https://launchpad.net/ubuntu/+archive/test-rebuild-20181220-gcc9/+build/15930158 RUN: /usr/share/launchpad-buildd/slavebin/slave-prep Forking launchpad-buildd slave process... Kernel version: Linux lcy01-amd64-017 4.4.0-141-generic #167-Ubuntu SMP Wed Dec 5 10:40:15 UTC 2018 x86_64 Buildd toolchain package versions: launchpad-buildd_165 python-lpbuildd_165 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_1:2.7.4-0ubuntu1.6 dpkg-dev_1.18.4ubuntu1.5 python-debian_0.1.27ubuntu2. Syncing the system clock with the buildd NTP service... 9 Jan 03:14:23 ntpdate[1822]: adjust time server 10.211.37.1 offset 0.001255 sec RUN: /usr/share/launchpad-buildd/slavebin/in-target unpack-chroot --backend=chroot --series=disco --arch=amd64 PACKAGEBUILD-15930158 /home/buildd/filecache-default/020b0022f770b890c357907d03d82568c584d50e Creating target for build PACKAGEBUILD-15930158 RUN: /usr/share/launchpad-buildd/slavebin/in-target mount-chroot --backend=chroot --series=disco --arch=amd64 PACKAGEBUILD-15930158 Starting target for build PACKAGEBUILD-15930158 RUN: /usr/share/launchpad-buildd/slavebin/in-target override-sources-list --backend=chroot --series=disco --arch=amd64 PACKAGEBUILD-15930158 'deb http://ppa.launchpad.net/ubuntu-toolchain-r/ppa/ubuntu disco main' 'deb http://ppa.launchpad.net/ubuntu-toolchain-r/volatile/ubuntu disco main' 'deb http://ftpmaster.internal/ubuntu disco main restricted universe multiverse' 'deb http://ftpmaster.internal/ubuntu disco-security main restricted universe multiverse' 'deb http://ftpmaster.internal/ubuntu disco-updates main restricted universe multiverse' Overriding sources.list in build-PACKAGEBUILD-15930158 RUN: /usr/share/launchpad-buildd/slavebin/in-target add-trusted-keys --backend=chroot --series=disco --arch=amd64 PACKAGEBUILD-15930158 Adding trusted keys to build-PACKAGEBUILD-15930158 Warning: apt-key output should not be parsed (stdout is not a terminal) OK Warning: apt-key output should not be parsed (stdout is not a terminal) /etc/apt/trusted.gpg -------------------- pub rsa1024 2009-10-22 [SC] 60C3 1780 3A41 BA51 845E 371A 1E93 77A2 BA9E F27F uid [ unknown] Launchpad Toolchain builds /etc/apt/trusted.gpg.d/ubuntu-keyring-2012-archive.gpg ------------------------------------------------------ pub rsa4096 2012-05-11 [SC] 790B C727 7767 219C 42C8 6F93 3B4F E6AC C0B2 1F32 uid [ unknown] Ubuntu Archive Automatic Signing Key (2012) /etc/apt/trusted.gpg.d/ubuntu-keyring-2012-cdimage.gpg ------------------------------------------------------ pub rsa4096 2012-05-11 [SC] 8439 38DF 228D 22F7 B374 2BC0 D94A A3F0 EFE2 1092 uid [ unknown] Ubuntu CD Image Automatic Signing Key (2012) /etc/apt/trusted.gpg.d/ubuntu-keyring-2018-archive.gpg ------------------------------------------------------ pub rsa4096 2018-09-17 [SC] F6EC B376 2474 EDA9 D21B 7022 8719 20D1 991B C93C uid [ unknown] Ubuntu Archive Automatic Signing Key (2018) RUN: /usr/share/launchpad-buildd/slavebin/in-target update-debian-chroot --backend=chroot --series=disco --arch=amd64 PACKAGEBUILD-15930158 Updating target for build PACKAGEBUILD-15930158 Get:1 http://ftpmaster.internal/ubuntu disco InRelease [243 kB] Get:2 http://ppa.launchpad.net/ubuntu-toolchain-r/ppa/ubuntu disco InRelease [15.4 kB] Get:3 http://ppa.launchpad.net/ubuntu-toolchain-r/volatile/ubuntu disco InRelease [15.4 kB] Get:4 http://ftpmaster.internal/ubuntu disco-security InRelease [65.4 kB] Get:5 http://ftpmaster.internal/ubuntu disco-updates InRelease [65.4 kB] Get:6 http://ppa.launchpad.net/ubuntu-toolchain-r/ppa/ubuntu disco/main amd64 Packages [43.1 kB] Get:7 http://ppa.launchpad.net/ubuntu-toolchain-r/ppa/ubuntu disco/main Translation-en [13.3 kB] Get:8 http://ppa.launchpad.net/ubuntu-toolchain-r/volatile/ubuntu disco/main amd64 Packages [198 kB] Get:9 http://ppa.launchpad.net/ubuntu-toolchain-r/volatile/ubuntu disco/main Translation-en [26.9 kB] Get:10 http://ftpmaster.internal/ubuntu disco/main amd64 Packages [1007 kB] Get:11 http://ftpmaster.internal/ubuntu disco/main Translation-en [514 kB] Get:12 http://ftpmaster.internal/ubuntu disco/restricted amd64 Packages [9964 B] Get:13 http://ftpmaster.internal/ubuntu disco/universe amd64 Packages [8944 kB] Get:14 http://ftpmaster.internal/ubuntu disco/universe Translation-en [5170 kB] Get:15 http://ftpmaster.internal/ubuntu disco/multiverse amd64 Packages [159 kB] Get:16 http://ftpmaster.internal/ubuntu disco/multiverse Translation-en [113 kB] Fetched 16.6 MB in 4s (3846 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages were automatically installed and are no longer required: g++-8 libstdc++-8-dev Use 'sudo apt autoremove' to remove them. The following NEW packages will be installed: cpp-9 g++-9 gcc-9 gcc-9-base libgcc-9-dev libstdc++-9-dev The following packages will be upgraded: binutils binutils-common binutils-x86-64-linux-gnu cpp cpp-8 dash dpkg dpkg-dev e2fslibs e2fsprogs g++ g++-8 gcc gcc-8 gcc-8-base grep init init-system-helpers libasan5 libassuan0 libatomic1 libbinutils libcc1-0 libcom-err2 libcomerr2 libdpkg-perl libext2fs2 libgcc-8-dev libgcc1 libgnutls30 libgomp1 libitm1 liblsan0 libmpx2 libquadmath0 libsemanage-common libsemanage1 libsqlite3-0 libss2 libstdc++-8-dev libstdc++6 libtsan0 libubsan1 libzstd1 sed tar tzdata 47 upgraded, 6 newly installed, 0 to remove and 0 not upgraded. Need to get 64.4 MB of archives. After this operation, 116 MB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu disco/main amd64 tar amd64 1.30+dfsg-4 [242 kB] Get:2 http://ppa.launchpad.net/ubuntu-toolchain-r/volatile/ubuntu disco/main amd64 gcc-9-base amd64 9-20190102-0ubuntu2 [187 kB] Get:3 http://ftpmaster.internal/ubuntu disco/main amd64 dpkg amd64 1.19.2ubuntu2 [1101 kB] Get:4 http://ppa.launchpad.net/ubuntu-toolchain-r/volatile/ubuntu disco/main amd64 libgcc1 amd64 1:9-20190102-0ubuntu2 [40.1 kB] Get:5 http://ppa.launchpad.net/ubuntu-toolchain-r/volatile/ubuntu disco/main amd64 libstdc++6 amd64 9-20190102-0ubuntu2 [413 kB] Get:6 http://ftpmaster.internal/ubuntu disco/main amd64 dash amd64 0.5.10.2-3ubuntu1 [86.0 kB] Get:7 http://ftpmaster.internal/ubuntu disco/main amd64 grep amd64 3.3-1 [149 kB] Get:8 http://ftpmaster.internal/ubuntu disco/main amd64 sed amd64 4.7-1 [190 kB] Get:9 http://ftpmaster.internal/ubuntu disco/main amd64 init-system-helpers all 1.56+nmu1 [38.2 kB] Get:10 http://ftpmaster.internal/ubuntu disco/main amd64 libext2fs2 amd64 1.44.5-1 [159 kB] Get:11 http://ftpmaster.internal/ubuntu disco/main amd64 e2fsprogs amd64 1.44.5-1 [514 kB] Get:12 http://ftpmaster.internal/ubuntu disco/main amd64 init amd64 1.56+nmu1 [6080 B] Get:13 http://ftpmaster.internal/ubuntu disco/main amd64 libsemanage-common all 2.8-2 [7016 B] Get:14 http://ftpmaster.internal/ubuntu disco/main amd64 libsemanage1 amd64 2.8-2 [85.2 kB] Get:15 http://ftpmaster.internal/ubuntu disco/main amd64 libzstd1 amd64 1.3.8+dfsg-3 [226 kB] Get:16 http://ppa.launchpad.net/ubuntu-toolchain-r/volatile/ubuntu disco/main amd64 libgomp1 amd64 9-20190102-0ubuntu2 [90.0 kB] Get:17 http://ftpmaster.internal/ubuntu disco/main amd64 libgnutls30 amd64 3.6.5-2ubuntu1 [759 kB] Get:18 http://ppa.launchpad.net/ubuntu-toolchain-r/volatile/ubuntu disco/main amd64 libitm1 amd64 9-20190102-0ubuntu2 [27.9 kB] Get:19 http://ftpmaster.internal/ubuntu disco/main amd64 libcom-err2 amd64 1.44.5-1 [9372 B] Get:20 http://ftpmaster.internal/ubuntu disco/main amd64 libss2 amd64 1.44.5-1 [11.1 kB] Get:21 http://ftpmaster.internal/ubuntu disco/main amd64 libsqlite3-0 amd64 3.26.0-3 [530 kB] Get:22 http://ftpmaster.internal/ubuntu disco/main amd64 tzdata all 2018i-1 [189 kB] Get:23 http://ftpmaster.internal/ubuntu disco/main amd64 dpkg-dev all 1.19.2ubuntu2 [549 kB] Get:24 http://ftpmaster.internal/ubuntu disco/main amd64 libdpkg-perl all 1.19.2ubuntu2 [227 kB] Get:25 http://ftpmaster.internal/ubuntu disco/main amd64 e2fslibs amd64 1.44.5-1 [2704 B] Get:26 http://ftpmaster.internal/ubuntu disco/main amd64 libassuan0 amd64 2.5.2-1 [35.1 kB] Get:27 http://ftpmaster.internal/ubuntu disco/main amd64 libcomerr2 amd64 1.44.5-1 [2700 B] Get:28 http://ppa.launchpad.net/ubuntu-toolchain-r/volatile/ubuntu disco/main amd64 libatomic1 amd64 9-20190102-0ubuntu2 [9244 B] Get:29 http://ppa.launchpad.net/ubuntu-toolchain-r/volatile/ubuntu disco/main amd64 libasan5 amd64 9-20190102-0ubuntu2 [394 kB] Get:30 http://ppa.launchpad.net/ubuntu-toolchain-r/volatile/ubuntu disco/main amd64 liblsan0 amd64 9-20190102-0ubuntu2 [140 kB] Get:31 http://ppa.launchpad.net/ubuntu-toolchain-r/volatile/ubuntu disco/main amd64 libtsan0 amd64 9-20190102-0ubuntu2 [300 kB] Get:32 http://ppa.launchpad.net/ubuntu-toolchain-r/volatile/ubuntu disco/main amd64 libubsan1 amd64 9-20190102-0ubuntu2 [129 kB] Get:33 http://ppa.launchpad.net/ubuntu-toolchain-r/ppa/ubuntu disco/main amd64 libmpx2 amd64 8.2.0-13ubuntu1 [11.7 kB] Get:34 http://ppa.launchpad.net/ubuntu-toolchain-r/volatile/ubuntu disco/main amd64 libquadmath0 amd64 9-20190102-0ubuntu2 [145 kB] Get:35 http://ppa.launchpad.net/ubuntu-toolchain-r/ppa/ubuntu disco/main amd64 g++-8 amd64 8.2.0-13ubuntu1 [8113 kB] Get:36 http://ppa.launchpad.net/ubuntu-toolchain-r/ppa/ubuntu disco/main amd64 gcc-8 amd64 8.2.0-13ubuntu1 [8004 kB] Get:37 http://ppa.launchpad.net/ubuntu-toolchain-r/ppa/ubuntu disco/main amd64 libstdc++-8-dev amd64 8.2.0-13ubuntu1 [1538 kB] Get:38 http://ppa.launchpad.net/ubuntu-toolchain-r/ppa/ubuntu disco/main amd64 libgcc-8-dev amd64 8.2.0-13ubuntu1 [2304 kB] Get:39 http://ppa.launchpad.net/ubuntu-toolchain-r/volatile/ubuntu disco/main amd64 libcc1-0 amd64 9-20190102-0ubuntu2 [40.3 kB] Get:40 http://ppa.launchpad.net/ubuntu-toolchain-r/ppa/ubuntu disco/main amd64 binutils-x86-64-linux-gnu amd64 2.31.1-11ubuntu1 [1829 kB] Get:41 http://ppa.launchpad.net/ubuntu-toolchain-r/ppa/ubuntu disco/main amd64 libbinutils amd64 2.31.1-11ubuntu1 [484 kB] Get:42 http://ppa.launchpad.net/ubuntu-toolchain-r/ppa/ubuntu disco/main amd64 binutils amd64 2.31.1-11ubuntu1 [3396 B] Get:43 http://ppa.launchpad.net/ubuntu-toolchain-r/ppa/ubuntu disco/main amd64 binutils-common amd64 2.31.1-11ubuntu1 [194 kB] Get:44 http://ppa.launchpad.net/ubuntu-toolchain-r/ppa/ubuntu disco/main amd64 cpp-8 amd64 8.2.0-13ubuntu1 [7221 kB] Get:45 http://ppa.launchpad.net/ubuntu-toolchain-r/ppa/ubuntu disco/main amd64 gcc-8-base amd64 8.2.0-13ubuntu1 [18.6 kB] Get:46 http://ppa.launchpad.net/ubuntu-toolchain-r/volatile/ubuntu disco/main amd64 cpp-9 amd64 9-20190102-0ubuntu2 [7372 kB] Get:47 http://ppa.launchpad.net/ubuntu-toolchain-r/volatile/ubuntu disco/main amd64 libgcc-9-dev amd64 9-20190102-0ubuntu2 [2362 kB] Get:48 http://ppa.launchpad.net/ubuntu-toolchain-r/volatile/ubuntu disco/main amd64 gcc-9 amd64 9-20190102-0ubuntu2 [8002 kB] Get:49 http://ppa.launchpad.net/ubuntu-toolchain-r/volatile/ubuntu disco/main amd64 libstdc++-9-dev amd64 9-20190102-0ubuntu2 [1603 kB] Get:50 http://ppa.launchpad.net/ubuntu-toolchain-r/volatile/ubuntu disco/main amd64 g++-9 amd64 9-20190102-0ubuntu2 [8244 kB] Get:51 http://ppa.launchpad.net/ubuntu-toolchain-r/volatile/ubuntu disco/main amd64 g++ amd64 4:9-20181126-1ubuntu3 [1576 B] Get:52 http://ppa.launchpad.net/ubuntu-toolchain-r/volatile/ubuntu disco/main amd64 gcc amd64 4:9-20181126-1ubuntu3 [5188 B] Get:53 http://ppa.launchpad.net/ubuntu-toolchain-r/volatile/ubuntu disco/main amd64 cpp amd64 4:9-20181126-1ubuntu3 [42.4 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 64.4 MB in 5s (13.8 MB/s) (Reading database ... 12665 files and directories currently installed.) Preparing to unpack .../tar_1.30+dfsg-4_amd64.deb ... Unpacking tar (1.30+dfsg-4) over (1.30+dfsg-3) ... Setting up tar (1.30+dfsg-4) ... (Reading database ... 12665 files and directories currently installed.) Preparing to unpack .../dpkg_1.19.2ubuntu2_amd64.deb ... Unpacking dpkg (1.19.2ubuntu2) over (1.19.2ubuntu1) ... Setting up dpkg (1.19.2ubuntu2) ... (Reading database ... 12665 files and directories currently installed.) Preparing to unpack .../dash_0.5.10.2-3ubuntu1_amd64.deb ... Unpacking dash (0.5.10.2-3ubuntu1) over (0.5.10.2-2) ... Setting up dash (0.5.10.2-3ubuntu1) ... (Reading database ... 12665 files and directories currently installed.) Preparing to unpack .../archives/grep_3.3-1_amd64.deb ... Unpacking grep (3.3-1) over (3.1-3) ... Setting up grep (3.3-1) ... (Reading database ... 12665 files and directories currently installed.) Preparing to unpack .../archives/sed_4.7-1_amd64.deb ... Unpacking sed (4.7-1) over (4.5-2) ... Setting up sed (4.7-1) ... 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Setting up libquadmath0:amd64 (9-20190102-0ubuntu2) ... Setting up libcom-err2:amd64 (1.44.5-1) ... Setting up libgomp1:amd64 (9-20190102-0ubuntu2) ... Setting up libatomic1:amd64 (9-20190102-0ubuntu2) ... Setting up libss2:amd64 (1.44.5-1) ... Setting up libcc1-0:amd64 (9-20190102-0ubuntu2) ... Setting up e2fslibs:amd64 (1.44.5-1) ... Setting up tzdata (2018i-1) ... Current default time zone: 'Etc/UTC' Local time is now: Wed Jan 9 03:14:52 UTC 2019. Universal Time is now: Wed Jan 9 03:14:52 UTC 2019. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up init (1.56+nmu1) ... Setting up libtsan0:amd64 (9-20190102-0ubuntu2) ... Setting up libdpkg-perl (1.19.2ubuntu2) ... Setting up e2fsprogs (1.44.5-1) ... Setting up liblsan0:amd64 (9-20190102-0ubuntu2) ... Setting up binutils-common:amd64 (2.31.1-11ubuntu1) ... Processing triggers for libc-bin (2.28-0ubuntu1) ... Setting up cpp-9 (9-20190102-0ubuntu2) ... Setting up gcc-8-base:amd64 (8.2.0-13ubuntu1) ... Setting up libsqlite3-0:amd64 (3.26.0-3) ... Setting up libcomerr2:amd64 (1.44.5-1) ... Setting up libasan5:amd64 (9-20190102-0ubuntu2) ... Setting up libassuan0:amd64 (2.5.2-1) ... Setting up libitm1:amd64 (9-20190102-0ubuntu2) ... Setting up libubsan1:amd64 (9-20190102-0ubuntu2) ... Setting up cpp-8 (8.2.0-13ubuntu1) ... Setting up cpp (4:9-20181126-1ubuntu3) ... Setting up libgcc-9-dev:amd64 (9-20190102-0ubuntu2) ... Setting up libbinutils:amd64 (2.31.1-11ubuntu1) ... Setting up libstdc++-9-dev:amd64 (9-20190102-0ubuntu2) ... Setting up libmpx2:amd64 (8.2.0-13ubuntu1) ... Setting up libgcc-8-dev:amd64 (8.2.0-13ubuntu1) ... Setting up binutils-x86-64-linux-gnu (2.31.1-11ubuntu1) ... Setting up libstdc++-8-dev:amd64 (8.2.0-13ubuntu1) ... Setting up binutils (2.31.1-11ubuntu1) ... Setting up gcc-9 (9-20190102-0ubuntu2) ... Setting up g++-9 (9-20190102-0ubuntu2) ... Setting up gcc (4:9-20181126-1ubuntu3) ... Setting up gcc-8 (8.2.0-13ubuntu1) ... Setting up g++-8 (8.2.0-13ubuntu1) ... Setting up dpkg-dev (1.19.2ubuntu2) ... Setting up g++ (4:9-20181126-1ubuntu3) ... Processing triggers for libc-bin (2.28-0ubuntu1) ... RUN: /usr/share/launchpad-buildd/slavebin/sbuild-package PACKAGEBUILD-15930158 amd64 disco -c chroot:build-PACKAGEBUILD-15930158 --arch=amd64 --dist=disco --nolog -A 'hhsuite_3.0~beta3+dfsg-1.dsc' Initiating build PACKAGEBUILD-15930158 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 4.4.0-141-generic #167-Ubuntu SMP Wed Dec 5 10:40:15 UTC 2018 x86_64 sbuild (Debian sbuild) 0.67.0 (26 Dec 2015) on lcy01-amd64-017.buildd +==============================================================================+ | hhsuite 3.0~beta3+dfsg-1 (amd64) 09 Jan 2019 03:14 | +==============================================================================+ Package: hhsuite Version: 3.0~beta3+dfsg-1 Source Version: 3.0~beta3+dfsg-1 Distribution: disco Machine Architecture: amd64 Host Architecture: amd64 Build Architecture: amd64 I: NOTICE: Log filtering will replace 'build/hhsuite-YIJq2H/hhsuite-3.0~beta3+dfsg' with '<>' I: NOTICE: Log filtering will replace 'build/hhsuite-YIJq2H' with '<>' I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-15930158/chroot-autobuild' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- hhsuite_3.0~beta3+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-nRJbOi/apt_archive/sbuild-build-depends-core-dummy.deb'. Ign:1 copy:/<>/resolver-nRJbOi/apt_archive ./ InRelease Get:2 copy:/<>/resolver-nRJbOi/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-nRJbOi/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-nRJbOi/apt_archive ./ Sources [214 B] Get:5 copy:/<>/resolver-nRJbOi/apt_archive ./ Packages [527 B] Fetched 2860 B in 0s (206 kB/s) Reading package lists... Reading package lists... +------------------------------------------------------------------------------+ | Install core build dependencies (apt-based resolver) | +------------------------------------------------------------------------------+ Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following packages were automatically installed and are no longer required: g++-8 libstdc++-8-dev Use 'apt autoremove' to remove them. The following NEW packages will be installed: sbuild-build-depends-core-dummy 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 856 B of archives. After this operation, 0 B of additional disk space will be used. Get:1 copy:/<>/resolver-nRJbOi/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [856 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 856 B in 0s (0 B/s) Selecting previously unselected package sbuild-build-depends-core-dummy. (Reading database ... 