RUN: /usr/share/launchpad-buildd/slavebin/slave-prep ['slave-prep'] Forking launchpad-buildd slave process... Kernel version: Linux lgw01-53 3.19.0-32-generic #37~14.04.1-Ubuntu SMP Thu Oct 22 09:41:40 UTC 2015 x86_64 Buildd toolchain package versions: launchpad-buildd_135 python-lpbuildd_135 sbuild_0.65.2-1ubuntu2~ubuntu14.04.1~ppa6 bzr-builder_0.7.3+bzr174~ppa13~ubuntu14.04.1 bzr_2.6.0+bzr6593-1ubuntu1.1 dpkg-dev_1.17.5ubuntu5.4 python-debian_0.1.27ubuntu1~ubuntu14.04.1~ppa1. Syncing the system clock with the buildd NTP service... 5 Nov 16:41:31 ntpdate[1649]: adjust time server 10.211.37.1 offset 0.099546 sec RUN: /usr/share/launchpad-buildd/slavebin/unpack-chroot ['unpack-chroot', 'PACKAGEBUILD-8268452', '/home/buildd/filecache-default/8204889cda79fca0b488b979ea0c52fb9d6dbd17'] Unpacking chroot for build PACKAGEBUILD-8268452 RUN: /usr/share/launchpad-buildd/slavebin/mount-chroot ['mount-chroot', 'PACKAGEBUILD-8268452'] Mounting chroot for build PACKAGEBUILD-8268452 RUN: /usr/share/launchpad-buildd/slavebin/override-sources-list ['override-sources-list', 'PACKAGEBUILD-8268452', 'deb http://ftpmaster.internal/ubuntu xenial main universe', 'deb http://ftpmaster.internal/ubuntu xenial-security main universe', 'deb http://ftpmaster.internal/ubuntu xenial-updates main universe', 'deb http://ftpmaster.internal/ubuntu xenial-proposed main universe'] Overriding sources.list in build-PACKAGEBUILD-8268452 RUN: /usr/share/launchpad-buildd/slavebin/update-debian-chroot ['update-debian-chroot', 'PACKAGEBUILD-8268452', 'amd64'] Updating debian chroot for build PACKAGEBUILD-8268452 Get:1 http://ftpmaster.internal xenial InRelease [218 kB] Get:2 http://ftpmaster.internal xenial-security InRelease [64.4 kB] Get:3 http://ftpmaster.internal xenial-updates InRelease [64.4 kB] Get:4 http://ftpmaster.internal xenial-proposed InRelease [218 kB] Get:5 http://ftpmaster.internal xenial/main amd64 Packages [1436 kB] Get:6 http://ftpmaster.internal xenial/universe amd64 Packages [6890 kB] Get:7 http://ftpmaster.internal xenial/main Translation-en [840 kB] Get:8 http://ftpmaster.internal xenial/universe Translation-en [4697 kB] Get:9 http://ftpmaster.internal xenial-security/main amd64 Packages [28 B] Get:10 http://ftpmaster.internal xenial-security/universe amd64 Packages [28 B] Get:11 http://ftpmaster.internal xenial-security/main Translation-en [28 B] Get:12 http://ftpmaster.internal xenial-security/universe Translation-en [28 B] Get:13 http://ftpmaster.internal xenial-updates/main amd64 Packages [28 B] Get:14 http://ftpmaster.internal xenial-updates/universe amd64 Packages [28 B] Get:15 http://ftpmaster.internal xenial-updates/main Translation-en [28 B] Get:16 http://ftpmaster.internal xenial-updates/universe Translation-en [28 B] Get:17 http://ftpmaster.internal xenial-proposed/main amd64 Packages [94.4 kB] Get:18 http://ftpmaster.internal xenial-proposed/universe amd64 Packages [375 kB] Get:19 http://ftpmaster.internal xenial-proposed/main Translation-en [51.2 kB] Get:20 http://ftpmaster.internal xenial-proposed/universe Translation-en [209 kB] Fetched 15.2 MB in 6s (2410 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... The following package was automatically installed and is no longer required: udev Use 'apt-get autoremove' to remove it. The following packages will be upgraded: advancecomp base-files binutils bsdutils cpp-5 diffutils dpkg dpkg-dev e2fslibs e2fsprogs g++-5 gcc-5 gcc-5-base init libasan2 libatomic1 libaudit-common libaudit1 libblkid1 libcap2 libcap2-bin libcc1-0 libcilkrts5 libcomerr2 libcurl3-gnutls libdpkg-perl libfdisk1 libgcc-5-dev libgcc1 libgcrypt20 libgnutls-deb0-28 libgomp1 libgpg-error0 libgssapi-krb5-2 libidn11 libitm1 libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblsan0 libmount1 libmpx0 libquadmath0 libsmartcols1 libsqlite3-0 libss2 libstdc++-5-dev libstdc++6 libsystemd0 libtasn1-6 libtsan0 libubsan0 libudev1 libuuid1 linux-libc-dev mount pkg-create-dbgsym systemd systemd-sysv tar udev util-linux 63 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 111 MB of archives. After this operation, 326 MB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu/ xenial/main base-files amd64 9.4ubuntu2 [62.2 kB] Get:2 http://ftpmaster.internal/ubuntu/ xenial-proposed/main bsdutils amd64 1:2.27.1-1ubuntu1 [51.8 kB] Get:3 http://ftpmaster.internal/ubuntu/ xenial/main diffutils amd64 1:3.3-2 [156 kB] Get:4 http://ftpmaster.internal/ubuntu/ xenial/main dpkg amd64 1.18.3ubuntu1 [2081 kB] Get:5 http://ftpmaster.internal/ubuntu/ xenial/main e2fslibs amd64 1.42.13-1ubuntu1 [188 kB] Get:6 http://ftpmaster.internal/ubuntu/ xenial/main e2fsprogs amd64 1.42.13-1ubuntu1 [771 kB] Get:7 http://ftpmaster.internal/ubuntu/ xenial/main init amd64 1.24ubuntu1 [4006 B] Get:8 http://ftpmaster.internal/ubuntu/ xenial-proposed/main libsmartcols1 amd64 2.27.1-1ubuntu1 [62.9 kB] Get:9 http://ftpmaster.internal/ubuntu/ xenial-proposed/main libuuid1 amd64 2.27.1-1ubuntu1 [15.2 kB] Get:10 http://ftpmaster.internal/ubuntu/ xenial-proposed/main libblkid1 amd64 2.27.1-1ubuntu1 [107 kB] Get:11 http://ftpmaster.internal/ubuntu/ xenial-proposed/main libfdisk1 amd64 2.27.1-1ubuntu1 [138 kB] Get:12 http://ftpmaster.internal/ubuntu/ xenial-proposed/main util-linux amd64 2.27.1-1ubuntu1 [848 kB] Get:13 http://ftpmaster.internal/ubuntu/ xenial-proposed/main mount amd64 2.27.1-1ubuntu1 [121 kB] Get:14 http://ftpmaster.internal/ubuntu/ xenial-proposed/main tar amd64 1.28-2ubuntu1 [208 kB] Get:15 http://ftpmaster.internal/ubuntu/ xenial/main udev amd64 227-2ubuntu1 [972 kB] Get:16 http://ftpmaster.internal/ubuntu/ xenial/main libudev1 amd64 227-2ubuntu1 [56.9 kB] Get:17 http://ftpmaster.internal/ubuntu/ xenial/main libaudit-common all 1:2.4.4-4ubuntu1 [3892 B] Get:18 http://ftpmaster.internal/ubuntu/ xenial/main libaudit1 amd64 1:2.4.4-4ubuntu1 [36.3 kB] Get:19 http://ftpmaster.internal/ubuntu/ xenial/main libcap2 amd64 1:2.24-12 [12.9 kB] Get:20 http://ftpmaster.internal/ubuntu/ xenial-proposed/main libmount1 amd64 2.27.1-1ubuntu1 [115 kB] Get:21 http://ftpmaster.internal/ubuntu/ xenial/main libcap2-bin amd64 1:2.24-12 [20.2 kB] Get:22 http://ftpmaster.internal/ubuntu/ xenial/main libsystemd0 amd64 227-2ubuntu1 [203 kB] Get:23 http://ftpmaster.internal/ubuntu/ xenial/main systemd amd64 227-2ubuntu1 [3443 kB] Get:24 http://ftpmaster.internal/ubuntu/ xenial/main systemd-sysv amd64 227-2ubuntu1 [15.0 kB] Get:25 http://ftpmaster.internal/ubuntu/ xenial/main libgomp1 amd64 5.2.1-23ubuntu1 [55.2 kB] Get:26 http://ftpmaster.internal/ubuntu/ xenial/main libitm1 amd64 5.2.1-23ubuntu1 [27.4 kB] Get:27 http://ftpmaster.internal/ubuntu/ xenial/main libatomic1 amd64 5.2.1-23ubuntu1 [8886 B] Get:28 http://ftpmaster.internal/ubuntu/ xenial/main libasan2 amd64 5.2.1-23ubuntu1 [269 kB] Get:29 http://ftpmaster.internal/ubuntu/ xenial/main liblsan0 amd64 5.2.1-23ubuntu1 [109 kB] Get:30 http://ftpmaster.internal/ubuntu/ xenial/main libtsan0 amd64 5.2.1-23ubuntu1 [249 kB] Get:31 http://ftpmaster.internal/ubuntu/ xenial/main libubsan0 amd64 5.2.1-23ubuntu1 [100 kB] Get:32 http://ftpmaster.internal/ubuntu/ xenial/main libcilkrts5 amd64 5.2.1-23ubuntu1 [40.0 kB] Get:33 http://ftpmaster.internal/ubuntu/ xenial/main libmpx0 amd64 5.2.1-23ubuntu1 [9738 B] Get:34 http://ftpmaster.internal/ubuntu/ xenial/main libquadmath0 amd64 5.2.1-23ubuntu1 [131 kB] Get:35 http://ftpmaster.internal/ubuntu/ xenial/main cpp-5 amd64 5.2.1-23ubuntu1 [26.4 MB] Get:36 http://ftpmaster.internal/ubuntu/ xenial/main libcc1-0 amd64 5.2.1-23ubuntu1 [30.9 kB] Get:37 http://ftpmaster.internal/ubuntu/ xenial/main binutils amd64 2.25.51.20151028-0ubuntu1 [2313 kB] Get:38 http://ftpmaster.internal/ubuntu/ xenial/main g++-5 amd64 5.2.1-23ubuntu1 [37.0 MB] Get:39 http://ftpmaster.internal/ubuntu/ xenial/main gcc-5 amd64 5.2.1-23ubuntu1 [26.6 MB] Get:40 http://ftpmaster.internal/ubuntu/ xenial/main libgcc-5-dev amd64 5.2.1-23ubuntu1 [2233 kB] Get:41 http://ftpmaster.internal/ubuntu/ xenial/main gcc-5-base amd64 5.2.1-23ubuntu1 [16.6 kB] Get:42 http://ftpmaster.internal/ubuntu/ xenial/main libstdc++6 amd64 5.2.1-23ubuntu1 [393 kB] Get:43 http://ftpmaster.internal/ubuntu/ xenial/main libstdc++-5-dev amd64 5.2.1-23ubuntu1 [1421 kB] Get:44 http://ftpmaster.internal/ubuntu/ xenial/main libgcc1 amd64 1:5.2.1-23ubuntu1 [38.8 kB] Get:45 http://ftpmaster.internal/ubuntu/ xenial/main libcomerr2 amd64 1.42.13-1ubuntu1 [65.7 kB] Get:46 http://ftpmaster.internal/ubuntu/ xenial/main libgpg-error0 amd64 1.20-1 [32.8 kB] Get:47 http://ftpmaster.internal/ubuntu/ xenial/main libgcrypt20 amd64 1.6.4-3 [336 kB] Get:48 http://ftpmaster.internal/ubuntu/ xenial/main libss2 amd64 1.42.13-1ubuntu1 [70.0 kB] Get:49 http://ftpmaster.internal/ubuntu/ xenial/main libdpkg-perl all 1.18.3ubuntu1 [195 kB] Get:50 http://ftpmaster.internal/ubuntu/ xenial/main dpkg-dev all 1.18.3ubuntu1 [583 kB] Get:51 http://ftpmaster.internal/ubuntu/ xenial/main libtasn1-6 amd64 4.7-2 [43.1 kB] Get:52 http://ftpmaster.internal/ubuntu/ xenial/main libgnutls-deb0-28 amd64 3.3.18-1ubuntu1 [520 kB] Get:53 http://ftpmaster.internal/ubuntu/ xenial/main libsqlite3-0 amd64 3.9.1-2 [395 kB] Get:54 http://ftpmaster.internal/ubuntu/ xenial/main libgssapi-krb5-2 amd64 1.13.2+dfsg-3 [119 kB] Get:55 http://ftpmaster.internal/ubuntu/ xenial/main libkrb5-3 amd64 1.13.2+dfsg-3 [273 kB] Get:56 http://ftpmaster.internal/ubuntu/ xenial/main libkrb5support0 amd64 1.13.2+dfsg-3 [30.2 kB] Get:57 http://ftpmaster.internal/ubuntu/ xenial/main libk5crypto3 amd64 1.13.2+dfsg-3 [81.3 kB] Get:58 http://ftpmaster.internal/ubuntu/ xenial-proposed/main libkeyutils1 amd64 1.5.9-8 [9824 B] Get:59 http://ftpmaster.internal/ubuntu/ xenial-proposed/main libidn11 amd64 1.32-3ubuntu1 [45.5 kB] Get:60 http://ftpmaster.internal/ubuntu/ xenial-proposed/main libcurl3-gnutls amd64 7.45.0-1ubuntu1 [183 kB] Get:61 http://ftpmaster.internal/ubuntu/ xenial/main advancecomp amd64 1.20-1 [160 kB] Get:62 http://ftpmaster.internal/ubuntu/ xenial-proposed/main linux-libc-dev amd64 4.2.0-17.21 [808 kB] Get:63 http://ftpmaster.internal/ubuntu/ xenial/main pkg-create-dbgsym all 0.70 [9046 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 111 MB in 7s (15.6 MB/s) (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 11690 files and directories currently installed.) Preparing to unpack .../base-files_9.4ubuntu2_amd64.deb ... Unpacking base-files (9.4ubuntu2) over (7.2ubuntu11) ... Setting up base-files (9.4ubuntu2) ... Installing new version of config file /etc/debian_version ... Installing new version of config file /etc/issue ... Installing new version of config file /etc/issue.net ... Installing new version of config file /etc/lsb-release ... Updating /etc/profile to current default. Updating /etc/nsswitch.conf to current default. Updating /root/.profile to current default. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 11692 files and directories currently installed.) Preparing to unpack .../bsdutils_1%3a2.27.1-1ubuntu1_amd64.deb ... Unpacking bsdutils (1:2.27.1-1ubuntu1) over (1:2.26.2-6ubuntu3) ... Setting up bsdutils (1:2.27.1-1ubuntu1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 11692 files and directories currently installed.) Preparing to unpack .../diffutils_1%3a3.3-2_amd64.deb ... Unpacking diffutils (1:3.3-2) over (1:3.3-1) ... Setting up diffutils (1:3.3-2) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 11692 files and directories currently installed.) Preparing to unpack .../dpkg_1.18.3ubuntu1_amd64.deb ... Unpacking dpkg (1.18.3ubuntu1) over (1.18.2ubuntu5) ... Setting up dpkg (1.18.3ubuntu1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 11692 files and directories currently installed.) Preparing to unpack .../e2fslibs_1.42.13-1ubuntu1_amd64.deb ... Unpacking e2fslibs:amd64 (1.42.13-1ubuntu1) over (1.42.12-1ubuntu2) ... Processing triggers for libc-bin (2.21-0ubuntu4) ... Setting up e2fslibs:amd64 (1.42.13-1ubuntu1) ... Processing triggers for libc-bin (2.21-0ubuntu4) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 11692 files and directories currently installed.) Preparing to unpack .../e2fsprogs_1.42.13-1ubuntu1_amd64.deb ... Unpacking e2fsprogs (1.42.13-1ubuntu1) over (1.42.12-1ubuntu2) ... Setting up e2fsprogs (1.42.13-1ubuntu1) ... Installing new version of config file /etc/mke2fs.conf ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 11693 files and directories currently installed.) Preparing to unpack .../init_1.24ubuntu1_amd64.deb ... Unpacking init (1.24ubuntu1) over (1.23ubuntu3) ... Setting up init (1.24ubuntu1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 11693 files and directories currently installed.) Preparing to unpack .../libsmartcols1_2.27.1-1ubuntu1_amd64.deb ... Unpacking libsmartcols1:amd64 (2.27.1-1ubuntu1) over (2.26.2-6ubuntu3) ... Processing triggers for libc-bin (2.21-0ubuntu4) ... Setting up libsmartcols1:amd64 (2.27.1-1ubuntu1) ... Processing triggers for libc-bin (2.21-0ubuntu4) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 11693 files and directories currently installed.) Preparing to unpack .../libuuid1_2.27.1-1ubuntu1_amd64.deb ... Unpacking libuuid1:amd64 (2.27.1-1ubuntu1) over (2.26.2-6ubuntu3) ... Processing triggers for libc-bin (2.21-0ubuntu4) ... Setting up libuuid1:amd64 (2.27.1-1ubuntu1) ... Processing triggers for libc-bin (2.21-0ubuntu4) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 11693 files and directories currently installed.) Preparing to unpack .../libblkid1_2.27.1-1ubuntu1_amd64.deb ... Unpacking libblkid1:amd64 (2.27.1-1ubuntu1) over (2.26.2-6ubuntu3) ... Processing triggers for libc-bin (2.21-0ubuntu4) ... Setting up libblkid1:amd64 (2.27.1-1ubuntu1) ... Processing triggers for libc-bin (2.21-0ubuntu4) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 11693 files and directories currently installed.) Preparing to unpack .../libfdisk1_2.27.1-1ubuntu1_amd64.deb ... Unpacking libfdisk1:amd64 (2.27.1-1ubuntu1) over (2.26.2-6ubuntu3) ... Processing triggers for libc-bin (2.21-0ubuntu4) ... Setting up libfdisk1:amd64 (2.27.1-1ubuntu1) ... Processing triggers for libc-bin (2.21-0ubuntu4) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 11693 files and directories currently installed.) Preparing to unpack .../util-linux_2.27.1-1ubuntu1_amd64.deb ... Unpacking util-linux (2.27.1-1ubuntu1) over (2.26.2-6ubuntu3) ... Setting up util-linux (2.27.1-1ubuntu1) ... Processing triggers for systemd (225-1ubuntu9) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 11701 files and directories currently installed.) Preparing to unpack .../mount_2.27.1-1ubuntu1_amd64.deb ... Unpacking mount (2.27.1-1ubuntu1) over (2.26.2-6ubuntu3) ... Setting up mount (2.27.1-1ubuntu1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 11701 files and directories currently installed.) Preparing to unpack .../tar_1.28-2ubuntu1_amd64.deb ... Unpacking tar (1.28-2ubuntu1) over (1.27.1-2) ... Setting up tar (1.28-2ubuntu1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 11701 files and directories currently installed.) Preparing to unpack .../udev_227-2ubuntu1_amd64.deb ... Unpacking udev (227-2ubuntu1) over (225-1ubuntu9) ... Preparing to unpack .../libudev1_227-2ubuntu1_amd64.deb ... Unpacking libudev1:amd64 (227-2ubuntu1) over (225-1ubuntu9) ... Processing triggers for libc-bin (2.21-0ubuntu4) ... Setting up libudev1:amd64 (227-2ubuntu1) ... Processing triggers for libc-bin (2.21-0ubuntu4) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 11701 files and directories currently installed.) Preparing to unpack .../libaudit-common_1%3a2.4.4-4ubuntu1_all.deb ... Unpacking libaudit-common (1:2.4.4-4ubuntu1) over (1:2.4.2-1ubuntu1) ... Setting up libaudit-common (1:2.4.4-4ubuntu1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 11701 files and directories currently installed.) Preparing to unpack .../libaudit1_1%3a2.4.4-4ubuntu1_amd64.deb ... Unpacking libaudit1:amd64 (1:2.4.4-4ubuntu1) over (1:2.4.2-1ubuntu1) ... Processing triggers for libc-bin (2.21-0ubuntu4) ... Setting up libaudit1:amd64 (1:2.4.4-4ubuntu1) ... Processing triggers for libc-bin (2.21-0ubuntu4) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 11701 files and directories currently installed.) Preparing to unpack .../libcap2_1%3a2.24-12_amd64.deb ... Unpacking libcap2:amd64 (1:2.24-12) over (1:2.24-9) ... Setting up libcap2:amd64 (1:2.24-12) ... Processing triggers for libc-bin (2.21-0ubuntu4) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 11701 files and directories currently installed.) Preparing to unpack .../libmount1_2.27.1-1ubuntu1_amd64.deb ... Unpacking libmount1:amd64 (2.27.1-1ubuntu1) over (2.26.2-6ubuntu3) ... Processing triggers for libc-bin (2.21-0ubuntu4) ... Setting up libmount1:amd64 (2.27.1-1ubuntu1) ... Processing triggers for libc-bin (2.21-0ubuntu4) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 11701 files and directories currently installed.) Preparing to unpack .../libcap2-bin_1%3a2.24-12_amd64.deb ... Unpacking libcap2-bin (1:2.24-12) over (1:2.24-9) ... Setting up libcap2-bin (1:2.24-12) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 11701 files and directories currently installed.) Preparing to unpack .../libsystemd0_227-2ubuntu1_amd64.deb ... Unpacking libsystemd0:amd64 (227-2ubuntu1) over (225-1ubuntu9) ... Processing triggers for libc-bin (2.21-0ubuntu4) ... Setting up libsystemd0:amd64 (227-2ubuntu1) ... Processing triggers for libc-bin (2.21-0ubuntu4) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 11701 files and directories currently installed.) Preparing to unpack .../systemd_227-2ubuntu1_amd64.deb ... Unpacking systemd (227-2ubuntu1) over (225-1ubuntu9) ... Setting up systemd (227-2ubuntu1) ... Installing new version of config file /etc/X11/xinit/xinitrc.d/50-systemd-user.sh ... Installing new version of config file /etc/systemd/journald.conf ... Installing new version of config file /etc/systemd/system.conf ... addgroup: The group `systemd-journal' already exists as a system group. Exiting. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 11701 files and directories currently installed.) Preparing to unpack .../systemd-sysv_227-2ubuntu1_amd64.deb ... Unpacking systemd-sysv (227-2ubuntu1) over (225-1ubuntu9) ... Setting up systemd-sysv (227-2ubuntu1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 11701 files and directories currently installed.) Preparing to unpack .../libgomp1_5.2.1-23ubuntu1_amd64.deb ... Unpacking libgomp1:amd64 (5.2.1-23ubuntu1) over (5.2.1-22ubuntu2) ... Preparing to unpack .../libitm1_5.2.1-23ubuntu1_amd64.deb ... Unpacking libitm1:amd64 (5.2.1-23ubuntu1) over (5.2.1-22ubuntu2) ... Preparing to unpack .../libatomic1_5.2.1-23ubuntu1_amd64.deb ... Unpacking libatomic1:amd64 (5.2.1-23ubuntu1) over (5.2.1-22ubuntu2) ... Preparing to unpack .../libasan2_5.2.1-23ubuntu1_amd64.deb ... Unpacking libasan2:amd64 (5.2.1-23ubuntu1) over (5.2.1-22ubuntu2) ... Preparing to unpack .../liblsan0_5.2.1-23ubuntu1_amd64.deb ... Unpacking liblsan0:amd64 (5.2.1-23ubuntu1) over (5.2.1-22ubuntu2) ... Preparing to unpack .../libtsan0_5.2.1-23ubuntu1_amd64.deb ... Unpacking libtsan0:amd64 (5.2.1-23ubuntu1) over (5.2.1-22ubuntu2) ... Preparing to unpack .../libubsan0_5.2.1-23ubuntu1_amd64.deb ... Unpacking libubsan0:amd64 (5.2.1-23ubuntu1) over (5.2.1-22ubuntu2) ... Preparing to unpack .../libcilkrts5_5.2.1-23ubuntu1_amd64.deb ... Unpacking libcilkrts5:amd64 (5.2.1-23ubuntu1) over (5.2.1-22ubuntu2) ... Preparing to unpack .../libmpx0_5.2.1-23ubuntu1_amd64.deb ... Unpacking libmpx0:amd64 (5.2.1-23ubuntu1) over (5.2.1-22ubuntu2) ... Preparing to unpack .../libquadmath0_5.2.1-23ubuntu1_amd64.deb ... Unpacking libquadmath0:amd64 (5.2.1-23ubuntu1) over (5.2.1-22ubuntu2) ... Preparing to unpack .../cpp-5_5.2.1-23ubuntu1_amd64.deb ... Unpacking cpp-5 (5.2.1-23ubuntu1) over (5.2.1-22ubuntu2) ... Preparing to unpack .../libcc1-0_5.2.1-23ubuntu1_amd64.deb ... Unpacking libcc1-0:amd64 (5.2.1-23ubuntu1) over (5.2.1-22ubuntu2) ... Preparing to unpack .../binutils_2.25.51.20151028-0ubuntu1_amd64.deb ... Unpacking binutils (2.25.51.20151028-0ubuntu1) over (2.25.1-6ubuntu1) ... Preparing to unpack .../g++-5_5.2.1-23ubuntu1_amd64.deb ... Unpacking g++-5 (5.2.1-23ubuntu1) over (5.2.1-22ubuntu2) ... Preparing to unpack .../gcc-5_5.2.1-23ubuntu1_amd64.deb ... Unpacking gcc-5 (5.2.1-23ubuntu1) over (5.2.1-22ubuntu2) ... Preparing to unpack .../libgcc-5-dev_5.2.1-23ubuntu1_amd64.deb ... Unpacking libgcc-5-dev:amd64 (5.2.1-23ubuntu1) over (5.2.1-22ubuntu2) ... Preparing to unpack .../gcc-5-base_5.2.1-23ubuntu1_amd64.deb ... Unpacking gcc-5-base:amd64 (5.2.1-23ubuntu1) over (5.2.1-22ubuntu2) ... Processing triggers for libc-bin (2.21-0ubuntu4) ... Setting up gcc-5-base:amd64 (5.2.1-23ubuntu1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 11721 files and directories currently installed.) Preparing to unpack .../libstdc++6_5.2.1-23ubuntu1_amd64.deb ... Unpacking libstdc++6:amd64 (5.2.1-23ubuntu1) over (5.2.1-22ubuntu2) ... Processing triggers for libc-bin (2.21-0ubuntu4) ... Setting up libstdc++6:amd64 (5.2.1-23ubuntu1) ... Processing triggers for libc-bin (2.21-0ubuntu4) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 11721 files and directories currently installed.) Preparing to unpack .../libstdc++-5-dev_5.2.1-23ubuntu1_amd64.deb ... Unpacking libstdc++-5-dev:amd64 (5.2.1-23ubuntu1) over (5.2.1-22ubuntu2) ... Preparing to unpack .../libgcc1_1%3a5.2.1-23ubuntu1_amd64.deb ... Unpacking libgcc1:amd64 (1:5.2.1-23ubuntu1) over (1:5.2.1-22ubuntu2) ... Processing triggers for libc-bin (2.21-0ubuntu4) ... Setting up libgcc1:amd64 (1:5.2.1-23ubuntu1) ... Processing triggers for libc-bin (2.21-0ubuntu4) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 11721 files and directories currently installed.) Preparing to unpack .../libcomerr2_1.42.13-1ubuntu1_amd64.deb ... Unpacking libcomerr2:amd64 (1.42.13-1ubuntu1) over (1.42.12-1ubuntu2) ... Processing triggers for libc-bin (2.21-0ubuntu4) ... Setting up libcomerr2:amd64 (1.42.13-1ubuntu1) ... Processing triggers for libc-bin (2.21-0ubuntu4) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 11721 files and directories currently installed.) Preparing to unpack .../libgpg-error0_1.20-1_amd64.deb ... Unpacking libgpg-error0:amd64 (1.20-1) over (1.19-2) ... Processing triggers for libc-bin (2.21-0ubuntu4) ... Setting up libgpg-error0:amd64 (1.20-1) ... Processing triggers for libc-bin (2.21-0ubuntu4) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 11721 files and directories currently installed.) Preparing to unpack .../libgcrypt20_1.6.4-3_amd64.deb ... Unpacking libgcrypt20:amd64 (1.6.4-3) over (1.6.3-2ubuntu1) ... Processing triggers for libc-bin (2.21-0ubuntu4) ... Setting up libgcrypt20:amd64 (1.6.4-3) ... Processing triggers for libc-bin (2.21-0ubuntu4) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 11721 files and directories currently installed.) Preparing to unpack .../libss2_1.42.13-1ubuntu1_amd64.deb ... Unpacking libss2:amd64 (1.42.13-1ubuntu1) over (1.42.12-1ubuntu2) ... Processing triggers for libc-bin (2.21-0ubuntu4) ... Setting up libss2:amd64 (1.42.13-1ubuntu1) ... Processing triggers for libc-bin (2.21-0ubuntu4) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 11721 files and directories currently installed.) Preparing to unpack .../libdpkg-perl_1.18.3ubuntu1_all.deb ... Unpacking libdpkg-perl (1.18.3ubuntu1) over (1.18.2ubuntu5) ... Preparing to unpack .../dpkg-dev_1.18.3ubuntu1_all.deb ... Unpacking dpkg-dev (1.18.3ubuntu1) over (1.18.2ubuntu5) ... Preparing to unpack .../libtasn1-6_4.7-2_amd64.deb ... Unpacking libtasn1-6:amd64 (4.7-2) over (4.5-2) ... Preparing to unpack .../libgnutls-deb0-28_3.3.18-1ubuntu1_amd64.deb ... Unpacking libgnutls-deb0-28:amd64 (3.3.18-1ubuntu1) over (3.3.15-5ubuntu2) ... Preparing to unpack .../libsqlite3-0_3.9.1-2_amd64.deb ... Unpacking libsqlite3-0:amd64 (3.9.1-2) over (3.8.11.1-1) ... Preparing to unpack .../libgssapi-krb5-2_1.13.2+dfsg-3_amd64.deb ... Unpacking libgssapi-krb5-2:amd64 (1.13.2+dfsg-3) over (1.13.2+dfsg-2) ... Preparing to unpack .../libkrb5-3_1.13.2+dfsg-3_amd64.deb ... Unpacking libkrb5-3:amd64 (1.13.2+dfsg-3) over (1.13.2+dfsg-2) ... Preparing to unpack .../libkrb5support0_1.13.2+dfsg-3_amd64.deb ... Unpacking libkrb5support0:amd64 (1.13.2+dfsg-3) over (1.13.2+dfsg-2) ... Preparing to unpack .../libk5crypto3_1.13.2+dfsg-3_amd64.deb ... Unpacking libk5crypto3:amd64 (1.13.2+dfsg-3) over (1.13.2+dfsg-2) ... Preparing to unpack .../libkeyutils1_1.5.9-8_amd64.deb ... Unpacking libkeyutils1:amd64 (1.5.9-8) over (1.5.9-5ubuntu1) ... Preparing to unpack .../libidn11_1.32-3ubuntu1_amd64.deb ... Unpacking libidn11:amd64 (1.32-3ubuntu1) over (1.28-1ubuntu2) ... Preparing to unpack .../libcurl3-gnutls_7.45.0-1ubuntu1_amd64.deb ... Unpacking libcurl3-gnutls:amd64 (7.45.0-1ubuntu1) over (7.43.0-1ubuntu2) ... Preparing to unpack .../advancecomp_1.20-1_amd64.deb ... Unpacking advancecomp (1.20-1) over (1.19-1) ... Preparing to unpack .../linux-libc-dev_4.2.0-17.21_amd64.deb ... Unpacking linux-libc-dev:amd64 (4.2.0-17.21) over (4.2.0-16.19) ... Preparing to unpack .../pkg-create-dbgsym_0.70_all.deb ... Unpacking pkg-create-dbgsym (0.70) over (0.69) ... Processing triggers for libc-bin (2.21-0ubuntu4) ... Setting up udev (227-2ubuntu1) ... Installing new version of config file /etc/init.d/udev ... addgroup: The group `input' already exists as a system group. Exiting. virtio network devices detected, disabling predictable interface names in /etc/systemd/network/50-virtio-kernel-names.link Running in chroot, ignoring request. invoke-rc.d: policy-rc.d denied execution of restart. Setting