RUN: /usr/share/launchpad-buildd/slavebin/slave-prep ['slave-prep'] Forking launchpad-buildd slave process... Kernel version: Linux lgw01-05 3.19.0-33-generic #38~14.04.1-Ubuntu SMP Fri Nov 6 18:17:28 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... 24 Nov 23:14:47 ntpdate[1651]: adjust time server 10.211.37.1 offset 0.000887 sec RUN: /usr/share/launchpad-buildd/slavebin/unpack-chroot ['unpack-chroot', 'PACKAGEBUILD-8339795', '/home/buildd/filecache-default/9ecf9f6874f6384eb09ac1764090b184b3b8f2b8'] Unpacking chroot for build PACKAGEBUILD-8339795 RUN: /usr/share/launchpad-buildd/slavebin/mount-chroot ['mount-chroot', 'PACKAGEBUILD-8339795'] Mounting chroot for build PACKAGEBUILD-8339795 RUN: /usr/share/launchpad-buildd/slavebin/override-sources-list ['override-sources-list', 'PACKAGEBUILD-8339795', '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-8339795 RUN: /usr/share/launchpad-buildd/slavebin/update-debian-chroot ['update-debian-chroot', 'PACKAGEBUILD-8339795', 'i386'] Updating debian chroot for build PACKAGEBUILD-8339795 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 i386 Packages [1441 kB] Get:6 http://ftpmaster.internal xenial/universe i386 Packages [6964 kB] Get:7 http://ftpmaster.internal xenial/main Translation-en [842 kB] Get:8 http://ftpmaster.internal xenial/universe Translation-en [4712 kB] Get:9 http://ftpmaster.internal xenial-security/main i386 Packages [28 B] Get:10 http://ftpmaster.internal xenial-security/universe i386 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 i386 Packages [28 B] Get:14 http://ftpmaster.internal xenial-updates/universe i386 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 i386 Packages [58.2 kB] Get:18 http://ftpmaster.internal xenial-proposed/universe i386 Packages [282 kB] Get:19 http://ftpmaster.internal xenial-proposed/main Translation-en [25.0 kB] Get:20 http://ftpmaster.internal xenial-proposed/universe Translation-en [119 kB] Fetched 15.0 MB in 8s (1702 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... The following packages were automatically installed and are no longer required: libisl13 udev Use 'apt-get autoremove' to remove them. The following NEW packages will be installed: libisl15 The following packages will be upgraded: advancecomp base-files binutils bsdutils cpp cpp-5 debconf diffutils dpkg dpkg-dev e2fslibs e2fsprogs findutils g++ g++-5 gcc gcc-5 gcc-5-base grep hostname init initscripts libapparmor1 libasan2 libatomic1 libaudit-common libaudit1 libblkid1 libcap2 libcap2-bin libcc1-0 libcilkrts5 libcomerr2 libcurl3-gnutls libdbus-1-3 libdpkg-perl libfdisk1 libgcc-5-dev libgcc1 libgcrypt20 libgmp10 libgnutls-deb0-28 libgomp1 libgpg-error0 libgssapi-krb5-2 libidn11 libitm1 libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 libmount1 libmpx0 libpng12-0 libquadmath0 libselinux1 libsemanage-common libsemanage1 libsepol1 libsmartcols1 libsqlite3-0 libss2 libssl1.0.0 libstdc++-5-dev libstdc++6 libsystemd0 libtasn1-6 libubsan0 libudev1 libuuid1 linux-libc-dev lsb-base mount openssl pkg-create-dbgsym systemd systemd-sysv sysv-rc sysvinit-utils tar udev util-linux 82 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 91.2 MB of archives. After this operation, 168 MB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu/ xenial/main base-files i386 9.4ubuntu2 [70.0 kB] Get:2 http://ftpmaster.internal/ubuntu/ xenial/main bsdutils i386 1:2.27.1-1ubuntu3 [53.7 kB] Get:3 http://ftpmaster.internal/ubuntu/ xenial/main diffutils i386 1:3.3-2 [159 kB] Get:4 http://ftpmaster.internal/ubuntu/ xenial/main dpkg i386 1.18.3ubuntu1 [2109 kB] Get:5 http://ftpmaster.internal/ubuntu/ xenial/main e2fslibs i386 1.42.13-1ubuntu1 [208 kB] Get:6 http://ftpmaster.internal/ubuntu/ xenial/main e2fsprogs i386 1.42.13-1ubuntu1 [793 kB] Get:7 http://ftpmaster.internal/ubuntu/ xenial/main findutils i386 4.4.2-10 [253 kB] Get:8 http://ftpmaster.internal/ubuntu/ xenial-proposed/main grep i386 2.22-1 [154 kB] Get:9 http://ftpmaster.internal/ubuntu/ xenial/main hostname i386 3.16ubuntu2 [11.8 kB] Get:10 http://ftpmaster.internal/ubuntu/ xenial/main init i386 1.24ubuntu2 [3966 B] Get:11 http://ftpmaster.internal/ubuntu/ xenial/main libsmartcols1 i386 2.27.1-1ubuntu3 [67.8 kB] Get:12 http://ftpmaster.internal/ubuntu/ xenial/main libuuid1 i386 2.27.1-1ubuntu3 [15.9 kB] Get:13 http://ftpmaster.internal/ubuntu/ xenial/main libblkid1 i386 2.27.1-1ubuntu3 [120 kB] Get:14 http://ftpmaster.internal/ubuntu/ xenial/main libfdisk1 i386 2.27.1-1ubuntu3 [154 kB] Get:15 http://ftpmaster.internal/ubuntu/ xenial/main debconf all 1.5.58ubuntu1 [136 kB] Get:16 http://ftpmaster.internal/ubuntu/ xenial/main sysvinit-utils i386 2.88dsf-59.2ubuntu3 [26.1 kB] Get:17 http://ftpmaster.internal/ubuntu/ xenial/main sysv-rc all 2.88dsf-59.2ubuntu3 [36.1 kB] Get:18 http://ftpmaster.internal/ubuntu/ xenial/main initscripts i386 2.88dsf-59.2ubuntu3 [24.8 kB] Get:19 http://ftpmaster.internal/ubuntu/ xenial/main util-linux i386 2.27.1-1ubuntu3 [873 kB] Get:20 http://ftpmaster.internal/ubuntu/ xenial/main libudev1 i386 228-2ubuntu1 [59.3 kB] Get:21 http://ftpmaster.internal/ubuntu/ xenial/main udev i386 228-2ubuntu1 [983 kB] Get:22 http://ftpmaster.internal/ubuntu/ xenial/main libsystemd0 i386 228-2ubuntu1 [219 kB] Get:23 http://ftpmaster.internal/ubuntu/ xenial/main systemd i386 228-2ubuntu1 [3514 kB] Get:24 http://ftpmaster.internal/ubuntu/ xenial-proposed/main libgomp1 i386 5.2.1-25ubuntu1 [58.7 kB] Get:25 http://ftpmaster.internal/ubuntu/ xenial-proposed/main libitm1 i386 5.2.1-25ubuntu1 [30.7 kB] Get:26 http://ftpmaster.internal/ubuntu/ xenial-proposed/main libatomic1 i386 5.2.1-25ubuntu1 [9662 B] Get:27 http://ftpmaster.internal/ubuntu/ xenial-proposed/main libasan2 i386 5.2.1-25ubuntu1 [271 kB] Get:28 http://ftpmaster.internal/ubuntu/ xenial-proposed/main gcc-5-base i386 5.2.1-25ubuntu1 [16.4 kB] Get:29 http://ftpmaster.internal/ubuntu/ xenial-proposed/main libgcc1 i386 1:5.2.1-25ubuntu1 [46.4 kB] Get:30 http://ftpmaster.internal/ubuntu/ xenial-proposed/main libubsan0 i386 5.2.1-25ubuntu1 [111 kB] Get:31 http://ftpmaster.internal/ubuntu/ xenial-proposed/main libcilkrts5 i386 5.2.1-25ubuntu1 [44.8 kB] Get:32 http://ftpmaster.internal/ubuntu/ xenial-proposed/main libmpx0 i386 5.2.1-25ubuntu1 [11.2 kB] Get:33 http://ftpmaster.internal/ubuntu/ xenial-proposed/main libquadmath0 i386 5.2.1-25ubuntu1 [203 kB] Get:34 http://ftpmaster.internal/ubuntu/ xenial-proposed/main libisl15 i386 0.15-3 [588 kB] Get:35 http://ftpmaster.internal/ubuntu/ xenial-proposed/main cpp-5 i386 5.2.1-25ubuntu1 [25.2 MB] Get:36 http://ftpmaster.internal/ubuntu/ xenial-proposed/main libcc1-0 i386 5.2.1-25ubuntu1 [32.4 kB] Get:37 http://ftpmaster.internal/ubuntu/ xenial/main binutils i386 2.25.51.20151113-2ubuntu1 [2483 kB] Get:38 http://ftpmaster.internal/ubuntu/ xenial-proposed/main g++-5 i386 5.2.1-25ubuntu1 [15.4 MB] Get:39 http://ftpmaster.internal/ubuntu/ xenial-proposed/main gcc-5 i386 5.2.1-25ubuntu1 [25.5 MB] Get:40 http://ftpmaster.internal/ubuntu/ xenial-proposed/main libgcc-5-dev i386 5.2.1-25ubuntu1 [2241 kB] Get:41 http://ftpmaster.internal/ubuntu/ xenial-proposed/main libstdc++-5-dev i386 5.2.1-25ubuntu1 [1452 kB] Get:42 http://ftpmaster.internal/ubuntu/ xenial-proposed/main libstdc++6 i386 5.2.1-25ubuntu1 [418 kB] Get:43 http://ftpmaster.internal/ubuntu/ xenial/main libgmp10 i386 2:6.1.0+dfsg-2 [246 kB] Get:44 http://ftpmaster.internal/ubuntu/ xenial-proposed/main libselinux1 i386 2.4-3 [61.0 kB] Get:45 http://ftpmaster.internal/ubuntu/ xenial/main libapparmor1 i386 2.10-0ubuntu8 [30.5 kB] Get:46 http://ftpmaster.internal/ubuntu/ xenial/main libaudit-common all 1:2.4.4-4ubuntu1 [3892 B] Get:47 http://ftpmaster.internal/ubuntu/ xenial/main libaudit1 i386 1:2.4.4-4ubuntu1 [37.4 kB] Get:48 http://ftpmaster.internal/ubuntu/ xenial/main libcap2 i386 1:2.24-12 [13.2 kB] Get:49 http://ftpmaster.internal/ubuntu/ xenial/main libmount1 i386 2.27.1-1ubuntu3 [125 kB] Get:50 http://ftpmaster.internal/ubuntu/ xenial/main libcap2-bin i386 1:2.24-12 [20.5 kB] Get:51 http://ftpmaster.internal/ubuntu/ xenial/main lsb-base all 9.20150917ubuntu1 [13.4 kB] Get:52 http://ftpmaster.internal/ubuntu/ xenial/main mount i386 2.27.1-1ubuntu3 [126 kB] Get:53 http://ftpmaster.internal/ubuntu/ xenial/main tar i386 1.28-2.1 [220 kB] Get:54 http://ftpmaster.internal/ubuntu/ xenial/main systemd-sysv i386 228-2ubuntu1 [14.9 kB] Get:55 http://ftpmaster.internal/ubuntu/ xenial/main libcomerr2 i386 1.42.13-1ubuntu1 [65.9 kB] Get:56 http://ftpmaster.internal/ubuntu/ xenial/main libgpg-error0 i386 1.20-1 [35.7 kB] Get:57 http://ftpmaster.internal/ubuntu/ xenial/main libgcrypt20 i386 1.6.4-3 [320 kB] Get:58 http://ftpmaster.internal/ubuntu/ xenial/main libsepol1 i386 2.4-2 [204 kB] Get:59 http://ftpmaster.internal/ubuntu/ xenial-proposed/main libsemanage-common all 2.4-3 [6744 B] Get:60 http://ftpmaster.internal/ubuntu/ xenial-proposed/main libsemanage1 i386 2.4-3 [86.8 kB] Get:61 http://ftpmaster.internal/ubuntu/ xenial/main libss2 i386 1.42.13-1ubuntu1 [70.6 kB] Get:62 http://ftpmaster.internal/ubuntu/ xenial/main libtasn1-6 i386 4.7-2 [45.1 kB] Get:63 http://ftpmaster.internal/ubuntu/ xenial/main libgnutls-deb0-28 i386 3.3.18-1ubuntu1 [540 kB] Get:64 http://ftpmaster.internal/ubuntu/ xenial/main libpng12-0 i386 1.2.54-1 [122 kB] Get:65 http://ftpmaster.internal/ubuntu/ xenial-proposed/main libsqlite3-0 i386 3.9.2-1 [419 kB] Get:66 http://ftpmaster.internal/ubuntu/ xenial/main libssl1.0.0 i386 1.0.2d-0ubuntu2 [907 kB] Get:67 http://ftpmaster.internal/ubuntu/ xenial/main libgssapi-krb5-2 i386 1.13.2+dfsg-4 [129 kB] Get:68 http://ftpmaster.internal/ubuntu/ xenial/main libkrb5-3 i386 1.13.2+dfsg-4 [298 kB] Get:69 http://ftpmaster.internal/ubuntu/ xenial/main libkrb5support0 i386 1.13.2+dfsg-4 [32.0 kB] Get:70 http://ftpmaster.internal/ubuntu/ xenial/main libk5crypto3 i386 1.13.2+dfsg-4 [83.4 kB] Get:71 http://ftpmaster.internal/ubuntu/ xenial-proposed/main libkeyutils1 i386 1.5.9-8 [10.1 kB] Get:72 http://ftpmaster.internal/ubuntu/ xenial/main libidn11 i386 1.32-3ubuntu1 [46.6 kB] Get:73 http://ftpmaster.internal/ubuntu/ xenial/main libcurl3-gnutls i386 7.45.0-1ubuntu1 [203 kB] Get:74 http://ftpmaster.internal/ubuntu/ xenial/main libdbus-1-3 i386 1.10.4-1ubuntu2 [173 kB] Get:75 http://ftpmaster.internal/ubuntu/ xenial/main openssl i386 1.0.2d-0ubuntu2 [526 kB] Get:76 http://ftpmaster.internal/ubuntu/ xenial/main advancecomp i386 1.20-1 [163 kB] Get:77 http://ftpmaster.internal/ubuntu/ xenial-proposed/main cpp i386 4:5.2.1-13ubuntu4 [27.5 kB] Get:78 http://ftpmaster.internal/ubuntu/ xenial/main dpkg-dev all 1.18.3ubuntu1 [583 kB] Get:79 http://ftpmaster.internal/ubuntu/ xenial/main libdpkg-perl all 1.18.3ubuntu1 [195 kB] Get:80 http://ftpmaster.internal/ubuntu/ xenial-proposed/main gcc i386 4:5.2.1-13ubuntu4 [5188 B] Get:81 http://ftpmaster.internal/ubuntu/ xenial-proposed/main g++ i386 4:5.2.1-13ubuntu4 [1488 B] Get:82 http://ftpmaster.internal/ubuntu/ xenial/main linux-libc-dev i386 4.2.0-19.23 [819 kB] Get:83 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 91.2 MB in 16s (5694 kB/s) 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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 ... 11679 files and directories currently installed.) Preparing to unpack .../bsdutils_1%3a2.27.1-1ubuntu3_i386.deb ... Unpacking bsdutils (1:2.27.1-1ubuntu3) over (1:2.26.2-6ubuntu3) ... Setting up bsdutils (1:2.27.1-1ubuntu3) ... (Reading database ... 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RUN: /usr/share/launchpad-buildd/slavebin/sbuild-package ['sbuild-package', 'PACKAGEBUILD-8339795', 'i386', 'xenial-proposed', '-c', 'chroot:autobuild', '--arch=i386', '--dist=xenial-proposed', '--purge=never', '--nolog', 'clustalo_1.2.1-2.dsc'] Initiating build PACKAGEBUILD-8339795 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 3.19.0-33-generic #38~14.04.1-Ubuntu SMP Fri Nov 6 18:17:28 UTC 2015 i686 sbuild (Debian sbuild) 0.65.2 (24 Mar 2015) on lgw01-05.buildd ╔══════════════════════════════════════════════════════════════════════════════╗ ║ clustalo 1.2.1-2 (i386) 24 Nov 2015 23:15 ║ ╚══════════════════════════════════════════════════════════════════════════════╝ Package: clustalo Version: 1.2.1-2 Source Version: 1.2.1-2 Distribution: xenial-proposed Machine Architecture: amd64 Host Architecture: i386 Build Architecture: i386 I: NOTICE: Log filtering will replace 'build/clustalo-q2nzvA/clustalo-1.2.1' with '«PKGBUILDDIR»' I: NOTICE: Log filtering will replace 'build/clustalo-q2nzvA' with '«BUILDDIR»' I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-8339795/chroot-autobuild' with '«CHROOT»' ┌──────────────────────────────────────────────────────────────────────────────┐ │ Fetch source files │ └──────────────────────────────────────────────────────────────────────────────┘ Local sources ───────────── clustalo_1.2.1-2.