https://launchpad.net/ubuntu/+source/augustus/3.3.1+dfsg-1/+build/14888203 RUN: /usr/share/launchpad-buildd/slavebin/slave-prep Forking launchpad-buildd slave process... Kernel version: Linux lcy01-amd64-006 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 05:10:53 ntpdate[1827]: adjust time server 10.211.37.1 offset 0.001941 sec RUN: /usr/share/launchpad-buildd/slavebin/in-target unpack-chroot --backend=chroot --series=cosmic --arch=amd64 PACKAGEBUILD-14888203 /home/buildd/filecache-default/b7d07d6b68ae68badf26a018a3a0291d50e41e42 Creating target for build PACKAGEBUILD-14888203 RUN: /usr/share/launchpad-buildd/slavebin/in-target mount-chroot --backend=chroot --series=cosmic --arch=amd64 PACKAGEBUILD-14888203 Starting target for build PACKAGEBUILD-14888203 RUN: /usr/share/launchpad-buildd/slavebin/in-target override-sources-list --backend=chroot --series=cosmic --arch=amd64 PACKAGEBUILD-14888203 '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-14888203 RUN: /usr/share/launchpad-buildd/slavebin/in-target update-debian-chroot --backend=chroot --series=cosmic --arch=amd64 PACKAGEBUILD-14888203 Updating target for build PACKAGEBUILD-14888203 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 amd64 Packages [1017 kB] Get:6 http://ftpmaster.internal/ubuntu cosmic/main Translation-en [517 kB] Get:7 http://ftpmaster.internal/ubuntu cosmic/universe amd64 Packages [8621 kB] Get:8 http://ftpmaster.internal/ubuntu cosmic/universe Translation-en [4980 kB] Get:9 http://ftpmaster.internal/ubuntu cosmic-proposed/main amd64 Packages [109 kB] Get:10 http://ftpmaster.internal/ubuntu cosmic-proposed/main Translation-en [48.6 kB] Get:11 http://ftpmaster.internal/ubuntu cosmic-proposed/universe amd64 Packages [472 kB] Get:12 http://ftpmaster.internal/ubuntu cosmic-proposed/universe Translation-en [202 kB] Fetched 16.4 MB in 4s (4031 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-x86-64-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 liblsan0 libmount1 libmpx2 libncurses5 libncursesw5 libp11-kit0 libperl5.26 libprocps6 libquadmath0 libreadline7 libslang2 libsmartcols1 libsqlite3-0 libss2 libstdc++-7-dev libstdc++6 libtinfo5 libtsan0 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 tar tzdata util-linux 80 upgraded, 3 newly installed, 0 to remove and 0 not upgraded. Need to get 49.2 MB of archives. After this operation, 1483 kB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu cosmic/main amd64 base-files amd64 10.1ubuntu4 [58.0 kB] Get:2 http://ftpmaster.internal/ubuntu cosmic/main amd64 libtinfo6 amd64 6.1+20180210-2ubuntu2 [83.8 kB] Get:3 http://ftpmaster.internal/ubuntu cosmic/main amd64 debianutils amd64 4.8.6 [85.6 kB] Get:4 http://ftpmaster.internal/ubuntu cosmic/main amd64 bash amd64 4.4.18-2ubuntu2 [614 kB] Get:5 http://ftpmaster.internal/ubuntu cosmic-proposed/main amd64 bsdutils amd64 1:2.32-0.1ubuntu1 [60.4 kB] Get:6 http://ftpmaster.internal/ubuntu cosmic-proposed/main amd64 tar amd64 1.30+dfsg-1 [240 kB] Get:7 http://ftpmaster.internal/ubuntu cosmic/main amd64 dpkg amd64 1.19.0.5ubuntu3 [1140 kB] Get:8 http://ftpmaster.internal/ubuntu cosmic/main amd64 libext2fs2 amd64 1.44.1-2 [157 kB] Get:9 http://ftpmaster.internal/ubuntu cosmic/main amd64 e2fsprogs amd64 1.44.1-2 [391 kB] Get:10 http://ftpmaster.internal/ubuntu cosmic/main amd64 ncurses-bin amd64 6.1+20180210-2ubuntu2 [163 kB] Get:11 http://ftpmaster.internal/ubuntu cosmic-proposed/main amd64 perl-modules-5.26 all 5.26.2-3 [2763 kB] Get:12 http://ftpmaster.internal/ubuntu cosmic-proposed/main amd64 libperl5.26 amd64 5.26.2-3 [3539 kB] Get:13 http://ftpmaster.internal/ubuntu cosmic-proposed/main amd64 perl amd64 5.26.2-3 [201 kB] Get:14 http://ftpmaster.internal/ubuntu cosmic-proposed/main amd64 perl-base amd64 5.26.2-3 [1390 kB] Get:15 http://ftpmaster.internal/ubuntu cosmic-proposed/main amd64 libuuid1 amd64 2.32-0.1ubuntu1 [19.9 kB] Get:16 http://ftpmaster.internal/ubuntu cosmic-proposed/main amd64 libblkid1 amd64 2.32-0.1ubuntu1 [128 kB] Get:17 http://ftpmaster.internal/ubuntu cosmic-proposed/main amd64 libfdisk1 amd64 2.32-0.1ubuntu1 [167 kB] Get:18 http://ftpmaster.internal/ubuntu cosmic/main amd64 libncursesw6 amd64 6.1+20180210-2ubuntu2 [130 kB] Get:19 http://ftpmaster.internal/ubuntu cosmic-proposed/main amd64 libmount1 amd64 2.32-0.1ubuntu1 [139 kB] Get:20 http://ftpmaster.internal/ubuntu cosmic-proposed/main amd64 libsmartcols1 amd64 2.32-0.1ubuntu1 [86.0 kB] Get:21 http://ftpmaster.internal/ubuntu cosmic-proposed/main amd64 fdisk amd64 2.32-0.1ubuntu1 [109 kB] Get:22 http://ftpmaster.internal/ubuntu cosmic-proposed/main amd64 util-linux amd64 2.32-0.1ubuntu1 [916 kB] Get:23 http://ftpmaster.internal/ubuntu cosmic/main amd64 base-passwd amd64 3.5.45 [47.4 kB] Get:24 http://ftpmaster.internal/ubuntu cosmic/main amd64 ncurses-base all 6.1+20180210-2ubuntu2 [17.8 kB] Get:25 http://ftpmaster.internal/ubuntu cosmic-proposed/main amd64 libquadmath0 amd64 8.1.0-3ubuntu2 [133 kB] Get:26 http://ftpmaster.internal/ubuntu cosmic-proposed/main amd64 libitm1 amd64 8.1.0-3ubuntu2 [28.1 kB] Get:27 http://ftpmaster.internal/ubuntu cosmic-proposed/main amd64 gcc-8-base amd64 8.1.0-3ubuntu2 [18.4 kB] Get:28 http://ftpmaster.internal/ubuntu cosmic-proposed/main amd64 libgcc1 amd64 1:8.1.0-3ubuntu2 [40.7 kB] Get:29 http://ftpmaster.internal/ubuntu cosmic-proposed/main amd64 libmpx2 amd64 8.1.0-3ubuntu2 [11.7 kB] Get:30 http://ftpmaster.internal/ubuntu cosmic-proposed/main amd64 liblsan0 amd64 8.1.0-3ubuntu2 [132 kB] Get:31 http://ftpmaster.internal/ubuntu cosmic-proposed/main amd64 libtsan0 amd64 8.1.0-3ubuntu2 [288 kB] Get:32 http://ftpmaster.internal/ubuntu cosmic-proposed/main amd64 libcc1-0 amd64 8.1.0-3ubuntu2 [39.4 kB] Get:33 http://ftpmaster.internal/ubuntu cosmic-proposed/main amd64 libatomic1 amd64 8.1.0-3ubuntu2 [9072 B] Get:34 http://ftpmaster.internal/ubuntu cosmic-proposed/main amd64 libgomp1 amd64 8.1.0-3ubuntu2 [76.5 kB] Get:35 http://ftpmaster.internal/ubuntu cosmic-proposed/main amd64 libstdc++6 amd64 8.1.0-3ubuntu2 [399 kB] Get:36 