RUN: /usr/share/launchpad-buildd/slavebin/slave-prep ['slave-prep'] Forking launchpad-buildd slave process... Kernel version: Linux lcy01-29 4.4.0-45-generic #66-Ubuntu SMP Wed Oct 19 14:12:37 UTC 2016 x86_64 Buildd toolchain package versions: launchpad-buildd_140 python-lpbuildd_140 sbuild_0.67.0-2ubuntu7 bzr-builder_0.7.3+bzr174~ppa13~ubuntu14.10.1 bzr_2.7.0-2ubuntu3 git-build-recipe_0.3.2 git_1:2.7.4-0ubuntu1 dpkg-dev_1.18.4ubuntu1.1 python-debian_0.1.27ubuntu2 qemu-user-static_1:2.5+dfsg-5ubuntu10.5. Syncing the system clock with the buildd NTP service... 3 Nov 23:15:13 ntpdate[1738]: adjust time server 10.211.37.1 offset -0.014327 sec RUN: /usr/share/launchpad-buildd/slavebin/unpack-chroot ['unpack-chroot', 'PACKAGEBUILD-11127343', '/home/buildd/filecache-default/5ce6418ad8acb4cb980a16cd30f1736d3291c7a9'] Unpacking chroot for build PACKAGEBUILD-11127343 RUN: /usr/share/launchpad-buildd/slavebin/mount-chroot ['mount-chroot', 'PACKAGEBUILD-11127343'] Mounting chroot for build PACKAGEBUILD-11127343 RUN: /usr/share/launchpad-buildd/slavebin/override-sources-list ['override-sources-list', 'PACKAGEBUILD-11127343', 'deb http://ftpmaster.internal/ubuntu zesty main universe', 'deb http://ftpmaster.internal/ubuntu zesty-security main universe', 'deb http://ftpmaster.internal/ubuntu zesty-updates main universe', 'deb http://ftpmaster.internal/ubuntu zesty-proposed main universe'] Overriding sources.list in build-PACKAGEBUILD-11127343 RUN: /usr/share/launchpad-buildd/slavebin/update-debian-chroot ['update-debian-chroot', 'PACKAGEBUILD-11127343', 'i386'] Updating debian chroot for build PACKAGEBUILD-11127343 Get:1 http://ftpmaster.internal/ubuntu zesty InRelease [247 kB] Get:2 http://ftpmaster.internal/ubuntu zesty-security InRelease [92.2 kB] Get:3 http://ftpmaster.internal/ubuntu zesty-updates InRelease [92.1 kB] Get:4 http://ftpmaster.internal/ubuntu zesty-proposed InRelease [95.6 kB] Get:5 http://ftpmaster.internal/ubuntu zesty/main i386 Packages [1232 kB] Get:6 http://ftpmaster.internal/ubuntu zesty/main Translation-en [587 kB] Get:7 http://ftpmaster.internal/ubuntu zesty/universe i386 Packages [7819 kB] Get:8 http://ftpmaster.internal/ubuntu zesty/universe Translation-en [4554 kB] Get:9 http://ftpmaster.internal/ubuntu zesty-proposed/main i386 Packages [186 kB] Get:10 http://ftpmaster.internal/ubuntu zesty-proposed/main Translation-en [96.1 kB] Get:11 http://ftpmaster.internal/ubuntu zesty-proposed/universe i386 Packages [488 kB] Get:12 http://ftpmaster.internal/ubuntu zesty-proposed/universe Translation-en [296 kB] Fetched 15.8 MB in 5s (3110 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages were automatically installed and are no longer required: libperl5.22 perl-modules-5.22 Use 'sudo apt autoremove' to remove them. The following NEW packages will be installed: libperl5.24 perl-modules-5.24 The following packages will be upgraded: adduser base-files bash binutils cpp-6 diffutils dmsetup g++-6 gcc-6 gcc-6-base grep libapparmor1 libasan3 libatomic1 libcc1-0 libcilkrts5 libcurl3-gnutls libdevmapper1.02.1 libgcc-6-dev libgcc1 libgomp1 libgssapi-krb5-2 libhogweed4 libitm1 libk5crypto3 libkrb5-3 libkrb5support0 libksba8 libldap-2.4-2 liblzma5 libmpx2 libnettle6 libpng16-16 libquadmath0 libsasl2-2 libsasl2-modules-db libselinux1 libsemanage-common libsemanage1 libsepol1 libslang2 libsqlite3-0 libstdc++-6-dev libstdc++6 libsystemd0 libubsan0 libudev1 linux-libc-dev perl perl-base pinentry-curses systemd systemd-sysv tar tzdata ubuntu-keyring xz-utils 57 upgraded, 2 newly installed, 0 to remove and 0 not upgraded. Need to get 45.2 MB of archives. After this operation, 34.0 MB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu zesty/main i386 base-files i386 9.6ubuntu6 [55.8 kB] Get:2 http://ftpmaster.internal/ubuntu zesty-proposed/main i386 bash i386 4.4-1ubuntu1 [621 kB] Get:3 http://ftpmaster.internal/ubuntu zesty/main i386 diffutils i386 1:3.5-1 [167 kB] Get:4 http://ftpmaster.internal/ubuntu zesty/main i386 grep i386 2.26-1 [158 kB] Get:5 http://ftpmaster.internal/ubuntu zesty/main i386 perl-modules-5.24 all 5.24.1~rc3-3 [2661 kB] Get:6 http://ftpmaster.internal/ubuntu zesty/main i386 libperl5.24 i386 5.24.1~rc3-3 [3094 kB] Get:7 http://ftpmaster.internal/ubuntu zesty/main i386 perl i386 5.24.1~rc3-3 [237 kB] Get:8 http://ftpmaster.internal/ubuntu zesty/main i386 perl-base i386 5.24.1~rc3-3 [1409 kB] Get:9 http://ftpmaster.internal/ubuntu zesty-proposed/main i386 tar i386 1.29b-1.1 [236 kB] Get:10 http://ftpmaster.internal/ubuntu zesty/main i386 libapparmor1 i386 2.10.95-4ubuntu5.2 [31.6 kB] Get:11 http://ftpmaster.internal/ubuntu zesty/main i386 liblzma5 i386 5.2.2-1.2 [98.7 kB] Get:12 http://ftpmaster.internal/ubuntu zesty-proposed/main i386 libselinux1 i386 2.6-1 [73.4 kB] Get:13 http://ftpmaster.internal/ubuntu zesty/main i386 adduser all 3.113+nmu3ubuntu5 [161 kB] Get:14 http://ftpmaster.internal/ubuntu zesty/main i386 systemd i386 231-10 [2324 kB] Get:15 http://ftpmaster.internal/ubuntu zesty/main i386 libsystemd0 i386 231-10 [227 kB] Get:16 http://ftpmaster.internal/ubuntu zesty/main i386 systemd-sysv i386 231-10 [14.3 kB] Get:17 http://ftpmaster.internal/ubuntu zesty-proposed/main i386 libitm1 i386 6.2.0-11ubuntu1 [31.2 kB] Get:18 http://ftpmaster.internal/ubuntu zesty-proposed/main i386 libcc1-0 i386 6.2.0-11ubuntu1 [33.0 kB] Get:19 http://ftpmaster.internal/ubuntu zesty-proposed/main i386 libgomp1 i386 6.2.0-11ubuntu1 [79.9 kB] Get:20 http://ftpmaster.internal/ubuntu zesty-proposed/main i386 libatomic1 i386 6.2.0-11ubuntu1 [9890 B] Get:21 http://ftpmaster.internal/ubuntu zesty-proposed/main i386 libasan3 i386 6.2.0-11ubuntu1 [300 kB] Get:22 http://ftpmaster.internal/ubuntu zesty-proposed/main i386 libubsan0 i386 6.2.0-11ubuntu1 [120 kB] Get:23 http://ftpmaster.internal/ubuntu zesty-proposed/main i386 libcilkrts5 i386 6.2.0-11ubuntu1 [45.8 kB] Get:24 http://ftpmaster.internal/ubuntu zesty-proposed/main i386 libmpx2 i386 6.2.0-11ubuntu1 [12.8 kB] Get:25 http://ftpmaster.internal/ubuntu zesty-proposed/main i386 libquadmath0 i386 6.2.0-11ubuntu1 [205 kB] Get:26 http://ftpmaster.internal/ubuntu zesty-proposed/main i386 gcc-6-base i386 6.2.0-11ubuntu1 [17.4 kB] Get:27 http://ftpmaster.internal/ubuntu zesty-proposed/main i386 libstdc++6 i386 6.2.0-11ubuntu1 [434 kB] Get:28 http://ftpmaster.internal/ubuntu zesty-proposed/main i386 g++-6 i386 6.2.0-11ubuntu1 [7620 kB] Get:29 