https://launchpad.net/ubuntu/+source/augustus/3.3.1+dfsg-1/+build/14888206 RUN: /usr/share/launchpad-buildd/slavebin/slave-prep Forking launchpad-buildd slave process... Kernel version: Linux lgw01-amd64-038 4.4.0-124-generic #148-Ubuntu SMP Wed May 2 13:00:18 UTC 2018 x86_64 Buildd toolchain package versions: launchpad-buildd_161 python-lpbuildd_161 sbuild_0.67.0-2ubuntu7.1 bzr-builder_0.7.3+bzr174~ppa13~ubuntu14.10.1 bzr_2.7.0-2ubuntu3.1 git-build-recipe_0.3.4~git201611291343.dcee459~ubuntu16.04.1 git_1:2.7.4-0ubuntu1.3 dpkg-dev_1.18.4ubuntu1.4 python-debian_0.1.27ubuntu2. Syncing the system clock with the buildd NTP service... 16 May 05:11:04 ntpdate[1799]: adjust time server 10.211.37.1 offset 0.005193 sec RUN: /usr/share/launchpad-buildd/slavebin/in-target unpack-chroot --backend=chroot --series=cosmic --arch=i386 PACKAGEBUILD-14888206 /home/buildd/filecache-default/ccc8a783f4c9fcf0282a95411cd13cfaeeda0fbe Creating target for build PACKAGEBUILD-14888206 RUN: /usr/share/launchpad-buildd/slavebin/in-target mount-chroot --backend=chroot --series=cosmic --arch=i386 PACKAGEBUILD-14888206 Starting target for build PACKAGEBUILD-14888206 RUN: /usr/share/launchpad-buildd/slavebin/in-target override-sources-list --backend=chroot --series=cosmic --arch=i386 PACKAGEBUILD-14888206 'deb http://ftpmaster.internal/ubuntu cosmic main universe' 'deb http://ftpmaster.internal/ubuntu cosmic-security main universe' 'deb http://ftpmaster.internal/ubuntu cosmic-updates main universe' 'deb http://ftpmaster.internal/ubuntu cosmic-proposed main universe' Overriding sources.list in build-PACKAGEBUILD-14888206 RUN: /usr/share/launchpad-buildd/slavebin/in-target update-debian-chroot --backend=chroot --series=cosmic --arch=i386 PACKAGEBUILD-14888206 Updating target for build PACKAGEBUILD-14888206 Get:1 http://ftpmaster.internal/ubuntu cosmic InRelease [242 kB] Get:2 http://ftpmaster.internal/ubuntu cosmic-security InRelease [65.4 kB] Get:3 http://ftpmaster.internal/ubuntu cosmic-updates InRelease [65.4 kB] Get:4 http://ftpmaster.internal/ubuntu cosmic-proposed InRelease [92.5 kB] Get:5 http://ftpmaster.internal/ubuntu cosmic/main i386 Packages [1005 kB] Get:6 http://ftpmaster.internal/ubuntu cosmic/main Translation-en [517 kB] Get:7 http://ftpmaster.internal/ubuntu cosmic/universe i386 Packages [8583 kB] Get:8 http://ftpmaster.internal/ubuntu cosmic/universe Translation-en [4980 kB] Get:9 http://ftpmaster.internal/ubuntu cosmic-proposed/main i386 Packages [98.9 kB] Get:10 http://ftpmaster.internal/ubuntu cosmic-proposed/main Translation-en [48.6 kB] Get:11 http://ftpmaster.internal/ubuntu cosmic-proposed/universe i386 Packages [450 kB] Get:12 http://ftpmaster.internal/ubuntu cosmic-proposed/universe Translation-en [202 kB] Fetched 16.3 MB in 4s (4372 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following package was automatically installed and is no longer required: libncursesw5 Use 'sudo apt autoremove' to remove it. The following NEW packages will be installed: libncurses6 libncursesw6 libtinfo6 The following packages will be upgraded: adduser apt base-files base-passwd bash binutils binutils-common binutils-i686-linux-gnu bsdutils build-essential cpp cpp-7 debianutils dpkg dpkg-dev e2fslibs e2fsprogs fdisk g++ g++-7 gcc gcc-7 gcc-7-base gcc-8-base libapt-pkg5.0 libargon2-0 libasan4 libatomic1 libaudit-common libaudit1 libbinutils libblkid1 libcap-ng0 libcc1-0 libcilkrts5 libcom-err2 libcomerr2 libdpkg-perl libext2fs2 libfdisk1 libgcc-7-dev libgcc1 libgmp10 libgomp1 libgpg-error0 libitm1 libmount1 libmpx2 libncurses5 libncursesw5 libp11-kit0 libperl5.26 libprocps6 libquadmath0 libreadline7 libslang2 libsmartcols1 libsqlite3-0 libss2 libstdc++-7-dev libstdc++6 libtinfo5 libubsan0 libusb-0.1-4 libuuid1 linux-libc-dev mount ncurses-base ncurses-bin perl perl-base perl-modules-5.26 pinentry-curses procps readline-common tzdata util-linux 77 upgraded, 3 newly installed, 0 to remove and 0 not upgraded. Need to get 49.8 MB of archives. After this operation, 1469 kB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu cosmic/main i386 base-files i386 10.1ubuntu4 [58.0 kB] Get:2 http://ftpmaster.internal/ubuntu cosmic/main i386 libtinfo6 i386 6.1+20180210-2ubuntu2 [84.6 kB] Get:3 http://ftpmaster.internal/ubuntu cosmic/main i386 debianutils i386 4.8.6 [86.1 kB] Get:4 http://ftpmaster.internal/ubuntu cosmic/main i386 bash i386 4.4.18-2ubuntu2 [645 kB] Get:5 http://ftpmaster.internal/ubuntu cosmic-proposed/main i386 bsdutils i386 1:2.32-0.1ubuntu1 [62.7 kB] Get:6 http://ftpmaster.internal/ubuntu cosmic/main i386 dpkg i386 1.19.0.5ubuntu3 [1162 kB] Get:7 http://ftpmaster.internal/ubuntu cosmic/main i386 libext2fs2 i386 1.44.1-2 [185 kB] Get:8 http://ftpmaster.internal/ubuntu cosmic/main i386 e2fsprogs i386 1.44.1-2 [428 kB] Get:9 http://ftpmaster.internal/ubuntu cosmic/main i386 ncurses-bin i386 6.1+20180210-2ubuntu2 [166 kB] Get:10 http://ftpmaster.internal/ubuntu cosmic-proposed/main i386 perl-modules-5.26 all 5.26.2-3 [2763 kB] Get:11 http://ftpmaster.internal/ubuntu cosmic-proposed/main i386 libperl5.26 i386 5.26.2-3 [3182 kB] Get:12 http://ftpmaster.internal/ubuntu cosmic-proposed/main i386 perl i386 5.26.2-3 [201 kB] Get:13 http://ftpmaster.internal/ubuntu cosmic-proposed/main i386 perl-base i386 5.26.2-3 [1495 kB] Get:14 http://ftpmaster.internal/ubuntu cosmic-proposed/main i386 libuuid1 i386 2.32-0.1ubuntu1 [20.6 kB] Get:15 http://ftpmaster.internal/ubuntu cosmic-proposed/main i386 libblkid1 i386 2.32-0.1ubuntu1 [143 kB] Get:16 http://ftpmaster.internal/ubuntu cosmic-proposed/main i386 libfdisk1 i386 2.32-0.1ubuntu1 [186 kB] Get:17 http://ftpmaster.internal/ubuntu cosmic/main i386 libncursesw6 i386 6.1+20180210-2ubuntu2 [141 kB] Get:18 http://ftpmaster.internal/ubuntu cosmic-proposed/main i386 libmount1 i386 2.32-0.1ubuntu1 [152 kB] Get:19 http://ftpmaster.internal/ubuntu cosmic-proposed/main i386 libsmartcols1 i386 2.32-0.1ubuntu1 [94.0 kB] Get:20 http://ftpmaster.internal/ubuntu cosmic-proposed/main i386 fdisk i386 2.32-0.1ubuntu1 [118 kB] Get:21 http://ftpmaster.internal/ubuntu cosmic-proposed/main i386 util-linux i386 2.32-0.1ubuntu1 [943 kB] Get:22 http://ftpmaster.internal/ubuntu cosmic/main i386 base-passwd i386 3.5.45 [47.9 kB] Get:23 http://ftpmaster.internal/ubuntu cosmic/main i386 ncurses-base all 6.1+20180210-2ubuntu2 [17.8 kB] Get:24 http://ftpmaster.internal/ubuntu cosmic-proposed/main i386 libquadmath0 i386 8.1.0-3ubuntu2 [208 kB] Get:25 http://ftpmaster.internal/ubuntu cosmic-proposed/main i386 libitm1 i386 8.1.0-3ubuntu2 [30.8 kB] Get:26 http://ftpmaster.internal/ubuntu cosmic-proposed/main i386 gcc-8-base i386 8.1.0-3ubuntu2 [18.4 kB] Get:27 http://ftpmaster.internal/ubuntu cosmic-proposed/main i386 libgcc1 i386 1:8.1.0-3ubuntu2 [48.1 kB] Get:28 http://ftpmaster.internal/ubuntu cosmic-proposed/main i386 libmpx2 i386 8.1.0-3ubuntu2 [12.9 kB] Get:29 http://ftpmaster.internal/ubuntu cosmic-proposed/main i386 libcc1-0 i386 8.1.0-3ubuntu2 [41.9 kB] Get:30 http://ftpmaster.internal/ubuntu cosmic-proposed/main i386 libatomic1 i386 8.1.0-3ubuntu2 [9632 B] Get:31 http://ftpmaster.internal/ubuntu cosmic-proposed/main i386 libgomp1 i386 8.1.0-3ubuntu2 [80.8 kB] Get:32 http://ftpmaster.internal/ubuntu cosmic-proposed/main i386 libstdc++6 i386 8.1.0-3ubuntu2 [430 kB] Get:33 http://ftpmaster.internal/ubuntu cosmic/main i386 libapt-pkg5.0 i386 1.7.0~alpha0ubuntu1 [872 kB] Get:34 http://ftpmaster.internal/ubuntu cosmic-proposed/main i386 adduser all 3.117ubuntu1 [163 kB] Get:35 http://ftpmaster.internal/ubuntu cosmic/main i386 apt i386 1.7.0~alpha0ubuntu1 [1195 kB] Get:36 http://ftpmaster.internal/ubuntu cosmic-proposed/main i386 mount i386 2.32-0.1ubuntu1 [110 kB] Get:37 http://ftpmaster.internal/ubuntu cosmic-proposed/main i386 libaudit-common all 1:2.8.3-1ubuntu1 [4052 B] Get:38 http://ftpmaster.internal/ubuntu cosmic/main i386 libcap-ng0 i386 0.7.9-1 [11.5 kB] Get:39 http://ftpmaster.internal/ubuntu cosmic-proposed/main i386 libaudit1 i386 1:2.8.3-1ubuntu1 [40.1 kB] Get:40 http://ftpmaster.internal/ubuntu cosmic/main i386 libcom-err2 i386 1.44.1-2 [9684 B] Get:41 http://ftpmaster.internal/ubuntu cosmic/main i386 libgpg-error0 i386 1.31-1 [60.9 kB] Get:42 http://ftpmaster.internal/ubuntu cosmic/main i386 libss2 i386 1.44.1-2 [11.6 kB] Get:43 http://ftpmaster.internal/ubuntu cosmic/main i386 libncurses5 i386 6.1+20180210-2ubuntu2 [101 kB] Get:44 http://ftpmaster.internal/ubuntu cosmic/main i386 libncursesw5 i386 6.1+20180210-2ubuntu2 [128 kB] Get:45 http://ftpmaster.internal/ubuntu cosmic/main i386 libtinfo5 i386 6.1+20180210-2ubuntu2 [79.7 kB] Get:46 http://ftpmaster.internal/ubuntu cosmic/main i386 libgmp10 i386 2:6.1.2+dfsg-3 [246 kB] Get:47 http://ftpmaster.internal/ubuntu cosmic/main i386 libp11-kit0 i386 0.23.10-2 [179 kB] Get:48 http://ftpmaster.internal/ubuntu cosmic/main i386 libprocps6 i386 2:3.3.12-3ubuntu2 [32.3 kB] Get:49 http://ftpmaster.internal/ubuntu cosmic/main i386 libncurses6 i386 6.1+20180210-2ubuntu2 [108 kB] Get:50 http://ftpmaster.internal/ubuntu cosmic/main i386 procps i386 2:3.3.12-3ubuntu2 [224 kB] Get:51 http://ftpmaster.internal/ubuntu cosmic/main i386 libargon2-0 i386 0~20161029-2 [25.0 kB] Get:52 http://ftpmaster.internal/ubuntu cosmic/main i386 readline-common all 7.0-5 [52.2 kB] Get:53 http://ftpmaster.internal/ubuntu cosmic/main i386 libreadline7 i386 7.0-5 [127 kB] Get:54 http://ftpmaster.internal/ubuntu cosmic/main i386 libslang2 i386 2.3.2-1ubuntu1 [426 kB] Get:55 http://ftpmaster.internal/ubuntu cosmic-proposed/main i386 libsqlite3-0 i386 3.23.1-1 [536 kB] Get:56 http://ftpmaster.internal/ubuntu cosmic/main i386 tzdata all 2018e-1 [188 kB] Get:57 http://ftpmaster.internal/ubuntu cosmic/main i386 binutils-common i386 2.30-17ubuntu1 [193 kB] Get:58 http://ftpmaster.internal/ubuntu cosmic/main i386 binutils i386 2.30-17ubuntu1 [3392 B] Get:59 http://ftpmaster.internal/ubuntu cosmic/main i386 binutils-i686-linux-gnu i386 2.30-17ubuntu1 [2028 kB] Get:60 http://ftpmaster.internal/ubuntu cosmic/main i386 libbinutils i386 2.30-17ubuntu1 [544 kB] Get:61 http://ftpmaster.internal/ubuntu cosmic-proposed/main i386 libasan4 i386 7.3.0-19ubuntu2 [361 kB] Get:62 http://ftpmaster.internal/ubuntu cosmic-proposed/main i386 libubsan0 i386 7.3.0-19ubuntu2 [141 kB] Get:63 http://ftpmaster.internal/ubuntu cosmic-proposed/main i386 libcilkrts5 i386 7.3.0-19ubuntu2 [47.3 kB] Get:64 http://ftpmaster.internal/ubuntu cosmic-proposed/main i386 g++-7 i386 7.3.0-19ubuntu2 [7817 kB] Get:65 http://ftpmaster.internal/ubuntu cosmic-proposed/main i386 gcc-7 i386 7.3.0-19ubuntu2 [7692 kB] Get:66 http://ftpmaster.internal/ubuntu cosmic-proposed/main i386 libstdc++-7-dev i386 7.3.0-19ubuntu2 [1505 kB] Get:67 http://ftpmaster.internal/ubuntu cosmic-proposed/main i386 libgcc-7-dev i386 7.3.0-19ubuntu2 [2395 kB] Get:68 http://ftpmaster.internal/ubuntu cosmic-proposed/main i386 cpp-7 i386 7.3.0-19ubuntu2 [6964 kB] Get:69 http://ftpmaster.internal/ubuntu cosmic-proposed/main i386 gcc-7-base i386 7.3.0-19ubuntu2 [18.9 kB] Get:70 http://ftpmaster.internal/ubuntu cosmic/main i386 cpp i386 4:7.3.0-3ubuntu3 [27.6 kB] Get:71 http://ftpmaster.internal/ubuntu cosmic/main i386 gcc i386 4:7.3.0-3ubuntu3 [5268 B] Get:72 http://ftpmaster.internal/ubuntu cosmic/main i386 g++ i386 4:7.3.0-3ubuntu3 [1596 B] Get:73 http://ftpmaster.internal/ubuntu cosmic/main i386 dpkg-dev all 1.19.0.5ubuntu3 [608 kB] Get:74 http://ftpmaster.internal/ubuntu cosmic/main i386 libdpkg-perl all 1.19.0.5ubuntu3 [211 kB] Get:75 http://ftpmaster.internal/ubuntu cosmic/main i386 build-essential i386 12.5ubuntu2 [4728 B] Get:76 http://ftpmaster.internal/ubuntu cosmic/main i386 e2fslibs i386 1.44.1-2 [2704 B] Get:77 http://ftpmaster.internal/ubuntu cosmic/main i386 libcomerr2 i386 1.44.1-2 [2692 B] Get:78 http://ftpmaster.internal/ubuntu cosmic/main i386 libusb-0.1-4 i386 2:0.1.12-32 [17.9 kB] Get:79 http://ftpmaster.internal/ubuntu cosmic-proposed/main i386 linux-libc-dev i386 4.15.0-21.22 [1007 kB] Get:80 http://ftpmaster.internal/ubuntu cosmic-proposed/main i386 pinentry-curses i386 1.1.0-1build1 [37.7 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 49.8 MB in 1s (40.1 MB/s) (Reading database ... 12632 files and directories currently installed.) Preparing to unpack .../base-files_10.1ubuntu4_i386.deb ... Unpacking base-files (10.1ubuntu4) over (10.1ubuntu2) ... Setting up base-files (10.1ubuntu4) ... Installing new version of config file /etc/issue ... Installing new version of config file /etc/issue.net ... Installing new version of config file /etc/lsb-release ... Selecting previously unselected package libtinfo6:i386. (Reading database ... 12632 files and directories currently installed.) Preparing to unpack .../libtinfo6_6.1+20180210-2ubuntu2_i386.deb ... Unpacking libtinfo6:i386 (6.1+20180210-2ubuntu2) ... Setting up libtinfo6:i386 (6.1+20180210-2ubuntu2) ... (Reading database ... 12641 files and directories currently installed.) Preparing to unpack .../debianutils_4.8.6_i386.deb ... Unpacking debianutils (4.8.6) over (4.8.4) ... Setting up debianutils (4.8.6) ... (Reading database ... 12641 files and directories currently installed.) Preparing to unpack .../bash_4.4.18-2ubuntu2_i386.deb ... 