DC-Build-Header: hhsuite 3.0~beta2+dfsg-3 / 2017-07-06 20:54:47 +0000 DC-Task: type:rebuild-binarch-only source:hhsuite version:3.0~beta2+dfsg-3 chroot:unstable esttime:97 logfile:/tmp/hhsuite_3.0~beta2+dfsg-3_unstable_clang4.0.log modes:clang40:binarch-only DC-Sbuild-call: su user42 -c 'sbuild -n --arch-any --apt-update -d unstable -v --chroot-setup-commands=/tmp/clang40 hhsuite_3.0~beta2+dfsg-3' sbuild (Debian sbuild) 0.73.0 (23 Dec 2016) on ip-172-31-36-161.eu-central-1.compute.internal +==============================================================================+ | hhsuite 3.0~beta2+dfsg-3 (amd64) Thu, 06 Jul 2017 20:54:48 +0000 | +==============================================================================+ Package: hhsuite Version: 3.0~beta2+dfsg-3 Source Version: 3.0~beta2+dfsg-3 Distribution: unstable Machine Architecture: amd64 Host Architecture: amd64 Build Architecture: amd64 Build Type: any I: NOTICE: Log filtering will replace 'var/run/schroot/mount/unstable-amd64-sbuild-68f3b218-256a-4a67-bffa-b39c6dddb910' with '<>' +------------------------------------------------------------------------------+ | Chroot Setup Commands | +------------------------------------------------------------------------------+ /tmp/clang40 ------------ + echo 'Entering customization script...' Entering customization script... + CLANG_VERSION=4.0 + echo 'Install of clang-4.0' Install of clang-4.0 + apt-get update Get:1 http://127.0.0.1:9999/debian unstable InRelease [255 kB] Get:2 http://127.0.0.1:9999/debian unstable/main Sources.diff/Index [27.9 kB] Get:3 http://127.0.0.1:9999/debian unstable/main amd64 Packages.diff/Index [27.9 kB] Get:4 http://127.0.0.1:9999/debian unstable/main Translation-en.diff/Index [27.9 kB] Get:5 http://127.0.0.1:9999/debian unstable/main Sources 2017-07-02-0216.39.pdiff [15.0 kB] Get:6 http://127.0.0.1:9999/debian unstable/main Sources 2017-07-02-0817.00.pdiff [7416 B] Get:7 http://127.0.0.1:9999/debian unstable/main Sources 2017-07-02-1415.16.pdiff [17.0 kB] Get:8 http://127.0.0.1:9999/debian unstable/main Sources 2017-07-02-2015.53.pdiff [15.2 kB] Get:9 http://127.0.0.1:9999/debian unstable/main Sources 2017-07-03-0215.43.pdiff [50.2 kB] Get:10 http://127.0.0.1:9999/debian unstable/main Sources 2017-07-03-0815.58.pdiff [5500 B] Get:11 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2017-07-04-1416.28.pdiff [484 B] Get:50 http://127.0.0.1:9999/debian unstable/main Translation-en 2017-07-04-2017.16.pdiff [1126 B] Get:51 http://127.0.0.1:9999/debian unstable/main Translation-en 2017-07-05-0215.45.pdiff [214 B] Get:52 http://127.0.0.1:9999/debian unstable/main Translation-en 2017-07-05-0817.10.pdiff [606 B] Get:53 http://127.0.0.1:9999/debian unstable/main Translation-en 2017-07-05-1416.09.pdiff [214 B] Get:54 http://127.0.0.1:9999/debian unstable/main Translation-en 2017-07-05-2019.56.pdiff [2615 B] Get:55 http://127.0.0.1:9999/debian unstable/main Translation-en 2017-07-06-0216.07.pdiff [1869 B] Get:56 http://127.0.0.1:9999/debian unstable/main Translation-en 2017-07-06-0817.23.pdiff [915 B] Get:56 http://127.0.0.1:9999/debian unstable/main Translation-en 2017-07-06-0817.23.pdiff [915 B] Fetched 974 kB in 1s (760 kB/s) Reading package lists... + apt-get install --yes --no-install-recommends --force-yes clang-4.0 Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: cpp-6 g++-6 gcc-6 gcc-6-base gcc-7-base libasan3 libatomic1 libbsd0 libcc1-0 libcilkrts5 libclang-common-4.0-dev libclang1-4.0 libedit2 libffi6 libgcc-6-dev libgcc1 libgomp1 libitm1 libjsoncpp1 libllvm4.0 liblsan0 libmpx2 libncurses5 libobjc-6-dev libobjc4 libquadmath0 libstdc++-6-dev libstdc++6 libtsan0 libubsan0 Suggested packages: gnustep gnustep-devel clang-4.0-doc libomp-dev gcc-6-locales g++-6-multilib gcc-6-doc libstdc++6-6-dbg gcc-6-multilib libgcc1-dbg libgomp1-dbg libitm1-dbg libatomic1-dbg libasan3-dbg liblsan0-dbg libtsan0-dbg libubsan0-dbg libcilkrts5-dbg libmpx2-dbg libquadmath0-dbg libstdc++-6-doc Recommended packages: llvm-4.0-dev python libgpm2 The following NEW packages will be installed: clang-4.0 