up libgomp1:amd64 (5.2.1-23ubuntu1) ... Setting up libitm1:amd64 (5.2.1-23ubuntu1) ... Setting up libatomic1:amd64 (5.2.1-23ubuntu1) ... Setting up libasan2:amd64 (5.2.1-23ubuntu1) ... Setting up liblsan0:amd64 (5.2.1-23ubuntu1) ... Setting up libtsan0:amd64 (5.2.1-23ubuntu1) ... Setting up libubsan0:amd64 (5.2.1-23ubuntu1) ... Setting up libcilkrts5:amd64 (5.2.1-23ubuntu1) ... Setting up libmpx0:amd64 (5.2.1-23ubuntu1) ... Setting up libquadmath0:amd64 (5.2.1-23ubuntu1) ... Setting up cpp-5 (5.2.1-23ubuntu1) ... Setting up libcc1-0:amd64 (5.2.1-23ubuntu1) ... Setting up binutils (2.25.51.20151028-0ubuntu1) ... Setting up libgcc-5-dev:amd64 (5.2.1-23ubuntu1) ... Setting up gcc-5 (5.2.1-23ubuntu1) ... Setting up libstdc++-5-dev:amd64 (5.2.1-23ubuntu1) ... Setting up g++-5 (5.2.1-23ubuntu1) ... Setting up libdpkg-perl (1.18.3ubuntu1) ... Setting up dpkg-dev (1.18.3ubuntu1) ... Setting up libtasn1-6:amd64 (4.7-2) ... Setting up libgnutls-deb0-28:amd64 (3.3.18-1ubuntu1) ... Setting up libsqlite3-0:amd64 (3.9.1-2) ... Setting up libkrb5support0:amd64 (1.13.2+dfsg-3) ... Setting up libk5crypto3:amd64 (1.13.2+dfsg-3) ... Setting up libkeyutils1:amd64 (1.5.9-8) ... Setting up libkrb5-3:amd64 (1.13.2+dfsg-3) ... Setting up libgssapi-krb5-2:amd64 (1.13.2+dfsg-3) ... Setting up libidn11:amd64 (1.32-3ubuntu1) ... Setting up libcurl3-gnutls:amd64 (7.45.0-1ubuntu1) ... Setting up advancecomp (1.20-1) ... Setting up linux-libc-dev:amd64 (4.2.0-17.21) ... Setting up pkg-create-dbgsym (0.70) ... Processing triggers for systemd (227-2ubuntu1) ... Processing triggers for libc-bin (2.21-0ubuntu4) ... RUN: /usr/share/launchpad-buildd/slavebin/sbuild-package ['sbuild-package', 'PACKAGEBUILD-8268452', 'amd64', 'xenial-proposed', '-c', 'chroot:autobuild', '--arch=amd64', '--dist=xenial-proposed', '--purge=never', '--nolog', '-A', 'libmems_1.6.0+4725-2.dsc'] Initiating build PACKAGEBUILD-8268452 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 3.19.0-32-generic #37~14.04.1-Ubuntu SMP Thu Oct 22 09:41:40 UTC 2015 x86_64 sbuild (Debian sbuild) 0.65.2 (24 Mar 2015) on lgw01-53.buildd ╔══════════════════════════════════════════════════════════════════════════════╗ ║ libmems 1.6.0+4725-2 (amd64) 05 Nov 2015 16:42 ║ ╚══════════════════════════════════════════════════════════════════════════════╝ Package: libmems Version: 1.6.0+4725-2 Source Version: 1.6.0+4725-2 Distribution: xenial-proposed Machine Architecture: amd64 Host Architecture: amd64 Build Architecture: amd64 I: NOTICE: Log filtering will replace 'build/libmems-kwjgZf/libmems-1.6.0+4725' with '«PKGBUILDDIR»' I: NOTICE: Log filtering will replace 'build/libmems-kwjgZf' with '«BUILDDIR»' I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-8268452/chroot-autobuild' with '«CHROOT»' ┌──────────────────────────────────────────────────────────────────────────────┐ │ Fetch source files │ └──────────────────────────────────────────────────────────────────────────────┘ Local sources ───────────── libmems_1.6.0+4725-2.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 '/«BUILDDIR»/resolver-CneLOA/apt_archive/sbuild-build-depends-core-dummy.deb'. Ign file: ./ InRelease Ign file: ./ Release.gpg Get:1 file: ./ Release [2119 B] Ign file: ./ Translation-en 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 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 0 B/772 B of archives. After this operation, 0 B of additional disk space will be used. WARNING: The following packages cannot be authenticated! sbuild-build-depends-core-dummy debconf: delaying package configuration, since apt-utils is not installed Authentication warning overridden. Selecting previously unselected package sbuild-build-depends-core-dummy. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 11716 files and directories currently installed.) Preparing to unpack .../sbuild-build-depends-core-dummy.deb ... Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ... Setting up sbuild-build-depends-core-dummy (0.invalid.0) ... Merged Build-Depends: base-files, base-passwd, bash, bsdutils, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, init, libc-bin, login, mount, ncurses-base, ncurses-bin, perl-base, sed, tar, util-linux, libc6-dev | libc-dev, gcc (>= 4:5.2), g++ (>= 4:5.2), make, dpkg-dev (>= 1.17.11), 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: base-files, base-passwd, bash, bsdutils, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, init, libc-bin, login, mount, ncurses-base, ncurses-bin, perl-base, sed, tar, util-linux, libc6-dev | libc-dev, gcc (>= 4:5.2), g++ (>= 4:5.2), make, dpkg-dev (>= 1.17.11), 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 '/«BUILDDIR»/resolver-rPDWnm/apt_archive/sbuild-build-depends-libmems-dummy.deb'. Ign file: ./ InRelease Ign file: ./ Release.gpg Get:1 file: ./ Release [2119 B] Ign file: ./ Translation-en 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 extra 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 libasprintf0v5 libboost-filesystem-dev libboost-filesystem1.58-dev libboost-filesystem1.58.0 libboost-iostreams-dev libboost-iostreams1.58-dev libboost-iostreams1.58.0 libboost-program-options-dev libboost-program-options1.58-dev libboost-program-options1.58.0 libboost-regex1.58-dev libboost-regex1.58.0 libboost-system1.58-dev libboost-system1.58.0 libboost1.58-dev libcroco3 libfile-stripnondeterminism-perl libgenome-1.3-0v5 libgenome-1.3-dev libglib2.0-0 libicu-dev libicu55 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 groff libboost1.58-doc libboost-atomic1.58-dev libboost-chrono1.58-dev libboost-context1.58-dev libboost-coroutine1.58-dev libboost-date-time1.58-dev libboost-exception1.58-dev libboost-graph1.58-dev libboost-graph-parallel1.58-dev libboost-locale1.58-dev libboost-log1.58-dev libboost-math1.58-dev libboost-mpi1.58-dev libboost-mpi-python1.58-dev libboost-python1.58-dev libboost-random1.58-dev libboost-serialization1.58-dev libboost-signals1.58-dev libboost-test1.58-dev libboost-thread1.58-dev libboost-timer1.58-dev libboost-wave1.58-dev libboost1.58-tools-dev libmpfrc++-dev libntl-dev icu-doc libtool-doc automaken gfortran fortran95-compiler gcj-jdk less www-browser libmail-box-perl Recommended packages: curl wget lynx-cur libasprintf-dev libgettextpo-dev 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 libasprintf0v5 libboost-filesystem-dev libboost-filesystem1.58-dev libboost-filesystem1.58.0 libboost-iostreams-dev libboost-iostreams1.58-dev libboost-iostreams1.58.0 libboost-program-options-dev libboost-program-options1.58-dev libboost-program-options1.58.0 libboost-regex1.58-dev libboost-regex1.58.0 libboost-system1.58-dev libboost-system1.58.0 libboost1.58-dev libcroco3 libfile-stripnondeterminism-perl libgenome-1.3-0v5 libgenome-1.3-dev libglib2.0-0 libicu-dev libicu55 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, 52 newly installed, 0 to remove and 0 not upgraded. Need to get 32.9 MB/32.9 MB of archives. After this operation, 219 MB of additional disk space will be used. WARNING: The following packages cannot be authenticated! sbuild-build-depends-libmems-dummy Authentication warning overridden. Get:1 http://ftpmaster.internal/ubuntu/ xenial/main libasprintf0v5 amd64 0.19.4-1ubuntu3 [6676 B] Get:2 http://ftpmaster.internal/ubuntu/ xenial/main groff-base amd64 1.22.3-1 [1183 kB] Get:3 http://ftpmaster.internal/ubuntu/ xenial/main bsdmainutils amd64 9.0.6ubuntu1 [175 kB] Get:4 http://ftpmaster.internal/ubuntu/ xenial/main libpipeline1 amd64 1.4.1-1 [24.9 kB] Get:5 http://ftpmaster.internal/ubuntu/ xenial/main man-db amd64 2.7.4-1 [858 kB] Get:6 http://ftpmaster.internal/ubuntu/ xenial-proposed/main libglib2.0-0 amd64 2.47.1-1 [1111 kB] Get:7 http://ftpmaster.internal/ubuntu/ xenial/main libicu55 amd64 55.1-4ubuntu1 [7652 kB] Get:8 http://ftpmaster.internal/ubuntu/ xenial/main libxml2 amd64 2.9.2+zdfsg1-4 [692 kB] Get:9 http://ftpmaster.internal/ubuntu/ xenial/main libcroco3 amd64 0.6.8-3 [83.2 kB] Get:10 http://ftpmaster.internal/ubuntu/ xenial/main libsigsegv2 amd64 2.10-4 [14.1 kB] Get:11 http://ftpmaster.internal/ubuntu/ xenial/main libunistring0 amd64 0.9.3-5.2ubuntu1 [279 kB] Get:12 http://ftpmaster.internal/ubuntu/ xenial/main libmagic1 amd64 1:5.22+15-2ubuntu1 [211 kB] Get:13 http://ftpmaster.internal/ubuntu/ xenial/main file amd64 1:5.22+15-2ubuntu1 [20.7 kB] Get:14 http://ftpmaster.internal/ubuntu/ xenial/main libtimedate-perl all 2.3000-2 [37.5 kB] Get:15 http://ftpmaster.internal/ubuntu/ xenial/main gettext-base amd64 0.19.4-1ubuntu3 [48.3 kB] Get:16 http://ftpmaster.internal/ubuntu/ xenial/main m4 amd64 1.4.17-4 [193 kB] Get:17 http://ftpmaster.internal/ubuntu/ xenial/main autoconf all 2.69-9 [321 kB] Get:18 http://ftpmaster.internal/ubuntu/ xenial/main autotools-dev all 20150820.1 [39.8 kB] Get:19 http://ftpmaster.internal/ubuntu/ xenial/main automake all 1:1.15-1ubuntu1 [511 kB] Get:20 http://ftpmaster.internal/ubuntu/ xenial/main autopoint all 0.19.4-1ubuntu3 [390 kB] Get:21 http://ftpmaster.internal/ubuntu/ xenial/main d-shlibs all 0.62ubuntu1 [9364 B] Get:22 http://ftpmaster.internal/ubuntu/ xenial/main gettext amd64 0.19.4-1ubuntu3 [857 kB] Get:23 http://ftpmaster.internal/ubuntu/ xenial/main intltool-debian all 0.35.0+20060710.4 [24.9 kB] Get:24 http://ftpmaster.internal/ubuntu/ xenial/main po-debconf all 1.0.18 [234 kB] Get:25 http://ftpmaster.internal/ubuntu/ xenial/main libarchive-zip-perl all 1.53-1 [87.0 kB] Get:26 http://ftpmaster.internal/ubuntu/ xenial/main libfile-stripnondeterminism-perl all 0.013-1 [10.4 kB] Get:27 http://ftpmaster.internal/ubuntu/ xenial/main dh-strip-nondeterminism all 0.013-1 [5600 B] Get:28 http://ftpmaster.internal/ubuntu/ xenial-proposed/main debhelper all 9.20151005ubuntu2 [730 kB] Get:29 http://ftpmaster.internal/ubuntu/ xenial/main libtool all 2.4.2-1.11 [180 kB] Get:30 http://ftpmaster.internal/ubuntu/ xenial/main dh-autoreconf all 10 [15.3 kB] Get:31 http://ftpmaster.internal/ubuntu/ xenial/main icu-devtools amd64 55.1-4ubuntu1 [168 kB] Get:32 http://ftpmaster.internal/ubuntu/ xenial/main libboost1.58-dev amd64 1.58.0+dfsg-3.1ubuntu1 [6234 kB] Get:33 http://ftpmaster.internal/ubuntu/ xenial/main libboost-system1.58.0 amd64 1.58.0+dfsg-3.1ubuntu1 [9102 B] Get:34 http://ftpmaster.internal/ubuntu/ xenial/main libboost-filesystem1.58.0 amd64 1.58.0+dfsg-3.1ubuntu1 [37.8 kB] Get:35 http://ftpmaster.internal/ubuntu/ xenial/main libboost-system1.58-dev amd64 1.58.0+dfsg-3.1ubuntu1 [8582 B] Get:36 http://ftpmaster.internal/ubuntu/ xenial/main libboost-filesystem1.58-dev amd64 1.58.0+dfsg-3.1ubuntu1 [46.3 kB] Get:37 http://ftpmaster.internal/ubuntu/ xenial/main libboost-filesystem-dev amd64 1.58.0.0ubuntu1 [2824 B] Get:38 http://ftpmaster.internal/ubuntu/ xenial/main libboost-regex1.58.0 amd64 1.58.0+dfsg-3.1ubuntu1 [263 kB] Get:39 http://ftpmaster.internal/ubuntu/ xenial/main libicu-dev amd64 55.1-4ubuntu1 [8546 kB] Get:40 http://ftpmaster.internal/ubuntu/ xenial/main libboost-regex1.58-dev amd64 1.58.0+dfsg-3.1ubuntu1 [322 kB] Get:41 http://ftpmaster.internal/ubuntu/ xenial/main libboost-iostreams1.58.0 amd64 1.58.0+dfsg-3.1ubuntu1 [28.3 kB] Get:42 http://ftpmaster.internal/ubuntu/ xenial/main libboost-iostreams1.58-dev amd64 1.58.0+dfsg-3.1ubuntu1 [36.1 kB] Get:43 http://ftpmaster.internal/ubuntu/ xenial/main libboost-iostreams-dev amd64 1.58.0.0ubuntu1 [2790 B] Get:44 http://ftpmaster.internal/ubuntu/ xenial/main libboost-program-options1.58.0 amd64 1.58.0+dfsg-3.1ubuntu1 [139 kB] Get:45 http://ftpmaster.internal/ubuntu/ xenial/main libboost-program-options1.58-dev amd64 1.58.0+dfsg-3.1ubuntu1 [169 kB] Get:46 http://ftpmaster.internal/ubuntu/ xenial/main libboost-program-options-dev amd64 1.58.0.0ubuntu1 [2818 B] Get:47 http://ftpmaster.internal/ubuntu/ xenial/universe libgenome-1.3-0v5 amd64 1.3.1-8 [106 kB] Get:48 http://ftpmaster.internal/ubuntu/ xenial/universe libgenome-1.3-dev amd64 1.3.1-8 [170 kB] Get:49 http://ftpmaster.internal/ubuntu/ xenial/universe libmuscle-3.7-1 amd64 3.7+4565-1 [238 kB] Get:50 http://ftpmaster.internal/ubuntu/ xenial/universe libmuscle-3.7-dev amd64 3.7+4565-1 [290 kB] Get:51 http://ftpmaster.internal/ubuntu/ xenial/main pkg-config amd64 0.28-1ubuntu1 [40.0 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 32.9 MB in 1s (20.6 MB/s) Selecting previously unselected package libasprintf0v5:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 11716 files and directories currently installed.) Preparing to unpack .../libasprintf0v5_0.19.4-1ubuntu3_amd64.deb ... Unpacking libasprintf0v5:amd64 (0.19.4-1ubuntu3) ... Selecting previously unselected package groff-base. Preparing to unpack .../groff-base_1.22.3-1_amd64.deb ... Unpacking groff-base (1.22.3-1) ... Selecting previously unselected package bsdmainutils. Preparing to unpack .../bsdmainutils_9.0.6ubuntu1_amd64.deb ... Unpacking bsdmainutils (9.0.6ubuntu1) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../libpipeline1_1.4.1-1_amd64.deb ... Unpacking libpipeline1:amd64 (1.4.1-1) ... Selecting previously unselected package man-db. Preparing to unpack .../man-db_2.7.4-1_amd64.deb ... Unpacking man-db (2.7.4-1) ... Selecting previously unselected package libglib2.0-0:amd64. Preparing to unpack .../libglib2.0-0_2.47.1-1_amd64.deb ... Unpacking libglib2.0-0:amd64 (2.47.1-1) ... Selecting previously unselected package libicu55:amd64. Preparing to unpack .../libicu55_55.1-4ubuntu1_amd64.deb ... Unpacking libicu55:amd64 (55.1-4ubuntu1) ... Selecting previously unselected package libxml2:amd64. Preparing to unpack .../libxml2_2.9.2+zdfsg1-4_amd64.deb ... Unpacking libxml2:amd64 (2.9.2+zdfsg1-4) ... Selecting previously unselected package libcroco3:amd64. Preparing to unpack .../libcroco3_0.6.8-3_amd64.deb ... Unpacking libcroco3:amd64 (0.6.8-3) ... Selecting previously unselected package libsigsegv2:amd64. Preparing to unpack .../libsigsegv2_2.10-4_amd64.deb ... Unpacking libsigsegv2:amd64 (2.10-4) ... Selecting previously unselected package libunistring0:amd64. Preparing to unpack .../libunistring0_0.9.3-5.2ubuntu1_amd64.deb ... Unpacking libunistring0:amd64 (0.9.3-5.2ubuntu1) ... Selecting previously unselected package libmagic1:amd64. Preparing to unpack .../libmagic1_1%3a5.22+15-2ubuntu1_amd64.deb ... Unpacking libmagic1:amd64 (1:5.22+15-2ubuntu1) ... Selecting previously unselected package file. Preparing to unpack .../file_1%3a5.22+15-2ubuntu1_amd64.deb ... Unpacking file (1:5.22+15-2ubuntu1) ... Selecting previously unselected package libtimedate-perl. Preparing to unpack .../libtimedate-perl_2.3000-2_all.deb ... Unpacking libtimedate-perl (2.3000-2) ... Selecting previously unselected package gettext-base. Preparing to unpack .../gettext-base_0.19.4-1ubuntu3_amd64.deb ... Unpacking gettext-base (0.19.4-1ubuntu3) ... Selecting previously unselected package m4. Preparing to unpack .../archives/m4_1.4.17-4_amd64.deb ... Unpacking m4 (1.4.17-4) ... Selecting previously unselected package autoconf. Preparing to unpack .../autoconf_2.69-9_all.deb ... Unpacking autoconf (2.69-9) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../autotools-dev_20150820.1_all.deb ... Unpacking autotools-dev (20150820.1) ... Selecting previously unselected package automake. Preparing to unpack .../automake_1%3a1.15-1ubuntu1_all.deb ... Unpacking automake (1:1.15-1ubuntu1) ... Selecting previously unselected package autopoint. Preparing to unpack .../autopoint_0.19.4-1ubuntu3_all.deb ... Unpacking autopoint (0.19.4-1ubuntu3) ... Selecting previously unselected package d-shlibs. Preparing to unpack .../d-shlibs_0.62ubuntu1_all.deb ... Unpacking d-shlibs (0.62ubuntu1) ... Selecting previously unselected package gettext. Preparing to unpack .../gettext_0.19.4-1ubuntu3_amd64.deb ... Unpacking gettext (0.19.4-1ubuntu3) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../intltool-debian_0.35.0+20060710.4_all.deb ... Unpacking intltool-debian (0.35.0+20060710.4) ... Selecting previously unselected package po-debconf. Preparing to unpack .../po-debconf_1.0.18_all.deb ... Unpacking po-debconf (1.0.18) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../libarchive-zip-perl_1.53-1_all.deb ... Unpacking libarchive-zip-perl (1.53-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../libfile-stripnondeterminism-perl_0.013-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (0.013-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../dh-strip-nondeterminism_0.013-1_all.deb ... Unpacking dh-strip-nondeterminism (0.013-1) ... Selecting previously unselected package debhelper. Preparing to unpack .../debhelper_9.20151005ubuntu2_all.deb ... Unpacking debhelper (9.20151005ubuntu2) ... Selecting previously unselected package libtool. Preparing to unpack .../libtool_2.4.2-1.11_all.deb ... Unpacking libtool (2.4.2-1.11) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../dh-autoreconf_10_all.deb ... Unpacking dh-autoreconf (10) ... Selecting previously unselected package icu-devtools. Preparing to unpack .../icu-devtools_55.1-4ubuntu1_amd64.deb ... Unpacking icu-devtools (55.1-4ubuntu1) ... Selecting previously unselected package libboost1.58-dev:amd64. Preparing to unpack .../libboost1.58-dev_1.58.0+dfsg-3.1ubuntu1_amd64.deb ... Unpacking libboost1.58-dev:amd64 (1.58.0+dfsg-3.1ubuntu1) ... Selecting previously unselected package libboost-system1.58.0:amd64. Preparing to unpack .../libboost-system1.58.0_1.58.0+dfsg-3.1ubuntu1_amd64.deb ... Unpacking libboost-system1.58.0:amd64 (1.58.0+dfsg-3.1ubuntu1) ... Selecting previously unselected package libboost-filesystem1.58.0:amd64. Preparing to unpack .../libboost-filesystem1.58.0_1.58.0+dfsg-3.1ubuntu1_amd64.deb ... Unpacking libboost-filesystem1.58.0:amd64 (1.58.0+dfsg-3.1ubuntu1) ... Selecting previously unselected package libboost-system1.58-dev:amd64. Preparing to unpack .../libboost-system1.58-dev_1.58.0+dfsg-3.1ubuntu1_amd64.deb ... Unpacking libboost-system1.58-dev:amd64 (1.58.0+dfsg-3.1ubuntu1) ... Selecting previously unselected package libboost-filesystem1.58-dev:amd64. Preparing to unpack .../libboost-filesystem1.58-dev_1.58.0+dfsg-3.1ubuntu1_amd64.deb ... Unpacking libboost-filesystem1.58-dev:amd64 (1.58.0+dfsg-3.1ubuntu1) ... Selecting previously unselected package libboost-filesystem-dev:amd64. Preparing to unpack .../libboost-filesystem-dev_1.58.0.0ubuntu1_amd64.deb ... Unpacking libboost-filesystem-dev:amd64 (1.58.0.0ubuntu1) ... Selecting previously unselected package libboost-regex1.58.0:amd64. Preparing to unpack .../libboost-regex1.58.0_1.58.0+dfsg-3.1ubuntu1_amd64.deb ... Unpacking libboost-regex1.58.0:amd64 (1.58.0+dfsg-3.1ubuntu1) ... Selecting previously unselected package libicu-dev:amd64. Preparing to unpack .../libicu-dev_55.1-4ubuntu1_amd64.deb ... Unpacking libicu-dev:amd64 (55.1-4ubuntu1) ... Selecting previously unselected package libboost-regex1.58-dev:amd64. Preparing to unpack .../libboost-regex1.58-dev_1.58.0+dfsg-3.1ubuntu1_amd64.deb ... Unpacking libboost-regex1.58-dev:amd64 (1.58.0+dfsg-3.1ubuntu1) ... Selecting previously unselected package libboost-iostreams1.58.0:amd64. Preparing to unpack .../libboost-iostreams1.58.0_1.58.0+dfsg-3.1ubuntu1_amd64.deb ... Unpacking libboost-iostreams1.58.0:amd64 (1.58.0+dfsg-3.1ubuntu1) ... Selecting previously unselected package libboost-iostreams1.58-dev:amd64. Preparing to unpack .../libboost-iostreams1.58-dev_1.58.0+dfsg-3.1ubuntu1_amd64.deb ... Unpacking libboost-iostreams1.58-dev:amd64 (1.58.0+dfsg-3.1ubuntu1) ... Selecting previously unselected package libboost-iostreams-dev:amd64. Preparing to unpack .../libboost-iostreams-dev_1.58.0.0ubuntu1_amd64.deb ... Unpacking libboost-iostreams-dev:amd64 (1.58.0.0ubuntu1) ... Selecting previously unselected package libboost-program-options1.58.0:amd64. Preparing to unpack .../libboost-program-options1.58.0_1.58.0+dfsg-3.1ubuntu1_amd64.deb ... Unpacking libboost-program-options1.58.0:amd64 (1.58.0+dfsg-3.1ubuntu1) ... Selecting previously unselected package libboost-program-options1.58-dev:amd64. Preparing to unpack .../libboost-program-options1.58-dev_1.58.0+dfsg-3.1ubuntu1_amd64.deb ... Unpacking libboost-program-options1.58-dev:amd64 (1.58.0+dfsg-3.1ubuntu1) ... Selecting previously unselected package libboost-program-options-dev:amd64. Preparing to unpack .../libboost-program-options-dev_1.58.0.0ubuntu1_amd64.deb ... Unpacking libboost-program-options-dev:amd64 (1.58.0.0ubuntu1) ... Selecting previously unselected package libgenome-1.3-0v5. Preparing to unpack .../libgenome-1.3-0v5_1.3.1-8_amd64.deb ... Unpacking libgenome-1.3-0v5 (1.3.1-8) ... Selecting previously unselected package libgenome-1.3-dev. Preparing to unpack .../libgenome-1.3-dev_1.3.1-8_amd64.deb ... Unpacking libgenome-1.3-dev (1.3.1-8) ... Selecting previously unselected package libmuscle-3.7-1. Preparing to unpack .../libmuscle-3.7-1_3.7+4565-1_amd64.deb ... Unpacking libmuscle-3.7-1 (3.7+4565-1) ... Selecting previously unselected package libmuscle-3.7-dev. Preparing to unpack .../libmuscle-3.7-dev_3.7+4565-1_amd64.deb ... Unpacking libmuscle-3.7-dev (3.7+4565-1) ... Selecting previously unselected package pkg-config. Preparing to unpack .../pkg-config_0.28-1ubuntu1_amd64.deb ... Unpacking pkg-config (0.28-1ubuntu1) ... Selecting previously unselected package sbuild-build-depends-libmems-dummy. Preparing to unpack .../sbuild-build-depends-libmems-dummy.deb ... Unpacking sbuild-build-depends-libmems-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.21-0ubuntu4) ... Setting up libasprintf0v5:amd64 (0.19.4-1ubuntu3) ... Setting up groff-base (1.22.3-1) ... Setting up bsdmainutils (9.0.6ubuntu1) ... 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 libpipeline1:amd64 (1.4.1-1) ... Setting up man-db (2.7.4-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libglib2.0-0:amd64 (2.47.1-1) ... No schema files found: doing nothing. Setting up libicu55:amd64 (55.1-4ubuntu1) ... Setting up libxml2:amd64 (2.9.2+zdfsg1-4) ... Setting up libcroco3:amd64 (0.6.8-3) ... Setting up libsigsegv2:amd64 (2.10-4) ... Setting up libunistring0:amd64 (0.9.3-5.2ubuntu1) ... Setting up libmagic1:amd64 (1:5.22+15-2ubuntu1) ... Setting up file (1:5.22+15-2ubuntu1) ... Setting up libtimedate-perl (2.3000-2) ... Setting up gettext-base (0.19.4-1ubuntu3) ... Setting up m4 (1.4.17-4) ... Setting up autoconf (2.69-9) ... Setting up autotools-dev (20150820.1) ... Setting up automake (1:1.15-1ubuntu1) ... update-alternatives: using /usr/bin/automake-1.15 to provide /usr/bin/automake (automake) in auto mode Setting up autopoint (0.19.4-1ubuntu3) ... Setting up d-shlibs (0.62ubuntu1) ... Setting up gettext (0.19.4-1ubuntu3) ... Setting up intltool-debian (0.35.0+20060710.4) ... Setting up po-debconf (1.0.18) ... Setting up libarchive-zip-perl (1.53-1) ... Setting up libfile-stripnondeterminism-perl (0.013-1) ... Setting up libtool (2.4.2-1.11) ... Setting up icu-devtools (55.1-4ubuntu1) ... Setting up libboost1.58-dev:amd64 (1.58.0+dfsg-3.1ubuntu1) ... Setting up libboost-system1.58.0:amd64 (1.58.0+dfsg-3.1ubuntu1) ... Setting up libboost-filesystem1.58.0:amd64 (1.58.0+dfsg-3.1ubuntu1) ... Setting up libboost-system1.58-dev:amd64 (1.58.0+dfsg-3.1ubuntu1) ... Setting up libboost-filesystem1.58-dev:amd64 (1.58.0+dfsg-3.1ubuntu1) ... Setting up libboost-filesystem-dev:amd64 (1.58.0.0ubuntu1) ... Setting up libboost-regex1.58.0:amd64 (1.58.0+dfsg-3.1ubuntu1) ... Setting up libicu-dev:amd64 (55.1-4ubuntu1) ... Setting up libboost-regex1.58-dev:amd64 (1.58.0+dfsg-3.1ubuntu1) ... Setting up libboost-iostreams1.58.0:amd64 (1.58.0+dfsg-3.1ubuntu1) ... Setting up libboost-iostreams1.58-dev:amd64 (1.58.0+dfsg-3.1ubuntu1) ... Setting up libboost-iostreams-dev:amd64 (1.58.0.0ubuntu1) ... Setting up libboost-program-options1.58.0:amd64 (1.58.0+dfsg-3.1ubuntu1) ... Setting up libboost-program-options1.58-dev:amd64 (1.58.0+dfsg-3.1ubuntu1) ... Setting up libboost-program-options-dev:amd64 (1.58.0.0ubuntu1) ... Setting up libgenome-1.3-0v5 (1.3.1-8) ... Setting up libgenome-1.3-dev (1.3.1-8) ... Setting up libmuscle-3.7-1 (3.7+4565-1) ... Setting up libmuscle-3.7-dev (3.7+4565-1) ... Setting up pkg-config (0.28-1ubuntu1) ... Setting up debhelper (9.20151005ubuntu2) ... Setting up dh-autoreconf (10) ... Setting up sbuild-build-depends-libmems-dummy (0.invalid.0) ... Setting up dh-strip-nondeterminism (0.013-1) ... Processing triggers for libc-bin (2.21-0ubuntu4) ... ┌──────────────────────────────────────────────────────────────────────────────┐ │ Build environment │ └──────────────────────────────────────────────────────────────────────────────┘ Kernel: Linux 3.19.0-32-generic amd64 (x86_64) Toolchain package versions: binutils_2.25.51.20151028-0ubuntu1 dpkg-dev_1.18.3ubuntu1 g++-5_5.2.1-23ubuntu1 gcc-5_5.2.1-23ubuntu1 libc6-dev_2.21-0ubuntu4 libstdc++-5-dev_5.2.1-23ubuntu1 libstdc++6_5.2.1-23ubuntu1 linux-libc-dev_4.2.0-17.21 Package versions: adduser_3.113+nmu3ubuntu4 advancecomp_1.20-1 apt_1.0.10.2ubuntu1 apt-transport-https_1.0.10.2ubuntu1 autoconf_2.69-9 automake_1:1.15-1ubuntu1 autopoint_0.19.4-1ubuntu3 autotools-dev_20150820.1 base-files_9.4ubuntu2 base-passwd_3.5.38 bash_4.3-14ubuntu1 binutils_2.25.51.20151028-0ubuntu1 bsdmainutils_9.0.6ubuntu1 bsdutils_1:2.27.1-1ubuntu1 build-essential_12.1ubuntu2 bzip2_1.0.6-8 ca-certificates_20150426ubuntu1 coreutils_8.23-4ubuntu2 cpp_4:5.2.1-3ubuntu1 cpp-5_5.2.1-23ubuntu1 d-shlibs_0.62ubuntu1 dash_0.5.7-4ubuntu2 debconf_1.5.57ubuntu1 debhelper_9.20151005ubuntu2 debianutils_4.5.1 dh-autoreconf_10 dh-strip-nondeterminism_0.013-1 diffutils_1:3.3-2 dmsetup_2:1.02.99-1ubuntu1 dpkg_1.18.3ubuntu1 dpkg-dev_1.18.3ubuntu1 e2fslibs_1.42.13-1ubuntu1 e2fsprogs_1.42.13-1ubuntu1 