2 s390x 2.1.27~72-g88d82a3+dfsg-1 [46.6 kB] Get:55 http://ftpmaster.internal/ubuntu zesty/main s390x libldap-2.4-2 s390x 2.4.42+dfsg-2ubuntu5 [151 kB] Get:56 http://ftpmaster.internal/ubuntu zesty/main s390x libslang2 s390x 2.3.1-5ubuntu1 [413 kB] Get:57 http://ftpmaster.internal/ubuntu zesty/main s390x pinentry-curses s390x 0.9.7-8 [31.2 kB] Get:58 http://ftpmaster.internal/ubuntu zesty/main s390x xz-utils s390x 5.2.2-1.2 [82.1 kB] Get:59 http://ftpmaster.internal/ubuntu zesty-proposed/main s390x libgssapi-krb5-2 s390x 1.15~beta1-1 [109 kB] Get:60 http://ftpmaster.internal/ubuntu zesty-proposed/main s390x libkrb5-3 s390x 1.15~beta1-1 [258 kB] Get:61 http://ftpmaster.internal/ubuntu zesty-proposed/main s390x libkrb5support0 s390x 1.15~beta1-1 [31.2 kB] Get:62 http://ftpmaster.internal/ubuntu zesty-proposed/main s390x libk5crypto3 s390x 1.15~beta1-1 [83.0 kB] Get:63 http://ftpmaster.internal/ubuntu zesty-proposed/main s390x libcurl3-gnutls s390x 7.50.1-1ubuntu2 [173 kB] Get:64 http://ftpmaster.internal/ubuntu zesty/main s390x libpng16-16 s390x 1.6.26-1 [170 kB] Get:65 http://ftpmaster.internal/ubuntu zesty-proposed/main s390x linux-libc-dev s390x 4.8.0-27.29 [844 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 36.0 MB in 19s (1814 kB/s) (Reading database ... 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Preparing to unpack .../28-linux-libc-dev_4.8.0-27.29_s390x.deb ... Unpacking linux-libc-dev:s390x (4.8.0-27.29) over (4.8.0-22.24) ... Setting up libgomp1:s390x (6.2.0-11ubuntu1) ... Setting up libatomic1:s390x (6.2.0-11ubuntu1) ... Setting up perl-modules-5.24 (5.24.1~rc3-3) ... Setting up libperl5.24:s390x (5.24.1~rc3-3) ... Setting up libnettle6:s390x (3.3-1) ... Setting up libcc1-0:s390x (6.2.0-11ubuntu1) ... Setting up libpng16-16:s390x (1.6.26-1) ... Setting up tzdata (2016i-1) ... Current default time zone: 'Etc/UTC' Local time is now: Wed Nov 9 05:29:12 UTC 2016. Universal Time is now: Wed Nov 9 05:29:12 UTC 2016. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up systemd-sysv (232-2git1) ... Setting up libsasl2-modules-db:s390x (2.1.27~72-g88d82a3+dfsg-1) ... Setting up linux-libc-dev:s390x (4.8.0-27.29) ... Setting up libsasl2-2:s390x (2.1.27~72-g88d82a3+dfsg-1) ... Setting up libroken18-heimdal:s390x (1.7~git20160703+dfsg-1) ... Setting up libksba8:s390x (1.3.5-2) ... Setting up libdevmapper1.02.1:s390x (2:1.02.133-1ubuntu1) ... Setting up libkrb5support0:s390x (1.15~beta1-1) ... Setting up libhogweed4:s390x (3.3-1) ... Setting up perl (5.24.1~rc3-3) ... Installing new version of config file /etc/perl/sitecustomize.pl ... Processing triggers for libc-bin (2.24-3ubuntu1) ... Setting up xz-utils (5.2.2-1.2) ... Setting up libheimbase1-heimdal:s390x (1.7~git20160703+dfsg-1) ... Setting up libsqlite3-0:s390x (3.15.1-1) ... Setting up dmsetup (2:1.02.133-1ubuntu1) ... Setting up pinentry-curses (0.9.7-8) ... Setting up binutils (2.27.51.20161108-1ubuntu1) ... Setting up cpp-6 (6.2.0-11ubuntu1) ... Setting up libslang2:s390x (2.3.1-5ubuntu1) ... Setting up libitm1:s390x (6.2.0-11ubuntu1) ... Setting up libk5crypto3:s390x (1.15~beta1-1) ... Setting up libgcc-6-dev:s390x (6.2.0-11ubuntu1) ... Setting up libstdc++-6-dev:s390x (6.2.0-11ubuntu1) ... Setting up libwind0-heimdal:s390x (1.7~git20160703+dfsg-1) ... Setting up init (1.46) ... Setting up libasn1-8-heimdal:s390x (1.7~git20160703+dfsg-1) ... Setting up libhcrypto4-heimdal:s390x (1.7~git20160703+dfsg-1) ... Setting up libhx509-5-heimdal:s390x (1.7~git20160703+dfsg-1) ... Setting up gcc-6 (6.2.0-11ubuntu1) ... Setting up g++-6 (6.2.0-11ubuntu1) ... Setting up libkrb5-3:s390x (1.15~beta1-1) ... Setting up libkrb5-26-heimdal:s390x (1.7~git20160703+dfsg-1) ... Setting up libheimntlm0-heimdal:s390x (1.7~git20160703+dfsg-1) ... Setting up libgssapi-krb5-2:s390x (1.15~beta1-1) ... Setting up libgssapi3-heimdal:s390x (1.7~git20160703+dfsg-1) ... Setting up libldap-2.4-2:s390x (2.4.42+dfsg-2ubuntu5) ... Setting up libcurl3-gnutls:s390x (7.50.1-1ubuntu2) ... Processing triggers for libc-bin (2.24-3ubuntu1) ... RUN: /usr/share/launchpad-buildd/slavebin/sbuild-package ['sbuild-package', 'PACKAGEBUILD-11168025', 's390x', 'zesty-proposed', '-c', 'chroot:autobuild', '--arch=s390x', '--dist=zesty-proposed', '--purge=never', '--nolog', 'libmems_1.6.0+4725-4.dsc'] Initiating build PACKAGEBUILD-11168025 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 4.4.0-43-generic #63-Ubuntu SMP Wed Oct 12 13:54:32 UTC 2016 s390x sbuild (Debian sbuild) 0.67.0 (26 Dec 2015) on z13-017.buildd +==============================================================================+ | libmems 1.6.0+4725-4 (s390x) 09 Nov 2016 05:29 | +==============================================================================+ Package: libmems Version: 1.6.0+4725-4 Source Version: 1.6.0+4725-4 Distribution: zesty-proposed Machine Architecture: s390x Host Architecture: s390x Build Architecture: s390x I: NOTICE: Log filtering will replace 'build/libmems-bVNtVC/libmems-1.6.0+4725' with '<>' I: NOTICE: Log filtering will replace 'build/libmems-bVNtVC' with '<>' I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-11168025/chroot-autobuild' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- libmems_1.6.0+4725-4.dsc exists in .; copying to chroot Check architectures ------------------- Check dependencies ------------------ Merged Build-Depends: build-essential, fakeroot Filtered Build-Depends: build-essential, fakeroot dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/<>/resolver-wAtWNr/apt_archive/sbuild-build-depends-core-dummy.deb'. Ign:1 copy:/<>/resolver-wAtWNr/apt_archive ./ InRelease Get:2 copy:/<>/resolver-wAtWNr/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-wAtWNr/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-wAtWNr/apt_archive ./ Sources [214 B] Get:5 copy:/<>/resolver-wAtWNr/apt_archive ./ Packages [525 B] Fetched 2858 B in 0s (0 B/s) Reading package lists... Reading package lists... +------------------------------------------------------------------------------+ | Install core build dependencies (apt-based resolver) | +------------------------------------------------------------------------------+ Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following packages were automatically installed and are no longer required: libperl5.22 perl-modules-5.22 Use 'sudo apt autoremove' to remove them. The following NEW packages will be installed: sbuild-build-depends-core-dummy 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 770 B of archives. After this operation, 0 B of additional disk space will be used. Get:1 copy:/<>/resolver-wAtWNr/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [770 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 770 B in 0s (0 B/s) Selecting previously unselected package sbuild-build-depends-core-dummy. (Reading database ... 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Merged Build-Depends: debhelper (>= 9), dh-autoreconf, d-shlibs, pkg-config, libgenome-1.3-dev, libboost-filesystem-dev, libboost-iostreams-dev, libboost-program-options-dev, libmuscle-3.7-dev Filtered Build-Depends: debhelper (>= 9), dh-autoreconf, d-shlibs, pkg-config, libgenome-1.3-dev, libboost-filesystem-dev, libboost-iostreams-dev, libboost-program-options-dev, libmuscle-3.7-dev dpkg-deb: building package 'sbuild-build-depends-libmems-dummy' in '/<>/resolver-tNgNSz/apt_archive/sbuild-build-depends-libmems-dummy.deb'. Ign:1 copy:/<>/resolver-tNgNSz/apt_archive ./ InRelease Get:2 copy:/<>/resolver-tNgNSz/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-tNgNSz/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-tNgNSz/apt_archive ./ Sources [287 B] Get:5 copy:/<>/resolver-tNgNSz/apt_archive ./ Packages [604 B] Fetched 3010 B in 0s (0 B/s) Reading package lists... Reading package lists... +------------------------------------------------------------------------------+ | Install libmems build dependencies (apt-based resolver) | +------------------------------------------------------------------------------+ Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following packages were automatically installed and are no longer required: libperl5.22 perl-modules-5.22 Use 'sudo apt autoremove' to remove them. The following additional packages will be installed: autoconf automake autopoint autotools-dev bsdmainutils d-shlibs debhelper dh-autoreconf dh-strip-nondeterminism file gettext gettext-base groff-base icu-devtools intltool-debian libarchive-zip-perl libboost-filesystem-dev libboost-filesystem1.62-dev libboost-filesystem1.62.0 libboost-iostreams-dev libboost-iostreams1.62-dev libboost-iostreams1.62.0 libboost-program-options-dev libboost-program-options1.62-dev libboost-program-options1.62.0 libboost-regex1.62-dev libboost-regex1.62.0 libboost-system1.62-dev libboost-system1.62.0 libboost1.62-dev libcroco3 libfile-stripnondeterminism-perl libgenome-1.3-0v5 libgenome-1.3-dev libglib2.0-0 libicu-dev libicu57 libmagic1 libmuscle-3.7-1 libmuscle-3.7-dev libpipeline1 libsigsegv2 libtimedate-perl libtool libunistring0 libxml2 m4 man-db pkg-config po-debconf Suggested packages: autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois vacation dh-make