libbsd0 libclang-common-4.0-dev libclang1-4.0 libedit2 libffi6 libjsoncpp1 libllvm4.0 libncurses5 libobjc-6-dev libobjc4 The following packages will be upgraded: cpp-6 g++-6 gcc-6 gcc-6-base gcc-7-base libasan3 libatomic1 libcc1-0 libcilkrts5 libgcc-6-dev libgcc1 libgomp1 libitm1 liblsan0 libmpx2 libquadmath0 libstdc++-6-dev libstdc++6 libtsan0 libubsan0 20 upgraded, 11 newly installed, 0 to remove and 13 not upgraded. Need to get 101 MB of archives. After this operation, 320 MB of additional disk space will be used. Get:1 http://127.0.0.1:9999/debian unstable/main amd64 libquadmath0 amd64 7.1.0-9 [132 kB] Get:2 http://127.0.0.1:9999/debian unstable/main amd64 libitm1 amd64 7.1.0-9 [27.2 kB] Get:3 http://127.0.0.1:9999/debian unstable/main amd64 gcc-7-base amd64 7.1.0-9 [180 kB] Get:4 http://127.0.0.1:9999/debian unstable/main amd64 libstdc++6 amd64 7.1.0-9 [398 kB] Get:5 http://127.0.0.1:9999/debian unstable/main amd64 libmpx2 amd64 7.1.0-9 [11.4 kB] Get:6 http://127.0.0.1:9999/debian unstable/main amd64 liblsan0 amd64 7.1.0-9 [124 kB] Get:7 http://127.0.0.1:9999/debian unstable/main amd64 libtsan0 amd64 7.1.0-9 [270 kB] Get:8 http://127.0.0.1:9999/debian unstable/main amd64 libubsan0 amd64 7.1.0-9 [117 kB] Get:9 http://127.0.0.1:9999/debian unstable/main amd64 libcilkrts5 amd64 7.1.0-9 [42.0 kB] Get:10 http://127.0.0.1:9999/debian unstable/main amd64 libcc1-0 amd64 7.1.0-9 [37.7 kB] Get:11 http://127.0.0.1:9999/debian unstable/main amd64 libatomic1 amd64 7.1.0-9 [8782 B] Get:12 http://127.0.0.1:9999/debian unstable/main amd64 libgomp1 amd64 7.1.0-9 [75.1 kB] Get:13 http://127.0.0.1:9999/debian unstable/main amd64 libgcc1 amd64 1:7.1.0-9 [39.3 kB] Get:14 http://127.0.0.1:9999/debian unstable/main amd64 libasan3 amd64 6.4.0-1 [310 kB] Get:15 http://127.0.0.1:9999/debian unstable/main amd64 g++-6 amd64 6.4.0-1 [7084 kB] Get:16 http://127.0.0.1:9999/debian unstable/main amd64 libstdc++-6-dev amd64 6.4.0-1 [1421 kB] Get:17 http://127.0.0.1:9999/debian unstable/main amd64 gcc-6 amd64 6.4.0-1 [6908 kB] Get:18 http://127.0.0.1:9999/debian unstable/main amd64 libgcc-6-dev amd64 6.4.0-1 [2297 kB] Get:19 http://127.0.0.1:9999/debian unstable/main amd64 cpp-6 amd64 6.4.0-1 [6549 kB] Get:20 http://127.0.0.1:9999/debian unstable/main amd64 gcc-6-base amd64 6.4.0-1 [180 kB] Get:21 http://127.0.0.1:9999/debian unstable/main amd64 libbsd0 amd64 0.8.5-1 [89.6 kB] Get:22 http://127.0.0.1:9999/debian unstable/main amd64 libncurses5 amd64 6.0+20161126-1 [93.4 kB] Get:23 http://127.0.0.1:9999/debian unstable/main amd64 libedit2 amd64 3.1-20170329-1 [85.2 kB] Get:24 http://127.0.0.1:9999/debian unstable/main amd64 libffi6 amd64 3.2.1-6 [20.4 kB] Get:25 http://127.0.0.1:9999/debian unstable/main amd64 libllvm4.0 amd64 1:4.0.1-1 [12.3 MB] Get:26 http://127.0.0.1:9999/debian unstable/main amd64 libclang1-4.0 amd64 1:4.0.1-1 [6355 kB] Get:27 http://127.0.0.1:9999/debian unstable/main amd64 libjsoncpp1 amd64 1.7.4-3 [75.6 kB] Get:28 http://127.0.0.1:9999/debian unstable/main amd64 libobjc4 amd64 7.1.0-9 [51.0 kB] Get:29 http://127.0.0.1:9999/debian unstable/main amd64 libobjc-6-dev amd64 6.4.0-1 [197 kB] Get:30 http://127.0.0.1:9999/debian unstable/main amd64 libclang-common-4.0-dev amd64 1:4.0.1-1 [2495 kB] Get:31 http://127.0.0.1:9999/debian unstable/main amd64 clang-4.0 amd64 1:4.0.1-1 [52.7 MB] debconf: delaying package configuration, since apt-utils is not installed Fetched 101 MB in 1s (97.1 MB/s) (Reading database ... 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Preparing to unpack .../16-libclang-common-4.0-dev_1%3a4.0.1-1_amd64.deb ... Unpacking libclang-common-4.0-dev (1:4.0.1-1) ... Selecting previously unselected package clang-4.0. Preparing to unpack .../17-clang-4.0_1%3a4.0.1-1_amd64.deb ... Unpacking clang-4.0 (1:4.0.1-1) ... Setting up libquadmath0:amd64 (7.1.0-9) ... Setting up libncurses5:amd64 (6.0+20161126-1) ... Setting up libgomp1:amd64 (7.1.0-9) ... Setting up libatomic1:amd64 (7.1.0-9) ... Setting up libcc1-0:amd64 (7.1.0-9) ... Setting up libobjc4:amd64 (7.1.0-9) ... Setting up libcilkrts5:amd64 (7.1.0-9) ... Setting up libubsan0:amd64 (7.1.0-9) ... Setting up libtsan0:amd64 (7.1.0-9) ... Setting up gcc-6-base:amd64 (6.4.0-1) ... Setting up libbsd0:amd64 (0.8.5-1) ... Setting up liblsan0:amd64 (7.1.0-9) ... Setting up libmpx2:amd64 (7.1.0-9) ... Processing triggers for libc-bin (2.24-12) ... Setting up libffi6:amd64 (3.2.1-6) ... Setting up cpp-6 (6.4.0-1) ... Setting up libitm1:amd64 (7.1.0-9) ... Setting up libjsoncpp1:amd64 (1.7.4-3) ... Setting up libedit2:amd64 (3.1-20170329-1) ... Setting up libasan3:amd64 (6.4.0-1) ... Setting up libgcc-6-dev:amd64 (6.4.0-1) ... Setting up libstdc++-6-dev:amd64 (6.4.0-1) ... Setting up gcc-6 (6.4.0-1) ... Setting up g++-6 (6.4.0-1) ... Setting up libllvm4.0:amd64 (1:4.0.1-1) ... Setting up libobjc-6-dev:amd64 (6.4.0-1) ... Setting up libclang1-4.0:amd64 (1:4.0.1-1) ... Setting up libclang-common-4.0-dev (1:4.0.1-1) ... Setting up clang-4.0 (1:4.0.1-1) ... Processing triggers for libc-bin (2.24-12) ... W: --force-yes is deprecated, use one of the options starting with --allow instead. + echo 'Replace gcc, g++ & cpp by clang' Replace gcc, g++ & cpp by clang + VERSIONS='4.6 4.7 4.8 4.9 5 6 7' + cd /usr/bin + for VERSION in $VERSIONS + rm -f g++-4.6 gcc-4.6 cpp-4.6 gcc + ln -s clang++-4.0 g++-4.6 + ln -s clang-4.0 gcc-4.6 + ln -s clang-4.0 cpp-4.6 + ln -s clang-4.0 gcc + echo 'gcc-4.6 hold' + dpkg --set-selections dpkg: warning: package not in status nor available database at line 1: gcc-4.6 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method; please see the FAQ + echo 'g++-4.6 hold' + dpkg --set-selections dpkg: warning: package not in status nor available database at line 1: g++-4.6 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method; please see the FAQ + for VERSION in $VERSIONS + rm -f g++-4.7 gcc-4.7 cpp-4.7 gcc + ln -s clang++-4.0 g++-4.7 + ln -s clang-4.0 gcc-4.7 + ln -s clang-4.0 cpp-4.7 + ln -s clang-4.0 gcc + echo 'gcc-4.7 hold' + dpkg --set-selections dpkg: warning: package not in status nor available database at line 1: gcc-4.7 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method; please see the FAQ + echo 'g++-4.7 hold' + dpkg --set-selections dpkg: warning: package not in status nor available database at line 1: g++-4.7 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method; please see the FAQ + for VERSION in $VERSIONS + rm -f g++-4.8 gcc-4.8 cpp-4.8 gcc + ln -s clang++-4.0 g++-4.8 + ln -s clang-4.0 gcc-4.8 + ln -s clang-4.0 cpp-4.8 + ln -s clang-4.0 gcc + echo 'gcc-4.8 hold' + dpkg --set-selections dpkg: warning: package not in status nor available database at line 1: gcc-4.8 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method; please see the FAQ + echo 'g++-4.8 hold' + dpkg --set-selections dpkg: warning: package not in status nor available database at line 1: g++-4.8 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method; please see the FAQ + for VERSION in $VERSIONS + rm -f g++-4.9 gcc-4.9 cpp-4.9 gcc + ln -s clang++-4.0 g++-4.9 + ln -s clang-4.0 gcc-4.9 + ln -s clang-4.0 cpp-4.9 + ln -s clang-4.0 gcc + echo 'gcc-4.9 hold' + dpkg --set-selections dpkg: warning: package not in status nor available database at line 1: gcc-4.9 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method; please see the FAQ + echo 'g++-4.9 hold' + dpkg --set-selections dpkg: warning: package not in status nor available database at line 1: g++-4.9 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method; please see the FAQ + for VERSION in $VERSIONS + rm -f g++-5 gcc-5 cpp-5 gcc + ln -s clang++-4.0 g++-5 + ln -s clang-4.0 gcc-5 + ln -s clang-4.0 cpp-5 + ln -s clang-4.0 gcc + echo 'gcc-5 hold' + dpkg --set-selections + echo 'g++-5 hold' + dpkg --set-selections + for VERSION in $VERSIONS + rm -f g++-6 gcc-6 cpp-6 gcc + ln -s clang++-4.0 g++-6 + ln -s clang-4.0 gcc-6 + ln -s clang-4.0 cpp-6 + ln -s clang-4.0 gcc + echo 'gcc-6 hold' + dpkg --set-selections + echo 'g++-6 hold' + dpkg --set-selections + for VERSION in $VERSIONS + rm -f g++-7 gcc-7 cpp-7 gcc + ln -s clang++-4.0 g++-7 + ln -s clang-4.0 gcc-7 + ln -s clang-4.0 cpp-7 + ln -s clang-4.0 gcc + echo 'gcc-7 hold' + dpkg --set-selections dpkg: warning: package not in status nor available database at line 1: gcc-7 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method; please see the FAQ + echo 'g++-7 hold' + dpkg --set-selections dpkg: warning: package not in status nor available database at line 1: g++-7 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method; please see the FAQ + cd - /build/hhsuite-ay0b98 + echo 'Check if gcc, g++ & cpp are actually clang' Check if gcc, g++ & cpp are actually clang + gcc --version + grep clang + cpp --version + grep clang + g++ --version + grep clang I: Finished running '/tmp/clang40'. Finished processing commands. -------------------------------------------------------------------------------- +------------------------------------------------------------------------------+ | Update chroot | +------------------------------------------------------------------------------+ Hit:1 http://127.0.0.1:9999/debian unstable InRelease Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following NEW packages will be installed: libgnutls30 libhogweed4 libidn2-0 libnettle6 libp11-kit0 libtasn1-6 libunistring2 The following packages will be upgraded: apt cpp debconf g++ gcc libapt-pkg5.0 libdebconfclient0 libperl5.24 libsystemd0 libudev1 perl perl-base perl-modules-5.24 13 upgraded, 7 newly installed, 0 to remove and 0 not upgraded. Need to get 12.5 MB of archives. After this operation, 6330 kB of additional disk space will be used. Get:1 http://127.0.0.1:9999/debian unstable/main amd64 libperl5.24 amd64 5.24.1-6 [3525 kB] Get:2 http://127.0.0.1:9999/debian unstable/main amd64 perl amd64 5.24.1-6 [218 kB] Get:3 http://127.0.0.1:9999/debian unstable/main amd64 perl-base amd64 5.24.1-6 [1344 kB] Get:4 http://127.0.0.1:9999/debian unstable/main amd64 perl-modules-5.24 all 5.24.1-6 [2723 kB] Get:5 http://127.0.0.1:9999/debian unstable/main amd64 libapt-pkg5.0 amd64 1.5~beta1 [922 kB] Get:6 http://127.0.0.1:9999/debian unstable/main amd64 libnettle6 amd64 3.3-1+b1 [191 kB] Get:7 http://127.0.0.1:9999/debian unstable/main amd64 libhogweed4 amd64 3.3-1+b1 [136 kB] Get:8 http://127.0.0.1:9999/debian unstable/main amd64 libunistring2 amd64 0.9.7-2 [377 kB] Get:9 http://127.0.0.1:9999/debian unstable/main amd64 libidn2-0 amd64 0.16-1+b1 [56.6 kB] Get:10 http://127.0.0.1:9999/debian unstable/main amd64 libp11-kit0 amd64 0.23.7-2 [193 kB] Get:11 http://127.0.0.1:9999/debian unstable/main amd64 libtasn1-6 amd64 4.12-2 [51.0 kB] Get:12 http://127.0.0.1:9999/debian unstable/main amd64 libgnutls30 amd64 3.5.13-2 [914 kB] Get:13 http://127.0.0.1:9999/debian unstable/main amd64 apt amd64 1.5~beta1 [1237 kB] Get:14 http://127.0.0.1:9999/debian unstable/main amd64 debconf all 1.5.62 [160 kB] Get:15 http://127.0.0.1:9999/debian unstable/main amd64 libsystemd0 amd64 233-10 [281 kB] Get:16 http://127.0.0.1:9999/debian unstable/main amd64 libudev1 amd64 233-10 [126 kB] Get:17 http://127.0.0.1:9999/debian unstable/main amd64 libdebconfclient0 amd64 0.229 [47.9 kB] Get:18 http://127.0.0.1:9999/debian unstable/main amd64 cpp amd64 4:6.3.0-4d1 [18.8 kB] Get:19 http://127.0.0.1:9999/debian unstable/main amd64 gcc amd64 4:6.3.0-4d1 [5252 B] Get:20 http://127.0.0.1:9999/debian unstable/main amd64 g++ amd64 4:6.3.0-4d1 [1548 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 12.5 MB in 0s (86.9 MB/s) (Reading database ... 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Setting up perl-modules-5.24 (5.24.1-6) ... Setting up libperl5.24:amd64 (5.24.1-6) ... Setting up gcc (4:6.3.0-4d1) ... Setting up perl (5.24.1-6) ... Processing triggers for libc-bin (2.24-12) ... Setting up g++ (4:6.3.0-4d1) ... +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Check APT --------- Checking available source versions... Download source files with APT ------------------------------ Reading package lists... NOTICE: 'hhsuite' packaging is maintained in the 'Git' version control system at: https://anonscm.debian.org/git/debian-med/hhsuite.git Please use: git clone https://anonscm.debian.org/git/debian-med/hhsuite.