13710 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 (>= 10), libffindex0-dev (>= 0.9.9.7+soedinglab), cmake, texlive-latex-base, texlive-latex-recommended, imagemagick, help2man Filtered Build-Depends: debhelper (>= 10), libffindex0-dev (>= 0.9.9.7+soedinglab), cmake, texlive-latex-base, texlive-latex-recommended, imagemagick, help2man dpkg-deb: building package 'sbuild-build-depends-hhsuite-dummy' in '/<>/resolver-NSIbxp/apt_archive/sbuild-build-depends-hhsuite-dummy.deb'. Ign:1 copy:/<>/resolver-NSIbxp/apt_archive ./ InRelease Get:2 copy:/<>/resolver-NSIbxp/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-NSIbxp/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-NSIbxp/apt_archive ./ Sources [277 B] Get:5 copy:/<>/resolver-NSIbxp/apt_archive ./ Packages [596 B] Fetched 2992 B in 0s (250 kB/s) Reading package lists... Reading package lists... +------------------------------------------------------------------------------+ | Install hhsuite build dependencies (apt-based resolver) | +------------------------------------------------------------------------------+ Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following packages were automatically installed and are no longer required: g++-8 libstdc++-8-dev Use 'apt autoremove' to remove them. The following additional packages will be installed: autoconf automake autopoint autotools-dev bsdmainutils cmake cmake-data debhelper dh-autoreconf dh-strip-nondeterminism dwz file fontconfig-config fonts-dejavu-core fonts-lmodern gettext gettext-base groff-base help2man hicolor-icon-theme imagemagick imagemagick-6-common imagemagick-6.q16 intltool-debian libarchive-zip-perl libarchive13 libasn1-8-heimdal libavahi-client3 libavahi-common-data libavahi-common3 libbrotli1 libbsd0 libcairo2 libcroco3 libcups2 libcupsimage2 libcurl4 libdbus-1-3 libelf1 libexpat1 libffindex0 libffindex0-dev libfftw3-double3 libfile-stripnondeterminism-perl libfontconfig1 libfreetype6 libglib2.0-0 libgraphite2-3 libgs9 libgs9-common libgssapi-krb5-2 libgssapi3-heimdal libharfbuzz-icu0 libharfbuzz0b libhcrypto4-heimdal libheimbase1-heimdal libheimntlm0-heimdal libhx509-5-heimdal libice6 libicu63 libijs-0.35 libjbig0 libjbig2dec0 libjpeg-turbo8 libjpeg8 libjsoncpp1 libk5crypto3 libkeyutils1 libkpathsea6 libkrb5-26-heimdal libkrb5-3 libkrb5support0 liblcms2-2 libldap-2.4-2 libldap-common liblocale-gettext-perl liblqr-1-0 libltdl7 libmagic-mgc libmagic1 libmagickcore-6.q16-6 libmagickwand-6.q16-6 libnghttp2-14 libpaper-utils libpaper1 libpipeline1 libpixman-1-0 libpotrace0 libpsl5 libptexenc1 librhash0 libroken18-heimdal librtmp1 libsasl2-2 libsasl2-modules-db libsigsegv2 libsm6 libsynctex2 libteckit0 libtexlua52 libtexlua53 libtexluajit2 libtiff5 libtool libuv1 libwebp6 libwind0-heimdal libwoff1 libx11-6 libx11-data libxau6 libxaw7 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxi6 libxml2 libxmu6 libxpm4 libxrender1 libxt6 libxxhash0 libzzip-0-13 m4 man-db po-debconf poppler-data t1utils tex-common texlive-base texlive-binaries texlive-latex-base texlive-latex-recommended ucf x11-common xdg-utils Suggested packages: autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois vacation cmake-doc ninja-build dh-make gettext-doc libasprintf-dev libgettextpo-dev groff imagemagick-doc autotrace cups-bsd | lpr | lprng curl enscript ffmpeg gimp gnuplot grads graphviz hp2xx html2ps libwmf-bin mplayer povray radiance sane-utils transfig ufraw-batch lrzip cups-common libfftw3-bin libfftw3-dev krb5-doc krb5-user liblcms2-utils libmagickcore-6.q16-6-extra libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc apparmor less www-browser libmail-box-perl poppler-utils ghostscript fonts-japanese-mincho | fonts-ipafont-mincho fonts-japanese-gothic | fonts-ipafont-gothic fonts-arphic-ukai fonts-arphic-uming fonts-nanum gv | postscript-viewer perl-tk xpdf-reader | pdf-viewer texlive-latex-base-doc texlive-latex-recommended-doc texlive-pstricks Recommended packages: curl | wget | lynx libmagickcore-6.q16-6-extra ghostscript netpbm libcupsfilters1 dbus libarchive-cpio-perl libglib2.0-data shared-mime-info xdg-user-dirs fonts-droid-fallback krb5-locales gsfonts publicsuffix libsasl2-modules libltdl-dev libmail-sendmail-perl lmodern libfile-mimeinfo-perl libnet-dbus-perl libx11-protocol-perl x11-utils x11-xserver-utils The following NEW packages will be installed: autoconf automake autopoint autotools-dev bsdmainutils cmake cmake-data debhelper dh-autoreconf dh-strip-nondeterminism dwz file fontconfig-config fonts-dejavu-core fonts-lmodern gettext gettext-base groff-base help2man hicolor-icon-theme imagemagick imagemagick-6-common imagemagick-6.q16 intltool-debian libarchive-zip-perl libarchive13 libasn1-8-heimdal libavahi-client3 libavahi-common-data libavahi-common3 libbrotli1 libbsd0 libcairo2 libcroco3 libcups2 libcupsimage2 libcurl4 libdbus-1-3 libelf1 libexpat1 libffindex0 libffindex0-dev libfftw3-double3 libfile-stripnondeterminism-perl libfontconfig1 libfreetype6 libglib2.0-0 libgraphite2-3 libgs9 libgs9-common libgssapi-krb5-2 libgssapi3-heimdal libharfbuzz-icu0 libharfbuzz0b libhcrypto4-heimdal libheimbase1-heimdal libheimntlm0-heimdal libhx509-5-heimdal libice6 libicu63 libijs-0.35 libjbig0 libjbig2dec0 libjpeg-turbo8 libjpeg8 libjsoncpp1 libk5crypto3 libkeyutils1 libkpathsea6 libkrb5-26-heimdal libkrb5-3 libkrb5support0 liblcms2-2 libldap-2.4-2 libldap-common liblocale-gettext-perl liblqr-1-0 libltdl7 libmagic-mgc libmagic1 libmagickcore-6.q16-6 libmagickwand-6.q16-6 libnghttp2-14 libpaper-utils libpaper1 libpipeline1 libpixman-1-0 libpotrace0 libpsl5 libptexenc1 librhash0 libroken18-heimdal librtmp1 libsasl2-2 libsasl2-modules-db libsigsegv2 libsm6 libsynctex2 libteckit0 libtexlua52 libtexlua53 libtexluajit2 libtiff5 libtool libuv1 libwebp6 libwind0-heimdal libwoff1 libx11-6 libx11-data libxau6 libxaw7 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxi6 libxml2 libxmu6 libxpm4 libxrender1 libxt6 libxxhash0 libzzip-0-13 m4 man-db po-debconf poppler-data sbuild-build-depends-hhsuite-dummy t1utils tex-common texlive-base texlive-binaries texlive-latex-base texlive-latex-recommended ucf x11-common xdg-utils 0 upgraded, 139 newly installed, 0 to remove and 0 not upgraded. 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Get:1 copy:/<>/resolver-NSIbxp/apt_archive ./ sbuild-build-depends-hhsuite-dummy 0.invalid.0 [928 B] Get:2 http://ftpmaster.internal/ubuntu disco/main amd64 liblocale-gettext-perl amd64 1.07-3build3 [16.4 kB] Get:3 http://ftpmaster.internal/ubuntu disco/main amd64 libxau6 amd64 1:1.0.8-1 [8376 B] Get:4 http://ftpmaster.internal/ubuntu disco/main amd64 libbsd0 amd64 0.9.1-1 [44.6 kB] Get:5 http://ftpmaster.internal/ubuntu disco/main amd64 libxdmcp6 amd64 1:1.1.2-3 [10.7 kB] Get:6 http://ftpmaster.internal/ubuntu disco/main amd64 libxcb1 amd64 1.13.1-2 [45.2 kB] Get:7 http://ftpmaster.internal/ubuntu disco/main amd64 libx11-data all 2:1.6.7-1 [113 kB] Get:8 http://ftpmaster.internal/ubuntu disco/main amd64 libx11-6 amd64 2:1.6.7-1 [572 kB] Get:9 http://ftpmaster.internal/ubuntu disco/main amd64 libxext6 amd64 2:1.3.3-1 [29.4 kB] Get:10 http://ftpmaster.internal/ubuntu disco/main amd64 bsdmainutils amd64 11.1.2ubuntu2 [181 kB] Get:11 http://ftpmaster.internal/ubuntu disco/main amd64 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imagemagick-6-common all 8:6.9.10.14+dfsg-7ubuntu2 [61.3 kB] Get:33 http://ftpmaster.internal/ubuntu disco/main amd64 libmagickcore-6.q16-6 amd64 8:6.9.10.14+dfsg-7ubuntu2 [1637 kB] Get:34 http://ftpmaster.internal/ubuntu disco/main amd64 libmagickwand-6.q16-6 amd64 8:6.9.10.14+dfsg-7ubuntu2 [305 kB] Get:35 http://ftpmaster.internal/ubuntu disco/main amd64 x11-common all 1:7.7+19ubuntu8 [22.5 kB] Get:36 http://ftpmaster.internal/ubuntu disco/main amd64 libice6 amd64 2:1.0.9-2 [40.2 kB] Get:37 http://ftpmaster.internal/ubuntu disco/main amd64 libsm6 amd64 2:1.2.2-1 [15.8 kB] Get:38 http://ftpmaster.internal/ubuntu disco/main amd64 poppler-data all 0.4.9-2 [1475 kB] Get:39 http://ftpmaster.internal/ubuntu disco/main amd64 tex-common all 6.10 [32.6 kB] Get:40 http://ftpmaster.internal/ubuntu disco/main amd64 libmagic-mgc amd64 1:5.34-2 [197 kB] Get:41 http://ftpmaster.internal/ubuntu disco/main amd64 libmagic1 amd64 1:5.34-2 [72.3 kB] Get:42 http://ftpmaster.internal/ubuntu disco/main amd64 file amd64 1:5.34-2 [22.8 kB] Get:43 http://ftpmaster.internal/ubuntu disco/main amd64 libdbus-1-3 amd64 1.12.10-1ubuntu2 [177 kB] Get:44 http://ftpmaster.internal/ubuntu disco/main amd64 libelf1 amd64 0.175-1 [44.2 kB] Get:45 http://ftpmaster.internal/ubuntu disco/main amd64 gettext-base amd64 0.19.8.1-9 [50.1 kB] Get:46 http://ftpmaster.internal/ubuntu disco/main amd64 libkrb5support0 amd64 1.16.1-1ubuntu1 [31.0 kB] Get:47 http://ftpmaster.internal/ubuntu disco/main amd64 libk5crypto3 amd64 1.16.1-1ubuntu1 [85.5 kB] Get:48 http://ftpmaster.internal/ubuntu disco/main amd64 libkeyutils1 amd64 1.5.9-9.3 [9640 B] Get:49 http://ftpmaster.internal/ubuntu disco/main amd64 libkrb5-3 amd64 1.16.1-1ubuntu1 [281 kB] Get:50 http://ftpmaster.internal/ubuntu disco/main amd64 libgssapi-krb5-2 amd64 1.16.1-1ubuntu1 [122 kB] Get:51 http://ftpmaster.internal/ubuntu disco/main amd64 libpsl5 amd64 0.20.2-2 [50.0 kB] Get:52 http://ftpmaster.internal/ubuntu disco/main amd64 libsigsegv2 amd64 2.12-2 [13.9 kB] Get:53 http://ftpmaster.internal/ubuntu disco/main amd64 m4 amd64 1.4.18-2 [199 kB] Get:54 http://ftpmaster.internal/ubuntu disco/main amd64 autoconf all 2.69-11 [322 kB] Get:55 http://ftpmaster.internal/ubuntu disco/main amd64 autotools-dev all 20180224.1 [39.6 kB] Get:56 http://ftpmaster.internal/ubuntu disco/main amd64 automake all 1:1.16.1-4 [522 kB] Get:57 http://ftpmaster.internal/ubuntu disco/main amd64 autopoint all 0.19.8.1-9 [412 kB] Get:58 http://ftpmaster.internal/ubuntu disco/main amd64 cmake-data all 3.13.2-1 [1457 kB] Get:59 http://ftpmaster.internal/ubuntu disco/main amd64 libarchive13 amd64 3.3.3-3 [305 kB] Get:60 http://ftpmaster.internal/ubuntu disco/main amd64 libroken18-heimdal amd64 7.5.0+dfsg-2.1 [41.4 kB] Get:61 http://ftpmaster.internal/ubuntu disco/main amd64 libasn1-8-heimdal amd64 7.5.0+dfsg-2.1 [182 kB] Get:62 http://ftpmaster.internal/ubuntu disco/main amd64 libheimbase1-heimdal amd64 7.5.0+dfsg-2.1 [29.4 kB] Get:63 http://ftpmaster.internal/ubuntu disco/main amd64 libhcrypto4-heimdal amd64 7.5.0+dfsg-2.1 [86.7 kB] Get:64 http://ftpmaster.internal/ubuntu disco/main amd64 libwind0-heimdal amd64 7.5.0+dfsg-2.1 [47.8 kB] Get:65 http://ftpmaster.internal/ubuntu disco/main amd64 libhx509-5-heimdal amd64 7.5.0+dfsg-2.1 [107 kB] Get:66 http://ftpmaster.internal/ubuntu disco/main amd64 libkrb5-26-heimdal amd64 7.5.0+dfsg-2.1 [206 kB] Get:67 http://ftpmaster.internal/ubuntu disco/main amd64 libheimntlm0-heimdal amd64 7.5.0+dfsg-2.1 [14.8 kB] Get:68 http://ftpmaster.internal/ubuntu disco/main amd64 libgssapi3-heimdal amd64 7.5.0+dfsg-2.1 [96.4 kB] Get:69 http://ftpmaster.internal/ubuntu disco/main amd64 libsasl2-modules-db amd64 2.1.27~101-g0780600+dfsg-3ubuntu2 [14.8 kB] Get:70 http://ftpmaster.internal/ubuntu disco/main amd64 libsasl2-2 amd64 2.1.27~101-g0780600+dfsg-3ubuntu2 [49.2 kB] Get:71 http://ftpmaster.internal/ubuntu disco/main amd64 libldap-common all 2.4.46+dfsg-5ubuntu3 [16.0 kB] Get:72 http://ftpmaster.internal/ubuntu disco/main amd64 libldap-2.4-2 amd64 2.4.46+dfsg-5ubuntu3 [154 kB] Get:73 http://ftpmaster.internal/ubuntu disco/main amd64 libnghttp2-14 amd64 1.35.1-1 [78.9 kB] Get:74 http://ftpmaster.internal/ubuntu disco/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2 [54.5 kB] Get:75 http://ftpmaster.internal/ubuntu disco/main amd64 libcurl4 amd64 7.61.0-1ubuntu2.2 [217 kB] Get:76 http://ftpmaster.internal/ubuntu disco/main amd64 libjsoncpp1 amd64 1.7.4-3 [73.6 kB] Get:77 http://ftpmaster.internal/ubuntu disco/main amd64 librhash0 amd64 1.3.7-1 [94.4 kB] Get:78 http://ftpmaster.internal/ubuntu disco/main amd64 libuv1 amd64 1.24.0-1 [69.3 kB] Get:79 http://ftpmaster.internal/ubuntu disco/main amd64 cmake amd64 3.13.2-1 [3466 kB] Get:80 http://ftpmaster.internal/ubuntu disco/main amd64 libtool all 2.4.6-6 [195 kB] Get:81 http://ftpmaster.internal/ubuntu disco/main amd64 dh-autoreconf all 19 [16.1 kB] Get:82 http://ftpmaster.internal/ubuntu disco/main amd64 libarchive-zip-perl all 1.64-1 [84.9 kB] Get:83 http://ftpmaster.internal/ubuntu disco/main amd64 libfile-stripnondeterminism-perl all 1.0.0-1 [13.9 kB] Get:84 http://ftpmaster.internal/ubuntu disco/main amd64 dh-strip-nondeterminism all 1.0.0-1 [5064 B] Get:85 http://ftpmaster.internal/ubuntu disco/main amd64 dwz amd64 0.12-3 [78.1 kB] Get:86 http://ftpmaster.internal/ubuntu disco/main amd64 libcroco3 amd64 0.6.12-3 [81.4 kB] Get:87 http://ftpmaster.internal/ubuntu disco/main amd64 gettext amd64 0.19.8.1-9 [896 kB] Get:88 http://ftpmaster.internal/ubuntu disco/main amd64 intltool-debian all 0.35.0+20060710.4 [24.9 kB] Get:89 http://ftpmaster.internal/ubuntu disco/main amd64 po-debconf all 1.0.21 [233 kB] Get:90 http://ftpmaster.internal/ubuntu disco/main amd64 debhelper all 11.5.3ubuntu1 [888 kB] Get:91 http://ftpmaster.internal/ubuntu disco/main amd64 fonts-lmodern all 2.004.5-5 [4532 kB] Get:92 http://ftpmaster.internal/ubuntu disco/universe amd64 help2man amd64 1.47.8 [169 kB] Get:93 http://ftpmaster.internal/ubuntu disco/main amd64 hicolor-icon-theme all 0.17-2 [9976 B] Get:94 http://ftpmaster.internal/ubuntu disco/universe amd64 imagemagick-6.q16 amd64 8:6.9.10.14+dfsg-7ubuntu2 [427 kB] Get:95 http://ftpmaster.internal/ubuntu disco/universe amd64 imagemagick amd64 8:6.9.10.14+dfsg-7ubuntu2 [14.4 kB] Get:96 http://ftpmaster.internal/ubuntu disco/main amd64 libavahi-common-data amd64 0.7-4ubuntu4 [21.4 kB] Get:97 http://ftpmaster.internal/ubuntu disco/main amd64 libavahi-common3 amd64 0.7-4ubuntu4 [21.5 kB] Get:98 http://ftpmaster.internal/ubuntu disco/main amd64 libavahi-client3 amd64 0.7-4ubuntu4 [25.2 kB] Get:99 http://ftpmaster.internal/ubuntu disco/main amd64 libbrotli1 amd64 1.0.7-2 [268 kB] Get:100 http://ftpmaster.internal/ubuntu disco/main amd64 libpixman-1-0 amd64 0.36.0-1 [229 kB] Get:101 http://ftpmaster.internal/ubuntu disco/main amd64 libxcb-render0 amd64 1.13.1-2 [14.8 kB] Get:102 http://ftpmaster.internal/ubuntu disco/main amd64 libxcb-shm0 amd64 1.13.1-2 [5548 B] Get:103 http://ftpmaster.internal/ubuntu disco/main amd64 libxrender1 amd64 1:0.9.10-1 [18.7 kB] Get:104 http://ftpmaster.internal/ubuntu disco/main amd64 libcairo2 amd64 1.16.0-1 [584 kB] Get:105 http://ftpmaster.internal/ubuntu disco/main amd64 libcups2 amd64 2.2.10-3 [212 kB] Get:106 http://ftpmaster.internal/ubuntu