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Setting up cpp-7 (7.3.0-19ubuntu2) ... Setting up procps (2:3.3.12-3ubuntu2) ... Setting up libstdc++-7-dev:i386 (7.3.0-19ubuntu2) ... Setting up perl (5.26.2-3) ... Setting up binutils-i686-linux-gnu (2.30-17ubuntu1) ... Processing triggers for systemd (237-3ubuntu10) ... Setting up binutils (2.30-17ubuntu1) ... Setting up cpp (4:7.3.0-3ubuntu3) ... Setting up gcc-7 (7.3.0-19ubuntu2) ... Setting up g++-7 (7.3.0-19ubuntu2) ... Setting up libdpkg-perl (1.19.0.5ubuntu3) ... Setting up gcc (4:7.3.0-3ubuntu3) ... Setting up dpkg-dev (1.19.0.5ubuntu3) ... Setting up g++ (4:7.3.0-3ubuntu3) ... Setting up build-essential (12.5ubuntu2) ... Processing triggers for libc-bin (2.27-3ubuntu1) ... RUN: /usr/share/launchpad-buildd/slavebin/sbuild-package PACKAGEBUILD-14888206 i386 cosmic-proposed -c chroot:build-PACKAGEBUILD-14888206 --arch=i386 --dist=cosmic-proposed --nolog augustus_3.3.1+dfsg-1.dsc Initiating build PACKAGEBUILD-14888206 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 4.4.0-124-generic #148-Ubuntu SMP Wed May 2 13:00:18 UTC 2018 i686 sbuild (Debian sbuild) 0.67.0 (26 Dec 2015) on lgw01-amd64-038.buildd +==============================================================================+ | augustus 3.3.1+dfsg-1 (i386) 16 May 2018 05:11 | +==============================================================================+ Package: augustus Version: 3.3.1+dfsg-1 Source Version: 3.3.1+dfsg-1 Distribution: cosmic-proposed Machine Architecture: amd64 Host Architecture: i386 Build Architecture: i386 I: NOTICE: Log filtering will replace 'build/augustus-E5WXFJ/augustus-3.3.1+dfsg' with '<>' I: NOTICE: Log filtering will replace 'build/augustus-E5WXFJ' with '<>' I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-14888206/chroot-autobuild' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- augustus_3.3.1+dfsg-1.dsc exists in .; copying to chroot Check architectures ------------------- Check dependencies ------------------ Merged Build-Depends: build-essential, fakeroot Filtered Build-Depends: build-essential, fakeroot dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/<>/resolver-jgcqCJ/apt_archive/sbuild-build-depends-core-dummy.deb'. Ign:1 copy:/<>/resolver-jgcqCJ/apt_archive ./ InRelease Get:2 copy:/<>/resolver-jgcqCJ/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-jgcqCJ/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-jgcqCJ/apt_archive ./ Sources [214 B] Get:5 copy:/<>/resolver-jgcqCJ/apt_archive ./ Packages [524 B] Fetched 2857 B in 0s (0 B/s) Reading package lists... Reading package lists... +------------------------------------------------------------------------------+ | Install core build dependencies (apt-based resolver) | +------------------------------------------------------------------------------+ Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following 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 852 B of archives. After this operation, 0 B of additional disk space will be used. Get:1 copy:/<>/resolver-jgcqCJ/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [852 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 852 B in 0s (0 B/s) Selecting previously unselected package sbuild-build-depends-core-dummy. (Reading database ... 12656 files and directories currently installed.) Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_i386.deb ... Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ... Setting up sbuild-build-depends-core-dummy (0.invalid.0) ... Merged Build-Depends: debhelper (>= 11), libsqlite3-dev, libboost-iostreams-dev, zlib1g-dev, libgsl-dev, liblpsolve55-dev, libbamtools-dev, libbam-dev, libbz2-dev, lzma-dev, libhts-dev, libncurses5-dev, asciidoctor Filtered Build-Depends: debhelper (>= 11), libsqlite3-dev, libboost-iostreams-dev, zlib1g-dev, libgsl-dev, liblpsolve55-dev, libbamtools-dev, libbam-dev, libbz2-dev, lzma-dev, libhts-dev, libncurses5-dev, asciidoctor dpkg-deb: building package 'sbuild-build-depends-augustus-dummy' in '/<>/resolver-4kjIid/apt_archive/sbuild-build-depends-augustus-dummy.deb'. Ign:1 copy:/<>/resolver-4kjIid/apt_archive ./ InRelease Get:2 copy:/<>/resolver-4kjIid/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-4kjIid/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-4kjIid/apt_archive ./ Sources [283 B] Get:5 copy:/<>/resolver-4kjIid/apt_archive ./ Packages [604 B] Fetched 3006 B in 0s (0 B/s) Reading package lists... Reading package lists... +------------------------------------------------------------------------------+ | Install augustus build dependencies (apt-based resolver) | +------------------------------------------------------------------------------+ Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: asciidoctor autoconf automake autopoint autotools-dev bsdmainutils debhelper dh-autoreconf dh-strip-nondeterminism file gettext gettext-base gir1.2-glib-2.0 gir1.2-harfbuzz-0.0 groff-base icu-devtools intltool-debian libamd2 libarchive-zip-perl libasn1-8-heimdal libbam-dev libbamtools-dev libbamtools2.5.1 libblas-dev libblas3 libboost-iostreams-dev libboost-iostreams1.65-dev libboost-iostreams1.65.1 libboost-regex1.65-dev libboost-regex1.65.1 libboost1.65-dev libbsd0 libbtf1 libbz2-dev libcamd2 libccolamd2 libcholmod3 libcolamd2 libcroco3 libcurl3-gnutls libcxsparse3 libelf1 libexpat1 libfile-stripnondeterminism-perl libfreetype6 libgfortran4 libgirepository-1.0-1 libglib2.0-0 libglib2.0-bin libglib2.0-data libglib2.0-dev libglib2.0-dev-bin libgraphblas2 libgraphite2-3 libgraphite2-dev libgsl-dev libgsl23 libgslcblas0 libgssapi-krb5-2 libgssapi3-heimdal libharfbuzz-dev libharfbuzz-gobject0 libharfbuzz-icu0 libharfbuzz0b libhcrypto4-heimdal libheimbase1-heimdal libheimntlm0-heimdal libhts-dev libhts2 libhx509-5-heimdal libicu-dev libicu-le-hb-dev libicu-le-hb0 libicu60 libiculx60 libk5crypto3 libkeyutils1 libklu1 libkrb5-26-heimdal libkrb5-3 libkrb5support0 liblapack-dev liblapack3 libldap-2.4-2 libldap-common libldl2 liblpsolve55-dev liblzma-dev libmagic-mgc libmagic1 libmetis5 libmpdec2 libncurses-dev libncurses5-dev libnghttp2-14 libpcre16-3 libpcre3-dev libpcre32-3 libpcrecpp0v5 libpipeline1 libpsl5 libpython3-stdlib libpython3.6-minimal libpython3.6-stdlib librbio2 libroken18-heimdal librtmp1 libruby2.5 libsasl2-2 libsasl2-modules-db libsigsegv2 libspqr2 libsqlite3-dev libsuitesparse-dev libsuitesparseconfig5 libtimedate-perl libtool libumfpack5 libwind0-heimdal libxml2 libyaml-0-2 lzma-dev m4 man-db mime-support pkg-config po-debconf python3 python3-distutils python3-lib2to3 python3-minimal python3.6 python3.6-minimal rake ruby ruby-asciidoctor ruby-did-you-mean ruby-minitest ruby-net-telnet ruby-power-assert ruby-test-unit ruby2.5 rubygems-integration zlib1g-dev Suggested packages: autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois vacation dh-make dwz gettext-doc libasprintf-dev libgettextpo-dev groff libbamtools-doc liblapack-doc libboost1.65-doc libboost-atomic1.65-dev libboost-chrono1.65-dev libboost-container1.65-dev libboost-context1.65-dev libboost-coroutine1.65-dev libboost-date-time1.65-dev libboost-exception1.65-dev libboost-fiber1.65-dev libboost-filesystem1.65-dev libboost-graph1.65-dev libboost-graph-parallel1.65-dev libboost-locale1.65-dev libboost-log1.65-dev libboost-math1.65-dev libboost-mpi1.65-dev libboost-mpi-python1.65-dev libboost-numpy1.65-dev libboost-program-options1.65-dev libboost-python1.65-dev libboost-random1.65-dev libboost-serialization1.65-dev libboost-signals1.65-dev libboost-stacktrace1.65-dev libboost-system1.65-dev libboost-test1.65-dev libboost-thread1.65-dev libboost-timer1.65-dev libboost-type-erasure1.65-dev libboost-wave1.65-dev libboost1.65-tools-dev libmpfrc++-dev libntl-dev libglib2.0-doc libgraphite2-utils gsl-ref-psdoc | gsl-doc-pdf | gsl-doc-info | gsl-ref-html krb5-doc krb5-user icu-doc liblzma-doc sqlite3-doc libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc apparmor less www-browser libmail-box-perl python3-doc python3-tk python3-venv python3.6-venv python3.6-doc binfmt-support ri ruby-dev bundler Recommended packages: curl | wget | lynx bzip2-doc libarchive-cpio-perl shared-mime-info xdg-user-dirs krb5-locales publicsuffix libsasl2-modules libltdl-dev libmail-sendmail-perl zip fonts-lato libjs-jquery The following NEW packages will be installed: asciidoctor autoconf automake autopoint autotools-dev bsdmainutils debhelper dh-autoreconf dh-strip-nondeterminism file gettext gettext-base gir1.2-glib-2.0 gir1.2-harfbuzz-0.0 groff-base icu-devtools intltool-debian libamd2 libarchive-zip-perl libasn1-8-heimdal libbam-dev libbamtools-dev libbamtools2.5.1 libblas-dev libblas3 libboost-iostreams-dev libboost-iostreams1.65-dev libboost-iostreams1.65.1 libboost-regex1.65-dev libboost-regex1.65.1 libboost1.65-dev libbsd0 libbtf1 libbz2-dev libcamd2 libccolamd2 libcholmod3 libcolamd2 libcroco3 libcurl3-gnutls libcxsparse3 libelf1 libexpat1 libfile-stripnondeterminism-perl libfreetype6 libgfortran4 libgirepository-1.0-1 libglib2.0-0 libglib2.0-bin libglib2.0-data libglib2.0-dev libglib2.0-dev-bin libgraphblas2 libgraphite2-3 libgraphite2-dev libgsl-dev libgsl23 libgslcblas0 libgssapi-krb5-2 libgssapi3-heimdal libharfbuzz-dev libharfbuzz-gobject0 libharfbuzz-icu0 libharfbuzz0b libhcrypto4-heimdal libheimbase1-heimdal libheimntlm0-heimdal libhts-dev libhts2 libhx509-5-heimdal libicu-dev libicu-le-hb-dev libicu-le-hb0 libicu60 libiculx60 libk5crypto3 libkeyutils1 libklu1 libkrb5-26-heimdal libkrb5-3 libkrb5support0 liblapack-dev liblapack3 libldap-2.4-2 libldap-common libldl2 liblpsolve55-dev liblzma-dev libmagic-mgc libmagic1 libmetis5 libmpdec2 libncurses-dev libncurses5-dev libnghttp2-14 libpcre16-3 libpcre3-dev libpcre32-3 libpcrecpp0v5 libpipeline1 libpsl5 libpython3-stdlib libpython3.6-minimal libpython3.6-stdlib librbio2 libroken18-heimdal librtmp1 libruby2.5 libsasl2-2 libsasl2-modules-db libsigsegv2 libspqr2 libsqlite3-dev libsuitesparse-dev libsuitesparseconfig5 libtimedate-perl libtool libumfpack5 libwind0-heimdal libxml2 libyaml-0-2 lzma-dev m4 man-db mime-support pkg-config po-debconf python3 python3-distutils python3-lib2to3 python3-minimal python3.6 python3.6-minimal rake ruby ruby-asciidoctor ruby-did-you-mean ruby-minitest ruby-net-telnet ruby-power-assert ruby-test-unit ruby2.5 rubygems-integration sbuild-build-depends-augustus-dummy zlib1g-dev 0 upgraded, 145 newly installed, 0 to remove and 0 not upgraded. Need to get 60.3 MB of archives. After this operation, 357 MB of additional disk space will be used. Get:1 copy:/<>/resolver-4kjIid/apt_archive ./ sbuild-build-depends-augustus-dummy 0.invalid.0 [932 B] Get:2 http://ftpmaster.internal/ubuntu cosmic/main i386 libpython3.6-minimal i386 3.6.5-9ubuntu1 [533 kB] Get:3 http://ftpmaster.internal/ubuntu cosmic/main i386 libexpat1 i386 2.2.5-3 [78.1 kB] Get:4 http://ftpmaster.internal/ubuntu cosmic/main i386 python3.6-minimal i386 3.6.5-9ubuntu1 [1616 kB] Get:5 http://ftpmaster.internal/ubuntu cosmic/main i386 python3-minimal i386 3.6.5-3 [23.8 kB] Get:6 http://ftpmaster.internal/ubuntu cosmic/main i386 mime-support all 3.60ubuntu1 [30.1 kB] Get:7 http://ftpmaster.internal/ubuntu cosmic/main i386 libmpdec2 i386 2.4.2-2 [80.0 kB] Get:8 http://ftpmaster.internal/ubuntu cosmic/main i386 libpython3.6-stdlib i386 3.6.5-9ubuntu1 [1742 kB] Get:9 http://ftpmaster.internal/ubuntu cosmic/main i386 python3.6 i386 3.6.5-9ubuntu1 [186 kB] Get:10 http://ftpmaster.internal/ubuntu cosmic/main i386 libpython3-stdlib i386 3.6.5-3 [7280 B] Get:11 http://ftpmaster.internal/ubuntu cosmic/main i386 python3 i386 3.6.5-3 [10.2 kB] Get:12 http://ftpmaster.internal/ubuntu cosmic/main i386 libbsd0 i386 0.8.7-1 [44.7 kB] Get:13 http://ftpmaster.internal/ubuntu cosmic/main i386 bsdmainutils i386 11.1.2ubuntu2 [183 kB] Get:14 http://ftpmaster.internal/ubuntu cosmic/main i386 groff-base i386 1.22.3-10 [1169 kB] Get:15 http://ftpmaster.internal/ubuntu cosmic/main i386 libpipeline1 i386 1.5.0-1 [27.2 kB] Get:16 http://ftpmaster.internal/ubuntu cosmic/main i386 man-db i386 2.8.3-2 [1028 kB] Get:17 http://ftpmaster.internal/ubuntu cosmic/main i386 libmagic-mgc i386 1:5.33-2 [193 kB] Get:18 http://ftpmaster.internal/ubuntu cosmic/main i386 libmagic1 i386 1:5.33-2 [76.6 kB] Get:19 http://ftpmaster.internal/ubuntu cosmic/main i386 file i386 1:5.33-2 [22.8 kB] Get:20 http://ftpmaster.internal/ubuntu cosmic/main i386 libglib2.0-0 i386 2.56.1-2ubuntu1 [1232 kB] Get:21 http://ftpmaster.internal/ubuntu cosmic/main i386 libgirepository-1.0-1 i386 1.56.1-1 [88.7 kB] Get:22 http://ftpmaster.internal/ubuntu cosmic/main i386 gir1.2-glib-2.0 i386 1.56.1-1 [131 kB] Get:23 http://ftpmaster.internal/ubuntu cosmic/main i386 libelf1 i386 0.170-0.4 [50.7 kB] Get:24 http://ftpmaster.internal/ubuntu cosmic/main i386 libglib2.0-data all 2.56.1-2ubuntu1 [4220 B] Get:25 http://ftpmaster.internal/ubuntu cosmic/main i386 libicu60 i386 60.2-6ubuntu1 [8192 kB] Get:26 http://ftpmaster.internal/ubuntu cosmic/main i386 libxml2 i386 2.9.4+dfsg1-6.1ubuntu1 [697 kB] Get:27 http://ftpmaster.internal/ubuntu cosmic/main i386 libyaml-0-2 i386 0.1.7-2ubuntu3 [49.3 kB] Get:28 http://ftpmaster.internal/ubuntu cosmic/main i386 gettext-base i386 0.19.8.1-6build1 [51.3 kB] Get:29 http://ftpmaster.internal/ubuntu cosmic/main i386 libkrb5support0 i386 1.16-2build1 [32.8 kB] Get:30 http://ftpmaster.internal/ubuntu cosmic/main i386 libk5crypto3 i386 1.16-2build1 [90.0 kB] Get:31 http://ftpmaster.internal/ubuntu cosmic/main i386 libkeyutils1 i386 1.5.9-9.2ubuntu3 [8940 B] Get:32 http://ftpmaster.internal/ubuntu cosmic/main i386 libkrb5-3 i386 1.16-2build1 [303 kB] Get:33 http://ftpmaster.internal/ubuntu cosmic/main i386 libgssapi-krb5-2 i386 1.16-2build1 [132 kB] Get:34 http://ftpmaster.internal/ubuntu cosmic/main i386 libpsl5 i386 0.20.1-1 [49.8 kB] Get:35 http://ftpmaster.internal/ubuntu cosmic/main i386 rubygems-integration all 1.11 [4994 B] Get:36 