http://ftpmaster.internal/ubuntu zesty-proposed/main i386 libstdc++-6-dev i386 6.2.0-11ubuntu1 [1445 kB] Get:30 http://ftpmaster.internal/ubuntu zesty-proposed/main i386 libgcc-6-dev i386 6.2.0-11ubuntu1 [2306 kB] Get:31 http://ftpmaster.internal/ubuntu zesty-proposed/main i386 gcc-6 i386 6.2.0-11ubuntu1 [7364 kB] Get:32 http://ftpmaster.internal/ubuntu zesty-proposed/main i386 cpp-6 i386 6.2.0-11ubuntu1 [6821 kB] Get:33 http://ftpmaster.internal/ubuntu zesty-proposed/main i386 libgcc1 i386 1:6.2.0-11ubuntu1 [48.0 kB] Get:34 http://ftpmaster.internal/ubuntu zesty-proposed/main i386 binutils i386 2.27-9ubuntu1 [2504 kB] Get:35 http://ftpmaster.internal/ubuntu zesty/main i386 libsepol1 i386 2.6-1 [240 kB] Get:36 http://ftpmaster.internal/ubuntu zesty-proposed/main i386 libsemanage-common all 2.6-1 [6832 B] Get:37 http://ftpmaster.internal/ubuntu zesty-proposed/main i386 libsemanage1 i386 2.6-1 [89.9 kB] Get:38 http://ftpmaster.internal/ubuntu zesty/main i386 libudev1 i386 231-10 [60.3 kB] Get:39 http://ftpmaster.internal/ubuntu zesty/main i386 ubuntu-keyring all 2016.10.27 [16.6 kB] Get:40 http://ftpmaster.internal/ubuntu zesty/main i386 tzdata all 2016h-1 [169 kB] Get:41 http://ftpmaster.internal/ubuntu zesty/main i386 libdevmapper1.02.1 i386 2:1.02.133-1ubuntu1 [172 kB] Get:42 http://ftpmaster.internal/ubuntu zesty/main i386 dmsetup i386 2:1.02.133-1ubuntu1 [79.6 kB] Get:43 http://ftpmaster.internal/ubuntu zesty/main i386 libhogweed4 i386 3.3-1 [137 kB] Get:44 http://ftpmaster.internal/ubuntu zesty/main i386 libnettle6 i386 3.3-1 [109 kB] Get:45 http://ftpmaster.internal/ubuntu zesty/main i386 libksba8 i386 1.3.5-2 [99.9 kB] Get:46 http://ftpmaster.internal/ubuntu zesty-proposed/main i386 libsasl2-modules-db i386 2.1.27~72-g88d82a3+dfsg-1 [16.0 kB] Get:47 http://ftpmaster.internal/ubuntu zesty-proposed/main i386 libsasl2-2 i386 2.1.27~72-g88d82a3+dfsg-1 [52.3 kB] Get:48 http://ftpmaster.internal/ubuntu zesty/main i386 libldap-2.4-2 i386 2.4.42+dfsg-2ubuntu5 [173 kB] Get:49 http://ftpmaster.internal/ubuntu zesty-proposed/main i386 libslang2 i386 2.3.1-4ubuntu1 [423 kB] Get:50 http://ftpmaster.internal/ubuntu zesty-proposed/main i386 libsqlite3-0 i386 3.15.0-1 [516 kB] Get:51 http://ftpmaster.internal/ubuntu zesty/main i386 pinentry-curses i386 0.9.7-6 [32.7 kB] Get:52 http://ftpmaster.internal/ubuntu zesty/main i386 xz-utils i386 5.2.2-1.2 [86.3 kB] Get:53 http://ftpmaster.internal/ubuntu zesty-proposed/main i386 libgssapi-krb5-2 i386 1.15~beta1-1 [129 kB] Get:54 http://ftpmaster.internal/ubuntu zesty-proposed/main i386 libkrb5-3 i386 1.15~beta1-1 [299 kB] Get:55 http://ftpmaster.internal/ubuntu zesty-proposed/main i386 libkrb5support0 i386 1.15~beta1-1 [33.7 kB] Get:56 http://ftpmaster.internal/ubuntu zesty-proposed/main i386 libk5crypto3 i386 1.15~beta1-1 [87.4 kB] Get:57 http://ftpmaster.internal/ubuntu zesty-proposed/main i386 libcurl3-gnutls i386 7.50.1-1ubuntu2 [208 kB] Get:58 http://ftpmaster.internal/ubuntu zesty-proposed/main i386 libpng16-16 i386 1.6.26-1 [182 kB] Get:59 http://ftpmaster.internal/ubuntu zesty-proposed/main i386 linux-libc-dev i386 4.8.0-27.29 [856 kB] debconf: delaying package configuration, since apt-utils is not installed 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Universal Time is now: Thu Nov 3 23:15:58 UTC 2016. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up systemd-sysv (231-10) ... Setting up libubsan0:i386 (6.2.0-11ubuntu1) ... Setting up libsasl2-modules-db:i386 (2.1.27~72-g88d82a3+dfsg-1) ... Setting up linux-libc-dev:i386 (4.8.0-27.29) ... Setting up libsasl2-2:i386 (2.1.27~72-g88d82a3+dfsg-1) ... Setting up libksba8:i386 (1.3.5-2) ... Setting up libdevmapper1.02.1:i386 (2:1.02.133-1ubuntu1) ... Setting up libkrb5support0:i386 (1.15~beta1-1) ... Setting up libhogweed4:i386 (3.3-1) ... Setting up perl (5.24.1~rc3-3) ... Installing new version of config file /etc/perl/sitecustomize.pl ... Setting up libmpx2:i386 (6.2.0-11ubuntu1) ... Processing triggers for libc-bin (2.24-3ubuntu1) ... Setting up libldap-2.4-2:i386 (2.4.42+dfsg-2ubuntu5) ... Setting up xz-utils (5.2.2-1.2) ... Setting up libsqlite3-0:i386 (3.15.0-1) ... Setting up dmsetup (2:1.02.133-1ubuntu1) ... Setting up pinentry-curses (0.9.7-6) ... Setting up binutils (2.27-9ubuntu1) ... Setting up cpp-6 (6.2.0-11ubuntu1) ... Setting up libslang2:i386 (2.3.1-4ubuntu1) ... Setting up libitm1:i386 (6.2.0-11ubuntu1) ... Setting up libk5crypto3:i386 (1.15~beta1-1) ... Setting up libgcc-6-dev:i386 (6.2.0-11ubuntu1) ... Setting up libstdc++-6-dev:i386 (6.2.0-11ubuntu1) ... Setting up gcc-6 (6.2.0-11ubuntu1) ... Setting up g++-6 (6.2.0-11ubuntu1) ... Setting up libkrb5-3:i386 (1.15~beta1-1) ... Setting up libgssapi-krb5-2:i386 (1.15~beta1-1) ... Setting up libcurl3-gnutls:i386 (7.50.1-1ubuntu2) ... Processing triggers for libc-bin (2.24-3ubuntu1) ... RUN: /usr/share/launchpad-buildd/slavebin/sbuild-package ['sbuild-package', 'PACKAGEBUILD-11127343', 'i386', 'zesty-proposed', '-c', 'chroot:autobuild', '--arch=i386', '--dist=zesty-proposed', '--purge=never', '--nolog', 'hisat2_2.0.4-2.dsc'] Initiating build PACKAGEBUILD-11127343 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 4.4.0-45-generic #66-Ubuntu SMP Wed Oct 19 14:12:37 UTC 2016 i686 sbuild (Debian sbuild) 0.67.0 (26 Dec 2015) on lcy01-29.buildd +==============================================================================+ | hisat2 2.0.4-2 (i386) 03 Nov 2016 23:16 | +==============================================================================+ Package: hisat2 Version: 2.0.4-2 Source Version: 2.0.4-2 Distribution: zesty-proposed Machine Architecture: amd64 Host Architecture: i386 Build Architecture: i386 I: NOTICE: Log filtering will replace 'build/hisat2-l8ZISh/hisat2-2.0.4' with '<>' I: NOTICE: Log filtering will replace 'build/hisat2-l8ZISh' with '<>' I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-11127343/chroot-autobuild' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- hisat2_2.0.4-2.