fakeroot_1.20.2-1ubuntu1 file_1:5.22+15-2ubuntu1 findutils_4.4.2-9build1 g++_4:5.2.1-3ubuntu1 g++-5_5.2.1-23ubuntu1 gcc_4:5.2.1-3ubuntu1 gcc-5_5.2.1-23ubuntu1 gcc-5-base_5.2.1-23ubuntu1 gettext_0.19.4-1ubuntu3 gettext-base_0.19.4-1ubuntu3 gnupg_1.4.18-7ubuntu1 gpgv_1.4.18-7ubuntu1 grep_2.21-2 groff-base_1.22.3-1 gzip_1.6-4ubuntu1 hostname_3.15ubuntu2 icu-devtools_55.1-4ubuntu1 init_1.24ubuntu1 initscripts_2.88dsf-59.2ubuntu2 insserv_1.14.0-5ubuntu3 intltool-debian_0.35.0+20060710.4 libacl1_2.2.52-2 libapparmor1_2.10-0ubuntu6 libapt-pkg4.16_1.0.10.2ubuntu1 libarchive-zip-perl_1.53-1 libasan2_5.2.1-23ubuntu1 libasn1-8-heimdal_1.6~rc2+dfsg-10ubuntu1 libasprintf0v5_0.19.4-1ubuntu3 libatomic1_5.2.1-23ubuntu1 libattr1_1:2.4.47-2 libaudit-common_1:2.4.4-4ubuntu1 libaudit1_1:2.4.4-4ubuntu1 libblkid1_2.27.1-1ubuntu1 libboost-filesystem-dev_1.58.0.0ubuntu1 libboost-filesystem1.58-dev_1.58.0+dfsg-3.1ubuntu1 libboost-filesystem1.58.0_1.58.0+dfsg-3.1ubuntu1 libboost-iostreams-dev_1.58.0.0ubuntu1 libboost-iostreams1.58-dev_1.58.0+dfsg-3.1ubuntu1 libboost-iostreams1.58.0_1.58.0+dfsg-3.1ubuntu1 libboost-program-options-dev_1.58.0.0ubuntu1 libboost-program-options1.58-dev_1.58.0+dfsg-3.1ubuntu1 libboost-program-options1.58.0_1.58.0+dfsg-3.1ubuntu1 libboost-regex1.58-dev_1.58.0+dfsg-3.1ubuntu1 libboost-regex1.58.0_1.58.0+dfsg-3.1ubuntu1 libboost-system1.58-dev_1.58.0+dfsg-3.1ubuntu1 libboost-system1.58.0_1.58.0+dfsg-3.1ubuntu1 libboost1.58-dev_1.58.0+dfsg-3.1ubuntu1 libbz2-1.0_1.0.6-8 libc-bin_2.21-0ubuntu4 libc-dev-bin_2.21-0ubuntu4 libc6_2.21-0ubuntu4 libc6-dev_2.21-0ubuntu4 libcap2_1:2.24-12 libcap2-bin_1:2.24-12 libcc1-0_5.2.1-23ubuntu1 libcilkrts5_5.2.1-23ubuntu1 libcomerr2_1.42.13-1ubuntu1 libcroco3_0.6.8-3 libcryptsetup4_2:1.6.6-5ubuntu2 libcurl3-gnutls_7.45.0-1ubuntu1 libdb5.3_5.3.28-11 libdbus-1-3_1.10.0-1ubuntu1 libdebconfclient0_0.192ubuntu1 libdevmapper1.02.1_2:1.02.99-1ubuntu1 libdpkg-perl_1.18.3ubuntu1 libfakeroot_1.20.2-1ubuntu1 libfdisk1_2.27.1-1ubuntu1 libffi6_3.2.1-3 libfile-stripnondeterminism-perl_0.013-1 libgcc-5-dev_5.2.1-23ubuntu1 libgcc1_1:5.2.1-23ubuntu1 libgcrypt20_1.6.4-3 libgdbm3_1.8.3-13.1 libgenome-1.3-0v5_1.3.1-8 libgenome-1.3-dev_1.3.1-8 libglib2.0-0_2.47.1-1 libgmp10_2:6.0.0+dfsg-7 libgnutls-deb0-28_3.3.18-1ubuntu1 libgomp1_5.2.1-23ubuntu1 libgpg-error0_1.20-1 libgssapi-krb5-2_1.13.2+dfsg-3 libgssapi3-heimdal_1.6~rc2+dfsg-10ubuntu1 libhcrypto4-heimdal_1.6~rc2+dfsg-10ubuntu1 libheimbase1-heimdal_1.6~rc2+dfsg-10ubuntu1 libheimntlm0-heimdal_1.6~rc2+dfsg-10ubuntu1 libhogweed4_3.1.1-4 libhx509-5-heimdal_1.6~rc2+dfsg-10ubuntu1 libicu-dev_55.1-4ubuntu1 libicu55_55.1-4ubuntu1 libidn11_1.32-3ubuntu1 libisl13_0.14-2 libitm1_5.2.1-23ubuntu1 libk5crypto3_1.13.2+dfsg-3 libkeyutils1_1.5.9-8 libkmod2_21-1ubuntu1 libkrb5-26-heimdal_1.6~rc2+dfsg-10ubuntu1 libkrb5-3_1.13.2+dfsg-3 libkrb5support0_1.13.2+dfsg-3 libldap-2.4-2_2.4.41+dfsg-1ubuntu2 liblockfile-bin_1.09-6ubuntu1 liblockfile1_1.09-6ubuntu1 liblsan0_5.2.1-23ubuntu1 liblzma5_5.1.1alpha+20120614-2ubuntu2 libmagic1_1:5.22+15-2ubuntu1 libmount1_2.27.1-1ubuntu1 libmpc3_1.0.3-1 libmpfr4_3.1.3-1 libmpx0_5.2.1-23ubuntu1 libmuscle-3.7-1_3.7+4565-1 libmuscle-3.7-dev_3.7+4565-1 libncurses5_5.9+20150516-2ubuntu1 libncursesw5_5.9+20150516-2ubuntu1 libnettle6_3.1.1-4 libnih-dbus1_1.0.3-4ubuntu27 libnih1_1.0.3-4ubuntu27 libp11-kit0_0.23.1-3 libpam-modules_1.1.8-3.1ubuntu3 libpam-modules-bin_1.1.8-3.1ubuntu3 libpam-runtime_1.1.8-3.1ubuntu3 libpam0g_1.1.8-3.1ubuntu3 libpcre3_2:8.35-7.1ubuntu1 libpipeline1_1.4.1-1 libpng12-0_1.2.51-0ubuntu3 libprocps3_1:3.3.9-1ubuntu8 libquadmath0_5.2.1-23ubuntu1 libreadline6_6.3-8ubuntu1 libroken18-heimdal_1.6~rc2+dfsg-10ubuntu1 librtmp1_2.4+20150115.gita107cef-1build1 libsasl2-2_2.1.26.dfsg1-14 libsasl2-modules-db_2.1.26.dfsg1-14 libseccomp2_2.2.3-2ubuntu1 libselinux1_2.3-2build1 libsemanage-common_2.3-1build2 libsemanage1_2.3-1build2 libsepol1_2.3-2 libsigsegv2_2.10-4 libslang2_2.3.0-2ubuntu1 libsmartcols1_2.27.1-1ubuntu1 libsqlite3-0_3.9.1-2 libss2_1.42.13-1ubuntu1 libssl1.0.0_1.0.2d-0ubuntu1 libstdc++-5-dev_5.2.1-23ubuntu1 libstdc++6_5.2.1-23ubuntu1 libsystemd0_227-2ubuntu1 libtasn1-6_4.7-2 libtimedate-perl_2.3000-2 libtinfo5_5.9+20150516-2ubuntu1 libtool_2.4.2-1.11 libtsan0_5.2.1-23ubuntu1 libubsan0_5.2.1-23ubuntu1 libudev1_227-2ubuntu1 libunistring0_0.9.3-5.2ubuntu1 libusb-0.1-4_2:0.1.12-27 libustr-1.0-1_1.0.4-5 libuuid1_2.27.1-1ubuntu1 libwind0-heimdal_1.6~rc2+dfsg-10ubuntu1 libxml2_2.9.2+zdfsg1-4 linux-libc-dev_4.2.0-17.21 lockfile-progs_0.1.17 login_1:4.1.5.1-1.1ubuntu7 lsb-base_4.1+Debian11ubuntu8 m4_1.4.17-4 make_4.0-8.2 man-db_2.7.4-1 mawk_1.3.3-17ubuntu2 mount_2.27.1-1ubuntu1 multiarch-support_2.21-0ubuntu4 ncurses-base_5.9+20150516-2ubuntu1 ncurses-bin_5.9+20150516-2ubuntu1 openssl_1.0.2d-0ubuntu1 optipng_0.7.5-1 passwd_1:4.1.5.1-1.1ubuntu7 patch_2.7.5-1 perl_5.20.2-6 perl-base_5.20.2-6 perl-modules_5.20.2-6 pkg-config_0.28-1ubuntu1 pkg-create-dbgsym_0.70 pkgbinarymangler_122 po-debconf_1.0.18 policyrcd-script-zg2_0.1-2 procps_1:3.3.9-1ubuntu8 readline-common_6.3-8ubuntu1 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-libmems-dummy_0.invalid.0 sed_4.2.2-6.1 sensible-utils_0.0.9 systemd_227-2ubuntu1 systemd-sysv_227-2ubuntu1 sysv-rc_2.88dsf-59.2ubuntu2 sysvinit-utils_2.88dsf-59.2ubuntu2 tar_1.28-2ubuntu1 tzdata_2015g-1 ubuntu-keyring_2012.05.19 udev_227-2ubuntu1 util-linux_2.27.1-1ubuntu1 xz-utils_5.1.1alpha+20120614-2ubuntu2 zlib1g_1:1.2.8.dfsg-2ubuntu4 ┌──────────────────────────────────────────────────────────────────────────────┐ │ Build │ └──────────────────────────────────────────────────────────────────────────────┘ Unpack source ───────────── gpgv: Signature made Tue Aug 18 21:50:17 2015 UTC using RSA key ID D1C646D1 gpgv: Can't check signature: public key not found dpkg-source: warning: failed to verify signature on ./libmems_1.6.0+4725-2.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+4725-2.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 Check disc space ──────────────── Sufficient free space for build User Environment ──────────────── DEB_BUILD_OPTIONS=parallel=4 HOME=/home/buildd LANG=C 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=/«BUILDDIR»/libmems-1.6.0+4725 SHELL=/bin/sh SUDO_COMMAND=/usr/sbin/chroot /«CHROOT» su buildd -s /bin/sh -c cd '/«BUILDDIR»/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: source package libmems dpkg-buildpackage: source version 1.6.0+4725-2 dpkg-buildpackage: source distribution unstable dpkg-source --before-build libmems-1.6.0+4725 dpkg-buildpackage: host architecture amd64 fakeroot debian/rules clean dh clean --with autoreconf dh_testdir dh_auto_clean dh_autoreconf_clean dh_clean debian/rules build dh build --with autoreconf dh_testdir dh_autoreconf libtoolize: putting auxiliary files in AC_CONFIG_AUX_DIR, `config'. libtoolize: copying file `config/ltmain.sh' libtoolize: putting macros in AC_CONFIG_MACRO_DIR, `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 ./configure --build=x86_64-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/x86_64-linux-gnu --libexecdir=\${prefix}/lib/x86_64-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... x86_64-pc-linux-gnu checking host system type... x86_64-pc-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 whether the shell understands some XSI constructs... yes checking whether the shell understands "+="... yes checking how to convert x86_64-pc-linux-gnu file names to x86_64-pc-linux-gnu format... func_convert_file_noop checking how to convert x86_64-pc-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 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 elf_x86_64) 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 elf_x86_64 checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld... yes checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) 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 elf_x86_64) 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_58 checking whether the compiler implements namespaces... yes configure: WARNING: could not figure out which toolset name to use for g++ checking for the toolset name used by Boost 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 make -j1 make[1]: Entering directory '/«BUILDDIR»/libmems-1.6.0+4725' make all-recursive make[2]: Entering directory '/«BUILDDIR»/libmems-1.6.0+4725' Making all in libMems make[3]: Entering directory '/«BUILDDIR»/libmems-1.6.0+4725/libMems' /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -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 -fstack-protector-strong -Wformat -Werror=format-security -c -o RepeatHash.lo RepeatHash.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -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 -fstack-protector-strong -Wformat -Werror=format-security -c RepeatHash.cpp -fPIC -DPIC -o .libs/RepeatHash.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -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 -fstack-protector-strong -Wformat -Werror=format-security -c RepeatHash.cpp -o RepeatHash.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -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 -fstack-protector-strong -Wformat -Werror=format-security -c -o DNAFileSML.lo DNAFileSML.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -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 -fstack-protector-strong -Wformat -Werror=format-security -c DNAFileSML.cpp -fPIC -DPIC -o .libs/DNAFileSML.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -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 -fstack-protector-strong -Wformat -Werror=format-security -c DNAFileSML.cpp -o DNAFileSML.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -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 -fstack-protector-strong -Wformat -Werror=format-security -c -o MatchFinder.lo MatchFinder.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -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 -fstack-protector-strong -Wformat -Werror=format-security -c MatchFinder.cpp -fPIC -DPIC -o .libs/MatchFinder.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -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 -fstack-protector-strong -Wformat -Werror=format-security -c MatchFinder.cpp -o MatchFinder.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -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 -fstack-protector-strong -Wformat -Werror=format-security -c -o DNAMemorySML.lo DNAMemorySML.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -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 -fstack-protector-strong -Wformat -Werror=format-security -c DNAMemorySML.cpp -fPIC -DPIC -o .libs/DNAMemorySML.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -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 -fstack-protector-strong -Wformat -Werror=format-security -c DNAMemorySML.cpp -o DNAMemorySML.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -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 -fstack-protector-strong -Wformat -Werror=format-security -c -o MemorySML.lo MemorySML.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -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 -fstack-protector-strong -Wformat -Werror=format-security -c MemorySML.cpp -fPIC -DPIC -o .libs/MemorySML.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -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 -fstack-protector-strong -Wformat -Werror=format-security -c MemorySML.cpp -o MemorySML.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -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 -fstack-protector-strong -Wformat -Werror=format-security -c -o SortedMerList.lo SortedMerList.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -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 -fstack-protector-strong -Wformat -Werror=format-security -c SortedMerList.cpp -fPIC -DPIC -o .libs/SortedMerList.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -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 -fstack-protector-strong -Wformat -Werror=format-security -c SortedMerList.cpp -o SortedMerList.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -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 -fstack-protector-strong -Wformat -Werror=format-security -c -o FileSML.lo FileSML.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -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 -fstack-protector-strong -Wformat -Werror=format-security -c FileSML.cpp -fPIC -DPIC -o .libs/FileSML.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -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 -fstack-protector-strong -Wformat -Werror=format-security -c FileSML.cpp -o FileSML.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -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 -fstack-protector-strong -Wformat -Werror=format-security -c -o MemHash.lo MemHash.