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 5304 kB of source archives. Get:1 http://127.0.0.1:9999/debian unstable/main hhsuite 3.0~beta2+dfsg-3 (dsc) [2282 B] Get:2 http://127.0.0.1:9999/debian unstable/main hhsuite 3.0~beta2+dfsg-3 (tar) [5287 kB] Get:3 http://127.0.0.1:9999/debian unstable/main hhsuite 3.0~beta2+dfsg-3 (diff) [14.6 kB] Fetched 5304 kB in 0s (22.9 MB/s) Download complete and in download only mode I: NOTICE: Log filtering will replace 'build/hhsuite-ay0b98/hhsuite-3.0~beta2+dfsg' with '<>' I: NOTICE: Log filtering will replace 'build/hhsuite-ay0b98' with '<>' +------------------------------------------------------------------------------+ | Install build-essential | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: build-essential, fakeroot Filtered Build-Depends: build-essential, fakeroot dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/<>/resolver-zbe7kL/apt_archive/sbuild-build-depends-core-dummy.deb'. dpkg-scanpackages: warning: Packages in archive but missing from override file: dpkg-scanpackages: warning: sbuild-build-depends-core-dummy dpkg-scanpackages: info: Wrote 1 entries to output Packages file. Ign:1 copy:/<>/resolver-zbe7kL/apt_archive ./ InRelease Get:2 copy:/<>/resolver-zbe7kL/apt_archive ./ Release [957 B] Ign:3 copy:/<>/resolver-zbe7kL/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-zbe7kL/apt_archive ./ Sources [349 B] Get:5 copy:/<>/resolver-zbe7kL/apt_archive ./ Packages [431 B] Fetched 1737 B in 0s (0 B/s) Reading package lists... Reading package lists... Install core build dependencies (apt-based resolver) ---------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following NEW packages will be installed: sbuild-build-depends-core-dummy 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 784 B of archives. After this operation, 0 B of additional disk space will be used. Get:1 copy:/<>/resolver-zbe7kL/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [784 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 784 B in 0s (0 B/s) Selecting previously unselected package sbuild-build-depends-core-dummy. (Reading database ... 10206 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) ... +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (amd64 included in amd64 all) +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper (>= 10), libffindex0-dev (>= 0.9.9.6-2), cmake, texlive-latex-base, texlive-latex-recommended, imagemagick, help2man Filtered Build-Depends: debhelper (>= 10), libffindex0-dev (>= 0.9.9.6-2), cmake, texlive-latex-base, texlive-latex-recommended, imagemagick, help2man dpkg-deb: building package 'sbuild-build-depends-hhsuite-dummy' in '/<>/resolver-zbe7kL/apt_archive/sbuild-build-depends-hhsuite-dummy.deb'. dpkg-scanpackages: warning: Packages in archive but missing from override file: dpkg-scanpackages: warning: sbuild-build-depends-core-dummy sbuild-build-depends-hhsuite-dummy dpkg-scanpackages: info: Wrote 2 entries to output Packages file. Ign:1 copy:/<>/resolver-zbe7kL/apt_archive ./ InRelease Get:2 copy:/<>/resolver-zbe7kL/apt_archive ./ Release [963 B] Ign:3 copy:/<>/resolver-zbe7kL/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-zbe7kL/apt_archive ./ Sources [547 B] Get:5 copy:/<>/resolver-zbe7kL/apt_archive ./ Packages [632 B] Fetched 2142 B in 0s (0 B/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 additional packages will be installed: autoconf automake autopoint autotools-dev bsdmainutils cmake cmake-data debhelper dh-autoreconf dh-strip-nondeterminism 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 libavahi-client3 libavahi-common-data libavahi-common3 libcairo2 libcroco3 libcups2 libcupsimage2 libcurl3 libdbus-1-3 libexpat1 libffindex0 libffindex0-dev libfftw3-double3 libfile-stripnondeterminism-perl libfontconfig1 libfreetype6 libglib2.0-0 libgraphite2-3 libgs9 libgs9-common libgssapi-krb5-2 libharfbuzz-icu0 libharfbuzz0b libice6 libicu57 libidn11 libijs-0.35 libjbig0 libjbig2dec0 libjpeg62-turbo libk5crypto3 libkeyutils1 libkpathsea6 libkrb5-3 