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-ACjUD8/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 packages were automatically installed and are no longer required: libisl13 udev Use 'apt-get 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 0 B/774 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 ... 11705 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, dh-linktree, libargtable2-dev, doxygen, graphviz, sphinx-common 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, dh-linktree, libargtable2-dev, doxygen, graphviz, sphinx-common dpkg-deb: building package 'sbuild-build-depends-clustalo-dummy' in '/«BUILDDIR»/resolver-JkxbfY/apt_archive/sbuild-build-depends-clustalo-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 clustalo 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: libisl13 udev Use 'apt-get autoremove' to remove them. The following extra packages will be installed: autoconf automake autopoint autotools-dev bsdmainutils debhelper dh-autoreconf dh-linktree dh-strip-nondeterminism doxygen file fontconfig fontconfig-config fonts-dejavu-core gettext gettext-base graphviz groff-base intltool-debian libarchive-zip-perl libargtable2-0 libargtable2-dev libargtable2-docs libasprintf0v5 libbsd0 libcairo2 libcdt5 libcgraph6 libclang1-3.6 libcroco3 libdatrie1 libedit2 libexpat1 libfile-stripnondeterminism-perl libfontconfig1 libfreetype6 libgd3 libglib2.0-0 libgraphite2-3 libgvc6 libgvpr2 libharfbuzz0b libice6 libicu55 libjbig0 libjpeg-turbo8 libjpeg8 libjs-jquery libjs-sphinxdoc libjs-underscore libllvm3.6v5 libltdl7 libmagic1 libobjc-5-dev libobjc4 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpathplan4 libpipeline1 libpixman-1-0 libsigsegv2 libsm6 libthai-data libthai0 libtiff5 libtimedate-perl libtool libunistring0 libvpx2 libx11-6 libx11-data libxapian22v5 libxau6 libxaw7 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxml2 libxmu6 libxpm4 libxrender1 libxt6 m4 man-db po-debconf sphinx-common ucf x11-common Suggested packages: autoconf-archive gnu-standards autoconf-doc wamerican wordlist whois vacation dh-make doxygen-latex doxygen-doc doxygen-gui gettext-doc gsfonts graphviz-doc groff libgd-tools javascript-common libtool-doc automaken gfortran fortran95-compiler gcj-jdk xapian-tools less www-browser libmail-box-perl Recommended packages: curl wget lynx-cur libasprintf-dev libgettextpo-dev fonts-liberation libglib2.0-data shared-mime-info xdg-user-dirs libltdl-dev xml-core libmail-sendmail-perl python-sphinx python3-sphinx The following NEW packages will be installed: autoconf automake autopoint autotools-dev bsdmainutils debhelper dh-autoreconf dh-linktree dh-strip-nondeterminism doxygen file fontconfig fontconfig-config fonts-dejavu-core gettext gettext-base graphviz groff-base intltool-debian libarchive-zip-perl libargtable2-0 libargtable2-dev libargtable2-docs libasprintf0v5 libbsd0 libcairo2 libcdt5 libcgraph6 libclang1-3.6 libcroco3 libdatrie1 libedit2 libexpat1 libfile-stripnondeterminism-perl libfontconfig1 libfreetype6 libgd3 libglib2.0-0 libgraphite2-3 libgvc6 libgvpr2 libharfbuzz0b libice6 libicu55 libjbig0 libjpeg-turbo8 libjpeg8 libjs-jquery libjs-sphinxdoc libjs-underscore libllvm3.6v5 libltdl7 libmagic1 libobjc-5-dev libobjc4 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpathplan4 libpipeline1 libpixman-1-0 libsigsegv2 libsm6 libthai-data libthai0 libtiff5 libtimedate-perl libtool libunistring0 libvpx2 libx11-6 libx11-data libxapian22v5 libxau6 libxaw7 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxml2 libxmu6 libxpm4 libxrender1 libxt6 m4 man-db po-debconf sbuild-build-depends-clustalo-dummy sphinx-common ucf x11-common 0 upgraded, 92 newly installed, 0 to remove and 0 not upgraded. Need to get 44.4 MB/44.4 MB of archives. After this operation, 170 MB of additional disk space will be used. WARNING: The following packages cannot be authenticated! sbuild-build-depends-clustalo-dummy Authentication warning overridden. Get:1 http://ftpmaster.internal/ubuntu/ xenial/main libbsd0 i386 0.7.0-2 [36.7 kB] Get:2 http://ftpmaster.internal/ubuntu/ xenial/main libasprintf0v5 i386 0.19.4-1ubuntu3 [6706 B] Get:3 http://ftpmaster.internal/ubuntu/ xenial/main libxau6 i386 1:1.0.8-1 [8352 B] Get:4 http://ftpmaster.internal/ubuntu/ xenial/main libxdmcp6 i386 1:1.1.2-1 [11.5 kB] Get:5 http://ftpmaster.internal/ubuntu/ xenial/main libxcb1 i386 1.11.1-1ubuntu1 [44.1 kB] Get:6 http://ftpmaster.internal/ubuntu/ xenial/main libx11-data all 2:1.6.3-1ubuntu2 [113 kB] Get:7 http://ftpmaster.internal/ubuntu/ xenial/main libx11-6 i386 2:1.6.3-1ubuntu2 [592 kB] Get:8 http://ftpmaster.internal/ubuntu/ xenial/main libxext6 i386 2:1.3.3-1 [31.6 kB] Get:9 http://ftpmaster.internal/ubuntu/ xenial/main groff-base i386 1.22.3-4 [1152 kB] Get:10 http://ftpmaster.internal/ubuntu/ xenial/main bsdmainutils i386 9.0.6ubuntu1 [175 kB] Get:11 http://ftpmaster.internal/ubuntu/ xenial/main libpipeline1 i386 1.4.1-1 [26.7 kB] Get:12 http://ftpmaster.internal/ubuntu/ xenial/main man-db i386 2.7.5-1 [865 kB] Get:13 http://ftpmaster.internal/ubuntu/ xenial/main fonts-dejavu-core all 2.35-1 [1039 kB] Get:14 http://ftpmaster.internal/ubuntu/ xenial/main ucf all 3.0031 [52.7 kB] Get:15 http://ftpmaster.internal/ubuntu/ xenial/main fontconfig-config all 2.11.1-0ubuntu6 [48.7 kB] Get:16 http://ftpmaster.internal/ubuntu/ xenial/main libexpat1 i386 2.1.0-7 [74.3 kB] Get:17 http://ftpmaster.internal/ubuntu/ xenial/main libfreetype6 i386 2.5.2-4ubuntu2 [326 kB] Get:18 http://ftpmaster.internal/ubuntu/ xenial/main libfontconfig1 i386 2.11.1-0ubuntu6 [135 kB] Get:19 http://ftpmaster.internal/ubuntu/ xenial/main fontconfig i386 2.11.1-0ubuntu6 [176 kB] Get:20 http://ftpmaster.internal/ubuntu/ xenial/main libgraphite2-3 i386 1.2.4-3ubuntu1 [57.5 kB] Get:21 http://ftpmaster.internal/ubuntu/ xenial/main x11-common all 1:7.7+12ubuntu1 [22.4 kB] Get:22 http://ftpmaster.internal/ubuntu/ xenial/main libice6 i386 2:1.0.9-1 [38.2 kB] Get:23 http://ftpmaster.internal/ubuntu/ xenial/main libjpeg-turbo8 i386 1.3.0-0ubuntu2 [107 kB] Get:24 http://ftpmaster.internal/ubuntu/ xenial/main libltdl7 i386 2.4.2-1.11 [36.8 kB] Get:25 http://ftpmaster.internal/ubuntu/ xenial/main libsigsegv2 i386 2.10-4 [14.0 kB] Get:26 http://ftpmaster.internal/ubuntu/ xenial/main libsm6 i386 2:1.2.2-1 [14.8 kB] Get:27 http://ftpmaster.internal/ubuntu/ xenial/main libunistring0 i386 0.9.3-5.2ubuntu1 [277 kB] Get:28 http://ftpmaster.internal/ubuntu/ xenial/main libxpm4 i386 1:3.5.11-1 [32.1 kB] Get:29 http://ftpmaster.internal/ubuntu/ xenial/main libjbig0 i386 2.1-3.1 [27.0 kB] Get:30 http://ftpmaster.internal/ubuntu/ xenial/main libmagic1 i386 1:5.25-2ubuntu1 [222 kB] Get:31 http://ftpmaster.internal/ubuntu/ xenial/main file i386 1:5.25-2ubuntu1 [21.1 kB] Get:32 http://ftpmaster.internal/ubuntu/ xenial/main gettext-base i386 0.19.4-1ubuntu3 [49.2 kB] Get:33 http://ftpmaster.internal/ubuntu/ xenial/main libedit2 i386 3.1-20150325-1ubuntu1 [80.9 kB] Get:34 http://ftpmaster.internal/ubuntu/ xenial/main libglib2.0-0 i386 2.47.1-1 [1178 kB] Get:35 http://ftpmaster.internal/ubuntu/ xenial/main libicu55 i386 55.1-6ubuntu1 [7755 kB] Get:36 http://ftpmaster.internal/ubuntu/ xenial/main libxml2 i386 2.9.2+zdfsg1-4ubuntu1 [729 kB] Get:37 http://ftpmaster.internal/ubuntu/ xenial/main m4 i386 1.4.17-4 [190 kB] Get:38 http://ftpmaster.internal/ubuntu/ xenial/main autoconf all 2.69-9 [321 kB] Get:39 http://ftpmaster.internal/ubuntu/ xenial/main autotools-dev all 20150820.1 [39.8 kB] Get:40 http://ftpmaster.internal/ubuntu/ xenial/main automake all 1:1.15-1ubuntu1 [511 kB] Get:41 http://ftpmaster.internal/ubuntu/ xenial/main autopoint all 0.19.4-1ubuntu3 [390 kB] Get:42 http://ftpmaster.internal/ubuntu/ xenial/main libcroco3 i386 0.6.9-1 [88.5 kB] Get:43 http://ftpmaster.internal/ubuntu/ xenial/main gettext i386 0.19.4-1ubuntu3 [864 kB] Get:44 http://ftpmaster.internal/ubuntu/ xenial/main intltool-debian all 0.35.0+20060710.4 [24.9 kB] Get:45 http://ftpmaster.internal/ubuntu/ xenial/main po-debconf all 1.0.18 [234 kB] Get:46 http://ftpmaster.internal/ubuntu/ xenial/main libarchive-zip-perl all 1.53-1 [87.0 kB] Get:47 http://ftpmaster.internal/ubuntu/ xenial/main libfile-stripnondeterminism-perl all 0.014-1 [10.1 kB] Get:48 http://ftpmaster.internal/ubuntu/ xenial/main libtimedate-perl all 2.3000-2 [37.5 kB] Get:49 http://ftpmaster.internal/ubuntu/ xenial/main dh-strip-nondeterminism all 0.014-1 [5596 B] Get:50 http://ftpmaster.internal/ubuntu/ xenial/main debhelper all 9.20151117ubuntu1 [742 kB] Get:51 http://ftpmaster.internal/ubuntu/ xenial/main libtool all 2.4.2-1.11 [180 kB] Get:52 http://ftpmaster.internal/ubuntu/ xenial/main dh-autoreconf all 10 [15.3 kB] Get:53 http://ftpmaster.internal/ubuntu/ xenial/universe dh-linktree all 0.4 [11.0 kB] Get:54 http://ftpmaster.internal/ubuntu/ xenial/main libllvm3.6v5 i386 1:3.6.2-3build1 [9011 kB] Get:55 http://ftpmaster.internal/ubuntu/ xenial-proposed/main libobjc4 i386 5.2.1-25ubuntu1 [118 kB] Get:56 http://ftpmaster.internal/ubuntu/ xenial-proposed/main libobjc-5-dev i386 5.2.1-25ubuntu1 [353 kB] Get:57 http://ftpmaster.internal/ubuntu/ xenial/main libclang1-3.6 i386 1:3.6.2-3build1 [4227 kB] Get:58 http://ftpmaster.internal/ubuntu/ xenial/main libxapian22v5 i386 1.2.21-1.2 [780 kB] Get:59 http://ftpmaster.internal/ubuntu/ xenial/main doxygen i386 1.8.9.1-5 [3100 kB] Get:60 http://ftpmaster.internal/ubuntu/ xenial/main libcdt5 i386 2.38.0-12 [23.6 kB] Get:61 http://ftpmaster.internal/ubuntu/ xenial/main libcgraph6 i386 2.38.0-12 [47.2 kB] Get:62 http://ftpmaster.internal/ubuntu/ xenial/main libjpeg8 i386 8c-2ubuntu8 [2188 B] Get:63 http://ftpmaster.internal/ubuntu/ xenial/main libtiff5 i386 4.0.5-1 [154 kB] Get:64 http://ftpmaster.internal/ubuntu/ xenial/main libvpx2 i386 1.4.0-4 [636 kB] Get:65 http://ftpmaster.internal/ubuntu/ xenial/main libgd3 i386 2.1.1-4build1 [128 kB] Get:66 http://ftpmaster.internal/ubuntu/ xenial/main libpixman-1-0 i386 0.33.4-1 [210 kB] Get:67 http://ftpmaster.internal/ubuntu/ xenial/main libxcb-render0 i386 1.11.1-1ubuntu1 [12.2 kB] Get:68 http://ftpmaster.internal/ubuntu/ xenial/main libxcb-shm0 i386 1.11.1-1ubuntu1 [5754 B] Get:69 http://ftpmaster.internal/ubuntu/ xenial/main libxrender1 i386 1:0.9.9-0ubuntu1 [19.2 kB] Get:70 http://ftpmaster.internal/ubuntu/ xenial/main libcairo2 i386 1.14.4-1 [614 kB] Get:71 http://ftpmaster.internal/ubuntu/ xenial/main libthai-data all 0.1.24-1 [131 kB] Get:72 http://ftpmaster.internal/ubuntu/ xenial/main libdatrie1 i386 0.2.10-1 [18.5 kB] Get:73 http://ftpmaster.internal/ubuntu/ xenial/main libthai0 i386 0.1.24-1 [18.0 kB] Get:74 http://ftpmaster.internal/ubuntu/ xenial/main libpango-1.0-0 i386 1.38.1-1 [154 kB] Get:75 http://ftpmaster.internal/ubuntu/ xenial/main libharfbuzz0b i386 1.0.1-1build2 [148 kB] Get:76 http://ftpmaster.internal/ubuntu/ xenial/main libpangoft2-1.0-0 i386 1.38.1-1 [36.5 kB] Get:77 http://ftpmaster.internal/ubuntu/ xenial/main libpangocairo-1.0-0 i386 1.38.1-1 [22.5 kB] Get:78 http://ftpmaster.internal/ubuntu/ xenial/main libpathplan4 i386 2.38.0-12 [26.7 kB] Get:79 http://ftpmaster.internal/ubuntu/ xenial/main libgvc6 i386 2.38.0-12 [616 kB] Get:80 http://ftpmaster.internal/ubuntu/ xenial/main libgvpr2 i386 2.38.0-12 [181 kB] Get:81 http://ftpmaster.internal/ubuntu/ xenial/main libxt6 i386 1:1.1.5-0ubuntu1 [164 kB] Get:82 http://ftpmaster.internal/ubuntu/ xenial/main libxmu6 i386 2:1.1.2-1ubuntu1 [48.4 kB] Get:83 http://ftpmaster.internal/ubuntu/ xenial/main libxaw7 i386 2:1.0.13-1 [182 kB] Get:84 http://ftpmaster.internal/ubuntu/ xenial/main graphviz i386 2.38.0-12 [682 kB] Get:85 http://ftpmaster.internal/ubuntu/ xenial/universe libargtable2-0 i386 12-1.1 [13.9 kB] Get:86 http://ftpmaster.internal/ubuntu/ xenial/universe libargtable2-docs all 12-1.1 [2620 kB] Get:87 http://ftpmaster.internal/ubuntu/ xenial/universe libargtable2-dev i386 12-1.1 [51.3 kB] Get:88 http://ftpmaster.internal/ubuntu/ xenial/main libjs-jquery all 1.7.2+dfsg-3ubuntu2 [69.0 kB] Get:89 http://ftpmaster.internal/ubuntu/ xenial/main libjs-underscore all 1.7.0~dfsg-1ubuntu1 [46.7 kB] Get:90 http://ftpmaster.internal/ubuntu/ xenial/main libjs-sphinxdoc all 1.3.1-7ubuntu2 [55.2 kB] Get:91 http://ftpmaster.internal/ubuntu/ xenial/main sphinx-common all 1.3.1-7ubuntu2 [322 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 44.4 MB in 5s (7534 kB/s) Selecting previously unselected package libbsd0:i386. 