http://ftpmaster.internal/ubuntu cosmic/main i386 rake all 12.3.1-3 [44.9 kB] Get:37 http://ftpmaster.internal/ubuntu cosmic/main i386 ruby-did-you-mean all 1.2.1-1 [9828 B] Get:38 http://ftpmaster.internal/ubuntu cosmic/main i386 ruby-minitest all 5.10.3-1 [38.6 kB] Get:39 http://ftpmaster.internal/ubuntu cosmic/main i386 ruby-net-telnet all 0.1.1-2 [12.6 kB] Get:40 http://ftpmaster.internal/ubuntu cosmic/main i386 ruby-power-assert all 0.3.0-1 [7952 B] Get:41 http://ftpmaster.internal/ubuntu cosmic-proposed/main i386 ruby-test-unit all 3.2.7-1 [61.4 kB] Get:42 http://ftpmaster.internal/ubuntu cosmic/main i386 libruby2.5 i386 2.5.1-1ubuntu1 [3182 kB] Get:43 http://ftpmaster.internal/ubuntu cosmic/main i386 ruby2.5 i386 2.5.1-1ubuntu1 [48.7 kB] Get:44 http://ftpmaster.internal/ubuntu cosmic/main i386 ruby i386 1:2.5.1 [5708 B] Get:45 http://ftpmaster.internal/ubuntu cosmic/universe i386 ruby-asciidoctor all 1.5.7-1 [157 kB] Get:46 http://ftpmaster.internal/ubuntu cosmic/universe i386 asciidoctor i386 1.5.7-1 [36.8 kB] Get:47 http://ftpmaster.internal/ubuntu cosmic/main i386 libsigsegv2 i386 2.12-2 [14.2 kB] Get:48 http://ftpmaster.internal/ubuntu cosmic/main i386 m4 i386 1.4.18-1 [196 kB] Get:49 http://ftpmaster.internal/ubuntu cosmic/main i386 autoconf all 2.69-11 [322 kB] Get:50 http://ftpmaster.internal/ubuntu cosmic/main i386 autotools-dev all 20180224.1 [39.6 kB] Get:51 http://ftpmaster.internal/ubuntu cosmic/main i386 automake all 1:1.15.1-3ubuntu2 [509 kB] Get:52 http://ftpmaster.internal/ubuntu cosmic/main i386 autopoint all 0.19.8.1-6build1 [412 kB] Get:53 http://ftpmaster.internal/ubuntu cosmic-proposed/main i386 libtool all 2.4.6-2.1 [195 kB] Get:54 http://ftpmaster.internal/ubuntu cosmic-proposed/main i386 dh-autoreconf all 18 [16.1 kB] Get:55 http://ftpmaster.internal/ubuntu cosmic/main i386 libarchive-zip-perl all 1.60-1 [83.9 kB] Get:56 http://ftpmaster.internal/ubuntu cosmic/main i386 libfile-stripnondeterminism-perl all 0.041-1 [15.3 kB] Get:57 http://ftpmaster.internal/ubuntu cosmic/main i386 libtimedate-perl all 2.3000-2 [37.5 kB] Get:58 http://ftpmaster.internal/ubuntu cosmic/main i386 dh-strip-nondeterminism all 0.041-1 [5188 B] Get:59 http://ftpmaster.internal/ubuntu cosmic/main i386 libcroco3 i386 0.6.12-2 [87.7 kB] Get:60 http://ftpmaster.internal/ubuntu cosmic/main i386 gettext i386 0.19.8.1-6build1 [902 kB] Get:61 http://ftpmaster.internal/ubuntu cosmic/main i386 intltool-debian all 0.35.0+20060710.4 [24.9 kB] Get:62 http://ftpmaster.internal/ubuntu cosmic/main i386 po-debconf all 1.0.20 [232 kB] Get:63 http://ftpmaster.internal/ubuntu cosmic/main i386 debhelper all 11.2.1ubuntu1 [906 kB] Get:64 http://ftpmaster.internal/ubuntu cosmic/main i386 libfreetype6 i386 2.8.1-2ubuntu2 [351 kB] Get:65 http://ftpmaster.internal/ubuntu cosmic/main i386 libgraphite2-3 i386 1.3.11-2 [81.9 kB] Get:66 http://ftpmaster.internal/ubuntu cosmic/main i386 libharfbuzz0b i386 1.7.6-1ubuntu1 [274 kB] Get:67 http://ftpmaster.internal/ubuntu cosmic/main i386 gir1.2-harfbuzz-0.0 i386 1.7.6-1ubuntu1 [18.6 kB] Get:68 http://ftpmaster.internal/ubuntu cosmic/main i386 icu-devtools i386 60.2-6ubuntu1 [189 kB] Get:69 http://ftpmaster.internal/ubuntu cosmic/main i386 libsuitesparseconfig5 i386 1:5.2.0+dfsg-1 [9244 B] Get:70 http://ftpmaster.internal/ubuntu cosmic/main i386 libamd2 i386 1:5.2.0+dfsg-1 [14.1 kB] Get:71 http://ftpmaster.internal/ubuntu cosmic/main i386 libroken18-heimdal i386 7.5.0+dfsg-1 [44.8 kB] Get:72 http://ftpmaster.internal/ubuntu cosmic/main i386 libasn1-8-heimdal i386 7.5.0+dfsg-1 [183 kB] Get:73 http://ftpmaster.internal/ubuntu cosmic/universe i386 libbam-dev i386 0.1.19-2 [134 kB] Get:74 http://ftpmaster.internal/ubuntu cosmic-proposed/universe i386 libbamtools2.5.1 i386 2.5.1+dfsg-3 [169 kB] Get:75 http://ftpmaster.internal/ubuntu cosmic-proposed/universe i386 libbamtools-dev i386 2.5.1+dfsg-3 [19.8 kB] Get:76 http://ftpmaster.internal/ubuntu cosmic/main i386 libblas3 i386 3.8.0-1 [124 kB] Get:77 http://ftpmaster.internal/ubuntu cosmic/main i386 libblas-dev i386 3.8.0-1 [129 kB] Get:78 http://ftpmaster.internal/ubuntu cosmic-proposed/main i386 libboost1.65-dev i386 1.65.1+dfsg-0ubuntu6 [7217 kB] Get:79 http://ftpmaster.internal/ubuntu cosmic-proposed/universe i386 libboost-regex1.65.1 i386 1.65.1+dfsg-0ubuntu6 [282 kB] Get:80 http://ftpmaster.internal/ubuntu cosmic/main i386 libicu-le-hb0 i386 1.0.3+git161113-5 [15.7 kB] Get:81 http://ftpmaster.internal/ubuntu cosmic/main i386 libiculx60 i386 60.2-6ubuntu1 [19.7 kB] Get:82 http://ftpmaster.internal/ubuntu cosmic/main i386 libharfbuzz-icu0 i386 1.7.6-1ubuntu1 [5860 B] Get:83 http://ftpmaster.internal/ubuntu cosmic/main i386 libharfbuzz-gobject0 i386 1.7.6-1ubuntu1 [12.5 kB] Get:84 http://ftpmaster.internal/ubuntu cosmic/main i386 libglib2.0-bin i386 2.56.1-2ubuntu1 [72.8 kB] Get:85 http://ftpmaster.internal/ubuntu cosmic/main i386 python3-lib2to3 all 3.6.5-3 [76.6 kB] Get:86 http://ftpmaster.internal/ubuntu cosmic/main i386 python3-distutils all 3.6.5-3 [141 kB] Get:87 http://ftpmaster.internal/ubuntu cosmic/main i386 libglib2.0-dev-bin i386 2.56.1-2ubuntu1 [102 kB] Get:88 http://ftpmaster.internal/ubuntu cosmic/main i386 libpcre16-3 i386 2:8.39-9 [147 kB] Get:89 http://ftpmaster.internal/ubuntu cosmic/main i386 libpcre32-3 i386 2:8.39-9 [138 kB] Get:90 http://ftpmaster.internal/ubuntu cosmic/main i386 libpcrecpp0v5 i386 2:8.39-9 [16.3 kB] Get:91 http://ftpmaster.internal/ubuntu cosmic/main i386 libpcre3-dev i386 2:8.39-9 [537 kB] Get:92 http://ftpmaster.internal/ubuntu cosmic/main i386 pkg-config i386 0.29.1-0ubuntu2 [45.8 kB] Get:93 http://ftpmaster.internal/ubuntu cosmic/main i386 zlib1g-dev i386 1:1.2.11.dfsg-0ubuntu2 [178 kB] Get:94 http://ftpmaster.internal/ubuntu cosmic/main i386 libglib2.0-dev i386 2.56.1-2ubuntu1 [1491 kB] Get:95 http://ftpmaster.internal/ubuntu cosmic/main i386 libgraphite2-dev i386 1.3.11-2 [14.5 kB] Get:96 http://ftpmaster.internal/ubuntu cosmic/main i386 libharfbuzz-dev i386 1.7.6-1ubuntu1 [371 kB] Get:97 http://ftpmaster.internal/ubuntu cosmic/main i386 libicu-le-hb-dev i386 1.0.3+git161113-5 [31.2 kB] Get:98 http://ftpmaster.internal/ubuntu cosmic/main i386 libicu-dev i386 60.2-6ubuntu1 [9073 kB] Get:99 http://ftpmaster.internal/ubuntu cosmic-proposed/universe i386 libboost-regex1.65-dev i386 1.65.1+dfsg-0ubuntu6 [335 kB] Get:100 http://ftpmaster.internal/ubuntu cosmic-proposed/main i386 libboost-iostreams1.65.1 i386 1.65.1+dfsg-0ubuntu6 [31.0 kB] Get:101 http://ftpmaster.internal/ubuntu cosmic-proposed/universe i386 libboost-iostreams1.65-dev i386 1.65.1+dfsg-0ubuntu6 [39.7 kB] Get:102 http://ftpmaster.internal/ubuntu cosmic/universe i386 libboost-iostreams-dev i386 1.65.1.0ubuntu1 [2916 B] Get:103 http://ftpmaster.internal/ubuntu cosmic/main i386 libbtf1 i386 1:5.2.0+dfsg-1 [9332 B] Get:104 http://ftpmaster.internal/ubuntu cosmic/main i386 libbz2-dev i386 1.0.6-8.1 [28.6 kB] Get:105 http://ftpmaster.internal/ubuntu cosmic/main i386 libcamd2 i386 1:5.2.0+dfsg-1 [14.8 kB] Get:106 http://ftpmaster.internal/ubuntu cosmic/main i386 libccolamd2 i386 1:5.2.0+dfsg-1 [15.8 kB] Get:107 http://ftpmaster.internal/ubuntu cosmic/main i386 libcolamd2 i386 1:5.2.0+dfsg-1 [12.2 kB] Get:108 http://ftpmaster.internal/ubuntu cosmic-proposed/main i386 libgfortran4 i386 7.3.0-19ubuntu2 [472 kB] Get:109 http://ftpmaster.internal/ubuntu cosmic/main i386 liblapack3 i386 3.8.0-1 [1935 kB] Get:110 http://ftpmaster.internal/ubuntu cosmic/main i386 libmetis5 i386 5.1.0.dfsg-5 [166 kB] Get:111 http://ftpmaster.internal/ubuntu cosmic/main i386 libcholmod3 i386 1:5.2.0+dfsg-1 [225 kB] Get:112 http://ftpmaster.internal/ubuntu cosmic/main i386 libheimbase1-heimdal i386 7.5.0+dfsg-1 [32.1 kB] Get:113 http://ftpmaster.internal/ubuntu cosmic/main i386 libhcrypto4-heimdal i386 7.5.0+dfsg-1 [92.6 kB] Get:114 http://ftpmaster.internal/ubuntu cosmic/main i386 libwind0-heimdal i386 7.5.0+dfsg-1 [48.3 kB] Get:115 http://ftpmaster.internal/ubuntu cosmic/main i386 libhx509-5-heimdal i386 7.5.0+dfsg-1 [118 kB] Get:116 http://ftpmaster.internal/ubuntu cosmic/main i386 libkrb5-26-heimdal i386 7.5.0+dfsg-1 [232 kB] Get:117 http://ftpmaster.internal/ubuntu cosmic/main i386 libheimntlm0-heimdal i386 7.5.0+dfsg-1 [16.4 kB] Get:118 http://ftpmaster.internal/ubuntu cosmic/main i386 libgssapi3-heimdal i386 7.5.0+dfsg-1 [106 kB] Get:119 http://ftpmaster.internal/ubuntu cosmic/main i386 libsasl2-modules-db i386 2.1.27~101-g0780600+dfsg-3ubuntu2 [15.6 kB] Get:120 http://ftpmaster.internal/ubuntu cosmic/main i386 libsasl2-2 i386 2.1.27~101-g0780600+dfsg-3ubuntu2 [52.8 kB] Get:121 http://ftpmaster.internal/ubuntu cosmic/main i386 libldap-common all 2.4.46+dfsg-5ubuntu1 [16.6 kB] Get:122 http://ftpmaster.internal/ubuntu cosmic/main i386 libldap-2.4-2 i386 2.4.46+dfsg-5ubuntu1 [167 kB] Get:123 http://ftpmaster.internal/ubuntu cosmic/main i386 libnghttp2-14 i386 1.30.0-1ubuntu1 [83.0 kB] Get:124 http://ftpmaster.internal/ubuntu cosmic/main i386 librtmp1 i386 2.4+20151223.gitfa8646d.1-1 [58.1 kB] Get:125 http://ftpmaster.internal/ubuntu cosmic/main i386 libcurl3-gnutls i386 7.58.0-2ubuntu3 [236 kB] Get:126 http://ftpmaster.internal/ubuntu cosmic/main i386 libcxsparse3 i386 1:5.2.0+dfsg-1 [46.8 kB] Get:127 http://ftpmaster.internal/ubuntu cosmic/main i386 libgraphblas2 i386 1:5.2.0+dfsg-1 [506 kB] Get:128 http://ftpmaster.internal/ubuntu cosmic/universe i386 libgslcblas0 i386 2.4+dfsg-6 [80.5 kB] Get:129 http://ftpmaster.internal/ubuntu cosmic/universe i386 libgsl23 i386 2.4+dfsg-6 [802 kB] Get:130 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i386 libsuitesparse-dev i386 1:5.2.0+dfsg-1 [1131 kB] Get:141 http://ftpmaster.internal/ubuntu cosmic/main i386 liblpsolve55-dev i386 5.5.0.15-4build1 [447 kB] Get:142 http://ftpmaster.internal/ubuntu cosmic/main i386 libncurses-dev i386 6.1+20180210-2ubuntu2 [360 kB] Get:143 http://ftpmaster.internal/ubuntu cosmic/main i386 libncurses5-dev i386 6.1+20180210-2ubuntu2 [972 B] Get:144 http://ftpmaster.internal/ubuntu cosmic-proposed/main i386 libsqlite3-dev i386 3.23.1-1 [672 kB] Get:145 http://ftpmaster.internal/ubuntu cosmic/universe i386 lzma-dev all 9.22-2ubuntu3 [41.2 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 60.3 MB in 4s (16.8 MB/s) Selecting previously unselected package libpython3.6-minimal:i386. 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Preparing to unpack .../135-sbuild-build-depends-augustus-dummy_0.invalid.0_i386.deb ... Unpacking sbuild-build-depends-augustus-dummy (0.invalid.0) ... Setting up libbtf1:i386 (1:5.2.0+dfsg-1) ... Setting up libldl2:i386 (1:5.2.0+dfsg-1) ... Setting up libcxsparse3:i386 (1:5.2.0+dfsg-1) ... Setting up libicu60:i386 (60.2-6ubuntu1) ... Setting up libboost-iostreams1.65.1:i386 (1.65.1+dfsg-0ubuntu6) ... Setting up libbz2-dev:i386 (1.0.6-8.1) ... Setting up libarchive-zip-perl (1.60-1) ... Setting up libnghttp2-14:i386 (1.30.0-1ubuntu1) ... Setting up mime-support (3.60ubuntu1) ... Setting up libgfortran4:i386 (7.3.0-19ubuntu2) ... Setting up libsqlite3-dev:i386 (3.23.1-1) ... Setting up libtimedate-perl (2.3000-2) ... Setting up libsigsegv2:i386 (2.12-2) ... Setting up libldap-common (2.4.46+dfsg-5ubuntu1) ... Setting up libpsl5:i386 (0.20.1-1) ... Setting up libelf1:i386 (0.170-0.4) ... Setting up groff-base (1.22.3-10) ... Setting up libglib2.0-0:i386 (2.56.1-2ubuntu1) ... No schema files found: doing nothing. Setting up libsasl2-modules-db:i386 (2.1.27~101-g0780600+dfsg-3ubuntu2) ... Setting up libsasl2-2:i386 (2.1.27~101-g0780600+dfsg-3ubuntu2) ... Setting up gettext-base (0.19.8.1-6build1) ... Setting up libgraphblas2:i386 (1:5.2.0+dfsg-1) ... Setting up libpipeline1:i386 (1.5.0-1) ... Setting up libroken18-heimdal:i386 (7.5.0+dfsg-1) ... Setting up librtmp1:i386 (2.4+20151223.gitfa8646d.1-1) ... Setting up m4 (1.4.18-1) ... Setting up libbsd0:i386 (0.8.7-1) ... Setting up libkrb5support0:i386 (1.16-2build1) ... Setting up libgirepository-1.0-1:i386 (1.56.1-1) ... Setting up libxml2:i386 (2.9.4+dfsg1-6.1ubuntu1) ... Setting up libfreetype6:i386 (2.8.1-2ubuntu2) ... Setting up libmagic-mgc (1:5.33-2) ... Setting up libmagic1:i386 (1:5.33-2) ... Setting up libgraphite2-3:i386 (1.3.11-2) ... Setting up libcroco3:i386 (0.6.12-2) ... Setting up pkg-config (0.29.1-0ubuntu2) ... Setting up ruby-did-you-mean (1.2.1-1) ... Setting up libyaml-0-2:i386 (0.1.7-2ubuntu3) ... Setting up libblas3:i386 (3.8.0-1) ... update-alternatives: using /usr/lib/i386-linux-gnu/blas/libblas.so.3 to provide /usr/lib/i386-linux-gnu/libblas.so.3 (libblas.so.3-i386-linux-gnu) in auto mode Setting up gir1.2-glib-2.0:i386 (1.56.1-1) ... Setting up libglib2.0-data (2.56.1-2ubuntu1) ... Processing triggers for libc-bin (2.27-3ubuntu1) ... Setting up autotools-dev (20180224.1) ... Setting up libheimbase1-heimdal:i386 (7.5.0+dfsg-1) ... Setting up libsuitesparseconfig5:i386 (1:5.2.0+dfsg-1) ... Setting up libmetis5:i386 (5.1.0.dfsg-5) ... Setting up libbamtools2.5.1:i386 (2.5.1+dfsg-3) ... Setting up ruby-net-telnet (0.1.1-2) ... Setting up libbam-dev (0.1.19-2) ... Setting up libcolamd2:i386 (1:5.2.0+dfsg-1) ... Setting up rubygems-integration (1.11) ... Setting up libccolamd2:i386 (1:5.2.0+dfsg-1) ... Setting up libpcrecpp0v5:i386 (2:8.39-9) ... Setting up libpcre32-3:i386 (2:8.39-9) ... Setting up icu-devtools (60.2-6ubuntu1) ... Setting up libpcre16-3:i386 (2:8.39-9) ... Setting up liblzma-dev:i386 (5.2.2-1.3) ... Setting up libkeyutils1:i386 (1.5.9-9.2ubuntu3) ... Setting up bsdmainutils (11.1.2ubuntu2) ... 