libkrb5support0 liblcms2-2 libldap-2.4-2 libldap-common liblocale-gettext-perl liblqr-1-0 libltdl7 liblzo2-2 libmagic-mgc libmagic1 libmagickcore-6.q16-3 libmagickwand-6.q16-3 libnghttp2-14 libnspr4 libnss3 libopenjp2-7 libpaper-utils libpaper1 libpipeline1 libpixman-1-0 libpng16-16 libpoppler64 libpotrace0 libprocps6 libpsl5 libptexenc1 librtmp1 libsasl2-2 libsasl2-modules-db libsigsegv2 libsm6 libsqlite3-0 libssh2-1 libssl1.0.2 libsynctex1 libtexlua52 libtexluajit2 libtiff5 libtimedate-perl libtool libuv1 libx11-6 libx11-data libxau6 libxaw7 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxi6 libxml2 libxmu6 libxpm4 libxrender1 libxt6 libzzip-0-13 lsb-base m4 man-db po-debconf poppler-data procps 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 codeblocks eclipse 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.q16-3-extra libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc 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-pstricks gvfs-bin Recommended packages: curl | wget | lynx-cur libmagickcore-6.q16-3-extra ghostscript netpbm libcupsfilters1 ca-certificates dbus libarchive-cpio-perl libglib2.0-data shared-mime-info xdg-user-dirs fonts-droid-fallback krb5-locales gsfonts publicsuffix libsasl2-modules libltdl-dev xml-core libmail-sendmail-perl psmisc lmodern python ruby wish texlive-latex-base-doc prosper texlive-latex-recommended-doc 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 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 libavahi-client3 libavahi-common-data libavahi-common3 libcairo2 libcroco3 libcups2 libcupsimage2 libcurl3 libdbus-1-3 libexpat1 libffindex0 libffindex0-dev libfftw3-double3 libfile-stripnondeterminism-perl libfontconfig1 libfreetype6 libglib2.0-0 libgraphite2-3 libgs9 libgs9-common libgssapi-krb5-2 libharfbuzz-icu0 libharfbuzz0b libice6 libicu57 libidn11 libijs-0.35 libjbig0 libjbig2dec0 libjpeg62-turbo libk5crypto3 libkeyutils1 libkpathsea6 libkrb5-3 libkrb5support0 liblcms2-2 libldap-2.4-2 libldap-common liblocale-gettext-perl liblqr-1-0 libltdl7 liblzo2-2 libmagic-mgc libmagic1 libmagickcore-6.q16-3 libmagickwand-6.q16-3 libnghttp2-14 libnspr4 libnss3 libopenjp2-7 libpaper-utils libpaper1 libpipeline1 libpixman-1-0 libpng16-16 libpoppler64 libpotrace0 libprocps6 libpsl5 libptexenc1 librtmp1 libsasl2-2 libsasl2-modules-db libsigsegv2 libsm6 libsqlite3-0 libssh2-1 libssl1.0.2 libsynctex1 libtexlua52 libtexluajit2 libtiff5 libtimedate-perl libtool libuv1 libx11-6 libx11-data libxau6 libxaw7 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxi6 libxml2 libxmu6 libxpm4 libxrender1 libxt6 libzzip-0-13 lsb-base m4 man-db po-debconf poppler-data procps 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, 132 newly installed, 0 to remove and 0 not upgraded. Need to get 102 MB of archives. After this operation, 319 MB of additional disk space will be used. Get:1 copy:/<>/resolver-zbe7kL/apt_archive ./ sbuild-build-depends-hhsuite-dummy 0.invalid.0 [848 B] Get:2 http://127.0.0.1:9999/debian unstable/main amd64 groff-base amd64 1.22.3-9 [1160 kB] Get:3 http://127.0.0.1:9999/debian unstable/main amd64 bsdmainutils amd64 9.0.12+nmu1 [186 kB] Get:4 http://127.0.0.1:9999/debian unstable/main amd64 libpipeline1 amd64 1.4.1-2 [27.6 kB] Get:5 http://127.0.0.1:9999/debian unstable/main amd64 man-db amd64 2.7.6.1-2 [1044 kB] Get:6 http://127.0.0.1:9999/debian unstable/main amd64 cmake-data all 3.7.2-1 [1216 kB] Get:7 http://127.0.0.1:9999/debian unstable/main amd64 libprocps6 amd64 2:3.3.12-3 [58.1 kB] Get:8 http://127.0.0.1:9999/debian unstable/main amd64 lsb-base all 9.20161125 [27.9 kB] Get:9 http://127.0.0.1:9999/debian unstable/main amd64 procps amd64 2:3.3.12-3 [249 kB] Get:10 http://127.0.0.1:9999/debian unstable/main amd64 liblzo2-2 amd64 2.08-1.2+b2 [55.0 kB] Get:11 http://127.0.0.1:9999/debian unstable/main amd64 libicu57 amd64 57.1-6 [7701 kB] Get:12 http://127.0.0.1:9999/debian unstable/main amd64 libxml2 amd64 2.9.4+dfsg1-3 [715 kB] Get:13 http://127.0.0.1:9999/debian unstable/main amd64 libarchive13 amd64 3.2.2-2 [294 kB] Get:14 