disco/main amd64 libcupsimage2 amd64 2.2.10-3 [18.4 kB] Get:107 http://ftpmaster.internal/ubuntu disco/main amd64 libgraphite2-3 amd64 1.3.12-1 [73.6 kB] Get:108 http://ftpmaster.internal/ubuntu disco/main amd64 libijs-0.35 amd64 0.35-13 [15.5 kB] Get:109 http://ftpmaster.internal/ubuntu disco/main amd64 libjbig2dec0 amd64 0.15-2 [58.5 kB] Get:110 http://ftpmaster.internal/ubuntu disco/main amd64 libpaper1 amd64 1.1.26 [12.9 kB] Get:111 http://ftpmaster.internal/ubuntu disco/main amd64 libgs9-common all 9.26~dfsg+0-0ubuntu3 [5092 kB] Get:112 http://ftpmaster.internal/ubuntu disco/main amd64 libgs9 amd64 9.26~dfsg+0-0ubuntu3 [2390 kB] Get:113 http://ftpmaster.internal/ubuntu disco/main amd64 libharfbuzz0b amd64 2.3.0-1 [365 kB] Get:114 http://ftpmaster.internal/ubuntu disco/main amd64 libharfbuzz-icu0 amd64 2.3.0-1 [5460 B] Get:115 http://ftpmaster.internal/ubuntu disco/main amd64 libkpathsea6 amd64 2018.20181218.49446-1 [56.1 kB] Get:116 http://ftpmaster.internal/ubuntu disco/main amd64 libpaper-utils amd64 1.1.26 [8320 B] Get:117 http://ftpmaster.internal/ubuntu disco/main amd64 libpotrace0 amd64 1.15-1 [17.5 kB] Get:118 http://ftpmaster.internal/ubuntu disco/main amd64 libptexenc1 amd64 2018.20181218.49446-1 [35.2 kB] Get:119 http://ftpmaster.internal/ubuntu disco/main amd64 libsynctex2 amd64 2018.20181218.49446-1 [54.0 kB] Get:120 http://ftpmaster.internal/ubuntu disco/main amd64 libteckit0 amd64 2.5.8+ds2-5ubuntu1 [317 kB] Get:121 http://ftpmaster.internal/ubuntu disco/main amd64 libtexlua52 amd64 2018.20181218.49446-1 [90.2 kB] Get:122 http://ftpmaster.internal/ubuntu disco/main amd64 libtexlua53 amd64 2018.20181218.49446-1 [103 kB] Get:123 http://ftpmaster.internal/ubuntu disco/main amd64 libtexluajit2 amd64 2018.20181218.49446-1 [234 kB] Get:124 http://ftpmaster.internal/ubuntu disco/main amd64 libwoff1 amd64 1.0.2-1build1 [42.1 kB] Get:125 http://ftpmaster.internal/ubuntu disco/main amd64 libxt6 amd64 1:1.1.5-1 [160 kB] Get:126 http://ftpmaster.internal/ubuntu disco/main amd64 libxmu6 amd64 2:1.1.2-2 [46.0 kB] Get:127 http://ftpmaster.internal/ubuntu disco/main amd64 libxpm4 amd64 1:3.5.12-1 [34.0 kB] Get:128 http://ftpmaster.internal/ubuntu disco/main amd64 libxaw7 amd64 2:1.0.13-1 [173 kB] Get:129 http://ftpmaster.internal/ubuntu disco/main amd64 libxi6 amd64 2:1.7.9-1 [29.2 kB] Get:130 http://ftpmaster.internal/ubuntu disco/main amd64 libxxhash0 amd64 0.6.5-2 [7180 B] Get:131 http://ftpmaster.internal/ubuntu disco/main amd64 libzzip-0-13 amd64 0.13.62-3.1ubuntu1 [26.0 kB] Get:132 http://ftpmaster.internal/ubuntu disco/main amd64 t1utils amd64 1.41-3 [56.1 kB] Get:133 http://ftpmaster.internal/ubuntu disco/main amd64 texlive-binaries amd64 2018.20181218.49446-1 [11.5 MB] Get:134 http://ftpmaster.internal/ubuntu disco/main amd64 xdg-utils all 1.1.3-1ubuntu2 [60.5 kB] Get:135 http://ftpmaster.internal/ubuntu disco/main amd64 texlive-base all 2018.20181214-1 [19.4 MB] Get:136 http://ftpmaster.internal/ubuntu disco/main amd64 texlive-latex-base all 2018.20181214-1 [956 kB] Get:137 http://ftpmaster.internal/ubuntu disco/main amd64 texlive-latex-recommended all 2018.20181214-1 [15.3 MB] Get:138 http://ftpmaster.internal/ubuntu disco/universe amd64 libffindex0 amd64 0.9.9.7+sog+git20160415.14274c9-1 [17.0 kB] Get:139 http://ftpmaster.internal/ubuntu disco/universe amd64 libffindex0-dev amd64 0.9.9.7+sog+git20160415.14274c9-1 [16.7 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 95.4 MB in 2s (40.5 MB/s) Selecting previously unselected package liblocale-gettext-perl. (Reading database ... 13710 files and directories currently installed.) Preparing to unpack .../000-liblocale-gettext-perl_1.07-3build3_amd64.deb ... Unpacking liblocale-gettext-perl (1.07-3build3) ... Selecting previously unselected package libxau6:amd64. Preparing to unpack .../001-libxau6_1%3a1.0.8-1_amd64.deb ... Unpacking libxau6:amd64 (1:1.0.8-1) ... Selecting previously unselected package libbsd0:amd64. Preparing to unpack .../002-libbsd0_0.9.1-1_amd64.deb ... Unpacking libbsd0:amd64 (0.9.1-1) ... Selecting previously unselected package libxdmcp6:amd64. Preparing to unpack .../003-libxdmcp6_1%3a1.1.2-3_amd64.deb ... Unpacking libxdmcp6:amd64 (1:1.1.2-3) ... Selecting previously unselected package libxcb1:amd64. Preparing to unpack .../004-libxcb1_1.13.1-2_amd64.deb ... Unpacking libxcb1:amd64 (1.13.1-2) ... Selecting previously unselected package libx11-data. Preparing to unpack .../005-libx11-data_2%3a1.6.7-1_all.deb ... Unpacking libx11-data (2:1.6.7-1) ... 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Preparing to unpack .../033-x11-common_1%3a7.7+19ubuntu8_all.deb ... dpkg-query: no packages found matching nux-tools Unpacking x11-common (1:7.7+19ubuntu8) ... Selecting previously unselected package libice6:amd64. Preparing to unpack .../034-libice6_2%3a1.0.9-2_amd64.deb ... Unpacking libice6:amd64 (2:1.0.9-2) ... Selecting previously unselected package libsm6:amd64. Preparing to unpack .../035-libsm6_2%3a1.2.2-1_amd64.deb ... Unpacking libsm6:amd64 (2:1.2.2-1) ... Selecting previously unselected package poppler-data. Preparing to unpack .../036-poppler-data_0.4.9-2_all.deb ... Unpacking poppler-data (0.4.9-2) ... Selecting previously unselected package tex-common. Preparing to unpack .../037-tex-common_6.10_all.deb ... Unpacking tex-common (6.10) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../038-libmagic-mgc_1%3a5.34-2_amd64.deb ... Unpacking libmagic-mgc (1:5.34-2) ... Selecting previously unselected package libmagic1:amd64. 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Setting up libexpat1:amd64 (2.2.6-1) ... Setting up libptexenc1:amd64 (2018.20181218.49446-1) ... Setting up libarchive-zip-perl (1.64-1) ... Setting up libnghttp2-14:amd64 (1.35.1-1) ... Setting up libwoff1:amd64 (1.0.2-1build1) ... Setting up libicu63:amd64 (63.1-5) ... Setting up liblcms2-2:amd64 (2.9-3) ... Setting up libjbig0:amd64 (2.1-3.1build1) ... Setting up libsigsegv2:amd64 (2.12-2) ... Setting up libldap-common (2.4.46+dfsg-5ubuntu3) ... Setting up fonts-dejavu-core (2.37-1) ... Setting up poppler-data (0.4.9-2) ... Setting up libuv1:amd64 (1.24.0-1) ... Setting up libpsl5:amd64 (0.20.2-2) ... Setting up libelf1:amd64 (0.175-1) ... Setting up groff-base (1.22.3-10) ... Setting up libglib2.0-0:amd64 (2.58.1-2) ... No schema files found: doing nothing. Setting up libtexlua53:amd64 (2018.20181218.49446-1) ... 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 (0.19.8.1-9) ... Setting up cmake-data (3.13.2-1) ... Setting up libsynctex2:amd64 (2018.20181218.49446-1) ... Setting up libjpeg-turbo8:amd64 (2.0.0-0ubuntu2) ... Setting up libffindex0 (0.9.9.7+sog+git20160415.14274c9-1) ... Setting up libpipeline1:amd64 (1.5.0-2) ... Setting up libroken18-heimdal:amd64 (7.5.0+dfsg-2.1) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2) ... Setting up m4 (1.4.18-2) ... Setting up libfftw3-double3:amd64 (3.3.8-2) ... Setting up libxxhash0:amd64 (0.6.5-2) ... Setting up libbsd0:amd64 (0.9.1-1) ... Setting up libkrb5support0:amd64 (1.16.1-1ubuntu1) ... Setting up ucf (3.0038) ... Setting up libxml2:amd64 (2.9.4+dfsg1-7ubuntu3) ... Setting up libfreetype6:amd64 (2.8.1-2ubuntu2) ... Setting up libmagic-mgc (1:5.34-2) ... Setting up libmagic1:amd64 (1:5.34-2) ... Setting up libgraphite2-3:amd64 (1.3.12-1) ... Setting up librhash0:amd64 (1.3.7-1) ... Setting up libcroco3:amd64 (0.6.12-3) ... Setting up liblqr-1-0:amd64 (0.4.2-2.1) ... Setting up libjbig2dec0:amd64 (0.15-2) ... Setting up libpixman-1-0:amd64 (0.36.0-1) ... Processing triggers for libc-bin (2.28-0ubuntu1) ... Setting up dwz (0.12-3) ... Setting up autotools-dev (20180224.1) ... Setting up t1utils (1.41-3) ... Setting up libheimbase1-heimdal:amd64 (7.5.0+dfsg-2.1) ... Processing triggers for systemd (239-7ubuntu15) ... Setting up libltdl7:amd64 (2.4.6-6) ... Setting up libijs-0.35:amd64 (0.35-13) ... Setting up liblocale-gettext-perl (1.07-3build3) ... Setting up libpotrace0:amd64 (1.15-1) ... Setting up libteckit0:amd64 (2.5.8+ds2-5ubuntu1) ... Setting up libxdmcp6:amd64 (1:1.1.2-3) ... Setting up libkeyutils1:amd64 (1.5.9-9.3) ... Setting up bsdmainutils (11.1.2ubuntu2) ... update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode Setting up x11-common (1:7.7+19ubuntu8) ... update-rc.d: warning: start and stop actions are no longer supported; falling back to defaults Running in chroot, ignoring request. invoke-rc.d: policy-rc.d denied execution of start. Setting up libzzip-0-13:amd64 (0.13.62-3.1ubuntu1) ... Setting up xdg-utils (1.1.3-1ubuntu2) ... Setting up hicolor-icon-theme (0.17-2) ... Setting up libtexluajit2:amd64 (2018.20181218.49446-1) ... Setting up libx11-data (2:1.6.7-1) ... Setting up libxau6:amd64 (1:1.0.8-1) ... Setting up autopoint (0.19.8.1-9) ... Setting up libdbus-1-3:amd64 (1.12.10-1ubuntu2) ... Setting up fonts-lmodern (2.004.5-5) ... Setting up libavahi-common-data:amd64 (0.7-4ubuntu4) ... Setting up libwebp6:amd64 (0.6.1-2) ... Setting up libfile-stripnondeterminism-perl (1.0.0-1) ... Setting up libjpeg8:amd64 (8c-2ubuntu8) ... Setting up libjsoncpp1:amd64 (1.7.4-3) ... Setting up libpaper1:amd64 (1.1.26) ... Creating config file /etc/papersize with new version Setting up libk5crypto3:amd64 (1.16.1-1ubuntu1) ... Setting up libpaper-utils (1.1.26) ... Setting up fontconfig-config (2.13.0-5ubuntu3) ... Setting up tex-common (6.10) ... update-language: texlive-base not installed and configured, doing nothing! Setting up libwind0-heimdal:amd64 (7.5.0+dfsg-2.1) ... Setting up gettext (0.19.8.1-9) ... Setting up libarchive13:amd64 (3.3.3-3) ... Setting up libffindex0-dev (0.9.9.7+sog+git20160415.14274c9-1) ... Setting up libasn1-8-heimdal:amd64 (7.5.0+dfsg-2.1) ... Setting up libhcrypto4-heimdal:amd64 (7.5.0+dfsg-2.1) ... Setting up libharfbuzz0b:amd64 (2.3.0-1) ... Setting up libtiff5:amd64 (4.0.10-3) ... Setting up autoconf (2.69-11) ... Setting up file (1:5.34-2) ... Setting up libhx509-5-heimdal:amd64 (7.5.0+dfsg-2.1) ... Setting up intltool-debian (0.35.0+20060710.4) ... Setting up automake (1:1.16.1-4) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up help2man (1.47.8) ... Setting up libice6:amd64 (2:1.0.9-2) ... Setting up man-db (2.8.5-1) ... Not building database; man-db/auto-update is not 'true'. Created symlink /etc/systemd/system/timers.target.wants/man-db.timer → /lib/systemd/system/man-db.timer. Setting up libkrb5-3:amd64 (1.16.1-1ubuntu1) ... Setting up libavahi-common3:amd64 (0.7-4ubuntu4) ... Setting up libkrb5-26-heimdal:amd64 (7.5.0+dfsg-2.1) ... Setting up libxcb1:amd64 (1.13.1-2) ... Setting up libheimntlm0-heimdal:amd64 (7.5.0+dfsg-2.1) ... Setting up libtool (2.4.6-6) ... Setting up libfontconfig1:amd64 (2.13.0-5ubuntu3) ... Setting up libsm6:amd64 (2:1.2.2-1) ... Setting up libxcb-render0:amd64 (1.13.1-2) ... Setting up libharfbuzz-icu0:amd64 (2.3.0-1) ... Setting up po-debconf (1.0.21) ... Setting up libx11-6:amd64 (2:1.6.7-1) ... Setting up libgssapi-krb5-2:amd64 (1.16.1-1ubuntu1) ... Setting up libxcb-shm0:amd64 (1.13.1-2) ... Setting up libxpm4:amd64 (1:3.5.12-1) ... Setting up libxt6:amd64 (1:1.1.5-1) ... Setting up libxrender1:amd64 (1:0.9.10-1) ... Setting up libavahi-client3:amd64 (0.7-4ubuntu4) ... Setting up libgssapi3-heimdal:amd64 (7.5.0+dfsg-2.1) ... Setting up libcups2:amd64 (2.2.10-3) ... Setting up libxext6:amd64 (2:1.3.3-1) ... Setting up libxmu6:amd64 (2:1.1.2-2) ... Setting up libcupsimage2:amd64 (2.2.10-3) ... Setting up libmagickcore-6.q16-6:amd64 (8:6.9.10.14+dfsg-7ubuntu2) ... Setting up libldap-2.4-2:amd64 (2.4.46+dfsg-5ubuntu3) ... Setting up libgs9:amd64 (9.26~dfsg+0-0ubuntu3) ... Setting up libxi6:amd64 (2:1.7.9-1) ... Setting up libxaw7:amd64 (2:1.0.13-1) ... Setting up libcairo2:amd64 (1.16.0-1) ... Setting up libcurl4:amd64 (7.61.0-1ubuntu2.2) ... Setting up texlive-binaries (2018.20181218.49446-1) ... update-alternatives: using /usr/bin/xdvi-xaw to provide /usr/bin/xdvi.bin (xdvi.bin) in auto mode update-alternatives: using /usr/bin/bibtex.original to provide /usr/bin/bibtex (bibtex) in auto mode Setting up libmagickwand-6.q16-6:amd64 (8:6.9.10.14+dfsg-7ubuntu2) ... Setting up texlive-base (2018.20181214-1) ... tl-paper: setting paper size for dvips to a4: /var/lib/texmf/dvips/config/config-paper.ps tl-paper: setting paper size for dvipdfmx to a4: /var/lib/texmf/dvipdfmx/dvipdfmx-paper.cfg tl-paper: setting paper size for xdvi to a4: /var/lib/texmf/xdvi/XDvi-paper tl-paper: setting paper size for pdftex to a4: /var/lib/texmf/tex/generic/config/pdftexconfig.tex tl-paper: setting paper size for dvipdfmx to letter: /var/lib/texmf/dvipdfmx/dvipdfmx-paper.cfg tl-paper: setting paper size for dvips to letter: /var/lib/texmf/dvips/config/config-paper.ps tl-paper: setting paper size for pdftex to letter: /var/lib/texmf/tex/generic/config/pdftexconfig.tex tl-paper: setting paper size for xdvi to letter: /var/lib/texmf/xdvi/XDvi-paper Setting up cmake (3.13.2-1) ... Setting up texlive-latex-base (2018.20181214-1) ... Setting up texlive-latex-recommended (2018.20181214-1) ... Setting up imagemagick-6.q16 (8:6.9.10.14+dfsg-7ubuntu2) ... update-alternatives: using /usr/bin/compare-im6.q16 to provide /usr/bin/compare (compare) in auto mode update-alternatives: using /usr/bin/compare-im6.q16 to provide /usr/bin/compare-im6 (compare-im6) in auto mode update-alternatives: using /usr/bin/animate-im6.q16 to provide /usr/bin/animate (animate) in auto mode update-alternatives: using /usr/bin/animate-im6.q16 to provide /usr/bin/animate-im6 (animate-im6) in auto mode update-alternatives: using /usr/bin/convert-im6.q16 to provide /usr/bin/convert (convert) in auto mode update-alternatives: using /usr/bin/convert-im6.q16 to provide /usr/bin/convert-im6 (convert-im6) in auto mode update-alternatives: using /usr/bin/composite-im6.q16 to provide /usr/bin/composite (composite) in auto mode update-alternatives: using /usr/bin/composite-im6.q16 to provide /usr/bin/composite-im6 (composite-im6) in auto mode update-alternatives: using /usr/bin/conjure-im6.q16 to provide /usr/bin/conjure (conjure) in auto mode update-alternatives: using /usr/bin/conjure-im6.q16 to provide /usr/bin/conjure-im6 (conjure-im6) in auto mode update-alternatives: using /usr/bin/import-im6.q16 to provide /usr/bin/import (import) in auto mode update-alternatives: using /usr/bin/import-im6.q16 to provide /usr/bin/import-im6 (import-im6) in auto mode update-alternatives: using /usr/bin/identify-im6.q16 to provide /usr/bin/identify (identify) in auto mode update-alternatives: using /usr/bin/identify-im6.q16 to provide /usr/bin/identify-im6 (identify-im6) in auto mode update-alternatives: using /usr/bin/stream-im6.q16 to provide /usr/bin/stream (stream) in auto mode update-alternatives: using /usr/bin/stream-im6.q16 to provide /usr/bin/stream-im6 (stream-im6) in auto mode update-alternatives: using /usr/bin/display-im6.q16 to provide /usr/bin/display (display) in auto mode update-alternatives: using /usr/bin/display-im6.q16 to provide /usr/bin/display-im6 (display-im6) in auto mode update-alternatives: using /usr/bin/montage-im6.q16 to provide /usr/bin/montage (montage) in auto mode update-alternatives: using /usr/bin/montage-im6.q16 to provide /usr/bin/montage-im6 (montage-im6) in auto mode update-alternatives: using /usr/bin/mogrify-im6.q16 to provide /usr/bin/mogrify (mogrify) in auto mode update-alternatives: using /usr/bin/mogrify-im6.q16 to provide /usr/bin/mogrify-im6 (mogrify-im6) in auto mode Setting up imagemagick (8:6.9.10.14+dfsg-7ubuntu2) ... Setting up dh-strip-nondeterminism (1.0.0-1) ... Setting up debhelper (11.5.3ubuntu1) ... Setting up dh-autoreconf (19) ... Setting up sbuild-build-depends-hhsuite-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.28-0ubuntu1) ... Processing triggers for systemd (239-7ubuntu15) ... Processing triggers for tex-common (6.10) ... Running updmap-sys. This