gettext-doc libasprintf-dev libgettextpo-dev groff libboost1.62-doc libboost-atomic1.62-dev libboost-chrono1.62-dev libboost-date-time1.62-dev libboost-exception1.62-dev libboost-graph1.62-dev libboost-graph-parallel1.62-dev libboost-locale1.62-dev libboost-log1.62-dev libboost-math1.62-dev libboost-mpi1.62-dev libboost-mpi-python1.62-dev libboost-python1.62-dev libboost-random1.62-dev libboost-serialization1.62-dev libboost-signals1.62-dev libboost-test1.62-dev libboost-thread1.62-dev libboost-timer1.62-dev libboost-type-erasure1.62-dev libboost-wave1.62-dev libboost1.62-tools-dev libmpfrc++-dev libntl-dev icu-doc libtool-doc gfortran | fortran95-compiler gcj-jdk less www-browser libmail-box-perl Recommended packages: curl | wget | lynx-cur libglib2.0-data shared-mime-info xdg-user-dirs libltdl-dev xml-core libmail-sendmail-perl The following NEW packages will be installed: autoconf automake autopoint autotools-dev bsdmainutils d-shlibs debhelper dh-autoreconf dh-strip-nondeterminism file gettext gettext-base groff-base icu-devtools intltool-debian libarchive-zip-perl libboost-filesystem-dev libboost-filesystem1.62-dev libboost-filesystem1.62.0 libboost-iostreams-dev libboost-iostreams1.62-dev libboost-iostreams1.62.0 libboost-program-options-dev libboost-program-options1.62-dev libboost-program-options1.62.0 libboost-regex1.62-dev libboost-regex1.62.0 libboost-system1.62-dev libboost-system1.62.0 libboost1.62-dev libcroco3 libfile-stripnondeterminism-perl libgenome-1.3-0v5 libgenome-1.3-dev libglib2.0-0 libicu-dev libicu57 libmagic1 libmuscle-3.7-1 libmuscle-3.7-dev libpipeline1 libsigsegv2 libtimedate-perl libtool libunistring0 libxml2 m4 man-db pkg-config po-debconf sbuild-build-depends-libmems-dummy 0 upgraded, 51 newly installed, 0 to remove and 0 not upgraded. Need to get 41.6 MB of archives. After this operation, 298 MB of additional disk space will be used. 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http://ftpmaster.internal/ubuntu zesty/main s390x libboost1.62-dev s390x 1.62.0+dfsg-2ubuntu1 [6985 kB] Get:33 http://ftpmaster.internal/ubuntu zesty/main s390x libboost-system1.62.0 s390x 1.62.0+dfsg-2ubuntu1 [9282 B] Get:34 http://ftpmaster.internal/ubuntu zesty/main s390x libboost-filesystem1.62.0 s390x 1.62.0+dfsg-2ubuntu1 [35.8 kB] Get:35 http://ftpmaster.internal/ubuntu zesty/main s390x libboost-system1.62-dev s390x 1.62.0+dfsg-2ubuntu1 [9290 B] Get:36 http://ftpmaster.internal/ubuntu zesty/main s390x libboost-filesystem1.62-dev s390x 1.62.0+dfsg-2ubuntu1 [43.7 kB] Get:37 http://ftpmaster.internal/ubuntu zesty/universe s390x libboost-filesystem-dev s390x 1.62.0.0ubuntu1 [2922 B] Get:38 http://ftpmaster.internal/ubuntu zesty/main s390x libboost-regex1.62.0 s390x 1.62.0+dfsg-2ubuntu1 [235 kB] Get:39 http://ftpmaster.internal/ubuntu zesty/main s390x libicu-dev s390x 57.1-4 [16.7 MB] Get:40 http://ftpmaster.internal/ubuntu zesty/main s390x libboost-regex1.62-dev s390x 1.62.0+dfsg-2ubuntu1 [289 kB] Get:41 http://ftpmaster.internal/ubuntu zesty/main s390x libboost-iostreams1.62.0 s390x 1.62.0+dfsg-2ubuntu1 [26.5 kB] Get:42 http://ftpmaster.internal/ubuntu zesty/main s390x libboost-iostreams1.62-dev s390x 1.62.0+dfsg-2ubuntu1 [31.0 kB] Get:43 http://ftpmaster.internal/ubuntu zesty/universe s390x libboost-iostreams-dev s390x 1.62.0.0ubuntu1 [2872 B] Get:44 http://ftpmaster.internal/ubuntu zesty/main s390x libboost-program-options1.62.0 s390x 1.62.0+dfsg-2ubuntu1 [120 kB] Get:45 http://ftpmaster.internal/ubuntu zesty/main s390x libboost-program-options1.62-dev s390x 1.62.0+dfsg-2ubuntu1 [142 kB] Get:46 http://ftpmaster.internal/ubuntu zesty/main s390x libboost-program-options-dev s390x 1.62.0.0ubuntu1 [2894 B] Get:47 http://ftpmaster.internal/ubuntu zesty/universe s390x libgenome-1.3-0v5 s390x 1.3.1-9 [104 kB] Get:48 http://ftpmaster.internal/ubuntu zesty/universe s390x libgenome-1.3-dev s390x 1.3.1-9 [166 kB] Get:49 http://ftpmaster.internal/ubuntu zesty/universe s390x libmuscle-3.7-1 s390x 3.7+4565-2 [230 kB] Get:50 http://ftpmaster.internal/ubuntu zesty/universe s390x libmuscle-3.7-dev s390x 3.7+4565-2 [284 kB] Get:51 http://ftpmaster.internal/ubuntu zesty/main s390x pkg-config s390x 0.29.1-0ubuntu1 [44.2 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 41.6 MB in 48s (860 kB/s) Selecting previously unselected package groff-base. 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Setting up autotools-dev (20160430.1) ... Setting up libunistring0:s390x (0.9.3-5.2ubuntu1) ... Setting up libmuscle-3.7-1 (3.7+4565-2) ... Setting up icu-devtools (57.1-4) ... Setting up libgenome-1.3-dev (1.3.1-9) ... Setting up bsdmainutils (9.0.6ubuntu3) ... update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode Setting up autopoint (0.19.8.1-1ubuntu2) ... Setting up libboost-system1.62.0:s390x (1.62.0+dfsg-2ubuntu1) ... Setting up libboost-program-options-dev:s390x (1.62.0.0ubuntu1) ... Setting up libfile-stripnondeterminism-perl (0.028-1) ... Setting up libmuscle-3.7-dev (3.7+4565-2) ... Setting up gettext (0.19.8.1-1ubuntu2) ... Setting up libboost-regex1.62.0:s390x (1.62.0+dfsg-2ubuntu1) ... Setting up autoconf (2.69-10) ... Setting up libicu-dev (57.1-4) ... Setting up file (1:5.28-2ubuntu1) ... Setting up intltool-debian (0.35.0+20060710.4) ... Setting up libboost-system1.62-dev:s390x (1.62.0+dfsg-2ubuntu1) ... Setting up libboost-filesystem1.62.0:s390x (1.62.0+dfsg-2ubuntu1) ... Setting up automake (1:1.15-4ubuntu1) ... update-alternatives: using /usr/bin/automake-1.15 to provide /usr/bin/automake (automake) in auto mode Setting up man-db (2.7.5-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libtool (2.4.6-2) ... Setting up libboost-filesystem1.62-dev:s390x (1.62.0+dfsg-2ubuntu1) ... Setting up po-debconf (1.0.20) ... Setting up libboost-regex1.62-dev:s390x (1.62.0+dfsg-2ubuntu1) ... Setting up libboost-iostreams1.62-dev:s390x (1.62.0+dfsg-2ubuntu1) ... Setting up libboost-filesystem-dev:s390x (1.62.0.0ubuntu1) ... Setting up libboost-iostreams-dev:s390x (1.62.0.0ubuntu1) ... Setting up dh-strip-nondeterminism (0.028-1) ... Setting up debhelper (10.2.2ubuntu1) ... Setting up dh-autoreconf (12) ... Setting up sbuild-build-depends-libmems-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.24-3ubuntu1) ... +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 4.4.0-43-generic s390x (s390x) Toolchain package versions: binutils_2.27.51.20161108-1ubuntu1 dpkg-dev_1.18.10ubuntu1 g++-6_6.2.0-11ubuntu1 gcc-6_6.2.0-11ubuntu1 libc6-dev_2.24-3ubuntu1 libstdc++-6-dev_6.2.0-11ubuntu1 libstdc++6_6.2.0-11ubuntu1 linux-libc-dev_4.8.0-27.29 Package versions: adduser_3.113+nmu3ubuntu5 advancecomp_1.20-1 apt_1.3.1 apt-transport-https_1.3.1 autoconf_2.69-10 automake_1:1.15-4ubuntu1 autopoint_0.19.8.1-1ubuntu2 autotools-dev_20160430.1 base-files_9.6ubuntu6 base-passwd_3.5.40 bash_4.4-1ubuntu1 binutils_2.27.51.20161108-1ubuntu1 bsdmainutils_9.0.6ubuntu3 bsdutils_1:2.28.2-1ubuntu1 build-essential_12.1ubuntu2 bzip2_1.0.6-8build1 ca-certificates_20160104ubuntu1 coreutils_8.25-2ubuntu2 cpp_4:6.1.1-1ubuntu2 cpp-6_6.2.0-11ubuntu1 d-shlibs_0.77ubuntu1 dash_0.5.8-2.3ubuntu1 debconf_1.5.59ubuntu1 debhelper_10.2.2ubuntu1 debianutils_4.8 dh-autoreconf_12 dh-strip-nondeterminism_0.028-1 diffutils_1:3.5-1 dmsetup_2:1.02.133-1ubuntu1 dpkg_1.18.10ubuntu1 dpkg-dev_1.18.10ubuntu1 e2fslibs_1.43.3-1 e2fsprogs_1.43.3-1 fakeroot_1.21-1ubuntu2 file_1:5.28-2ubuntu1 findutils_4.6.0+git+20160703-2 g++_4:6.1.1-1ubuntu2 g++-6_6.2.0-11ubuntu1 gcc_4:6.1.1-1ubuntu2 gcc-6_6.2.0-11ubuntu1 gcc-6-base_6.2.0-11ubuntu1 gettext_0.19.8.1-1ubuntu2 gettext-base_0.19.8.1-1ubuntu2 gnupg_2.1.15-1ubuntu6 gnupg-agent_2.1.15-1ubuntu6 gpgv_2.1.15-1ubuntu6 grep_2.26-1 groff-base_1.22.3-8 gzip_1.6-4ubuntu1 hostname_3.18 icu-devtools_57.1-4 init_1.46 init-system-helpers_1.46 initscripts_2.88dsf-59.3ubuntu2 insserv_1.14.0-5ubuntu3 intltool-debian_0.35.0+20060710.4 libacl1_2.2.52-3 libapparmor1_2.10.95-4ubuntu5.2 libapt-pkg5.0_1.3.1 libarchive-zip-perl_1.59-1 libasn1-8-heimdal_1.7~git20160703+dfsg-1 libassuan0_2.4.3-1 libatomic1_6.2.0-11ubuntu1 libattr1_1:2.4.47-2 libaudit-common_1:2.6.6-1ubuntu1 libaudit1_1:2.6.6-1ubuntu1 libblkid1_2.28.2-1ubuntu1 libboost-filesystem-dev_1.62.0.0ubuntu1 libboost-filesystem1.62-dev_1.62.0+dfsg-2ubuntu1 libboost-filesystem1.62.0_1.62.0+dfsg-2ubuntu1 libboost-iostreams-dev_1.62.0.0ubuntu1 libboost-iostreams1.62-dev_1.62.0+dfsg-2ubuntu1 libboost-iostreams1.62.0_1.62.0+dfsg-2ubuntu1 libboost-program-options-dev_1.62.0.0ubuntu1 libboost-program-options1.62-dev_1.62.0+dfsg-2ubuntu1 libboost-program-options1.62.0_1.62.0+dfsg-2ubuntu1 libboost-regex1.62-dev_1.62.0+dfsg-2ubuntu1 libboost-regex1.62.0_1.62.0+dfsg-2ubuntu1 libboost-system1.62-dev_1.62.0+dfsg-2ubuntu1 libboost-system1.62.0_1.62.0+dfsg-2ubuntu1 libboost1.62-dev_1.62.0+dfsg-2ubuntu1 libbz2-1.0_1.0.6-8build1 libc-bin_2.24-3ubuntu1 libc-dev-bin_2.24-3ubuntu1 libc6_2.24-3ubuntu1 libc6-dev_2.24-3ubuntu1 libcap-ng0_0.7.7-3 libcap2_1:2.25-1 libcc1-0_6.2.0-11ubuntu1 libcomerr2_1.43.3-1 libcroco3_0.6.11-2 libcryptsetup4_2:1.7.2-0ubuntu1 libcurl3-gnutls_7.50.1-1ubuntu2 libdb5.3_5.3.28-12 libdebconfclient0_0.213ubuntu1 libdevmapper1.02.1_2:1.02.133-1ubuntu1 libdpkg-perl_1.18.10ubuntu1 