http://ftpmaster.internal/ubuntu cosmic/main amd64 libapt-pkg5.0 amd64 1.7.0~alpha0ubuntu1 [801 kB] Get:37 http://ftpmaster.internal/ubuntu cosmic-proposed/main amd64 adduser all 3.117ubuntu1 [163 kB] Get:38 http://ftpmaster.internal/ubuntu cosmic/main amd64 apt amd64 1.7.0~alpha0ubuntu1 [1166 kB] Get:39 http://ftpmaster.internal/ubuntu cosmic-proposed/main amd64 mount amd64 2.32-0.1ubuntu1 [104 kB] Get:40 http://ftpmaster.internal/ubuntu cosmic-proposed/main amd64 libaudit-common all 1:2.8.3-1ubuntu1 [4052 B] Get:41 http://ftpmaster.internal/ubuntu cosmic/main amd64 libcap-ng0 amd64 0.7.9-1 [11.3 kB] Get:42 http://ftpmaster.internal/ubuntu cosmic-proposed/main amd64 libaudit1 amd64 1:2.8.3-1ubuntu1 [38.8 kB] Get:43 http://ftpmaster.internal/ubuntu cosmic/main amd64 libcom-err2 amd64 1.44.1-2 [9392 B] Get:44 http://ftpmaster.internal/ubuntu cosmic/main amd64 libgpg-error0 amd64 1.31-1 [56.0 kB] Get:45 http://ftpmaster.internal/ubuntu cosmic/main amd64 libss2 amd64 1.44.1-2 [11.1 kB] Get:46 http://ftpmaster.internal/ubuntu cosmic/main amd64 libncurses5 amd64 6.1+20180210-2ubuntu2 [95.2 kB] Get:47 http://ftpmaster.internal/ubuntu cosmic/main amd64 libncursesw5 amd64 6.1+20180210-2ubuntu2 [117 kB] Get:48 http://ftpmaster.internal/ubuntu cosmic/main amd64 libtinfo5 amd64 6.1+20180210-2ubuntu2 [79.3 kB] Get:49 http://ftpmaster.internal/ubuntu cosmic/main amd64 libgmp10 amd64 2:6.1.2+dfsg-3 [240 kB] Get:50 http://ftpmaster.internal/ubuntu cosmic/main amd64 libp11-kit0 amd64 0.23.10-2 [186 kB] Get:51 http://ftpmaster.internal/ubuntu cosmic/main amd64 libprocps6 amd64 2:3.3.12-3ubuntu2 [31.5 kB] Get:52 http://ftpmaster.internal/ubuntu cosmic/main amd64 libncurses6 amd64 6.1+20180210-2ubuntu2 [100 kB] Get:53 http://ftpmaster.internal/ubuntu cosmic/main amd64 procps amd64 2:3.3.12-3ubuntu2 [225 kB] Get:54 http://ftpmaster.internal/ubuntu cosmic/main amd64 libargon2-0 amd64 0~20161029-2 [19.9 kB] Get:55 http://ftpmaster.internal/ubuntu cosmic/main amd64 readline-common all 7.0-5 [52.2 kB] Get:56 http://ftpmaster.internal/ubuntu cosmic/main amd64 libreadline7 amd64 7.0-5 [123 kB] Get:57 http://ftpmaster.internal/ubuntu cosmic/main amd64 libslang2 amd64 2.3.2-1ubuntu1 [425 kB] Get:58 http://ftpmaster.internal/ubuntu cosmic-proposed/main amd64 libsqlite3-0 amd64 3.23.1-1 [501 kB] Get:59 http://ftpmaster.internal/ubuntu cosmic/main amd64 tzdata all 2018e-1 [188 kB] Get:60 http://ftpmaster.internal/ubuntu cosmic/main amd64 binutils-x86-64-linux-gnu amd64 2.30-17ubuntu1 [1855 kB] Get:61 http://ftpmaster.internal/ubuntu cosmic/main amd64 binutils-common amd64 2.30-17ubuntu1 [193 kB] Get:62 http://ftpmaster.internal/ubuntu cosmic/main amd64 binutils amd64 2.30-17ubuntu1 [3392 B] Get:63 http://ftpmaster.internal/ubuntu cosmic/main amd64 libbinutils amd64 2.30-17ubuntu1 [502 kB] Get:64 http://ftpmaster.internal/ubuntu cosmic-proposed/main amd64 libasan4 amd64 7.3.0-19ubuntu2 [358 kB] Get:65 http://ftpmaster.internal/ubuntu cosmic-proposed/main amd64 libubsan0 amd64 7.3.0-19ubuntu2 [126 kB] Get:66 http://ftpmaster.internal/ubuntu cosmic-proposed/main amd64 libcilkrts5 amd64 7.3.0-19ubuntu2 [42.5 kB] Get:67 http://ftpmaster.internal/ubuntu cosmic-proposed/main amd64 g++-7 amd64 7.3.0-19ubuntu2 [7565 kB] Get:68 http://ftpmaster.internal/ubuntu cosmic-proposed/main amd64 gcc-7 amd64 7.3.0-19ubuntu2 [7445 kB] Get:69 http://ftpmaster.internal/ubuntu cosmic-proposed/main amd64 libstdc++-7-dev amd64 7.3.0-19ubuntu2 [1462 kB] Get:70 http://ftpmaster.internal/ubuntu cosmic-proposed/main amd64 libgcc-7-dev amd64 7.3.0-19ubuntu2 [2378 kB] Get:71 http://ftpmaster.internal/ubuntu cosmic-proposed/main amd64 cpp-7 amd64 7.3.0-19ubuntu2 [6732 kB] Get:72 http://ftpmaster.internal/ubuntu cosmic-proposed/main amd64 gcc-7-base amd64 7.3.0-19ubuntu2 [18.9 kB] Get:73 http://ftpmaster.internal/ubuntu cosmic/main amd64 cpp amd64 4:7.3.0-3ubuntu3 [27.5 kB] Get:74 http://ftpmaster.internal/ubuntu cosmic/main amd64 gcc amd64 4:7.3.0-3ubuntu3 [5216 B] Get:75 http://ftpmaster.internal/ubuntu cosmic/main amd64 g++ amd64 4:7.3.0-3ubuntu3 [1592 B] Get:76 http://ftpmaster.internal/ubuntu cosmic/main amd64 dpkg-dev all 1.19.0.5ubuntu3 [608 kB] Get:77 http://ftpmaster.internal/ubuntu cosmic/main amd64 libdpkg-perl all 1.19.0.5ubuntu3 [211 kB] Get:78 http://ftpmaster.internal/ubuntu cosmic/main amd64 build-essential amd64 12.5ubuntu2 [4732 B] Get:79 http://ftpmaster.internal/ubuntu cosmic/main amd64 e2fslibs amd64 1.44.1-2 [2704 B] Get:80 http://ftpmaster.internal/ubuntu cosmic/main amd64 libcomerr2 amd64 1.44.1-2 [2692 B] Get:81 http://ftpmaster.internal/ubuntu cosmic/main amd64 libusb-0.1-4 amd64 2:0.1.12-32 [17.4 kB] Get:82 http://ftpmaster.internal/ubuntu cosmic-proposed/main amd64 linux-libc-dev amd64 4.15.0-21.22 [1007 kB] Get:83 http://ftpmaster.internal/ubuntu cosmic-proposed/main amd64 pinentry-curses amd64 1.1.0-1build1 [35.8 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 49.2 MB in 2s (26.9 MB/s) (Reading database ... 12637 files and directories currently installed.) Preparing to unpack .../base-files_10.1ubuntu4_amd64.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:amd64. (Reading database ... 12637 files and directories currently installed.) Preparing to unpack .../libtinfo6_6.1+20180210-2ubuntu2_amd64.deb ... Unpacking libtinfo6:amd64 (6.1+20180210-2ubuntu2) ... Setting up libtinfo6:amd64 (6.1+20180210-2ubuntu2) ... (Reading database ... 12646 files and directories currently installed.) Preparing to unpack .../debianutils_4.8.6_amd64.deb ... Unpacking debianutils (4.8.6) over (4.8.4) ... Setting up debianutils (4.8.6) ... (Reading database ... 12646 files and directories currently installed.) Preparing to unpack .../bash_4.4.18-2ubuntu2_amd64.deb ... 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Setting up binutils-x86-64-linux-gnu (2.30-17ubuntu1) ... Setting up cpp (4:7.3.0-3ubuntu3) ... Setting up libdpkg-perl (1.19.0.5ubuntu3) ... Setting up binutils (2.30-17ubuntu1) ... Setting up gcc-7 (7.3.0-19ubuntu2) ... Setting up g++-7 (7.3.0-19ubuntu2) ... 