may take some time... done. Running mktexlsr /var/lib/texmf ... done. Building format(s) --all. This may take some time... done. +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 4.4.0-141-generic amd64 (x86_64) Toolchain package versions: binutils_2.31.1-11ubuntu1 dpkg-dev_1.19.2ubuntu2 g++-8_8.2.0-13ubuntu1 g++-9_9-20190102-0ubuntu2 gcc-8_8.2.0-13ubuntu1 gcc-9_9-20190102-0ubuntu2 libc6-dev_2.28-0ubuntu1 libstdc++-8-dev_8.2.0-13ubuntu1 libstdc++-9-dev_9-20190102-0ubuntu2 libstdc++6_9-20190102-0ubuntu2 linux-libc-dev_4.18.0-11.12 Package versions: adduser_3.117ubuntu1 advancecomp_2.1-1 apt_1.8.0~alpha2ubuntu1 autoconf_2.69-11 automake_1:1.16.1-4 autopoint_0.19.8.1-9 autotools-dev_20180224.1 base-files_10.1ubuntu8 base-passwd_3.5.45 bash_4.4.18-2ubuntu3 binutils_2.31.1-11ubuntu1 binutils-common_2.31.1-11ubuntu1 binutils-x86-64-linux-gnu_2.31.1-11ubuntu1 bsdmainutils_11.1.2ubuntu2 bsdutils_1:2.32-0.1ubuntu2 build-essential_12.5ubuntu2 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libcap-ng0_0.7.9-1build1 libcap2_1:2.25-1.2 libcc1-0_9-20190102-0ubuntu2 libcom-err2_1.44.5-1 libcomerr2_1.44.5-1 libcroco3_0.6.12-3 libcryptsetup12_2:2.0.4-2ubuntu2 libcups2_2.2.10-3 libcupsimage2_2.2.10-3 libcurl4_7.61.0-1ubuntu2.2 libdb5.3_5.3.28+dfsg1-0.2 libdbus-1-3_1.12.10-1ubuntu2 libdebconfclient0_0.244ubuntu1 libdevmapper1.02.1_2:1.02.145-4.1ubuntu4 libdpkg-perl_1.19.2ubuntu2 libelf1_0.175-1 libexpat1_2.2.6-1 libext2fs2_1.44.5-1 libfakeroot_1.23-1 libfdisk1_2.32-0.1ubuntu2 libffi6_3.2.1-9 libffindex0_0.9.9.7+sog+git20160415.14274c9-1 libffindex0-dev_0.9.9.7+sog+git20160415.14274c9-1 libfftw3-double3_3.3.8-2 libfile-stripnondeterminism-perl_1.0.0-1 libfontconfig1_2.13.0-5ubuntu3 libfreetype6_2.8.1-2ubuntu2 libgcc-8-dev_8.2.0-13ubuntu1 libgcc-9-dev_9-20190102-0ubuntu2 libgcc1_1:9-20190102-0ubuntu2 libgcrypt20_1.8.4-3ubuntu1 libgdbm-compat4_1.18.1-2 libgdbm6_1.18.1-2 libglib2.0-0_2.58.1-2 libgmp10_2:6.1.2+dfsg-4 libgnutls30_3.6.5-2ubuntu1 libgomp1_9-20190102-0ubuntu2 libgpg-error0_1.32-3 libgraphite2-3_1.3.12-1 libgs9_9.26~dfsg+0-0ubuntu3 libgs9-common_9.26~dfsg+0-0ubuntu3 libgssapi-krb5-2_1.16.1-1ubuntu1 libgssapi3-heimdal_7.5.0+dfsg-2.1 libharfbuzz-icu0_2.3.0-1 libharfbuzz0b_2.3.0-1 libhcrypto4-heimdal_7.5.0+dfsg-2.1 libheimbase1-heimdal_7.5.0+dfsg-2.1 libheimntlm0-heimdal_7.5.0+dfsg-2.1 libhogweed4_3.4.1~rc1-1 libhx509-5-heimdal_7.5.0+dfsg-2.1 libice6_2:1.0.9-2 libicu63_63.1-5 libidn11_1.33-2.2ubuntu1 libidn2-0_2.0.5-1 libijs-0.35_0.35-13 libip4tc0_1.6.1-2ubuntu3 libisl19_0.20-2 libitm1_9-20190102-0ubuntu2 libjbig0_2.1-3.1build1 libjbig2dec0_0.15-2 libjpeg-turbo8_2.0.0-0ubuntu2 libjpeg8_8c-2ubuntu8 libjson-c3_0.12.1-1.3 libjsoncpp1_1.7.4-3 libk5crypto3_1.16.1-1ubuntu1 libkeyutils1_1.5.9-9.3 libkmod2_25-1ubuntu2 libkpathsea6_2018.20181218.49446-1 libkrb5-26-heimdal_7.5.0+dfsg-2.1 libkrb5-3_1.16.1-1ubuntu1 libkrb5support0_1.16.1-1ubuntu1 liblcms2-2_2.9-3 libldap-2.4-2_2.4.46+dfsg-5ubuntu3 libldap-common_2.4.46+dfsg-5ubuntu3 liblocale-gettext-perl_1.07-3build3 liblockfile-bin_1.14-1.1 liblockfile1_1.14-1.1 liblqr-1-0_0.4.2-2.1 liblsan0_9-20190102-0ubuntu2 libltdl7_2.4.6-6 liblz4-1_1.8.2-1ubuntu1 liblzma5_5.2.2-1.3 libmagic-mgc_1:5.34-2 libmagic1_1:5.34-2 libmagickcore-6.q16-6_8:6.9.10.14+dfsg-7ubuntu2 libmagickwand-6.q16-6_8:6.9.10.14+dfsg-7ubuntu2 libmount1_2.32-0.1ubuntu2 libmpc3_1.1.0-1 libmpfr6_4.0.1-2 libmpx2_8.2.0-13ubuntu1 libncurses6_6.1+20180210-4ubuntu1 libncursesw6_6.1+20180210-4ubuntu1 libnettle6_3.4.1~rc1-1 libnghttp2-14_1.35.1-1 libnpth0_1.6-1 libp11-kit0_0.23.14-2 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 libpaper-utils_1.1.26 libpaper1_1.1.26 libpcre3_2:8.39-11 libperl5.28_5.28.1-3 libpipeline1_1.5.0-2 libpixman-1-0_0.36.0-1 libpng16-16_1.6.34-2 libpotrace0_1.15-1 libprocps7_2:3.3.15-2ubuntu1 libpsl5_0.20.2-2 libptexenc1_2018.20181218.49446-1 libquadmath0_9-20190102-0ubuntu2 libreadline7_7.0-5 librhash0_1.3.7-1 libroken18-heimdal_7.5.0+dfsg-2.1 librtmp1_2.4+20151223.gitfa8646d.1-2 libsasl2-2_2.1.27~101-g0780600+dfsg-3ubuntu2 libsasl2-modules-db_2.1.27~101-g0780600+dfsg-3ubuntu2 libseccomp2_2.3.3-3ubuntu2 libselinux1_2.8-1build2 libsemanage-common_2.8-2 libsemanage1_2.8-2 libsepol1_2.8-1 libsigsegv2_2.12-2 libslang2_2.3.2-1ubuntu1 libsm6_2:1.2.2-1 libsmartcols1_2.32-0.1ubuntu2 libsqlite3-0_3.26.0-3 libss2_1.44.5-1 libssl1.1_1.1.1a-1ubuntu2 libstdc++-8-dev_8.2.0-13ubuntu1 libstdc++-9-dev_9-20190102-0ubuntu2 libstdc++6_9-20190102-0ubuntu2 libsynctex2_2018.20181218.49446-1 libsystemd0_239-7ubuntu15 libtasn1-6_4.13-3 libteckit0_2.5.8+ds2-5ubuntu1 libtexlua52_2018.20181218.49446-1 libtexlua53_2018.20181218.49446-1 libtexluajit2_2018.20181218.49446-1 libtiff5_4.0.10-3 libtinfo6_6.1+20180210-4ubuntu1 libtool_2.4.6-6 libtsan0_9-20190102-0ubuntu2 libubsan1_9-20190102-0ubuntu2 libudev1_239-7ubuntu15 libunistring2_0.9.10-1ubuntu1 libusb-0.1-4_2:0.1.12-32 libuuid1_2.32-0.1ubuntu2 libuv1_1.24.0-1 libwebp6_0.6.1-2 libwind0-heimdal_7.5.0+dfsg-2.1 libwoff1_1.0.2-1build1 libx11-6_2:1.6.7-1 libx11-data_2:1.6.7-1 libxau6_1:1.0.8-1 libxaw7_2:1.0.13-1 libxcb-render0_1.13.1-2 libxcb-shm0_1.13.1-2 libxcb1_1.13.1-2 libxdmcp6_1:1.1.2-3 libxext6_2:1.3.3-1 libxi6_2:1.7.9-1 libxml2_2.9.4+dfsg1-7ubuntu3 libxmu6_2:1.1.2-2 libxpm4_1:3.5.12-1 libxrender1_1:0.9.10-1 libxt6_1:1.1.5-1 libxxhash0_0.6.5-2 libzstd1_1.3.8+dfsg-3 libzzip-0-13_0.13.62-3.1ubuntu1 linux-libc-dev_4.18.0-11.12 lockfile-progs_0.1.18 login_1:4.5-1ubuntu1 lsb-base_9.20170808ubuntu1 m4_1.4.18-2 make_4.2.1-1.2 man-db_2.8.5-1 mawk_1.3.3-17ubuntu3 mount_2.32-0.1ubuntu2 multiarch-support_2.28-0ubuntu1 ncurses-base_6.1+20180210-4ubuntu1 ncurses-bin_6.1+20180210-4ubuntu1 openssl_1.1.1a-1ubuntu2 optipng_0.7.6-1.1 passwd_1:4.5-1ubuntu1 patch_2.7.6-3 perl_5.28.1-3 perl-base_5.28.1-3 perl-modules-5.28_5.28.1-3 pinentry-curses_1.1.0-1build2 pkgbinarymangler_143 po-debconf_1.0.21 policyrcd-script-zg2_0.1-3 poppler-data_0.4.9-2 procps_2:3.3.15-2ubuntu1 readline-common_7.0-5 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-hhsuite-dummy_0.invalid.0 sed_4.7-1 sensible-utils_0.0.12 systemd_239-7ubuntu15 systemd-sysv_239-7ubuntu15 sysv-rc_2.88dsf-59.3ubuntu2 sysvinit-utils_2.88dsf-59.10ubuntu2 t1utils_1.41-3 tar_1.30+dfsg-4 tex-common_6.10 texlive-base_2018.20181214-1 texlive-binaries_2018.20181218.49446-1 texlive-latex-base_2018.20181214-1 texlive-latex-recommended_2018.20181214-1 tzdata_2018i-1 ubuntu-keyring_2018.09.18.1 ucf_3.0038 util-linux_2.32-0.1ubuntu2 x11-common_1:7.7+19ubuntu8 xdg-utils_1.1.3-1ubuntu2 xz-utils_5.2.2-1.3 zlib1g_1:1.2.11.dfsg-0ubuntu2 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- gpgv: Signature made Tue Aug 21 19:23:54 2018 UTC gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./hhsuite_3.0~beta3+dfsg-1.dsc dpkg-source: info: extracting hhsuite in hhsuite-3.0~beta3+dfsg dpkg-source: info: unpacking hhsuite_3.0~beta3+dfsg.orig.tar.xz dpkg-source: info: unpacking hhsuite_3.0~beta3+dfsg-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying perlscript_uselib dpkg-source: info: applying perl_interpreter dpkg-source: info: applying add_Makefile_in_data.patch dpkg-source: info: applying disable-ffindex-build.patch dpkg-source: info: applying drop-fmemopen.h.patch dpkg-source: info: applying build-own-manual-PDF.patch dpkg-source: info: applying set-default-HHLIB-dir.patch dpkg-source: info: applying disable-AVX-SSE.patch Check disc space ---------------- Sufficient free space for build User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf DEB_BUILD_OPTIONS=noautodbgsym 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-15930158 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-15930158 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-15930158 SCHROOT_UID=2001 SCHROOT_USER=buildd SHELL=/bin/sh TERM=unknown USER=buildd V=1 dpkg-buildpackage ----------------- dpkg-buildpackage: info: source package hhsuite dpkg-buildpackage: info: source version 3.0~beta3+dfsg-1 dpkg-buildpackage: info: source distribution unstable dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 fakeroot debian/rules clean dh clean --builddirectory=mybuild debian/rules override_dh_auto_clean make[1]: Entering directory '/<>/hhsuite-3.0~beta3+dfsg' dh_auto_clean rm -f hhalign.1 hhblits.1 hhblits_omp.1 hhconsensus.1 hhfilter.1 hhmake.1 hhsearch.1 find . -name "*.rej" -delete find . -name "*~" -delete dh_clean make[1]: Leaving directory '/<>/hhsuite-3.0~beta3+dfsg' dh_autoreconf_clean -O--builddirectory=mybuild dh_clean -O--builddirectory=mybuild debian/rules build dh build --builddirectory=mybuild dh_update_autotools_config -O--builddirectory=mybuild dh_autoreconf -O--builddirectory=mybuild dh_auto_configure -O--builddirectory=mybuild cd mybuild && cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=None -DCMAKE_INSTALL_SYSCONFDIR=/etc -DCMAKE_INSTALL_LOCALSTATEDIR=/var -DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/x86_64-linux-gnu .. -- The CXX compiler identification is GNU 9.0.0 -- Check for working CXX compiler: /usr/bin/c++ -- Check for working CXX compiler: /usr/bin/c++ -- works -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Detecting CXX compile features -- Detecting CXX compile features - done -- Compiler is GNU -- Processor is x86_64 -- Using CPU native flags for SSE optimization: -march=native -- Performing Test HAVE_MM_MALLOC -- Performing Test HAVE_MM_MALLOC - Success -- Performing Test HAVE_POSIX_MEMALIGN -- Performing Test HAVE_POSIX_MEMALIGN - Success -- Performing Test HAVE_AVX2_EXTENSIONS -- Performing Test HAVE_AVX2_EXTENSIONS - Success -- Performing Test HAVE_AVX_EXTENSIONS -- Performing Test HAVE_AVX_EXTENSIONS - Success -- Performing Test HAVE_SSE4_2_EXTENSIONS -- Performing Test HAVE_SSE4_2_EXTENSIONS - Success -- Performing Test HAVE_SSE4_1_EXTENSIONS -- Performing Test HAVE_SSE4_1_EXTENSIONS - Success -- Performing Test HAVE_SSSE3_EXTENSIONS -- Performing Test HAVE_SSSE3_EXTENSIONS - Success -- Performing Test HAVE_SSE3_EXTENSIONS -- Performing Test HAVE_SSE3_EXTENSIONS - Success -- Performing Test HAVE_SSE2_EXTENSIONS -- Performing Test HAVE_SSE2_EXTENSIONS - Success -- Performing Test HAVE_SSE_EXTENSIONS -- Performing Test HAVE_SSE_EXTENSIONS - Success -- Found SSE4.2 extensions, using flags: -march=native -msse4.2 -mfpmath=sse -- Found OpenMP_CXX: -fopenmp (found version "4.5") -- Found OpenMP: TRUE (found version "4.5") -- Found OpenMP -- Found LATEX: /usr/bin/latex -- Found UnixCommands: /bin/bash -- I could not find the ps2pdf command. -- I could not find the pdftops command. -- I could not find the latex2html command. -- Configuring done -- Generating done CMake Warning: Manually-specified variables were not used by the project: CMAKE_EXPORT_NO_PACKAGE_REGISTRY CMAKE_INSTALL_LIBDIR CMAKE_INSTALL_LOCALSTATEDIR CMAKE_INSTALL_SYSCONFDIR -- Build files have been written to: /<>/hhsuite-3.0~beta3+dfsg/mybuild debian/rules override_dh_auto_build make[1]: Entering directory '/<>/hhsuite-3.0~beta3+dfsg' dh_auto_build -- NO_PNG=1 cd mybuild && make V=1 -j4 NO_PNG=1 make[2]: Entering directory '/<>/hhsuite-3.0~beta3+dfsg/mybuild' /usr/bin/cmake -S"/<>/hhsuite-3.0~beta3+dfsg" -B"/<>/hhsuite-3.0~beta3+dfsg/mybuild" --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start "/<>/hhsuite-3.0~beta3+dfsg/mybuild/CMakeFiles" "/<>/hhsuite-3.0~beta3+dfsg/mybuild/CMakeFiles/progress.marks" make -f CMakeFiles/Makefile2 all make[3]: Entering directory '/<>/hhsuite-3.0~beta3+dfsg/mybuild' make -f src/CMakeFiles/HH_OBJECTS.dir/build.make src/CMakeFiles/HH_OBJECTS.dir/depend make[4]: Entering directory '/<>/hhsuite-3.0~beta3+dfsg/mybuild' cd "/<>/hhsuite-3.0~beta3+dfsg/mybuild" && /usr/bin/cmake -E cmake_depends "Unix Makefiles" "/<>/hhsuite-3.0~beta3+dfsg" "/<>/hhsuite-3.0~beta3+dfsg/src" "/<>/hhsuite-3.0~beta3+dfsg/mybuild" "/<>/hhsuite-3.0~beta3+dfsg/mybuild/src" "/<>/hhsuite-3.0~beta3+dfsg/mybuild/src/CMakeFiles/HH_OBJECTS.dir/DependInfo.cmake" --color= make -f src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/build.make src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/depend make -f src/CMakeFiles/CS_OBJECTS.dir/build.make src/CMakeFiles/CS_OBJECTS.dir/depend make -f src/CMakeFiles/hhviterbialgorithm_and_ss.dir/build.make src/CMakeFiles/hhviterbialgorithm_and_ss.dir/depend make[4]: Entering directory '/<>/hhsuite-3.0~beta3+dfsg/mybuild' cd "/<>/hhsuite-3.0~beta3+dfsg/mybuild" && /usr/bin/cmake -E cmake_depends "Unix Makefiles" "/<>/hhsuite-3.0~beta3+dfsg" "/<>/hhsuite-3.0~beta3+dfsg/src" "/<>/hhsuite-3.0~beta3+dfsg/mybuild" "/<>/hhsuite-3.0~beta3+dfsg/mybuild/src" "/<>/hhsuite-3.0~beta3+dfsg/mybuild/src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/DependInfo.cmake" --color= make[4]: Entering directory '/<>/hhsuite-3.0~beta3+dfsg/mybuild' cd "/<>/hhsuite-3.0~beta3+dfsg/mybuild" && /usr/bin/cmake -E cmake_depends "Unix Makefiles" "/<>/hhsuite-3.0~beta3+dfsg" "/<>/hhsuite-3.0~beta3+dfsg/src" "/<>/hhsuite-3.0~beta3+dfsg/mybuild" "/<>/hhsuite-3.0~beta3+dfsg/mybuild/src" "/<>/hhsuite-3.0~beta3+dfsg/mybuild/src/CMakeFiles/CS_OBJECTS.dir/DependInfo.cmake" --color= make[4]: Entering directory '/<>/hhsuite-3.0~beta3+dfsg/mybuild' cd "/<>/hhsuite-3.0~beta3+dfsg/mybuild" && /usr/bin/cmake -E cmake_depends "Unix Makefiles" "/<>/hhsuite-3.0~beta3+dfsg" "/<>/hhsuite-3.0~beta3+dfsg/src" "/<>/hhsuite-3.0~beta3+dfsg/mybuild" "/<>/hhsuite-3.0~beta3+dfsg/mybuild/src" "/<>/hhsuite-3.0~beta3+dfsg/mybuild/src/CMakeFiles/hhviterbialgorithm_and_ss.dir/DependInfo.cmake" --color= Scanning dependencies of target CS_OBJECTS make[4]: Leaving directory '/<>/hhsuite-3.0~beta3+dfsg/mybuild' make -f src/CMakeFiles/CS_OBJECTS.dir/build.make src/CMakeFiles/CS_OBJECTS.dir/build Scanning dependencies of target hhviterbialgorithm_and_ss make[4]: Leaving directory '/<>/hhsuite-3.0~beta3+dfsg/mybuild' make -f src/CMakeFiles/hhviterbialgorithm_and_ss.dir/build.make src/CMakeFiles/hhviterbialgorithm_and_ss.dir/build Scanning dependencies of target hhviterbialgorithm_with_celloff_and_ss make[4]: Leaving directory '/<>/hhsuite-3.0~beta3+dfsg/mybuild' make -f src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/build.make src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/build make[4]: Entering directory '/<>/hhsuite-3.0~beta3+dfsg/mybuild' make[4]: Entering directory '/<>/hhsuite-3.0~beta3+dfsg/mybuild' make[4]: Entering directory '/<>/hhsuite-3.0~beta3+dfsg/mybuild' [ 1%] Building CXX object src/CMakeFiles/CS_OBJECTS.dir/cs/aa.cc.o cd "/<>/hhsuite-3.0~beta3+dfsg/mybuild/src" && /usr/bin/c++ -DOPENMP -DSSE -I"/<>/hhsuite-3.0~beta3+dfsg/src" -I"/<>/hhsuite-3.0~beta3+dfsg/src/cs" -I"/<>/hhsuite-3.0~beta3+dfsg/mybuild" -g -O2 -fdebug-prefix-map=/<>/hhsuite-3.0~beta3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -march=native -msse4.2 -mfpmath=sse -fopenmp -fno-strict-aliasing -o CMakeFiles/CS_OBJECTS.dir/cs/aa.cc.o -c "/<>/hhsuite-3.0~beta3+dfsg/src/cs/aa.cc" [ 2%] Building CXX object src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/hhviterbialgorithm.cpp.o cd "/<>/hhsuite-3.0~beta3+dfsg/mybuild/src" && /usr/bin/c++ -DOPENMP -DSSE -I"/<>/hhsuite-3.0~beta3+dfsg/src" -I"/<>/hhsuite-3.0~beta3+dfsg/src/cs" -I"/<>/hhsuite-3.0~beta3+dfsg/mybuild" -g -O2 -fdebug-prefix-map=/<>/hhsuite-3.0~beta3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -march=native -msse4.2 -mfpmath=sse -fopenmp -fno-strict-aliasing -DVITERBI_CELLOFF=1 -DVITERBI_SS_SCORE=1 -o CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/hhviterbialgorithm.cpp.o -c "/<>/hhsuite-3.0~beta3+dfsg/src/hhviterbialgorithm.cpp" [ 4%] Building CXX object src/CMakeFiles/hhviterbialgorithm_and_ss.dir/hhviterbialgorithm.cpp.o cd "/<>/hhsuite-3.0~beta3+dfsg/mybuild/src" && /usr/bin/c++ -DOPENMP -DSSE -I"/<>/hhsuite-3.0~beta3+dfsg/src" -I"/<>/hhsuite-3.0~beta3+dfsg/src/cs" -I"/<>/hhsuite-3.0~beta3+dfsg/mybuild" -g -O2 -fdebug-prefix-map=/<>/hhsuite-3.0~beta3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -march=native -msse4.2 -mfpmath=sse -fopenmp -fno-strict-aliasing -DVITERBI_SS_SCORE=1 -o CMakeFiles/hhviterbialgorithm_and_ss.dir/hhviterbialgorithm.cpp.o -c "/<>/hhsuite-3.0~beta3+dfsg/src/hhviterbialgorithm.cpp" Scanning dependencies of target HH_OBJECTS make[4]: Leaving directory '/<>/hhsuite-3.0~beta3+dfsg/mybuild' make -f src/CMakeFiles/HH_OBJECTS.dir/build.make src/CMakeFiles/HH_OBJECTS.dir/build make[4]: Entering directory '/<>/hhsuite-3.0~beta3+dfsg/mybuild' [ 5%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhblits.cpp.o cd "/<>/hhsuite-3.0~beta3+dfsg/mybuild/src" && /usr/bin/c++ -DOPENMP -DSSE -I"/<>/hhsuite-3.0~beta3+dfsg/src" -I"/<>/hhsuite-3.0~beta3+dfsg/src/cs" -I"/<>/hhsuite-3.0~beta3+dfsg/mybuild" -g -O2 -fdebug-prefix-map=/<>/hhsuite-3.0~beta3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -march=native -msse4.2 -mfpmath=sse -fopenmp -fno-strict-aliasing -o CMakeFiles/HH_OBJECTS.dir/hhblits.cpp.o -c "/<>/hhsuite-3.0~beta3+dfsg/src/hhblits.cpp" [ 7%] Building CXX object src/CMakeFiles/CS_OBJECTS.dir/cs/as.cc.o cd "/<>/hhsuite-3.0~beta3+dfsg/mybuild/src" && /usr/bin/c++ -DOPENMP -DSSE -I"/<>/hhsuite-3.0~beta3+dfsg/src" -I"/<>/hhsuite-3.0~beta3+dfsg/src/cs" -I"/<>/hhsuite-3.0~beta3+dfsg/mybuild" -g -O2 -fdebug-prefix-map=/<>/hhsuite-3.0~beta3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -march=native -msse4.2 -mfpmath=sse -fopenmp -fno-strict-aliasing -o CMakeFiles/CS_OBJECTS.dir/cs/as.cc.o -c "/<>/hhsuite-3.0~beta3+dfsg/src/cs/as.cc" make[4]: Leaving directory '/<>/hhsuite-3.0~beta3+dfsg/mybuild' [ 7%] Built target hhviterbialgorithm_and_ss make -f src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/build.make src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/depend make[4]: Entering directory '/<>/hhsuite-3.0~beta3+dfsg/mybuild' cd "/<>/hhsuite-3.0~beta3+dfsg/mybuild" && /usr/bin/cmake -E cmake_depends "Unix Makefiles" "/<>/hhsuite-3.0~beta3+dfsg" "/<>/hhsuite-3.0~beta3+dfsg/src" "/<>/hhsuite-3.0~beta3+dfsg/mybuild" "/<>/hhsuite-3.0~beta3+dfsg/mybuild/src" "/<>/hhsuite-3.0~beta3+dfsg/mybuild/src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/DependInfo.cmake" --color= Scanning dependencies of target hhviterbialgorithm_with_celloff make[4]: Leaving directory '/<>/hhsuite-3.0~beta3+dfsg/mybuild' make -f src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/build.make src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/build make[4]: Entering directory '/<>/hhsuite-3.0~beta3+dfsg/mybuild' [ 8%] Building CXX object src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/hhviterbialgorithm.cpp.o cd "/<>/hhsuite-3.0~beta3+dfsg/mybuild/src" && /usr/bin/c++ -DOPENMP -DSSE -I"/<>/hhsuite-3.0~beta3+dfsg/src" -I"/<>/hhsuite-3.0~beta3+dfsg/src/cs" -I"/<>/hhsuite-3.0~beta3+dfsg/mybuild" -g -O2 -fdebug-prefix-map=/<>/hhsuite-3.0~beta3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -march=native -msse4.2 -mfpmath=sse -fopenmp -fno-strict-aliasing -DVITERBI_CELLOFF=1 -o CMakeFiles/hhviterbialgorithm_with_celloff.dir/hhviterbialgorithm.cpp.o -c "/<>/hhsuite-3.0~beta3+dfsg/src/hhviterbialgorithm.cpp" make[4]: Leaving directory '/<>/hhsuite-3.0~beta3+dfsg/mybuild' [ 8%] Built target hhviterbialgorithm_with_celloff_and_ss make -f src/CMakeFiles/A3M_COMPRESS_OBJECT.dir/build.make src/CMakeFiles/A3M_COMPRESS_OBJECT.dir/depend make[4]: Entering directory '/<>/hhsuite-3.0~beta3+dfsg/mybuild' cd "/<>/hhsuite-3.0~beta3+dfsg/mybuild" && /usr/bin/cmake -E cmake_depends "Unix Makefiles" "/<>/hhsuite-3.0~beta3+dfsg" "/<>/hhsuite-3.0~beta3+dfsg/src" "/<>/hhsuite-3.0~beta3+dfsg/mybuild" "/<>/hhsuite-3.0~beta3+dfsg/mybuild/src" "/<>/hhsuite-3.0~beta3+dfsg/mybuild/src/CMakeFiles/A3M_COMPRESS_OBJECT.dir/DependInfo.cmake" --color= Scanning dependencies of target A3M_COMPRESS_OBJECT make[4]: Leaving directory '/<>/hhsuite-3.0~beta3+dfsg/mybuild' make -f src/CMakeFiles/A3M_COMPRESS_OBJECT.dir/build.make src/CMakeFiles/A3M_COMPRESS_OBJECT.dir/build make[4]: Entering directory '/<>/hhsuite-3.0~beta3+dfsg/mybuild' [ 10%] Building CXX object src/CMakeFiles/A3M_COMPRESS_OBJECT.dir/a3m_compress.cpp.o cd "/<>/hhsuite-3.0~beta3+dfsg/mybuild/src" && /usr/bin/c++ -DOPENMP -DSSE -I"/<>/hhsuite-3.0~beta3+dfsg/src" -I"/<>/hhsuite-3.0~beta3+dfsg/src/cs" -I"/<>/hhsuite-3.0~beta3+dfsg/mybuild" -g -O2 -fdebug-prefix-map=/<>/hhsuite-3.0~beta3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -march=native -msse4.2 -mfpmath=sse -fopenmp -fno-strict-aliasing -o CMakeFiles/A3M_COMPRESS_OBJECT.dir/a3m_compress.cpp.o -c "/<>/hhsuite-3.0~beta3+dfsg/src/a3m_compress.cpp" [ 11%] Building CXX object src/CMakeFiles/CS_OBJECTS.dir/cs/assert_helpers.cc.o cd "/<>/hhsuite-3.0~beta3+dfsg/mybuild/src" && /usr/bin/c++ -DOPENMP -DSSE -I"/<>/hhsuite-3.0~beta3+dfsg/src" -I"/<>/hhsuite-3.0~beta3+dfsg/src/cs" -I"/<>/hhsuite-3.0~beta3+dfsg/mybuild" -g -O2 -fdebug-prefix-map=/<>/hhsuite-3.0~beta3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -march=native -msse4.2 -mfpmath=sse -fopenmp -fno-strict-aliasing -o CMakeFiles/CS_OBJECTS.dir/cs/assert_helpers.cc.o -c "/<>/hhsuite-3.0~beta3+dfsg/src/cs/assert_helpers.cc" [ 13%] Building CXX object src/CMakeFiles/CS_OBJECTS.dir/cs/blosum_matrix.cc.o cd "/<>/hhsuite-3.0~beta3+dfsg/mybuild/src" && /usr/bin/c++ -DOPENMP -DSSE -I"/<>/hhsuite-3.0~beta3+dfsg/src" -I"/<>/hhsuite-3.0~beta3+dfsg/src/cs" -I"/<>/hhsuite-3.0~beta3+dfsg/mybuild" -g -O2 -fdebug-prefix-map=/<>/hhsuite-3.0~beta3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -march=native -msse4.2 -mfpmath=sse -fopenmp -fno-strict-aliasing -o CMakeFiles/CS_OBJECTS.dir/cs/blosum_matrix.cc.o -c "/<>/hhsuite-3.0~beta3+dfsg/src/cs/blosum_matrix.cc" make[4]: Leaving directory '/<>/hhsuite-3.0~beta3+dfsg/mybuild' [ 13%] Built target hhviterbialgorithm_with_celloff make -f doc/CMakeFiles/pdf.dir/build.make doc/CMakeFiles/pdf.dir/depend make[4]: Entering directory '/<>/hhsuite-3.0~beta3+dfsg/mybuild' cd "/<>/hhsuite-3.0~beta3+dfsg/mybuild" && /usr/bin/cmake -E cmake_depends "Unix Makefiles" "/<>/hhsuite-3.0~beta3+dfsg" "/<>/hhsuite-3.0~beta3+dfsg/doc" "/<>/hhsuite-3.0~beta3+dfsg/mybuild" "/<>/hhsuite-3.0~beta3+dfsg/mybuild/doc" "/<>/hhsuite-3.0~beta3+dfsg/mybuild/doc/CMakeFiles/pdf.dir/DependInfo.cmake" --color= Scanning dependencies of target pdf make[4]: Leaving directory '/<>/hhsuite-3.0~beta3+dfsg/mybuild' make -f doc/CMakeFiles/pdf.dir/build.make doc/CMakeFiles/pdf.dir/build make[4]: Entering directory '/<>/hhsuite-3.0~beta3+dfsg/mybuild' [ 14%] Generating hhsuite-userguide.bib cd "/<>/hhsuite-3.0~beta3+dfsg/mybuild/doc" && /usr/bin/cmake -E copy /<>/hhsuite-3.0~beta3+dfsg/doc/hhsuite-userguide.bib /<>/hhsuite-3.0~beta3+dfsg/mybuild/doc/hhsuite-userguide.bib make[4]: Leaving directory '/<>/hhsuite-3.0~beta3+dfsg/mybuild' [ 15%] Generating hhblits-hhsearch.png [ 15%] Built target A3M_COMPRESS_OBJECT cd "/<>/hhsuite-3.0~beta3+dfsg/mybuild/doc" && /usr/bin/cmake -E copy /<>/hhsuite-3.0~beta3+dfsg/doc/hhblits-hhsearch.png /<>/hhsuite-3.0~beta3+dfsg/mybuild/doc/hhblits-hhsearch.png [ 17%] Generating hhsuite-userguide.tex make -f src/CMakeFiles/a3m_database_reduce.dir/build.make src/CMakeFiles/a3m_database_reduce.dir/depend cd "/<>/hhsuite-3.0~beta3+dfsg/mybuild/doc" && /usr/bin/cmake -E copy /<>/hhsuite-3.0~beta3+dfsg/doc/hhsuite-userguide.tex /<>/hhsuite-3.0~beta3+dfsg/mybuild/doc/hhsuite-userguide.tex make[4]: Entering directory '/<>/hhsuite-3.0~beta3+dfsg/mybuild' cd "/<>/hhsuite-3.0~beta3+dfsg/mybuild" && /usr/bin/cmake -E cmake_depends "Unix Makefiles" "/<>/hhsuite-3.0~beta3+dfsg" "/<>/hhsuite-3.0~beta3+dfsg/src" "/<>/hhsuite-3.0~beta3+dfsg/mybuild" "/<>/hhsuite-3.0~beta3+dfsg/mybuild/src" "/<>/hhsuite-3.0~beta3+dfsg/mybuild/src/CMakeFiles/a3m_database_reduce.dir/DependInfo.cmake" --color= Scanning dependencies of target a3m_database_reduce make[4]: Leaving directory '/<>/hhsuite-3.0~beta3+dfsg/mybuild' make -f src/CMakeFiles/a3m_database_reduce.dir/build.make src/CMakeFiles/a3m_database_reduce.dir/build make[4]: Entering directory '/<>/hhsuite-3.0~beta3+dfsg/mybuild' [ 18%] Generating hhsuite-userguide.pdf cd "/<>/hhsuite-3.0~beta3+dfsg/mybuild/doc" && /usr/bin/cmake -E chdir /<>/hhsuite-3.0~beta3+dfsg/mybuild/doc /usr/bin/pdflatex -interaction=nonstopmode hhsuite-userguide.tex [ 20%] Building CXX object src/CMakeFiles/a3m_database_reduce.dir/a3m_database_reduce.cpp.o cd "/<>/hhsuite-3.0~beta3+dfsg/mybuild/src" && /usr/bin/c++ -DOPENMP -DSSE -I"/<>/hhsuite-3.0~beta3+dfsg/src" -I"/<>/hhsuite-3.0~beta3+dfsg/src/cs" -I"/<>/hhsuite-3.0~beta3+dfsg/mybuild" -g -O2 -fdebug-prefix-map=/<>/hhsuite-3.0~beta3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security 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[5] Underfull \hbox (badness 10000) in paragraph at lines 235--236 Overfull \hbox (30.66537pt too wide) in paragraph at lines 240--240 []\OT1/cmtt/m/n/10.95 $ wget https://github.com/soedinglab/hh-suite/releases/.. ./hhsuite-3.0-beta.1-Linux.rpm[] Underfull \hbox (badness 10000) in paragraph at lines 243--245 [6] Overfull \hbox (82.40356pt too wide) in paragraph at lines 307--307 []\OT1/cmtt/m/n/10.95 $ wget http://wwwuser.gwdg.de/~compbiol/data/hhsuite/data bases/hhsuite_dbs/uniprot20_2015_06.tgz[] LaTeX Warning: Citation `uniprot:2010' on page 7 undefined on input line 312. LaTeX Warning: Citation `Higgins:2011' on page 7 undefined on input line 312. LaTeX Warning: Reference `building_dbs' on page 7 undefined on input line 316. [7] LaTeX Warning: Reference `efficiency' on page 8 undefined on input line 318. [8] LaTeX Warning: Reference `MAC' on page 9 undefined on input line 434. [9] LaTeX Warning: Reference `installation' on page 10 undefined on input line 438. 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[14] Underfull \hbox (badness 10000) in paragraph at lines 648--649 [15] Overfull \hbox (7.67062pt too wide) in paragraph at lines 697--697 []\OT1/cmtt/m/n/10.95 $ ffindex_order sorting.dat _hhm.ff{data,index} _ hhm_ordered.ff{data,index}[] Overfull \hbox (7.67062pt too wide) in paragraph at lines 697--697 []\OT1/cmtt/m/n/10.95 $ ffindex_order sorting.dat _a3m.ff{data,index} _ a3m_ordered.ff{data,index}[] Overfull \hbox (7.67062pt too wide) in paragraph at lines 717--717 []\OT1/cmtt/m/n/10.95 $ python3 cif2fasta.py -i -o pdb100.fas -c -p pdb_filter.dat[] LaTeX Warning: Reference `building_dbs' on page 16 undefined on input line 721. [16] LaTeX Warning: Reference `building_dbs' on page 17 undefined on input line 738. 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[34] Overfull \hbox (8.27538pt too wide) in paragraph at lines 1713--1713 [] \OT1/cmtt/m/n/10 -add_cons generate consensus sequence as master sequen ce of query MSA (default=don't)[] Overfull \hbox (8.27538pt too wide) in paragraph at lines 1713--1713 [] \OT1/cmtt/m/n/10 -maxfilt max number of hits allowed to pas s 2nd prefilter (default=20000)[] Overfull \hbox (50.27501pt too wide) in paragraph at lines 1713--1713 [] \OT1/cmtt/m/n/10 -pre_evalue_thresh max E-value threshold of Smith-Wa terman prefilter score (default=1000.0)[] Overfull \hbox (18.77528pt too wide) in paragraph at lines 1713--1713 [] \OT1/cmtt/m/n/10 -pre_bitfactor prefilter scores are in units of 1 bit / pre_bitfactor (default=4)[] Overfull \hbox (24.02524pt too wide) in paragraph at lines 1713--1713 [] \OT1/cmtt/m/n/10 -pre_gap_open gap open penalty in prefilter Smi th-Waterman alignment (default=20)[] Overfull \hbox (29.27519pt too wide) in paragraph at lines 1713--1713 [] \OT1/cmtt/m/n/10 -pre_gap_extend gap extend penalty in prefilter S mith-Waterman alignment (default=4)[] Overfull \hbox (55.52496pt too wide) in paragraph at lines 1713--1713 [] \OT1/cmtt/m/n/10 -pre_score_offset offset on sequence profile scores in prefilter S-W alignment (default=50)[] [35] Overfull \hbox (45.02505pt too wide) in paragraph at lines 1713--1713 [] \OT1/cmtt/m/n/10 -ovlp banded alignment: forbid larges t diagonals |i-j| of DP matrix (def=0)[] Overfull \hbox (24.02524pt too wide) in paragraph at lines 1713--1713 [] \OT1/cmtt/m/n/10 -alt show up to this many alternative align ments with raw score > smin(def=4)[] Overfull \hbox (29.27519pt too wide) in paragraph at lines 1713--1713 [] \OT1/cmtt/m/n/10 -ssa [0,1] ss confusion matrix = (1-ssa)*I + ssa* psipred-confusion-matrix [def=1.00)[] Overfull \hbox (29.27519pt too wide) in paragraph at lines 1713--1713 [] \OT1/cmtt/m/n/10 -pc_hhm_contxt_mode {0,..,3} position dependence of pc a dmixture 'tau' (pc mode, default=2)[] Overfull \hbox (92.27464pt too wide) in paragraph at lines 1713--1713 [] \OT1/cmtt/m/n/10 Context independent hhm pseudocounts (used for templates; 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u sed for query if contxt file is not available):[] Overfull \hbox (39.7751pt too wide) in paragraph at lines 1844--1844 [] \OT1/cmtt/m/n/10 -pc_hhm_nocontxt_mode {0,..,3} position dependence of pc admixture 'tau' (pc mode, default=2)[] Overfull \hbox (129.02432pt too wide) in paragraph at lines 1844--1844 [] \OT1/cmtt/m/n/10 -contxt context file for computing context-specific pseudocounts (default=${HHLIB}/data/context_data.crf)[] [39] Overfull \hbox (29.27519pt too wide) in paragraph at lines 1943--1943 [] \OT1/cmtt/m/n/10 -pc_hhm_contxt_mode {0,..,3} position dependence of pc a dmixture 'tau' (pc mode, default=0)[] [40] Overfull \hbox (92.27464pt too wide) in paragraph at lines 1943--1943 [] \OT1/cmtt/m/n/10 Context independent hhm pseudocounts (used for templates; u sed for query if contxt file is not available):[] Overfull \hbox (39.7751pt too wide) in paragraph at lines 1943--1943 [] \OT1/cmtt/m/n/10 -pc_hhm_nocontxt_mode {0,..,3} position dependence of pc admixture 'tau' (pc mode, default=2)[] Overfull \hbox (129.02432pt too wide) in paragraph at lines 1943--1943 [] \OT1/cmtt/m/n/10 -contxt context file for computing context-specific pseudocounts (default=${HHLIB}/data/context_data.crf)[] Overfull \hbox (29.27519pt too wide) in paragraph at lines 2003--2003 [] \OT1/cmtt/m/n/10 -oa3m write query alignment in a3m or PSI-BLAST fo rmat (-opsi) to file (default=none)[] Overfull \hbox (76.52478pt too wide) in paragraph at lines 2003--2003 [] \OT1/cmtt/m/n/10 -aa3m append query alignment in a3m (-aa3m) or PSI -BLAST format (-apsi )to file (default=none)[] Overfull \hbox (8.27538pt too wide) in paragraph at lines 2003--2003 [] \OT1/cmtt/m/n/10 -add_cons generate consensus sequence as master sequen ce of query MSA (default=don't)[] [41] [42] [43] LaTeX Warning: Citation `Sali:1993' on page 44 undefined on input line 2101. LaTeX Warning: Citation `Sali:1993' on page 44 undefined on input line 2138. [44] Overfull \hbox (50.27501pt too wide) in paragraph at lines 2215--2215 []\OT1/cmtt/m/n/10 Write files into current directory and name each file by the first word after ">" in the name line.[] Overfull \hbox (50.27501pt too wide) in paragraph at lines 2237--2237 [] \OT1/cmtt/m/n/10 The program reads an input sequence in FASTA/A3M which must have a SCOP domain, PDB chain, or DALI[] [45] Overfull \hbox (50.27501pt too wide) in paragraph at lines 2237--2237 [] \OT1/cmtt/m/n/10 domain identifier (e.g. d1hz4a_, 1hz4_A, or 1hz4A_1). It re ads the corresponding PDB file from the[] Overfull \hbox (39.7751pt too wide) in paragraph at lines 2237--2237 [] \OT1/cmtt/m/n/10 given pdb directory and generates a new PDB file by aligni ng the input sequence to the sequence[] Overfull \hbox (29.27519pt too wide) in paragraph at lines 2237--2237 [] \OT1/cmtt/m/n/10 extracted from the ATOM records of the corresponding pdb ch ain and renumbering the residues in[] Overfull \hbox (24.02524pt too wide) in paragraph at lines 2237--2237 [] \OT1/cmtt/m/n/10 (HETATM records for MSE (selenomethionine) will be interpre ted as ATOM records for MET in the[] LaTeX Warning: Reference `building_dbs' on page 46 undefined on input line 2242 . LaTeX Warning: Reference `building_dbs' on page 46 undefined on input line 2265 . [46] [47] Overfull \hbox (170.34192pt too wide) in paragraph at lines 2357--2359 []\OT1/cmr/m/n/10.95 All er-ror mes-sages are now writ-ten to stderr (not std-o ut) and are of the form [][]\OT1/cmtt/m/n/10.95 Error in : []\OT1/cmr/m/n/10.95 . LaTeX Warning: Citation `Remmert:2011' on page 48 undefined on input line 2386. [48] [49] [50] LaTeX Warning: Citation `Farrar:2007' on page 51 undefined on input line 2548. Underfull \hbox (badness 10000) in paragraph at lines 2573--2581 [51] No file hhsuite-userguide.bbl. [52] (./hhsuite-userguide.aux) LaTeX Warning: There were undefined references. LaTeX Warning: Label(s) may have changed. Rerun to get cross-references right. ) (see the transcript file for additional information) Output written on hhsuite-userguide.pdf (52 pages, 379486 bytes). 