libfakeroot_1.21-1ubuntu2 libfdisk1_2.28.2-1ubuntu1 libffi6_3.2.1-6 libfile-stripnondeterminism-perl_0.028-1 libgcc-6-dev_6.2.0-11ubuntu1 libgcc1_1:6.2.0-11ubuntu1 libgcrypt20_1.7.2-2ubuntu1 libgdbm3_1.8.3-14 libgenome-1.3-0v5_1.3.1-9 libgenome-1.3-dev_1.3.1-9 libglib2.0-0_2.50.2-1 libgmp10_2:6.1.1+dfsg-1 libgnutls30_3.5.3-5ubuntu1 libgomp1_6.2.0-11ubuntu1 libgpg-error0_1.24-1 libgssapi-krb5-2_1.15~beta1-1 libgssapi3-heimdal_1.7~git20160703+dfsg-1 libhcrypto4-heimdal_1.7~git20160703+dfsg-1 libheimbase1-heimdal_1.7~git20160703+dfsg-1 libheimntlm0-heimdal_1.7~git20160703+dfsg-1 libhogweed4_3.3-1 libhx509-5-heimdal_1.7~git20160703+dfsg-1 libicu-dev_57.1-4 libicu57_57.1-4 libidn11_1.33-1 libip4tc0_1.6.0-3ubuntu2 libisl15_0.17.1-1 libitm1_6.2.0-11ubuntu1 libk5crypto3_1.15~beta1-1 libkeyutils1_1.5.9-9ubuntu1 libkmod2_22-1.1ubuntu1 libkrb5-26-heimdal_1.7~git20160703+dfsg-1 libkrb5-3_1.15~beta1-1 libkrb5support0_1.15~beta1-1 libksba8_1.3.5-2 libldap-2.4-2_2.4.42+dfsg-2ubuntu5 liblockfile-bin_1.09-6ubuntu1 liblockfile1_1.09-6ubuntu1 liblz4-1_0.0~r131-2ubuntu2 liblzma5_5.2.2-1.2 libmagic1_1:5.28-2ubuntu1 libmount1_2.28.2-1ubuntu1 libmpc3_1.0.3-1 libmpfr4_3.1.5-1 libmuscle-3.7-1_3.7+4565-2 libmuscle-3.7-dev_3.7+4565-2 libncurses5_6.0+20160625-1ubuntu1 libncursesw5_6.0+20160625-1ubuntu1 libnettle6_3.3-1 libnpth0_1.2-3 libp11-kit0_0.23.2-5 libpam-modules_1.1.8-3.2ubuntu2 libpam-modules-bin_1.1.8-3.2ubuntu2 libpam-runtime_1.1.8-3.2ubuntu2 libpam0g_1.1.8-3.2ubuntu2 libpcre3_2:8.39-2 libperl5.22_5.22.2-3 libperl5.24_5.24.1~rc3-3 libpipeline1_1.4.1-2 libpng16-16_1.6.26-1 libprocps6_2:3.3.12-1ubuntu2 libreadline7_7.0-0ubuntu2 libroken18-heimdal_1.7~git20160703+dfsg-1 librtmp1_2.4+20151223.gitfa8646d.1-1 libsasl2-2_2.1.27~72-g88d82a3+dfsg-1 libsasl2-modules-db_2.1.27~72-g88d82a3+dfsg-1 libseccomp2_2.3.1-2ubuntu2 libselinux1_2.6-3 libsemanage-common_2.6-1 libsemanage1_2.6-1 libsepol1_2.6-1 libsigsegv2_2.10-5 libslang2_2.3.1-5ubuntu1 libsmartcols1_2.28.2-1ubuntu1 libsqlite3-0_3.15.1-1 libss2_1.43.3-1 libssl1.0.0_1.0.2g-1ubuntu9 libstdc++-6-dev_6.2.0-11ubuntu1 libstdc++6_6.2.0-11ubuntu1 libsystemd0_232-2git1 libtasn1-6_4.9-4 libtimedate-perl_2.3000-2 libtinfo5_6.0+20160625-1ubuntu1 libtool_2.4.6-2 libudev1_232-2git1 libunistring0_0.9.3-5.2ubuntu1 libusb-0.1-4_2:0.1.12-30 libustr-1.0-1_1.0.4-5 libuuid1_2.28.2-1ubuntu1 libwind0-heimdal_1.7~git20160703+dfsg-1 libxml2_2.9.4+dfsg1-2.1 linux-libc-dev_4.8.0-27.29 lockfile-progs_0.1.17 login_1:4.2-3.2ubuntu1 lsb-base_9.20160110ubuntu5 m4_1.4.17-5 make_4.1-9 man-db_2.7.5-1 mawk_1.3.3-17ubuntu2 mount_2.28.2-1ubuntu1 multiarch-support_2.24-3ubuntu1 ncurses-base_6.0+20160625-1ubuntu1 ncurses-bin_6.0+20160625-1ubuntu1 openssl_1.0.2g-1ubuntu9 optipng_0.7.6-1build1 passwd_1:4.2-3.2ubuntu1 patch_2.7.5-1 perl_5.24.1~rc3-3 perl-base_5.24.1~rc3-3 perl-modules-5.22_5.22.2-3 perl-modules-5.24_5.24.1~rc3-3 pinentry-curses_0.9.7-8 pkg-config_0.29.1-0ubuntu1 pkg-create-dbgsym_0.72 pkgbinarymangler_131 po-debconf_1.0.20 policyrcd-script-zg2_0.1-3 procps_2:3.3.12-1ubuntu2 readline-common_7.0-0ubuntu2 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-libmems-dummy_0.invalid.0 sed_4.2.2-8 sensible-utils_0.0.9 systemd_232-2git1 systemd-sysv_232-2git1 sysv-rc_2.88dsf-59.3ubuntu2 sysvinit-utils_2.88dsf-59.8git1 tar_1.29b-1.1 tzdata_2016i-1 ubuntu-keyring_2016.10.27 util-linux_2.28.2-1ubuntu1 xz-utils_5.2.2-1.2 zlib1g_1:1.2.8.dfsg-2ubuntu5 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- gpgv: Signature made Tue Nov 8 17:13:02 2016 UTC gpgv: using RSA key gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./libmems_1.6.0+4725-4.dsc dpkg-source: info: extracting libmems in libmems-1.6.0+4725 dpkg-source: info: unpacking libmems_1.6.0+4725.orig.tar.xz dpkg-source: info: unpacking libmems_1.6.0+4725-4.debian.tar.xz dpkg-source: info: applying 01_fix_ctors.patch dpkg-source: info: applying 02_fix_a_Wformat.patch dpkg-source: info: applying pkg-config-directive.patch dpkg-source: info: applying 03_update_boost_m4_to_git_d9ff75.patch dpkg-source: info: applying 04_add_dependend_libs_to_link_command.patch dpkg-source: info: applying 05_gcc-6.patch dpkg-source: info: applying boost1.62.patch Check disc space ---------------- Sufficient free space for build User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf DEB_BUILD_OPTIONS=parallel=4 HOME=/home/buildd LANG=C.UTF-8 LC_ALL=C.UTF-8 LOGNAME=buildd MAIL=/var/mail/buildd OLDPWD=/ PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games PWD=/<>/libmems-1.6.0+4725 SHELL=/bin/sh SUDO_COMMAND=/usr/sbin/chroot /<> su buildd -s /bin/sh -c cd '/<>/libmems-1.6.0+4725' && 'env' SUDO_GID=2501 SUDO_UID=2001 SUDO_USER=buildd TERM=unknown USER=buildd USERNAME=root dpkg-buildpackage ----------------- dpkg-buildpackage: info: source package libmems dpkg-buildpackage: info: source version 1.6.0+4725-4 dpkg-buildpackage: info: source distribution unstable dpkg-source --before-build libmems-1.6.0+4725 dpkg-buildpackage: info: host architecture s390x fakeroot debian/rules clean dh clean --with autoreconf dh_testdir dh_auto_clean dh_autoreconf_clean dh_clean debian/rules build-arch dh build-arch --with autoreconf dh_testdir -a dh_update_autotools_config -a dh_autoreconf -a libtoolize: putting auxiliary files in AC_CONFIG_AUX_DIR, 'config'. libtoolize: copying file 'config/ltmain.sh' libtoolize: putting macros in AC_CONFIG_MACRO_DIRS, 'm4'. libtoolize: copying file 'm4/libtool.m4' libtoolize: copying file 'm4/ltoptions.m4' libtoolize: copying file 'm4/ltsugar.m4' libtoolize: copying file 'm4/ltversion.m4' libtoolize: copying file 'm4/lt~obsolete.m4' configure.ac:54: warning: AM_INIT_AUTOMAKE: two- and three-arguments forms are deprecated. For more info, see: configure.ac:54: http://www.gnu.org/software/automake/manual/automake.html#Modernize-AM_005fINIT_005fAUTOMAKE-invocation configure.ac:66: installing 'config/compile' configure.ac:66: installing 'config/config.guess' configure.ac:66: installing 'config/config.sub' configure.ac:54: installing 'config/install-sh' configure.ac:54: installing 'config/missing' libMems/Makefile.am:48: warning: source file 'HomologyHMM/algebras.cc' is in a subdirectory, libMems/Makefile.am:48: but option 'subdir-objects' is disabled automake: warning: possible forward-incompatibility. automake: At least a source file is in a subdirectory, but the 'subdir-objects' automake: automake option hasn't been enabled. For now, the corresponding output automake: object file(s) will be placed in the top-level directory. However, automake: this behaviour will change in future Automake versions: they will automake: unconditionally cause object files to be placed in the same subdirectory automake: of the corresponding sources. automake: You are advised to start using 'subdir-objects' option throughout your automake: project, to avoid future incompatibilities. libMems/Makefile.am:48: warning: source file 'HomologyHMM/homology.cc' is in a subdirectory, libMems/Makefile.am:48: but option 'subdir-objects' is disabled libMems/Makefile.am:48: warning: source file 'HomologyHMM/homologymain.cc' is in a subdirectory, libMems/Makefile.am:48: but option 'subdir-objects' is disabled libMems/Makefile.am:51: warning: source file 'dmSML/asyncio.c' is in a subdirectory, libMems/Makefile.am:51: but option 'subdir-objects' is disabled libMems/Makefile.am:51: warning: source file 'dmSML/alinuxaio.c' is in a subdirectory, libMems/Makefile.am:51: but option 'subdir-objects' is disabled libMems/Makefile.am:51: warning: source file 'dmSML/aPOSIXaio.c' is in a subdirectory, libMems/Makefile.am:51: but option 'subdir-objects' is disabled libMems/Makefile.am:51: warning: source file 'dmSML/alibc.c' is in a subdirectory, libMems/Makefile.am:51: but option 'subdir-objects' is disabled libMems/Makefile.am:51: warning: source file 'dmSML/awin32aio.c' is in a subdirectory, libMems/Makefile.am:51: but option 'subdir-objects' is disabled libMems/Makefile.am:51: warning: source file 'dmSML/buffer.c' is in a subdirectory, libMems/Makefile.am:51: but option 'subdir-objects' is disabled libMems/Makefile.am:51: warning: source file 'dmSML/util.c' is in a subdirectory, libMems/Makefile.am:51: but option 'subdir-objects' is disabled libMems/Makefile.am:51: warning: source file 'dmSML/sorting.c' is in a subdirectory, libMems/Makefile.am:51: but option 'subdir-objects' is disabled libMems/Makefile.am:51: warning: source file 'dmSML/dmsort.c' is in a subdirectory, libMems/Makefile.am:51: but option 'subdir-objects' is disabled libMems/Makefile.am:51: warning: source file 'dmSML/timing.c' is in a subdirectory, libMems/Makefile.am:51: but option 'subdir-objects' is disabled libMems/Makefile.am:51: warning: source file 'dmSML/sml.c' is in a subdirectory, libMems/Makefile.am:51: but option 'subdir-objects' is disabled libMems/Makefile.am: installing 'config/depcomp' dh_auto_configure -a ./configure --build=s390x-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-silent-rules --libdir=\${prefix}/lib/s390x-linux-gnu --libexecdir=\${prefix}/lib/s390x-linux-gnu --disable-maintainer-mode --disable-dependency-tracking configure: WARNING: unrecognized options: --disable-maintainer-mode checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /bin/mkdir -p checking for gawk... no checking for mawk... mawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking for g++... g++ checking whether the C++ compiler works... yes checking for C++ compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C++ compiler... yes checking whether g++ accepts -g... yes checking for style of include used by make... GNU checking dependency style of g++... none checking whether ln -s works... yes checking build system type... s390x-ibm-linux-gnu checking host system type... s390x-ibm-linux-gnu checking how to print strings... printf checking for gcc... gcc checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking whether gcc understands -c and -o together... yes checking dependency style of gcc... none checking for a sed that does not truncate output... /bin/sed checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking for fgrep... /bin/grep -F checking for ld used by gcc... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B checking the name lister (/usr/bin/nm -B) interface... BSD nm checking the maximum length of command line arguments... 1572864 checking how to convert s390x-ibm-linux-gnu file names to s390x-ibm-linux-gnu format... func_convert_file_noop checking how to convert s390x-ibm-linux-gnu file names to toolchain format... func_convert_file_noop checking for /usr/bin/ld option to reload object files... -r checking for objdump... objdump checking how to recognize dependent libraries... pass_all checking for dlltool... no checking how to associate runtime and link libraries... printf %s\n checking for ar... ar checking for archiver @FILE support... @ checking for strip... strip checking for ranlib... ranlib checking command to parse /usr/bin/nm -B output from gcc object... ok checking for sysroot... no checking for a working dd... /bin/dd checking how to truncate binary pipes... /bin/dd bs=4096 count=1 checking for mt... no checking if : is a manifest tool... no checking how to run the C preprocessor... gcc -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking for dlfcn.h... yes checking for objdir... .libs checking if gcc supports -fno-rtti -fno-exceptions... no checking for gcc option to produce PIC... -fPIC -DPIC checking if gcc PIC flag -fPIC -DPIC works... yes checking if gcc static flag -static works... yes checking if gcc supports -c -o file.o... yes checking if gcc supports -c -o file.o... (cached) yes checking whether the gcc linker (/usr/bin/ld -m elf64_s390) supports shared libraries... yes checking whether -lc should be explicitly linked in... no checking dynamic linker characteristics... GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... yes checking whether to build static libraries... yes checking how to run the C++ preprocessor... g++ -E checking for ld used by g++... /usr/bin/ld -m elf64_s390 checking if the linker (/usr/bin/ld -m elf64_s390) is GNU ld... yes checking whether the g++ linker (/usr/bin/ld -m elf64_s390) supports shared libraries... yes checking for g++ option to produce PIC... -fPIC -DPIC checking if g++ PIC flag -fPIC -DPIC works... yes checking if g++ static flag -static works... yes checking if g++ supports -c -o file.o... yes checking if g++ supports -c -o file.o... (cached) yes checking whether the g++ linker (/usr/bin/ld -m elf64_s390) supports shared libraries... yes checking dynamic linker characteristics... (cached) GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking for special C compiler options needed for large files... no checking for _FILE_OFFSET_BITS value needed for large files... no checking for ANSI C header files... (cached) yes checking for Boost headers version >= 1.34.0... yes checking for Boost's header version... 1_62 checking whether the compiler implements namespaces... yes checking for the toolset name used by Boost for g++... configure: WARNING: could not figure out which toolset name to use for g++ checking boost/system/error_code.hpp usability... yes checking boost/system/error_code.hpp presence... yes checking for boost/system/error_code.hpp... yes checking for the Boost system library... yes checking boost/filesystem/path.hpp usability... yes checking boost/filesystem/path.hpp presence... yes checking for boost/filesystem/path.hpp... yes checking for the Boost filesystem library... (cached) yes checking boost/program_options.hpp usability... yes checking boost/program_options.hpp presence... yes checking for boost/program_options.hpp... yes checking for the Boost program_options library... (cached) yes checking boost/iostreams/device/file_descriptor.hpp usability... yes checking boost/iostreams/device/file_descriptor.hpp presence... yes checking for boost/iostreams/device/file_descriptor.hpp... yes checking for the Boost iostreams library... (cached) yes checking for pkg-config... /usr/bin/pkg-config checking pkg-config is at least version 0.9.0... yes checking for DEPS... yes checking for sys/types.h... (cached) yes checking sys/aio.h usability... no checking sys/aio.h presence... no checking for sys/aio.h... no checking aio.h usability... yes checking aio.h presence... yes checking for aio.h... yes checking features.h usability... yes checking features.h presence... yes checking for features.h... yes checking for pthread_mutex_unlock in -lpthread... yes checking for aio_write in -lrt... yes checking for doxygen... no configure: WARNING: doxygen not found - will not generate any doxygen documentation checking for perl... /usr/bin/perl checking for an ANSI C-conforming const... yes checking for inline... inline checking whether time.h and sys/time.h may both be included... yes checking whether gcc needs -traditional... no checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating libMems/Makefile config.status: creating libMems-1.6.pc config.status: creating config.h config.status: executing depfiles commands config.status: executing libtool commands configure: WARNING: unrecognized options: --disable-maintainer-mode dh_auto_build -a make -j1 make[1]: Entering directory '/<>/libmems-1.6.0+4725' make all-recursive make[2]: Entering directory '/<>/libmems-1.6.0+4725' Making all in libMems make[3]: Entering directory '/<>/libmems-1.6.0+4725/libMems' /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -g -O2 -fdebug-prefix-map=/<>/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c -o RepeatHash.lo RepeatHash.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -g -O2 -fdebug-prefix-map=/<>/libmems-1.6.0+4725=. 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Aligner.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -g -O2 -fdebug-prefix-map=/<>/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c Aligner.cpp -fPIC -DPIC -o .libs/Aligner.o In file included from /usr/include/c++/6/ext/hash_map:60:0, from ../libMems/HomologyHMM/dptables.h:43, from ../libMems/HomologyHMM/homology.h:27, from ../libMems/Islands.h:25, from Aligner.cpp:10: /usr/include/c++/6/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp] #warning \ ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -g -O2 -fdebug-prefix-map=/<>/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c Aligner.cpp -o Aligner.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -g -O2 -fdebug-prefix-map=/<>/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c -o Islands.lo Islands.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -g -O2 -fdebug-prefix-map=/<>/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c Islands.cpp -fPIC -DPIC -o .libs/Islands.o In file included from /usr/include/c++/6/ext/hash_map:60:0, from ../libMems/HomologyHMM/dptables.h:43, from ../libMems/HomologyHMM/homology.h:27, from ../libMems/Islands.h:25, from Islands.cpp:13: /usr/include/c++/6/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp] #warning \ ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -g -O2 -fdebug-prefix-map=/<>/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c Islands.cpp -o Islands.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -g -O2 -fdebug-prefix-map=/<>/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c -o MaskedMemHash.lo MaskedMemHash.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -g -O2 -fdebug-prefix-map=/<>/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c MaskedMemHash.cpp -fPIC -DPIC -o .libs/MaskedMemHash.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -g -O2 -fdebug-prefix-map=/<>/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c MaskedMemHash.cpp -o MaskedMemHash.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -g -O2 -fdebug-prefix-map=/<>/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c -o GappedAlignment.lo GappedAlignment.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -g -O2 -fdebug-prefix-map=/<>/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c GappedAlignment.cpp -fPIC -DPIC -o .libs/GappedAlignment.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -g -O2 -fdebug-prefix-map=/<>/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c GappedAlignment.cpp -o GappedAlignment.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -g -O2 -fdebug-prefix-map=/<>/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c -o MuscleInterface.lo MuscleInterface.