http://127.0.0.1:9999/debian unstable/main amd64 libkeyutils1 amd64 1.5.9-9 [12.4 kB] Get:15 http://127.0.0.1:9999/debian unstable/main amd64 libkrb5support0 amd64 1.15-1 [61.7 kB] Get:16 http://127.0.0.1:9999/debian unstable/main amd64 libk5crypto3 amd64 1.15-1 [119 kB] Get:17 http://127.0.0.1:9999/debian unstable/main amd64 libkrb5-3 amd64 1.15-1 [311 kB] Get:18 http://127.0.0.1:9999/debian unstable/main amd64 libgssapi-krb5-2 amd64 1.15-1 [154 kB] Get:19 http://127.0.0.1:9999/debian unstable/main amd64 libsasl2-modules-db amd64 2.1.27~101-g0780600+dfsg-3 [68.2 kB] Get:20 http://127.0.0.1:9999/debian unstable/main amd64 libsasl2-2 amd64 2.1.27~101-g0780600+dfsg-3 [105 kB] Get:21 http://127.0.0.1:9999/debian unstable/main amd64 libldap-common all 2.4.44+dfsg-7 [85.2 kB] Get:22 http://127.0.0.1:9999/debian unstable/main amd64 libldap-2.4-2 amd64 2.4.44+dfsg-7 [219 kB] Get:23 http://127.0.0.1:9999/debian unstable/main amd64 libnghttp2-14 amd64 1.24.0-1 [81.6 kB] Get:24 http://127.0.0.1:9999/debian unstable/main amd64 libpsl5 amd64 0.17.0-4+b1 [43.0 kB] Get:25 http://127.0.0.1:9999/debian unstable/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-1+b1 [60.4 kB] Get:26 http://127.0.0.1:9999/debian unstable/main amd64 libssh2-1 amd64 1.8.0-1 [138 kB] Get:27 http://127.0.0.1:9999/debian unstable/main amd64 libssl1.0.2 amd64 1.0.2l-2 [1294 kB] Get:28 http://127.0.0.1:9999/debian unstable/main amd64 libcurl3 amd64 7.52.1-5 [291 kB] Get:29 http://127.0.0.1:9999/debian unstable/main amd64 libexpat1 amd64 2.2.1-3 [85.6 kB] Get:30 http://127.0.0.1:9999/debian unstable/main amd64 libuv1 amd64 1.9.1-3 [84.4 kB] Get:31 http://127.0.0.1:9999/debian unstable/main amd64 cmake amd64 3.7.2-1 [3038 kB] Get:32 http://127.0.0.1:9999/debian unstable/main amd64 liblocale-gettext-perl amd64 1.07-3+b1 [18.7 kB] Get:33 http://127.0.0.1:9999/debian unstable/main amd64 libglib2.0-0 amd64 2.52.3-1 [2742 kB] Get:34 http://127.0.0.1:9999/debian unstable/main amd64 liblqr-1-0 amd64 0.4.2-2+b2 [24.8 kB] Get:35 http://127.0.0.1:9999/debian unstable/main amd64 libfftw3-double3 amd64 3.3.6p2-1 [732 kB] Get:36 http://127.0.0.1:9999/debian unstable/main amd64 libpng16-16 amd64 1.6.29-3 [281 kB] Get:37 http://127.0.0.1:9999/debian unstable/main amd64 libfreetype6 amd64 2.8-0.2 [449 kB] Get:38 http://127.0.0.1:9999/debian unstable/main amd64 ucf all 3.0036 [70.2 kB] Get:39 http://127.0.0.1:9999/debian unstable/main amd64 fonts-dejavu-core all 2.37-1 [1068 kB] Get:40 http://127.0.0.1:9999/debian unstable/main amd64 fontconfig-config all 2.12.3-0.1 [303 kB] Get:41 http://127.0.0.1:9999/debian unstable/main amd64 libfontconfig1 amd64 2.12.3-0.1 [366 kB] Get:42 http://127.0.0.1:9999/debian unstable/main amd64 libjbig0 amd64 2.1-3.1+b2 [31.0 kB] Get:43 http://127.0.0.1:9999/debian unstable/main amd64 libjpeg62-turbo amd64 1:1.5.1-2 [134 kB] Get:44 http://127.0.0.1:9999/debian unstable/main amd64 liblcms2-2 amd64 2.8-4 [143 kB] Get:45 http://127.0.0.1:9999/debian unstable/main amd64 libltdl7 amd64 2.4.6-2 [389 kB] Get:46 http://127.0.0.1:9999/debian unstable/main amd64 libopenjp2-7 amd64 2.1.2-1.1 [121 kB] Get:47 http://127.0.0.1:9999/debian unstable/main amd64 libtiff5 amd64 4.0.8-3 [237 kB] Get:48 http://127.0.0.1:9999/debian unstable/main amd64 libxau6 amd64 1:1.0.8-1 [20.7 kB] Get:49 http://127.0.0.1:9999/debian unstable/main amd64 libxdmcp6 amd64 1:1.1.2-3 [26.3 kB] Get:50 http://127.0.0.1:9999/debian unstable/main amd64 libxcb1 amd64 1.12-1 [133 kB] Get:51 http://127.0.0.1:9999/debian unstable/main amd64 libx11-data all 2:1.6.4-3 [290 kB] Get:52 http://127.0.0.1:9999/debian unstable/main amd64 libx11-6 amd64 2:1.6.4-3 [747 kB] Get:53 http://127.0.0.1:9999/debian unstable/main amd64 libxext6 amd64 2:1.3.3-1+b2 [52.5 kB] Get:54 http://127.0.0.1:9999/debian unstable/main amd64 imagemagick-6-common all 8:6.9.7.4+dfsg-11 [182 kB] Get:55 http://127.0.0.1:9999/debian unstable/main amd64 libmagickcore-6.q16-3 amd64 8:6.9.7.4+dfsg-11 [1738 kB] Get:56 http://127.0.0.1:9999/debian unstable/main amd64 libmagickwand-6.q16-3 amd64 8:6.9.7.4+dfsg-11 [419 kB] Get:57 