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[15] Underfull \hbox (badness 10000) in paragraph at lines 648--649 [16] Overfull \hbox (7.67062pt too wide) in paragraph at lines 697--697 []\OT1/cmtt/m/n/10.95 $ ffindex_order sorting.dat _hhm.ff{data,index} _ hhm_ordered.ff{data,index}[] Overfull \hbox (7.67062pt too wide) in paragraph at lines 697--697 []\OT1/cmtt/m/n/10.95 $ ffindex_order sorting.dat _a3m.ff{data,index} _ a3m_ordered.ff{data,index}[] Overfull \hbox (7.67062pt too wide) in paragraph at lines 717--717 []\OT1/cmtt/m/n/10.95 $ python3 cif2fasta.py -i -o pdb100.fas -c -p pdb_filter.dat[] [17] Overfull \hbox (18.0163pt too wide) in paragraph at lines 738--739 []\OT1/cmr/m/n/10.95 which both were cre-ated by [][]\OT1/cmtt/m/n/10.95 cif2fa sta.py[]\OT1/cmr/m/n/10.95 , and the clus-ter as-sign-ments from MM-Seqs ([][]\ OT1/cmtt/m/n/10.95 pdb70_clu.tsv[]\OT1/cmr/m/n/10.95 ) Overfull \hbox (7.67062pt too wide) in paragraph at lines 769--769 []\OT1/cmtt/m/n/10.95 $ ffindex_order sorting.dat _hhm.ff{data,index} _ hhm_ordered.ff{data,index}[] Overfull \hbox (7.67062pt too wide) in paragraph at lines 769--769 []\OT1/cmtt/m/n/10.95 $ ffindex_order sorting.dat _a3m.ff{data,index} _ a3m_ordered.ff{data,index}[] [18] Overfull \hbox (36.41406pt too wide) in paragraph at lines 784--784 []\OT1/cmtt/m/n/10.95 $ hhsuitedb.py -o --cpu 1 --ia3m= --ics219 = --ihhm=[] LaTeX Warning: Citation `Todd:2001' on page 19 undefined on input line 801. 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[25] Overfull \hbox (116.89569pt too wide) in paragraph at lines 989--989 []\OT1/cmtt/m/n/10.95 Q ss_pred CcEEEeeCCCC-CCCeEEEEEECCeeEEEEEEECC CCcEEEEEEeeCCHHHHHHHHhhCCCccceeEEEecccCCCCCCe[] Overfull \hbox (180.13126pt too wide) in paragraph at lines 989--989 []\OT1/cmtt/m/n/10.95 Q Pr_1 81 GAFLIRESESA-PGDFSLSVKFGNDVQHFKVLRDG AGKYFLWVVKFNSLNELVDYHRSTSVSRNQQIFLRDIEQVPQQPT 159 (217)[] Overfull \hbox (180.13126pt too wide) in paragraph at lines 989--989 []\OT1/cmtt/m/n/10.95 Q Consensus 81 ~~~~~~~~~~~-~~~~~~s~~~~~~~~~~~i~~~~ ~~~~~~~~~~f~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 159 (217)[] Overfull \hbox (116.89569pt too wide) in paragraph at lines 989--989 [] \OT1/cmtt/m/n/10.95 |.+++|.+... ++.+.+ +..++.++|+++.... .+.|+.+...|.++..++.++...+....................[] Overfull \hbox (180.13126pt too wide) in paragraph at lines 989--989 []\OT1/cmtt/m/n/10.95 T Consensus 81 G~flvR~s~~~~~~~~~l-v~~~~~v~h~~i~~~~ ~g~~~~~~~~f~sl~~Lv~~y~~~~~~~~~~~~l~~~~~~~~~~~ 159 (217)[] Overfull \hbox (180.13126pt too wide) in paragraph at lines 989--989 []\OT1/cmtt/m/n/10.95 T 1gri_A 81 GAFLIRESESAPGDFSLS-VKFGNDVQHFKVLRDG AGKYFLWVVKFNSLNELVDYHRSTSVSRNQQIFLRDIEQVPQQPT 159 (217)[] Overfull \hbox (116.89569pt too wide) in paragraph at lines 989--989 []\OT1/cmtt/m/n/10.95 T ss_dssp TCEEEEECSSSTTCEEEE-EEETTEEEEEEEEECS SSCEESSSCEESSHHHHHHHHHHSCSSSSTTCCCCBCCCCCCCCC[] Overfull \hbox (116.89569pt too wide) in paragraph at lines 989--989 []\OT1/cmtt/m/n/10.95 T ss_pred CeEEEEECCCCCCCcEEE-EECCCceeEEEEEECC CCcEEEeeEecCCHHHHHHHhhcCCCccccceeccccccccCCce[] [26] [27] [28] [29] [30] [31] Overfull \hbox (3.64589pt too wide) in paragraph at lines 1363--1363 [][]\OT1/cmr/bx/n/10.95 Secondary struc-ture in-for-ma-tion in A3M/A2M or FASTA MSAs for HH-search/HHblits [32] Overfull \hbox (16.43517pt too wide) in paragraph at lines 1431--1436 \OT1/cmr/m/n/10.95 duced when us-ing HMMER-format, be-cause HM-MER adds more ps eu-do-counts than HH-search/HHblits [33] [34] [35] Overfull \hbox (8.27538pt too wide) in paragraph at lines 1713--1713 [] \OT1/cmtt/m/n/10 -add_cons generate consensus sequence as master sequen ce of query MSA (default=don't)[] Overfull \hbox (8.27538pt too wide) in paragraph at lines 1713--1713 [] \OT1/cmtt/m/n/10 -maxfilt max number of hits allowed to pas s 2nd prefilter (default=20000)[] Overfull \hbox (50.27501pt too wide) in paragraph at lines 1713--1713 [] \OT1/cmtt/m/n/10 -pre_evalue_thresh max E-value threshold of Smith-Wa terman prefilter score (default=1000.0)[] Overfull \hbox (18.77528pt too wide) in paragraph at lines 1713--1713 [] \OT1/cmtt/m/n/10 -pre_bitfactor prefilter scores are in units of 1 bit / pre_bitfactor (default=4)[] Overfull \hbox (24.02524pt too wide) in paragraph at lines 1713--1713 [] \OT1/cmtt/m/n/10 -pre_gap_open gap open penalty in prefilter Smi th-Waterman alignment (default=20)[] Overfull \hbox (29.27519pt too wide) in paragraph at lines 1713--1713 [] \OT1/cmtt/m/n/10 -pre_gap_extend gap extend penalty in prefilter S mith-Waterman alignment (default=4)[] Overfull \hbox (55.52496pt too wide) in paragraph at lines 1713--1713 [] \OT1/cmtt/m/n/10 -pre_score_offset offset on sequence profile scores in prefilter S-W alignment (default=50)[] [36] Overfull \hbox (45.02505pt too wide) in paragraph at lines 1713--1713 [] \OT1/cmtt/m/n/10 -ovlp banded alignment: forbid larges t diagonals |i-j| of DP matrix (def=0)[] Overfull \hbox (24.02524pt too wide) in paragraph at lines 1713--1713 [] \OT1/cmtt/m/n/10 -alt show up to this many alternative align ments with raw score > smin(def=4)[] Overfull \hbox (29.27519pt too wide) in paragraph at lines 1713--1713 [] \OT1/cmtt/m/n/10 -ssa [0,1] ss confusion matrix = (1-ssa)*I + ssa* psipred-confusion-matrix [def=1.00)[] Overfull \hbox (29.27519pt too wide) in paragraph at lines 1713--1713 [] \OT1/cmtt/m/n/10 -pc_hhm_contxt_mode {0,..,3} position dependence of pc a dmixture 'tau' (pc mode, default=2)[] Overfull \hbox (92.27464pt too wide) in paragraph at lines 1713--1713 [] \OT1/cmtt/m/n/10 Context independent hhm pseudocounts (used for templates; u sed for query if contxt file is not available):[] Overfull \hbox (39.7751pt too wide) in paragraph at lines 1713--1713 [] \OT1/cmtt/m/n/10 -pc_hhm_nocontxt_mode {0,..,3} position dependence of pc admixture 'tau' (pc mode, default=2)[] [37] Overfull \hbox (60.77492pt too wide) in paragraph at lines 1713--1713 [] \OT1/cmtt/m/n/10 -pc_prefilter_contxt_mode {0,..,3} position dependence o f pc admixture 'tau' (pc mode, default=3)[] Overfull \hbox (71.27483pt too wide) in paragraph at lines 1713--1713 [] \OT1/cmtt/m/n/10 -pc_prefilter_nocontxt_mode {0,..,3} position dependence of pc admixture 'tau' (pc mode, default=2)[] Overfull \hbox (129.02432pt too wide) in paragraph at lines 1713--1713 [] \OT1/cmtt/m/n/10 -contxt context file for computing context-specific pseudocounts (default=${HHLIB}/data/context_data.crf)[] [38] Overfull \hbox (8.27538pt too wide) in paragraph at lines 1844--1844 [] \OT1/cmtt/m/n/10 -add_cons generate consensus sequence as master sequen ce of query MSA (default=don't)[] Overfull \hbox (39.7751pt too wide) in paragraph at lines 1844--1844 [] \OT1/cmtt/m/n/10 -ovlp banded alignment: forbid largest diagonals |i-j| of DP matrix (def=0)[] Overfull \hbox (18.77528pt too wide) in paragraph at lines 1844--1844 [] \OT1/cmtt/m/n/10 -alt show up to this many alternative alignm ents with raw score > smin(def=4)[] Overfull \hbox (45.02505pt too wide) in paragraph at lines 1844--1844 [] \OT1/cmtt/m/n/10 -ssa [0,1] SS substitution matrix = (1-ssa)*I + ss a*full-SS-substition-matrix [def=1.00)[] [39] Overfull \hbox (29.27519pt too wide) in paragraph at lines 1844--1844 [] \OT1/cmtt/m/n/10 -pc_hhm_contxt_mode {0,..,3} position dependence of pc a dmixture 'tau' (pc mode, default=2)[] Overfull \hbox (92.27464pt too wide) in paragraph at lines 1844--1844 [] \OT1/cmtt/m/n/10 Context independent hhm pseudocounts (used for templates; u sed for query if contxt file is not available):[] Overfull \hbox (39.7751pt too wide) in paragraph at lines 1844--1844 [] \OT1/cmtt/m/n/10 -pc_hhm_nocontxt_mode {0,..,3} position dependence of pc admixture 'tau' (pc mode, default=2)[] Overfull \hbox (129.02432pt too wide) in paragraph at lines 1844--1844 [] \OT1/cmtt/m/n/10 -contxt context file for computing context-specific pseudocounts (default=${HHLIB}/data/context_data.crf)[] [40] Overfull \hbox (29.27519pt too wide) in paragraph at lines 1943--1943 [] \OT1/cmtt/m/n/10 -pc_hhm_contxt_mode {0,..,3} position dependence of pc a dmixture 'tau' (pc mode, default=0)[] [41] Overfull \hbox (92.27464pt too wide) in paragraph at lines 1943--1943 [] \OT1/cmtt/m/n/10 Context independent hhm pseudocounts (used for templates; u sed for query if contxt file is not available):[] Overfull \hbox (39.7751pt too wide) in paragraph at lines 1943--1943 [] \OT1/cmtt/m/n/10 -pc_hhm_nocontxt_mode {0,..,3} position dependence of pc admixture 'tau' (pc mode, default=2)[] Overfull \hbox (129.02432pt too wide) in paragraph at lines 1943--1943 [] \OT1/cmtt/m/n/10 -contxt context file for computing context-specific pseudocounts (default=${HHLIB}/data/context_data.crf)[] Overfull \hbox (29.27519pt too wide) in paragraph at lines 2003--2003 [] \OT1/cmtt/m/n/10 -oa3m write query alignment in a3m or PSI-BLAST fo rmat (-opsi) to file (default=none)[] Overfull \hbox (76.52478pt too wide) in paragraph at lines 2003--2003 [] \OT1/cmtt/m/n/10 -aa3m append query alignment in a3m (-aa3m) or PSI -BLAST format (-apsi )to file (default=none)[] Overfull \hbox (8.27538pt too wide) in paragraph at lines 2003--2003 [] \OT1/cmtt/m/n/10 -add_cons generate consensus sequence as master sequen ce of query MSA (default=don't)[] [42] [43] [44] LaTeX Warning: Citation `Sali:1993' on page 45 undefined on input line 2101. LaTeX Warning: Citation `Sali:1993' on page 45 undefined on input line 2138. [45] Overfull \hbox (50.27501pt too wide) in paragraph at lines 2215--2215 []\OT1/cmtt/m/n/10 Write files into current directory and name each file by the first word after ">" in the name line.[] Overfull \hbox (50.27501pt too wide) in paragraph at lines 2237--2237 [] \OT1/cmtt/m/n/10 The program reads an input sequence in FASTA/A3M which must have a SCOP domain, PDB chain, or DALI[] [46] Overfull \hbox (50.27501pt too wide) in paragraph at lines 2237--2237 [] \OT1/cmtt/m/n/10 domain identifier (e.g. d1hz4a_, 1hz4_A, or 1hz4A_1). It re ads the corresponding PDB file from the[] Overfull \hbox (39.7751pt too wide) in paragraph at lines 2237--2237 [] \OT1/cmtt/m/n/10 given pdb directory and generates a new PDB file by aligni ng the input sequence to the sequence[] Overfull \hbox (29.27519pt too wide) in paragraph at lines 2237--2237 [] \OT1/cmtt/m/n/10 extracted from the ATOM records of the corresponding pdb ch ain and renumbering the residues in[] Overfull \hbox (24.02524pt too wide) in paragraph at lines 2237--2237 [] \OT1/cmtt/m/n/10 (HETATM records for MSE (selenomethionine) will be interpre ted as ATOM records for MET in the[] [47] [48] Overfull \hbox (170.34192pt too wide) in paragraph at lines 2357--2359 []\OT1/cmr/m/n/10.95 All er-ror mes-sages are now writ-ten to stderr (not std-o ut) and are of the form [][]\OT1/cmtt/m/n/10.95 Error in : []\OT1/cmr/m/n/10.95 . LaTeX Warning: Citation `Remmert:2011' on page 49 undefined on input line 2386. [49] [50] [51] LaTeX Warning: Citation `Farrar:2007' on page 52 undefined on input line 2548. Underfull \hbox (badness 10000) in paragraph at lines 2573--2581 [52] (./hhsuite-userguide.bbl [53] [54]) [55] (./hhsuite-userguide.aux) LaTeX Warning: There were undefined references. LaTeX Warning: Label(s) may have changed. Rerun to get cross-references right. ) (see the transcript file for additional information) Output written on hhsuite-userguide.pdf (55 pages, 393238 bytes). Transcript written on hhsuite-userguide.log. cd "/<>/hhsuite-3.0~beta3+dfsg/mybuild/doc" && /usr/bin/cmake -E chdir /<>/hhsuite-3.0~beta3+dfsg/mybuild/doc /usr/bin/pdflatex -interaction=nonstopmode hhsuite-userguide.tex This is pdfTeX, Version 3.14159265-2.6-1.40.19 (TeX Live 2019/dev/Debian) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./hhsuite-userguide.tex LaTeX2e <2018-12-01> (/usr/share/texlive/texmf-dist/tex/latex/base/article.cls Document Class: article 2018/09/03 v1.4i Standard LaTeX document class (/usr/share/texlive/texmf-dist/tex/latex/base/size11.clo)) (/usr/share/texlive/texmf-dist/tex/latex/url/url.sty) (/usr/share/texlive/texmf-dist/tex/latex/cite/cite.sty) (/usr/share/texlive/texmf-dist/tex/latex/tools/longtable.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphicx.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphics.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/trig.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/graphics.cfg) (/usr/share/texlive/texmf-dist/tex/latex/graphics-def/pdftex.def))) (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsmath.sty For additional information on amsmath, use the `?' option. (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amstext.sty (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsgen.sty)) (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsbsy.sty) (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsopn.sty)) (/usr/share/texlive/texmf-dist/tex/latex/fancyvrb/fancyvrb.sty Style option: `fancyvrb' v3.1a <2018/11/20> (tvz) (/usr/share/texlive/texmf-dist/tex/latex/xcolor/xcolor.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/color.cfg))) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/bookmark.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/pdfescape.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ltxcmds.sty) (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/pdftexcmds.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/infwarerr.sty) (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifluatex.sty) (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifpdf.sty))) (/usr/share/texlive/texmf-dist/tex/generic/ifxetex/ifxetex.sty) (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifvtex.sty) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/hyperref.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/hobsub-hyperref.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/hobsub-generic.sty)) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/auxhook.sty) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/kvoptions.sty) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/pd1enc.defIn file included from /<>/hhsuite-3.0~beta3+dfsg/src/cs/getopt_pp.cc:22: /<>/hhsuite-3.0~beta3+dfsg/src/cs/getopt_pp.h:353:31: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 353 | void end_of_options() const throw(GetOptEx) { | ^~~~~ /<>/hhsuite-3.0~beta3+dfsg/src/cs/getopt_pp.h:363:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 363 | GETOPT_INLINE GetOpt_pp& operator >> (const _Option& opt) throw(GetOptEx); | ^~~~~ /<>/hhsuite-3.0~beta3+dfsg/src/cs/getopt_pp.h:371:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 371 | const std::string& long_opt) throw(GetOptEx) { | ^~~~~ /<>/hhsuite-3.0~beta3+dfsg/src/cs/getopt_pp.h:386:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 386 | template inline T getopt(char short_opt) throw(GetOptEx) { | ^~~~~ ) (/usr/share/texlive/texmf-dist/tex/latex/latexconfig/hyperref.cfg)) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/hpdftex.def (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/rerunfilecheck.sty))/<>/hhsuite-3.0~beta3+dfsg/src/cs/getopt_pp.cc:115:25: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 115 | const _Option& opt) throw (GetOptEx) { | ^~~~~ (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/bkm-pdftex.def)) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/puenc.def) (./hhsuite-userguide.aux) (/usr/share/texlive/texmf-dist/tex/context/base/mkii/supp-pdf.mkii [Loading MPS to PDF converter (version 2006.09.02).] ) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/epstopdf-base.sty (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/grfext.sty) (/usr/share/texlive/texmf-dist/tex/latex/latexconfig/epstopdf-sys.cfg)) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/nameref.