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 ruby-minitest (5.10.3-1) ... Setting up libgslcblas0:i386 (2.4+dfsg-6) ... Setting up libncurses-dev:i386 (6.1+20180210-2ubuntu2) ... Setting up libglib2.0-bin (2.56.1-2ubuntu1) ... Setting up libboost1.65-dev:i386 (1.65.1+dfsg-0ubuntu6) ... Setting up libgraphite2-dev:i386 (1.3.11-2) ... Setting up autopoint (0.19.8.1-6build1) ... Setting up libmpdec2:i386 (2.4.2-2) ... Setting up ruby-power-assert (0.3.0-1) ... Setting up libboost-regex1.65.1:i386 (1.65.1+dfsg-0ubuntu6) ... Setting up zlib1g-dev:i386 (1:1.2.11.dfsg-0ubuntu2) ... Setting up libfile-stripnondeterminism-perl (0.041-1) ... Setting up libpython3.6-stdlib:i386 (3.6.5-9ubuntu1) ... Setting up libk5crypto3:i386 (1.16-2build1) ... Setting up libpcre3-dev:i386 (2:8.39-9) ... Setting up lzma-dev (9.22-2ubuntu3) ... Setting up python3.6 (3.6.5-9ubuntu1) ... Setting up libwind0-heimdal:i386 (7.5.0+dfsg-1) ... Setting up ruby-test-unit (3.2.7-1) ... Setting up libgsl23:i386 (2.4+dfsg-6) ... Setting up gettext (0.19.8.1-6build1) ... Setting up libblas-dev:i386 (3.8.0-1) ... update-alternatives: using /usr/lib/i386-linux-gnu/blas/libblas.so to provide /usr/lib/i386-linux-gnu/libblas.so (libblas.so-i386-linux-gnu) in auto mode Setting up libgsl-dev (2.4+dfsg-6) ... Setting up libasn1-8-heimdal:i386 (7.5.0+dfsg-1) ... Setting up liblapack3:i386 (3.8.0-1) ... update-alternatives: using /usr/lib/i386-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/i386-linux-gnu/liblapack.so.3 (liblapack.so.3-i386-linux-gnu) in auto mode Setting up librbio2:i386 (1:5.2.0+dfsg-1) ... Setting up libcamd2:i386 (1:5.2.0+dfsg-1) ... Setting up libbamtools-dev:i386 (2.5.1+dfsg-3) ... Setting up libhcrypto4-heimdal:i386 (7.5.0+dfsg-1) ... Setting up libharfbuzz0b:i386 (1.7.6-1ubuntu1) ... Setting up autoconf (2.69-11) ... Setting up file (1:5.33-2) ... Setting up libhx509-5-heimdal:i386 (7.5.0+dfsg-1) ... Setting up libncurses5-dev:i386 (6.1+20180210-2ubuntu2) ... Setting up intltool-debian (0.35.0+20060710.4) ... Setting up libamd2:i386 (1:5.2.0+dfsg-1) ... Setting up gir1.2-harfbuzz-0.0:i386 (1.7.6-1ubuntu1) ... Setting up automake (1:1.15.1-3ubuntu2) ... update-alternatives: using /usr/bin/automake-1.15 to provide /usr/bin/automake (automake) in auto mode Setting up man-db (2.8.3-2) ... Not building database; man-db/auto-update is not 'true'. Setting up libkrb5-3:i386 (1.16-2build1) ... Setting up libkrb5-26-heimdal:i386 (7.5.0+dfsg-1) ... Setting up libharfbuzz-gobject0:i386 (1.7.6-1ubuntu1) ... Setting up libheimntlm0-heimdal:i386 (7.5.0+dfsg-1) ... Setting up liblapack-dev:i386 (3.8.0-1) ... update-alternatives: using /usr/lib/i386-linux-gnu/lapack/liblapack.so to provide /usr/lib/i386-linux-gnu/liblapack.so (liblapack.so-i386-linux-gnu) in auto mode Setting up libtool (2.4.6-2.1) ... Setting up libpython3-stdlib:i386 (3.6.5-3) ... Setting up libharfbuzz-icu0:i386 (1.7.6-1ubuntu1) ... Setting up po-debconf (1.0.20) ... Setting up python3 (3.6.5-3) ... Setting up libicu-le-hb0:i386 (1.0.3+git161113-5) ... Setting up libklu1:i386 (1:5.2.0+dfsg-1) ... Setting up libcholmod3:i386 (1:5.2.0+dfsg-1) ... Setting up libgssapi-krb5-2:i386 (1.16-2build1) ... Setting up libiculx60:i386 (60.2-6ubuntu1) ... Setting up libgssapi3-heimdal:i386 (7.5.0+dfsg-1) ... Setting up python3-lib2to3 (3.6.5-3) ... Setting up python3-distutils (3.6.5-3) ... Setting up libspqr2:i386 (1:5.2.0+dfsg-1) ... Setting up libglib2.0-dev-bin (2.56.1-2ubuntu1) ... Setting up libumfpack5:i386 (1:5.2.0+dfsg-1) ... Setting up libglib2.0-dev:i386 (2.56.1-2ubuntu1) ... Setting up libldap-2.4-2:i386 (2.4.46+dfsg-5ubuntu1) ... Setting up libsuitesparse-dev:i386 (1:5.2.0+dfsg-1) ... Setting up libcurl3-gnutls:i386 (7.58.0-2ubuntu3) ... Setting up liblpsolve55-dev (5.5.0.15-4build1) ... Setting up libhts2:i386 (1.7-2) ... Setting up libhts-dev:i386 (1.7-2) ... Setting up libharfbuzz-dev:i386 (1.7.6-1ubuntu1) ... Setting up dh-autoreconf (18) ... Setting up libicu-le-hb-dev:i386 (1.0.3+git161113-5) ... Setting up rake (12.3.1-3) ... Setting up libicu-dev (60.2-6ubuntu1) ... Setting up dh-strip-nondeterminism (0.041-1) ... Setting up libboost-regex1.65-dev:i386 (1.65.1+dfsg-0ubuntu6) ... Setting up debhelper (11.2.1ubuntu1) ... Setting up libruby2.5:i386 (2.5.1-1ubuntu1) ... Setting up libboost-iostreams1.65-dev:i386 (1.65.1+dfsg-0ubuntu6) ... Setting up libboost-iostreams-dev:i386 (1.65.1.0ubuntu1) ... Setting up ruby2.5 (2.5.1-1ubuntu1) ... Setting up ruby (1:2.5.1) ... Setting up ruby-asciidoctor (1.5.7-1) ... Setting up asciidoctor (1.5.7-1) ... Setting up sbuild-build-depends-augustus-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.27-3ubuntu1) ... +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 4.4.0-124-generic amd64 (i686) Toolchain package versions: binutils_2.30-17ubuntu1 dpkg-dev_1.19.0.5ubuntu3 g++-7_7.3.0-19ubuntu2 gcc-7_7.3.0-19ubuntu2 libc6-dev_2.27-3ubuntu1 libstdc++-7-dev_7.3.0-19ubuntu2 libstdc++6_8.1.0-3ubuntu2 linux-libc-dev_4.15.0-21.22 Package versions: adduser_3.117ubuntu1 advancecomp_2.1-1 apt_1.7.0~alpha0ubuntu1 asciidoctor_1.5.7-1 autoconf_2.69-11 automake_1:1.15.1-3ubuntu2 autopoint_0.19.8.1-6build1 autotools-dev_20180224.1 base-files_10.1ubuntu4 base-passwd_3.5.45 bash_4.4.18-2ubuntu2 binutils_2.30-17ubuntu1 binutils-common_2.30-17ubuntu1 binutils-i686-linux-gnu_2.30-17ubuntu1 bsdmainutils_11.1.2ubuntu2 bsdutils_1:2.32-0.1ubuntu1 build-essential_12.5ubuntu2 bzip2_1.0.6-8.1 ca-certificates_20180409 coreutils_8.28-1ubuntu1 cpp_4:7.3.0-3ubuntu3 cpp-7_7.3.0-19ubuntu2 dash_0.5.8-2.10 debconf_1.5.66 debhelper_11.2.1ubuntu1 debianutils_4.8.6 dh-autoreconf_18 dh-strip-nondeterminism_0.041-1 diffutils_1:3.6-1 dmsetup_2:1.02.145-4.1ubuntu3 dpkg_1.19.0.5ubuntu3 dpkg-dev_1.19.0.5ubuntu3 e2fslibs_1.44.1-2 e2fsprogs_1.44.1-2 fakeroot_1.22-2ubuntu1 fdisk_2.32-0.1ubuntu1 file_1:5.33-2 findutils_4.6.0+git+20170828-2 g++_4:7.3.0-3ubuntu3 g++-7_7.3.0-19ubuntu2 gcc_4:7.3.0-3ubuntu3 gcc-7_7.3.0-19ubuntu2 gcc-7-base_7.3.0-19ubuntu2 gcc-8-base_8.1.0-3ubuntu2 gettext_0.19.8.1-6build1 gettext-base_0.19.8.1-6build1 gir1.2-glib-2.0_1.56.1-1 gir1.2-harfbuzz-0.0_1.7.6-1ubuntu1 gpg_2.2.4-1ubuntu1 gpg-agent_2.2.4-1ubuntu1 gpgconf_2.2.4-1ubuntu1 gpgv_2.2.4-1ubuntu1 grep_3.1-2 groff-base_1.22.3-10 gzip_1.6-5ubuntu1 hostname_3.20 icu-devtools_60.2-6ubuntu1 init_1.51 init-system-helpers_1.51 initscripts_2.88dsf-59.3ubuntu2 insserv_1.14.0-5ubuntu3 intltool-debian_0.35.0+20060710.4 libacl1_2.2.52-3build1 libamd2_1:5.2.0+dfsg-1 libapparmor1_2.12-4ubuntu5 libapt-pkg5.0_1.7.0~alpha0ubuntu1 libarchive-zip-perl_1.60-1 libargon2-0_0~20161029-2 libasan4_7.3.0-19ubuntu2 libasn1-8-heimdal_7.5.0+dfsg-1 libassuan0_2.5.1-2 libatomic1_8.1.0-3ubuntu2 libattr1_1:2.4.47-2build1 libaudit-common_1:2.8.3-1ubuntu1 libaudit1_1:2.8.3-1ubuntu1 libbam-dev_0.1.19-2 libbamtools-dev_2.5.1+dfsg-3 libbamtools2.5.1_2.5.1+dfsg-3 libbinutils_2.30-17ubuntu1 libblas-dev_3.8.0-1 libblas3_3.8.0-1 libblkid1_2.32-0.1ubuntu1 libboost-iostreams-dev_1.65.1.0ubuntu1 libboost-iostreams1.65-dev_1.65.1+dfsg-0ubuntu6 libboost-iostreams1.65.1_1.65.1+dfsg-0ubuntu6 libboost-regex1.65-dev_1.65.1+dfsg-0ubuntu6 libboost-regex1.65.1_1.65.1+dfsg-0ubuntu6 libboost1.65-dev_1.65.1+dfsg-0ubuntu6 libbsd0_0.8.7-1 libbtf1_1:5.2.0+dfsg-1 libbz2-1.0_1.0.6-8.1 libbz2-dev_1.0.6-8.1 libc-bin_2.27-3ubuntu1 libc-dev-bin_2.27-3ubuntu1 libc6_2.27-3ubuntu1 libc6-dev_2.27-3ubuntu1 libcamd2_1:5.2.0+dfsg-1 libcap-ng0_0.7.9-1 libcap2_1:2.25-1.2 libcc1-0_8.1.0-3ubuntu2 libccolamd2_1:5.2.0+dfsg-1 libcholmod3_1:5.2.0+dfsg-1 libcilkrts5_7.3.0-19ubuntu2 libcolamd2_1:5.2.0+dfsg-1 libcom-err2_1.44.1-2 libcomerr2_1.44.1-2 libcroco3_0.6.12-2 libcryptsetup12_2:2.0.2-1ubuntu1 libcurl3-gnutls_7.58.0-2ubuntu3 libcxsparse3_1:5.2.0+dfsg-1 libdb5.3_5.3.28-13.1ubuntu1 libdebconfclient0_0.213ubuntu1 libdevmapper1.02.1_2:1.02.145-4.1ubuntu3 libdpkg-perl_1.19.0.5ubuntu3 libelf1_0.170-0.4 libexpat1_2.2.5-3 libext2fs2_1.44.1-2 libfakeroot_1.22-2ubuntu1 libfdisk1_2.32-0.1ubuntu1 libffi6_3.2.1-8 libfile-stripnondeterminism-perl_0.041-1 libfreetype6_2.8.1-2ubuntu2 libgcc-7-dev_7.3.0-19ubuntu2 libgcc1_1:8.1.0-3ubuntu2 libgcrypt20_1.8.1-4ubuntu1 libgdbm-compat4_1.14.1-6 libgdbm5_1.14.1-6 libgfortran4_7.3.0-19ubuntu2 libgirepository-1.0-1_1.56.1-1 libglib2.0-0_2.56.1-2ubuntu1 libglib2.0-bin_2.56.1-2ubuntu1 libglib2.0-data_2.56.1-2ubuntu1 libglib2.0-dev_2.56.1-2ubuntu1 libglib2.0-dev-bin_2.56.1-2ubuntu1 libgmp10_2:6.1.2+dfsg-3 libgnutls30_3.5.18-1ubuntu1 libgomp1_8.1.0-3ubuntu2 libgpg-error0_1.31-1 libgraphblas2_1:5.2.0+dfsg-1 libgraphite2-3_1.3.11-2 libgraphite2-dev_1.3.11-2 libgsl-dev_2.4+dfsg-6 libgsl23_2.4+dfsg-6 libgslcblas0_2.4+dfsg-6 libgssapi-krb5-2_1.16-2build1 libgssapi3-heimdal_7.5.0+dfsg-1 libharfbuzz-dev_1.7.6-1ubuntu1 libharfbuzz-gobject0_1.7.6-1ubuntu1 libharfbuzz-icu0_1.7.6-1ubuntu1 libharfbuzz0b_1.7.6-1ubuntu1 libhcrypto4-heimdal_7.5.0+dfsg-1 libheimbase1-heimdal_7.5.0+dfsg-1 libheimntlm0-heimdal_7.5.0+dfsg-1 libhogweed4_3.4-1 libhts-dev_1.7-2 libhts2_1.7-2 libhx509-5-heimdal_7.5.0+dfsg-1 libicu-dev_60.2-6ubuntu1 libicu-le-hb-dev_1.0.3+git161113-5 libicu-le-hb0_1.0.3+git161113-5 libicu60_60.2-6ubuntu1 libiculx60_60.2-6ubuntu1 libidn11_1.33-2.1ubuntu1 libidn2-0_2.0.4-1.1build2 libip4tc0_1.6.1-2ubuntu2 libisl19_0.19-1 libitm1_8.1.0-3ubuntu2 libjson-c3_0.12.1-1.3 libk5crypto3_1.16-2build1 libkeyutils1_1.5.9-9.2ubuntu3 libklu1_1:5.2.0+dfsg-1 libkmod2_24-1ubuntu3 libkrb5-26-heimdal_7.5.0+dfsg-1 libkrb5-3_1.16-2build1 libkrb5support0_1.16-2build1 liblapack-dev_3.8.0-1 liblapack3_3.8.0-1 libldap-2.4-2_2.4.46+dfsg-5ubuntu1 libldap-common_2.4.46+dfsg-5ubuntu1 libldl2_1:5.2.0+dfsg-1 liblockfile-bin_1.14-1.1 liblockfile1_1.14-1.1 liblpsolve55-dev_5.5.0.15-4build1 liblz4-1_0.0~r131-2ubuntu3 liblzma-dev_5.2.2-1.3 liblzma5_5.2.2-1.3 libmagic-mgc_1:5.33-2 libmagic1_1:5.33-2 libmetis5_5.1.0.dfsg-5 libmount1_2.32-0.1ubuntu1 libmpc3_1.1.0-1 libmpdec2_2.4.2-2 libmpfr6_4.0.1-1 libmpx2_8.1.0-3ubuntu2 libncurses-dev_6.1+20180210-2ubuntu2 libncurses5_6.1+20180210-2ubuntu2 libncurses5-dev_6.1+20180210-2ubuntu2 libncurses6_6.1+20180210-2ubuntu2 libncursesw5_6.1+20180210-2ubuntu2 libncursesw6_6.1+20180210-2ubuntu2 libnettle6_3.4-1 libnghttp2-14_1.30.0-1ubuntu1 libnpth0_1.5-3 libp11-kit0_0.23.10-2 libpam-modules_1.1.8-3.6ubuntu2 libpam-modules-bin_1.1.8-3.6ubuntu2 libpam-runtime_1.1.8-3.6ubuntu2 libpam0g_1.1.8-3.6ubuntu2 libpcre16-3_2:8.39-9 libpcre3_2:8.39-9 libpcre3-dev_2:8.39-9 libpcre32-3_2:8.39-9 libpcrecpp0v5_2:8.39-9 libperl5.26_5.26.2-3 libpipeline1_1.5.0-1 libpng16-16_1.6.34-1 libprocps6_2:3.3.12-3ubuntu2 libpsl5_0.20.1-1 libpython3-stdlib_3.6.5-3 libpython3.6-minimal_3.6.5-9ubuntu1 libpython3.6-stdlib_3.6.5-9ubuntu1 libquadmath0_8.1.0-3ubuntu2 librbio2_1:5.2.0+dfsg-1 libreadline7_7.0-5 libroken18-heimdal_7.5.0+dfsg-1 librtmp1_2.4+20151223.gitfa8646d.1-1 libruby2.5_2.5.1-1ubuntu1 libsasl2-2_2.1.27~101-g0780600+dfsg-3ubuntu2 libsasl2-modules-db_2.1.27~101-g0780600+dfsg-3ubuntu2 libseccomp2_2.3.1-2.1ubuntu4 libselinux1_2.7-2build2 libsemanage-common_2.7-2build2 libsemanage1_2.7-2build2 libsepol1_2.7-1 libsigsegv2_2.12-2 libslang2_2.3.2-1ubuntu1 libsmartcols1_2.32-0.1ubuntu1 libspqr2_1:5.2.0+dfsg-1 libsqlite3-0_3.23.1-1 libsqlite3-dev_3.23.1-1 libss2_1.44.1-2 libssl1.1_1.1.0g-2ubuntu4 libstdc++-7-dev_7.3.0-19ubuntu2 libstdc++6_8.1.0-3ubuntu2 libsuitesparse-dev_1:5.2.0+dfsg-1 libsuitesparseconfig5_1:5.2.0+dfsg-1 libsystemd0_237-3ubuntu10 libtasn1-6_4.13-2 libtimedate-perl_2.3000-2 libtinfo5_6.1+20180210-2ubuntu2 libtinfo6_6.1+20180210-2ubuntu2 libtool_2.4.6-2.1 libubsan0_7.3.0-19ubuntu2 libudev1_237-3ubuntu10 libumfpack5_1:5.2.0+dfsg-1 libunistring2_0.9.9-0ubuntu1 libusb-0.1-4_2:0.1.12-32 libuuid1_2.32-0.1ubuntu1 libwind0-heimdal_7.5.0+dfsg-1 libxml2_2.9.4+dfsg1-6.1ubuntu1 libyaml-0-2_0.1.7-2ubuntu3 libzstd1_1.3.3+dfsg-2ubuntu1 linux-libc-dev_4.15.0-21.22 lockfile-progs_0.1.17build1 login_1:4.5-1ubuntu1 lsb-base_9.20170808ubuntu1 lzma-dev_9.22-2ubuntu3 m4_1.4.18-1 make_4.1-9.1ubuntu1 man-db_2.8.3-2 mawk_1.3.3-17ubuntu3 mime-support_3.60ubuntu1 mount_2.32-0.1ubuntu1 multiarch-support_2.27-3ubuntu1 ncurses-base_6.1+20180210-2ubuntu2 ncurses-bin_6.1+20180210-2ubuntu2 openssl_1.1.0g-2ubuntu4 optipng_0.7.6-1.1 passwd_1:4.5-1ubuntu1 patch_2.7.6-2ubuntu1 perl_5.26.2-3 perl-base_5.26.2-3 perl-modules-5.26_5.26.2-3 pinentry-curses_1.1.0-1build1 pkg-config_0.29.1-0ubuntu2 pkgbinarymangler_138 po-debconf_1.0.20 policyrcd-script-zg2_0.1-3 procps_2:3.3.12-3ubuntu2 python3_3.6.5-3 python3-distutils_3.6.5-3 python3-lib2to3_3.6.5-3 python3-minimal_3.6.5-3 python3.6_3.6.5-9ubuntu1 python3.6-minimal_3.6.5-9ubuntu1 rake_12.3.1-3 readline-common_7.0-5 ruby_1:2.5.1 ruby-asciidoctor_1.5.7-1 ruby-did-you-mean_1.2.1-1 ruby-minitest_5.10.3-1 ruby-net-telnet_0.1.1-2 ruby-power-assert_0.3.0-1 ruby-test-unit_3.2.7-1 ruby2.5_2.5.1-1ubuntu1 rubygems-integration_1.11 sbuild-build-depends-augustus-dummy_0.invalid.0 sbuild-build-depends-core-dummy_0.invalid.0 sed_4.4-2 sensible-utils_0.0.12 systemd_237-3ubuntu10 systemd-sysv_237-3ubuntu10 sysv-rc_2.88dsf-59.3ubuntu2 sysvinit-utils_2.88dsf-59.10ubuntu1 tar_1.29b-2 tzdata_2018e-1 ubuntu-keyring_2018.02.28 util-linux_2.32-0.1ubuntu1 xz-utils_5.2.2-1.3 zlib1g_1:1.2.11.dfsg-0ubuntu2 zlib1g-dev_1:1.2.11.dfsg-0ubuntu2 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- gpgv: Signature made Tue May 15 22:38:01 2018 UTC gpgv: using RSA key 8451F9178172E7E2DC73F79551F84A8FECCA7E09 gpgv: issuer "satta@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./augustus_3.3.1+dfsg-1.dsc dpkg-source: info: extracting augustus in augustus-3.3.1+dfsg dpkg-source: info: unpacking augustus_3.3.1+dfsg.orig.tar.xz dpkg-source: info: unpacking