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -g -O2 -fdebug-prefix-map=/<>/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c MuscleInterface.cpp -fPIC -DPIC -o .libs/MuscleInterface.o In file included from MuscleInterface.cpp:18:0: /usr/include/libMUSCLE-3.7/libMUSCLE/muscle.h:54:0: warning: "assert" redefined #define assert(exp) ((void)0) In file included from /usr/include/boost/integer/integer_log2.hpp:18:0, from /usr/include/boost/pending/integer_log2.hpp:7, from /usr/include/boost/pending/lowest_bit.hpp:18, from /usr/include/boost/dynamic_bitset/dynamic_bitset.hpp:46, from /usr/include/boost/dynamic_bitset.hpp:15, from ../libMems/AbstractMatch.h:22, from ../libMems/SparseAbstractMatch.h:18, from ../libMems/GappedAlignment.h:18, from ../libMems/MuscleInterface.h:19, from MuscleInterface.cpp:13: /usr/include/assert.h:88:0: note: this is the location of the previous definition # define assert(expr) \ libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -g -O2 -fdebug-prefix-map=/<>/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c MuscleInterface.cpp -o MuscleInterface.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -g -O2 -fdebug-prefix-map=/<>/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c -o PhyloTree.lo PhyloTree.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -g -O2 -fdebug-prefix-map=/<>/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c PhyloTree.cpp -fPIC -DPIC -o .libs/PhyloTree.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -g -O2 -fdebug-prefix-map=/<>/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c PhyloTree.cpp -o PhyloTree.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -g -O2 -fdebug-prefix-map=/<>/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c -o RepeatMatchList.lo RepeatMatchList.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -g -O2 -fdebug-prefix-map=/<>/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c RepeatMatchList.cpp -fPIC -DPIC -o .libs/RepeatMatchList.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -g -O2 -fdebug-prefix-map=/<>/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c RepeatMatchList.cpp -o RepeatMatchList.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -g -O2 -fdebug-prefix-map=/<>/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c -o RepeatMatch.lo RepeatMatch.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -g -O2 -fdebug-prefix-map=/<>/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c RepeatMatch.cpp -fPIC -DPIC -o .libs/RepeatMatch.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -g -O2 -fdebug-prefix-map=/<>/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c RepeatMatch.cpp -o RepeatMatch.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -g -O2 -fdebug-prefix-map=/<>/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c -o Backbone.lo Backbone.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -g -O2 -fdebug-prefix-map=/<>/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c Backbone.cpp -fPIC -DPIC -o .libs/Backbone.o In file included from /usr/include/c++/6/ext/hash_map:60:0, from ../libMems/HomologyHMM/dptables.h:43, from ../libMems/HomologyHMM/homology.h:27, from ../libMems/Islands.h:25, from ../libMems/ProgressiveAligner.h:21, from Backbone.cpp:13: /usr/include/c++/6/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp] #warning \ ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -g -O2 -fdebug-prefix-map=/<>/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c Backbone.cpp -o Backbone.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -g -O2 -fdebug-prefix-map=/<>/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c -o PairwiseMatchFinder.lo PairwiseMatchFinder.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -g -O2 -fdebug-prefix-map=/<>/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c PairwiseMatchFinder.cpp -fPIC -DPIC -o .libs/PairwiseMatchFinder.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -g -O2 -fdebug-prefix-map=/<>/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c PairwiseMatchFinder.cpp -o PairwiseMatchFinder.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -g -O2 -fdebug-prefix-map=/<>/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c -o ProgressiveAligner.lo ProgressiveAligner.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -g -O2 -fdebug-prefix-map=/<>/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c ProgressiveAligner.cpp -fPIC -DPIC -o .libs/ProgressiveAligner.o In file included from /usr/include/c++/6/ext/hash_map:60:0, from ../libMems/HomologyHMM/dptables.h:43, from ../libMems/HomologyHMM/homology.h:27, from ../libMems/Islands.h:25, from ../libMems/ProgressiveAligner.h:21, from ProgressiveAligner.cpp:14: /usr/include/c++/6/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp] #warning \ ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -g -O2 -fdebug-prefix-map=/<>/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c ProgressiveAligner.cpp -o ProgressiveAligner.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -g -O2 -fdebug-prefix-map=/<>/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c -o SuperInterval.lo SuperInterval.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -g -O2 -fdebug-prefix-map=/<>/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c SuperInterval.cpp -fPIC -DPIC -o .libs/SuperInterval.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -g -O2 -fdebug-prefix-map=/<>/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c SuperInterval.cpp -o SuperInterval.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -g -O2 -fdebug-prefix-map=/<>/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c -o GreedyBreakpointElimination.lo GreedyBreakpointElimination.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -g -O2 -fdebug-prefix-map=/<>/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c GreedyBreakpointElimination.cpp -fPIC -DPIC -o .libs/GreedyBreakpointElimination.o In file included from /usr/include/c++/6/ext/hash_map:60:0, from ../libMems/HomologyHMM/dptables.h:43, from ../libMems/HomologyHMM/homology.h:27, from ../libMems/Islands.h:25, from ../libMems/ProgressiveAligner.h:21, from GreedyBreakpointElimination.cpp:7: /usr/include/c++/6/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp] #warning \ ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -g -O2 -fdebug-prefix-map=/<>/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c GreedyBreakpointElimination.cpp -o GreedyBreakpointElimination.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -g -O2 -fdebug-prefix-map=/<>/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c -o algebras.lo `test -f 'HomologyHMM/algebras.cc' || echo './'`HomologyHMM/algebras.cc libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -g -O2 -fdebug-prefix-map=/<>/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c HomologyHMM/algebras.cc -fPIC -DPIC -o .libs/algebras.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -g -O2 -fdebug-prefix-map=/<>/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c HomologyHMM/algebras.cc -o algebras.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -g -O2 -fdebug-prefix-map=/<>/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c -o homology.lo `test -f 'HomologyHMM/homology.cc' || echo './'`HomologyHMM/homology.cc libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -g -O2 -fdebug-prefix-map=/<>/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c HomologyHMM/homology.cc -fPIC -DPIC -o .libs/homology.o In file included from /usr/include/c++/6/ext/hash_map:60:0, from HomologyHMM/dptables.h:43, from HomologyHMM/homology.h:27, from HomologyHMM/homology.cc:24: /usr/include/c++/6/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp] #warning \ ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -g -O2 -fdebug-prefix-map=/<>/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c HomologyHMM/homology.cc -o homology.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -g -O2 -fdebug-prefix-map=/<>/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c -o homologymain.lo `test -f 'HomologyHMM/homologymain.cc' || echo './'`HomologyHMM/homologymain.cc libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -g -O2 -fdebug-prefix-map=/<>/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c HomologyHMM/homologymain.cc -fPIC -DPIC -o .libs/homologymain.o In file included from /usr/include/c++/6/ext/hash_map:60:0, from HomologyHMM/dptables.h:43, from HomologyHMM/homology.h:27, from HomologyHMM/homologymain.cc:21: /usr/include/c++/6/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp] #warning \ ^~~~~~~ libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -g -O2 -fdebug-prefix-map=/<>/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c HomologyHMM/homologymain.cc -o homologymain.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -DUSE_POSIX_AIO -g -O2 -fdebug-prefix-map=/<>/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c -o asyncio.lo `test -f 'dmSML/asyncio.c' || echo './'`dmSML/asyncio.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -DUSE_POSIX_AIO -g -O2 -fdebug-prefix-map=/<>/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c dmSML/asyncio.c -fPIC -DPIC -o .libs/asyncio.