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Preparing to unpack .../libjs-underscore_1.7.0~dfsg-1ubuntu1_all.deb ... Unpacking libjs-underscore (1.7.0~dfsg-1ubuntu1) ... Selecting previously unselected package libjs-sphinxdoc. Preparing to unpack .../libjs-sphinxdoc_1.3.1-7ubuntu2_all.deb ... Unpacking libjs-sphinxdoc (1.3.1-7ubuntu2) ... Selecting previously unselected package sphinx-common. Preparing to unpack .../sphinx-common_1.3.1-7ubuntu2_all.deb ... Unpacking sphinx-common (1.3.1-7ubuntu2) ... Selecting previously unselected package sbuild-build-depends-clustalo-dummy. Preparing to unpack .../sbuild-build-depends-clustalo-dummy.deb ... Unpacking sbuild-build-depends-clustalo-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.21-0ubuntu4) ... Processing triggers for systemd (228-2ubuntu1) ... Setting up libbsd0:i386 (0.7.0-2) ... Setting up libasprintf0v5:i386 (0.19.4-1ubuntu3) ... Setting up libxau6:i386 (1:1.0.8-1) ... Setting up libxdmcp6:i386 (1:1.1.2-1) ... Setting up libxcb1:i386 (1.11.1-1ubuntu1) ... Setting up libx11-data (2:1.6.3-1ubuntu2) ... Setting up libx11-6:i386 (2:1.6.3-1ubuntu2) ... Setting up libxext6:i386 (2:1.3.3-1) ... Setting up groff-base (1.22.3-4) ... 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:i386 (1.4.1-1) ... Setting up man-db (2.7.5-1) ... Not building database; man-db/auto-update is not 'true'. Setting up fonts-dejavu-core (2.35-1) ... Setting up ucf (3.0031) ... Setting up fontconfig-config (2.11.1-0ubuntu6) ... Setting up libexpat1:i386 (2.1.0-7) ... Setting up libfreetype6:i386 (2.5.2-4ubuntu2) ... Setting up libfontconfig1:i386 (2.11.1-0ubuntu6) ... Setting up fontconfig (2.11.1-0ubuntu6) ... Regenerating fonts cache... done. Setting up libgraphite2-3:i386 (1.2.4-3ubuntu1) ... Setting up x11-common (1:7.7+12ubuntu1) ... update-rc.d: warning: start and stop actions are no longer supported; falling back to defaults Running in chroot, ignoring request. invoke-rc.d: policy-rc.d denied execution of start. Setting up libice6:i386 (2:1.0.9-1) ... Setting up libjpeg-turbo8:i386 (1.3.0-0ubuntu2) ... Setting up libltdl7:i386 (2.4.2-1.11) ... Setting up libsigsegv2:i386 (2.10-4) ... Setting up libsm6:i386 (2:1.2.2-1) ... Setting up libunistring0:i386 (0.9.3-5.2ubuntu1) ... Setting up libxpm4:i386 (1:3.5.11-1) ... Setting up libjbig0:i386 (2.1-3.1) ... Setting up libmagic1:i386 (1:5.25-2ubuntu1) ... Setting up file (1:5.25-2ubuntu1) ... Setting up gettext-base (0.19.4-1ubuntu3) ... Setting up libedit2:i386 (3.1-20150325-1ubuntu1) ... Setting up libglib2.0-0:i386 (2.47.1-1) ... No schema files found: doing nothing. Setting up libicu55:i386 (55.1-6ubuntu1) ... Setting up libxml2:i386 (2.9.2+zdfsg1-4ubuntu1) ... 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 libcroco3:i386 (0.6.9-1) ... 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 (0.014-1) ... Setting up libtimedate-perl (2.3000-2) ... Setting up libtool (2.4.2-1.11) ... Setting up libllvm3.6v5:i386 (1:3.6.2-3build1) ... Setting up libobjc4:i386 (5.2.1-25ubuntu1) ... Setting up libobjc-5-dev:i386 (5.2.1-25ubuntu1) ... Setting up libclang1-3.6:i386 (1:3.6.2-3build1) ... Setting up libxapian22v5 (1.2.21-1.2) ... Setting up doxygen (1.8.9.1-5) ... Setting up libcdt5 (2.38.0-12) ... Setting up libcgraph6 (2.38.0-12) ... Setting up libjpeg8:i386 (8c-2ubuntu8) ... Setting up libtiff5:i386 (4.0.5-1) ... Setting up libvpx2:i386 (1.4.0-4) ... Setting up libgd3:i386 (2.1.1-4build1) ... Setting up libpixman-1-0:i386 (0.33.4-1) ... Setting up libxcb-render0:i386 (1.11.1-1ubuntu1) ... Setting up libxcb-shm0:i386 (1.11.1-1ubuntu1) ... Setting up libxrender1:i386 (1:0.9.9-0ubuntu1) ... Setting up libcairo2:i386 (1.14.4-1) ... Setting up libthai-data (0.1.24-1) ... Setting up libdatrie1:i386 (0.2.10-1) ... Setting up libthai0:i386 (0.1.24-1) ... Setting up libpango-1.0-0:i386 (1.38.1-1) ... Setting up libharfbuzz0b:i386 (1.0.1-1build2) ... Setting up libpangoft2-1.0-0:i386 (1.38.1-1) ... Setting up libpangocairo-1.0-0:i386 (1.38.1-1) ... Setting up libpathplan4 (2.38.0-12) ... Setting up libgvc6 (2.38.0-12) ... Setting up libgvpr2 (2.38.0-12) ... Setting up libxt6:i386 (1:1.1.5-0ubuntu1) ... Setting up libxmu6:i386 (2:1.1.2-1ubuntu1) ... Setting up libxaw7:i386 (2:1.0.13-1) ... Setting up graphviz (2.38.0-12) ... Setting up libargtable2-0 (12-1.1) ... Setting up libargtable2-docs (12-1.1) ... Setting up libargtable2-dev (12-1.1) ... Setting up libjs-jquery (1.7.2+dfsg-3ubuntu2) ... Setting up libjs-underscore (1.7.0~dfsg-1ubuntu1) ... Setting up libjs-sphinxdoc (1.3.1-7ubuntu2) ... Setting up sphinx-common (1.3.1-7ubuntu2) ... Setting up debhelper (9.20151117ubuntu1) ... Setting up dh-autoreconf (10) ... Setting up dh-linktree (0.4) ... Setting up sbuild-build-depends-clustalo-dummy (0.invalid.0) ... Setting up dh-strip-nondeterminism (0.014-1) ... Processing triggers for libc-bin (2.21-0ubuntu4) ... Processing triggers for systemd (228-2ubuntu1) ... ┌──────────────────────────────────────────────────────────────────────────────┐ │ Build environment │ └──────────────────────────────────────────────────────────────────────────────┘ Kernel: Linux 3.19.0-33-generic amd64 (i686) Toolchain package versions: binutils_2.25.51.20151113-2ubuntu1 dpkg-dev_1.18.3ubuntu1 g++-5_5.2.1-25ubuntu1 gcc-5_5.2.1-25ubuntu1 libc6-dev_2.21-0ubuntu4 libstdc++-5-dev_5.2.1-25ubuntu1 libstdc++6_5.2.1-25ubuntu1 linux-libc-dev_4.2.0-19.23 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_2.25.51.20151113-2ubuntu1 bsdmainutils_9.0.6ubuntu1 bsdutils_1:2.27.1-1ubuntu3 build-essential_12.1ubuntu2 bzip2_1.0.6-8 ca-certificates_20150426ubuntu1 coreutils_8.23-4ubuntu2 cpp_4:5.2.1-13ubuntu4 cpp-5_5.2.1-25ubuntu1 dash_0.5.7-4ubuntu2 debconf_1.5.58ubuntu1 debhelper_9.20151117ubuntu1 debianutils_4.5.1 dh-autoreconf_10 dh-linktree_0.4 dh-strip-nondeterminism_0.014-1 diffutils_1:3.3-2 dmsetup_2:1.02.99-1ubuntu1 doxygen_1.8.9.1-5 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_1:5.25-2ubuntu1 findutils_4.4.2-10 fontconfig_2.11.1-0ubuntu6 fontconfig-config_2.11.1-0ubuntu6 fonts-dejavu-core_2.35-1 g++_4:5.2.1-13ubuntu4 g++-5_5.2.1-25ubuntu1 gcc_4:5.2.1-13ubuntu4 gcc-5_5.2.1-25ubuntu1 gcc-5-base_5.2.1-25ubuntu1 gettext_0.19.4-1ubuntu3 gettext-base_0.19.4-1ubuntu3 gnupg_1.4.18-7ubuntu1 gpgv_1.4.18-7ubuntu1 graphviz_2.38.0-12 grep_2.22-1 groff-base_1.22.3-4 gzip_1.6-4ubuntu1 hostname_3.16ubuntu2 init_1.24ubuntu2 initscripts_2.88dsf-59.2ubuntu3 insserv_1.14.0-5ubuntu3 intltool-debian_0.35.0+20060710.4 libacl1_2.2.52-2 libapparmor1_2.10-0ubuntu8 libapt-pkg4.16_1.0.10.2ubuntu1 libarchive-zip-perl_1.53-1 libargtable2-0_12-1.1 libargtable2-dev_12-1.1 libargtable2-docs_12-1.1 libasan2_5.2.1-25ubuntu1 libasn1-8-heimdal_1.6~rc2+dfsg-10ubuntu1 libasprintf0v5_0.19.4-1ubuntu3 libatomic1_5.2.1-25ubuntu1 libattr1_1:2.4.47-2 libaudit-common_1:2.4.4-4ubuntu1 libaudit1_1:2.4.4-4ubuntu1 libblkid1_2.27.1-1ubuntu3 libbsd0_0.7.0-2 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 libcairo2_1.14.4-1 libcap2_1:2.24-12 libcap2-bin_1:2.24-12 libcc1-0_5.2.1-25ubuntu1 libcdt5_2.38.0-12 libcgraph6_2.38.0-12 libcilkrts5_5.2.1-25ubuntu1 libclang1-3.6_1:3.6.2-3build1 libcomerr2_1.42.13-1ubuntu1 libcroco3_0.6.9-1 libcryptsetup4_2:1.6.6-5ubuntu2 libcurl3-gnutls_7.45.0-1ubuntu1 libdatrie1_0.2.10-1 libdb5.3_5.3.28-11 libdbus-1-3_1.10.4-1ubuntu2 libdebconfclient0_0.192ubuntu1 libdevmapper1.02.1_2:1.02.99-1ubuntu1 libdpkg-perl_1.18.3ubuntu1 libedit2_3.1-20150325-1ubuntu1 libexpat1_2.1.0-7 libfakeroot_1.20.2-1ubuntu1 libfdisk1_2.27.1-1ubuntu3 libffi6_3.2.1-3 libfile-stripnondeterminism-perl_0.014-1 libfontconfig1_2.11.1-0ubuntu6 libfreetype6_2.5.2-4ubuntu2 libgcc-5-dev_5.2.1-25ubuntu1 libgcc1_1:5.2.1-25ubuntu1 libgcrypt20_1.6.4-3 libgd3_2.1.1-4build1 libgdbm3_1.8.3-13.1 libglib2.0-0_2.47.1-1 libgmp10_2:6.1.0+dfsg-2 libgnutls-deb0-28_3.3.18-1ubuntu1 libgomp1_5.2.1-25ubuntu1 libgpg-error0_1.20-1 libgraphite2-3_1.2.4-3ubuntu1 libgssapi-krb5-2_1.13.2+dfsg-4 libgssapi3-heimdal_1.6~rc2+dfsg-10ubuntu1 libgvc6_2.38.0-12 libgvpr2_2.38.0-12 libharfbuzz0b_1.0.1-1build2 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 libice6_2:1.0.9-1 libicu55_55.1-6ubuntu1 libidn11_1.32-3ubuntu1 libisl13_0.14-2 libisl15_0.15-3 libitm1_5.2.1-25ubuntu1 libjbig0_2.1-3.1 libjpeg-turbo8_1.3.0-0ubuntu2 libjpeg8_8c-2ubuntu8 libjs-jquery_1.7.2+dfsg-3ubuntu2 libjs-sphinxdoc_1.3.1-7ubuntu2 libjs-underscore_1.7.0~dfsg-1ubuntu1 libk5crypto3_1.13.2+dfsg-4 libkeyutils1_1.5.9-8 libkmod2_21-1ubuntu1 libkrb5-26-heimdal_1.6~rc2+dfsg-10ubuntu1 libkrb5-3_1.13.2+dfsg-4 libkrb5support0_1.13.2+dfsg-4 libldap-2.4-2_2.4.41+dfsg-1ubuntu2 libllvm3.6v5_1:3.6.2-3build1 liblockfile-bin_1.09-6ubuntu1 liblockfile1_1.09-6ubuntu1 libltdl7_2.4.2-1.11 liblzma5_5.1.1alpha+20120614-2ubuntu2 libmagic1_1:5.25-2ubuntu1 libmount1_2.27.1-1ubuntu3 libmpc3_1.0.3-1 libmpfr4_3.1.3-1 libmpx0_5.2.1-25ubuntu1 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 libobjc-5-dev_5.2.1-25ubuntu1 libobjc4_5.2.1-25ubuntu1 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 libpango-1.0-0_1.38.1-1 libpangocairo-1.0-0_1.38.1-1 libpangoft2-1.0-0_1.38.1-1 libpathplan4_2.38.0-12 libpcre3_2:8.35-7.1ubuntu1 libpipeline1_1.4.1-1 libpixman-1-0_0.33.4-1 libpng12-0_1.2.54-1 libprocps3_1:3.3.9-1ubuntu8 libquadmath0_5.2.1-25ubuntu1 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_2.4-3 libsemanage-common_2.4-3 libsemanage1_2.4-3 libsepol1_2.4-2 libsigsegv2_2.10-4 libslang2_2.3.0-2ubuntu1 libsm6_2:1.2.2-1 libsmartcols1_2.27.1-1ubuntu3 libsqlite3-0_3.9.2-1 libss2_1.42.13-1ubuntu1 libssl1.0.0_1.0.2d-0ubuntu2 libstdc++-5-dev_5.2.1-25ubuntu1 libstdc++6_5.2.1-25ubuntu1 libsystemd0_228-2ubuntu1 libtasn1-6_4.7-2 libthai-data_0.1.24-1 libthai0_0.1.24-1 libtiff5_4.0.5-1 libtimedate-perl_2.3000-2 libtinfo5_5.9+20150516-2ubuntu1 libtool_2.4.2-1.11 libubsan0_5.2.1-25ubuntu1 libudev1_228-2ubuntu1 libunistring0_0.9.3-5.2ubuntu1 libusb-0.1-4_2:0.1.12-27 libustr-1.0-1_1.0.4-5 libuuid1_2.27.1-1ubuntu3 libvpx2_1.4.0-4 libwind0-heimdal_1.6~rc2+dfsg-10ubuntu1 libx11-6_2:1.6.3-1ubuntu2 libx11-data_2:1.6.3-1ubuntu2 libxapian22v5_1.2.21-1.2 libxau6_1:1.0.8-1 libxaw7_2:1.0.13-1 libxcb-render0_1.11.1-1ubuntu1 libxcb-shm0_1.11.1-1ubuntu1 libxcb1_1.11.1-1ubuntu1 libxdmcp6_1:1.1.2-1 libxext6_2:1.3.3-1 libxml2_2.9.2+zdfsg1-4ubuntu1 libxmu6_2:1.1.2-1ubuntu1 libxpm4_1:3.5.11-1 libxrender1_1:0.9.9-0ubuntu1 libxt6_1:1.1.5-0ubuntu1 linux-libc-dev_4.2.0-19.23 lockfile-progs_0.1.17 login_1:4.1.5.1-1.1ubuntu7 lsb-base_9.20150917ubuntu1 m4_1.4.17-4 make_4.0-8.2 man-db_2.7.5-1 mawk_1.3.3-17ubuntu2 mount_2.27.1-1ubuntu3 multiarch-support_2.21-0ubuntu4 ncurses-base_5.9+20150516-2ubuntu1 ncurses-bin_5.9+20150516-2ubuntu1 openssl_1.0.2d-0ubuntu2 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-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-clustalo-dummy_0.invalid.0 sbuild-build-depends-core-dummy_0.invalid.0 sed_4.2.2-6.1 sensible-utils_0.0.9 sphinx-common_1.3.1-7ubuntu2 systemd_228-2ubuntu1 systemd-sysv_228-2ubuntu1 sysv-rc_2.88dsf-59.2ubuntu3 sysvinit-utils_2.88dsf-59.2ubuntu3 tar_1.28-2.1 tzdata_2015g-1 ubuntu-keyring_2012.05.19 ucf_3.0031 udev_228-2ubuntu1 util-linux_2.27.1-1ubuntu3 x11-common_1:7.7+12ubuntu1 xz-utils_5.1.1alpha+20120614-2ubuntu2 zlib1g_1:1.2.8.dfsg-2ubuntu4 ┌──────────────────────────────────────────────────────────────────────────────┐ │ Build │ └──────────────────────────────────────────────────────────────────────────────┘ Unpack source ───────────── gpgv: Signature made Tue Nov 24 17:17:38 2015 UTC using RSA key ID D1C646D1 gpgv: Can't check signature: public key not found dpkg-source: warning: failed to verify signature on ./clustalo_1.2.1-2.dsc dpkg-source: info: extracting clustalo in clustalo-1.2.1 dpkg-source: info: unpacking