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 '/<>/resolver-T4fAMj/apt_archive/sbuild-build-depends-core-dummy.deb'. Ign:1 copy:/<>/resolver-T4fAMj/apt_archive ./ InRelease Get:2 copy:/<>/resolver-T4fAMj/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-T4fAMj/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-T4fAMj/apt_archive ./ Sources [214 B] Get:5 copy:/<>/resolver-T4fAMj/apt_archive ./ Packages [526 B] Fetched 2859 B in 0s (153 kB/s) Reading package lists... Reading package lists... +------------------------------------------------------------------------------+ | Install core build dependencies (apt-based resolver) | +------------------------------------------------------------------------------+ Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following packages were automatically installed and are no longer required: libperl5.22 perl-modules-5.22 Use 'sudo apt autoremove' to remove them. The following NEW packages will be installed: sbuild-build-depends-core-dummy 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 770 B of archives. After this operation, 0 B of additional disk space will be used. Get:1 copy:/<>/resolver-T4fAMj/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [770 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 770 B in 0s (0 B/s) Selecting previously unselected package sbuild-build-depends-core-dummy. (Reading database ... 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Merged Build-Depends: debhelper (>= 9), help2man, pandoc, python Filtered Build-Depends: debhelper (>= 9), help2man, pandoc, python dpkg-deb: building package 'sbuild-build-depends-hisat2-dummy' in '/<>/resolver-EyGw4a/apt_archive/sbuild-build-depends-hisat2-dummy.deb'. Ign:1 copy:/<>/resolver-EyGw4a/apt_archive ./ InRelease Get:2 copy:/<>/resolver-EyGw4a/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-EyGw4a/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-EyGw4a/apt_archive ./ Sources [226 B] Get:5 copy:/<>/resolver-EyGw4a/apt_archive ./ Packages [541 B] Fetched 2886 B in 0s (188 kB/s) Reading package lists... Reading package lists... +------------------------------------------------------------------------------+ | Install hisat2 build dependencies (apt-based resolver) | +------------------------------------------------------------------------------+ Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following packages were automatically installed and are no longer required: libperl5.22 perl-modules-5.22 Use 'sudo apt autoremove' to remove them. The following additional packages will be installed: autoconf automake autopoint autotools-dev bsdmainutils debhelper dh-autoreconf dh-strip-nondeterminism file gettext gettext-base groff-base help2man intltool-debian libarchive-zip-perl libcroco3 libexpat1 libfile-stripnondeterminism-perl libglib2.0-0 libicu57 liblocale-gettext-perl liblua5.1-0 libluajit-5.1-2 libluajit-5.1-common libmagic1 libpipeline1 libpython-stdlib libpython2.7-minimal libpython2.7-stdlib libsigsegv2 libtimedate-perl libtool libunistring0 libxml2 libyaml-0-2 m4 man-db mime-support pandoc pandoc-data po-debconf python python-minimal python2.7 python2.7-minimal Suggested packages: autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois vacation dh-make gettext-doc libasprintf-dev libgettextpo-dev groff libtool-doc gfortran | fortran95-compiler gcj-jdk less www-browser texlive-latex-recommended texlive-xetex texlive-luatex pandoc-citeproc texlive-latex-extra wkhtmltopdf libmail-box-perl python-doc python-tk python2.7-doc binfmt-support Recommended packages: curl | wget | lynx-cur libglib2.0-data shared-mime-info xdg-user-dirs libltdl-dev xml-core libmail-sendmail-perl The following NEW packages will be installed: autoconf automake autopoint autotools-dev bsdmainutils debhelper dh-autoreconf dh-strip-nondeterminism file gettext gettext-base groff-base help2man intltool-debian libarchive-zip-perl libcroco3 libexpat1 libfile-stripnondeterminism-perl libglib2.0-0 libicu57 liblocale-gettext-perl liblua5.1-0 libluajit-5.1-2 libluajit-5.1-common libmagic1 libpipeline1 libpython-stdlib libpython2.7-minimal libpython2.7-stdlib libsigsegv2 libtimedate-perl libtool libunistring0 libxml2 libyaml-0-2 m4 man-db mime-support pandoc pandoc-data po-debconf python python-minimal python2.7 python2.7-minimal sbuild-build-depends-hisat2-dummy 0 upgraded, 46 newly installed, 0 to remove and 0 not upgraded. Need to get 28.4 MB of archives. After this operation, 128 MB of additional disk space will be used. Get:1 copy:/<>/resolver-EyGw4a/apt_archive ./ sbuild-build-depends-hisat2-dummy 0.invalid.0 [788 B] Get:2 http://ftpmaster.internal/ubuntu zesty/main i386 liblocale-gettext-perl i386 1.07-3build1 [17.2 kB] Get:3 http://ftpmaster.internal/ubuntu zesty/main i386 groff-base i386 1.22.3-8 [1150 kB] Get:4 http://ftpmaster.internal/ubuntu zesty/main i386 bsdmainutils i386 9.0.6ubuntu3 [175 kB] Get:5 http://ftpmaster.internal/ubuntu zesty/main i386 libpipeline1 i386 1.4.1-2 [26.5 kB] Get:6 http://ftpmaster.internal/ubuntu zesty/main i386 man-db i386 2.7.5-1 [865 kB] Get:7 http://ftpmaster.internal/ubuntu zesty/main i386 libunistring0 i386 0.9.3-5.2ubuntu1 [277 kB] Get:8 http://ftpmaster.internal/ubuntu zesty-proposed/main i386 libpython2.7-minimal i386 2.7.12-4 [340 kB] Get:9 http://ftpmaster.internal/ubuntu zesty-proposed/main i386 python2.7-minimal i386 2.7.12-4 [1359 kB] Get:10 http://ftpmaster.internal/ubuntu zesty/main i386 python-minimal i386 2.7.11-2 [28.3 kB] Get:11 http://ftpmaster.internal/ubuntu zesty/main i386 mime-support all 3.60ubuntu1 [30.1 kB] Get:12 http://ftpmaster.internal/ubuntu zesty/main i386 libexpat1 i386 2.2.0-1 [74.9 kB] Get:13 http://ftpmaster.internal/ubuntu zesty-proposed/main i386 libpython2.7-stdlib i386 2.7.12-4 [1940 kB] Get:14 http://ftpmaster.internal/ubuntu zesty-proposed/main i386 python2.7 i386 2.7.12-4 [228 kB] Get:15 http://ftpmaster.internal/ubuntu zesty/main i386 libpython-stdlib i386 2.7.11-2 [7850 B] Get:16 http://ftpmaster.internal/ubuntu zesty/main i386 python i386 2.7.11-2 [139 kB] Get:17 http://ftpmaster.internal/ubuntu zesty/main i386 libmagic1 i386 1:5.28-2ubuntu1 [240 kB] Get:18 http://ftpmaster.internal/ubuntu zesty/main i386 file i386 1:5.28-2ubuntu1 [21.7 kB] Get:19 http://ftpmaster.internal/ubuntu zesty/main i386 gettext-base i386 0.19.8.1-1ubuntu2 [49.0 kB] Get:20 http://ftpmaster.internal/ubuntu zesty-proposed/main i386 libglib2.0-0 i386 2.50.1-1 [1213 kB] Get:21 http://ftpmaster.internal/ubuntu zesty/main i386 libicu57 i386 57.1-4 [7816 kB] Get:22 http://ftpmaster.internal/ubuntu zesty-proposed/main i386 libxml2 i386 2.9.4+dfsg1-2.1 [733 kB] Get:23 http://ftpmaster.internal/ubuntu zesty-proposed/main i386 libyaml-0-2 i386 0.1.7-2 [49.3 kB] Get:24 http://ftpmaster.internal/ubuntu zesty/main i386 libsigsegv2 i386 2.10-5 [14.3 