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -DUSE_POSIX_AIO -g -O2 -fdebug-prefix-map=/<>/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c dmSML/asyncio.c -o asyncio.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -DUSE_POSIX_AIO -g -O2 -fdebug-prefix-map=/<>/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c -o alinuxaio.lo `test -f 'dmSML/alinuxaio.c' || echo './'`dmSML/alinuxaio.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -DUSE_POSIX_AIO -g -O2 -fdebug-prefix-map=/<>/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c dmSML/alinuxaio.c -fPIC -DPIC -o .libs/alinuxaio.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -DUSE_POSIX_AIO -g -O2 -fdebug-prefix-map=/<>/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c dmSML/alinuxaio.c -o alinuxaio.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -DUSE_POSIX_AIO -g -O2 -fdebug-prefix-map=/<>/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c -o aPOSIXaio.lo `test -f 'dmSML/aPOSIXaio.c' || echo './'`dmSML/aPOSIXaio.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -DUSE_POSIX_AIO -g -O2 -fdebug-prefix-map=/<>/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c dmSML/aPOSIXaio.c -fPIC -DPIC -o .libs/aPOSIXaio.o dmSML/aPOSIXaio.c: In function ‘QueryLastCompletePAIO’: dmSML/aPOSIXaio.c:115:21: warning: passing argument 1 of ‘aio_suspend’ from incompatible pointer type [-Wincompatible-pointer-types] rval = aio_suspend(request_array, 1, &zero_wait); ^~~~~~~~~~~~~ In file included from /usr/include/features.h:364:0, from /usr/include/s390x-linux-gnu/sys/types.h:25, from ../libMems/dmSML/asyncio.h:24, from ../libMems/dmSML/aPOSIXaio.h:8, from dmSML/aPOSIXaio.c:5: /usr/include/aio.h:199:12: note: expected ‘const struct aiocb * const*’ but argument is of type ‘struct aiocb **’ extern int __REDIRECT_NTH (aio_suspend, ^ libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -DUSE_POSIX_AIO -g -O2 -fdebug-prefix-map=/<>/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c dmSML/aPOSIXaio.c -o aPOSIXaio.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -DUSE_POSIX_AIO -g -O2 -fdebug-prefix-map=/<>/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c -o alibc.lo `test -f 'dmSML/alibc.c' || echo './'`dmSML/alibc.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -DUSE_POSIX_AIO -g -O2 -fdebug-prefix-map=/<>/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c dmSML/alibc.c -fPIC -DPIC -o .libs/alibc.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -DUSE_POSIX_AIO -g -O2 -fdebug-prefix-map=/<>/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c dmSML/alibc.c -o alibc.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -DUSE_POSIX_AIO -g -O2 -fdebug-prefix-map=/<>/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c -o awin32aio.lo `test -f 'dmSML/awin32aio.c' || echo './'`dmSML/awin32aio.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -DUSE_POSIX_AIO -g -O2 -fdebug-prefix-map=/<>/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c dmSML/awin32aio.c -fPIC -DPIC -o .libs/awin32aio.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -DUSE_POSIX_AIO -g -O2 -fdebug-prefix-map=/<>/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c dmSML/awin32aio.c -o awin32aio.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -DUSE_POSIX_AIO -g -O2 -fdebug-prefix-map=/<>/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c -o buffer.lo `test -f 'dmSML/buffer.c' || echo './'`dmSML/buffer.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -DUSE_POSIX_AIO -g -O2 -fdebug-prefix-map=/<>/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c dmSML/buffer.c -fPIC -DPIC -o .libs/buffer.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -DUSE_POSIX_AIO -g -O2 -fdebug-prefix-map=/<>/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c dmSML/buffer.c -o buffer.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -DUSE_POSIX_AIO -g -O2 -fdebug-prefix-map=/<>/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c -o util.lo `test -f 'dmSML/util.c' || echo './'`dmSML/util.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -DUSE_POSIX_AIO -g -O2 -fdebug-prefix-map=/<>/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c dmSML/util.c -fPIC -DPIC -o .libs/util.o dmSML/util.c: In function ‘removeFile’: dmSML/util.c:126:24: warning: assignment discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] rm_cmd = Fmt( "/bin/rm -fv %s", filename ); ^ dmSML/util.c:128:24: warning: assignment discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] rm_cmd = Fmt( "/bin/rm -f %s", filename ); ^ dmSML/util.c:129:16: warning: implicit declaration of function ‘system’ [-Wimplicit-function-declaration] return system( rm_cmd ); ^~~~~~ libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -DUSE_POSIX_AIO -g -O2 -fdebug-prefix-map=/<>/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c dmSML/util.c -o util.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -DUSE_POSIX_AIO -g -O2 -fdebug-prefix-map=/<>/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c -o sorting.lo `test -f 'dmSML/sorting.c' || echo './'`dmSML/sorting.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -DUSE_POSIX_AIO -g -O2 -fdebug-prefix-map=/<>/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c dmSML/sorting.c -fPIC -DPIC -o .libs/sorting.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -DUSE_POSIX_AIO -g -O2 -fdebug-prefix-map=/<>/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c dmSML/sorting.c -o sorting.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -DUSE_POSIX_AIO -g -O2 -fdebug-prefix-map=/<>/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c -o dmsort.lo `test -f 'dmSML/dmsort.c' || echo './'`dmSML/dmsort.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -DUSE_POSIX_AIO -g -O2 -fdebug-prefix-map=/<>/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c dmSML/dmsort.c -fPIC -DPIC -o .libs/dmsort.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -DUSE_POSIX_AIO -g -O2 -fdebug-prefix-map=/<>/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c dmSML/dmsort.c -o dmsort.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -DUSE_POSIX_AIO -g -O2 -fdebug-prefix-map=/<>/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c -o timing.lo `test -f 'dmSML/timing.c' || echo './'`dmSML/timing.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -DUSE_POSIX_AIO -g -O2 -fdebug-prefix-map=/<>/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c dmSML/timing.c -fPIC -DPIC -o .libs/timing.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -DUSE_POSIX_AIO -g -O2 -fdebug-prefix-map=/<>/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c dmSML/timing.c -o timing.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -DUSE_POSIX_AIO -g -O2 -fdebug-prefix-map=/<>/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c -o sml.lo `test -f 'dmSML/sml.c' || echo './'`dmSML/sml.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -DUSE_POSIX_AIO -g -O2 -fdebug-prefix-map=/<>/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c dmSML/sml.c -fPIC -DPIC -o .libs/sml.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -DUSE_POSIX_AIO -g -O2 -fdebug-prefix-map=/<>/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -c dmSML/sml.c -o sml.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CXX --mode=link g++ -O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -I/usr/include/libGenome-1.3 -I/usr/include/libMUSCLE-3.7 -g -O2 -fdebug-prefix-map=/<>/libmems-1.6.0+4725=. -fstack-protector-strong -Wformat -Werror=format-security -version-info 1:0:0 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o libMems-1.6.la -rpath /usr/lib/s390x-linux-gnu RepeatHash.lo DNAFileSML.lo MatchFinder.lo DNAMemorySML.lo MemorySML.lo SortedMerList.lo FileSML.lo MemHash.lo MatchHashEntry.lo Interval.lo IntervalList.lo twister.lo gnAlignedSequences.lo MatchList.lo Aligner.lo Islands.lo MaskedMemHash.lo GappedAlignment.lo MuscleInterface.lo PhyloTree.lo RepeatMatchList.lo RepeatMatch.lo Backbone.lo PairwiseMatchFinder.lo ProgressiveAligner.lo SuperInterval.lo GreedyBreakpointElimination.lo algebras.lo homology.lo homologymain.lo asyncio.lo alinuxaio.lo aPOSIXaio.lo alibc.lo awin32aio.lo buffer.lo util.lo sorting.lo dmsort.lo timing.lo sml.lo -lGenome-1.3 -lMUSCLE-3.7 -lboost_filesystem -lboost_iostreams -lboost_system -lrt -lpthread libtool: link: g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/s390x-linux-gnu/6/../../../s390x-linux-gnu/crti.o /usr/lib/gcc/s390x-linux-gnu/6/crtbeginS.o .libs/RepeatHash.o .libs/DNAFileSML.o .libs/MatchFinder.o .libs/DNAMemorySML.o .libs/MemorySML.o .libs/SortedMerList.o .libs/FileSML.o .libs/MemHash.o .libs/MatchHashEntry.o .libs/Interval.o .libs/IntervalList.o .libs/twister.o .libs/gnAlignedSequences.o .libs/MatchList.o .libs/Aligner.o .libs/Islands.o .libs/MaskedMemHash.o .libs/GappedAlignment.o .libs/MuscleInterface.o .libs/PhyloTree.o .libs/RepeatMatchList.o .libs/RepeatMatch.o .libs/Backbone.o .libs/PairwiseMatchFinder.o .libs/ProgressiveAligner.o .libs/SuperInterval.o .libs/GreedyBreakpointElimination.o .libs/algebras.o .libs/homology.o .libs/homologymain.o .libs/asyncio.o .libs/alinuxaio.o .libs/aPOSIXaio.o .libs/alibc.o .libs/awin32aio.o .libs/buffer.o .libs/util.o .libs/sorting.o .libs/dmsort.o .libs/timing.o .libs/sml.o -lGenome-1.3 -lMUSCLE-3.7 -lboost_filesystem -lboost_iostreams -lboost_system -lrt -lpthread -L/usr/lib/gcc/s390x-linux-gnu/6 -L/usr/lib/gcc/s390x-linux-gnu/6/../../../s390x-linux-gnu -L/usr/lib/gcc/s390x-linux-gnu/6/../../../../lib -L/lib/s390x-linux-gnu -L/lib/../lib -L/usr/lib/s390x-linux-gnu -L/usr/lib/../lib -L/usr/lib/gcc/s390x-linux-gnu/6/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/s390x-linux-gnu/6/crtendS.o /usr/lib/gcc/s390x-linux-gnu/6/../../../s390x-linux-gnu/crtn.o -O2 -g -O2 -fstack-protector-strong -Wl,-Bsymbolic-functions -Wl,-z -Wl,relro -Wl,-z -Wl,now -Wl,-soname -Wl,libMems-1.6.so.1 -o .libs/libMems-1.6.so.1.0.0 libtool: link: (cd ".libs" && rm -f "libMems-1.6.so.1" && ln -s "libMems-1.6.so.1.0.0" "libMems-1.6.so.1") libtool: link: (cd ".libs" && rm -f "libMems-1.6.so" && ln -s "libMems-1.6.so.1.0.0" "libMems-1.6.so") libtool: link: ar cru .libs/libMems-1.6.a RepeatHash.o DNAFileSML.o MatchFinder.o DNAMemorySML.o MemorySML.o SortedMerList.o FileSML.o MemHash.o MatchHashEntry.o Interval.o IntervalList.o twister.o gnAlignedSequences.o MatchList.o Aligner.o Islands.o MaskedMemHash.o GappedAlignment.o MuscleInterface.o PhyloTree.o RepeatMatchList.o RepeatMatch.o Backbone.o PairwiseMatchFinder.o ProgressiveAligner.o SuperInterval.o GreedyBreakpointElimination.o algebras.o homology.o homologymain.o asyncio.o alinuxaio.o aPOSIXaio.o alibc.o awin32aio.o buffer.o util.o sorting.o dmsort.o timing.o sml.o ar: `u' modifier ignored since `D' is the default (see `U') libtool: link: ranlib .libs/libMems-1.6.a libtool: link: ( cd ".libs" && rm -f "libMems-1.6.la" && ln -s "../libMems-1.6.la" "libMems-1.6.la" ) make[3]: Leaving directory '/<>/libmems-1.6.0+4725/libMems' make[3]: Entering directory '/<>/libmems-1.6.0+4725' make[3]: Nothing to be done for 'all-am'. make[3]: Leaving directory '/<>/libmems-1.6.0+4725' make[2]: Leaving directory '/<>/libmems-1.6.0+4725' make[1]: Leaving directory '/<>/libmems-1.6.0+4725' dh_auto_test -a make -j1 check VERBOSE=1 make[1]: Entering directory '/<>/libmems-1.6.0+4725' Making check in libMems make[2]: Entering directory '/<>/libmems-1.6.0+4725/libMems' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/<>/libmems-1.6.0+4725/libMems' make[2]: Entering directory '/<>/libmems-1.6.0+4725' make[2]: Nothing to be done for 'check-am'. make[2]: Leaving directory '/<>/libmems-1.6.0+4725' make[1]: Leaving directory '/<>/libmems-1.6.0+4725' fakeroot debian/rules binary-arch dh binary-arch --with autoreconf dh_testroot -a dh_prep -a dh_auto_install -a make -j1 install DESTDIR=/<>/libmems-1.6.0\+4725/debian/tmp AM_UPDATE_INFO_DIR=no make[1]: Entering directory '/<>/libmems-1.6.0+4725' Making install in libMems make[2]: Entering directory '/<>/libmems-1.6.0+4725/libMems' make[3]: Entering directory '/<>/libmems-1.6.0+4725/libMems' /bin/mkdir -p '/<>/libmems-1.6.0+4725/debian/tmp/usr/lib/s390x-linux-gnu' /bin/bash ../libtool --mode=install /usr/bin/install -c libMems-1.6.la '/<>/libmems-1.6.0+4725/debian/tmp/usr/lib/s390x-linux-gnu' libtool: install: /usr/bin/install -c .libs/libMems-1.6.so.1.0.0 /<>/libmems-1.6.0+4725/debian/tmp/usr/lib/s390x-linux-gnu/libMems-1.6.so.1.0.0 libtool: install: (cd /<>/libmems-1.6.0+4725/debian/tmp/usr/lib/s390x-linux-gnu && { ln -s -f libMems-1.6.so.1.0.0 libMems-1.6.so.1 || { rm -f libMems-1.6.so.1 && ln -s libMems-1.6.so.1.0.0 libMems-1.6.so.1; }; }) libtool: install: (cd /<>/libmems-1.6.0+4725/debian/tmp/usr/lib/s390x-linux-gnu && { ln -s -f libMems-1.6.so.1.0.0 libMems-1.6.so || { rm -f libMems-1.6.so && ln -s libMems-1.6.so.1.0.0 libMems-1.6.so; }; }) libtool: install: /usr/bin/install -c .libs/libMems-1.6.lai /<>/libmems-1.6.0+4725/debian/tmp/usr/lib/s390x-linux-gnu/libMems-1.6.la libtool: install: /usr/bin/install -c .libs/libMems-1.6.a /<>/libmems-1.6.0+4725/debian/tmp/usr/lib/s390x-linux-gnu/libMems-1.6.a libtool: install: chmod 644 /<>/libmems-1.6.0+4725/debian/tmp/usr/lib/s390x-linux-gnu/libMems-1.6.a libtool: install: ranlib /<>/libmems-1.6.0+4725/debian/tmp/usr/lib/s390x-linux-gnu/libMems-1.6.a libtool: warning: remember to run 'libtool --finish /usr/lib/s390x-linux-gnu' /bin/mkdir -p '/<>/libmems-1.6.0+4725/debian/tmp/usr/include/libMems-1.6/libMems/dmSML' /usr/bin/install -c -m 644 dmSML/asyncio.h dmSML/alinuxaio.h dmSML/aPOSIXaio.h dmSML/alibc.h dmSML/awin32aio.h dmSML/buffer.h dmSML/util.h dmSML/sorting.h dmSML/dmsort.h dmSML/timing.h dmSML/sml.h '/<>/libmems-1.6.0+4725/debian/tmp/usr/include/libMems-1.6/libMems/dmSML' /bin/mkdir -p '/<>/libmems-1.6.0+4725/debian/tmp/usr/include/libMems-1.6/libMems/HomologyHMM' /usr/bin/install -c -m 644 HomologyHMM/homology.h HomologyHMM/dptables.h HomologyHMM/algebras.h HomologyHMM/parameters.h '/<>/libmems-1.6.0+4725/debian/tmp/usr/include/libMems-1.6/libMems/HomologyHMM' /bin/mkdir -p '/<>/libmems-1.6.0+4725/debian/tmp/usr/include/libMems-1.6/libMems' /usr/bin/install -c -m 644 RepeatHash.h MatchHashEntry.h DNAFileSML.h MemorySML.h MatchProjectionAdapter.h DNAMemorySML.h MatchFinder.h SortedMerList.h IntervalList.h FileSML.h gnAlignedSequences.h Interval.h MemHash.h AbstractMatch.h SlotAllocator.h Aligner.h Match.h MatchList.h Matrix.h NumericMatrix.h Islands.h MaskedMemHash.h SeedMasks.h GappedAlignment.h MuscleInterface.h GappedAligner.h PhyloTree.h SparseAbstractMatch.h DenseAbstractMatch.h RepeatMatch.h UngappedLocalAlignment.h AbstractGappedAlignment.h CompactGappedAlignment.h HybridAbstractMatch.h twister.h SubstitutionMatrix.h RepeatMatchList.h Backbone.h ProgressiveAligner.h PairwiseMatchAdapter.h '/<>/libmems-1.6.0+4725/debian/tmp/usr/include/libMems-1.6/libMems' /usr/bin/install -c -m 644 PairwiseMatchFinder.h SeedOccurrenceList.h TreeUtilities.h SuperInterval.h GreedyBreakpointElimination.h LCB.h DistanceMatrix.h Scoring.h configuration.h Memory.h Files.h gnRAWSequence.h '/<>/libmems-1.6.0+4725/debian/tmp/usr/include/libMems-1.6/libMems' make[3]: Leaving directory '/<>/libmems-1.6.0+4725/libMems' make[2]: Leaving directory '/<>/libmems-1.6.0+4725/libMems' make[2]: Entering directory '/<>/libmems-1.6.0+4725' make[3]: Entering directory '/<>/libmems-1.6.0+4725' make[3]: Nothing to be done for 'install-exec-am'. /bin/mkdir -p '/<>/libmems-1.6.0+4725/debian/tmp/usr/lib/s390x-linux-gnu/pkgconfig' /usr/bin/install -c -m 644 libMems-1.6.pc '/<>/libmems-1.6.0+4725/debian/tmp/usr/lib/s390x-linux-gnu/pkgconfig' make[3]: Leaving directory '/<>/libmems-1.6.0+4725' make[2]: Leaving directory '/<>/libmems-1.6.0+4725' make[1]: Leaving directory '/<>/libmems-1.6.0+4725' debian/rules override_dh_install make[1]: Entering directory '/<>/libmems-1.6.0+4725' dh_install d-shlibmove --commit \ --multiarch \ --v5 \ --devunversioned \ --exclude-la \ --movedev debian/tmp/usr/include usr \ --movedev "debian/tmp/usr/lib/*/pkgconfig/*.pc" usr/lib/s390x-linux-gnu/pkgconfig \ debian/tmp/usr/lib/*/*.so Library package automatic movement utility --> libboost-filesystem1.62-dev package exists. --> libboost-iostreams1.62-dev package exists. --> libboost-system1.62-dev package exists. --> libgenome-1.3-dev package exists. --> libmuscle-3.7-dev package exists. set -e install -d -m 755 debian/libmems-1.6-dev/usr/lib/s390x-linux-gnu install -d -m 755 debian/libmems-1.6-1v5/usr/lib/s390x-linux-gnu mv debian/tmp/usr/lib/s390x-linux-gnu/libMems-1.6.a debian/libmems-1.6-dev/usr/lib/s390x-linux-gnu mv debian/tmp/usr/lib/s390x-linux-gnu/libMems-1.6.so debian/libmems-1.6-dev/usr/lib/s390x-linux-gnu mv /<>/libmems-1.6.0+4725/debian/tmp/usr/lib/s390x-linux-gnu/libMems-1.6.so.1 debian/libmems-1.6-1v5/usr/lib/s390x-linux-gnu mv /<>/libmems-1.6.0+4725/debian/tmp/usr/lib/s390x-linux-gnu/libMems-1.6.so.1.0.0 debian/libmems-1.6-1v5/usr/lib/s390x-linux-gnu PKGDEV=libmems-1.6-dev PKGSHL=libmems-1.6-1v5 install -d -m 755 debian/libmems-1.6-dev/usr mv debian/tmp/usr/include debian/libmems-1.6-dev/usr install -d -m 755 debian/libmems-1.6-dev/usr/lib/s390x-linux-gnu/pkgconfig mv debian/tmp/usr/lib/*/pkgconfig/*.pc debian/libmems-1.6-dev/usr/lib/s390x-linux-gnu/pkgconfig make[1]: Leaving directory '/<>/libmems-1.6.0+4725' dh_installdocs -a dh_installchangelogs -a dh_perl -a dh_link -a dh_strip_nondeterminism -a dh_compress -a dh_fixperms -a dh_strip -a dh_strip debug symbol extraction: enabling -a due to Build-Debug-Symbols: yes in /CurrentlyBuilding dh_strip debug symbol extraction: all non-arch-all packages for this build platform s390x: libmems-1.6-dev libmems-1.6-1v5 dh_strip debug symbol extraction: packages to act on: libmems-1.6-dev libmems-1.6-1v5 dh_strip debug symbol extraction: ignored packages: Using buildid for compat level >= 9 libmems-1.6-dev has no unstripped objects, ignoring find: ‘/<>/libmems-1.6.0+4725/debian/libmems-1.6-dev-dbgsym’: No such file or directory /usr/bin/pkg_create_dbgsym: nothing in /<>/libmems-1.6.0+4725/debian/libmems-1.6-dev-dbgsym and no dbgdepends, ignoring Using buildid for compat level >= 9 dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe /usr/bin/pkg_create_dbgsym: deferring build of .ddeb to