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -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 -fstack-protector-strong -Wformat -Werror=format-security -c MemHash.cpp -fPIC -DPIC -o .libs/MemHash.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -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 -fstack-protector-strong -Wformat -Werror=format-security -c MemHash.cpp -o MemHash.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -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 -fstack-protector-strong -Wformat -Werror=format-security -c -o MatchHashEntry.lo MatchHashEntry.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -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 -fstack-protector-strong -Wformat -Werror=format-security -c MatchHashEntry.cpp -fPIC -DPIC -o .libs/MatchHashEntry.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -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 -fstack-protector-strong -Wformat -Werror=format-security -c MatchHashEntry.cpp -o MatchHashEntry.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -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 -fstack-protector-strong -Wformat -Werror=format-security -c -o Interval.lo Interval.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -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 -fstack-protector-strong -Wformat -Werror=format-security -c Interval.cpp -fPIC -DPIC -o .libs/Interval.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -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 -fstack-protector-strong -Wformat -Werror=format-security -c Interval.cpp -o Interval.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -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 -fstack-protector-strong -Wformat -Werror=format-security -c -o IntervalList.lo IntervalList.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -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 -fstack-protector-strong -Wformat -Werror=format-security -c IntervalList.cpp -fPIC -DPIC -o .libs/IntervalList.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -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 -fstack-protector-strong -Wformat -Werror=format-security -c IntervalList.cpp -o IntervalList.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -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 -fstack-protector-strong -Wformat -Werror=format-security -c -o twister.lo twister.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -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 -fstack-protector-strong -Wformat -Werror=format-security -c twister.c -fPIC -DPIC -o .libs/twister.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -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 -fstack-protector-strong -Wformat -Werror=format-security -c twister.c -o twister.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -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 -fstack-protector-strong -Wformat -Werror=format-security -c -o gnAlignedSequences.lo gnAlignedSequences.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -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 -fstack-protector-strong -Wformat -Werror=format-security -c gnAlignedSequences.cpp -fPIC -DPIC -o .libs/gnAlignedSequences.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -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 -fstack-protector-strong -Wformat -Werror=format-security -c gnAlignedSequences.cpp -o gnAlignedSequences.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -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 -fstack-protector-strong -Wformat -Werror=format-security -c -o MatchList.lo MatchList.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -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 -fstack-protector-strong -Wformat -Werror=format-security -c MatchList.cpp -fPIC -DPIC -o .libs/MatchList.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -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 -fstack-protector-strong -Wformat -Werror=format-security -c MatchList.cpp -o MatchList.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -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 -fstack-protector-strong -Wformat -Werror=format-security -c -o Aligner.lo Aligner.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -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 -fstack-protector-strong -Wformat -Werror=format-security -c Aligner.cpp -fPIC -DPIC -o .libs/Aligner.o In file included from /usr/include/c++/5/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++/5/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.. -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 -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.. -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 -fstack-protector-strong -Wformat -Werror=format-security -c -o Islands.lo Islands.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -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 -fstack-protector-strong -Wformat -Werror=format-security -c Islands.cpp -fPIC -DPIC -o .libs/Islands.o In file included from /usr/include/c++/5/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++/5/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.. -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 -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.. -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 -fstack-protector-strong -Wformat -Werror=format-security -c -o MaskedMemHash.lo MaskedMemHash.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -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 -fstack-protector-strong -Wformat -Werror=format-security -c MaskedMemHash.cpp -fPIC -DPIC -o .libs/MaskedMemHash.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -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 -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.. -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 -fstack-protector-strong -Wformat -Werror=format-security -c -o GappedAlignment.lo GappedAlignment.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -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 -fstack-protector-strong -Wformat -Werror=format-security -c GappedAlignment.cpp -fPIC -DPIC -o .libs/GappedAlignment.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -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 -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.. -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 -fstack-protector-strong -Wformat -Werror=format-security -c -o MuscleInterface.lo MuscleInterface.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -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 -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:21, 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.. -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 -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.. -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 -fstack-protector-strong -Wformat -Werror=format-security -c -o PhyloTree.lo PhyloTree.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -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 -fstack-protector-strong -Wformat -Werror=format-security -c PhyloTree.cpp -fPIC -DPIC -o .libs/PhyloTree.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -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 -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.. -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 -fstack-protector-strong -Wformat -Werror=format-security -c -o RepeatMatchList.lo RepeatMatchList.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -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 -fstack-protector-strong -Wformat -Werror=format-security -c RepeatMatchList.cpp -fPIC -DPIC -o .libs/RepeatMatchList.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -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 -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.. -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 -fstack-protector-strong -Wformat -Werror=format-security -c -o RepeatMatch.lo RepeatMatch.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -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 -fstack-protector-strong -Wformat -Werror=format-security -c RepeatMatch.cpp -fPIC -DPIC -o .libs/RepeatMatch.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -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 -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.. -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 -fstack-protector-strong -Wformat -Werror=format-security -c -o Backbone.lo Backbone.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -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 -fstack-protector-strong -Wformat -Werror=format-security -c Backbone.cpp -fPIC -DPIC -o .libs/Backbone.o In file included from /usr/include/c++/5/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++/5/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.. -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 -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.. -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 -fstack-protector-strong -Wformat -Werror=format-security -c -o PairwiseMatchFinder.lo PairwiseMatchFinder.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -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 -fstack-protector-strong -Wformat -Werror=format-security -c PairwiseMatchFinder.cpp -fPIC -DPIC -o .libs/PairwiseMatchFinder.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -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 -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.. -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 -fstack-protector-strong -Wformat -Werror=format-security -c -o ProgressiveAligner.lo ProgressiveAligner.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -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 -fstack-protector-strong -Wformat -Werror=format-security -c ProgressiveAligner.cpp -fPIC -DPIC -o .libs/ProgressiveAligner.o In file included from /usr/include/c++/5/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++/5/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.. -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 -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.. -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 -fstack-protector-strong -Wformat -Werror=format-security -c -o SuperInterval.lo SuperInterval.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -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 -fstack-protector-strong -Wformat -Werror=format-security -c SuperInterval.cpp -fPIC -DPIC -o .libs/SuperInterval.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -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 -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.. -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 -fstack-protector-strong -Wformat -Werror=format-security -c -o GreedyBreakpointElimination.lo GreedyBreakpointElimination.