kB] Get:25 http://ftpmaster.internal/ubuntu zesty/main i386 m4 i386 1.4.17-5 [195 kB] Get:26 http://ftpmaster.internal/ubuntu zesty/main i386 autoconf all 2.69-10 [321 kB] Get:27 http://ftpmaster.internal/ubuntu zesty/main i386 autotools-dev all 20160430.1 [39.6 kB] Get:28 http://ftpmaster.internal/ubuntu zesty/main i386 automake all 1:1.15-4ubuntu1 [510 kB] Get:29 http://ftpmaster.internal/ubuntu zesty/main i386 autopoint all 0.19.8.1-1ubuntu2 [412 kB] Get:30 http://ftpmaster.internal/ubuntu zesty-proposed/main i386 libtool all 2.4.6-2 [194 kB] Get:31 http://ftpmaster.internal/ubuntu zesty/main i386 dh-autoreconf all 12 [15.8 kB] Get:32 http://ftpmaster.internal/ubuntu zesty/main i386 libarchive-zip-perl all 1.59-1 [84.0 kB] Get:33 http://ftpmaster.internal/ubuntu zesty/main i386 libfile-stripnondeterminism-perl all 0.028-1 [12.5 kB] Get:34 http://ftpmaster.internal/ubuntu zesty/main i386 libtimedate-perl all 2.3000-2 [37.5 kB] Get:35 http://ftpmaster.internal/ubuntu zesty/main i386 dh-strip-nondeterminism all 0.028-1 [4820 B] Get:36 http://ftpmaster.internal/ubuntu zesty/main i386 libcroco3 i386 0.6.11-2 [87.1 kB] Get:37 http://ftpmaster.internal/ubuntu zesty/main i386 gettext i386 0.19.8.1-1ubuntu2 [1086 kB] Get:38 http://ftpmaster.internal/ubuntu zesty/main i386 intltool-debian all 0.35.0+20060710.4 [24.9 kB] Get:39 http://ftpmaster.internal/ubuntu zesty/main i386 po-debconf all 1.0.20 [232 kB] Get:40 http://ftpmaster.internal/ubuntu zesty/main i386 debhelper all 10.2.2ubuntu1 [742 kB] Get:41 http://ftpmaster.internal/ubuntu zesty/universe i386 help2man i386 1.47.4 [155 kB] Get:42 http://ftpmaster.internal/ubuntu zesty/main i386 liblua5.1-0 i386 5.1.5-8.1build1 [115 kB] Get:43 http://ftpmaster.internal/ubuntu zesty/universe i386 libluajit-5.1-common all 2.0.4+dfsg-1 [35.3 kB] Get:44 http://ftpmaster.internal/ubuntu zesty/universe i386 libluajit-5.1-2 i386 2.0.4+dfsg-1 [215 kB] Get:45 http://ftpmaster.internal/ubuntu zesty/universe i386 pandoc-data all 1.17.2~dfsg-1build4 [84.3 kB] Get:46 http://ftpmaster.internal/ubuntu zesty/universe i386 pandoc i386 1.17.2~dfsg-1build4 [6961 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 28.4 MB in 3s (7977 kB/s) Selecting previously unselected package liblocale-gettext-perl. (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 ... 14095 files and directories currently installed.) Preparing to unpack .../00-liblocale-gettext-perl_1.07-3build1_i386.deb ... Unpacking liblocale-gettext-perl (1.07-3build1) ... Selecting previously unselected package groff-base. Preparing to unpack .../01-groff-base_1.22.3-8_i386.deb ... Unpacking groff-base (1.22.3-8) ... Selecting previously unselected package bsdmainutils. 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Unpacking sbuild-build-depends-hisat2-dummy (0.invalid.0) ... Setting up libexpat1:i386 (2.2.0-1) ... Setting up libarchive-zip-perl (1.59-1) ... Setting up libluajit-5.1-common (2.0.4+dfsg-1) ... Setting up mime-support (3.60ubuntu1) ... Setting up libtimedate-perl (2.3000-2) ... Setting up libsigsegv2:i386 (2.10-5) ... Setting up groff-base (1.22.3-8) ... Setting up libglib2.0-0:i386 (2.50.1-1) ... No schema files found: doing nothing. Setting up pandoc-data (1.17.2~dfsg-1build4) ... Setting up gettext-base (0.19.8.1-1ubuntu2) ... Setting up libpipeline1:i386 (1.4.1-2) ... Setting up m4 (1.4.17-5) ... Setting up libicu57:i386 (57.1-4) ... Setting up libxml2:i386 (2.9.4+dfsg1-2.1) ... Setting up libmagic1:i386 (1:5.28-2ubuntu1) ... Setting up libcroco3:i386 (0.6.11-2) ... Setting up libyaml-0-2:i386 (0.1.7-2) ... Processing triggers for libc-bin (2.24-3ubuntu1) ... Setting up autotools-dev (20160430.1) ... Setting up libunistring0:i386 (0.9.3-5.2ubuntu1) ... Setting up libluajit-5.1-2:i386 (2.0.4+dfsg-1) ... Setting up liblocale-gettext-perl (1.07-3build1) ... Setting up liblua5.1-0:i386 (5.1.5-8.1build1) ... Setting up bsdmainutils (9.0.6ubuntu3) ... update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode Setting up libpython2.7-stdlib:i386 (2.7.12-4) ... Setting up autopoint (0.19.8.1-1ubuntu2) ... Setting up libfile-stripnondeterminism-perl (0.028-1) ... Setting up pandoc (1.17.2~dfsg-1build4) ... Setting up gettext (0.19.8.1-1ubuntu2) ... Setting up python2.7 (2.7.12-4) ... Setting up autoconf (2.69-10) ... Setting up file (1:5.28-2ubuntu1) ... Setting up libpython-stdlib:i386 (2.7.11-2) ... Setting up intltool-debian (0.35.0+20060710.4) ... Setting up automake (1:1.15-4ubuntu1) ... update-alternatives: using /usr/bin/automake-1.15 to provide /usr/bin/automake (automake) in auto mode Setting up help2man (1.47.4) ... Setting up man-db (2.7.5-1) ... Not building database; man-db/auto-update is not 'true'. Setting up python (2.7.11-2) ... Setting up libtool (2.4.6-2) ... Setting up po-debconf (1.0.20) ... Setting up dh-autoreconf (12) ... Setting up dh-strip-nondeterminism (0.028-1) ... Setting up debhelper (10.2.2ubuntu1) ... Setting up sbuild-build-depends-hisat2-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.24-3ubuntu1) ... +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 4.4.0-45-generic amd64 (i686) Toolchain package versions: binutils_2.27-9ubuntu1 dpkg-dev_1.18.10ubuntu1 g++-6_6.2.0-11ubuntu1 gcc-6_6.2.0-11ubuntu1 libc6-dev_2.24-3ubuntu1 libstdc++-6-dev_6.2.0-11ubuntu1 libstdc++6_6.2.0-11ubuntu1 linux-libc-dev_4.8.0-27.29 Package versions: adduser_3.113+nmu3ubuntu5 advancecomp_1.20-1 apt_1.3.1 apt-transport-https_1.3.1 autoconf_2.69-10 automake_1:1.15-4ubuntu1 autopoint_0.19.8.1-1ubuntu2 autotools-dev_20160430.1 base-files_9.6ubuntu6 base-passwd_3.5.40 bash_4.4-1ubuntu1 binutils_2.27-9ubuntu1 bsdmainutils_9.0.6ubuntu3 bsdutils_1:2.28.2-1ubuntu1 build-essential_12.1ubuntu2 bzip2_1.0.6-8build1 ca-certificates_20160104ubuntu1 coreutils_8.25-2ubuntu2 cpp_4:6.1.1-1ubuntu2 cpp-6_6.2.0-11ubuntu1 dash_0.5.8-2.3ubuntu1 debconf_1.5.59ubuntu1 debhelper_10.2.2ubuntu1 debianutils_4.8 dh-autoreconf_12 dh-strip-nondeterminism_0.028-1 diffutils_1:3.5-1 dmsetup_2:1.02.133-1ubuntu1 dpkg_1.18.10ubuntu1 dpkg-dev_1.18.10ubuntu1 e2fslibs_1.43.3-1 e2fsprogs_1.43.3-1 fakeroot_1.21-1ubuntu2 file_1:5.28-2ubuntu1 findutils_4.6.0+git+20160703-2 g++_4:6.1.1-1ubuntu2 g++-6_6.2.0-11ubuntu1 gcc_4:6.1.1-1ubuntu2 gcc-6_6.2.0-11ubuntu1 gcc-6-base_6.2.0-11ubuntu1 gettext_0.19.8.1-1ubuntu2 gettext-base_0.19.8.1-1ubuntu2 gnupg_2.1.15-1ubuntu6 gnupg-agent_2.1.15-1ubuntu6 gpgv_2.1.15-1ubuntu6 grep_2.26-1 