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-14888203 amd64 cosmic-proposed -c chroot:build-PACKAGEBUILD-14888203 --arch=amd64 --dist=cosmic-proposed --nolog -A augustus_3.3.1+dfsg-1.dsc Initiating build PACKAGEBUILD-14888203 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 x86_64 sbuild (Debian sbuild) 0.67.0 (26 Dec 2015) on lcy01-amd64-006.buildd +==============================================================================+ | augustus 3.3.1+dfsg-1 (amd64) 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: amd64 Build Architecture: amd64 I: NOTICE: Log filtering will replace 'build/augustus-ybiSOF/augustus-3.3.1+dfsg' with '<>' I: NOTICE: Log filtering will replace 'build/augustus-ybiSOF' with '<>' I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-14888203/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-BHdnTX/apt_archive/sbuild-build-depends-core-dummy.deb'. Ign:1 copy:/<>/resolver-BHdnTX/apt_archive ./ InRelease Get:2 copy:/<>/resolver-BHdnTX/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-BHdnTX/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-BHdnTX/apt_archive ./ Sources [214 B] Get:5 copy:/<>/resolver-BHdnTX/apt_archive ./ Packages [526 B] Fetched 2859 B in 0s (229 kB/s) Reading package lists... Reading package lists... +------------------------------------------------------------------------------+ | Install core build dependencies (apt-based resolver) | +------------------------------------------------------------------------------+ Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following 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-BHdnTX/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 ... 12661 files and directories currently installed.) Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_amd64.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-SqULdH/apt_archive/sbuild-build-depends-augustus-dummy.deb'. Ign:1 copy:/<>/resolver-SqULdH/apt_archive ./ InRelease Get:2 copy:/<>/resolver-SqULdH/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-SqULdH/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-SqULdH/apt_archive ./ Sources [283 B] Get:5 copy:/<>/resolver-SqULdH/apt_archive ./ Packages [605 B] Fetched 3007 B in 0s (249 kB/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 59.8 MB of archives. After this operation, 358 MB of additional disk space will be used. Get:1 copy:/<>/resolver-SqULdH/apt_archive ./ sbuild-build-depends-augustus-dummy 0.invalid.0 [932 B] Get:2 http://ftpmaster.internal/ubuntu cosmic/main amd64 libpython3.6-minimal amd64 3.6.5-9ubuntu1 [531 kB] Get:3 http://ftpmaster.internal/ubuntu cosmic/main amd64 libexpat1 amd64 2.2.5-3 [80.2 kB] Get:4 http://ftpmaster.internal/ubuntu cosmic/main amd64 python3.6-minimal amd64 3.6.5-9ubuntu1 [1601 kB] Get:5 http://ftpmaster.internal/ubuntu cosmic/main amd64 python3-minimal amd64 3.6.5-3 [23.8 kB] Get:6 http://ftpmaster.internal/ubuntu cosmic/main amd64 mime-support all 3.60ubuntu1 [30.1 kB] Get:7 http://ftpmaster.internal/ubuntu cosmic/main amd64 libmpdec2 amd64 2.4.2-2 [84.1 kB] Get:8 http://ftpmaster.internal/ubuntu cosmic/main amd64 libpython3.6-stdlib amd64 3.6.5-9ubuntu1 [1728 kB] Get:9 http://ftpmaster.internal/ubuntu cosmic/main amd64 python3.6 amd64 3.6.5-9ubuntu1 [186 kB] Get:10 http://ftpmaster.internal/ubuntu cosmic/main amd64 libpython3-stdlib amd64 3.6.5-3 [7276 B] Get:11 http://ftpmaster.internal/ubuntu cosmic/main amd64 python3 amd64 3.6.5-3 [10.2 kB] Get:12 http://ftpmaster.internal/ubuntu cosmic/main amd64 libbsd0 amd64 0.8.7-1 [41.5 kB] Get:13 http://ftpmaster.internal/ubuntu cosmic/main amd64 bsdmainutils amd64 11.1.2ubuntu2 [181 kB] Get:14 http://ftpmaster.internal/ubuntu cosmic/main amd64 groff-base amd64 1.22.3-10 [1153 kB] Get:15 http://ftpmaster.internal/ubuntu cosmic/main amd64 libpipeline1 amd64 1.5.0-1 [25.3 kB] Get:16 http://ftpmaster.internal/ubuntu cosmic/main amd64 man-db amd64 2.8.3-2 [1019 kB] Get:17 http://ftpmaster.internal/ubuntu cosmic/main amd64 libmagic-mgc amd64 1:5.33-2 [193 kB] Get:18 http://ftpmaster.internal/ubuntu cosmic/main amd64 libmagic1 amd64 1:5.33-2 [69.8 kB] Get:19 http://ftpmaster.internal/ubuntu cosmic/main amd64 file amd64 1:5.33-2 [22.9 kB] Get:20 http://ftpmaster.internal/ubuntu cosmic/main amd64 libglib2.0-0 amd64 2.56.1-2ubuntu1 [1167 kB] Get:21 http://ftpmaster.internal/ubuntu cosmic/main amd64 libgirepository-1.0-1 amd64 1.56.1-1 [82.0 kB] Get:22 http://ftpmaster.internal/ubuntu cosmic/main amd64 gir1.2-glib-2.0 amd64 1.56.1-1 [131 kB] Get:23 http://ftpmaster.internal/ubuntu cosmic/main amd64 libelf1 amd64 0.170-0.4 [44.1 kB] Get:24 http://ftpmaster.internal/ubuntu cosmic/main amd64 libglib2.0-data all 2.56.1-2ubuntu1 [4220 B] Get:25 http://ftpmaster.internal/ubuntu cosmic/main amd64 libicu60 amd64 60.2-6ubuntu1 [8055 kB] Get:26 http://ftpmaster.internal/ubuntu cosmic/main amd64 libxml2 amd64 2.9.4+dfsg1-6.1ubuntu1 [662 kB] Get:27 http://ftpmaster.internal/ubuntu cosmic/main amd64 libyaml-0-2 amd64 0.1.7-2ubuntu3 [47.2 kB] Get:28 http://ftpmaster.internal/ubuntu cosmic/main amd64 gettext-base amd64 0.19.8.1-6build1 [50.0 kB] Get:29 http://ftpmaster.internal/ubuntu cosmic/main amd64 libkrb5support0 amd64 1.16-2build1 [31.1 kB] Get:30 http://ftpmaster.internal/ubuntu cosmic/main amd64 libk5crypto3 amd64 1.16-2build1 [85.6 kB] Get:31 http://ftpmaster.internal/ubuntu cosmic/main amd64 libkeyutils1 amd64 1.5.9-9.2ubuntu3 [8704 B] Get:32 http://ftpmaster.internal/ubuntu cosmic/main amd64 libkrb5-3 amd64 1.16-2build1 [279 kB] Get:33 http://ftpmaster.internal/ubuntu cosmic/main amd64 libgssapi-krb5-2 amd64 1.16-2build1 [122 kB] Get:34 http://ftpmaster.internal/ubuntu cosmic/main amd64 libpsl5 amd64 0.20.1-1 [49.2 kB] Get:35 http://ftpmaster.internal/ubuntu cosmic/main amd64 rubygems-integration all 1.11 [4994 B] Get:36 http://ftpmaster.internal/ubuntu cosmic/main amd64 rake all 12.3.1-3 [44.9 kB] Get:37 http://ftpmaster.internal/ubuntu cosmic/main amd64 ruby-did-you-mean all 1.2.1-1 [9828 B] Get:38 http://ftpmaster.internal/ubuntu cosmic/main amd64 ruby-minitest