augustus_3.3.1+dfsg-1.debian.tar.xz dpkg-source: info: applying search_config_path dpkg-source: info: applying set_installdir dpkg-source: info: applying keep_cflags dpkg-source: info: applying buildflags.patch dpkg-source: info: applying spelling.patch Check disc space ---------------- Sufficient free space for build User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf DEB_BUILD_OPTIONS=parallel=4 HOME=/sbuild-nonexistent LANG=C.UTF-8 LC_ALL=C.UTF-8 LOGNAME=buildd PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games SCHROOT_ALIAS_NAME=build-PACKAGEBUILD-14888206 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-14888206 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-14888206 SCHROOT_UID=2001 SCHROOT_USER=buildd SHELL=/bin/sh TERM=unknown USER=buildd V=1 dpkg-buildpackage ----------------- dpkg-buildpackage: info: source package augustus dpkg-buildpackage: info: source version 3.3.1+dfsg-1 dpkg-buildpackage: info: source distribution unstable dpkg-source --before-build augustus-3.3.1+dfsg dpkg-buildpackage: info: host architecture i386 fakeroot debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/<>/augustus-3.3.1+dfsg' /usr/bin/make -C auxprogs/bam2hints clean make[2]: Entering directory '/<>/augustus-3.3.1+dfsg/auxprogs/bam2hints' rm -f bam2hints.o bam2hints ../../bin/bam2hints make[2]: Leaving directory '/<>/augustus-3.3.1+dfsg/auxprogs/bam2hints' /usr/bin/make -C auxprogs/homGeneMapping clean make[2]: Entering directory '/<>/augustus-3.3.1+dfsg/auxprogs/homGeneMapping' (cd src; make clean; cd ../bin; rm -f homGeneMapping; cd ../../../bin; rm -f homGeneMapping) make[3]: Entering directory '/<>/augustus-3.3.1+dfsg/auxprogs/homGeneMapping/src' rm -f homGeneMapping gene.o genome.o make[3]: Leaving directory '/<>/augustus-3.3.1+dfsg/auxprogs/homGeneMapping/src' /bin/sh: 1: cd: can't cd to ../../../bin make[2]: Leaving directory '/<>/augustus-3.3.1+dfsg/auxprogs/homGeneMapping' /usr/bin/make -C auxprogs/joingenes clean make[2]: Entering directory '/<>/augustus-3.3.1+dfsg/auxprogs/joingenes' rm -rf *o joingenes; rm -rf ../../bin/joingenes make[2]: Leaving directory '/<>/augustus-3.3.1+dfsg/auxprogs/joingenes' /usr/bin/make -C auxprogs/aln2wig clean make[2]: Entering directory '/<>/augustus-3.3.1+dfsg/auxprogs/aln2wig' rm -f aln2wig aln2wig.o; rm -f ../../bin/aln2wig make[2]: Leaving directory '/<>/augustus-3.3.1+dfsg/auxprogs/aln2wig' /usr/bin/make -C auxprogs/bam2wig clean make[2]: Entering directory '/<>/augustus-3.3.1+dfsg/auxprogs/bam2wig' rm -f bam2wig bam2wig.o rm -f ../../bin/bam2wig make[2]: Leaving directory '/<>/augustus-3.3.1+dfsg/auxprogs/bam2wig' /usr/bin/make -C auxprogs/checkTargetSortedness clean make[2]: Entering directory '/<>/augustus-3.3.1+dfsg/auxprogs/checkTargetSortedness' rm -f *.o checkTargetSortedness make[2]: Leaving directory '/<>/augustus-3.3.1+dfsg/auxprogs/checkTargetSortedness' /usr/bin/make -C auxprogs/compileSpliceCands clean make[2]: Entering directory '/<>/augustus-3.3.1+dfsg/auxprogs/compileSpliceCands' rm -f compileSpliceCands compileSpliceCands.o ../../bin/compileSpliceCands list.o make[2]: Leaving directory '/<>/augustus-3.3.1+dfsg/auxprogs/compileSpliceCands' /usr/bin/make -C auxprogs/filterBam clean make[2]: Entering directory '/<>/augustus-3.3.1+dfsg/auxprogs/filterBam' (cd src; make clean;) make[3]: Entering directory '/<>/augustus-3.3.1+dfsg/auxprogs/filterBam/src' rm -f *~ filterBam.o MatePairs.o getReferenceName.o initOptions.o SingleAlignment.o printElapsedTime.o sumMandIOperations.o sumDandIOperations.o PairednessCoverage.o rm -f ../../../bin/filterBam make[3]: Leaving directory '/<>/augustus-3.3.1+dfsg/auxprogs/filterBam/src' make[2]: Leaving directory '/<>/augustus-3.3.1+dfsg/auxprogs/filterBam' rm -rf bin make[1]: Leaving directory '/<>/augustus-3.3.1+dfsg' dh_clean debian/rules build-arch dh build-arch dh_update_autotools_config -a dh_autoreconf -a dh_auto_configure -a debian/rules override_dh_auto_build make[1]: Entering directory '/<>/augustus-3.3.1+dfsg' mkdir -p bin /usr/bin/make -C auxprogs/aln2wig make[2]: Entering directory '/<>/augustus-3.3.1+dfsg/auxprogs/aln2wig' gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/augustus-3.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wno-sign-compare -ansi -pedantic -O2 -ggdb -g -O2 -fdebug-prefix-map=/<>/augustus-3.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -c aln2wig.c gcc -Wall -Wno-sign-compare -ansi -pedantic -O2 -ggdb -g -O2 -fdebug-prefix-map=/<>/augustus-3.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/augustus-3.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o aln2wig aln2wig.o; cp aln2wig ../../bin make[2]: Leaving directory '/<>/augustus-3.3.1+dfsg/auxprogs/aln2wig' /usr/bin/make -C auxprogs/bam2hints make[2]: Entering directory '/<>/augustus-3.3.1+dfsg/auxprogs/bam2hints' g++ -Wall -O2 -g -O2 -fdebug-prefix-map=/<>/augustus-3.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -c bam2hints.cc -o bam2hints.o -I/usr/include/bamtools g++ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O2 -g -O2 -fdebug-prefix-map=/<>/augustus-3.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o bam2hints bam2hints.o -lbamtools -lz cp bam2hints ../../bin make[2]: Leaving directory '/<>/augustus-3.3.1+dfsg/auxprogs/bam2hints' /usr/bin/make -C auxprogs/bam2wig make[2]: Entering directory '/<>/augustus-3.3.1+dfsg/auxprogs/bam2wig' cc -Wall -O2 -I/usr/include/samtools/ -I. -I/usr/include/htslib/ -I/usr/include/bcftools/ -I/usr/include/tabix/ -g -O2 -fdebug-prefix-map=/<>/augustus-3.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -c bam2wig.c -o bam2wig.o cc -Wall -O2 -I/usr/include/samtools/ -I. -I/usr/include/htslib/ -I/usr/include/bcftools/ -I/usr/include/tabix/ -g -O2 -fdebug-prefix-map=/<>/augustus-3.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now bam2wig.o -o bam2wig /usr/lib/libbam.a -lhts -lcurses -lm -lz -lpthread -lbz2 -llzma cp bam2wig ../../bin/bam2wig make[2]: Leaving directory '/<>/augustus-3.3.1+dfsg/auxprogs/bam2wig' /usr/bin/make -C auxprogs/checkTargetSortedness make[2]: Entering directory '/<>/augustus-3.3.1+dfsg/auxprogs/checkTargetSortedness' cc -g -Wall -O2 -g -O2 -fdebug-prefix-map=/<>/augustus-3.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -c checkTargetSortedness.c -o checkTargetSortedness.o -I/usr/include/samtools -I. cc -g -Wall -O2 -g -O2 -fdebug-prefix-map=/<>/augustus-3.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now checkTargetSortedness.o -o checkTargetSortedness -lbam -lcurses -lm -lz -lpthread make[2]: Leaving directory '/<>/augustus-3.3.1+dfsg/auxprogs/checkTargetSortedness' /usr/bin/make -C auxprogs/compileSpliceCands make[2]: Entering directory '/<>/augustus-3.3.1+dfsg/auxprogs/compileSpliceCands' cc -Wall -pedantic -ansi -g -O2 -fdebug-prefix-map=/<>/augustus-3.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c compileSpliceCands.c compileSpliceCands.c: In function ‘getChromosome’: compileSpliceCands.c:226:2: warning: this decimal constant is unsigned only in ISO C90 s = malloc(3500000000); ^ compileSpliceCands.c:226:4: warning: argument 1 value ‘3500000000’ exceeds maximum object size 2147483647 [-Walloc-size-larger-than=] s = malloc(3500000000); ~~^~~~~~~~~~~~~~~~~~~~ In file included from compileSpliceCands.c:14:0: /usr/include/stdlib.h:539:14: note: in a call to allocation function ‘malloc’ declared here extern void *malloc (size_t __size) __THROW __attribute_malloc__ __wur; ^~~~~~ compileSpliceCands.c: In function ‘parseList’: compileSpliceCands.c:350:32: warning: ‘left’ may be used uninitialized in this function [-Wmaybe-uninitialized] findPossibleSpliceSites(left->name,actualChromosome,left->startPos,left->endPos,right->startPos,right->endPos,left->strand,right->strand); ^~~~ compileSpliceCands.c: In function ‘main’: compileSpliceCands.c:563:3: warning: ‘chromosomeLength’ may be used uninitialized in this function [-Wmaybe-uninitialized] parseList(&L,actualChromosome,chromosomeLength,oldname,maxSpliceSiteDiff,threshold,maxIntronLength); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cc -g -O2 -fdebug-prefix-map=/<>/augustus-3.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o list.o list.c cc -o compileSpliceCands compileSpliceCands.o list.o -g -O2 -fdebug-prefix-map=/<>/augustus-3.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now; make[2]: Leaving directory '/<>/augustus-3.3.1+dfsg/auxprogs/compileSpliceCands' /usr/bin/make -C auxprogs/filterBam make[2]: Entering directory '/<>/augustus-3.3.1+dfsg/auxprogs/filterBam' (cd src;make) make[3]: Entering directory '/<>/augustus-3.3.1+dfsg/auxprogs/filterBam/src' g++ -std=c++0x -g -O2 -fdebug-prefix-map=/<>/augustus-3.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -std=c++0x -g -O2 -fdebug-prefix-map=/<>/augustus-3.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c filterBam.cc -o filterBam.o -I/usr/include/bamtools -Iheaders -I./bamtools g++ -std=c++0x -g -O2 -fdebug-prefix-map=/<>/augustus-3.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -std=c++0x -g -O2 -fdebug-prefix-map=/<>/augustus-3.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c functions/MatePairs.cc -o MatePairs.o -I/usr/include/bamtools -Iheaders -I./bamtools g++ -std=c++0x -g -O2 -fdebug-prefix-map=/<>/augustus-3.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -std=c++0x -g -O2 -fdebug-prefix-map=/<>/augustus-3.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c functions/getReferenceName.cc -o getReferenceName.o -I/usr/include/bamtools -Iheaders -I./bamtools g++ -std=c++0x -g -O2 -fdebug-prefix-map=/<>/augustus-3.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -std=c++0x -g -O2 -fdebug-prefix-map=/<>/augustus-3.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c functions/initOptions.cc -o initOptions.o -I/usr/include/bamtools -Iheaders -I./bamtools g++ -std=c++0x -g -O2 -fdebug-prefix-map=/<>/augustus-3.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -std=c++0x -g -O2 -fdebug-prefix-map=/<>/augustus-3.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c functions/SingleAlignment.cc -o SingleAlignment.o -I/usr/include/bamtools -Iheaders -I./bamtools g++ -std=c++0x -g -O2 -fdebug-prefix-map=/<>/augustus-3.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -std=c++0x -g -O2 -fdebug-prefix-map=/<>/augustus-3.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c functions/printElapsedTime.cc -o printElapsedTime.o -I/usr/include/bamtools -Iheaders -I./bamtools g++ -std=c++0x -g -O2 -fdebug-prefix-map=/<>/augustus-3.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -std=c++0x -g -O2 -fdebug-prefix-map=/<>/augustus-3.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c functions/sumMandIOperations.cc -o sumMandIOperations.o -I/usr/include/bamtools -Iheaders -I./bamtools g++ -std=c++0x -g -O2 -fdebug-prefix-map=/<>/augustus-3.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -std=c++0x -g -O2 -fdebug-prefix-map=/<>/augustus-3.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c functions/sumDandIOperations.cc -o sumDandIOperations.o -I/usr/include/bamtools -Iheaders -I./bamtools g++ -std=c++0x -g -O2 -fdebug-prefix-map=/<>/augustus-3.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -std=c++0x -g -O2 -fdebug-prefix-map=/<>/augustus-3.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c functions/PairednessCoverage.cc -o PairednessCoverage.o -I/usr/include/bamtools -Iheaders -I./bamtools g++ -std=c++0x -g -O2 -fdebug-prefix-map=/<>/augustus-3.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -std=c++0x -g -O2 -fdebug-prefix-map=/<>/augustus-3.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now filterBam.o MatePairs.o getReferenceName.o initOptions.o SingleAlignment.o printElapsedTime.o sumMandIOperations.o sumDandIOperations.o PairednessCoverage.o -o filterBam -lbamtools -lz filterBam compiled with BAMTOOLS=/usr/include/bamtools mv filterBam ../../../bin/filterBam make[3]: Leaving directory '/<>/augustus-3.3.1+dfsg/auxprogs/filterBam/src' make[2]: Leaving directory '/<>/augustus-3.3.1+dfsg/auxprogs/filterBam' /usr/bin/make -C auxprogs/homGeneMapping/src make[2]: Entering directory '/<>/augustus-3.3.1+dfsg/auxprogs/homGeneMapping/src' g++ -c -g -O2 -fdebug-prefix-map=/<>/augustus-3.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wno-sign-compare -ansi -pedantic -std=c++0x -pthread -o gene.o gene.cc -I../include g++ -c -g -O2 -fdebug-prefix-map=/<>/augustus-3.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wno-sign-compare -ansi -pedantic -std=c++0x -pthread -o genome.o genome.cc -I../include g++ -g -O2 -fdebug-prefix-map=/<>/augustus-3.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wno-sign-compare -ansi -pedantic -std=c++0x -pthread -o homGeneMapping main.cc gene.o genome.o -I../include -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now cp homGeneMapping ../../../bin/homGeneMapping make[2]: Leaving directory '/<>/augustus-3.3.1+dfsg/auxprogs/homGeneMapping/src' /usr/bin/make -C auxprogs/joingenes make[2]: Entering directory '/<>/augustus-3.3.1+dfsg/auxprogs/joingenes' g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/augustus-3.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -std=gnu++0x joingenes.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/augustus-3.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -std=gnu++0x jg_transcript.cpp g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/augustus-3.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -std=gnu++0x jg_ios.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>/augustus-3.