dh_gencontrol dh_makeshlibs -a dh_shlibdeps -a dh_installdeb -a dh_gencontrol -a dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe dh_gencontrol debug symbol wrapper: all non-arch-all packages for this build platform s390x: libmems-1.6-dev libmems-1.6-1v5 dh_gencontrol debug symbol wrapper: packages to act on: libmems-1.6-dev libmems-1.6-1v5 dh_gencontrol debug symbol wrapper: ignored packages: dh_gencontrol debug symbol wrapper: no debian/libmems-1.6-dev-dbgsym, skipping package libmems-1.6-dev dh_gencontrol debug symbol wrapper: processing package libmems-1.6-1v5 (pkgdir debian/libmems-1.6-1v5, ddeb package dir debian/libmems-1.6-1v5-dbgsym) dh_gencontrol debug symbol wrapper: building libmems-1.6-1v5-dbgsym_1.6.0+4725-4_s390x.ddeb dpkg-deb: building package 'libmems-1.6-1v5-dbgsym' in '../libmems-1.6-1v5-dbgsym_1.6.0+4725-4_s390x.ddeb'. dh_gencontrol debug symbol wrapper: dpkg-distaddfile libmems-1.6-1v5-dbgsym_1.6.0+4725-4_s390x.ddeb libs extra dpkg-distaddfile: warning: File::FcntlLock not available; using flock which is not NFS-safe dh_md5sums -a dh_builddeb -a INFO: pkgstriptranslations version 131 INFO: pkgstriptranslations version 131 pkgstriptranslations: processing libmems-1.6-dev (in debian/libmems-1.6-dev); do_strip: , oemstrip: pkgstriptranslations: processing libmems-1.6-1v5 (in debian/libmems-1.6-1v5); do_strip: , oemstrip: pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/libmems-1.6-dev/DEBIAN/control, package libmems-1.6-dev, directory debian/libmems-1.6-dev Searching for duplicated docs in dependency libmems-1.6-1v5... symlinking changelog.Debian.gz in libmems-1.6-dev to file in libmems-1.6-1v5 pkgstripfiles: Running PNG optimization (using 4 cpus) for package libmems-1.6-dev ... pkgstripfiles: No PNG files. dpkg-deb: building package 'libmems-1.6-dev' in '../libmems-1.6-dev_1.6.0+4725-4_s390x.deb'. pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/libmems-1.6-1v5/DEBIAN/control, package libmems-1.6-1v5, directory debian/libmems-1.6-1v5 pkgstripfiles: Running PNG optimization (using 4 cpus) for package libmems-1.6-1v5 ... pkgstripfiles: No PNG files. dpkg-deb: building package 'libmems-1.6-1v5' in '../libmems-1.6-1v5_1.6.0+4725-4_s390x.deb'. dpkg-genchanges --build=any -mLaunchpad Build Daemon >../libmems_1.6.0+4725-4_s390x.changes dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included) dpkg-source --after-build libmems-1.6.0+4725 dpkg-buildpackage: info: binary-only upload (no source included) -------------------------------------------------------------------------------- Build finished at 20161109-0535 Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Post Build Chroot | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ libmems_1.6.0+4725-4_s390x.changes: ----------------------------------- Format: 1.8 Date: Tue, 08 Nov 2016 14:16:07 +0100 Source: libmems Binary: libmems-1.6-dev libmems-1.6-1v5 Architecture: s390x Version: 1.6.0+4725-4 Distribution: zesty-proposed Urgency: medium Maintainer: Launchpad Build Daemon Changed-By: Andreas Tille Description: libmems-1.6-1v5 - library to support DNA string matching and comparative genomics libmems-1.6-dev - development library to support DNA string matching and comparativ Closes: 843628 Changes: libmems (1.6.0+4725-4) unstable; urgency=medium . * Use fake watch file * Add missing include so that BOOST_WORKAROUND is defined (thanks to (Graham Inggs for the patch) Closes: #843628 * Add patch to really drop explicit version in package names but do not activate the patch due to transition freeze Checksums-Sha1: fca1974de9e81831268d9f7c7c2aaf74bc26c6bf 4858930 libmems-1.6-1v5-dbgsym_1.6.0+4725-4_s390x.ddeb 994e5afbd0a0a114654429a417b10c1fbce89a04 550166 libmems-1.6-1v5_1.6.0+4725-4_s390x.deb 4a0788620ac11807cd317eea9bc899b63f21bbfa 816792 libmems-1.6-dev_1.6.0+4725-4_s390x.deb Checksums-Sha256: 6dcad8640507f8f661ec8add0452e21faeca969480475d7f050c4f7862e5b343 4858930 libmems-1.6-1v5-dbgsym_1.6.0+4725-4_s390x.ddeb 56b2290d3a8968bddad088f72d9f7f8c45f4c851c34a4b0f8cfe82b37951f44b 550166 libmems-1.6-1v5_1.6.0+4725-4_s390x.deb 853389d6e816669b1e61071dea2e0d2a60af0a08b141a50967a1e8db7527f03a 816792 libmems-1.6-dev_1.6.0+4725-4_s390x.deb Files: acea19763a1156691bd51f5351846baa 4858930 libs extra libmems-1.6-1v5-dbgsym_1.6.0+4725-4_s390x.ddeb b3da1d6d8382afbd71265ff61417bacc 550166 libs optional libmems-1.6-1v5_1.6.0+4725-4_s390x.deb dbd8c2379d223e37b8c35424dd73b344 816792 libdevel optional libmems-1.6-dev_1.6.0+4725-4_s390x.deb +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ libmems-1.6-1v5_1.6.0+4725-4_s390x.deb -------------------------------------- new debian package, version 2.0. size 550166 bytes: control archive=1125 bytes. 1293 bytes, 25 lines control 237 bytes, 3 lines md5sums 30 bytes, 1 lines shlibs 60 bytes, 2 lines triggers Package: libmems-1.6-1v5 Source: libmems Version: 1.6.0+4725-4 Architecture: s390x Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 1906 Depends: libboost-filesystem1.62.0, libboost-iostreams1.62.0, libboost-system1.62.0, libc6 (>= 2.7), libgcc1 (>= 1:3.0), libgenome-1.3-0v5, libmuscle-3.7-1, libstdc++6 (>= 5.2) Conflicts: libmems-1.6-1 Replaces: libmems-1.6-1 Section: libs Priority: optional Multi-Arch: same Homepage: http://sourceforge.net/p/mauve/code/HEAD/tree/libMems/trunk/ Description: library to support DNA string matching and comparative genomics libMems is a freely available software development library to support DNA string matching and comparative genomics. Among other things, libMems implements an algorithm to perform approximate multi-MUM and multi-MEM identification. The algorithm uses spaced seed patterns in conjunction with a seed-and-extend style hashing method to identify matches. The method is efficient, requiring a maximum of only 16 bytes per base of the largest input sequence, and this data can be stored externally (i.e. on disk) to further reduce memory requirements. . This package contains the dynamic library. drwxr-xr-x root/root 0 2016-11-08 13:16 ./ drwxr-xr-x root/root 0 2016-11-08 13:16 ./usr/ drwxr-xr-x root/root 0 2016-11-08 13:16 ./usr/lib/ drwxr-xr-x root/root 0 2016-11-08 13:16 ./usr/lib/s390x-linux-gnu/ lrwxrwxrwx root/root 0 2016-11-08 13:16 ./usr/lib/s390x-linux-gnu/libMems-1.6.so.1 -> libMems-1.6.so.1.0.0 -rw-r--r-- root/root 1936352 2016-11-08 13:16 ./usr/lib/s390x-linux-gnu/libMems-1.6.so.1.0.0 drwxr-xr-x root/root 0 2016-11-08 13:16 ./usr/share/ drwxr-xr-x root/root 0 2016-11-08 13:16 ./usr/share/doc/ drwxr-xr-x root/root 0 2016-11-08 13:16 ./usr/share/doc/libmems-1.6-1v5/ -rw-r--r-- root/root 699 2016-11-08 13:16 ./usr/share/doc/libmems-1.6-1v5/changelog.Debian.gz -rw-r--r-- root/root 2365 2016-11-08 13:16 ./usr/share/doc/libmems-1.6-1v5/copyright libmems-1.6-dev_1.6.0+4725-4_s390x.deb -------------------------------------- new debian package, version 2.0. size 816792 bytes: control archive=2984 bytes. 1307 bytes, 24 lines control 5742 bytes, 70 lines md5sums Package: libmems-1.6-dev Source: libmems Version: 1.6.0+4725-4 Architecture: s390x Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 6758 Depends: libmems-1.6-1v5 (= 1.6.0+4725-4), libboost-filesystem1.62-dev, libboost-iostreams1.62-dev, libboost-system1.62-dev, libgenome-1.3-dev, libmuscle-3.7-dev Provides: libmems-1.6-dev Section: libdevel Priority: optional Homepage: http://sourceforge.net/p/mauve/code/HEAD/tree/libMems/trunk/ Description: development library to support DNA string matching and comparative genomics libMems is a freely available software development library to support DNA string matching and comparative genomics. Among other things, libMems implements an algorithm to perform approximate multi-MUM and multi-MEM identification. The algorithm uses spaced seed patterns in conjunction with a seed-and-extend style hashing method to identify matches. The method is efficient, requiring a maximum of only 16 bytes per base of the largest input sequence, and this data can be stored externally (i.e. on disk) to further reduce memory requirements. . 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+------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Not removing build depends: as requested Keeping session: +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: s390x Build-Space: 288404 Build-Time: 330 Distribution: zesty-proposed Host Architecture: s390x Install-Time: 62 Job: libmems_1.6.0+4725-4.dsc Machine Architecture: s390x Package: libmems Package-Time: 392 Source-Version: 1.6.0+4725-4 Space: 288404 Status: successful Version: 1.6.0+4725-4 -------------------------------------------------------------------------------- Finished at 20161109-0535 Build needed 00:06:32, 288404k disc space RUN: /usr/share/launchpad-buildd/slavebin/scan-for-processes ['scan-for-processes', 'PACKAGEBUILD-11168025'] Scanning for processes to kill in build /home/buildd/build-PACKAGEBUILD-11168025/chroot-autobuild... RUN: /usr/share/launchpad-buildd/slavebin/umount-chroot ['umount-chroot', 'PACKAGEBUILD-11168025'] Unmounting chroot for build PACKAGEBUILD-11168025... RUN: /usr/share/launchpad-buildd/slavebin/remove-build ['remove-build', 'PACKAGEBUILD-11168025'] Removing build PACKAGEBUILD-11168025