all 5.10.3-1 [38.6 kB] Get:39 http://ftpmaster.internal/ubuntu cosmic/main amd64 ruby-net-telnet all 0.1.1-2 [12.6 kB] Get:40 http://ftpmaster.internal/ubuntu cosmic/main amd64 ruby-power-assert all 0.3.0-1 [7952 B] Get:41 http://ftpmaster.internal/ubuntu cosmic-proposed/main amd64 ruby-test-unit all 3.2.7-1 [61.4 kB] Get:42 http://ftpmaster.internal/ubuntu cosmic/main amd64 libruby2.5 amd64 2.5.1-1ubuntu1 [3066 kB] Get:43 http://ftpmaster.internal/ubuntu cosmic/main amd64 ruby2.5 amd64 2.5.1-1ubuntu1 [48.6 kB] Get:44 http://ftpmaster.internal/ubuntu cosmic/main amd64 ruby amd64 1:2.5.1 [5712 B] Get:45 http://ftpmaster.internal/ubuntu cosmic/universe amd64 ruby-asciidoctor all 1.5.7-1 [157 kB] Get:46 http://ftpmaster.internal/ubuntu cosmic/universe amd64 asciidoctor amd64 1.5.7-1 [36.8 kB] Get:47 http://ftpmaster.internal/ubuntu cosmic/main amd64 libsigsegv2 amd64 2.12-2 [13.9 kB] Get:48 http://ftpmaster.internal/ubuntu cosmic/main amd64 m4 amd64 1.4.18-1 [197 kB] Get:49 http://ftpmaster.internal/ubuntu cosmic/main amd64 autoconf all 2.69-11 [322 kB] Get:50 http://ftpmaster.internal/ubuntu cosmic/main amd64 autotools-dev all 20180224.1 [39.6 kB] Get:51 http://ftpmaster.internal/ubuntu cosmic/main amd64 automake all 1:1.15.1-3ubuntu2 [509 kB] Get:52 http://ftpmaster.internal/ubuntu cosmic/main amd64 autopoint all 0.19.8.1-6build1 [412 kB] Get:53 http://ftpmaster.internal/ubuntu cosmic-proposed/main amd64 libtool all 2.4.6-2.1 [195 kB] Get:54 http://ftpmaster.internal/ubuntu cosmic-proposed/main amd64 dh-autoreconf all 18 [16.1 kB] Get:55 http://ftpmaster.internal/ubuntu cosmic/main amd64 libarchive-zip-perl all 1.60-1 [83.9 kB] Get:56 http://ftpmaster.internal/ubuntu cosmic/main amd64 libfile-stripnondeterminism-perl all 0.041-1 [15.3 kB] Get:57 http://ftpmaster.internal/ubuntu cosmic/main amd64 libtimedate-perl all 2.3000-2 [37.5 kB] Get:58 http://ftpmaster.internal/ubuntu cosmic/main amd64 dh-strip-nondeterminism all 0.041-1 [5188 B] Get:59 http://ftpmaster.internal/ubuntu cosmic/main amd64 libcroco3 amd64 0.6.12-2 [81.3 kB] Get:60 http://ftpmaster.internal/ubuntu cosmic/main amd64 gettext amd64 0.19.8.1-6build1 [895 kB] Get:61 http://ftpmaster.internal/ubuntu cosmic/main amd64 intltool-debian all 0.35.0+20060710.4 [24.9 kB] Get:62 http://ftpmaster.internal/ubuntu cosmic/main amd64 po-debconf all 1.0.20 [232 kB] Get:63 http://ftpmaster.internal/ubuntu cosmic/main amd64 debhelper all 11.2.1ubuntu1 [906 kB] Get:64 http://ftpmaster.internal/ubuntu cosmic/main amd64 libfreetype6 amd64 2.8.1-2ubuntu2 [335 kB] Get:65 http://ftpmaster.internal/ubuntu cosmic/main amd64 libgraphite2-3 amd64 1.3.11-2 [78.7 kB] Get:66 http://ftpmaster.internal/ubuntu cosmic/main amd64 libharfbuzz0b amd64 1.7.6-1ubuntu1 [264 kB] Get:67 http://ftpmaster.internal/ubuntu cosmic/main amd64 gir1.2-harfbuzz-0.0 amd64 1.7.6-1ubuntu1 [18.7 kB] Get:68 http://ftpmaster.internal/ubuntu cosmic/main amd64 icu-devtools amd64 60.2-6ubuntu1 [181 kB] Get:69 http://ftpmaster.internal/ubuntu cosmic/main amd64 libsuitesparseconfig5 amd64 1:5.2.0+dfsg-1 [9256 B] Get:70 http://ftpmaster.internal/ubuntu cosmic/main amd64 libamd2 amd64 1:5.2.0+dfsg-1 [19.6 kB] Get:71 http://ftpmaster.internal/ubuntu cosmic/main amd64 libroken18-heimdal amd64 7.5.0+dfsg-1 [41.3 kB] Get:72 http://ftpmaster.internal/ubuntu cosmic/main amd64 libasn1-8-heimdal amd64 7.5.0+dfsg-1 [175 kB] Get:73 http://ftpmaster.internal/ubuntu cosmic/universe amd64 libbam-dev amd64 0.1.19-2 [124 kB] Get:74 http://ftpmaster.internal/ubuntu cosmic-proposed/universe amd64 libbamtools2.5.1 amd64 2.5.1+dfsg-3 [151 kB] Get:75 http://ftpmaster.internal/ubuntu cosmic-proposed/universe amd64 libbamtools-dev amd64 2.5.1+dfsg-3 [19.8 kB] Get:76 http://ftpmaster.internal/ubuntu cosmic/main amd64 libblas3 amd64 3.8.0-1 [140 kB] Get:77 http://ftpmaster.internal/ubuntu cosmic/main amd64 libblas-dev amd64 3.8.0-1 [143 kB] Get:78 http://ftpmaster.internal/ubuntu cosmic-proposed/main amd64 libboost1.65-dev amd64 1.65.1+dfsg-0ubuntu6 [7217 kB] Get:79 http://ftpmaster.internal/ubuntu cosmic-proposed/universe amd64 libboost-regex1.65.1 amd64 1.65.1+dfsg-0ubuntu6 [259 kB] Get:80 http://ftpmaster.internal/ubuntu cosmic/main amd64 libicu-le-hb0 amd64 1.0.3+git161113-5 [14.4 kB] Get:81 http://ftpmaster.internal/ubuntu cosmic/main amd64 libiculx60 amd64 60.2-6ubuntu1 [19.0 kB] Get:82 http://ftpmaster.internal/ubuntu cosmic/main amd64 libharfbuzz-icu0 amd64 1.7.6-1ubuntu1 [5600 B] Get:83 http://ftpmaster.internal/ubuntu cosmic/main amd64 libharfbuzz-gobject0 amd64 1.7.6-1ubuntu1 [13.4 kB] Get:84 http://ftpmaster.internal/ubuntu cosmic/main amd64 libglib2.0-bin amd64 2.56.1-2ubuntu1 [68.8 kB] Get:85 http://ftpmaster.internal/ubuntu cosmic/main amd64 python3-lib2to3 all 3.6.5-3 [76.6 kB] Get:86 http://ftpmaster.internal/ubuntu cosmic/main amd64 python3-distutils all 3.6.5-3 [141 kB] Get:87 http://ftpmaster.internal/ubuntu cosmic/main amd64 libglib2.0-dev-bin amd64 2.56.1-2ubuntu1 [102 kB] Get:88 http://ftpmaster.internal/ubuntu cosmic/main amd64 libpcre16-3 amd64 2:8.39-9 [147 kB] Get:89 http://ftpmaster.internal/ubuntu cosmic/main amd64 libpcre32-3 amd64 2:8.39-9 [138 kB] Get:90 http://ftpmaster.internal/ubuntu cosmic/main amd64 libpcrecpp0v5 amd64 2:8.39-9 [15.3 kB] Get:91 http://ftpmaster.internal/ubuntu cosmic/main amd64 libpcre3-dev amd64 2:8.39-9 [537 kB] Get:92 http://ftpmaster.internal/ubuntu cosmic/main amd64 pkg-config amd64 0.29.1-0ubuntu2 [45.0 kB] Get:93 http://ftpmaster.internal/ubuntu cosmic/main amd64 zlib1g-dev amd64 1:1.2.11.dfsg-0ubuntu2 [176 kB] Get:94 http://ftpmaster.internal/ubuntu cosmic/main amd64 libglib2.0-dev amd64 2.56.1-2ubuntu1 [1382 kB] Get:95 http://ftpmaster.internal/ubuntu cosmic/main amd64 libgraphite2-dev amd64 1.3.11-2 [14.5 kB] Get:96 http://ftpmaster.internal/ubuntu cosmic/main amd64 libharfbuzz-dev amd64 1.7.6-1ubuntu1 [354 kB] Get:97 http://ftpmaster.internal/ubuntu cosmic/main amd64 libicu-le-hb-dev amd64 1.0.3+git161113-5 [29.6 kB] Get:98 http://ftpmaster.internal/ubuntu cosmic/main amd64 libicu-dev amd64 