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -std=gnu++0x joingenes.o jg_transcript.o jg_ios.o -o joingenes -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now cp joingenes ../../bin/ make[2]: Leaving directory '/<>/augustus-3.3.1+dfsg/auxprogs/joingenes' dh_auto_build make -j4 -Oline "INSTALL=install --strip-program=true" make[2]: Entering directory '/<>/augustus-3.3.1+dfsg' mkdir -p bin make[2]: Leaving directory '/<>/augustus-3.3.1+dfsg' cd src && make make[3]: Entering directory '/<>/augustus-3.3.1+dfsg/src' g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -pedantic -O3 -g -O2 -fdebug-prefix-map=/<>/augustus-3.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o pp_hitseq.o pp_hitseq.cc -I../include make[3]: Leaving directory '/<>/augustus-3.3.1+dfsg/src' make[3]: Entering directory '/<>/augustus-3.3.1+dfsg/src' g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -pedantic -O3 -g -O2 -fdebug-prefix-map=/<>/augustus-3.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o genbank.o genbank.cc -I../include make[3]: Leaving directory '/<>/augustus-3.3.1+dfsg/src' make[3]: Entering directory '/<>/augustus-3.3.1+dfsg/src' g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -pedantic -O3 -g -O2 -fdebug-prefix-map=/<>/augustus-3.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o pp_profile.o pp_profile.cc -I../include make[3]: Leaving directory '/<>/augustus-3.3.1+dfsg/src' make[3]: Entering directory '/<>/augustus-3.3.1+dfsg/src' g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -pedantic -O3 -g -O2 -fdebug-prefix-map=/<>/augustus-3.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o properties.o properties.cc -I../include make[3]: Leaving directory '/<>/augustus-3.3.1+dfsg/src' make[3]: Entering directory '/<>/augustus-3.3.1+dfsg/src' g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -pedantic -O3 -g -O2 -fdebug-prefix-map=/<>/augustus-3.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o pp_scoring.o pp_scoring.cc -I../include make[3]: Leaving directory '/<>/augustus-3.3.1+dfsg/src' make[3]: Entering directory '/<>/augustus-3.3.1+dfsg/src' g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -pedantic -O3 -g -O2 -fdebug-prefix-map=/<>/augustus-3.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o types.o types.cc -I../include make[3]: Leaving directory '/<>/augustus-3.3.1+dfsg/src' make[3]: Entering directory '/<>/augustus-3.3.1+dfsg/src' g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -pedantic -O3 -g -O2 -fdebug-prefix-map=/<>/augustus-3.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o statemodel.o statemodel.cc -I../include make[3]: Leaving directory '/<>/augustus-3.3.1+dfsg/src' make[3]: Entering directory '/<>/augustus-3.3.1+dfsg/src' g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -pedantic -O3 -g -O2 -fdebug-prefix-map=/<>/augustus-3.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o motif.o motif.cc -I../include make[3]: Leaving directory '/<>/augustus-3.3.1+dfsg/src' make[3]: Entering directory '/<>/augustus-3.3.1+dfsg/src' g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -pedantic -O3 -g -O2 -fdebug-prefix-map=/<>/augustus-3.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o namgene.o namgene.cc -I../include make[3]: Leaving directory '/<>/augustus-3.3.1+dfsg/src' make[3]: Entering directory '/<>/augustus-3.3.1+dfsg/src' g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -pedantic -O3 -g -O2 -fdebug-prefix-map=/<>/augustus-3.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o evaluation.o evaluation.cc -I../include make[3]: Leaving directory '/<>/augustus-3.3.1+dfsg/src' make[3]: Entering directory '/<>/augustus-3.3.1+dfsg/src' g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -pedantic -O3 -g -O2 -fdebug-prefix-map=/<>/augustus-3.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o geneticcode.o geneticcode.cc -I../include make[3]: Leaving directory '/<>/augustus-3.3.1+dfsg/src' make[3]: Entering directory '/<>/augustus-3.3.1+dfsg/src' g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -pedantic -O3 -g -O2 -fdebug-prefix-map=/<>/augustus-3.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o projectio.o projectio.cc -I../include make[3]: Leaving directory '/<>/augustus-3.3.1+dfsg/src' make[3]: Entering directory '/<>/augustus-3.3.1+dfsg/src' g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -pedantic -O3 -g -O2 -fdebug-prefix-map=/<>/augustus-3.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o hints.o hints.cc -I../include make[3]: Leaving directory '/<>/augustus-3.3.1+dfsg/src' make[3]: Entering directory '/<>/augustus-3.3.1+dfsg/src' g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -pedantic -O3 -g -O2 -fdebug-prefix-map=/<>/augustus-3.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o gene.o gene.cc -I../include make[3]: Leaving directory '/<>/augustus-3.3.1+dfsg/src' make[3]: Entering directory '/<>/augustus-3.3.1+dfsg/src' g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -pedantic -O3 -g -O2 -fdebug-prefix-map=/<>/augustus-3.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o intronmodel.o intronmodel.cc -I../include make[3]: Leaving directory '/<>/augustus-3.3.1+dfsg/src' make[3]: Entering directory '/<>/augustus-3.3.1+dfsg/src' g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -pedantic -O3 -g -O2 -fdebug-prefix-map=/<>/augustus-3.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o exonmodel.o exonmodel.cc -I../include make[3]: Leaving directory '/<>/augustus-3.3.1+dfsg/src' make[3]: Entering directory '/<>/augustus-3.3.1+dfsg/src' g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -pedantic -O3 -g -O2 -fdebug-prefix-map=/<>/augustus-3.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o igenicmodel.o igenicmodel.cc -I../include make[3]: Leaving directory '/<>/augustus-3.3.1+dfsg/src' make[3]: Entering directory '/<>/augustus-3.3.1+dfsg/src' g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -pedantic -O3 -g -O2 -fdebug-prefix-map=/<>/augustus-3.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o vitmatrix.o vitmatrix.cc -I../include make[3]: Leaving directory '/<>/augustus-3.3.1+dfsg/src' make[3]: Entering directory '/<>/augustus-3.3.1+dfsg/src' g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -pedantic -O3 -g -O2 -fdebug-prefix-map=/<>/augustus-3.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o lldouble.o lldouble.cc -I../include make[3]: Leaving directory '/<>/augustus-3.3.1+dfsg/src' make[3]: Entering directory '/<>/augustus-3.3.1+dfsg/src' g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -pedantic -O3 -g -O2 -fdebug-prefix-map=/<>/augustus-3.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o extrinsicinfo.o extrinsicinfo.cc -I../include make[3]: Leaving directory '/<>/augustus-3.3.1+dfsg/src' make[3]: Entering directory '/<>/augustus-3.3.1+dfsg/src' g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -pedantic -O3 -g -O2 -fdebug-prefix-map=/<>/augustus-3.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o utrmodel.o utrmodel.cc -I../include make[3]: Leaving directory '/<>/augustus-3.3.1+dfsg/src' make[3]: Entering directory '/<>/augustus-3.3.1+dfsg/src' g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -pedantic -O3 -g -O2 -fdebug-prefix-map=/<>/augustus-3.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o mea.o mea.cc -I../include make[3]: Leaving directory '/<>/augustus-3.3.1+dfsg/src' make[3]: Entering directory '/<>/augustus-3.3.1+dfsg/src' g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -pedantic -O3 -g -O2 -fdebug-prefix-map=/<>/augustus-3.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o merkmal.o merkmal.cc -I../include make[3]: Leaving directory '/<>/augustus-3.3.1+dfsg/src' make[3]: Entering directory '/<>/augustus-3.3.1+dfsg/src' g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -pedantic -O3 -g -O2 -fdebug-prefix-map=/<>/augustus-3.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o meaPath.o meaPath.cc -I../include make[3]: Leaving directory '/<>/augustus-3.3.1+dfsg/src' make[3]: Entering directory '/<>/augustus-3.3.1+dfsg/src' g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -pedantic -O3 -g -O2 -fdebug-prefix-map=/<>/augustus-3.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o fasta.o fasta.cc -I../include make[3]: Leaving directory '/<>/augustus-3.3.1+dfsg/src' make[3]: Entering directory '/<>/augustus-3.3.1+dfsg/src' g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -pedantic -O3 -g -O2 -fdebug-prefix-map=/<>/augustus-3.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o exoncand.o exoncand.cc -I../include make[3]: Leaving directory '/<>/augustus-3.3.1+dfsg/src' make[3]: Entering directory '/<>/augustus-3.3.1+dfsg/src' g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -pedantic -O3 -g -O2 -fdebug-prefix-map=/<>/augustus-3.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o graph.o graph.cc -I../include make[3]: Leaving directory '/<>/augustus-3.3.1+dfsg/src' make[3]: Entering directory '/<>/augustus-3.3.1+dfsg/src' g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -pedantic -O3 -g -O2 -fdebug-prefix-map=/<>/augustus-3.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o commontrain.o commontrain.cc -I../include make[3]: Leaving directory '/<>/augustus-3.3.1+dfsg/src' make[3]: Entering directory '/<>/augustus-3.3.1+dfsg/src' g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -pedantic -O3 -g -O2 -fdebug-prefix-map=/<>/augustus-3.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o ncmodel.o ncmodel.cc -I../include make[3]: Leaving directory '/<>/augustus-3.3.1+dfsg/src' make[3]: Entering directory '/<>/augustus-3.3.1+dfsg/src' g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -pedantic -O3 -g -O2 -fdebug-prefix-map=/<>/augustus-3.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o igenictrain.o igenictrain.cc -I../include make[3]: Leaving directory '/<>/augustus-3.3.1+dfsg/src' make[3]: Entering directory '/<>/augustus-3.3.1+dfsg/src' g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -pedantic -O3 -g -O2 -fdebug-prefix-map=/<>/augustus-3.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o randseqaccess.o randseqaccess.cc -I../include make[3]: Leaving directory '/<>/augustus-3.3.1+dfsg/src' make[3]: Entering directory '/<>/augustus-3.3.1+dfsg/src' g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -pedantic -O3 -g -O2 -fdebug-prefix-map=/<>/augustus-3.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o dummy.o dummy.cc -I../include make[3]: Leaving directory '/<>/augustus-3.3.1+dfsg/src' make[3]: Entering directory '/<>/augustus-3.3.1+dfsg/src' g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -pedantic -O3 -g -O2 -fdebug-prefix-map=/<>/augustus-3.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o introntrain.o introntrain.cc -I../include make[3]: Leaving directory '/<>/augustus-3.3.1+dfsg/src' make[3]: Entering directory '/<>/augustus-3.3.1+dfsg/src' g++ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -pedantic -O3 -g -O2 -fdebug-prefix-map=/<>/augustus-3.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o prepareAlign pp_prepare_align.cc make[3]: Leaving directory '/<>/augustus-3.3.1+dfsg/src' make[3]: Entering directory '/<>/augustus-3.3.1+dfsg/src' cp prepareAlign ../bin/ make[3]: Leaving directory '/<>/augustus-3.3.1+dfsg/src' make[3]: Entering directory '/<>/augustus-3.3.1+dfsg/src' echo "-Wall -Wno-sign-compare -Wno-strict-overflow -pedantic -O3 -g -O2 -fdebug-prefix-map=/<>/augustus-3.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security" > cxxflags make[3]: Leaving directory '/<>/augustus-3.3.1+dfsg/src' make[3]: Entering directory '/<>/augustus-3.3.1+dfsg/src' g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -pedantic -O3 -g -O2 -fdebug-prefix-map=/<>/augustus-3.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o pp_fastBlockSearcher.o pp_fastBlockSearcher.cc -I../include make[3]: Leaving directory '/<>/augustus-3.3.1+dfsg/src' make[3]: Entering directory '/<>/augustus-3.3.1+dfsg/src' g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -pedantic -O3 -g -O2 -fdebug-prefix-map=/<>/augustus-3.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o exontrain.o exontrain.cc -I../include make[3]: Leaving directory '/<>/augustus-3.3.1+dfsg/src' make[3]: Entering directory '/<>/augustus-3.3.1+dfsg/src' g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -pedantic -O3 -g -O2 -fdebug-prefix-map=/<>/augustus-3.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o utrtrain.o utrtrain.cc -I../include make[3]: Leaving directory '/<>/augustus-3.3.1+dfsg/src' make[3]: Entering directory '/<>/augustus-3.3.1+dfsg/src' g++ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -pedantic -O3 -g -O2 -fdebug-prefix-map=/<>/augustus-3.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o augustus augustus.cc genbank.o properties.o pp_profile.o pp_hitseq.o pp_scoring.o statemodel.o namgene.o types.o gene.o evaluation.o motif.o geneticcode.o hints.o extrinsicinfo.o projectio.o intronmodel.o exonmodel.o igenicmodel.o utrmodel.o merkmal.o vitmatrix.o lldouble.o mea.o graph.o meaPath.o exoncand.o randseqaccess.o fasta.o ncmodel.o dummy.o -I../include make[3]: Leaving directory '/<>/augustus-3.3.1+dfsg/src' make[3]: Entering directory '/<>/augustus-3.3.1+dfsg/src' cp augustus ../bin/ make[3]: Leaving directory '/<>/augustus-3.3.1+dfsg/src' make[3]: Entering directory '/<>/augustus-3.3.1+dfsg/src' g++ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -pedantic -O3 -g -O2 -fdebug-prefix-map=/<>/augustus-3.