clustalo_1.2.1.orig.tar.gz dpkg-source: info: unpacking clustalo_1.2.1-2.debian.tar.xz 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=/«PKGBUILDDIR» SHELL=/bin/sh SUDO_COMMAND=/usr/sbin/chroot /«CHROOT» su buildd -s /bin/sh -c cd '/«PKGBUILDDIR»' && 'env' SUDO_GID=2501 SUDO_UID=2001 SUDO_USER=buildd TERM=unknown USER=buildd USERNAME=root dpkg-buildpackage ───────────────── dpkg-buildpackage: source package clustalo dpkg-buildpackage: source version 1.2.1-2 dpkg-buildpackage: source distribution unstable dpkg-source --before-build clustalo-1.2.1 dpkg-buildpackage: host architecture i386 fakeroot debian/rules clean dh clean --with autoreconf --with linktree dh_testdir dh_auto_clean dh_autoreconf_clean debian/rules override_dh_clean make[1]: Entering directory '/«PKGBUILDDIR»' dh_clean rm -f _configs.sed rm -rf doc make[1]: Leaving directory '/«PKGBUILDDIR»' debian/rules build-arch dh build-arch --with autoreconf --with linktree dh_testdir -a dh_autoreconf -a configure.ac:141: warning: AC_LANG_CONFTEST: no AC_LANG_SOURCE call detected in body ../../lib/autoconf/lang.m4:193: AC_LANG_CONFTEST is expanded from... ../../lib/autoconf/general.m4:2672: _AC_LINK_IFELSE is expanded from... ../../lib/autoconf/general.m4:2689: AC_LINK_IFELSE is expanded from... m4/libtool.m4:1022: _LT_SYS_MODULE_PATH_AIX is expanded from... m4/libtool.m4:4170: _LT_LINKER_SHLIBS is expanded from... m4/libtool.m4:5249: _LT_LANG_C_CONFIG is expanded from... m4/libtool.m4:138: _LT_SETUP is expanded from... m4/libtool.m4:67: LT_INIT is expanded from... configure.ac:141: the top level configure.ac:141: warning: AC_LANG_CONFTEST: no AC_LANG_SOURCE call detected in body ../../lib/autoconf/lang.m4:193: AC_LANG_CONFTEST is expanded from... ../../lib/autoconf/general.m4:2672: _AC_LINK_IFELSE is expanded from... ../../lib/autoconf/general.m4:2689: AC_LINK_IFELSE is expanded from... m4/libtool.m4:4170: _LT_LINKER_SHLIBS is expanded from... m4/libtool.m4:5249: _LT_LANG_C_CONFIG is expanded from... m4/libtool.m4:138: _LT_SETUP is expanded from... m4/libtool.m4:67: LT_INIT is expanded from... configure.ac:141: the top level configure.ac:163: warning: AC_LANG_CONFTEST: no AC_LANG_SOURCE call detected in body ../../lib/autoconf/lang.m4:193: AC_LANG_CONFTEST is expanded from... ../../lib/autoconf/general.m4:2672: _AC_LINK_IFELSE is expanded from... ../../lib/autoconf/general.m4:2689: AC_LINK_IFELSE is expanded from... m4/libtool.m4:1022: _LT_SYS_MODULE_PATH_AIX is expanded from... m4/libtool.m4:5356: _LT_LANG_CXX_CONFIG is expanded from... m4/libtool.m4:785: _LT_LANG is expanded from... m4/libtool.m4:768: LT_LANG is expanded from... configure.ac:163: the top level configure.ac:141: warning: AC_LANG_CONFTEST: no AC_LANG_SOURCE call detected in body ../../lib/autoconf/lang.m4:193: AC_LANG_CONFTEST is expanded from... ../../lib/autoconf/general.m4:2672: _AC_LINK_IFELSE is expanded from... ../../lib/autoconf/general.m4:2689: AC_LINK_IFELSE is expanded from... m4/libtool.m4:1022: _LT_SYS_MODULE_PATH_AIX is expanded from... m4/libtool.m4:4170: _LT_LINKER_SHLIBS is expanded from... m4/libtool.m4:5249: _LT_LANG_C_CONFIG is expanded from... m4/libtool.m4:138: _LT_SETUP is expanded from... m4/libtool.m4:67: LT_INIT is expanded from... configure.ac:141: the top level configure.ac:141: warning: AC_LANG_CONFTEST: no AC_LANG_SOURCE call detected in body ../../lib/autoconf/lang.m4:193: AC_LANG_CONFTEST is expanded from... ../../lib/autoconf/general.m4:2672: _AC_LINK_IFELSE is expanded from... ../../lib/autoconf/general.m4:2689: AC_LINK_IFELSE is expanded from... m4/libtool.m4:4170: _LT_LINKER_SHLIBS is expanded from... m4/libtool.m4:5249: _LT_LANG_C_CONFIG is expanded from... m4/libtool.m4:138: _LT_SETUP is expanded from... m4/libtool.m4:67: LT_INIT is expanded from... configure.ac:141: the top level configure.ac:163: warning: AC_LANG_CONFTEST: no AC_LANG_SOURCE call detected in body ../../lib/autoconf/lang.m4:193: AC_LANG_CONFTEST is expanded from... ../../lib/autoconf/general.m4:2672: _AC_LINK_IFELSE is expanded from... ../../lib/autoconf/general.m4:2689: AC_LINK_IFELSE is expanded from... m4/libtool.m4:1022: _LT_SYS_MODULE_PATH_AIX is expanded from... m4/libtool.m4:5356: _LT_LANG_CXX_CONFIG is expanded from... m4/libtool.m4:785: _LT_LANG is expanded from... m4/libtool.m4:768: LT_LANG is expanded from... configure.ac:163: the top level configure.ac:141: warning: AC_LANG_CONFTEST: no AC_LANG_SOURCE call detected in body ../../lib/autoconf/lang.m4:193: AC_LANG_CONFTEST is expanded from... ../../lib/autoconf/general.m4:2672: _AC_LINK_IFELSE is expanded from... ../../lib/autoconf/general.m4:2689: AC_LINK_IFELSE is expanded from... m4/libtool.m4:1022: _LT_SYS_MODULE_PATH_AIX is expanded from... m4/libtool.m4:4170: _LT_LINKER_SHLIBS is expanded from... m4/libtool.m4:5249: _LT_LANG_C_CONFIG is expanded from... m4/libtool.m4:138: _LT_SETUP is expanded from... m4/libtool.m4:67: LT_INIT is expanded from... configure.ac:141: the top level configure.ac:141: warning: AC_LANG_CONFTEST: no AC_LANG_SOURCE call detected in body ../../lib/autoconf/lang.m4:193: AC_LANG_CONFTEST is expanded from... ../../lib/autoconf/general.m4:2672: _AC_LINK_IFELSE is expanded from... ../../lib/autoconf/general.m4:2689: AC_LINK_IFELSE is expanded from... m4/libtool.m4:4170: _LT_LINKER_SHLIBS is expanded from... m4/libtool.m4:5249: _LT_LANG_C_CONFIG is expanded from... m4/libtool.m4:138: _LT_SETUP is expanded from... m4/libtool.m4:67: LT_INIT is expanded from... configure.ac:141: the top level configure.ac:163: warning: AC_LANG_CONFTEST: no AC_LANG_SOURCE call detected in body ../../lib/autoconf/lang.m4:193: AC_LANG_CONFTEST is expanded from... ../../lib/autoconf/general.m4:2672: _AC_LINK_IFELSE is expanded from... ../../lib/autoconf/general.m4:2689: AC_LINK_IFELSE is expanded from... m4/libtool.m4:1022: _LT_SYS_MODULE_PATH_AIX is expanded from... m4/libtool.m4:5356: _LT_LANG_CXX_CONFIG is expanded from... m4/libtool.m4:785: _LT_LANG is expanded from... m4/libtool.m4:768: LT_LANG is expanded from... configure.ac:163: the top level libtoolize: putting auxiliary files in `.'. libtoolize: copying file `./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:124: installing './compile' dh_auto_configure -a ./configure --build=i686-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/i386-linux-gnu --libexecdir=\${prefix}/lib/i386-linux-gnu --disable-maintainer-mode --disable-dependency-tracking configure: WARNING: unrecognized options: --disable-maintainer-mode configure: Welcome to Clustal Omega - version 1.2.1 (AndreaGiacomo) +NMMMMMMMMMS= MMMMM? :MMMMM8 IMMMMS MMMMM, ~MMMMN ,MMMMM =MMMMM MMMMM ?MMMMM +MMMMM MMMMMS MMMMM MMMMM MMMMM: MMMMM MMMMM+ MMMMM MMMMM~ MMMMM MMMMM MMMMMZ MMMMM MMMMM ,MMMMZ MMMM8 MMMM+ MMMMS MMMM, MMMMO MMMM ,N SMMM MMM8 +8 ,M7 M+ M+ :M8 ,MMMMMMMMMMMMI MMMMMMMMMMMM8 ,MMMMMMMMMMMM8 MMMMMMMMMMMM8 ,MMMMMMMMMMMMN MMMMMMMMMMMM8 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 style of include used by make... GNU checking for gcc... gcc 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 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 how to run the C preprocessor... gcc -E checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -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 minix/config.h usability... no checking minix/config.h presence... no checking for minix/config.h... no checking whether it is safe to define __EXTENSIONS__... yes checking build system type... i686-pc-linux-gnu checking host system type... i686-pc-linux-gnu checking whether make sets $(MAKE)... (cached) yes checking how to print strings... printf checking for a sed that does not truncate output... /bin/sed 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 whether ln -s works... yes 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 i686-pc-linux-gnu file names to i686-pc-linux-gnu format... func_convert_file_noop checking how to convert i686-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 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) 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 for gcc... (cached) gcc checking whether we are using the GNU C compiler... (cached) yes checking whether gcc accepts -g... (cached) yes checking for gcc option to accept ISO C89... (cached) none needed checking whether gcc understands -c and -o together... (cached) yes checking dependency style of gcc... (cached) none checking how to run the C preprocessor... gcc -E checking for g++... g++ checking whether we are using the GNU C++ compiler... yes checking whether g++ accepts -g... yes checking dependency style of g++... none checking how to run the C++ preprocessor... g++ -E checking for ld used by g++... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking whether the g++ linker (/usr/bin/ld) 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) supports shared libraries... yes checking dynamic linker characteristics... (cached) GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking how to run the C++ preprocessor... g++ -E checking for ANSI C header files... (cached) yes checking assert.h usability... yes checking assert.h presence... yes checking for assert.h... yes checking ctype.h usability... yes checking ctype.h presence... yes checking for ctype.h... yes checking float.h usability... yes checking float.h presence... yes checking for float.h... yes checking limits.h usability... yes checking limits.h presence... yes checking for limits.h... yes checking math.h usability... yes checking math.h presence... yes checking for math.h... yes checking for memory.h... (cached) yes checking stdarg.h usability... yes checking stdarg.h presence... yes checking for stdarg.h... yes checking stdio.h usability... yes checking stdio.h presence... yes checking for stdio.h... yes checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking time.h usability... yes checking time.h presence... yes checking for time.h... yes checking for unistd.h... (cached) yes checking for an ANSI C-conforming const... yes checking for size_t... yes checking for inline... inline checking for log in -lm... yes checking for log2 in -lm... yes checking argtable2.h usability... yes checking argtable2.h presence... yes checking for argtable2.h... yes checking for arg_parse in -largtable2... yes checking for OpenMP flag of C compiler... -fopenmp checking whether byte ordering is bigendian... no checking for ntohs... yes checking for ntohl... yes checking for ntons... no checking for ntonl... no checking size of unsigned short... 2 checking size of unsigned int... 4 checking size of unsigned long... 4 checking size of unsigned long long... 8 checking for stroul... no checking for strtoull... yes checking for ftello... yes checking for fseeko... yes checking for ftello64... yes checking for fseeko64... yes checking for ftell64... no checking for fseek64... no checking for off_t... yes checking size of fpos_t... 12 checking if malloc debugging is wanted... no checking whether to build with debug information... no checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating src/Makefile config.status: creating clustalo.pc config.status: creating Doxyfile config.status: creating src/clustal/Makefile config.status: creating src/hhalign/Makefile config.status: creating src/kmpp/Makefile config.status: creating src/squid/Makefile config.status: creating src/config.h config.status: executing src/clustal-omega-config.h commands config.status: creating src/clustal-omega-config.h - prefix CLUSTAL_OMEGA for src/config.h defines config.status: executing depfiles commands config.status: executing libtool commands configure: WARNING: unrecognized options: --disable-maintainer-mode dh_auto_build -a make -j1 make[1]: Entering directory '/«PKGBUILDDIR»' Making all in src make[2]: Entering directory '/«PKGBUILDDIR»/src' make all-recursive make[3]: Entering directory '/«PKGBUILDDIR»/src' Making all in hhalign make[4]: Entering directory '/«PKGBUILDDIR»/src/hhalign' /bin/bash ../../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../../src -D_FORTIFY_SOURCE=2 -fno-strict-aliasing -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -fopenmp -O3 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c -o hhalign.lo hhalign.