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -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 -fstack-protector-strong -Wformat -Werror=format-security -c GreedyBreakpointElimination.cpp -fPIC -DPIC -o .libs/GreedyBreakpointElimination.o In file included from /usr/include/c++/5/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++/5/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.. -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 -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.. -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 -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.. -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 -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.. -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 -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.. -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 -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.. -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 -fstack-protector-strong -Wformat -Werror=format-security -c HomologyHMM/homology.cc -fPIC -DPIC -o .libs/homology.o In file included from /usr/include/c++/5/ext/hash_map:60:0, from HomologyHMM/dptables.h:43, from HomologyHMM/homology.h:27, from HomologyHMM/homology.cc:24: /usr/include/c++/5/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.. -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 -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.. -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 -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.. -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 -fstack-protector-strong -Wformat -Werror=format-security -c HomologyHMM/homologymain.cc -fPIC -DPIC -o .libs/homologymain.o In file included from /usr/include/c++/5/ext/hash_map:60:0, from HomologyHMM/dptables.h:43, from HomologyHMM/homology.h:27, from HomologyHMM/homologymain.cc:21: /usr/include/c++/5/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.. -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 -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.. -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 -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.. -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 -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.. -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 -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.. -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 -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.. -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 -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.. -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 -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.. -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 -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.. -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 -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/x86_64-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.. -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 -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.. -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 -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.. -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 -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.. -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 -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.. -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 -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.. -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 -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.. -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 -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.. -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 -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.. -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 -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.. -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 -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.. -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 -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.. -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 -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.. -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 -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.. -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 -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.. -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 -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.. -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 -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.. -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 -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.. -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 -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.. -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 -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.. -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 -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.. -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 -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.. -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 -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.. -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 -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.. -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 -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.. -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 -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 -fstack-protector-strong -Wformat -Werror=format-security -version-info 1:0:0 -Wl,-Bsymbolic-functions -Wl,-z,relro -o libMems-1.6.la -rpath /usr/lib/x86_64-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/x86_64-linux-gnu/5/../../../x86_64-linux-gnu/crti.o /usr/lib/gcc/x86_64-linux-gnu/5/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/x86_64-linux-gnu/5 -L/usr/lib/gcc/x86_64-linux-gnu/5/../../../x86_64-linux-gnu -L/usr/lib/gcc/x86_64-linux-gnu/5/../../../../lib -L/lib/x86_64-linux-gnu -L/lib/../lib -L/usr/lib/x86_64-linux-gnu -L/usr/lib/../lib -L/usr/lib/gcc/x86_64-linux-gnu/5/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/x86_64-linux-gnu/5/crtendS.o /usr/lib/gcc/x86_64-linux-gnu/5/../../../x86_64-linux-gnu/crtn.o -O2 -O2 -Wl,-Bsymbolic-functions -Wl,-z -Wl,relro -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 '/«BUILDDIR»/libmems-1.6.0+4725/libMems' make[3]: Entering directory '/«BUILDDIR»/libmems-1.6.0+4725' make[3]: Leaving directory '/«BUILDDIR»/libmems-1.6.0+4725' make[2]: Leaving directory '/«BUILDDIR»/libmems-1.6.0+4725' make[1]: Leaving directory '/«BUILDDIR»/libmems-1.6.0+4725' dh_auto_test make -j1 check make[1]: Entering directory '/«BUILDDIR»/libmems-1.6.0+4725' Making check in libMems make[2]: Entering directory '/«BUILDDIR»/libmems-1.6.0+4725/libMems' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/«BUILDDIR»/libmems-1.6.0+4725/libMems' make[2]: Entering directory '/«BUILDDIR»/libmems-1.6.0+4725' make[2]: Leaving directory '/«BUILDDIR»/libmems-1.6.0+4725' make[1]: Leaving directory '/«BUILDDIR»/libmems-1.6.0+4725' fakeroot debian/rules binary dh binary --with autoreconf dh_testroot dh_prep dh_auto_install make -j1 install DESTDIR=/«BUILDDIR»/libmems-1.6.0\+4725/debian/tmp AM_UPDATE_INFO_DIR=no make[1]: Entering directory '/«BUILDDIR»/libmems-1.6.0+4725' Making install in libMems make[2]: Entering directory '/«BUILDDIR»/libmems-1.6.0+4725/libMems' make[3]: Entering directory '/«BUILDDIR»/libmems-1.6.0+4725/libMems' /bin/mkdir -p '/«BUILDDIR»/libmems-1.6.0+4725/debian/tmp/usr/lib/x86_64-linux-gnu' /bin/bash ../libtool --mode=install /usr/bin/install -c libMems-1.6.la '/«BUILDDIR»/libmems-1.6.0+4725/debian/tmp/usr/lib/x86_64-linux-gnu' libtool: install: /usr/bin/install -c .libs/libMems-1.6.so.1.0.0 /«BUILDDIR»/libmems-1.6.0+4725/debian/tmp/usr/lib/x86_64-linux-gnu/libMems-1.6.so.1.0.0 libtool: install: (cd /«BUILDDIR»/libmems-1.6.0+4725/debian/tmp/usr/lib/x86_64-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 /«BUILDDIR»/libmems-1.6.0+4725/debian/tmp/usr/lib/x86_64-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 /«BUILDDIR»/libmems-1.6.0+4725/debian/tmp/usr/lib/x86_64-linux-gnu/libMems-1.6.la libtool: install: /usr/bin/install -c .libs/libMems-1.6.a /«BUILDDIR»/libmems-1.6.0+4725/debian/tmp/usr/lib/x86_64-linux-gnu/libMems-1.6.a libtool: install: chmod 644 /«BUILDDIR»/libmems-1.6.0+4725/debian/tmp/usr/lib/x86_64-linux-gnu/libMems-1.6.a libtool: install: ranlib /«BUILDDIR»/libmems-1.6.0+4725/debian/tmp/usr/lib/x86_64-linux-gnu/libMems-1.6.a libtool: install: warning: remember to run `libtool --finish /usr/lib/x86_64-linux-gnu' /bin/mkdir -p '/«BUILDDIR»/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 '/«BUILDDIR»/libmems-1.6.0+4725/debian/tmp/usr/include/libMems-1.6/libMems/dmSML' /bin/mkdir -p '/«BUILDDIR»/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 '/«BUILDDIR»/libmems-1.6.0+4725/debian/tmp/usr/include/libMems-1.6/libMems/HomologyHMM' /bin/mkdir -p '/«BUILDDIR»/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 '/«BUILDDIR»/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 '/«BUILDDIR»/libmems-1.6.0+4725/debian/tmp/usr/include/libMems-1.6/libMems' make[3]: Leaving directory '/«BUILDDIR»/libmems-1.6.0+4725/libMems' make[2]: Leaving directory '/«BUILDDIR»/libmems-1.6.0+4725/libMems' make[2]: Entering directory '/«BUILDDIR»/libmems-1.6.0+4725' make[3]: Entering directory '/«BUILDDIR»/libmems-1.6.0+4725' make[3]: Nothing to be done for 'install-exec-am'. /bin/mkdir -p '/«BUILDDIR»/libmems-1.6.0+4725/debian/tmp/usr/lib/x86_64-linux-gnu/pkgconfig' /usr/bin/install -c -m 644 libMems-1.6.pc '/«BUILDDIR»/libmems-1.6.0+4725/debian/tmp/usr/lib/x86_64-linux-gnu/pkgconfig' make[3]: Leaving directory '/«BUILDDIR»/libmems-1.6.0+4725' make[2]: Leaving directory '/«BUILDDIR»/libmems-1.6.0+4725' make[1]: Leaving directory '/«BUILDDIR»/libmems-1.6.0+4725' debian/rules override_dh_install make[1]: Entering directory '/«BUILDDIR»/libmems-1.6.0+4725' dh_install d-shlibmove --commit \ --multiarch \ --v5 \ --devunversioned \ --override s/libGenome-1.3-0-dev/libgenome-1.3-dev/ \ --override s/libMUSCLE-3.7-1-dev/libmuscle-3.7-dev/ \ --exclude-la \ --movedev debian/tmp/usr/include/* usr/include \ --movedev "debian/tmp/usr/lib/*/pkgconfig/*.pc" usr/lib/x86_64-linux-gnu/pkgconfig \ debian/tmp/usr/lib/*/*.so Library package automatic movement utility --> libboost-filesystem1.58-dev package exists. --> libboost-iostreams1.58-dev package exists. --> libboost-system1.58-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/x86_64-linux-gnu install -d -m 755 debian/libmems-1.6-1v5/usr/lib/x86_64-linux-gnu mv debian/tmp/usr/lib/x86_64-linux-gnu/libMems-1.6.a debian/libmems-1.6-dev/usr/lib/x86_64-linux-gnu mv debian/tmp/usr/lib/x86_64-linux-gnu/libMems-1.6.so debian/libmems-1.6-dev/usr/lib/x86_64-linux-gnu mv /«BUILDDIR»/libmems-1.6.0+4725/debian/tmp/usr/lib/x86_64-linux-gnu/libMems-1.6.so.1 debian/libmems-1.6-1v5/usr/lib/x86_64-linux-gnu mv /«BUILDDIR»/libmems-1.6.0+4725/debian/tmp/usr/lib/x86_64-linux-gnu/libMems-1.6.so.1.0.0 debian/libmems-1.6-1v5/usr/lib/x86_64-linux-gnu PKGDEV=libmems-1.6-dev PKGSHL=libmems-1.6-1v5 install -d -m 755 debian/libmems-1.6-dev/usr/include mv debian/tmp/usr/include/libMems-1.6 debian/libmems-1.6-dev/usr/include install -d -m 755 debian/libmems-1.6-dev/usr/lib/x86_64-linux-gnu/pkgconfig mv debian/tmp/usr/lib/*/pkgconfig/*.pc debian/libmems-1.6-dev/usr/lib/x86_64-linux-gnu/pkgconfig make[1]: Leaving directory '/«BUILDDIR»/libmems-1.6.0+4725' dh_installdocs dh_installchangelogs dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_strip 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 amd64: 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: `/«BUILDDIR»/libmems-1.6.0+4725/debian/libmems-1.6-dev-dbgsym': No such file or directory /usr/bin/pkg_create_dbgsym: nothing in /«BUILDDIR»/libmems-1.6.0+4725/debian/libmems-1.6-dev-dbgsym and no dbgdepends, ignoring Using buildid for compat level >= 9 dpkg-gencontrol: warning: -is is deprecated; it is without effect dpkg-gencontrol: warning: -ip is deprecated; it is without effect 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 dh_shlibdeps dh_installdeb dh_gencontrol 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 amd64: 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+4725-2_amd64.ddeb dpkg-deb: building package 'libmems-1.6-1v5-dbgsym' in '../libmems-1.6-1v5-dbgsym_1.6.0+4725-2_amd64.ddeb'. dh_gencontrol debug symbol wrapper: dpkg-distaddfile libmems-1.6-1v5-dbgsym_1.6.0+4725-2_amd64.ddeb libs extra dpkg-distaddfile: warning: File::FcntlLock not available; using flock which is not NFS-safe dh_md5sums dh_builddeb INFO: pkgstriptranslations version 122 pkgstriptranslations: processing libmems-1.6-dev (in debian/libmems-1.6-dev); 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: PNG optimization for package libmems-1.6-dev took 0 s dpkg-deb: building package 'libmems-1.6-dev' in '../libmems-1.6-dev_1.6.0+4725-2_amd64.deb'. INFO: pkgstriptranslations version 122 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-1.6-1v5/DEBIAN/control, package libmems-1.6-1v5, directory debian/libmems-1.6-1v5 pkgstripfiles: PNG optimization for package libmems-1.6-1v5 took 0 s dpkg-deb: building package 'libmems-1.6-1v5' in '../libmems-1.6-1v5_1.6.0+4725-2_amd64.deb'. dpkg-genchanges -b -mLaunchpad Build Daemon >../libmems_1.6.0+4725-2_amd64.changes dpkg-genchanges: binary-only upload (no source code included) dpkg-source --after-build libmems-1.6.0+4725 dpkg-buildpackage: binary-only upload (no source included) ──────────────────────────────────────────────────────────────────────────────── Build finished at 20151105-1654 Finished ──────── I: Built successfully ┌──────────────────────────────────────────────────────────────────────────────┐ │ Post Build Chroot │ └──────────────────────────────────────────────────────────────────────────────┘ ┌──────────────────────────────────────────────────────────────────────────────┐ │ Changes │ └──────────────────────────────────────────────────────────────────────────────┘ libmems_1.6.0+4725-2_amd64.changes: ─────────────────────────────────── Format: 1.8 Date: Tue, 18 Aug 2015 23:39:39 +0200 Source: libmems Binary: libmems-1.6-dev libmems-1.6-1v5 Architecture: amd64 Version: 1.6.0+4725-2 Distribution: xenial-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: 795344 Changes: libmems (1.6.0+4725-2) unstable; urgency=medium . * Add Multi-Arch: same and Pre-Depends: ${misc:Pre-Depends} according to https://wiki.debian.org/Multiarch/Implementation * Rename library packages for g++5 ABI transition. * properly link to its dependencies Closes: #795344 Checksums-Sha1: b9d387dace8a13dba722e1ebfd3f1170dc430658 4688850 libmems-1.6-1v5-dbgsym_1.6.0+4725-2_amd64.ddeb fdd1f20e30d6d3891b742c82a0240764a0fbd82c 666366 libmems-1.6-1v5_1.6.0+4725-2_amd64.deb 999f757640bf9ca8785d7be2c3987b1572a680ea 967280 libmems-1.6-dev_1.6.0+4725-2_amd64.deb Checksums-Sha256: b0e54dbc32cb7d92b86cdecb7ec35994a37703bd20c6b72dbc7ba42b64803027 4688850 libmems-1.6-1v5-dbgsym_1.6.0+4725-2_amd64.ddeb 3addc7c5c4c5bcfe736acb9092b0e86c7aebae1e57f90266fd930f43c3428719 666366 libmems-1.6-1v5_1.6.0+4725-2_amd64.deb d26586dc1f4f88ec71ea010c6b43bbb4e3274576558e82f76b00092c5633483a 967280 libmems-1.6-dev_1.6.0+4725-2_amd64.deb Files: ff12415e51ce1bad12cdde46e79e1071 4688850 libs extra libmems-1.6-1v5-dbgsym_1.6.0+4725-2_amd64.ddeb abf9b8baac2c9b3460f50d5c9518921b 666366 libs optional libmems-1.6-1v5_1.6.0+4725-2_amd64.deb ef322e247e34c119531e9632517ab2f7 967280 libdevel optional libmems-1.6-dev_1.6.0+4725-2_amd64.deb ┌──────────────────────────────────────────────────────────────────────────────┐ │ Package contents │ └──────────────────────────────────────────────────────────────────────────────┘ libmems-1.6-1v5_1.6.0+4725-2_amd64.deb ────────────────────────────────────── new debian package, version 2.0. size 666366 bytes: control archive=1134 bytes. 1296 bytes, 25 lines control 238 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+4725-2 Architecture: amd64 Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 1998 Depends: libboost-filesystem1.58.0, libboost-iostreams1.58.0, libboost-system1.58.0, libc6 (>= 2.14), libgcc1 (>= 1:4.1.1), 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 2015-11-05 16:54 ./ drwxr-xr-x root/root 0 2015-11-05 16:54 ./usr/ drwxr-xr-x root/root 0 2015-11-05 16:54 ./usr/lib/ drwxr-xr-x root/root 0 2015-11-05 16:54 ./usr/lib/x86_64-linux-gnu/ lrwxrwxrwx root/root 0 2015-11-05 16:54 ./usr/lib/x86_64-linux-gnu/libMems-1.6.so.1 -> libMems-1.6.so.1.0.0 -rw-r--r-- root/root 2029984 2015-11-05 16:54 ./usr/lib/x86_64-linux-gnu/libMems-1.6.so.1.0.0 drwxr-xr-x root/root 0 2015-11-05 16:54 ./usr/share/ drwxr-xr-x root/root 0 2015-11-05 16:54 ./usr/share/doc/ drwxr-xr-x root/root 0 2015-11-05 16:54 ./usr/share/doc/libmems-1.6-1v5/ -rw-r--r-- root/root 334 2015-08-18 21:43 ./usr/share/doc/libmems-1.6-1v5/changelog.Debian.gz -rw-r--r-- root/root 2365 2015-08-18 21:43 ./usr/share/doc/libmems-1.6-1v5/copyright libmems-1.6-dev_1.6.0+4725-2_amd64.deb ────────────────────────────────────── new debian package, version 2.0. size 967280 bytes: control archive=2991 bytes. 1307 bytes, 24 lines control 5744 bytes, 70 lines md5sums Package: libmems-1.6-dev Source: libmems Version: 1.6.0+4725-2 Architecture: amd64 Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 7677 Depends: libmems-1.6-1v5 (= 1.6.0+4725-2), libboost-filesystem1.58-dev, libboost-iostreams1.58-dev, libboost-system1.58-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. . This is the development package containing the statically linked library and the header files. drwxr-xr-x root/root 0 2015-11-05 16:54 ./ drwxr-xr-x root/root 0 2015-11-05 16:54 ./usr/ drwxr-xr-x root/root 0 2015-11-05 16:54 ./usr/include/ drwxr-xr-x root/root 0 2015-11-05 16:54 ./usr/include/libMems-1.6/ drwxr-xr-x root/root 0 2015-11-05 16:54 ./usr/include/libMems-1.6/libMems/ -rw-r--r-- root/root 3614 2015-11-05 16:54 ./usr/include/libMems-1.6/libMems/AbstractGappedAlignment.h -rw-r--r-- root/root 12989 2015-11-05 16:54 ./usr/include/libMems-1.6/libMems/AbstractMatch.h -rw-r--r-- root/root 11670 2015-11-05 16:54 ./usr/include/libMems-1.6/libMems/Aligner.h -rw-r--r-- root/root 8161 2015-11-05 16:54 ./usr/include/libMems-1.6/libMems/Backbone.h -rw-r--r-- root/root 26662 2015-11-05 16:54 ./usr/include/libMems-1.6/libMems/CompactGappedAlignment.h -rw-r--r-- root/root 2075 2015-11-05 16:54 ./usr/include/libMems-1.6/libMems/DNAFileSML.h -rw-r--r-- root/root 1905 2015-11-05 16:54 ./usr/include/libMems-1.6/libMems/DNAMemorySML.h -rw-r--r-- root/root 5031 2015-11-05 16:54 ./usr/include/libMems-1.6/libMems/DenseAbstractMatch.h -rw-r--r-- root/root 10891 2015-11-05 16:54 ./usr/include/libMems-1.6/libMems/DistanceMatrix.h -rw-r--r-- root/root 4590 2015-11-05 16:54 ./usr/include/libMems-1.6/libMems/FileSML.h -rw-r--r-- root/root 5777 2015-11-05 16:54 ./usr/include/libMems-1.6/libMems/Files.h -rw-r--r-- root/root 2513 2015-11-05 16:54 ./usr/include/libMems-1.6/libMems/GappedAligner.h -rw-r--r-- root/root 8478 2015-11-05 16:54 ./usr/include/libMems-1.6/libMems/GappedAlignment.h -rw-r--r-- root/root 29239 2015-11-05 16:54 ./usr/include/libMems-1.6/libMems/GreedyBreakpointElimination.h drwxr-xr-x root/root 0 2015-11-05 16:54 ./usr/include/libMems-1.6/libMems/HomologyHMM/ -rw-r--r-- root/root 20861 2015-11-05 16:54 ./usr/include/libMems-1.6/libMems/HomologyHMM/algebras.h -rw-r--r-- root/root 13161 2015-11-05 16:54 ./usr/include/libMems-1.6/libMems/HomologyHMM/dptables.h -rw-r--r-- root/root 7163 2015-11-05 16:54 ./usr/include/libMems-1.6/libMems/HomologyHMM/homology.h -rw-r--r-- root/root 7759 2015-11-05 16:54 ./usr/include/libMems-1.6/libMems/HomologyHMM/parameters.h -rw-r--r-- root/root 9786 2015-11-05 16:54 ./usr/include/libMems-1.6/libMems/HybridAbstractMatch.h -rw-r--r-- root/root 30049 2015-11-05 16:54 ./usr/include/libMems-1.6/libMems/Interval.h -rw-r--r-- root/root 27519 2015-11-05 16:54 ./usr/include/libMems-1.6/libMems/IntervalList.h -rw-r--r-- root/root 13712 2015-11-05 16:54 ./usr/include/libMems-1.6/libMems/Islands.h -rw-r--r-- root/root 1825 2015-11-05 16:54 ./usr/include/libMems-1.6/libMems/LCB.h -rw-r--r-- root/root 1416 2015-11-05 16:54 ./usr/include/libMems-1.6/libMems/MaskedMemHash.h -rw-r--r-- root/root 926 2015-11-05 16:54 ./usr/include/libMems-1.6/libMems/Match.h -rw-r--r-- root/root 13449 2015-11-05 16:54 ./usr/include/libMems-1.6/libMems/MatchFinder.h -rw-r--r-- root/root 4728 2015-11-05 16:54 ./usr/include/libMems-1.6/libMems/MatchHashEntry.h -rw-r--r-- root/root 22769 2015-11-05 16:54 ./usr/include/libMems-1.6/libMems/MatchList.h -rw-r--r-- root/root 4377 2015-11-05 16:54 ./usr/include/libMems-1.6/libMems/MatchProjectionAdapter.h -rw-r--r-- root/root 4016 2015-11-05 16:54 ./usr/include/libMems-1.6/libMems/Matrix.h -rw-r--r-- root/root 7182 2015-11-05 16:54 ./usr/include/libMems-1.6/libMems/MemHash.h -rw-r--r-- root/root 1543 2015-11-05 16:54 ./usr/include/libMems-1.6/libMems/Memory.h -rw-r--r-- root/root 1988 2015-11-05 16:54 ./usr/include/libMems-1.6/libMems/MemorySML.h -rw-r--r-- root/root 5235 2015-11-05 16:54 ./usr/include/libMems-1.6/libMems/MuscleInterface.h -rw-r--r-- root/root 4605 2015-11-05 16:54 ./usr/include/libMems-1.6/libMems/NumericMatrix.h -rw-r--r-- root/root 3674 2015-11-05 16:54 ./usr/include/libMems-1.6/libMems/PairwiseMatchAdapter.h -rw-r--r-- root/root 1013 2015-11-05 16:54 ./usr/include/libMems-1.6/libMems/PairwiseMatchFinder.h -rw-r--r-- root/root 10333 2015-11-05 16:54 ./usr/include/libMems-1.6/libMems/PhyloTree.h -rw-r--r-- root/root 24671 2015-11-05 16:54 ./usr/include/libMems-1.6/libMems/ProgressiveAligner.h -rw-r--r-- root/root 1428 2015-11-05 16:54 ./usr/include/libMems-1.6/libMems/RepeatHash.h -rw-r--r-- root/root 1453 2015-11-05 16:54 ./usr/include/libMems-1.6/libMems/RepeatMatch.h -rw-r--r-- root/root 2195 2015-11-05 16:54 ./usr/include/libMems-1.6/libMems/RepeatMatchList.h -rw-r--r-- root/root 10167 2015-11-05 16:54 ./usr/include/libMems-1.6/libMems/Scoring.h -rw-r--r-- root/root 9694 2015-11-05 16:54 ./usr/include/libMems-1.6/libMems/SeedMasks.h -rw-r--r-- root/root 2483 2015-11-05 16:54 ./usr/include/libMems-1.6/libMems/SeedOccurrenceList.h -rw-r--r-- root/root 4383 2015-11-05 16:54 ./usr/include/libMems-1.6/libMems/SlotAllocator.h -rw-r--r-- root/root 12250 2015-11-05 16:54 ./usr/include/libMems-1.6/libMems/SortedMerList.h -rw-r--r-- root/root 7625 2015-11-05 16:54 ./usr/include/libMems-1.6/libMems/SparseAbstractMatch.h -rw-r--r-- root/root 3100 2015-11-05 16:54 ./usr/include/libMems-1.6/libMems/SubstitutionMatrix.h -rw-r--r-- root/root 1879 2015-11-05 16:54 ./usr/include/libMems-1.6/libMems/SuperInterval.h -rw-r--r-- root/root 4590 2015-11-05 16:54 ./usr/include/libMems-1.6/libMems/TreeUtilities.h -rw-r--r-- root/root 7254 2015-11-05 16:54 ./usr/include/libMems-1.6/libMems/UngappedLocalAlignment.h -rw-r--r-- root/root 1214 2015-11-05 16:54 ./usr/include/libMems-1.6/libMems/configuration.h drwxr-xr-x root/root 0 2015-11-05 16:54 ./usr/include/libMems-1.6/libMems/dmSML/ -rw-r--r-- root/root 381 2015-11-05 16:54 ./usr/include/libMems-1.6/libMems/dmSML/aPOSIXaio.h -rw-r--r-- root/root 328 2015-11-05 16:54 ./usr/include/libMems-1.6/libMems/dmSML/alibc.h -rw-r--r-- root/root 387 2015-11-05 16:54 ./usr/include/libMems-1.6/libMems/dmSML/alinuxaio.h -rw-r--r-- root/root 4402 2015-11-05 16:54 ./usr/include/libMems-1.6/libMems/dmSML/asyncio.h -rw-r--r-- root/root 377 2015-11-05 16:54 ./usr/include/libMems-1.6/libMems/dmSML/awin32aio.h -rw-r--r-- root/root 7161 2015-11-05 16:54 ./usr/include/libMems-1.6/libMems/dmSML/buffer.h -rw-r--r-- root/root 4979 2015-11-05 16:54 ./usr/include/libMems-1.6/libMems/dmSML/dmsort.h -rw-r--r-- root/root 2197 2015-11-05 16:54 ./usr/include/libMems-1.6/libMems/dmSML/sml.h -rw-r--r-- root/root 2438 2015-11-05 16:54 ./usr/include/libMems-1.6/libMems/dmSML/sorting.h -rw-r--r-- root/root 393 2015-11-05 16:54 ./usr/include/libMems-1.6/libMems/dmSML/timing.h -rw-r--r-- root/root 731 2015-11-05 16:54 ./usr/include/libMems-1.6/libMems/dmSML/util.h -rw-r--r-- root/root 13038 2015-11-05 16:54 ./usr/include/libMems-1.6/libMems/gnAlignedSequences.h -rw-r--r-- root/root 7484 2015-11-05 16:54 ./usr/include/libMems-1.6/libMems/gnRAWSequence.h -rw-r--r-- root/root 309 2015-11-05 16:54 ./usr/include/libMems-1.6/libMems/twister.h drwxr-xr-x root/root 0 2015-11-05 16:54 ./usr/lib/ drwxr-xr-x root/root 0 2015-11-05 16:54 ./usr/lib/x86_64-linux-gnu/ -rw-r--r-- root/root 7314102 2015-11-05 16:54 ./usr/lib/x86_64-linux-gnu/libMems-1.6.a lrwxrwxrwx root/root 0 2015-11-05 16:54 ./usr/lib/x86_64-linux-gnu/libMems-1.6.so -> libMems-1.6.so.1.0.0 drwxr-xr-x root/root 0 2015-11-05 16:54 ./usr/lib/x86_64-linux-gnu/pkgconfig/ -rw-r--r-- root/root 406 2015-11-05 16:54 ./usr/lib/x86_64-linux-gnu/pkgconfig/libMems-1.6.pc drwxr-xr-x root/root 0 2015-11-05 16:54 ./usr/share/ drwxr-xr-x root/root 0 2015-11-05 16:54 ./usr/share/doc/ drwxr-xr-x root/root 0 2015-11-05 16:54 ./usr/share/doc/libmems-1.6-dev/ lrwxrwxrwx root/root 0 2015-11-05 16:54 ./usr/share/doc/libmems-1.6-dev/changelog.Debian.gz -> ../libmems-1.6-1v5/changelog.Debian.gz -rw-r--r-- root/root 2365 2015-08-18 21:43 ./usr/share/doc/libmems-1.6-dev/copyright ┌──────────────────────────────────────────────────────────────────────────────┐ │ Post Build │ └──────────────────────────────────────────────────────────────────────────────┘ ┌──────────────────────────────────────────────────────────────────────────────┐ │ Cleanup │ └──────────────────────────────────────────────────────────────────────────────┘ Not removing build depends: as requested Keeping session: ┌──────────────────────────────────────────────────────────────────────────────┐ │ Summary │ └──────────────────────────────────────────────────────────────────────────────┘ Build Architecture: amd64 Build-Space: 277796 Build-Time: 724 Distribution: xenial-proposed Host Architecture: amd64 Install-Time: 21 Job: libmems_1.6.0+4725-2.dsc Machine Architecture: amd64 Package: libmems Package-Time: 746 Source-Version: 1.6.0+4725-2 Space: 277796 Status: successful Version: 1.6.0+4725-2 ──────────────────────────────────────────────────────────────────────────────── Finished at 20151105-1654 Build needed 00:12:26, 277796k disc space RUN: /usr/share/launchpad-buildd/slavebin/scan-for-processes ['scan-for-processes', 'PACKAGEBUILD-8268452'] Scanning for processes to kill in build /home/buildd/build-PACKAGEBUILD-8268452/chroot-autobuild... RUN: /usr/share/launchpad-buildd/slavebin/umount-chroot ['umount-chroot', 'PACKAGEBUILD-8268452'] Unmounting chroot for build PACKAGEBUILD-8268452... RUN: /usr/share/launchpad-buildd/slavebin/remove-build ['remove-build', 'PACKAGEBUILD-8268452'] Removing build PACKAGEBUILD-8268452