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o fastBlockSearch fastBlockSearch.cc pp_fastBlockSearcher.o types.o properties.o geneticcode.o pp_profile.o lldouble.o -I../include make[3]: Leaving directory '/<>/augustus-3.3.1+dfsg/src' make[3]: Entering directory '/<>/augustus-3.3.1+dfsg/src' cp fastBlockSearch ../bin/ make[3]: Leaving directory '/<>/augustus-3.3.1+dfsg/src' make[3]: Entering directory '/<>/augustus-3.3.1+dfsg/src' g++ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -pedantic -O3 -g -O2 -fdebug-prefix-map=/<>/augustus-3.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o etraining etraining.cc commontrain.o igenictrain.o introntrain.o exontrain.o utrtrain.o genbank.o properties.o pp_profile.o pp_hitseq.o pp_scoring.o statemodel.o namgene.o types.o gene.o evaluation.o motif.o geneticcode.o hints.o extrinsicinfo.o projectio.o intronmodel.o exonmodel.o igenicmodel.o utrmodel.o merkmal.o vitmatrix.o lldouble.o mea.o graph.o meaPath.o exoncand.o randseqaccess.o fasta.o ncmodel.o -I../include make[3]: Leaving directory '/<>/augustus-3.3.1+dfsg/src' make[3]: Entering directory '/<>/augustus-3.3.1+dfsg/src' cp etraining ../bin/ make[3]: Leaving directory '/<>/augustus-3.3.1+dfsg/src' cd auxprogs && make make[3]: Entering directory '/<>/augustus-3.3.1+dfsg/auxprogs' cd bam2hints; make; make[4]: Entering directory '/<>/augustus-3.3.1+dfsg/auxprogs/bam2hints' make[4]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. make[4]: Leaving directory '/<>/augustus-3.3.1+dfsg/auxprogs/bam2hints' make[4]: 'bam2hints' is up to date. make[3]: Leaving directory '/<>/augustus-3.3.1+dfsg/auxprogs' make[3]: Entering directory '/<>/augustus-3.3.1+dfsg/auxprogs' cd compileSpliceCands; make; make[4]: Entering directory '/<>/augustus-3.3.1+dfsg/auxprogs/compileSpliceCands' make[4]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. make[4]: Leaving directory '/<>/augustus-3.3.1+dfsg/auxprogs/compileSpliceCands' make[4]: 'compileSpliceCands' is up to date. make[3]: Leaving directory '/<>/augustus-3.3.1+dfsg/auxprogs' make[3]: Entering directory '/<>/augustus-3.3.1+dfsg/auxprogs' cd filterBam; make; make[4]: Entering directory '/<>/augustus-3.3.1+dfsg/auxprogs/filterBam' make[4]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. make[4]: Leaving directory '/<>/augustus-3.3.1+dfsg/auxprogs/filterBam' make[4]: Entering directory '/<>/augustus-3.3.1+dfsg/auxprogs/filterBam' (cd src;make) make[5]: Entering directory '/<>/augustus-3.3.1+dfsg/auxprogs/filterBam/src' g++ -std=c++0x -g -O2 -fdebug-prefix-map=/<>/augustus-3.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -std=c++0x -g -O2 -fdebug-prefix-map=/<>/augustus-3.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now filterBam.o MatePairs.o getReferenceName.o initOptions.o SingleAlignment.o printElapsedTime.o sumMandIOperations.o sumDandIOperations.o PairednessCoverage.o -o filterBam -lbamtools -lz make[5]: Leaving directory '/<>/augustus-3.3.1+dfsg/auxprogs/filterBam/src' make[5]: Entering directory '/<>/augustus-3.3.1+dfsg/auxprogs/filterBam/src' filterBam compiled with BAMTOOLS=/usr/include/bamtools make[5]: Leaving directory '/<>/augustus-3.3.1+dfsg/auxprogs/filterBam/src' make[5]: Entering directory '/<>/augustus-3.3.1+dfsg/auxprogs/filterBam/src' mv filterBam ../../../bin/filterBam make[5]: Leaving directory '/<>/augustus-3.3.1+dfsg/auxprogs/filterBam/src' make[4]: Leaving directory '/<>/augustus-3.3.1+dfsg/auxprogs/filterBam' make[3]: Leaving directory '/<>/augustus-3.3.1+dfsg/auxprogs' make[3]: Entering directory '/<>/augustus-3.3.1+dfsg/auxprogs' cd homGeneMapping; make; make[4]: Entering directory '/<>/augustus-3.3.1+dfsg/auxprogs/homGeneMapping' make[4]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. make[4]: Leaving directory '/<>/augustus-3.3.1+dfsg/auxprogs/homGeneMapping' make[4]: Entering directory '/<>/augustus-3.3.1+dfsg/auxprogs/homGeneMapping' (cd src; make) make[5]: Nothing to be done for 'all'. make[4]: Leaving directory '/<>/augustus-3.3.1+dfsg/auxprogs/homGeneMapping' make[3]: Leaving directory '/<>/augustus-3.3.1+dfsg/auxprogs' make[3]: Entering directory '/<>/augustus-3.3.1+dfsg/auxprogs' cd joingenes; make; make[4]: Entering directory '/<>/augustus-3.3.1+dfsg/auxprogs/joingenes' make[4]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. make[4]: Leaving directory '/<>/augustus-3.3.1+dfsg/auxprogs/joingenes' make[4]: Nothing to be done for 'all'. make[3]: Leaving directory '/<>/augustus-3.3.1+dfsg/auxprogs' make[3]: Entering directory '/<>/augustus-3.3.1+dfsg/auxprogs' cd bam2wig; make; make[4]: Entering directory '/<>/augustus-3.3.1+dfsg/auxprogs/bam2wig' make[4]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. make[4]: Leaving directory '/<>/augustus-3.3.1+dfsg/auxprogs/bam2wig' make[4]: 'bam2wig' is up to date. make[3]: Leaving directory '/<>/augustus-3.3.1+dfsg/auxprogs' make[3]: Entering directory '/<>/augustus-3.3.1+dfsg/auxprogs' cd utrrnaseq/Debug; make all; make[4]: Entering directory '/<>/augustus-3.3.1+dfsg/auxprogs/utrrnaseq/Debug' make[4]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. make[4]: Leaving directory '/<>/augustus-3.3.1+dfsg/auxprogs/utrrnaseq/Debug' make[4]: Entering directory '/<>/augustus-3.3.1+dfsg/auxprogs/utrrnaseq/Debug' Building file: ../src/Compute_UTRs.cpp make[4]: Leaving directory '/<>/augustus-3.3.1+dfsg/auxprogs/utrrnaseq/Debug' make[4]: Entering directory '/<>/augustus-3.3.1+dfsg/auxprogs/utrrnaseq/Debug' Invoking: GCC C++ Compiler make[4]: Leaving directory '/<>/augustus-3.3.1+dfsg/auxprogs/utrrnaseq/Debug' make[4]: Entering directory '/<>/augustus-3.3.1+dfsg/auxprogs/utrrnaseq/Debug' g++ -I/usr/include/boost -O0 -g3 -pedantic -Wall -c -fmessage-length=0 -MMD -MP -MF"src/Compute_UTRs.d" -MT"src/Compute_UTRs.o" -o "src/Compute_UTRs.o" "../src/Compute_UTRs.cpp" make[4]: Leaving directory '/<>/augustus-3.3.1+dfsg/auxprogs/utrrnaseq/Debug' make[4]: Entering directory '/<>/augustus-3.3.1+dfsg/auxprogs/utrrnaseq/Debug' Finished building: ../src/Compute_UTRs.cpp make[4]: Leaving directory '/<>/augustus-3.3.1+dfsg/auxprogs/utrrnaseq/Debug' make[4]: Entering directory '/<>/augustus-3.3.1+dfsg/auxprogs/utrrnaseq/Debug' make[4]: Leaving directory '/<>/augustus-3.3.1+dfsg/auxprogs/utrrnaseq/Debug' make[4]: Entering directory '/<>/augustus-3.3.1+dfsg/auxprogs/utrrnaseq/Debug' Building file: ../src/Coord_Transform.cpp make[4]: Leaving directory '/<>/augustus-3.3.1+dfsg/auxprogs/utrrnaseq/Debug' make[4]: Entering directory '/<>/augustus-3.3.1+dfsg/auxprogs/utrrnaseq/Debug' Invoking: GCC C++ Compiler make[4]: Leaving directory '/<>/augustus-3.3.1+dfsg/auxprogs/utrrnaseq/Debug' make[4]: Entering directory '/<>/augustus-3.3.1+dfsg/auxprogs/utrrnaseq/Debug' g++ -I/usr/include/boost -O0 -g3 -pedantic -Wall -c -fmessage-length=0 -MMD -MP -MF"src/Coord_Transform.d" -MT"src/Coord_Transform.o" -o "src/Coord_Transform.o" "../src/Coord_Transform.cpp" make[4]: Leaving directory '/<>/augustus-3.3.1+dfsg/auxprogs/utrrnaseq/Debug' make[4]: Entering directory '/<>/augustus-3.3.1+dfsg/auxprogs/utrrnaseq/Debug' Finished building: ../src/Coord_Transform.cpp make[4]: Leaving directory '/<>/augustus-3.3.1+dfsg/auxprogs/utrrnaseq/Debug' make[4]: Entering directory '/<>/augustus-3.3.1+dfsg/auxprogs/utrrnaseq/Debug' make[4]: Leaving directory '/<>/augustus-3.3.1+dfsg/auxprogs/utrrnaseq/Debug' make[4]: Entering directory '/<>/augustus-3.3.1+dfsg/auxprogs/utrrnaseq/Debug' Building file: ../src/Genomic_Data.cpp make[4]: Leaving directory '/<>/augustus-3.3.1+dfsg/auxprogs/utrrnaseq/Debug' make[4]: Entering directory '/<>/augustus-3.3.1+dfsg/auxprogs/utrrnaseq/Debug' Invoking: GCC C++ Compiler make[4]: Leaving directory '/<>/augustus-3.3.1+dfsg/auxprogs/utrrnaseq/Debug' make[4]: Entering directory '/<>/augustus-3.3.1+dfsg/auxprogs/utrrnaseq/Debug' g++ -I/usr/include/boost -O0 -g3 -pedantic -Wall -c -fmessage-length=0 -MMD -MP -MF"src/Genomic_Data.d" -MT"src/Genomic_Data.o" -o "src/Genomic_Data.o" "../src/Genomic_Data.cpp" make[4]: Leaving directory '/<>/augustus-3.3.1+dfsg/auxprogs/utrrnaseq/Debug' make[4]: Entering directory '/<>/augustus-3.3.1+dfsg/auxprogs/utrrnaseq/Debug' Finished building: ../src/Genomic_Data.cpp make[4]: Leaving directory '/<>/augustus-3.3.1+dfsg/auxprogs/utrrnaseq/Debug' make[4]: Entering directory '/<>/augustus-3.3.1+dfsg/auxprogs/utrrnaseq/Debug' make[4]: Leaving directory '/<>/augustus-3.3.1+dfsg/auxprogs/utrrnaseq/Debug' make[4]: Entering directory '/<>/augustus-3.3.1+dfsg/auxprogs/utrrnaseq/Debug' Building file: ../src/Splice_Sites.cpp make[4]: Leaving directory '/<>/augustus-3.3.1+dfsg/auxprogs/utrrnaseq/Debug' make[4]: Entering directory '/<>/augustus-3.3.1+dfsg/auxprogs/utrrnaseq/Debug' Invoking: GCC C++ Compiler make[4]: Leaving directory '/<>/augustus-3.3.1+dfsg/auxprogs/utrrnaseq/Debug' make[4]: Entering directory '/<>/augustus-3.3.1+dfsg/auxprogs/utrrnaseq/Debug' g++ -I/usr/include/boost -O0 -g3 -pedantic -Wall -c -fmessage-length=0 -MMD -MP -MF"src/Splice_Sites.d" -MT"src/Splice_Sites.o" -o "src/Splice_Sites.o" "../src/Splice_Sites.cpp" make[4]: Leaving directory '/<>/augustus-3.3.1+dfsg/auxprogs/utrrnaseq/Debug' make[4]: Entering directory '/<>/augustus-3.3.1+dfsg/auxprogs/utrrnaseq/Debug' Finished building: ../src/Splice_Sites.cpp make[4]: Leaving directory '/<>/augustus-3.3.1+dfsg/auxprogs/utrrnaseq/Debug' make[4]: Entering directory '/<>/augustus-3.3.1+dfsg/auxprogs/utrrnaseq/Debug' make[4]: Leaving directory '/<>/augustus-3.3.1+dfsg/auxprogs/utrrnaseq/Debug' make[4]: Entering directory '/<>/augustus-3.3.1+dfsg/auxprogs/utrrnaseq/Debug' Building file: ../src/Supporting_Methods.cpp make[4]: Leaving directory '/<>/augustus-3.3.1+dfsg/auxprogs/utrrnaseq/Debug' make[4]: Entering directory '/<>/augustus-3.3.1+dfsg/auxprogs/utrrnaseq/Debug' Invoking: GCC C++ Compiler make[4]: Leaving directory '/<>/augustus-3.3.1+dfsg/auxprogs/utrrnaseq/Debug' make[4]: Entering directory '/<>/augustus-3.3.1+dfsg/auxprogs/utrrnaseq/Debug' g++ -I/usr/include/boost -O0 -g3 -pedantic -Wall -c -fmessage-length=0 -MMD -MP -MF"src/Supporting_Methods.d" -MT"src/Supporting_Methods.o" -o "src/Supporting_Methods.o" "../src/Supporting_Methods.cpp" make[4]: Leaving directory '/<>/augustus-3.3.1+dfsg/auxprogs/utrrnaseq/Debug' make[4]: Entering directory '/<>/augustus-3.3.1+dfsg/auxprogs/utrrnaseq/Debug' Finished building: ../src/Supporting_Methods.cpp make[4]: Leaving directory '/<>/augustus-3.3.1+dfsg/auxprogs/utrrnaseq/Debug' make[4]: Entering directory '/<>/augustus-3.3.1+dfsg/auxprogs/utrrnaseq/Debug' make[4]: Leaving directory '/<>/augustus-3.3.1+dfsg/auxprogs/utrrnaseq/Debug' make[4]: Entering directory '/<>/augustus-3.3.1+dfsg/auxprogs/utrrnaseq/Debug' Building file: ../src/Test.cpp make[4]: Leaving directory '/<>/augustus-3.3.1+dfsg/auxprogs/utrrnaseq/Debug' make[4]: Entering directory '/<>/augustus-3.3.1+dfsg/auxprogs/utrrnaseq/Debug' Invoking: GCC C++ Compiler make[4]: Leaving directory '/<>/augustus-3.3.1+dfsg/auxprogs/utrrnaseq/Debug' make[4]: Entering directory '/<>/augustus-3.3.1+dfsg/auxprogs/utrrnaseq/Debug' g++ -I/usr/include/boost -O0 -g3 -pedantic -Wall -c -fmessage-length=0 -MMD -MP -MF"src/Test.d" -MT"src/Test.o" -o "src/Test.o" "../src/Test.cpp" make[4]: Leaving directory '/<>/augustus-3.3.1+dfsg/auxprogs/utrrnaseq/Debug' make[4]: Entering directory '/<>/augustus-3.3.1+dfsg/auxprogs/utrrnaseq/Debug' Finished building: ../src/Test.cpp make[4]: Leaving directory '/<>/augustus-3.3.1+dfsg/auxprogs/utrrnaseq/Debug' make[4]: Entering directory '/<>/augustus-3.3.1+dfsg/auxprogs/utrrnaseq/Debug' make[4]: Leaving directory '/<>/augustus-3.3.1+dfsg/auxprogs/utrrnaseq/Debug' make[4]: Entering directory '/<>/augustus-3.3.1+dfsg/auxprogs/utrrnaseq/Debug' Building file: ../src/UTRs.cpp make[4]: Leaving directory '/<>/augustus-3.3.1+dfsg/auxprogs/utrrnaseq/Debug' make[4]: Entering directory '/<>/augustus-3.3.1+dfsg/auxprogs/utrrnaseq/Debug' Invoking: GCC C++ Compiler make[4]: Leaving directory '/<>/augustus-3.3.1+dfsg/auxprogs/utrrnaseq/Debug' make[4]: Entering directory '/<>/augustus-3.3.1+dfsg/auxprogs/utrrnaseq/Debug' g++ -I/usr/include/boost -O0 -g3 -pedantic -Wall -c -fmessage-length=0 -MMD -MP -MF"src/UTRs.d" -MT"src/UTRs.o" -o "src/UTRs.o" "../src/UTRs.cpp" make[4]: Leaving directory '/<>/augustus-3.3.1+dfsg/auxprogs/utrrnaseq/Debug' make[4]: Entering directory '/<>/augustus-3.3.1+dfsg/auxprogs/utrrnaseq/Debug' Finished building: ../src/UTRs.cpp make[4]: Leaving directory '/<>/augustus-3.3.1+dfsg/auxprogs/utrrnaseq/Debug' make[4]: Entering directory '/<>/augustus-3.3.1+dfsg/auxprogs/utrrnaseq/Debug' make[4]: Leaving directory '/<>/augustus-3.3.1+dfsg/auxprogs/utrrnaseq/Debug' make[4]: Entering directory '/<>/augustus-3.3.1+dfsg/auxprogs/utrrnaseq/Debug' Building file: ../src/main.cpp make[4]: Leaving directory '/<>/augustus-3.3.1+dfsg/auxprogs/utrrnaseq/Debug' make[4]: Entering directory '/<>/augustus-3.3.1+dfsg/auxprogs/utrrnaseq/Debug' Invoking: GCC C++ Compiler make[4]: Leaving directory '/<>/augustus-3.3.1+dfsg/auxprogs/utrrnaseq/Debug' make[4]: Entering directory '/<>/augustus-3.3.1+dfsg/auxprogs/utrrnaseq/Debug' g++ -I/usr/include/boost -O0 -g3 -pedantic -Wall -c -fmessage-length=0 -MMD -MP -MF"src/main.d" -MT"src/main.o" -o "src/main.o" "../src/main.cpp" make[4]: Leaving directory '/<>/augustus-3.3.1+dfsg/auxprogs/utrrnaseq/Debug' make[4]: Entering directory '/<>/augustus-3.3.1+dfsg/auxprogs/utrrnaseq/Debug' Finished building: ../src/main.cpp make[4]: Leaving directory '/<>/augustus-3.3.1+dfsg/auxprogs/utrrnaseq/Debug' make[4]: Entering directory '/<>/augustus-3.3.1+dfsg/auxprogs/utrrnaseq/Debug' make[4]: Leaving directory '/<>/augustus-3.3.1+dfsg/auxprogs/utrrnaseq/Debug' make[4]: Entering directory '/<>/augustus-3.3.1+dfsg/auxprogs/utrrnaseq/Debug' Building target: utrrnaseq make[4]: Leaving directory '/<>/augustus-3.3.1+dfsg/auxprogs/utrrnaseq/Debug' make[4]: Entering directory '/<>/augustus-3.3.1+dfsg/auxprogs/utrrnaseq/Debug' Invoking: GCC C++ Linker make[4]: Leaving directory '/<>/augustus-3.3.1+dfsg/auxprogs/utrrnaseq/Debug' make[4]: Entering directory '/<>/augustus-3.3.1+dfsg/auxprogs/utrrnaseq/Debug' g++ -o "utrrnaseq" ./src/Compute_UTRs.o ./src/Coord_Transform.o ./src/Genomic_Data.o ./src/Splice_Sites.o ./src/Supporting_Methods.o ./src/Test.o ./src/UTRs.o ./src/main.o make[4]: Leaving directory '/<>/augustus-3.3.1+dfsg/auxprogs/utrrnaseq/Debug' make[4]: Entering directory '/<>/augustus-3.3.1+dfsg/auxprogs/utrrnaseq/Debug' Finished building target: utrrnaseq make[4]: Leaving directory '/<>/augustus-3.3.1+dfsg/auxprogs/utrrnaseq/Debug' make[4]: Entering directory '/<>/augustus-3.3.1+dfsg/auxprogs/utrrnaseq/Debug' make[4]: Leaving directory '/<>/augustus-3.3.1+dfsg/auxprogs/utrrnaseq/Debug' make[4]: Entering directory '/<>/augustus-3.3.1+dfsg/auxprogs/utrrnaseq/Debug' cp utrrnaseq ../../../bin/utrrnaseq make[4]: Leaving directory '/<>/augustus-3.3.1+dfsg/auxprogs/utrrnaseq/Debug' make[3]: Leaving directory '/<>/augustus-3.3.1+dfsg/auxprogs' asciidoctor -a docdate='' -b manpage debian/mansrc/*adoc make[1]: Leaving directory '/<>/augustus-3.3.1+dfsg' dh_auto_test -a create-stamp debian/debhelper-build-stamp fakeroot debian/rules binary-arch dh binary-arch dh_testroot -a dh_prep -a debian/rules override_dh_auto_install make[1]: Entering directory '/<>/augustus-3.3.1+dfsg' mkdir -p debian/augustus/usr/bin install bin/* debian/augustus/usr/bin install auxprogs/checkTargetSortedness/checkTargetSortedness \ debian/augustus/usr/bin install auxprogs/bam2wig/bam2wig \ debian/augustus/usr/bin install auxprogs/compileSpliceCands/compileSpliceCands \ debian/augustus/usr/bin install auxprogs/homGeneMapping/src/homGeneMapping \ debian/augustus/usr/bin install auxprogs/joingenes/joingenes \ debian/augustus/usr/bin mkdir -p debian/augustus/usr/share/augustus cp -r scripts debian/augustus/usr/share/augustus chmod -R -x debian/augustus/usr/share/augustus/scripts/* rm -rf debian/augustus/usr/share/augustus/scripts/*.patch \ debian/augustus/usr/share/augustus/scripts/aln2wig chmod +x debian/augustus/usr/share/augustus/scripts/checkUTR \ debian/augustus/usr/share/augustus/scripts/*.pl* mkdir -p debian/augustus-doc/usr/share/doc/augustus cp README* debian/augustus-doc/usr/share/doc/augustus cp docs/*.txt debian/augustus-doc/usr/share/doc/augustus cp -r docs/tutorial \ debian/augustus-doc/usr/share/doc/augustus mkdir -p debian/augustus-data/usr/share/augustus cp -r config debian/augustus-data/usr/share/augustus find debian/augustus-data/usr/share/augustus \ -type f -exec chmod -x {} \; make[1]: Leaving directory '/<>/augustus-3.3.1+dfsg' dh_installdocs -a debian/rules override_dh_installchangelogs make[1]: Entering directory '/<>/augustus-3.3.1+dfsg' dh_installchangelogs -k HISTORY.TXT make[1]: Leaving directory '/<>/augustus-3.3.1+dfsg' dh_installman -a dh_perl -a dh_link -a dh_strip_nondeterminism -a debian/rules override_dh_compress make[1]: Entering directory '/<>/augustus-3.3.1+dfsg' dh_compress -Xtutorial make[1]: Leaving directory '/<>/augustus-3.3.1+dfsg' dh_fixperms -a dh_missing -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dh_installdeb -a dh_gencontrol -a dpkg-gencontrol: warning: package augustus: unused substitution variable ${perl:Depends} dpkg-gencontrol: warning: package augustus: unused substitution variable ${perl:Depends} dh_md5sums -a dh_builddeb -a INFO: pkgstriptranslations version 138 INFO: pkgstriptranslations version 138 pkgstriptranslations: processing augustus (in debian/augustus); do_strip: , oemstrip: pkgstriptranslations: processing augustus-dbgsym (in debian/.debhelper/augustus/dbgsym-root); do_strip: , oemstrip: pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/augustus/DEBIAN/control, package augustus, directory debian/augustus .. removing usr/share/doc/augustus/changelog.gz pkgstripfiles: Running PNG optimization (using 4 cpus) for package augustus ... pkgstripfiles: No PNG files. dpkg-deb: building package 'augustus' in '../augustus_3.3.1+dfsg-1_i386.deb'. pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/.debhelper/augustus/dbgsym-root/DEBIAN/control, package augustus-dbgsym, directory debian/.debhelper/augustus/dbgsym-root pkgstripfiles: Running PNG optimization (using 4 cpus) for package augustus-dbgsym ... pkgstripfiles: No PNG files. dpkg-deb: building package 'augustus-dbgsym' in 'debian/.debhelper/scratch-space/build-augustus/augustus-dbgsym_3.3.1+dfsg-1_i386.deb'. Renaming augustus-dbgsym_3.3.1+dfsg-1_i386.deb to augustus-dbgsym_3.3.1+dfsg-1_i386.ddeb dpkg-genbuildinfo --build=any dpkg-genchanges --build=any -mLaunchpad Build Daemon >../augustus_3.3.1+dfsg-1_i386.changes dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included) dpkg-source --after-build augustus-3.3.1+dfsg dpkg-buildpackage: info: binary-only upload (no source included) -------------------------------------------------------------------------------- Build finished at 20180516-0513 Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Post Build Chroot | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ augustus_3.3.1+dfsg-1_i386.changes: ----------------------------------- Format: 1.8 Date: Sat, 12 May 2018 08:25:35 +0200 Source: augustus Binary: augustus augustus-data augustus-doc Architecture: i386 Version: 3.3.1+dfsg-1 Distribution: cosmic-proposed Urgency: medium Maintainer: Launchpad Build Daemon Changed-By: Sascha Steinbiss Description: augustus - gene prediction in eukaryotic genomes augustus-data - data files for AUGUSTUS augustus-doc - documentation files for AUGUSTUS Changes: augustus (3.3.1+dfsg-1) unstable; urgency=medium . [ Steffen Moeller ] * debian/upstream/metadata: RRID -> SciCrunch . [ Sascha Steinbiss ] * New upstream release. * Fix typo in manpage. * Remove obsolete Testsuite entry. * Bump Standards-Version. * Remove old patches. * Update VCS-* links. * Bump debhelper requirement to version 11. Checksums-Sha1: 7230a7599a915ee8bb29e7665db106d452d0fde3 16399692 augustus-dbgsym_3.3.1+dfsg-1_i386.ddeb edb045a9b058fea37ad52d9925a273ee52bcde25 9381 augustus_3.3.1+dfsg-1_i386.buildinfo 243892815dba1ac388d6d6c6c2b4dcd174503661 1235160 augustus_3.3.1+dfsg-1_i386.deb Checksums-Sha256: a269aaea4a969c26bb81eca1489a9267c05b0e1512f31e9b9d35910f8b84a433 16399692 augustus-dbgsym_3.3.1+dfsg-1_i386.ddeb a60bb6fa34caef73e7b5c4353e3c89c324271c3200079cc0024cceec72145d92 9381 augustus_3.3.1+dfsg-1_i386.buildinfo 0c7b8238bc18fd648b2322112aa5c21560f85c8098a6673c43f8178208056346 1235160 augustus_3.3.1+dfsg-1_i386.deb Files: 6839154156760b23ec4a717ec1f46593 16399692 debug optional augustus-dbgsym_3.3.1+dfsg-1_i386.ddeb cfb680cac36252a55c445311f2cd2d73 9381 science optional augustus_3.3.1+dfsg-1_i386.buildinfo fcd00b7ed2f1f2c6d356b368e8480400 1235160 science optional augustus_3.3.1+dfsg-1_i386.deb +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ augustus_3.3.1+dfsg-1_i386.deb ------------------------------ new debian package, version 2.0. size 1235160 bytes: control archive=4596 bytes. 1309 bytes, 23 lines control 9519 bytes, 127 lines md5sums Package: augustus Version: 3.3.1+dfsg-1 Architecture: i386 Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 5200 Depends: libbamtools2.5.1, libc6 (>= 2.15), libgcc1 (>= 1:3.0), libstdc++6 (>= 6), zlib1g (>= 1:1.2.3.3), augustus-data Built-Using: samtools-legacy (= 0.1.19-2) Section: science Priority: optional Homepage: http://bioinf.uni-greifswald.de/augustus/ Description: gene prediction in eukaryotic genomes AUGUSTUS is a software for gene prediction in eukaryotic genomic sequences that is based on a generalized hidden Markov model (HMM), a probabilistic model of a sequence and its gene structure. After learning gene structures from a reference annotation, AUGUSTUS uses the HMM to recognize genes in a new sequence and annotates it with the regions of identified genes. External hints, e.g. from RNA sequencing, EST or protein alignments etc. can be used to guide and improve the gene finding process. The result is the set of most likely gene structures that comply with all given user constraints, if such gene structures exist. AUGUSTUS already includes prebuilt HMMs for many species, as well as scripts to train custom models using annotated genomes. drwxr-xr-x root/root 0 2018-05-12 06:25 ./ drwxr-xr-x root/root 0 2018-05-12 06:25 ./usr/ drwxr-xr-x root/root 0 2018-05-12 06:25 ./usr/bin/ -rwxr-xr-x root/root 13672 2018-05-12 06:25 ./usr/bin/aln2wig -rwxr-xr-x root/root 1442200 2018-05-12 06:25 ./usr/bin/augustus -rwxr-xr-x root/root 34644 2018-05-12 06:25 ./usr/bin/bam2hints -rwxr-xr-x root/root 129452 2018-05-12 06:25 ./usr/bin/bam2wig -rwxr-xr-x root/root 121260 2018-05-12 06:25 ./usr/bin/checkTargetSortedness -rwxr-xr-x root/root 17768 2018-05-12 06:25 ./usr/bin/compileSpliceCands -rwxr-xr-x root/root 1622456 2018-05-12 06:25 ./usr/bin/etraining -rwxr-xr-x root/root 298888 2018-05-12 06:25 ./usr/bin/fastBlockSearch -rwxr-xr-x root/root 202236 2018-05-12 06:25 ./usr/bin/filterBam -rwxr-xr-x root/root 149208 2018-05-12 06:25 ./usr/bin/homGeneMapping -rwxr-xr-x root/root 157148 2018-05-12 06:25 ./usr/bin/joingenes -rwxr-xr-x root/root 30140 2018-05-12 06:25 ./usr/bin/prepareAlign -rwxr-xr-x root/root 284464 2018-05-12 06:25 ./usr/bin/utrrnaseq drwxr-xr-x root/root 0 2018-05-12 06:25 ./usr/share/ drwxr-xr-x root/root 0 2018-05-12 06:25 ./usr/share/augustus/ drwxr-xr-x root/root 0 2018-05-12 06:25 ./usr/share/augustus/scripts/ -rw-r--r-- root/root 12539 2018-05-12 06:25 ./usr/share/augustus/scripts/README.autoAug -rw-r--r-- root/root 12247 2018-05-12 06:25 ./usr/share/augustus/scripts/SplicedAlignment.pm -rwxr-xr-x root/root 13828 2018-05-12 06:25 ./usr/share/augustus/scripts/aa2nonred.pl -rwxr-xr-x root/root 3022 2018-05-12 06:25 ./usr/share/augustus/scripts/augustus2browser.pl -rwxr-xr-x root/root 389 2018-05-12 06:25 ./usr/share/augustus/scripts/augustus2gbrowse.pl -rwxr-xr-x root/root 49009 2018-05-12 06:25 ./usr/share/augustus/scripts/autoAug.pl -rwxr-xr-x root/root 20477 2018-05-12 06:25 ./usr/share/augustus/scripts/autoAugPred.pl -rwxr-xr-x root/root 44543 2018-05-12 06:25 ./usr/share/augustus/scripts/autoAugTrain.pl -rw-r--r-- root/root 195 2018-05-12 06:25 ./usr/share/augustus/scripts/autoRun.pathInfo -rwxr-xr-x root/root 3370 2018-05-12 06:25 ./usr/share/augustus/scripts/bedgraph2wig.pl -rwxr-xr-x root/root 4442 2018-05-12 06:25 ./usr/share/augustus/scripts/blat2gbrowse.pl -rwxr-xr-x root/root 30278 2018-05-12 06:25 ./usr/share/augustus/scripts/blat2hints.pl -rwxr-xr-x root/root 11310 2018-05-12 06:25 ./usr/share/augustus/scripts/block2prfl.pl -rwxr-xr-x root/root 2233 2018-05-12 06:25 ./usr/share/augustus/scripts/cegma2gff.pl -rwxr-xr-x root/root 3843 2018-05-12 06:25 ./usr/share/augustus/scripts/checkParamArchive.pl -rwxr-xr-x root/root 1151 2018-05-12 06:25 ./usr/share/augustus/scripts/checkUTR -rwxr-xr-x root/root 535 2018-05-12 06:25 ./usr/share/augustus/scripts/cleanDOSfasta.pl -rwxr-xr-x root/root 7558 2018-05-12 06:25 ./usr/share/augustus/scripts/clusterAndSplitGenes.pl -rwxr-xr-x root/root 2363 2018-05-12 06:25 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2018-05-12 06:25 ./usr/share/man/man1/bam2hints.1.gz -rw-r--r-- root/root 719 2018-05-12 06:25 ./usr/share/man/man1/bam2wig.1.gz -rw-r--r-- root/root 612 2018-05-12 06:25 ./usr/share/man/man1/checkTargetSortedness.1.gz -rw-r--r-- root/root 838 2018-05-12 06:25 ./usr/share/man/man1/compileSpliceCands.1.gz -rw-r--r-- root/root 717 2018-05-12 06:25 ./usr/share/man/man1/etraining.1.gz -rw-r--r-- root/root 1340 2018-05-12 06:25 ./usr/share/man/man1/fastBlockSearch.1.gz -rw-r--r-- root/root 1746 2018-05-12 06:25 ./usr/share/man/man1/filterBam.1.gz -rw-r--r-- root/root 1505 2018-05-12 06:25 ./usr/share/man/man1/homGeneMapping.1.gz -rw-r--r-- root/root 2039 2018-05-12 06:25 ./usr/share/man/man1/joingenes.1.gz -rw-r--r-- root/root 673 2018-05-12 06:25 ./usr/share/man/man1/prepareAlign.1.gz -rw-r--r-- root/root 1380 2018-05-12 06:25 ./usr/share/man/man1/utrrnaseq.1.gz +------------------------------------------------------------------------------+ | Post Build | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not removing build depends: as requested +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: i386 Build-Space: 862956 Build-Time: 94 Distribution: cosmic-proposed Host Architecture: i386 Install-Time: 24 Job: augustus_3.3.1+dfsg-1.dsc Machine Architecture: amd64 Package: augustus Package-Time: 128 Source-Version: 3.3.1+dfsg-1 Space: 862956 Status: successful Version: 3.3.1+dfsg-1 -------------------------------------------------------------------------------- Finished at 20180516-0513 Build needed 00:02:08, 862956k disc space RUN: /usr/share/launchpad-buildd/slavebin/in-target scan-for-processes --backend=chroot --series=cosmic --arch=i386 PACKAGEBUILD-14888206 Scanning for processes to kill in build PACKAGEBUILD-14888206 RUN: /usr/share/launchpad-buildd/slavebin/in-target umount-chroot --backend=chroot --series=cosmic --arch=i386 PACKAGEBUILD-14888206 Stopping target for build PACKAGEBUILD-14888206 RUN: /usr/share/launchpad-buildd/slavebin/in-target remove-build --backend=chroot --series=cosmic --arch=i386 PACKAGEBUILD-14888206 Removing build PACKAGEBUILD-14888206