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I../../src -D_FORTIFY_SOURCE=2 -fno-strict-aliasing -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -fopenmp -O3 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c hhalign.cpp -fPIC -DPIC -o .libs/hhalign.o In file included from hhalign.cpp:62:0: hhutil-C.h: In function 'void ReadDefaultsFile(int&, char**)': hhutil-C.h:516:53: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] argv_conf[argc_conf]=new(char[strlen(c_first)+1]); ^ hhutil-C.h:521:56: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] argv_conf[argc_conf]=new(char[strlen(c_first)+1]); ^ In file included from hhalign.cpp:70:0: hhhmm-C.h: In member function 'HMM& HMM::operator=(HMM&)': hhhmm-C.h:188:44: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] sname[k]=new(char[strlen(q.sname[k])+1]); ^ hhhmm-C.h:193:40: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] seq[k]=new(char[strlen(q.seq[k])+1]); ^ hhhmm-C.h: In member function 'int HMM::Read(FILE*, char*)': hhhmm-C.h:329:48: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] char *cur_seq = new(char[par.maxColCnt]); //Sequence currently read in ^ hhhmm-C.h:360:43: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] seq[k-1]=new(char[strlen(cur_seq)+1]); ^ hhhmm-C.h:367:43: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] sname[k] = new (char[strlen(line+1)+1]); //+1 for terminating '\0' ^ hhhmm-C.h:463:40: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] seq[k]=new(char[strlen(cur_seq)+1]); ^ hhhmm-C.h: In member function 'int HMM::ReadHMMer(FILE*, char*)': hhhmm-C.h:735:59: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] seq[nsa_dssp] = new(char[/*MAXRES*/par.maxResLen+2]); ^ hhhmm-C.h:756:59: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] seq[nss_pred] = new(char[/*MAXRES*/par.maxResLen+2]); ^ hhhmm-C.h:777:59: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] seq[nss_conf] = new(char[/*MAXRES*/par.maxResLen+2]); ^ hhhmm-C.h:859:55: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] seq[nss_dssp] = new(char[/*MAXRES*/par.maxResLen+2]); ^ hhhmm-C.h:1035:46: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] sname[k+1]=new(char[strlen(longname)+1]); ^ hhhmm-C.h:1037:27: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] seq[k]=new(char[L+2]); ^ hhhmm-C.h:1040:29: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] seq[k+1]=new(char[L+2]); ^ hhhmm-C.h:1058:44: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] sname[k]=new(char[strlen(longname)+1]); ^ hhhmm-C.h:1062:27: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] seq[k]=new(char[L+2]); ^ hhhmm-C.h: In member function 'int HMM::ReadHMMer3(FILE*, char*)': hhhmm-C.h:1237:77: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] seq[nsa_dssp] = new(char[/*MAXRES*/par.maxResLen+2]); ^ hhhmm-C.h:1258:77: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] seq[nss_pred] = new(char[/*MAXRES*/par.maxResLen+2]); ^ hhhmm-C.h:1279:77: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] seq[nss_conf] = new(char[/*MAXRES*/par.maxResLen+2]); ^ hhhmm-C.h:1349:69: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] seq[nss_dssp] = new(char[/*MAXRES*/par.maxResLen+2]); ^ hhhmm-C.h:1529:49: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] sname[k+1]=new(char[strlen(longname)+1]); ^ hhhmm-C.h:1531:30: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] seq[k]=new(char[L+2]); ^ hhhmm-C.h:1534:32: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] seq[k+1]=new(char[L+2]); ^ hhhmm-C.h:1552:47: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] sname[k]=new(char[strlen(longname)+1]); ^ hhhmm-C.h:1554:30: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] seq[k]=new(char[L+2]); ^ hhhmm-C.h: In member function 'void HMM::InsertCalibration(char*)': hhhmm-C.h:2109:39: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] char** lines = new(char*[3*L+100000]); ^ hhhmm-C.h:2138:44: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] lines[nline]=new(char[strlen(line)+1]); ^ In file included from hhalign.cpp:71:0: hhalignment-C.h: In constructor 'Alignment::Alignment(int, int)': hhalignment-C.h:80:30: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] sname = new(char*[maxseq+2]); /* MR1 */ ^ hhalignment-C.h:81:28: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] seq = new(char*[maxseq+2]); /* MR1 */ ^ hhalignment-C.h:82:22: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] l = new(int[maxres]); ^ hhalignment-C.h:83:26: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] X = new(char*[maxseq+2]); /* MR1 */ ^ hhalignment-C.h:84:40: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] I = new(short unsigned int*[maxseq+2]); /* MR1 */ ^ hhalignment-C.h:85:28: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] keep = new(char[maxseq+2]); /* MR1 */ ^ hhalignment-C.h:86:31: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] display = new(char[maxseq+2]); /* MR1 */ ^ hhalignment-C.h:87:27: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] wg = new(float[maxseq+2]); /* MR1 */ ^ hhalignment-C.h:88:28: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] nseqs = new(int[maxres+2]); /* MR1 */ ^ hhalignment-C.h: In member function 'void Alignment::Read(FILE*, char*, char*)': hhalignment-C.h:141:40: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] char *cur_seq=new(char[par.maxColCnt]); ^ hhalignment-C.h:183:61: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] seq[k]=new(char[strlen(cur_seq)+2]); ^ hhalignment-C.h:185:59: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] X[k]=new(char[strlen(cur_seq)+2]); ^ hhalignment-C.h:187:73: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] I[k]=new(short unsigned int[strlen(cur_seq)+2]); ^ In file included from hhalign.cpp:71:0: hhalignment-C.h:236:58: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] sname[k] = new(char[strlen(cur_name)+1]); ^ hhalignment-C.h:351:45: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] seq[k]=new(char[strlen(cur_seq)+2]); ^ hhalignment-C.h:353:43: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] X[k]=new(char[strlen(cur_seq)+2]); ^ hhalignment-C.h:355:57: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] I[k]=new(short unsigned int[strlen(cur_seq)+2]); ^ hhalignment-C.h: In member function 'void Alignment::Compress(const char*)': hhalignment-C.h:423:43: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] h = new(/*short*/ unsigned int[N_in+2]); /* short -> overflow, FS, r235 -> r236 */ ^ hhalignment-C.h:555:52: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] percent_gaps = new(float[par.maxColCnt]); ^ hhalignment-C.h:561:47: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] if (nres==NULL) nres=new(int[N_in]); ^ hhalignment-C.h:783:50: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] match_state = new(char[par.maxColCnt]); ^ hhalignment-C.h: In member function 'int Alignment::FilterForDisplay(int, int, int, float, int)': hhalignment-C.h:945:35: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] char *dummy = new(char[N_in+1]); ^ hhalignment-C.h: In member function 'int Alignment::Filter2(char*, int, int, float, int, int, int)': hhalignment-C.h:1008:30: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] char* in=new(char[N_in+1]); // in[k]=1: seq k has been accepted; in[k]=0: seq k has not yet been accepted at current seqid ^ hhalignment-C.h:1009:32: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] char* inkk=new(char[N_in+1]); // inkk[k]=1 iff in[ksort[k]]=1 else 0; ^ hhalignment-C.h:1010:27: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] int* Nmax=new(int[L+2]); // position-dependent maximum-sequence-identity threshold for filtering /* MR1, used to be called idmax*/ ^ hhalignment-C.h:1011:31: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] int* idmaxwin=new(int[L+2]); // minimum value of idmax[i-WFIL,i+WFIL] ^ hhalignment-C.h:1012:36: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] int* seqid_prev=new(int[N_in+1]); // maximum-sequence-identity threshold used in previous round of filtering (with lower seqid) ^ hhalignment-C.h:1013:24: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] int* N=new(int[L+2]); // N[i] number of already accepted sequences at position i ^ hhalignment-C.h:1042:32: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] first=new(int[N_in]);// first non-gap position in sequence k ^ hhalignment-C.h:1043:32: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] last =new(int[N_in]);// last non-gap position in sequence k ^ hhalignment-C.h:1056:31: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] nres=new(int[N_in]); ^ hhalignment-C.h:1070:32: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] ksort=new(int[N_in]); // never reuse alignment object for new alignment with more sequences ^ hhalignment-C.h: In member function 'int Alignment::HomologyFilter(int, float, float)': hhalignment-C.h:1313:33: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] char* coreseq=new(char[N_in]); // coreseq[k]=1 if sequence belongs to core of alignment (i.e. it is very similar to query) ^ hhalignment-C.h: In member function 'int Alignment::FilterWithCoreHMM(char*, float, HMM&)': hhalignment-C.h:1364:36: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] float** logodds=new(float*[L+1]); // log-odds ratios for HMM qcore ^ hhalignment-C.h:1373:32: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] first=new(int[N_in]);// first non-gap position in sequence k ^ hhalignment-C.h:1374:32: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] last =new(int[N_in]);// last non-gap position in sequence k ^ hhalignment-C.h:1387:31: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] nres=new(int[N_in]); ^ hhalignment-C.h: In member function 'void Alignment::FrequenciesAndTransitions(HMM&, char*)': hhalignment-C.h:1669:49: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] q.seq[q.ncons]=new(char[L+2]); ^ hhalignment-C.h:1676:64: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] q.sname[q.nfirst]=new(char[strlen(name)+11]); ^ hhalignment-C.h:1680:50: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] q.seq[q.nfirst]=new(char[L+2]); ^ hhalignment-C.h:1738:61: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] q.sname[nn]=new(char[strlen(sname[k])+1]); ^ hhalignment-C.h:1741:57: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] q.seq[nn]=new(char[strlen(seq[k])+1]); ^ hhalignment-C.h: In member function 'void Alignment::Amino_acid_frequencies_and_transitions_from_M_state(HMM&, char*)': hhalignment-C.h:1828:41: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] float *Neff = new(float[par.maxResLen]); // diversity of subalignment i ^ hhalignment-C.h:1835:25: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] wi = new(float[N_in+2]); ^ hhalignment-C.h:1844:20: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] n = new(int*[L+2]); ^ hhalignment-C.h: In member function 'void Alignment::Transitions_from_I_state(HMM&, char*)': hhalignment-C.h:2054:43: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] float *Neff = new(float[par.maxResLen]); // diversity of subalignment i ^ hhalignment-C.h:2062:27: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] wi = new(float[N_in+2]); ^ hhalignment-C.h:2073:22: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] n = new(int*[L+2]); ^ hhalignment-C.h: In member function 'void Alignment::Transitions_from_D_state(HMM&, char*)': hhalignment-C.h:2256:43: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] float *Neff = new(float[par.maxResLen]); // diversity of subalignment i ^ hhalignment-C.h:2265:27: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] wi = new(float[N_in+2]); /* FIXME: FS */ ^ hhalignment-C.h:2275:22: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] n = new(int*[L+2]); ^ hhalignment-C.h: In member function 'void Alignment::MergeMasterSlave(Hit&, char*)': hhalignment-C.h:2546:31: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] int* imatch=new(int[hit.j2+1]); ^ hhalignment-C.h:2678:34: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] char* new_seq=new(char[2*maxcol]); ^ hhalignment-C.h:2691:23: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] seq[N_in]=new(char[h]); ^ hhalignment-C.h:2694:21: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] X[N_in]=new(char[h]); ^ hhalignment-C.h:2696:35: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] I[N_in]=new(short