60.2-6ubuntu1 [8894 kB] Get:99 http://ftpmaster.internal/ubuntu cosmic-proposed/universe amd64 libboost-regex1.65-dev amd64 1.65.1+dfsg-0ubuntu6 [312 kB] Get:100 http://ftpmaster.internal/ubuntu cosmic-proposed/main amd64 libboost-iostreams1.65.1 amd64 1.65.1+dfsg-0ubuntu6 [29.1 kB] Get:101 http://ftpmaster.internal/ubuntu cosmic-proposed/universe amd64 libboost-iostreams1.65-dev amd64 1.65.1+dfsg-0ubuntu6 [37.0 kB] Get:102 http://ftpmaster.internal/ubuntu cosmic/universe amd64 libboost-iostreams-dev amd64 1.65.1.0ubuntu1 [2916 B] Get:103 http://ftpmaster.internal/ubuntu cosmic/main amd64 libbtf1 amd64 1:5.2.0+dfsg-1 [10.7 kB] Get:104 http://ftpmaster.internal/ubuntu cosmic/main amd64 libbz2-dev amd64 1.0.6-8.1 [29.5 kB] Get:105 http://ftpmaster.internal/ubuntu cosmic/main amd64 libcamd2 amd64 1:5.2.0+dfsg-1 [21.0 kB] Get:106 http://ftpmaster.internal/ubuntu cosmic/main amd64 libccolamd2 amd64 1:5.2.0+dfsg-1 [21.8 kB] Get:107 http://ftpmaster.internal/ubuntu cosmic/main amd64 libcolamd2 amd64 1:5.2.0+dfsg-1 [16.4 kB] Get:108 http://ftpmaster.internal/ubuntu cosmic-proposed/main amd64 libgfortran4 amd64 7.3.0-19ubuntu2 [492 kB] Get:109 http://ftpmaster.internal/ubuntu cosmic/main amd64 liblapack3 amd64 3.8.0-1 [2133 kB] Get:110 http://ftpmaster.internal/ubuntu cosmic/main amd64 libmetis5 amd64 5.1.0.dfsg-5 [169 kB] Get:111 http://ftpmaster.internal/ubuntu cosmic/main amd64 libcholmod3 amd64 1:5.2.0+dfsg-1 [300 kB] Get:112 http://ftpmaster.internal/ubuntu cosmic/main amd64 libheimbase1-heimdal amd64 7.5.0+dfsg-1 [29.3 kB] Get:113 http://ftpmaster.internal/ubuntu cosmic/main amd64 libhcrypto4-heimdal amd64 7.5.0+dfsg-1 [85.9 kB] Get:114 http://ftpmaster.internal/ubuntu cosmic/main amd64 libwind0-heimdal amd64 7.5.0+dfsg-1 [47.8 kB] Get:115 http://ftpmaster.internal/ubuntu cosmic/main amd64 libhx509-5-heimdal amd64 7.5.0+dfsg-1 [107 kB] Get:116 http://ftpmaster.internal/ubuntu cosmic/main amd64 libkrb5-26-heimdal amd64 7.5.0+dfsg-1 [206 kB] Get:117 http://ftpmaster.internal/ubuntu cosmic/main amd64 libheimntlm0-heimdal amd64 7.5.0+dfsg-1 [14.8 kB] Get:118 http://ftpmaster.internal/ubuntu cosmic/main amd64 libgssapi3-heimdal amd64 7.5.0+dfsg-1 [96.5 kB] Get:119 http://ftpmaster.internal/ubuntu cosmic/main amd64 libsasl2-modules-db amd64 2.1.27~101-g0780600+dfsg-3ubuntu2 [14.8 kB] Get:120 http://ftpmaster.internal/ubuntu cosmic/main amd64 libsasl2-2 amd64 2.1.27~101-g0780600+dfsg-3ubuntu2 [49.2 kB] Get:121 http://ftpmaster.internal/ubuntu cosmic/main amd64 libldap-common all 2.4.46+dfsg-5ubuntu1 [16.6 kB] Get:122 http://ftpmaster.internal/ubuntu cosmic/main amd64 libldap-2.4-2 amd64 2.4.46+dfsg-5ubuntu1 [155 kB] Get:123 http://ftpmaster.internal/ubuntu cosmic/main amd64 libnghttp2-14 amd64 1.30.0-1ubuntu1 [77.8 kB] Get:124 http://ftpmaster.internal/ubuntu cosmic/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-1 [54.2 kB] Get:125 http://ftpmaster.internal/ubuntu cosmic/main amd64 libcurl3-gnutls amd64 7.58.0-2ubuntu3 [212 kB] Get:126 http://ftpmaster.internal/ubuntu cosmic/main amd64 libcxsparse3 amd64 1:5.2.0+dfsg-1 [64.1 kB] Get:127 http://ftpmaster.internal/ubuntu cosmic/main amd64 libgraphblas2 amd64 1:5.2.0+dfsg-1 [386 kB] Get:128 http://ftpmaster.internal/ubuntu cosmic/universe amd64 libgslcblas0 amd64 2.4+dfsg-6 [79.7 kB] Get:129 http://ftpmaster.internal/ubuntu cosmic/universe amd64 libgsl23 amd64 2.4+dfsg-6 [823 kB] Get:130 http://ftpmaster.internal/ubuntu cosmic/universe amd64 libgsl-dev amd64 2.4+dfsg-6 [1023 kB] Get:131 http://ftpmaster.internal/ubuntu cosmic/universe amd64 libhts2 amd64 1.7-2 [300 kB] Get:132 http://ftpmaster.internal/ubuntu cosmic/main amd64 liblzma-dev amd64 5.2.2-1.3 [145 kB] Get:133 http://ftpmaster.internal/ubuntu cosmic/universe amd64 libhts-dev amd64 1.7-2 [381 kB] Get:134 http://ftpmaster.internal/ubuntu cosmic/main amd64 libklu1 amd64 1:5.2.0+dfsg-1 [69.4 kB] Get:135 http://ftpmaster.internal/ubuntu cosmic/main amd64 liblapack-dev amd64 3.8.0-1 [2161 kB] Get:136 http://ftpmaster.internal/ubuntu cosmic/main amd64 libldl2 amd64 1:5.2.0+dfsg-1 [10.4 kB] Get:137 http://ftpmaster.internal/ubuntu cosmic/main amd64 libumfpack5 amd64 1:5.2.0+dfsg-1 [229 kB] Get:138 http://ftpmaster.internal/ubuntu cosmic/main amd64 librbio2 amd64 1:5.2.0+dfsg-1 [24.1 kB] Get:139 http://ftpmaster.internal/ubuntu cosmic/main amd64 libspqr2 amd64 1:5.2.0+dfsg-1 [64.3 kB] Get:140 http://ftpmaster.internal/ubuntu cosmic/main amd64 libsuitesparse-dev amd64 1:5.2.0+dfsg-1 [1238 kB] Get:141 http://ftpmaster.internal/ubuntu cosmic/main amd64 liblpsolve55-dev amd64 5.5.0.15-4build1 [400 kB] Get:142 http://ftpmaster.internal/ubuntu cosmic/main amd64 libncurses-dev amd64 6.1+20180210-2ubuntu2 [333 kB] Get:143 http://ftpmaster.internal/ubuntu cosmic/main amd64 libncurses5-dev amd64 6.1+20180210-2ubuntu2 [976 B] Get:144 http://ftpmaster.internal/ubuntu cosmic-proposed/main amd64 libsqlite3-dev amd64 3.23.1-1 [639 kB] Get:145 http://ftpmaster.internal/ubuntu cosmic/universe amd64 lzma-dev all 9.22-2ubuntu3 [41.2 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 59.8 MB in 2s (24.9 MB/s) Selecting previously unselected package libpython3.6-minimal:amd64. 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Setting up libsigsegv2:amd64 (2.12-2) ... Setting up libldap-common (2.4.46+dfsg-5ubuntu1) ... Setting up libpsl5:amd64 (0.20.1-1) ... Setting up libelf1:amd64 (0.170-0.4) ... Setting up groff-base (1.22.3-10) ... Setting up libglib2.0-0:amd64 (2.56.1-2ubuntu1) ... No schema files found: doing nothing. Setting up libsasl2-modules-db:amd64 (2.1.27~101-g0780600+dfsg-3ubuntu2) ... Setting up libsasl2-2:amd64 (2.1.27~101-g0780600+dfsg-3ubuntu2) ... Setting up gettext-base (0.19.8.1-6build1) ... Setting up libgraphblas2:amd64 (1:5.2.0+dfsg-1) ... Setting up libpipeline1:amd64 (1.5.0-1) ... Setting up libroken18-heimdal:amd64 (7.5.0+dfsg-1) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-1) ... Setting up m4 (1.4.18-1) ... Setting up libbsd0:amd64 (0.8.7-1) ... Setting up libkrb5support0:amd64 (1.16-2build1) ... Setting up libgirepository-1.0-1:amd64 (1.56.1-1) ... Setting up libxml2:amd64 (2.9.4+dfsg1-6.1ubuntu1) ... Setting up libfreetype6:amd64 (2.8.1-2ubuntu2) ... Setting up libmagic-mgc (1:5.33-2) ... Setting up libmagic1:amd64 (1:5.33-2) ... Setting up libgraphite2-3:amd64 (1.3.11-2) ... Setting up libcroco3:amd64 (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:amd64 (0.1.7-2ubuntu3) ... Setting up libblas3:amd64 (3.8.0-1) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode Setting up gir1.2-glib-2.0:amd64 (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:amd64 (7.5.0+dfsg-1) ... Setting up libsuitesparseconfig5:amd64 (1:5.2.0+dfsg-1) ... Setting up libmetis5:amd64 (5.1.0.dfsg-5) ... Setting up libbamtools2.5.1:amd64 (2.5.1+dfsg-3) ... Setting up ruby-net-telnet (0.1.1-2) ... Setting up libbam-dev (0.1.19-2) ... 