groff-base_1.22.3-8 gzip_1.6-4ubuntu1 help2man_1.47.4 hostname_3.18 init_1.45 init-system-helpers_1.45 initscripts_2.88dsf-59.3ubuntu2 insserv_1.14.0-5ubuntu3 intltool-debian_0.35.0+20060710.4 libacl1_2.2.52-3 libapparmor1_2.10.95-4ubuntu5.2 libapt-pkg5.0_1.3.1 libarchive-zip-perl_1.59-1 libasan3_6.2.0-11ubuntu1 libasn1-8-heimdal_1.7~git20150920+dfsg-4ubuntu1 libassuan0_2.4.3-1 libatomic1_6.2.0-11ubuntu1 libattr1_1:2.4.47-2 libaudit-common_1:2.6.6-1ubuntu1 libaudit1_1:2.6.6-1ubuntu1 libblkid1_2.28.2-1ubuntu1 libbz2-1.0_1.0.6-8build1 libc-bin_2.24-3ubuntu1 libc-dev-bin_2.24-3ubuntu1 libc6_2.24-3ubuntu1 libc6-dev_2.24-3ubuntu1 libcap-ng0_0.7.7-3 libcap2_1:2.25-1 libcc1-0_6.2.0-11ubuntu1 libcilkrts5_6.2.0-11ubuntu1 libcomerr2_1.43.3-1 libcroco3_0.6.11-2 libcryptsetup4_2:1.7.2-0ubuntu1 libcurl3-gnutls_7.50.1-1ubuntu2 libdb5.3_5.3.28-12 libdebconfclient0_0.213ubuntu1 libdevmapper1.02.1_2:1.02.133-1ubuntu1 libdpkg-perl_1.18.10ubuntu1 libexpat1_2.2.0-1 libfakeroot_1.21-1ubuntu2 libfdisk1_2.28.2-1ubuntu1 libffi6_3.2.1-6 libfile-stripnondeterminism-perl_0.028-1 libgcc-6-dev_6.2.0-11ubuntu1 libgcc1_1:6.2.0-11ubuntu1 libgcrypt20_1.7.2-2ubuntu1 libgdbm3_1.8.3-14 libglib2.0-0_2.50.1-1 libgmp10_2:6.1.1+dfsg-1 libgnutls30_3.5.3-5ubuntu1 libgomp1_6.2.0-11ubuntu1 libgpg-error0_1.24-1 libgssapi-krb5-2_1.15~beta1-1 libgssapi3-heimdal_1.7~git20150920+dfsg-4ubuntu1 libhcrypto4-heimdal_1.7~git20150920+dfsg-4ubuntu1 libheimbase1-heimdal_1.7~git20150920+dfsg-4ubuntu1 libheimntlm0-heimdal_1.7~git20150920+dfsg-4ubuntu1 libhogweed4_3.3-1 libhx509-5-heimdal_1.7~git20150920+dfsg-4ubuntu1 libicu57_57.1-4 libidn11_1.33-1 libip4tc0_1.6.0-3ubuntu2 libisl15_0.17.1-1 libitm1_6.2.0-11ubuntu1 libk5crypto3_1.15~beta1-1 libkeyutils1_1.5.9-9ubuntu1 libkmod2_22-1.1ubuntu1 libkrb5-26-heimdal_1.7~git20150920+dfsg-4ubuntu1 libkrb5-3_1.15~beta1-1 libkrb5support0_1.15~beta1-1 libksba8_1.3.5-2 libldap-2.4-2_2.4.42+dfsg-2ubuntu5 liblocale-gettext-perl_1.07-3build1 liblockfile-bin_1.09-6ubuntu1 liblockfile1_1.09-6ubuntu1 liblua5.1-0_5.1.5-8.1build1 libluajit-5.1-2_2.0.4+dfsg-1 libluajit-5.1-common_2.0.4+dfsg-1 liblz4-1_0.0~r131-2ubuntu2 liblzma5_5.2.2-1.2 libmagic1_1:5.28-2ubuntu1 libmount1_2.28.2-1ubuntu1 libmpc3_1.0.3-1 libmpfr4_3.1.5-1 libmpx2_6.2.0-11ubuntu1 libncurses5_6.0+20160625-1ubuntu1 libncursesw5_6.0+20160625-1ubuntu1 libnettle6_3.3-1 libnpth0_1.2-3 libp11-kit0_0.23.2-5 libpam-modules_1.1.8-3.2ubuntu2 libpam-modules-bin_1.1.8-3.2ubuntu2 libpam-runtime_1.1.8-3.2ubuntu2 libpam0g_1.1.8-3.2ubuntu2 libpcre3_2:8.39-2 libperl5.22_5.22.2-3 libperl5.24_5.24.1~rc3-3 libpipeline1_1.4.1-2 libpng16-16_1.6.26-1 libprocps6_2:3.3.12-1ubuntu2 libpython-stdlib_2.7.11-2 libpython2.7-minimal_2.7.12-4 libpython2.7-stdlib_2.7.12-4 libquadmath0_6.2.0-11ubuntu1 libreadline7_7.0-0ubuntu2 libroken18-heimdal_1.7~git20150920+dfsg-4ubuntu1 librtmp1_2.4+20151223.gitfa8646d.1-1 libsasl2-2_2.1.27~72-g88d82a3+dfsg-1 libsasl2-modules-db_2.1.27~72-g88d82a3+dfsg-1 libseccomp2_2.3.1-2ubuntu2 libselinux1_2.6-1 libsemanage-common_2.6-1 libsemanage1_2.6-1 libsepol1_2.6-1 libsigsegv2_2.10-5 libslang2_2.3.1-4ubuntu1 libsmartcols1_2.28.2-1ubuntu1 libsqlite3-0_3.15.0-1 libss2_1.43.3-1 libssl1.0.0_1.0.2g-1ubuntu9 libstdc++-6-dev_6.2.0-11ubuntu1 libstdc++6_6.2.0-11ubuntu1 libsystemd0_231-10 libtasn1-6_4.9-4 libtimedate-perl_2.3000-2 libtinfo5_6.0+20160625-1ubuntu1 libtool_2.4.6-2 libubsan0_6.2.0-11ubuntu1 libudev1_231-10 libunistring0_0.9.3-5.2ubuntu1 libusb-0.1-4_2:0.1.12-30 libustr-1.0-1_1.0.4-5 libuuid1_2.28.2-1ubuntu1 libwind0-heimdal_1.7~git20150920+dfsg-4ubuntu1 libxml2_2.9.4+dfsg1-2.1 libyaml-0-2_0.1.7-2 linux-libc-dev_4.8.0-27.29 lockfile-progs_0.1.17 login_1:4.2-3.2ubuntu1 lsb-base_9.20160110ubuntu5 m4_1.4.17-5 make_4.1-9 man-db_2.7.5-1 mawk_1.3.3-17ubuntu2 mime-support_3.60ubuntu1 mount_2.28.2-1ubuntu1 multiarch-support_2.24-3ubuntu1 ncurses-base_6.0+20160625-1ubuntu1 ncurses-bin_6.0+20160625-1ubuntu1 openssl_1.0.2g-1ubuntu9 optipng_0.7.6-1build1 pandoc_1.17.2~dfsg-1build4 pandoc-data_1.17.2~dfsg-1build4 passwd_1:4.2-3.2ubuntu1 patch_2.7.5-1 perl_5.24.1~rc3-3 perl-base_5.24.1~rc3-3 perl-modules-5.22_5.22.2-3 perl-modules-5.24_5.24.1~rc3-3 pinentry-curses_0.9.7-6 pkg-create-dbgsym_0.72 pkgbinarymangler_131 po-debconf_1.0.20 policyrcd-script-zg2_0.1-3 procps_2:3.3.12-1ubuntu2 python_2.7.11-2 python-minimal_2.7.11-2 python2.7_2.7.12-4 python2.7-minimal_2.7.12-4 readline-common_7.0-0ubuntu2 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-hisat2-dummy_0.invalid.0 sed_4.2.2-8 sensible-utils_0.0.9 systemd_231-10 systemd-sysv_231-10 sysv-rc_2.88dsf-59.3ubuntu2 sysvinit-utils_2.88dsf-59.8git1 tar_1.29b-1.1 tzdata_2016h-1 ubuntu-keyring_2016.10.27 util-linux_2.28.2-1ubuntu1 xz-utils_5.2.2-1.2 zlib1g_1:1.2.8.dfsg-2ubuntu5 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- gpgv: Signature made Thu Aug 25 20:29:30 2016 UTC gpgv: using RSA key gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./hisat2_2.0.4-2.dsc dpkg-source: info: extracting hisat2 in hisat2-2.0.4 dpkg-source: info: unpacking hisat2_2.0.4.orig.tar.bz2 dpkg-source: info: unpacking hisat2_2.0.4-2.debian.tar.xz dpkg-source: info: applying hardening dpkg-source: info: applying reproducibile dpkg-source: info: applying fix-freebsd dpkg-source: info: applying compilerflags Check disc space ---------------- Sufficient free space for build User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf DEB_BUILD_OPTIONS=parallel=4 HOME=/home/buildd LANG=C.UTF-8 LC_ALL=C.UTF-8 LOGNAME=buildd MAIL=/var/mail/buildd OLDPWD=/ PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games PWD=/<> SHELL=/bin/sh SUDO_COMMAND=/usr/sbin/chroot /<> su buildd -s /bin/sh -c cd '/<>' && 'env' SUDO_GID=2501 SUDO_UID=2001 SUDO_USER=buildd TERM=unknown USER=buildd USERNAME=root dpkg-buildpackage ----------------- dpkg-buildpackage: info: source package hisat2 dpkg-buildpackage: info: source version 2.0.4-2 dpkg-buildpackage: info: source distribution unstable dpkg-source --before-build hisat2-2.0.4 dpkg-buildpackage: info: host architecture i386 fakeroot debian/rules clean dh clean dh_testdir dh_auto_clean make -j1 clean make[1]: Entering directory '/<>' rm -f hisat2-build-s hisat2-build-l hisat2-align-s hisat2-align-l hisat2-inspect-s hisat2-inspect-l hisat2-build-s-debug hisat2-build-l-debug hisat2-align-s-debug hisat2-align-l-debug hisat2-inspect-s-debug hisat2-inspect-l-debug \ hisat2-build-s.exe hisat2-build-l.exe hisat2-align-s.exe hisat2-align-l.exe hisat2-inspect-s.exe hisat2-inspect-l.exe hisat2-build-s-debug.exe hisat2-build-l-debug.exe hisat2-align-s-debug.exe hisat2-align-l-debug.exe hisat2-inspect-s-debug.exe hisat2-inspect-l-debug.exe \ hisat2-src.zip hisat2-bin.zip rm -f core.