unsigned int[h]); ^ hhalignment-C.h:2698:47: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] sname[N_in]=new(char[strlen(Tali.sname[k])+1]); ^ hhalignment-C.h: In member function 'void Alignment::AddSequence(char*, int*)': hhalignment-C.h:2729:23: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] X[N_in]=new(char[L+2]); ^ hhalignment-C.h: In member function 'void Alignment::GetPositionSpecificWeights(float**)': hhalignment-C.h:2779:19: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] n = new(int*[L+2]); ^ hhalignment-C.h: In member function 'void Alignment::Transfer(char**, int)': hhalignment-C.h:2896:59: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] I[k] = new(short unsigned int[iLen+2+GOOD_MEASURE]); ^ hhalignment-C.h:2897:45: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] X[k] = new(char[iLen+2+GOOD_MEASURE]); ^ hhalignment-C.h:2898:47: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] seq[k] = new(char[iLen+2+GOOD_MEASURE]); ^ In file included from hhalign.cpp:72:0: hhhit-C.h: In member function 'void Hit::AllocateBacktraceMatrix(int, int)': hhhit-C.h:179:20: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] bMM=new(char*[Nq]); ^ hhhit-C.h:180:20: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] bMI=new(char*[Nq]); ^ hhhit-C.h:181:20: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] bIM=new(char*[Nq]); ^ hhhit-C.h:182:20: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] bDG=new(char*[Nq]); ^ hhhit-C.h:183:20: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] bGD=new(char*[Nq]); ^ hhhit-C.h:184:25: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] cell_off=new(char*[Nq]); ^ hhhit-C.h:187:26: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] bMM[i]=new(char[Nt]); ^ hhhit-C.h:188:26: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] bMI[i]=new(char[Nt]); ^ hhhit-C.h:189:26: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] bIM[i]=new(char[Nt]); ^ hhhit-C.h:190:26: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] bGD[i]=new(char[Nt]); ^ hhhit-C.h:191:26: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] bDG[i]=new(char[Nt]); ^ hhhit-C.h:192:31: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] cell_off[i]=new(char[Nt]); ^ hhhit-C.h: In member function 'void Hit::AllocateForwardMatrix(int, int)': hhhit-C.h:239:23: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] F_MM=new(double*[Nq]); ^ hhhit-C.h:240:23: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] F_MI=new(double*[Nq]); ^ hhhit-C.h:241:23: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] F_DG=new(double*[Nq]); ^ hhhit-C.h:242:23: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] F_IM=new(double*[Nq]); ^ hhhit-C.h:243:23: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] F_GD=new(double*[Nq]); ^ hhhit-C.h:244:25: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] scale=new(double[Nq+1]); // need Nq+3? ^ hhhit-C.h:247:31: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] F_MM[i] = new(double[Nt]); ^ hhhit-C.h:248:31: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] F_MI[i] = new(double[Nt]); ^ hhhit-C.h:249:31: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] F_DG[i] = new(double[Nt]); ^ hhhit-C.h:250:31: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] F_IM[i] = new(double[Nt]); ^ hhhit-C.h:251:31: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] F_GD[i] = new(double[Nt]); ^ hhhit-C.h: In member function 'void Hit::AllocateBackwardMatrix(int, int)': hhhit-C.h:296:23: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] B_MM=new(double*[Nq]); ^ hhhit-C.h:303:31: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] B_MM[i] = new(double[Nt]); ^ hhhit-C.h: In member function 'void Hit::Viterbi(HMM&, HMM&, float**)': hhhit-C.h:376:42: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] float *sMM = new(float[par.maxResLen]); // sMM[i][j] = score of best alignment up to indices (i,j) ending in (Match,Match) ^ hhhit-C.h:377:42: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] float *sGD = new(float[par.maxResLen]); // sGD[i][j] = score of best alignment up to indices (i,j) ending in (Gap,Delete) ^ hhhit-C.h:378:42: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] float *sDG = new(float[par.maxResLen]); // sDG[i][j] = score of best alignment up to indices (i,j) ending in (Delete,Gap) ^ hhhit-C.h:379:42: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] float *sIM = new(float[par.maxResLen]); // sIM[i][j] = score of best alignment up to indices (i,j) ending in (Ins,Match) ^ hhhit-C.h:380:42: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] float *sMI = new(float[par.maxResLen]); // sMI[i][j] = score of best alignment up to indices (i,j) ending in (Match,Ins) ^ hhhit-C.h: In member function 'void Hit::Backtrace(HMM&, HMM&)': hhhit-C.h:1126:40: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] if (t.Xcons) Xcons = new( char[q.L+2]); // for template consensus sequence aligned to query ^ hhhit-C.h:1127:30: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] S = new( float[nsteps+1]); ^ hhhit-C.h:1128:30: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] S_ss = new( float[nsteps+1]); ^ hhhit-C.h: In member function 'void Hit::StochasticBacktrace(HMM&, HMM&, char)': hhhit-C.h:1228:40: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] double* scale_cum = new(double[q.L+2]); ^ hhhit-C.h:1247:39: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] double* sumF=new(double[q.L+t.L]); ^ hhhit-C.h:1371:40: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] if (t.Xcons) Xcons = new( char[q.L+2]); // for template consensus sequence aligned to query ^ hhhit-C.h:1372:30: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] S = new( float[nsteps+1]); ^ hhhit-C.h:1373:30: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] S_ss = new( float[nsteps+1]); ^ hhhit-C.h: In member function 'void Hit::BacktraceMAC(HMM&, HMM&)': hhhit-C.h:1475:40: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] if (t.Xcons) Xcons = new( char[q.L+2]); // for template consensus sequence aligned to query ^ hhhit-C.h:1476:30: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] S = new( float[nsteps+1]); ^ hhhit-C.h:1477:30: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] S_ss = new( float[nsteps+1]); ^ hhhit-C.h:1478:37: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] P_posterior = new( float[nsteps+1]); ^ hhhit-C.h: In member function 'void Hit::InitializeBacktrace(HMM&, HMM&)': hhhit-C.h:1683:54: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] longname=new(char[strlen(t.longname)+1])(); ^ hhhit-C.h:1684:50: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] name =new(char[strlen(t.name)+1])(); ^ hhhit-C.h:1685:50: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] file =new(char[strlen(t.file)+1])(); ^ hhhit-C.h:1696:43: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] sname=new(char*[t.n_display])(); // Call Compare only once with irep=1 ^ hhhit-C.h:1697:43: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] seq =new(char*[t.n_display])(); // Call Compare only once with irep=1 ^ hhhit-C.h:1730:34: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] this->i = new( int[i2+j2+2])(); ^ hhhit-C.h:1731:34: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] this->j = new( int[i2+j2+2])(); ^ hhhit-C.h:1732:35: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] states = new( char[i2+j2+2])(); ^ In file included from hhalign.cpp:73:0: hhhalfalignment-C.h: In constructor 'HalfAlignment::HalfAlignment(int)': hhhalfalignment-C.h:66:25: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] h = new(int[maxseqdis]); //h[k] = next position of sequence k to be written ^ hhhalfalignment-C.h:67:27: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] s = new(char*[maxseqdis]); //s[k][h] = character in column h, sequence k of output alignment ^ hhhalfalignment-C.h:68:26: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] l = new(int*[maxseqdis]); //counts non-gap residues: l[k][i] = index of last residue AT OR BEFORE match state i in seq k ^ hhhalfalignment-C.h:69:26: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] m = new(int*[maxseqdis]); //counts positions: m[k][i] = position of match state i in string seq[k] ^ In file included from hhalign.cpp:74:0: hhfullalignment-C.h: In member function 'void FullAlignment::PrintHHR(FILE*, Hit&)': hhfullalignment-C.h:359:39: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] lq = new(short unsigned int[qa->n+2]); ^ hhfullalignment-C.h:360:39: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] lt = new(short unsigned int[ta->n+2]); ^ In file included from hhalign.cpp:75:0: hhhitlist-C.h: In member function 'void HitList::TransitiveScoring()': hhhitlist-C.h:1285:20: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] Z = new(float*[N]); ^ hhhitlist-C.h:1288:26: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] Z[k] = new(float[N]); ^ hhhitlist-C.h:1293:20: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] C = new(float*[N]); ^ hhhitlist-C.h:1296:26: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] C[k] = new(float[N]); ^ hhhitlist-C.h:1303:20: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] Zq = new(float[N]); ^ hhhitlist-C.h:1304:21: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] Ztq = new(float[N]); ^ hhhitlist-C.h:1305:21: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] Zrq = new(float[N]); ^ hhhitlist-C.h:1306:22: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] fold = new(char*[N]); ^ hhhitlist-C.h:1307:21: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] fam = new(char*[N]); ^ hhhitlist-C.h:1308:22: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] Prob = new(float[N]); ^ hhhitlist-C.h:1309:18: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] ll = new(int[N]); ^ hhhitlist-C.h:1310:19: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] w = new(float[N]); ^ hhhitlist-C.h:1373:37: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] double** Csub = new(double*[M]); ^ hhhitlist-C.h:1374:37: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] double** Cinv = new(double*[M]); ^ hhhitlist-C.h:1377:27: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] Csub[m] = new(double[M]); ^ hhhitlist-C.h:1378:27: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] Cinv[m] = new(double[M]); ^ hhhitlist-C.h:1453:34: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] double** Csub = new(double*[M]); ^ hhhitlist-C.h:1456:31: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] Csub[m] = new(double[M]); ^ hhhitlist-C.h:1470:38: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] double** Cinv = new(double*[M]); ^ hhhitlist-C.h:1471:51: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] for (m=0; m/dev/null 2>&1 /bin/bash ../../libtool --tag=CXX --mode=link g++ -fno-strict-aliasing -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -fopenmp -O3 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -o libhhalign.la hhalign.lo -largtable2 -lm libtool: link: ar cru .libs/libhhalign.a .libs/hhalign.o ar: `u' modifier ignored since `D' is the default (see `U') libtool: link: ranlib .libs/libhhalign.a libtool: link: ( cd ".libs" && rm -f "libhhalign.la" && ln -s "../libhhalign.la" "libhhalign.la" ) make[4]: Leaving directory '/«PKGBUILDDIR»/src/hhalign' Making all in squid make[4]: Entering directory '/«PKGBUILDDIR»/src/squid' /bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c -o a2m.lo a2m.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c a2m.c -fPIC -DPIC -o .libs/a2m.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c a2m.c -o a2m.o >/dev/null 2>&1 /bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c -o aligneval.lo aligneval.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c aligneval.c -fPIC -DPIC -o .libs/aligneval.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c aligneval.c -o aligneval.o >/dev/null 2>&1 /bin/bash ../../libtool 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compile: gcc -DHAVE_CONFIG_H -I. -I../../src -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c clustal.c -o clustal.o >/dev/null 2>&1 /bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c -o cluster.lo cluster.