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Setting up libmpdec2:amd64 (2.4.2-2) ... Setting up ruby-power-assert (0.3.0-1) ... Setting up libboost-regex1.65.1:amd64 (1.65.1+dfsg-0ubuntu6) ... Setting up zlib1g-dev:amd64 (1:1.2.11.dfsg-0ubuntu2) ... Setting up libfile-stripnondeterminism-perl (0.041-1) ... Setting up libpython3.6-stdlib:amd64 (3.6.5-9ubuntu1) ... Setting up libk5crypto3:amd64 (1.16-2build1) ... Setting up libpcre3-dev:amd64 (2:8.39-9) ... Setting up lzma-dev (9.22-2ubuntu3) ... Setting up python3.6 (3.6.5-9ubuntu1) ... Setting up libwind0-heimdal:amd64 (7.5.0+dfsg-1) ... Setting up ruby-test-unit (3.2.7-1) ... Setting up libgsl23:amd64 (2.4+dfsg-6) ... Setting up gettext (0.19.8.1-6build1) ... Setting up libblas-dev:amd64 (3.8.0-1) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so to provide /usr/lib/x86_64-linux-gnu/libblas.so (libblas.so-x86_64-linux-gnu) in auto mode Setting up libgsl-dev (2.4+dfsg-6) ... Setting up libasn1-8-heimdal:amd64 (7.5.0+dfsg-1) ... Setting up liblapack3:amd64 (3.8.0-1) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode Setting up librbio2:amd64 (1:5.2.0+dfsg-1) ... Setting up libcamd2:amd64 (1:5.2.0+dfsg-1) ... Setting up libbamtools-dev:amd64 (2.5.1+dfsg-3) ... Setting up libhcrypto4-heimdal:amd64 (7.5.0+dfsg-1) ... Setting up libharfbuzz0b:amd64 (1.7.6-1ubuntu1) ... Setting up autoconf (2.69-11) ... Setting up file (1:5.33-2) ... Setting up libhx509-5-heimdal:amd64 (7.5.0+dfsg-1) ... Setting up libncurses5-dev:amd64 (6.1+20180210-2ubuntu2) ... Setting up intltool-debian (0.35.0+20060710.4) ... Setting up libamd2:amd64 (1:5.2.0+dfsg-1) ... Setting up gir1.2-harfbuzz-0.0:amd64 (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:amd64 (1.16-2build1) ... Setting up libkrb5-26-heimdal:amd64 (7.5.0+dfsg-1) ... Setting up libharfbuzz-gobject0:amd64 (1.7.6-1ubuntu1) ... Setting up libheimntlm0-heimdal:amd64 (7.5.0+dfsg-1) ... Setting up liblapack-dev:amd64 (3.8.0-1) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so to provide /usr/lib/x86_64-linux-gnu/liblapack.so (liblapack.so-x86_64-linux-gnu) in auto mode Setting up libtool (2.4.6-2.1) ... Setting up libpython3-stdlib:amd64 (3.6.5-3) ... Setting up libharfbuzz-icu0:amd64 (1.7.6-1ubuntu1) ... Setting up po-debconf (1.0.20) ... Setting up python3 (3.6.5-3) ... Setting up libicu-le-hb0:amd64 (1.0.3+git161113-5) ... Setting up libklu1:amd64 (1:5.2.0+dfsg-1) ... Setting up libcholmod3:amd64 (1:5.2.0+dfsg-1) ... Setting up libgssapi-krb5-2:amd64 (1.16-2build1) ... Setting up libiculx60:amd64 (60.2-6ubuntu1) ... Setting up libgssapi3-heimdal:amd64 (7.5.0+dfsg-1) ... Setting up python3-lib2to3 (3.6.5-3) ... Setting up python3-distutils (3.6.5-3) ... Setting up libspqr2:amd64 (1:5.2.0+dfsg-1) ... Setting up libglib2.0-dev-bin (2.56.1-2ubuntu1) ... Setting up libumfpack5:amd64 (1:5.2.0+dfsg-1) ... Setting up libglib2.0-dev:amd64 (2.56.1-2ubuntu1) ... Setting up libldap-2.4-2:amd64 (2.4.46+dfsg-5ubuntu1) ... Setting up libsuitesparse-dev:amd64 (1:5.2.0+dfsg-1) ... Setting up libcurl3-gnutls:amd64 (7.58.0-2ubuntu3) ... Setting up liblpsolve55-dev (5.5.0.15-4build1) ... Setting up libhts2:amd64 (1.7-2) ... Setting up libhts-dev:amd64 (1.7-2) ... Setting up libharfbuzz-dev:amd64 (1.7.6-1ubuntu1) ... Setting up dh-autoreconf (18) ... Setting up libicu-le-hb-dev:amd64 (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:amd64 (1.65.1+dfsg-0ubuntu6) ... Setting up debhelper (11.2.1ubuntu1) ... Setting up libruby2.5:amd64 (2.5.1-1ubuntu1) ... Setting up libboost-iostreams1.65-dev:amd64 (1.65.1+dfsg-0ubuntu6) ... Setting up libboost-iostreams-dev:amd64 (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 (x86_64) 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-x86-64-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 liblsan0_8.1.0-3ubuntu2 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 libtsan0_8.1.0-3ubuntu2 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_1.30+dfsg-1 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-14888203 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-14888203 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-14888203 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 amd64 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 dh build dh_update_autotools_config dh_autoreconf dh_auto_configure 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 ‘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 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 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 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 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 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 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 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 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 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 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 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 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++ -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' 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++ -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' 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 create-stamp debian/debhelper-build-stamp fakeroot debian/rules binary dh binary dh_testroot dh_prep 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 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 dh_perl dh_link dh_strip_nondeterminism 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 dh_missing dh_strip dh_makeshlibs dh_shlibdeps dh_installdeb dh_gencontrol dpkg-gencontrol: warning: package augustus: unused substitution variable ${perl:Depends} dpkg-gencontrol: warning: package augustus: unused substitution variable ${perl:Depends} dh_md5sums dh_builddeb INFO: pkgstriptranslations version 138 INFO: pkgstriptranslations version 138 INFO: pkgstriptranslations version 138 INFO: pkgstriptranslations version 138 pkgstriptranslations: processing augustus-dbgsym (in debian/.debhelper/augustus/dbgsym-root); do_strip: , oemstrip: pkgstriptranslations: processing augustus-doc (in debian/augustus-doc); do_strip: , oemstrip: pkgstriptranslations: processing augustus (in debian/augustus); do_strip: , oemstrip: pkgstriptranslations: processing augustus-data (in debian/augustus-data); do_strip: , oemstrip: pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/augustus-doc/DEBIAN/control, package augustus-doc, directory debian/augustus-doc .. removing usr/share/doc/augustus-doc/changelog.gz INFO: pkgstripfiles: waiting for lock (augustus-doc) ... pkgstripfiles: processing control file: debian/augustus-data/DEBIAN/control, package augustus-data, directory debian/augustus-data .. removing usr/share/doc/augustus-data/changelog.gz INFO: pkgstripfiles: waiting for lock (augustus-data) ... INFO: pkgstripfiles: waiting for lock (augustus-doc) ... INFO: pkgstripfiles: waiting for lock (augustus-data) ... INFO: pkgstripfiles: waiting for lock (augustus-doc) ... INFO: pkgstripfiles: waiting for lock (augustus-data) ... INFO: pkgstripfiles: waiting for lock (augustus-doc) ... INFO: pkgstripfiles: waiting for lock (augustus-data) ... INFO: pkgstripfiles: waiting for lock (augustus-doc) ... INFO: pkgstripfiles: waiting for lock (augustus-data) ... pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " 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_amd64.deb'. INFO: pkgstripfiles: waiting for lock (augustus-doc) ... pkgstripfiles: processing control file: debian/augustus/DEBIAN/control, package augustus, directory debian/augustus .. removing usr/share/doc/augustus/changelog.gz Skipping arch: any to arch: all dependency to augustus-data 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_amd64.deb'. pkgstripfiles: Running PNG optimization (using 4 cpus) for package augustus-data ... pkgstripfiles: No PNG files. dpkg-deb: building package 'augustus-data' in '../augustus-data_3.3.1+dfsg-1_all.deb'. pkgstripfiles: Disabled PNG optimization for -doc package augustus-doc (to save build time) dpkg-deb: building package 'augustus-doc' in '../augustus-doc_3.3.1+dfsg-1_all.deb'. Renaming augustus-dbgsym_3.3.1+dfsg-1_amd64.deb to augustus-dbgsym_3.3.1+dfsg-1_amd64.ddeb dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary -mLaunchpad Build Daemon >../augustus_3.3.1+dfsg-1_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build augustus-3.3.1+dfsg dpkg-buildpackage: info: binary-only upload (no source included) -------------------------------------------------------------------------------- Build finished at 20180516-0515 Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Post Build Chroot | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ augustus_3.3.1+dfsg-1_amd64.changes: ------------------------------------ Format: 1.8 Date: Sat, 12 May 2018 08:25:35 +0200 Source: augustus Binary: augustus augustus-data augustus-doc Architecture: all amd64 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: 845972e75c16de406afaa48da3692c73e7c3adca 15420984 augustus-data_3.3.1+dfsg-1_all.deb 792b3fc087359d5013b25aa3c6d804a4f4c948b1 16929716 augustus-dbgsym_3.3.1+dfsg-1_amd64.ddeb bc1860540940853665b4156e439200dceece30d9 16914256 augustus-doc_3.3.1+dfsg-1_all.deb af3324dcc009854577e3512a67cd2821de3420e8 10004 augustus_3.3.1+dfsg-1_amd64.buildinfo 339417cd61fb6fcfba4897c2e674ad9aae8e2a9b 1186548 augustus_3.3.1+dfsg-1_amd64.deb Checksums-Sha256: b90a2678a6d27adc86da8dfb143152b673337d2cdfd9b44a90bffe4af38e2628 15420984 augustus-data_3.3.1+dfsg-1_all.deb de3955aface707622612fba0be03ab4c10f821fc5d4e826420b5c236277f1383 16929716 augustus-dbgsym_3.3.1+dfsg-1_amd64.ddeb fc65b5a7d8187984538c82f17939ebcefb27c3565b18bede88317986c4e39b42 16914256 augustus-doc_3.3.1+dfsg-1_all.deb 8cb17339d79cce04a999c685d5ccc7cafccb957749574828a89a62cf9955a4fc 10004 augustus_3.3.1+dfsg-1_amd64.buildinfo 4a486328df9a78a44e8feb8d3bcbf2da46abb7d5473fce727132aa476bc4bc85 1186548 augustus_3.3.1+dfsg-1_amd64.deb Files: 3caaf35810b0ba1586e656f3b113a0a8 15420984 science optional augustus-data_3.3.1+dfsg-1_all.deb 95afeb2c57baf7fa907fc25d4319c96e 16929716 debug optional augustus-dbgsym_3.3.1+dfsg-1_amd64.ddeb a4dac203630fd6361e86f14bcd4ee359 16914256 doc optional augustus-doc_3.3.1+dfsg-1_all.deb 098a9defa3fd28f3bd775eaa33063a21 10004 science optional augustus_3.3.1+dfsg-1_amd64.buildinfo f5e14990d2ce6e28e6c1b228b0185e45 1186548 science optional augustus_3.3.1+dfsg-1_amd64.deb +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ augustus-data_3.3.1+dfsg-1_all.deb ---------------------------------- new debian package, version 2.0. size 15420984 bytes: control archive=16436 bytes. 605 bytes, 14 lines control 97579 bytes, 855 lines md5sums Package: augustus-data Source: augustus Version: 3.3.1+dfsg-1 Architecture: all Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 108600 Section: science Priority: optional Homepage: http://bioinf.uni-greifswald.de/augustus/ Description: data files for AUGUSTUS This package contains pre-trained species models and other required architecture-independent data files for the AUGUSTUS gene finder. These are needed to identify gene structures in these or related organisms. 