* .tmp.head rm -rf *.dSYM make[1]: Leaving directory '/<>' dh_clean debian/rules build-arch dh build-arch dh_testdir -a dh_update_autotools_config -a dh_auto_configure -a debian/rules override_dh_auto_build make[1]: Entering directory '/<>' make BUILD_HOST='Debian unstable' \ BUILD_TIME="Thu Aug 25 15:46:42 UTC 2016" \ all doc make[2]: Entering directory '/<>' /usr/bin/g++ -O3 -funroll-loops -g3 -Wdate-time -D_FORTIFY_SOURCE=2 -DCOMPILER_OPTIONS="\"-O3 -funroll-loops -g3 -Wdate-time -D_FORTIFY_SOURCE=2 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY \ -fno-strict-aliasing -DHISAT2_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"Debian unstable\"" -DBUILD_TIME="\"Thu Aug 25 15:46:42 UTC 2016\"" -DCOMPILER_VERSION="\"`/usr/bin/g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -g -O2 -fdebug-prefix-map=/<>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DBOWTIE2 -DNDEBUG -Wall -DMASSIVE_DATA_RLCSA \ -I third_party \ -o hisat2-build-s hisat2_build.cpp \ ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp gfm.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp tinythread.cpp diff_sample.cpp hisat2_build_main.cpp \ -lpthread -Wl,-Bsymbolic-functions -fPIE -pie -Wl,-z,relro -Wl,-z,now In file included from blockwise_sa.h:29:0, from gfm.h:43, from hisat2_build.cpp:35: diff_sample.h: In function ‘void calcExhaustiveDC(T, bool, bool)’: diff_sample.h:175:6: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] if(!diffs[d1]) diffCnt++; diffs[d1] = true; ^~ diff_sample.h:175:32: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the ‘if’ if(!diffs[d1]) diffCnt++; diffs[d1] = true; ^~~~~ diff_sample.h:176:6: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] if(!diffs[d2]) diffCnt++; diffs[d2] = true; ^~ diff_sample.h:176:32: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the ‘if’ if(!diffs[d2]) diffCnt++; diffs[d2] = true; ^~~~~ In file included from hisat2_build.cpp:35:0: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1042:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] auto_ptr ss(new stringstream()); ^~~~~~~~ In file included from /usr/include/c++/6/bits/locale_conv.h:41:0, from /usr/include/c++/6/locale:43, from /usr/include/c++/6/iomanip:43, from timer.h:26, from hisat2_build.cpp:30: /usr/include/c++/6/bits/unique_ptr.h:49:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from hisat2_build.cpp:35:0: gfm.h:1046:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] auto_ptr fb(new FileBuf(ss.get())); ^~~~~~~~ In file included from /usr/include/c++/6/bits/locale_conv.h:41:0, from /usr/include/c++/6/locale:43, from /usr/include/c++/6/iomanip:43, from timer.h:26, from hisat2_build.cpp:30: /usr/include/c++/6/bits/unique_ptr.h:49:28: note: declared here template class auto_ptr; ^~~~~~~~ gfm.h: Assembler messages: gfm.h:547: Error: invalid instruction suffix for `popcnt' gfm.h:547: Error: invalid instruction suffix for `popcnt' gfm.h:547: Error: invalid instruction suffix for `popcnt' gfm.h:547: Error: invalid instruction suffix for `popcnt' gfm.h:547: Error: invalid instruction suffix for `popcnt' gfm.h:547: Error: invalid instruction suffix for `popcnt' gfm.h:547: Error: invalid instruction suffix for `popcnt' gfm.h:547: Error: invalid instruction suffix for `popcnt' gfm.h:547: Error: invalid instruction suffix for `popcnt' gfm.h:547: Error: invalid instruction suffix for `popcnt' gfm.h:547: Error: invalid instruction suffix for `popcnt' gfm.h:547: Error: invalid instruction suffix for `popcnt' gfm.h:547: Error: invalid instruction suffix for `popcnt' gfm.h:547: Error: invalid instruction suffix for `popcnt' gfm.h:547: Error: invalid instruction suffix for `popcnt' gfm.h:547: Error: invalid instruction suffix for `popcnt' gfm.h:547: Error: invalid instruction suffix for `popcnt' gfm.h:547: Error: invalid instruction suffix for `popcnt' gfm.h:547: Error: invalid instruction suffix for `popcnt' gfm.h:547: Error: invalid instruction suffix for `popcnt' gfm.h:547: Error: invalid instruction suffix for `popcnt' gfm.h:547: Error: invalid instruction suffix for `popcnt' gfm.h:547: Error: invalid instruction suffix for `popcnt' gfm.h:547: Error: invalid instruction suffix for `popcnt' gfm.h:547: Error: invalid instruction suffix for `popcnt' gfm.h:547: Error: invalid instruction suffix for `popcnt' gfm.h:547: Error: invalid instruction suffix for `popcnt' gfm.h:547: Error: invalid instruction suffix for `popcnt' gfm.h:547: Error: invalid instruction suffix for `popcnt' gfm.h:547: Error: invalid instruction suffix for `popcnt' gfm.h:547: Error: invalid instruction suffix for `popcnt' gfm.h:547: Error: invalid instruction suffix for `popcnt' gfm.h:547: Error: invalid instruction suffix for `popcnt' gfm.h:547: Error: invalid instruction suffix for `popcnt' gfm.h:547: Error: invalid instruction suffix for `popcnt' gfm.h:547: Error: invalid instruction suffix for `popcnt' gfm.h:547: Error: invalid instruction suffix for `popcnt' gfm.h:547: Error: invalid instruction suffix for `popcnt' gfm.h:547: Error: invalid instruction suffix for `popcnt' gfm.h:547: Error: invalid instruction suffix for `popcnt' gfm.h:547: Error: invalid instruction suffix for `popcnt' gfm.h:547: Error: invalid instruction suffix for `popcnt' gfm.h:547: Error: invalid instruction suffix for `popcnt' gfm.h:547: Error: invalid instruction suffix for `popcnt' gfm.h:547: Error: invalid instruction suffix for `popcnt' gfm.h:547: Error: invalid instruction suffix for `popcnt' gfm.h:547: Error: invalid instruction suffix for `popcnt' gfm.h:547: Error: invalid instruction suffix for `popcnt' gfm.h:547: Error: invalid instruction suffix for `popcnt' gfm.h:547: Error: invalid instruction suffix for `popcnt' gfm.h:547: Error: invalid instruction suffix for `popcnt' gfm.h:547: Error: invalid instruction suffix for `popcnt' gfm.h:547: Error: invalid instruction suffix for `popcnt' gfm.h:547: Error: invalid instruction suffix for `popcnt' gfm.h:547: Error: invalid instruction suffix for `popcnt' gfm.h:547: Error: invalid instruction suffix for `popcnt' gfm.h:547: Error: invalid instruction suffix for `popcnt' gfm.h:547: Error: invalid