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c cluster.c -fPIC -DPIC -o .libs/cluster.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../src -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c cluster.c -o cluster.o >/dev/null 2>&1 /bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../src -D_FORTIFY_SOURCE=2 -DCLUSTALO -O3 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c -o dayhoff.lo 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.libs/ktuple_pair.o .libs/list.o .libs/log.o .libs/muscle_upgma.o .libs/muscle_tree.o .libs/mbed.o .libs/pair_dist.o .libs/progress.o .libs/seq.o .libs/symmatrix.o .libs/tree.o .libs/util.o .libs/weights.o ar: `u' modifier ignored since `D' is the default (see `U') libtool: link: ranlib .libs/libclustal.a libtool: link: ( cd ".libs" && rm -f "libclustal.la" && ln -s "../libclustal.la" "libclustal.la" ) make[4]: Leaving directory '/«PKGBUILDDIR»/src/clustal' make[4]: Entering directory '/«PKGBUILDDIR»/src' /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -O3 -fopenmp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c -o clustal-omega.lo clustal-omega.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -O3 -fopenmp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c clustal-omega.c -fPIC -DPIC -o .libs/clustal-omega.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -O3 -fopenmp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c clustal-omega.c -o clustal-omega.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CC --mode=link gcc -O3 -fopenmp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -static -Wl,-Bsymbolic-functions -Wl,-z,relro -o libclustalo.la -rpath /usr/lib/i386-linux-gnu clustal-omega.lo clustal/libclustal.la hhalign/libhhalign.la squid/libsquid.la kmpp/libkmpp.la -largtable2 -lm libtool: link: (cd .libs/libclustalo.lax/libclustal.a && ar x "/«PKGBUILDDIR»/src/clustal/.libs/libclustal.a") libtool: link: (cd .libs/libclustalo.lax/libhhalign.a && ar x "/«PKGBUILDDIR»/src/hhalign/.libs/libhhalign.a") libtool: link: (cd .libs/libclustalo.lax/libsquid.a && ar x "/«PKGBUILDDIR»/src/squid/.libs/libsquid.a") libtool: link: (cd .libs/libclustalo.lax/libkmpp.a && ar x "/«PKGBUILDDIR»/src/kmpp/.libs/libkmpp.a") libtool: link: ar cru .libs/libclustalo.a clustal-omega.o .libs/libclustalo.lax/libclustal.a/hhalign_wrapper.o .libs/libclustalo.lax/libclustal.a/ktuple_pair.o .libs/libclustalo.lax/libclustal.a/list.o .libs/libclustalo.lax/libclustal.a/log.o .libs/libclustalo.lax/libclustal.a/mbed.o .libs/libclustalo.lax/libclustal.a/muscle_tree.o .libs/libclustalo.lax/libclustal.a/muscle_upgma.o .libs/libclustalo.lax/libclustal.a/pair_dist.o .libs/libclustalo.lax/libclustal.a/progress.o .libs/libclustalo.lax/libclustal.a/seq.o .libs/libclustalo.lax/libclustal.a/symmatrix.o .libs/libclustalo.lax/libclustal.a/tree.o .libs/libclustalo.lax/libclustal.a/util.o .libs/libclustalo.lax/libclustal.a/weights.o .libs/libclustalo.lax/libhhalign.a/hhalign.o .libs/libclustalo.lax/libsquid.a/a2m.o .libs/libclustalo.lax/libsquid.a/aligneval.o .libs/libclustalo.lax/libsquid.a/alignio.o .libs/libclustalo.lax/libsquid.a/clustal.o .libs/libclustalo.lax/libsquid.a/cluster.o .libs/libclustalo.lax/libsquid.a/dayhoff.o .libs/libclustalo.lax/libsquid.a/eps.o .libs/libclustalo.lax/libsquid.a/file.o .libs/libclustalo.lax/libsquid.a/getopt.o .libs/libclustalo.lax/libsquid.a/gki.o .libs/libclustalo.lax/libsquid.a/gsi.o .libs/libclustalo.lax/libsquid.a/gsi64.o .libs/libclustalo.lax/libsquid.a/hsregex.o .libs/libclustalo.lax/libsquid.a/iupac.o .libs/libclustalo.lax/libsquid.a/msa.o .libs/libclustalo.lax/libsquid.a/msf.o .libs/libclustalo.lax/libsquid.a/phylip.o .libs/libclustalo.lax/libsquid.a/revcomp.o .libs/libclustalo.lax/libsquid.a/rk.o .libs/libclustalo.lax/libsquid.a/selex.o .libs/libclustalo.lax/libsquid.a/seqencode.o .libs/libclustalo.lax/libsquid.a/shuffle.o .libs/libclustalo.lax/libsquid.a/sqerror.o .libs/libclustalo.lax/libsquid.a/sqio.o .libs/libclustalo.lax/libsquid.a/squidcore.o .libs/libclustalo.lax/libsquid.a/sre_ctype.o .libs/libclustalo.lax/libsquid.a/sre_math.o .libs/libclustalo.lax/libsquid.a/sre_random.o .libs/libclustalo.lax/libsquid.a/sre_string.o .libs/libclustalo.lax/libsquid.a/ssi.o .libs/libclustalo.lax/libsquid.a/stack.o .libs/libclustalo.lax/libsquid.a/stockholm.o .libs/libclustalo.lax/libsquid.a/stopwatch.o .libs/libclustalo.lax/libsquid.a/translate.o .libs/libclustalo.lax/libsquid.a/types.o .libs/libclustalo.lax/libsquid.a/vectorops.o .libs/libclustalo.lax/libsquid.a/weight.o .libs/libclustalo.lax/libkmpp.a/KMeans.o .libs/libclustalo.lax/libkmpp.a/KmTree.o .libs/libclustalo.lax/libkmpp.a/KmUtils.o ar: `u' modifier ignored since `D' is the default (see `U') libtool: link: ranlib .libs/libclustalo.a libtool: link: rm -fr .libs/libclustalo.lax libtool: link: ( cd ".libs" && rm -f "libclustalo.la" && ln -s "../libclustalo.la" "libclustalo.la" ) g++ -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -O3 -fopenmp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c -o main.o main.cpp gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -O3 -fopenmp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c -o mymain.o mymain.c /bin/bash ../libtool --tag=CXX --mode=link g++ -O3 -fopenmp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -o clustalo main.o mymain.o libclustalo.la -largtable2 -lm libtool: link: g++ -O3 -fopenmp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z -Wl,relro -o clustalo main.o mymain.o ./.libs/libclustalo.a /usr/lib/libargtable2.so -lm -fopenmp ./.libs/libclustalo.a(clustal-omega.o): In function `AlnToHHMFile': /«PKGBUILDDIR»/src/clustal-omega.c:392: warning: the use of `mktemp' is dangerous, better use `mkstemp' or `mkdtemp' make[4]: Leaving directory '/«PKGBUILDDIR»/src' make[3]: Leaving directory '/«PKGBUILDDIR»/src' make[2]: Leaving directory '/«PKGBUILDDIR»/src' make[2]: Entering directory '/«PKGBUILDDIR»' make[2]: Nothing to be done for 'all-am'. make[2]: Leaving directory '/«PKGBUILDDIR»' make[1]: Leaving directory '/«PKGBUILDDIR»' dh_auto_test -a make -j1 check make[1]: Entering directory '/«PKGBUILDDIR»' Making check in src make[2]: Entering directory '/«PKGBUILDDIR»/src' Making check in hhalign make[3]: Entering directory '/«PKGBUILDDIR»/src/hhalign' make[3]: Nothing to be done for 'check'. make[3]: Leaving directory '/«PKGBUILDDIR»/src/hhalign' Making check in squid make[3]: Entering directory '/«PKGBUILDDIR»/src/squid' make[3]: Nothing to be done for 'check'. make[3]: Leaving directory '/«PKGBUILDDIR»/src/squid' Making check in kmpp make[3]: Entering directory '/«PKGBUILDDIR»/src/kmpp' make[3]: Nothing to be done for 'check'. make[3]: Leaving directory '/«PKGBUILDDIR»/src/kmpp' Making check in clustal make[3]: Entering directory '/«PKGBUILDDIR»/src/clustal' make[3]: Nothing to be done for 'check'. make[3]: Leaving directory '/«PKGBUILDDIR»/src/clustal' make[3]: Entering directory '/«PKGBUILDDIR»/src' make[3]: Leaving directory '/«PKGBUILDDIR»/src' make[2]: Leaving directory '/«PKGBUILDDIR»/src' make[2]: Entering directory '/«PKGBUILDDIR»' make[2]: Nothing to be done for 'check-am'. make[2]: Leaving directory '/«PKGBUILDDIR»' make[1]: Leaving directory '/«PKGBUILDDIR»' fakeroot debian/rules binary-arch dh binary-arch --with autoreconf --with linktree dh_testroot -a dh_prep -a dh_installdirs -a debian/rules override_dh_auto_install-arch make[1]: Entering directory '/«PKGBUILDDIR»' dh_auto_install -a make -j1 install DESTDIR=/«PKGBUILDDIR»/debian/tmp AM_UPDATE_INFO_DIR=no make[2]: Entering directory '/«PKGBUILDDIR»' Making install in src make[3]: Entering directory '/«PKGBUILDDIR»/src' Making install in hhalign make[4]: Entering directory '/«PKGBUILDDIR»/src/hhalign' make[5]: Entering directory '/«PKGBUILDDIR»/src/hhalign' make[5]: Nothing to be done for 'install-exec-am'. /bin/mkdir -p '/«PKGBUILDDIR»/debian/tmp/usr/include/clustalo/hhalign' /usr/bin/install -c -m 644 general.h hhfunc.h '/«PKGBUILDDIR»/debian/tmp/usr/include/clustalo/hhalign' make[5]: Leaving directory '/«PKGBUILDDIR»/src/hhalign' make[4]: Leaving directory '/«PKGBUILDDIR»/src/hhalign' Making install in squid make[4]: Entering directory '/«PKGBUILDDIR»/src/squid' make[5]: Entering directory '/«PKGBUILDDIR»/src/squid' make[5]: Nothing to be done for 'install-exec-am'. /bin/mkdir -p '/«PKGBUILDDIR»/debian/tmp/usr/include/clustalo/squid' /usr/bin/install -c -m 644 gki.h gsi64.h msa.h rk.h squid.h stopwatch.h sqfuncs.h sre_random.h ssi.h stockholm.h vectorops.h version.h '/«PKGBUILDDIR»/debian/tmp/usr/include/clustalo/squid' make[5]: Leaving directory '/«PKGBUILDDIR»/src/squid' make[4]: Leaving directory '/«PKGBUILDDIR»/src/squid' Making install in kmpp make[4]: Entering directory '/«PKGBUILDDIR»/src/kmpp' make[5]: Entering directory '/«PKGBUILDDIR»/src/kmpp' make[5]: Nothing to be done for 'install-exec-am'. make[5]: Nothing to be done for 'install-data-am'. make[5]: Leaving directory '/«PKGBUILDDIR»/src/kmpp' make[4]: Leaving directory '/«PKGBUILDDIR»/src/kmpp' Making install in clustal make[4]: Entering directory '/«PKGBUILDDIR»/src/clustal' make[5]: Entering directory '/«PKGBUILDDIR»/src/clustal' make[5]: Nothing to be done for 'install-exec-am'. /bin/mkdir -p '/«PKGBUILDDIR»/debian/tmp/usr/include/clustalo/clustal' /usr/bin/install -c -m 644 hhalign_wrapper.h ktuple_pair.h log.h mbed.h muscle_tree.h pair_dist.h progress.h seq.h symmatrix.h tree.h util.h weights.h '/«PKGBUILDDIR»/debian/tmp/usr/include/clustalo/clustal' make[5]: Leaving directory '/«PKGBUILDDIR»/src/clustal' make[4]: Leaving directory '/«PKGBUILDDIR»/src/clustal' make[4]: Entering directory '/«PKGBUILDDIR»/src' make[5]: Entering directory '/«PKGBUILDDIR»/src' /bin/mkdir -p '/«PKGBUILDDIR»/debian/tmp/usr/lib/i386-linux-gnu' /bin/bash ../libtool --mode=install /usr/bin/install -c libclustalo.la '/«PKGBUILDDIR»/debian/tmp/usr/lib/i386-linux-gnu' libtool: install: /usr/bin/install -c .libs/libclustalo.lai /«PKGBUILDDIR»/debian/tmp/usr/lib/i386-linux-gnu/libclustalo.la libtool: install: /usr/bin/install -c .libs/libclustalo.a /«PKGBUILDDIR»/debian/tmp/usr/lib/i386-linux-gnu/libclustalo.a libtool: install: chmod 644 /«PKGBUILDDIR»/debian/tmp/usr/lib/i386-linux-gnu/libclustalo.a libtool: install: ranlib /«PKGBUILDDIR»/debian/tmp/usr/lib/i386-linux-gnu/libclustalo.a libtool: install: warning: remember to run `libtool --finish /usr/lib/i386-linux-gnu' /bin/mkdir -p '/«PKGBUILDDIR»/debian/tmp/usr/bin' /bin/bash ../libtool --mode=install /usr/bin/install -c clustalo '/«PKGBUILDDIR»/debian/tmp/usr/bin' libtool: install: /usr/bin/install -c clustalo /«PKGBUILDDIR»/debian/tmp/usr/bin/clustalo /bin/mkdir -p '/«PKGBUILDDIR»/debian/tmp/usr/include/clustalo/' /usr/bin/install -c -m 644 clustal-omega-config.h clustal-omega.h '/«PKGBUILDDIR»/debian/tmp/usr/include/clustalo/' make[5]: Leaving directory '/«PKGBUILDDIR»/src' make[4]: Leaving directory '/«PKGBUILDDIR»/src' make[3]: Leaving directory '/«PKGBUILDDIR»/src' make[3]: Entering directory '/«PKGBUILDDIR»' make[4]: Entering directory '/«PKGBUILDDIR»' make[4]: Nothing to be done for 'install-exec-am'. /bin/mkdir -p '/«PKGBUILDDIR»/debian/tmp/usr/share/doc/clustal-omega' /usr/bin/install -c -m 644 README '/«PKGBUILDDIR»/debian/tmp/usr/share/doc/clustal-omega' /bin/mkdir -p '/«PKGBUILDDIR»/debian/tmp/usr/lib/i386-linux-gnu/pkgconfig' /usr/bin/install -c -m 644 clustalo.pc '/«PKGBUILDDIR»/debian/tmp/usr/lib/i386-linux-gnu/pkgconfig' make[4]: Leaving directory '/«PKGBUILDDIR»' make[3]: Leaving directory '/«PKGBUILDDIR»' make[2]: Leaving directory '/«PKGBUILDDIR»' rm -rf debian/tmp/usr/lib/pkgconfig rm -f debian/tmp/usr/lib/*/libclustalo.la mv debian/tmp/usr/include debian/libclustalo-dev/usr mv debian/tmp/usr/lib debian/libclustalo-dev/usr mv debian/tmp/usr/bin debian/clustalo/usr make[1]: Leaving directory '/«PKGBUILDDIR»' dh_installdocs -a dh_installchangelogs -a dh_installman -a dh_perl -a dh_link -a dh_linktree -a dh_strip_nondeterminism -a dh_compress -a dh_fixperms -a dh_strip -a dh_strip debug symbol extraction: enabling -a due to Build-Debug-Symbols: yes in /CurrentlyBuilding dh_strip debug symbol extraction: all non-arch-all packages for this build platform i386: clustalo libclustalo-dev dh_strip debug symbol extraction: packages to act on: clustalo libclustalo-dev dh_strip debug symbol extraction: ignored packages: 