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/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/config/ drwxr-xr-x root/root 0 2018-05-12 06:25 ./usr/share/augustus/config/cgp/ -rw-r--r-- root/root 1173 2018-05-12 06:25 ./usr/share/augustus/config/cgp/log_reg_parameters_arabidopsis.cfg -rw-r--r-- root/root 1546 2018-05-12 06:25 ./usr/share/augustus/config/cgp/log_reg_parameters_default.cfg -rw-r--r-- root/root 2628 2018-05-12 06:25 ./usr/share/augustus/config/cgp/log_reg_parameters_fly.cfg -rw-r--r-- root/root 1161 2018-05-12 06:25 ./usr/share/augustus/config/cgp/log_reg_parameters_human.cfg -rw-r--r-- root/root 861 2018-05-12 06:25 ./usr/share/augustus/config/cgp/log_reg_parameters_primates.cfg -rw-r--r-- root/root 937 2018-05-12 06:25 ./usr/share/augustus/config/cgp/log_reg_parameters_s_aureus.cfg drwxr-xr-x root/root 0 2018-05-12 06:25 ./usr/share/augustus/config/extrinsic/ -rw-r--r-- root/root 6731 2018-05-12 06:25 ./usr/share/augustus/config/extrinsic/extrinsic-cgp.cfg -rw-r--r-- root/root 2349 2018-05-12 06:25 ./usr/share/augustus/config/extrinsic/extrinsic.E.XNT.cfg -rw-r--r-- root/root 2033 2018-05-12 06:25 ./usr/share/augustus/config/extrinsic/extrinsic.E.cfg -rw-r--r-- root/root 2723 2018-05-12 06:25 ./usr/share/augustus/config/extrinsic/extrinsic.M.RM.E.W.P.cfg -rw-r--r-- root/root 2552 2018-05-12 06:25 ./usr/share/augustus/config/extrinsic/extrinsic.M.RM.E.W.cfg -rw-r--r-- root/root 2441 2018-05-12 06:25 ./usr/share/augustus/config/extrinsic/extrinsic.M.RM.PB.cfg -rw-r--r-- root/root 2003 2018-05-12 06:25 ./usr/share/augustus/config/extrinsic/extrinsic.ME.cfg -rw-r--r-- root/root 2574 2018-05-12 06:25 ./usr/share/augustus/config/extrinsic/extrinsic.MEMS.cfg -rw-r--r-- root/root 2057 2018-05-12 06:25 ./usr/share/augustus/config/extrinsic/extrinsic.MP.cfg -rw-r--r-- root/root 2608 2018-05-12 06:25 ./usr/share/augustus/config/extrinsic/extrinsic.MPE.cfg -rw-r--r-- root/root 2350 2018-05-12 06:25 ./usr/share/augustus/config/extrinsic/extrinsic.MT.cfg -rw-r--r-- root/root 9979 2018-05-12 06:25 ./usr/share/augustus/config/extrinsic/extrinsic.cfg drwxr-xr-x root/root 0 2018-05-12 06:25 ./usr/share/augustus/config/model/ -rw-r--r-- root/root 3385 2018-05-12 06:25 ./usr/share/augustus/config/model/constraints_shadow_partial.txt -rw-r--r-- root/root 4114 2018-05-12 06:25 ./usr/share/augustus/config/model/constraints_shadow_partial_utr.txt -rw-r--r-- root/root 2400 2018-05-12 06:25 ./usr/share/augustus/config/model/ovlp_len.pbl -rw-r--r-- root/root 2374 2018-05-12 06:25 ./usr/share/augustus/config/model/ovlp_len_archaea.pbl -rw-r--r-- root/root 5594 2018-05-12 06:25 ./usr/share/augustus/config/model/states_shadow.cfg -rw-r--r-- root/root 5672 2018-05-12 06:25 ./usr/share/augustus/config/model/states_shadow_2igenic.cfg -rw-r--r-- root/root 866 2018-05-12 06:25 ./usr/share/augustus/config/model/states_shadow_bacterium.cfg -rw-r--r-- root/root 856 2018-05-12 06:25 ./usr/share/augustus/config/model/states_shadow_intronless.cfg -rw-r--r-- root/root 8509 2018-05-12 06:25 ./usr/share/augustus/config/model/states_shadow_utr.cfg -rw-r--r-- root/root 10075 2018-05-12 06:25 ./usr/share/augustus/config/model/states_shadow_utr_nc.cfg -rw-r--r-- root/root 3019 2018-05-12 06:25 ./usr/share/augustus/config/model/states_singlestrand.cfg -rw-r--r-- root/root 3086 2018-05-12 06:25 ./usr/share/augustus/config/model/states_singlestrand_2igenic.cfg -rw-r--r-- root/root 6885 2018-05-12 06:25 ./usr/share/augustus/config/model/trans_shadow_atleastone.pbl -rw-r--r-- root/root 1354 2018-05-12 06:25 ./usr/share/augustus/config/model/trans_shadow_bacterium.pbl -rw-r--r-- root/root 6436 2018-05-12 06:25 ./usr/share/augustus/config/model/trans_shadow_complete.pbl 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./usr/share/doc/augustus-data/ lrwxrwxrwx root/root 0 2018-05-12 06:25 ./usr/share/doc/augustus-data/HISTORY.TXT.gz -> changelog.gz -rw-r--r-- root/root 944 2018-05-12 06:25 ./usr/share/doc/augustus-data/changelog.Debian.gz -rw-r--r-- root/root 3495 2018-05-11 10:24 ./usr/share/doc/augustus-data/copyright augustus-doc_3.3.1+dfsg-1_all.deb --------------------------------- new debian package, version 2.0. size 16914256 bytes: control archive=2472 bytes. 601 bytes, 14 lines control 5871 bytes, 68 lines md5sums Package: augustus-doc Source: augustus Version: 3.3.1+dfsg-1 Architecture: all Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 125011 Section: doc Priority: optional Homepage: http://bioinf.uni-greifswald.de/augustus/ Description: documentation files for AUGUSTUS This package contains documentation for AUGUSTUS: a comprehensive manual-style README both for AUGUSTUS in general as well as for its comparative gene prediction (cgp) mode, as 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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. 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+------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not removing build depends: as requested +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: amd64 Build-Space: 945404 Build-Time: 224 Distribution: cosmic-proposed Host Architecture: amd64 Install-Time: 27 Job: augustus_3.3.1+dfsg-1.dsc Machine Architecture: amd64 Package: augustus Package-Time: 262 Source-Version: 3.3.1+dfsg-1 Space: 945404 Status: successful Version: 3.3.1+dfsg-1 -------------------------------------------------------------------------------- Finished at 20180516-0515 Build needed 00:04:22, 945404k disc space RUN: /usr/share/launchpad-buildd/slavebin/in-target scan-for-processes --backend=chroot --series=cosmic --arch=amd64 PACKAGEBUILD-14888203 Scanning for processes to kill in build PACKAGEBUILD-14888203 RUN: /usr/share/launchpad-buildd/slavebin/in-target umount-chroot --backend=chroot --series=cosmic --arch=amd64 PACKAGEBUILD-14888203 Stopping target for build PACKAGEBUILD-14888203 RUN: /usr/share/launchpad-buildd/slavebin/in-target remove-build --backend=chroot --series=cosmic --arch=amd64 PACKAGEBUILD-14888203 Removing build PACKAGEBUILD-14888203