instruction suffix for `popcnt' gfm.h:547: Error: invalid instruction suffix for `popcnt' gfm.h:547: Error: invalid instruction suffix for `popcnt' gfm.h:547: Error: invalid instruction suffix for `popcnt' gfm.h:547: Error: invalid instruction suffix for `popcnt' gfm.h:547: Error: invalid instruction suffix for `popcnt' gfm.h:547: Error: invalid instruction suffix for `popcnt' gfm.h:547: Error: invalid instruction suffix for `popcnt' gfm.h:547: Error: invalid instruction suffix for `popcnt' gfm.h:547: Error: invalid instruction suffix for `popcnt' gfm.h:547: Error: invalid instruction suffix for `popcnt' gfm.h:547: Error: invalid instruction suffix for `popcnt' gfm.h:547: Error: invalid instruction suffix for `popcnt' gfm.h:547: Error: invalid instruction suffix for `popcnt' gfm.h:547: Error: invalid instruction suffix for `popcnt' gfm.h:547: Error: invalid instruction suffix for `popcnt' gfm.h:547: Error: invalid instruction suffix for `popcnt' gfm.h:547: Error: invalid instruction suffix for `popcnt' gfm.h:547: Error: invalid instruction suffix for `popcnt' gfm.h:547: Error: invalid instruction suffix for `popcnt' gfm.h:547: Error: invalid instruction suffix for `popcnt' gfm.h:547: Error: invalid instruction suffix for `popcnt' gfm.h:547: Error: invalid instruction suffix for `popcnt' gfm.h:547: Error: invalid instruction suffix for `popcnt' gfm.h:547: Error: invalid instruction suffix for `popcnt' gfm.h:547: Error: invalid instruction suffix for `popcnt' gfm.h:547: Error: invalid instruction suffix for `popcnt' gfm.h:547: Error: invalid instruction suffix for `popcnt' gfm.h:547: Error: invalid instruction suffix for `popcnt' gfm.h:547: Error: invalid instruction suffix for `popcnt' gfm.h:547: Error: invalid instruction suffix for `popcnt' gfm.h:547: Error: invalid instruction suffix for `popcnt' gfm.h:547: Error: invalid instruction suffix for `popcnt' gfm.h:547: Error: invalid instruction suffix for `popcnt' gfm.h:547: Error: invalid instruction suffix for `popcnt' gfm.h:547: Error: invalid instruction suffix for `popcnt' gfm.h:547: Error: invalid instruction suffix for `popcnt' gfm.h:547: Error: invalid instruction suffix for `popcnt' gfm.h:547: Error: invalid instruction suffix for `popcnt' gfm.h:547: Error: invalid instruction suffix for `popcnt' gfm.h:547: Error: invalid instruction suffix for `popcnt' gfm.h:547: Error: invalid instruction suffix for `popcnt' gfm.h:547: Error: invalid instruction suffix for `popcnt' gfm.h:547: Error: invalid instruction suffix for `popcnt' gfm.h:547: Error: invalid instruction suffix for `popcnt' gfm.h:547: Error: invalid instruction suffix for `popcnt' gfm.h:547: Error: invalid instruction suffix for `popcnt' gfm.h:547: Error: invalid instruction suffix for `popcnt' gfm.h:547: Error: invalid instruction suffix for `popcnt' gfm.h:547: Error: invalid instruction suffix for `popcnt' gfm.h:547: Error: invalid instruction suffix for `popcnt' gfm.h:547: Error: invalid instruction suffix for `popcnt' gfm.h:547: Error: invalid instruction suffix for `popcnt' gfm.h:547: Error: invalid instruction suffix for `popcnt' gfm.h:547: Error: invalid instruction suffix for `popcnt' gfm.h:547: Error: invalid instruction suffix for `popcnt' gfm.h:547: Error: invalid instruction suffix for `popcnt' gfm.h:547: Error: invalid instruction suffix for `popcnt' gfm.h:547: Error: invalid instruction suffix for `popcnt' gfm.h:547: Error: invalid instruction suffix for `popcnt' gfm.h:547: Error: invalid instruction suffix for `popcnt' gfm.h:547: Error: invalid instruction suffix for `popcnt' gfm.h:547: Error: invalid instruction suffix for `popcnt' gfm.h:547: Error: invalid instruction suffix for `popcnt' gfm.h:547: Error: invalid instruction suffix for `popcnt' gfm.h:547: Error: invalid instruction suffix for `popcnt' gfm.h:547: Error: invalid instruction suffix for `popcnt' gfm.h:547: Error: invalid instruction suffix for `popcnt' gfm.h:547: Error: invalid instruction suffix for `popcnt' gfm.h:547: Error: invalid instruction suffix for `popcnt' gfm.h:547: Error: invalid instruction suffix for `popcnt' gfm.h:547: Error: invalid instruction suffix for `popcnt' gfm.h:547: Error: invalid instruction suffix for `popcnt' gfm.h:547: Error: invalid instruction suffix for `popcnt' gfm.h:547: Error: invalid instruction suffix for `popcnt' gfm.h:547: Error: invalid instruction suffix for `popcnt' gfm.h:547: Error: invalid instruction suffix for `popcnt' gfm.h:547: Error: invalid instruction suffix for `popcnt' gfm.h:547: Error: invalid instruction suffix for `popcnt' gfm.h:547: Error: invalid instruction suffix for `popcnt' gfm.h:547: Error: invalid instruction suffix for `popcnt' gfm.h:547: Error: invalid instruction suffix for `popcnt' gfm.h:547: Error: invalid instruction suffix for `popcnt' gfm.h:547: Error: invalid instruction suffix for `popcnt' gfm.h:547: Error: invalid instruction suffix for `popcnt' gfm.h:547: Error: invalid instruction suffix for `popcnt' gfm.h:547: Error: invalid instruction suffix for `popcnt' gfm.h:547: Error: invalid instruction suffix for `popcnt' gfm.h:547: Error: invalid instruction suffix for `popcnt' gfm.h:547: Error: invalid instruction suffix for `popcnt' gfm.h:547: Error: invalid instruction suffix for `popcnt' gfm.h:547: Error: invalid instruction suffix for `popcnt' gfm.h:547: Error: invalid instruction suffix for `popcnt' gfm.h:547: Error: invalid instruction suffix for `popcnt' gfm.h:547: Error: invalid instruction suffix for `popcnt' gfm.h:547: Error: invalid instruction suffix for `popcnt' gfm.h:547: Error: invalid instruction suffix for `popcnt' gfm.h:547: Error: invalid instruction suffix for `popcnt' gfm.h:547: Error: invalid instruction suffix for `popcnt' gfm.h:547: Error: invalid instruction suffix for `popcnt' gfm.h:547: Error: invalid instruction suffix for `popcnt' gfm.h:547: Error: invalid instruction suffix for `popcnt' gfm.h:547: Error: invalid instruction suffix for `popcnt' gfm.h:547: Error: invalid instruction suffix for `popcnt' gfm.h:547: Error: invalid instruction suffix for `popcnt' gfm.h:547: Error: invalid instruction suffix for `popcnt' gfm.h:547: Error: invalid instruction suffix for `popcnt' gfm.h:547: Error: invalid instruction suffix for `popcnt' gfm.h:547: Error: invalid instruction suffix for `popcnt' gfm.h:547: Error: invalid instruction suffix for `popcnt' gfm.h:547: Error: invalid instruction suffix for `popcnt' gfm.h:547: Error: invalid instruction suffix for `popcnt' In file included from blockwise_sa.h:29:0, from gfm.h:43, from splice_site.h:34, from edit.h:30, from edit.cpp:21: diff_sample.h: In function ‘void calcExhaustiveDC(T, bool, bool)’: diff_sample.h:175:6: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] if(!diffs[d1]) diffCnt++; diffs[d1] = true; ^~ diff_sample.h:175:32: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the ‘if’ if(!diffs[d1]) diffCnt++; diffs[d1] = true; ^~~~~ diff_sample.h:176:6: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] if(!diffs[d2]) diffCnt++; diffs[d2] = true; ^~ diff_sample.h:176:32: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the ‘if’ if(!diffs[d2]) diffCnt++; diffs[d2] = true; ^~~~~ In file included from splice_site.h:34:0, from edit.h:30, from edit.cpp:21: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1042:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] auto_ptr ss(new stringstream()); ^~~~~~~~ In file included from /usr/include/c++/6/bits/locale_conv.h:41:0, from /usr/include/c++/6/locale:43, from /usr/include/c++/6/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from edit.cpp:21: /usr/include/c++/6/bits/unique_ptr.h:49:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from splice_site.h:34:0, from edit.h:30, from edit.cpp:21: gfm.h:1046:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] auto_ptr fb(new FileBuf(ss.get())); ^~~~~~~~ In file included from /usr/include/c++/6/bits/locale_conv.h:41:0, from /usr/include/c++/6/locale:43, from /usr/include/c++/6/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from edit.cpp:21: /usr/include/c++/6/bits/unique_ptr.h:49:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from blockwise_sa.h:29:0, from gfm.h:43, from gfm.cpp:21: diff_sample.h: In function ‘void calcExhaustiveDC(T, bool, bool)’: diff_sample.h:175:6: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] if(!diffs[d1]) diffCnt++; diffs[d1] = true; ^~ diff_sample.h:175:32: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the ‘if’ if(!diffs[d1]) diffCnt++; diffs[d1] = true; ^~~~~ diff_sample.h:176:6: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] if(!diffs[d2]) diffCnt++; diffs[d2] = true; ^~ diff_sample.h:176:32: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the ‘if’ if(!diffs[d2]) diffCnt++; diffs[d2] = true; ^~~~~ In file included from gfm.cpp:21:0: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1042:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] auto_ptr ss(new stringstream()); ^~~~~~~~ In file included from /usr/include/c++/6/memory:81:0, from gfm.h:28, from gfm.cpp:21: /usr/include/c++/6/bits/unique_ptr.h:49:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from gfm.cpp:21:0: gfm.h:1046:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] auto_ptr fb(new FileBuf(ss.get())); ^~~~~~~~ In file included from /usr/include/c++/6/memory:81:0, from gfm.h:28, from gfm.cpp:21: /usr/include/c++/6/bits/unique_ptr.h:49:28: note: declared here template class auto_ptr; ^~~~~~~~ reference.cpp: In member function ‘int BitPairReference::getStretch(uint32_t*, size_t, size_t, size_t) const’: reference.cpp:456:12: warning: variable ‘origBufOff’ set but not used [-Wunused-but-set-variable] uint64_t origBufOff = bufOff; ^~~~~~~~~~ reference.cpp:450:7: warning: variable ‘binarySearched’ set but not used [-Wunused-but-set-variable] bool binarySearched = false; ^~~~~~~~~~~~~~ In file included from multikey_qsort.h:27:0, from multikey_qsort.cpp:20: diff_sample.h: In function ‘void calcExhaustiveDC(T, bool, bool)’: diff_sample.h:175:6: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] if(!diffs[d1]) diffCnt++; diffs[d1] = true; ^~ diff_sample.h:175:32: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the ‘if’ if(!diffs[d1]) diffCnt++; diffs[d1] = true; ^~~~~ diff_sample.h:176:6: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] if(!diffs[d2]) diffCnt++; diffs[d2] = true; ^~ diff_sample.h:176:32: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the ‘if’ if(!diffs[d2]) diffCnt++; diffs[d2] = true; ^~~~~ In file included from diff_sample.cpp:20:0: diff_sample.h: In function ‘void calcExhaustiveDC(T, bool, bool)’: diff_sample.h:175:6: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] if(!diffs[d1]) diffCnt++; diffs[d1] = true; ^~ diff_sample.h:175:32: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the ‘if’ if(!diffs[d1]) diffCnt++; diffs[d1] = true; ^~~~~ diff_sample.h:176:6: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] if(!diffs[d2]) diffCnt++; diffs[d2] = true; ^~ diff_sample.h:176:32: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the ‘if’ if(!diffs[d2]) diffCnt++; diffs[d2] = true; ^~~~~ Makefile:278: recipe for target 'hisat2-build-s' failed make[2]: *** [hisat2-build-s] Error 1 make[2]: Leaving directory '/<>' debian/rules:16: recipe for target 'override_dh_auto_build' failed make[1]: *** [override_dh_auto_build] Error 2 make[1]: Leaving directory '/<>' debian/rules:13: recipe for target 'build-arch' failed make: *** [build-arch] Error 2 dpkg-buildpackage: error: debian/rules build-arch gave error exit status 2 -------------------------------------------------------------------------------- Build finished at 20161103-2317 Finished -------- E: Build failure (dpkg-buildpackage died) +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Not removing build depends: as requested Keeping session: +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: i386 Build-Space: 13392 Build-Time: 53 Distribution: zesty-proposed Fail-Stage: build Host Architecture: i386 Install-Time: 18 Job: hisat2_2.0.4-2.dsc Machine Architecture: amd64 Package: hisat2 Package-Time: 74 Source-Version: 2.0.4-2 Space: 13392 Status: attempted Version: 2.0.4-2 -------------------------------------------------------------------------------- Finished at 20161103-2317 Build needed 00:01:14, 13392k disc space RUN: /usr/share/launchpad-buildd/slavebin/scan-for-processes ['scan-for-processes', 'PACKAGEBUILD-11127343'] Scanning for processes to kill in build /home/buildd/build-PACKAGEBUILD-11127343/chroot-autobuild... RUN: /usr/share/launchpad-buildd/slavebin/umount-chroot ['umount-chroot', 'PACKAGEBUILD-11127343'] Unmounting chroot for build PACKAGEBUILD-11127343... RUN: /usr/share/launchpad-buildd/slavebin/remove-build ['remove-build', 'PACKAGEBUILD-11127343'] Removing build PACKAGEBUILD-11127343