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/gettitlestring.sty)) (/usr/share/texlive/texmf-dist/tex/latex/base/omscmr.fd) Underfull \hbox (badness 10000) in paragraph at lines 69--71 [1{/var/lib/texmf/fonts/map/pdftex/updmap/pdftex.map}] (./hhsuite-userguide.toc [2]) [3] [4] [5] Overfull \hbox (13.45457pt too wide) in paragraph at lines 148--150 []\OT1/cmr/m/n/10.95 However, you may limit the used in-struc-tion set to SSSE3 with the cmake com-pile flag [][]\OT1/cmtt/m/n/10.95 -DHAVE_SSSE3=1 Overfull \hbox (53.66013pt too wide) in paragraph at lines 166--166 []\OT1/cmtt/m/n/10.95 $ wget https://github.com/soedinglab/hh-suite/releases/.. ./hhsuite-3.0-beta.1-Source.tar.gz[] Overfull \hbox (15.30725pt too wide) in paragraph at lines 200--202 []\OT1/cmr/m/n/10.95 Set HH-LIB and paths: In your shell, set the en-vi-ron-men t vari-able HH-LIB to [][]\OT1/cmtt/m/n/10.95 ${INSTALL_BASE_DIR}[]\OT1/cmr/m/n /10.95 , Overfull \hbox (2.56387pt too wide) in paragraph at lines 205--209 \OT1/cmr/m/n/10.95 col-umn state li-brary file [][]\OT1/cmtt/m/n/10.95 cs219.li b []\OT1/cmr/m/n/10.95 and the con-text li-brary file [][]\OT1/cmtt/m/n/10.95 c ontext_data.crf []\OT1/cmr/m/n/10.95 in [][]\OT1/cmtt/m/n/10.95 $HHLIB/data/[]\ OT1/cmr/m/n/10.95 . [6] Underfull \hbox (badness 10000) in paragraph at lines 235--236 Overfull \hbox (30.66537pt too wide) in paragraph at lines 240--240 []\OT1/cmtt/m/n/10.95 $ wget https://github.com/soedinglab/hh-suite/releases/.. ./hhsuite-3.0-beta.1-Linux.rpm[] Underfull \hbox (badness 10000) in paragraph at lines 243--245 [7] Overfull \hbox (82.40356pt too wide) in paragraph at lines 307--307 []\OT1/cmtt/m/n/10.95 $ wget http://wwwuser.gwdg.de/~compbiol/data/hhsuite/data bases/hhsuite_dbs/uniprot20_2015_06.tgz[] [8] [9] [10] [11 <./hhblits-hhsearch.png>] [12] [13] [14] [15] Underfull \hbox (badness 10000) in paragraph at lines 648--649 [16] Overfull \hbox (7.67062pt too wide) in paragraph at lines 697--697 []\OT1/cmtt/m/n/10.95 $ ffindex_order sorting.dat _hhm.ff{data,index} _ hhm_ordered.ff{data,index}[] Overfull \hbox (7.67062pt too wide) in paragraph at lines 697--697 []\OT1/cmtt/m/n/10.95 $ ffindex_order sorting.dat _a3m.ff{data,index} _ a3m_ordered.ff{data,index}[] Overfull \hbox (7.67062pt too wide) in paragraph at lines 717--717 []\OT1/cmtt/m/n/10.95 $ python3 cif2fasta.py -i -o pdb100.fas -c -p pdb_filter.dat[] [17] Overfull \hbox (18.0163pt too wide) in paragraph at lines 738--739 []\OT1/cmr/m/n/10.95 which both were cre-ated by [][]\OT1/cmtt/m/n/10.95 cif2fa sta.py[]\OT1/cmr/m/n/10.95 , and the clus-ter as-sign-ments from MM-Seqs ([][]\ OT1/cmtt/m/n/10.95 pdb70_clu.tsv[]\OT1/cmr/m/n/10.95 ) Overfull \hbox (7.67062pt too wide) in paragraph at lines 769--769 []\OT1/cmtt/m/n/10.95 $ ffindex_order sorting.dat _hhm.ff{data,index} _ hhm_ordered.ff{data,index}[] Overfull \hbox (7.67062pt too wide) in paragraph at lines 769--769 []\OT1/cmtt/m/n/10.95 $ ffindex_order sorting.dat _a3m.ff{data,index} _ a3m_ordered.ff{data,index}[] [18] Overfull \hbox (36.41406pt too wide) in paragraph at lines 784--784 []\OT1/cmtt/m/n/10.95 $ hhsuitedb.py -o --cpu 1 --ia3m= --ics219 = --ihhm=[] [19] [20] [21] [22] [23] [24] [25] Overfull \hbox (116.89569pt too wide) in paragraph at lines 989--989 []\OT1/cmtt/m/n/10.95 Q ss_pred CcEEEeeCCCC-CCCeEEEEEECCeeEEEEEEECC CCcEEEEEEeeCCHHHHHHHHhhCCCccceeEEEecccCCCCCCe[] Overfull \hbox (180.13126pt too wide) in paragraph at lines 989--989 []\OT1/cmtt/m/n/10.95 Q Pr_1 81 GAFLIRESESA-PGDFSLSVKFGNDVQHFKVLRDG AGKYFLWVVKFNSLNELVDYHRSTSVSRNQQIFLRDIEQVPQQPT 159 (217)[] Overfull \hbox (180.13126pt too wide) in paragraph at lines 989--989 []\OT1/cmtt/m/n/10.95 Q Consensus 81 ~~~~~~~~~~~-~~~~~~s~~~~~~~~~~~i~~~~ ~~~~~~~~~~f~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 159 (217)[] Overfull \hbox (116.89569pt too wide) in paragraph at lines 989--989 [] \OT1/cmtt/m/n/10.95 |.+++|.+... ++.+.+ +..++.++|+++.... .+.|+.+...|.++..++.++...+....................[] Overfull \hbox (180.13126pt too wide) in paragraph at lines 989--989 []\OT1/cmtt/m/n/10.95 T Consensus 81 G~flvR~s~~~~~~~~~l-v~~~~~v~h~~i~~~~ ~g~~~~~~~~f~sl~~Lv~~y~~~~~~~~~~~~l~~~~~~~~~~~ 159 (217)[] Overfull \hbox (180.13126pt too wide) in paragraph at lines 989--989 []\OT1/cmtt/m/n/10.95 T 1gri_A 81 GAFLIRESESAPGDFSLS-VKFGNDVQHFKVLRDG AGKYFLWVVKFNSLNELVDYHRSTSVSRNQQIFLRDIEQVPQQPT 159 (217)[] Overfull \hbox (116.89569pt too wide) in paragraph at lines 989--989 []\OT1/cmtt/m/n/10.95 T ss_dssp TCEEEEECSSSTTCEEEE-EEETTEEEEEEEEECS SSCEESSSCEESSHHHHHHHHHHSCSSSSTTCCCCBCCCCCCCCC[] Overfull \hbox (116.89569pt too wide) in paragraph at lines 989--989 []\OT1/cmtt/m/n/10.95 T ss_pred CeEEEEECCCCCCCcEEE-EECCCceeEEEEEECC CCcEEEeeEecCCHHHHHHHhhcCCCccccceeccccccccCCce[] [26] [27] [28] [29] [30] [31] Overfull \hbox (3.64589pt too wide) in paragraph at lines 1363--1363 [][]\OT1/cmr/bx/n/10.95 Secondary struc-ture in-for-ma-tion in A3M/A2M or FASTA MSAs for HH-search/HHblits [32] Overfull \hbox (16.43517pt too wide) in paragraph at lines 1431--1436 \OT1/cmr/m/n/10.95 duced when us-ing HMMER-format, be-cause HM-MER adds more ps eu-do-counts than HH-search/HHblits [33] [34] [35] Overfull \hbox (8.27538pt too wide) in paragraph at lines 1713--1713 [] \OT1/cmtt/m/n/10 -add_cons generate consensus sequence as master sequen ce of query MSA (default=don't)[] Overfull \hbox (8.27538pt too wide) in paragraph at lines 1713--1713 [] \OT1/cmtt/m/n/10 -maxfilt max number of hits allowed to pas s 2nd prefilter (default=20000)[] Overfull \hbox (50.27501pt too wide) in paragraph at lines 1713--1713 [] \OT1/cmtt/m/n/10 -pre_evalue_thresh max E-value threshold of Smith-Wa terman prefilter score (default=1000.0)[] Overfull \hbox (18.77528pt too wide) in paragraph at lines 1713--1713 [] \OT1/cmtt/m/n/10 -pre_bitfactor prefilter scores are in units of 1 bit / pre_bitfactor (default=4)[] Overfull \hbox (24.02524pt too wide) in paragraph at lines 1713--1713 [] \OT1/cmtt/m/n/10 -pre_gap_open gap open penalty in prefilter Smi th-Waterman alignment (default=20)[] Overfull \hbox (29.27519pt too wide) in paragraph at lines 1713--1713 [] \OT1/cmtt/m/n/10 -pre_gap_extend gap extend penalty in prefilter S mith-Waterman alignment (default=4)[] Overfull \hbox (55.52496pt too wide) in paragraph at lines 1713--1713 [] \OT1/cmtt/m/n/10 -pre_score_offset offset on sequence profile scores in prefilter S-W alignment (default=50)[] [36] Overfull \hbox (45.02505pt too wide) in paragraph at lines 1713--1713 [] \OT1/cmtt/m/n/10 -ovlp banded alignment: forbid larges t diagonals |i-j| of DP matrix (def=0)[] Overfull \hbox (24.02524pt too wide) in paragraph at lines 1713--1713 [] \OT1/cmtt/m/n/10 -alt show up to this many alternative align ments with raw score > smin(def=4)[] Overfull \hbox (29.27519pt too wide) in paragraph at lines 1713--1713 [] \OT1/cmtt/m/n/10 -ssa [0,1] ss confusion matrix = (1-ssa)*I + ssa* psipred-confusion-matrix [def=1.00)[] Overfull \hbox (29.27519pt too wide) in paragraph at lines 1713--1713 [] \OT1/cmtt/m/n/10 -pc_hhm_contxt_mode {0,..,3} position dependence of pc a dmixture 'tau' (pc mode, default=2)[] Overfull \hbox (92.27464pt too wide) in paragraph at lines 1713--1713 [] \OT1/cmtt/m/n/10 Context independent hhm pseudocounts (used for templates; u sed for query if contxt file is not available):[] Overfull \hbox (39.7751pt too wide) in paragraph at lines 1713--1713 [] \OT1/cmtt/m/n/10 -pc_hhm_nocontxt_mode {0,..,3} position dependence of pc admixture 'tau' (pc mode, default=2)[] [37] Overfull \hbox (60.77492pt too wide) in paragraph at lines 1713--1713 [] \OT1/cmtt/m/n/10 -pc_prefilter_contxt_mode {0,..,3} position dependence o f pc admixture 'tau' (pc mode, default=3)[] Overfull \hbox (71.27483pt too wide) in paragraph at lines 1713--1713 [] \OT1/cmtt/m/n/10 -pc_prefilter_nocontxt_mode {0,..,3} position dependence of pc admixture 'tau' (pc mode, default=2)[] Overfull \hbox (129.02432pt too wide) in paragraph at lines 1713--1713 [] \OT1/cmtt/m/n/10 -contxt context file for computing context-specific pseudocounts (default=${HHLIB}/data/context_data.crf)[] [38] Overfull \hbox (8.27538pt too wide) in paragraph at lines 1844--1844 [] \OT1/cmtt/m/n/10 -add_cons generate consensus sequence as master sequen ce of query MSA (default=don't)[] Overfull \hbox (39.7751pt too wide) in paragraph at lines 1844--1844 [] \OT1/cmtt/m/n/10 -ovlp banded alignment: forbid largest diagonals |i-j| of DP matrix (def=0)[] Overfull \hbox (18.77528pt too wide) in paragraph at lines 1844--1844 [] \OT1/cmtt/m/n/10 -alt show up to this many alternative alignm ents with raw score > smin(def=4)[] Overfull \hbox (45.02505pt too wide) in paragraph at lines 1844--1844 [] \OT1/cmtt/m/n/10 -ssa [0,1] SS substitution matrix = (1-ssa)*I + ss a*full-SS-substition-matrix [def=1.00)[] [39] Overfull \hbox (29.27519pt too wide) in paragraph at lines 1844--1844 [] \OT1/cmtt/m/n/10 -pc_hhm_contxt_mode {0,..,3} position dependence of pc a dmixture 'tau' (pc mode, default=2)[] Overfull \hbox (92.27464pt too wide) in paragraph at lines 1844--1844 [] \OT1/cmtt/m/n/10 Context independent hhm pseudocounts (used for templates; u sed for query if contxt file is not available):[] Overfull \hbox (39.7751pt too wide) in paragraph at lines 1844--1844 [] \OT1/cmtt/m/n/10 -pc_hhm_nocontxt_mode {0,..,3} position dependence of pc admixture 'tau' (pc mode, default=2)[] Overfull \hbox (129.02432pt too wide) in paragraph at lines 1844--1844 [] \OT1/cmtt/m/n/10 -contxt context file for computing context-specific pseudocounts (default=${HHLIB}/data/context_data.crf)[] [40] Overfull \hbox (29.27519pt too wide) in paragraph at lines 1943--1943 [] \OT1/cmtt/m/n/10 -pc_hhm_contxt_mode {0,..,3} position dependence of pc a dmixture 'tau' (pc mode, default=0)[] [41] Overfull \hbox (92.27464pt too wide) in paragraph at lines 1943--1943 [] \OT1/cmtt/m/n/10 Context independent hhm pseudocounts (used for templates; u sed for query if contxt file is not available):[] Overfull \hbox (39.7751pt too wide) in paragraph at lines 1943--1943 [] \OT1/cmtt/m/n/10 -pc_hhm_nocontxt_mode {0,..,3} position dependence of pc admixture 'tau' (pc mode, default=2)[] Overfull \hbox (129.02432pt too wide) in paragraph at lines 1943--1943 [] \OT1/cmtt/m/n/10 -contxt context file for computing context-specific pseudocounts (default=${HHLIB}/data/context_data.crf)[] Overfull \hbox (29.27519pt too wide) in paragraph at lines 2003--2003 [] \OT1/cmtt/m/n/10 -oa3m write query alignment in a3m or PSI-BLAST fo rmat (-opsi) to file (default=none)[] Overfull \hbox (76.52478pt too wide) in paragraph at lines 2003--2003 [] \OT1/cmtt/m/n/10 -aa3m append query alignment in a3m (-aa3m) or PSI -BLAST format (-apsi )to file (default=none)[] Overfull \hbox (8.27538pt too wide) in paragraph at lines 2003--2003 [] \OT1/cmtt/m/n/10 -add_cons generate consensus sequence as master sequen ce of query MSA (default=don't)[] [42] [43] [44] [45] Overfull \hbox (50.27501pt too wide) in paragraph at lines 2215--2215 []\OT1/cmtt/m/n/10 Write files into current directory and name each file by the first word after ">" in the name line.[] Overfull \hbox (50.27501pt too wide) in paragraph at lines 2237--2237 [] \OT1/cmtt/m/n/10 The program reads an input sequence in FASTA/A3M which must have a SCOP domain, PDB chain, or DALI[] [46] Overfull \hbox (50.27501pt too wide) in paragraph at lines 2237--2237 [] \OT1/cmtt/m/n/10 domain identifier (e.g. d1hz4a_, 1hz4_A, or 1hz4A_1). It re ads the corresponding PDB file from the[] Overfull \hbox (39.7751pt too wide) in paragraph at lines 2237--2237 [] \OT1/cmtt/m/n/10 given pdb directory and generates a new PDB file by aligni ng the input sequence to the sequence[] Overfull \hbox (29.27519pt too wide) in paragraph at lines 2237--2237 [] \OT1/cmtt/m/n/10 extracted from the ATOM records of the corresponding pdb ch ain and renumbering the residues in[] Overfull \hbox (24.02524pt too wide) in paragraph at lines 2237--2237 [] \OT1/cmtt/m/n/10 (HETATM records for MSE (selenomethionine) will be interpre ted as ATOM records for MET in the[] [47] [48] Overfull \hbox (170.34192pt too wide) in paragraph at lines 2357--2359 []\OT1/cmr/m/n/10.95 All er-ror mes-sages are now writ-ten to stderr (not std-o ut) and are of the form [][]\OT1/cmtt/m/n/10.95 Error in : []\OT1/cmr/m/n/10.95 . [49] [50] [51] Underfull \hbox (badness 10000) in paragraph at lines 2573--2581 [52] (./hhsuite-userguide.bbl [53] [54]) [55] (./hhsuite-userguide.aux) ) (see the transcript file for additional information) Output written on hhsuite-userguide.pdf (55 pages, 394812 bytes). Transcript written on hhsuite-userguide.log. make[4]: Leaving directory '/<>/hhsuite-3.0~beta3+dfsg/mybuild' [ 23%] Built target pdf [ 24%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhhit.cpp.o cd "/<>/hhsuite-3.0~beta3+dfsg/mybuild/src" && /usr/bin/c++ -DOPENMP -DSSE -I"/<>/hhsuite-3.0~beta3+dfsg/src" -I"/<>/hhsuite-3.0~beta3+dfsg/src/cs" -I"/<>/hhsuite-3.0~beta3+dfsg/mybuild" -g -O2 -fdebug-prefix-map=/<>/hhsuite-3.0~beta3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -march=native -msse4.2 -mfpmath=sse -fopenmp -fno-strict-aliasing -o CMakeFiles/HH_OBJECTS.dir/hhhit.cpp.o -c "/<>/hhsuite-3.0~beta3+dfsg/src/hhhit.cpp" [ 26%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhmatrices.cpp.o cd "/<>/hhsuite-3.0~beta3+dfsg/mybuild/src" && /usr/bin/c++ -DOPENMP -DSSE -I"/<>/hhsuite-3.0~beta3+dfsg/src" -I"/<>/hhsuite-3.0~beta3+dfsg/src/cs" -I"/<>/hhsuite-3.0~beta3+dfsg/mybuild" -g -O2 -fdebug-prefix-map=/<>/hhsuite-3.0~beta3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -march=native -msse4.2 -mfpmath=sse -fopenmp -fno-strict-aliasing -o CMakeFiles/HH_OBJECTS.dir/hhmatrices.cpp.o -c "/<>/hhsuite-3.0~beta3+dfsg/src/hhmatrices.cpp" [ 27%] Building CXX object src/CMakeFiles/CS_OBJECTS.dir/cs/log.cc.o cd "/<>/hhsuite-3.0~beta3+dfsg/mybuild/src" && /usr/bin/c++ -DOPENMP -DSSE -I"/<>/hhsuite-3.0~beta3+dfsg/src" -I"/<>/hhsuite-3.0~beta3+dfsg/src/cs" -I"/<>/hhsuite-3.0~beta3+dfsg/mybuild" -g -O2 -fdebug-prefix-map=/<>/hhsuite-3.0~beta3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -march=native -msse4.2 -mfpmath=sse -fopenmp -fno-strict-aliasing -o CMakeFiles/CS_OBJECTS.dir/cs/log.cc.o -c "/<>/hhsuite-3.0~beta3+dfsg/src/cs/log.cc" [ 28%] Building CXX object src/CMakeFiles/CS_OBJECTS.dir/cs/application.cc.o cd "/<>/hhsuite-3.0~beta3+dfsg/mybuild/src" && /usr/bin/c++ -DOPENMP -DSSE -I"/<>/hhsuite-3.0~beta3+dfsg/src" -I"/<>/hhsuite-3.0~beta3+dfsg/src/cs" -I"/<>/hhsuite-3.0~beta3+dfsg/mybuild" -g -O2 -fdebug-prefix-map=/<>/hhsuite-3.0~beta3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -march=native -msse4.2 -mfpmath=sse -fopenmp -fno-strict-aliasing -o CMakeFiles/CS_OBJECTS.dir/cs/application.cc.o -c "/<>/hhsuite-3.0~beta3+dfsg/src/cs/application.cc" [ 30%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhsearch.cpp.o cd "/<>/hhsuite-3.0~beta3+dfsg/mybuild/src" && /usr/bin/c++ -DOPENMP -DSSE -I"/<>/hhsuite-3.0~beta3+dfsg/src" -I"/<>/hhsuite-3.0~beta3+dfsg/src/cs" -I"/<>/hhsuite-3.0~beta3+dfsg/mybuild" -g -O2 -fdebug-prefix-map=/<>/hhsuite-3.0~beta3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -march=native -msse4.2 -mfpmath=sse -fopenmp -fno-strict-aliasing -o CMakeFiles/HH_OBJECTS.dir/hhsearch.cpp.o -c "/<>/hhsuite-3.0~beta3+dfsg/src/hhsearch.cpp" [ 31%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhalign.cpp.o cd "/<>/hhsuite-3.0~beta3+dfsg/mybuild/src" && /usr/bin/c++ -DOPENMP -DSSE -I"/<>/hhsuite-3.0~beta3+dfsg/src" -I"/<>/hhsuite-3.0~beta3+dfsg/src/cs" -I"/<>/hhsuite-3.0~beta3+dfsg/mybuild" -g -O2 -fdebug-prefix-map=/<>/hhsuite-3.0~beta3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -march=native -msse4.2 -mfpmath=sse -fopenmp -fno-strict-aliasing -o CMakeFiles/HH_OBJECTS.dir/hhalign.cpp.o -c "/<>/hhsuite-3.0~beta3+dfsg/src/hhalign.cpp" In file included from /<>/hhsuite-3.0~beta3+dfsg/src/cs/application.h:29, from /<>/hhsuite-3.0~beta3+dfsg/src/cs/application.cc:21: /<>/hhsuite-3.0~beta3+dfsg/src/cs/getopt_pp.h:353:31: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 353 | void end_of_options() const throw(GetOptEx) { | ^~~~~ /<>/hhsuite-3.0~beta3+dfsg/src/cs/getopt_pp.h:363:61: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 363 | GETOPT_INLINE GetOpt_pp& operator >> (const _Option& opt) throw(GetOptEx); | ^~~~~ /<>/hhsuite-3.0~beta3+dfsg/src/cs/getopt_pp.h:371:67: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 371 | const std::string& long_opt) throw(GetOptEx) { | ^~~~~ /<>/hhsuite-3.0~beta3+dfsg/src/cs/getopt_pp.h:386:54: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 386 | template inline T getopt(char short_opt) throw(GetOptEx) { | ^~~~~ make[4]: Leaving directory '/<>/hhsuite-3.0~beta3+dfsg/mybuild' [ 31%] Built target CS_OBJECTS [ 33%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhhitlist.cpp.o cd "/<>/hhsuite-3.0~beta3+dfsg/mybuild/src" && /usr/bin/c++ -DOPENMP -DSSE -I"/<>/hhsuite-3.0~beta3+dfsg/src" -I"/<>/hhsuite-3.0~beta3+dfsg/src/cs" -I"/<>/hhsuite-3.0~beta3+dfsg/mybuild" -g -O2 -fdebug-prefix-map=/<>/hhsuite-3.0~beta3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -march=native -msse4.2 -mfpmath=sse -fopenmp -fno-strict-aliasing -o CMakeFiles/HH_OBJECTS.dir/hhhitlist.cpp.o -c "/<>/hhsuite-3.0~beta3+dfsg/src/hhhitlist.cpp" [ 34%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhposteriordecoder.cpp.o cd "/<>/hhsuite-3.0~beta3+dfsg/mybuild/src" && /usr/bin/c++ -DOPENMP -DSSE -I"/<>/hhsuite-3.0~beta3+dfsg/src" -I"/<>/hhsuite-3.0~beta3+dfsg/src/cs" -I"/<>/hhsuite-3.0~beta3+dfsg/mybuild" -g -O2 -fdebug-prefix-map=/<>/hhsuite-3.0~beta3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -march=native -msse4.2 -mfpmath=sse -fopenmp -fno-strict-aliasing -o CMakeFiles/HH_OBJECTS.dir/hhposteriordecoder.cpp.o -c "/<>/hhsuite-3.0~beta3+dfsg/src/hhposteriordecoder.cpp" [ 36%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhutil.cpp.o cd "/<>/hhsuite-3.0~beta3+dfsg/mybuild/src" && /usr/bin/c++ -DOPENMP -DSSE -I"/<>/hhsuite-3.0~beta3+dfsg/src" -I"/<>/hhsuite-3.0~beta3+dfsg/src/cs" -I"/<>/hhsuite-3.0~beta3+dfsg/mybuild" -g -O2 -fdebug-prefix-map=/<>/hhsuite-3.0~beta3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -march=native -msse4.2 -mfpmath=sse -fopenmp -fno-strict-aliasing -o CMakeFiles/HH_OBJECTS.dir/hhutil.cpp.o -c "/<>/hhsuite-3.0~beta3+dfsg/src/hhutil.cpp" [ 37%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/util.cpp.o cd "/<>/hhsuite-3.0~beta3+dfsg/mybuild/src" && /usr/bin/c++ -DOPENMP -DSSE -I"/<>/hhsuite-3.0~beta3+dfsg/src" -I"/<>/hhsuite-3.0~beta3+dfsg/src/cs" -I"/<>/hhsuite-3.0~beta3+dfsg/mybuild" -g -O2 -fdebug-prefix-map=/<>/hhsuite-3.0~beta3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -march=native -msse4.2 -mfpmath=sse -fopenmp -fno-strict-aliasing -o CMakeFiles/HH_OBJECTS.dir/util.cpp.o -c "/<>/hhsuite-3.0~beta3+dfsg/src/util.cpp" [ 39%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhalignment.cpp.o cd "/<>/hhsuite-3.0~beta3+dfsg/mybuild/src" && /usr/bin/c++ -DOPENMP -DSSE -I"/<>/hhsuite-3.0~beta3+dfsg/src" -I"/<>/hhsuite-3.0~beta3+dfsg/src/cs" -I"/<>/hhsuite-3.0~beta3+dfsg/mybuild" -g -O2 -fdebug-prefix-map=/<>/hhsuite-3.0~beta3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -march=native -msse4.2 -mfpmath=sse -fopenmp -fno-strict-aliasing -o CMakeFiles/HH_OBJECTS.dir/hhalignment.cpp.o -c "/<>/hhsuite-3.0~beta3+dfsg/src/hhalignment.cpp" [ 40%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhforwardalgorithm.cpp.o cd "/<>/hhsuite-3.0~beta3+dfsg/mybuild/src" && /usr/bin/c++ -DOPENMP -DSSE -I"/<>/hhsuite-3.0~beta3+dfsg/src" -I"/<>/hhsuite-3.0~beta3+dfsg/src/cs" -I"/<>/hhsuite-3.0~beta3+dfsg/mybuild" -g -O2 -fdebug-prefix-map=/<>/hhsuite-3.0~beta3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -march=native -msse4.2 -mfpmath=sse -fopenmp -fno-strict-aliasing -o CMakeFiles/HH_OBJECTS.dir/hhforwardalgorithm.cpp.o -c "/<>/hhsuite-3.0~beta3+dfsg/src/hhforwardalgorithm.cpp" [ 42%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhhmm.cpp.o cd "/<>/hhsuite-3.0~beta3+dfsg/mybuild/src" && /usr/bin/c++ -DOPENMP -DSSE -I"/<>/hhsuite-3.0~beta3+dfsg/src" -I"/<>/hhsuite-3.0~beta3+dfsg/src/cs" -I"/<>/hhsuite-3.0~beta3+dfsg/mybuild" -g -O2 -fdebug-prefix-map=/<>/hhsuite-3.0~beta3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -march=native -msse4.2 -mfpmath=sse -fopenmp -fno-strict-aliasing -o CMakeFiles/HH_OBJECTS.dir/hhhmm.cpp.o -c "/<>/hhsuite-3.0~beta3+dfsg/src/hhhmm.cpp" [ 43%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhposteriordecoderrunner.cpp.o cd "/<>/hhsuite-3.0~beta3+dfsg/mybuild/src" && /usr/bin/c++ -DOPENMP -DSSE -I"/<>/hhsuite-3.0~beta3+dfsg/src" -I"/<>/hhsuite-3.0~beta3+dfsg/src/cs" -I"/<>/hhsuite-3.0~beta3+dfsg/mybuild" -g -O2 -fdebug-prefix-map=/<>/hhsuite-3.0~beta3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -march=native -msse4.2 -mfpmath=sse -fopenmp -fno-strict-aliasing -o CMakeFiles/HH_OBJECTS.dir/hhposteriordecoderrunner.cpp.o -c "/<>/hhsuite-3.0~beta3+dfsg/src/hhposteriordecoderrunner.cpp" /<>/hhsuite-3.0~beta3+dfsg/src/hhalignment.cpp: In member function ‘int Alignment::Filter2(char*, int, int, float, int, int, int, const float (*)[20])’: /<>/hhsuite-3.0~beta3+dfsg/src/hhalignment.cpp:1797:39: warning: ‘%s’ directive writing up to 4095 bytes into a region of size 86 [-Wformat-overflow=] 1797 | sprintf(details, "The alingment %s does not contain any sequences.", | ^~ In file included from /usr/include/stdio.h:873, from /usr/include/c++/9/cstdio:42, from /usr/include/c++/9/ext/string_conversions.h:43, from /usr/include/c++/9/bits/basic_string.h:6464, from /usr/include/c++/9/string:55, from /usr/include/c++/9/bits/locale_classes.h:40, from /usr/include/c++/9/bits/ios_base.h:41, from /usr/include/c++/9/ios:42, from /usr/include/c++/9/ostream:38, from /usr/include/c++/9/iostream:39, from /<>/hhsuite-3.0~beta3+dfsg/src/hhalignment.h:3, from /<>/hhsuite-3.0~beta3+dfsg/src/hhalignment.cpp:8: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:34: note: ‘__builtin___sprintf_chk’ output between 47 and 4142 bytes into a destination of size 100 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 44%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhviterbialgorithm.cpp.o cd "/<>/hhsuite-3.0~beta3+dfsg/mybuild/src" && /usr/bin/c++ -DOPENMP -DSSE -I"/<>/hhsuite-3.0~beta3+dfsg/src" -I"/<>/hhsuite-3.0~beta3+dfsg/src/cs" -I"/<>/hhsuite-3.0~beta3+dfsg/mybuild" -g -O2 -fdebug-prefix-map=/<>/hhsuite-3.0~beta3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -march=native -msse4.2 -mfpmath=sse -fopenmp -fno-strict-aliasing -o CMakeFiles/HH_OBJECTS.dir/hhviterbialgorithm.cpp.o -c "/<>/hhsuite-3.0~beta3+dfsg/src/hhviterbialgorithm.cpp" [ 46%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhfullalignment.cpp.o cd "/<>/hhsuite-3.0~beta3+dfsg/mybuild/src" && /usr/bin/c++ -DOPENMP -DSSE -I"/<>/hhsuite-3.0~beta3+dfsg/src" -I"/<>/hhsuite-3.0~beta3+dfsg/src/cs" -I"/<>/hhsuite-3.0~beta3+dfsg/mybuild" -g -O2 -fdebug-prefix-map=/<>/hhsuite-3.0~beta3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -march=native -msse4.2 -mfpmath=sse -fopenmp -fno-strict-aliasing -o CMakeFiles/HH_OBJECTS.dir/hhfullalignment.cpp.o -c "/<>/hhsuite-3.0~beta3+dfsg/src/hhfullalignment.cpp" [ 47%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhhmmsimd.cpp.o cd "/<>/hhsuite-3.0~beta3+dfsg/mybuild/src" && /usr/bin/c++ -DOPENMP -DSSE -I"/<>/hhsuite-3.0~beta3+dfsg/src" -I"/<>/hhsuite-3.0~beta3+dfsg/src/cs" -I"/<>/hhsuite-3.0~beta3+dfsg/mybuild" -g -O2 -fdebug-prefix-map=/<>/hhsuite-3.0~beta3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -march=native -msse4.2 -mfpmath=sse -fopenmp -fno-strict-aliasing -o CMakeFiles/HH_OBJECTS.dir/hhhmmsimd.cpp.o -c "/<>/hhsuite-3.0~beta3+dfsg/src/hhhmmsimd.cpp" [ 49%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhposteriormatrix.cpp.o cd "/<>/hhsuite-3.0~beta3+dfsg/mybuild/src" && /usr/bin/c++ -DOPENMP -DSSE -I"/<>/hhsuite-3.0~beta3+dfsg/src" -I"/<>/hhsuite-3.0~beta3+dfsg/src/cs" -I"/<>/hhsuite-3.0~beta3+dfsg/mybuild" -g -O2 -fdebug-prefix-map=/<>/hhsuite-3.0~beta3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -march=native -msse4.2 -mfpmath=sse -fopenmp -fno-strict-aliasing -o CMakeFiles/HH_OBJECTS.dir/hhposteriormatrix.cpp.o -c "/<>/hhsuite-3.0~beta3+dfsg/src/hhposteriormatrix.cpp" [ 50%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhviterbi.cpp.o cd "/<>/hhsuite-3.0~beta3+dfsg/mybuild/src" && /usr/bin/c++ -DOPENMP -DSSE -I"/<>/hhsuite-3.0~beta3+dfsg/src" -I"/<>/hhsuite-3.0~beta3+dfsg/src/cs" -I"/<>/hhsuite-3.0~beta3+dfsg/mybuild" -g -O2 -fdebug-prefix-map=/<>/hhsuite-3.0~beta3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -march=native -msse4.2 -mfpmath=sse -fopenmp -fno-strict-aliasing -o CMakeFiles/HH_OBJECTS.dir/hhviterbi.cpp.o -c "/<>/hhsuite-3.0~beta3+dfsg/src/hhviterbi.cpp" [ 52%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhbacktracemac.cpp.o cd "/<>/hhsuite-3.0~beta3+dfsg/mybuild/src" && /usr/bin/c++ -DOPENMP -DSSE -I"/<>/hhsuite-3.0~beta3+dfsg/src" -I"/<>/hhsuite-3.0~beta3+dfsg/src/cs" -I"/<>/hhsuite-3.0~beta3+dfsg/mybuild" -g -O2 -fdebug-prefix-map=/<>/hhsuite-3.0~beta3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -march=native -msse4.2 -mfpmath=sse -fopenmp -fno-strict-aliasing -o CMakeFiles/HH_OBJECTS.dir/hhbacktracemac.cpp.o -c "/<>/hhsuite-3.0~beta3+dfsg/src/hhbacktracemac.cpp" [ 53%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhmacalgorithm.cpp.o cd "/<>/hhsuite-3.0~beta3+dfsg/mybuild/src" && /usr/bin/c++ -DOPENMP -DSSE -I"/<>/hhsuite-3.0~beta3+dfsg/src" -I"/<>/hhsuite-3.0~beta3+dfsg/src/cs" -I"/<>/hhsuite-3.0~beta3+dfsg/mybuild" -g -O2 -fdebug-prefix-map=/<>/hhsuite-3.0~beta3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -march=native -msse4.2 -mfpmath=sse -fopenmp -fno-strict-aliasing -o CMakeFiles/HH_OBJECTS.dir/hhmacalgorithm.cpp.o -c "/<>/hhsuite-3.0~beta3+dfsg/src/hhmacalgorithm.cpp" [ 55%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhprefilter.cpp.o cd "/<>/hhsuite-3.0~beta3+dfsg/mybuild/src" && /usr/bin/c++ -DOPENMP -DSSE -I"/<>/hhsuite-3.0~beta3+dfsg/src" -I"/<>/hhsuite-3.0~beta3+dfsg/src/cs" -I"/<>/hhsuite-3.0~beta3+dfsg/mybuild" -g -O2 -fdebug-prefix-map=/<>/hhsuite-3.0~beta3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -march=native -msse4.2 -mfpmath=sse -fopenmp -fno-strict-aliasing -o CMakeFiles/HH_OBJECTS.dir/hhprefilter.cpp.o -c "/<>/hhsuite-3.0~beta3+dfsg/src/hhprefilter.cpp" [ 56%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhviterbimatrix.cpp.o cd "/<>/hhsuite-3.0~beta3+dfsg/mybuild/src" && /usr/bin/c++ -DOPENMP -DSSE -I"/<>/hhsuite-3.0~beta3+dfsg/src" -I"/<>/hhsuite-3.0~beta3+dfsg/src/cs" -I"/<>/hhsuite-3.0~beta3+dfsg/mybuild" -g -O2 -fdebug-prefix-map=/<>/hhsuite-3.0~beta3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -march=native -msse4.2 -mfpmath=sse -fopenmp -fno-strict-aliasing -o CMakeFiles/HH_OBJECTS.dir/hhviterbimatrix.cpp.o -c "/<>/hhsuite-3.0~beta3+dfsg/src/hhviterbimatrix.cpp" [ 57%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhbackwardalgorithm.cpp.o cd "/<>/hhsuite-3.0~beta3+dfsg/mybuild/src" && /usr/bin/c++ -DOPENMP -DSSE -I"/<>/hhsuite-3.0~beta3+dfsg/src" -I"/<>/hhsuite-3.0~beta3+dfsg/src/cs" -I"/<>/hhsuite-3.0~beta3+dfsg/mybuild" -g -O2 -fdebug-prefix-map=/<>/hhsuite-3.0~beta3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -march=native -msse4.2 -mfpmath=sse -fopenmp -fno-strict-aliasing -o CMakeFiles/HH_OBJECTS.dir/hhbackwardalgorithm.cpp.o -c "/<>/hhsuite-3.0~beta3+dfsg/src/hhbackwardalgorithm.cpp" [ 59%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhdatabase.cpp.o cd "/<>/hhsuite-3.0~beta3+dfsg/mybuild/src" && /usr/bin/c++ -DOPENMP -DSSE -I"/<>/hhsuite-3.0~beta3+dfsg/src" -I"/<>/hhsuite-3.0~beta3+dfsg/src/cs" -I"/<>/hhsuite-3.0~beta3+dfsg/mybuild" -g -O2 -fdebug-prefix-map=/<>/hhsuite-3.0~beta3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -march=native -msse4.2 -mfpmath=sse -fopenmp -fno-strict-aliasing -o CMakeFiles/HH_OBJECTS.dir/hhdatabase.cpp.o -c "/<>/hhsuite-3.0~beta3+dfsg/src/hhdatabase.cpp" [ 60%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhhalfalignment.cpp.o cd "/<>/hhsuite-3.0~beta3+dfsg/mybuild/src" && /usr/bin/c++ -DOPENMP -DSSE -I"/<>/hhsuite-3.0~beta3+dfsg/src" -I"/<>/hhsuite-3.0~beta3+dfsg/src/cs" -I"/<>/hhsuite-3.0~beta3+dfsg/mybuild" -g -O2 -fdebug-prefix-map=/<>/hhsuite-3.0~beta3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -march=native -msse4.2 -mfpmath=sse -fopenmp -fno-strict-aliasing -o CMakeFiles/HH_OBJECTS.dir/hhhalfalignment.cpp.o -c "/<>/hhsuite-3.0~beta3+dfsg/src/hhhalfalignment.cpp" [ 62%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhviterbirunner.cpp.o cd "/<>/hhsuite-3.0~beta3+dfsg/mybuild/src" && /usr/bin/c++ -DOPENMP -DSSE -I"/<>/hhsuite-3.0~beta3+dfsg/src" -I"/<>/hhsuite-3.0~beta3+dfsg/src/cs" -I"/<>/hhsuite-3.0~beta3+dfsg/mybuild" -g -O2 -fdebug-prefix-map=/<>/hhsuite-3.0~beta3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -march=native -msse4.2 -mfpmath=sse -fopenmp -fno-strict-aliasing -o CMakeFiles/HH_OBJECTS.dir/hhviterbirunner.cpp.o -c "/<>/hhsuite-3.0~beta3+dfsg/src/hhviterbirunner.cpp" [ 63%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhfunc.cpp.o cd "/<>/hhsuite-3.0~beta3+dfsg/mybuild/src" && /usr/bin/c++ -DOPENMP -DSSE -I"/<>/hhsuite-3.0~beta3+dfsg/src" -I"/<>/hhsuite-3.0~beta3+dfsg/src/cs" -I"/<>/hhsuite-3.0~beta3+dfsg/mybuild" -g -O2 -fdebug-prefix-map=/<>/hhsuite-3.0~beta3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -march=native -msse4.2 -mfpmath=sse -fopenmp -fno-strict-aliasing -o CMakeFiles/HH_OBJECTS.dir/hhfunc.cpp.o -c "/<>/hhsuite-3.0~beta3+dfsg/src/hhfunc.cpp" make[4]: Leaving directory '/<>/hhsuite-3.0~beta3+dfsg/mybuild' [ 63%] Built target HH_OBJECTS make[3]: Leaving directory '/<>/hhsuite-3.0~beta3+dfsg/mybuild' make[2]: *** [Makefile:166: all] Error 2 make[2]: Leaving directory '/<>/hhsuite-3.0~beta3+dfsg/mybuild' dh_auto_build: cd mybuild && make V=1 -j4 NO_PNG=1 returned exit code 2 make[1]: *** [debian/rules:39: override_dh_auto_build] Error 2 make[1]: Leaving directory '/<>/hhsuite-3.0~beta3+dfsg' make: *** [debian/rules:42: build] Error 2 dpkg-buildpackage: error: debian/rules build subprocess returned exit status 2 -------------------------------------------------------------------------------- Build finished at 20190109-0316 Finished -------- E: Build failure (dpkg-buildpackage died) +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not removing build depends: as requested +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: amd64 Build-Space: 60564 Build-Time: 40 Distribution: disco Fail-Stage: build Host Architecture: amd64 Install-Time: 35 Job: hhsuite_3.0~beta3+dfsg-1.dsc Machine Architecture: amd64 Package: hhsuite Package-Time: 78 Source-Version: 3.0~beta3+dfsg-1 Space: 60564 Status: attempted Version: 3.0~beta3+dfsg-1 -------------------------------------------------------------------------------- Finished at 20190109-0316 Build needed 00:01:18, 60564k disc space RUN: /usr/share/launchpad-buildd/slavebin/in-target scan-for-processes --backend=chroot --series=disco --arch=amd64 PACKAGEBUILD-15930158 Scanning for processes to kill in build PACKAGEBUILD-15930158