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 Using buildid for compat level >= 9 libclustalo-dev has no unstripped objects, ignoring find: `/«PKGBUILDDIR»/debian/libclustalo-dev-dbgsym': No such file or directory /usr/bin/pkg_create_dbgsym: nothing in /«PKGBUILDDIR»/debian/libclustalo-dev-dbgsym and no dbgdepends, ignoring dh_makeshlibs -a dh_shlibdeps -a dh_installdeb -a dh_gencontrol -a dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe dpkg-gencontrol: warning: Depends field of package libclustalo-dev: unknown substitution variable ${shlibs:Depends} 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 i386: clustalo libclustalo-dev dh_gencontrol debug symbol wrapper: packages to act on: clustalo libclustalo-dev dh_gencontrol debug symbol wrapper: ignored packages: dh_gencontrol debug symbol wrapper: processing package clustalo (pkgdir debian/clustalo, ddeb package dir debian/clustalo-dbgsym) dh_gencontrol debug symbol wrapper: building clustalo-dbgsym_1.2.1-2_i386.ddeb dpkg-deb: building package 'clustalo-dbgsym' in '../clustalo-dbgsym_1.2.1-2_i386.ddeb'. dh_gencontrol debug symbol wrapper: dpkg-distaddfile clustalo-dbgsym_1.2.1-2_i386.ddeb science extra dpkg-distaddfile: warning: File::FcntlLock not available; using flock which is not NFS-safe dh_gencontrol debug symbol wrapper: no debian/libclustalo-dev-dbgsym, skipping package libclustalo-dev dh_md5sums -a dh_builddeb -a INFO: pkgstriptranslations version 122 pkgstriptranslations: processing clustalo (in debian/clustalo); do_strip: , oemstrip: pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/clustalo/DEBIAN/control, package clustalo, directory debian/clustalo pkgstripfiles: PNG optimization for package clustalo took 0 s dpkg-deb: building package 'clustalo' in '../clustalo_1.2.1-2_i386.deb'. INFO: pkgstriptranslations version 122 pkgstriptranslations: processing libclustalo-dev (in debian/libclustalo-dev); do_strip: , oemstrip: pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/libclustalo-dev/DEBIAN/control, package libclustalo-dev, directory debian/libclustalo-dev Searching for duplicated docs in dependency clustalo... symlinking changelog.Debian.gz in libclustalo-dev to file in clustalo pkgstripfiles: PNG optimization for package libclustalo-dev took 0 s dpkg-deb: building package 'libclustalo-dev' in '../libclustalo-dev_1.2.1-2_i386.deb'. dpkg-genchanges -B -mLaunchpad Build Daemon >../clustalo_1.2.1-2_i386.changes dpkg-genchanges: binary-only arch-specific upload (source code and arch-indep packages not included) dpkg-source --after-build clustalo-1.2.1 dpkg-buildpackage: binary-only upload (no source included) ──────────────────────────────────────────────────────────────────────────────── Build finished at 20151124-2317 Finished ──────── I: Built successfully ┌──────────────────────────────────────────────────────────────────────────────┐ │ Post Build Chroot │ └──────────────────────────────────────────────────────────────────────────────┘ ┌──────────────────────────────────────────────────────────────────────────────┐ │ Changes │ └──────────────────────────────────────────────────────────────────────────────┘ clustalo_1.2.1-2_i386.changes: ────────────────────────────── Format: 1.8 Date: Tue, 24 Nov 2015 17:58:56 +0100 Source: clustalo Binary: clustalo libclustalo-dev libclustalo-doc Architecture: i386 Version: 1.2.1-2 Distribution: xenial-proposed Urgency: medium Maintainer: Launchpad Build Daemon Changed-By: Andreas Tille Description: clustalo - General purpose multiple sequence alignment program for proteins libclustalo-dev - library to embed Clustal Omega libclustalo-doc - API documentation for library to embed Clustal Omega Closes: 806007 Changes: clustalo (1.2.1-2) unstable; urgency=medium . [ Steffen Möller] * Added debian/upstream/edam . [ Andreas Tille ] * cme fix dpkg-control * debian/rules: enable building architecture independent package only Closes: #806007 * more verbose descriptions * use linktree to get rid of jquery.js copy * fix order in debian/copyright Checksums-Sha1: 5d702b517237540ed221032511a758f7b196c09f 395944 clustalo-dbgsym_1.2.1-2_i386.ddeb c973c8483bea6a1239b2be893921c07831516f19 259116 clustalo_1.2.1-2_i386.deb 2d6b8fea1eff3d3996a6cab6ae06fd8be7879d4b 321190 libclustalo-dev_1.2.1-2_i386.deb Checksums-Sha256: 0292e390dd5442eac5654664a09657844c7c72ed602e28b5d74df61dde11efd3 395944 clustalo-dbgsym_1.2.1-2_i386.ddeb 43395818cf527b63aa7edc6085d8be42556b2b9a8703ae8179d15b6629348bee 259116 clustalo_1.2.1-2_i386.deb 79f7c4c10c617f11959405faeec216fc5971f4cae331925df4fc7038dfa4a72d 321190 libclustalo-dev_1.2.1-2_i386.deb Files: 063f887aa7bd67e5dd47e74b256fc383 395944 science extra clustalo-dbgsym_1.2.1-2_i386.ddeb 9ee593905782366ca63e9a75344a4888 259116 science optional clustalo_1.2.1-2_i386.deb 8e09c892590983e98e157fb64f1e3ff1 321190 libdevel optional libclustalo-dev_1.2.1-2_i386.deb ┌──────────────────────────────────────────────────────────────────────────────┐ │ Package contents │ └──────────────────────────────────────────────────────────────────────────────┘ clustalo_1.2.1-2_i386.deb ───────────────────────── new debian package, version 2.0. size 259116 bytes: control archive=776 bytes. 729 bytes, 15 lines control 329 bytes, 5 lines md5sums Package: clustalo Version: 1.2.1-2 Architecture: i386 Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 661 Depends: libargtable2-0 (>= 7), libc6 (>= 2.4), libgcc1 (>= 1:4.1.1), libgomp1 (>= 4.9), libstdc++6 (>= 5.2) Section: science Priority: optional Homepage: http://www.clustal.org/omega/ Description: General purpose multiple sequence alignment program for proteins Clustal-Omega is a general purpose multiple sequence alignment (MSA) program for dna/rna/proteins. It produces high quality MSAs and is capable of handling data-sets of hundreds of thousands of sequences in reasonable time. drwxr-xr-x root/root 0 2015-11-24 23:17 ./ drwxr-xr-x root/root 0 2015-11-24 23:17 ./usr/ drwxr-xr-x root/root 0 2015-11-24 23:17 ./usr/bin/ -rwxr-xr-x root/root 650716 2015-11-24 23:17 ./usr/bin/clustalo drwxr-xr-x root/root 0 2015-11-24 23:17 ./usr/share/ drwxr-xr-x root/root 0 2015-11-24 23:17 ./usr/share/doc/ drwxr-xr-x root/root 0 2015-11-24 23:17 ./usr/share/doc/clustalo/ -rw-r--r-- root/root 10994 2013-08-27 12:07 ./usr/share/doc/clustalo/README.gz -rw-r--r-- root/root 626 2015-11-24 17:15 ./usr/share/doc/clustalo/changelog.Debian.gz -rw-r--r-- root/root 1174 2015-11-24 17:15 ./usr/share/doc/clustalo/copyright drwxr-xr-x root/root 0 2015-11-24 23:17 ./usr/share/man/ drwxr-xr-x root/root 0 2015-11-24 23:17 ./usr/share/man/man1/ -rw-r--r-- root/root 1083 2015-11-24 23:17 ./usr/share/man/man1/clustalo.1.gz libclustalo-dev_1.2.1-2_i386.deb ──────────────────────────────── new debian package, version 2.0. size 321190 bytes: control archive=1461 bytes. 583 bytes, 16 lines control 2238 bytes, 31 lines md5sums Package: libclustalo-dev Source: clustalo Version: 1.2.1-2 Architecture: i386 Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 1102 Depends: libargtable2-dev, clustalo (= 1.2.1-2) Suggests: libclustalo-doc Section: libdevel Priority: optional Homepage: http://www.clustal.org/omega/ Description: library to embed Clustal Omega This package contains headers and libraries to include Clustal Omega in a program. It provides clustal usage with an API. drwxr-xr-x root/root 0 2015-11-24 23:17 ./ drwxr-xr-x root/root 0 2015-11-24 23:17 ./usr/ drwxr-xr-x root/root 0 2015-11-24 23:17 ./usr/include/ drwxr-xr-x root/root 0 2015-11-24 23:17 ./usr/include/clustalo/ -rw-r--r-- root/root 9529 2015-11-24 23:17 ./usr/include/clustalo/clustal-omega-config.h -rw-r--r-- root/root 4640 2015-11-24 23:17 ./usr/include/clustalo/clustal-omega.h drwxr-xr-x root/root 0 2015-11-24 23:17 ./usr/include/clustalo/clustal/ -rw-r--r-- root/root 1159 2015-11-24 23:17 ./usr/include/clustalo/clustal/hhalign_wrapper.h -rw-r--r-- root/root 1251 2015-11-24 23:17 ./usr/include/clustalo/clustal/ktuple_pair.h -rw-r--r-- root/root 1787 2015-11-24 23:17 ./usr/include/clustalo/clustal/log.h -rw-r--r-- root/root 866 2015-11-24 23:17 ./usr/include/clustalo/clustal/mbed.h -rw-r--r-- root/root 4112 2015-11-24 23:17 ./usr/include/clustalo/clustal/muscle_tree.h -rw-r--r-- root/root 1275 2015-11-24 23:17 ./usr/include/clustalo/clustal/pair_dist.h -rw-r--r-- root/root 1257 2015-11-24 23:17 ./usr/include/clustalo/clustal/progress.h -rw-r--r-- root/root 3936 2015-11-24 23:17 ./usr/include/clustalo/clustal/seq.h -rw-r--r-- root/root 2310 2015-11-24 23:17 ./usr/include/clustalo/clustal/symmatrix.h -rw-r--r-- root/root 1066 2015-11-24 23:17 ./usr/include/clustalo/clustal/tree.h -rw-r--r-- root/root 2308 2015-11-24 23:17 ./usr/include/clustalo/clustal/util.h -rw-r--r-- root/root 741 2015-11-24 23:17 ./usr/include/clustalo/clustal/weights.h drwxr-xr-x root/root 0 2015-11-24 23:17 ./usr/include/clustalo/hhalign/ -rw-r--r-- root/root 2961 2015-11-24 23:17 ./usr/include/clustalo/hhalign/general.h -rw-r--r-- root/root 859 2015-11-24 23:17 ./usr/include/clustalo/hhalign/hhfunc.h drwxr-xr-x root/root 0 2015-11-24 23:17 ./usr/include/clustalo/squid/ -rw-r--r-- root/root 1381 2015-11-24 23:17 ./usr/include/clustalo/squid/gki.h -rw-r--r-- root/root 3473 2015-11-24 23:17 ./usr/include/clustalo/squid/gsi64.h -rw-r--r-- root/root 13096 2015-11-24 23:17 ./usr/include/clustalo/squid/msa.h -rw-r--r-- root/root 1264 2015-11-24 23:17 ./usr/include/clustalo/squid/rk.h -rw-r--r-- root/root 10390 2015-11-24 23:17 ./usr/include/clustalo/squid/sqfuncs.h -rw-r--r-- root/root 19433 2015-11-24 23:17 ./usr/include/clustalo/squid/squid.h -rw-r--r-- root/root 489 2015-11-24 23:17 ./usr/include/clustalo/squid/sre_random.h -rw-r--r-- root/root 7610 2015-11-24 23:17 ./usr/include/clustalo/squid/ssi.h -rw-r--r-- root/root 1868 2015-11-24 23:17 ./usr/include/clustalo/squid/stockholm.h -rw-r--r-- root/root 1937 2015-11-24 23:17 ./usr/include/clustalo/squid/stopwatch.h -rw-r--r-- root/root 1434 2015-11-24 23:17 ./usr/include/clustalo/squid/vectorops.h -rw-r--r-- root/root 333 2015-11-24 23:17 ./usr/include/clustalo/squid/version.h drwxr-xr-x root/root 0 2015-11-24 23:17 ./usr/lib/ drwxr-xr-x root/root 0 2015-11-24 23:17 ./usr/lib/i386-linux-gnu/ -rw-r--r-- root/root 992246 2015-11-24 23:17 ./usr/lib/i386-linux-gnu/libclustalo.a drwxr-xr-x root/root 0 2015-11-24 23:17 ./usr/lib/i386-linux-gnu/pkgconfig/ -rw-r--r-- root/root 245 2015-11-24 23:17 ./usr/lib/i386-linux-gnu/pkgconfig/clustalo.pc drwxr-xr-x root/root 0 2015-11-24 23:17 ./usr/share/ drwxr-xr-x root/root 0 2015-11-24 23:17 ./usr/share/doc/ drwxr-xr-x root/root 0 2015-11-24 23:17 ./usr/share/doc/libclustalo-dev/ lrwxrwxrwx root/root 0 2015-11-24 23:17 ./usr/share/doc/libclustalo-dev/changelog.Debian.gz -> ../clustalo/changelog.Debian.gz -rw-r--r-- root/root 1174 2015-11-24 17:15 ./usr/share/doc/libclustalo-dev/copyright ┌──────────────────────────────────────────────────────────────────────────────┐ │ Post Build │ └──────────────────────────────────────────────────────────────────────────────┘ ┌──────────────────────────────────────────────────────────────────────────────┐ │ Cleanup │ └──────────────────────────────────────────────────────────────────────────────┘ Not removing build depends: as requested Keeping session: ┌──────────────────────────────────────────────────────────────────────────────┐ │ Summary │ └──────────────────────────────────────────────────────────────────────────────┘ Build Architecture: i386 Build-Space: 24068 Build-Time: 83 Distribution: xenial-proposed Host Architecture: i386 Install-Time: 26 Job: clustalo_1.2.1-2.dsc Machine Architecture: amd64 Package: clustalo Package-Time: 110 Source-Version: 1.2.1-2 Space: 24068 Status: successful Version: 1.2.1-2 ──────────────────────────────────────────────────────────────────────────────── Finished at 20151124-2317 Build needed 00:01:50, 24068k disc space RUN: /usr/share/launchpad-buildd/slavebin/scan-for-processes ['scan-for-processes', 'PACKAGEBUILD-8339795'] Scanning for processes to kill in build /home/buildd/build-PACKAGEBUILD-8339795/chroot-autobuild... RUN: /usr/share/launchpad-buildd/slavebin/umount-chroot ['umount-chroot', 'PACKAGEBUILD-8339795'] Unmounting chroot for build PACKAGEBUILD-8339795... RUN: /usr/share/launchpad-buildd/slavebin/remove-build ['remove-build', 'PACKAGEBUILD-8339795'] Removing build PACKAGEBUILD-8339795