http://127.0.0.1:9999/debian unstable/main amd64 poppler-data all 0.4.7-8 [1451 kB] Get:58 http://127.0.0.1:9999/debian unstable/main amd64 tex-common all 6.07 [566 kB] Get:59 http://127.0.0.1:9999/debian unstable/main amd64 libmagic-mgc amd64 1:5.30-1 [222 kB] Get:60 http://127.0.0.1:9999/debian unstable/main amd64 libmagic1 amd64 1:5.30-1 [111 kB] Get:61 http://127.0.0.1:9999/debian unstable/main amd64 file amd64 1:5.30-1 [63.9 kB] Get:62 http://127.0.0.1:9999/debian unstable/main amd64 gettext-base amd64 0.19.8.1-2+b1 [122 kB] Get:63 http://127.0.0.1:9999/debian unstable/main amd64 libidn11 amd64 1.33-1 [115 kB] Get:64 http://127.0.0.1:9999/debian unstable/main amd64 libsqlite3-0 amd64 3.16.2-5 [572 kB] Get:65 http://127.0.0.1:9999/debian unstable/main amd64 libsigsegv2 amd64 2.11-1 [29.9 kB] Get:66 http://127.0.0.1:9999/debian unstable/main amd64 m4 amd64 1.4.18-1 [202 kB] Get:67 http://127.0.0.1:9999/debian unstable/main amd64 autoconf all 2.69-10 [338 kB] Get:68 http://127.0.0.1:9999/debian unstable/main amd64 autotools-dev all 20161112.1 [73.4 kB] Get:69 http://127.0.0.1:9999/debian unstable/main amd64 automake all 1:1.15.1-2 [736 kB] Get:70 http://127.0.0.1:9999/debian unstable/main amd64 autopoint all 0.19.8.1-2 [433 kB] Get:71 http://127.0.0.1:9999/debian unstable/main amd64 libtool all 2.4.6-2 [545 kB] Get:72 http://127.0.0.1:9999/debian unstable/main amd64 dh-autoreconf all 14 [15.9 kB] Get:73 http://127.0.0.1:9999/debian unstable/main amd64 libarchive-zip-perl all 1.59-1 [95.5 kB] Get:74 http://127.0.0.1:9999/debian unstable/main amd64 libfile-stripnondeterminism-perl all 0.035-2 [17.0 kB] Get:75 http://127.0.0.1:9999/debian unstable/main amd64 libtimedate-perl all 2.3000-2 [42.2 kB] Get:76 http://127.0.0.1:9999/debian unstable/main amd64 dh-strip-nondeterminism all 0.035-2 [10.7 kB] Get:77 http://127.0.0.1:9999/debian unstable/main amd64 libcroco3 amd64 0.6.12-1 [144 kB] Get:78 http://127.0.0.1:9999/debian unstable/main amd64 gettext amd64 0.19.8.1-2+b1 [1301 kB] Get:79 http://127.0.0.1:9999/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.4 [26.3 kB] Get:80 http://127.0.0.1:9999/debian unstable/main amd64 po-debconf all 1.0.20 [247 kB] Get:81 http://127.0.0.1:9999/debian unstable/main amd64 debhelper all 10.6.2 [968 kB] Get:82 http://127.0.0.1:9999/debian unstable/main amd64 fonts-lmodern all 2.004.5-3 [4540 kB] Get:83 http://127.0.0.1:9999/debian unstable/main amd64 help2man amd64 1.47.4 [162 kB] Get:84 http://127.0.0.1:9999/debian unstable/main amd64 hicolor-icon-theme all 0.15-1 [9550 B] Get:85 http://127.0.0.1:9999/debian unstable/main amd64 imagemagick-6.q16 amd64 8:6.9.7.4+dfsg-11 [560 kB] Get:86 http://127.0.0.1:9999/debian unstable/main amd64 imagemagick amd64 8:6.9.7.4+dfsg-11 [139 kB] Get:87 http://127.0.0.1:9999/debian unstable/main amd64 libavahi-common-data amd64 0.6.32-2 [118 kB] Get:88 http://127.0.0.1:9999/debian unstable/main amd64 libavahi-common3 amd64 0.6.32-2 [52.0 kB] Get:89 http://127.0.0.1:9999/debian unstable/main amd64 libdbus-1-3 amd64 1.10.20-1 [193 kB] Get:90 http://127.0.0.1:9999/debian unstable/main amd64 libavahi-client3 amd64 0.6.32-2 [55.3 kB] Get:91 http://127.0.0.1:9999/debian unstable/main amd64 libpixman-1-0 amd64 0.34.0-1 [530 kB] Get:92 http://127.0.0.1:9999/debian unstable/main amd64 libxcb-render0 amd64 1.12-1 [105 kB] Get:93 http://127.0.0.1:9999/debian unstable/main amd64 libxcb-shm0 amd64 1.12-1 [95.9 kB] Get:94 http://127.0.0.1:9999/debian unstable/main amd64 libxrender1 amd64 1:0.9.10-1 [33.0 kB] Get:95 http://127.0.0.1:9999/debian unstable/main amd64 libcairo2 amd64 1.14.10-1 [774 kB] Get:96 http://127.0.0.1:9999/debian unstable/main amd64 libcups2 amd64 2.2.4-1 [313 kB] Get:97 http://127.0.0.1:9999/debian unstable/main amd64 libcupsimage2 amd64 2.2.4-1 [125 kB] Get:98 http://127.0.0.1:9999/debian unstable/main amd64 libffindex0 amd64 0.9.9.7-4 [16.5 kB] Get:99 http://127.0.0.1:9999/debian unstable/main amd64 libffindex0-dev amd64 0.9.9.7-4 [17.9 kB] Get:100 http://127.0.0.1:9999/debian unstable/main amd64 libgraphite2-3 amd64 1.3.10-2 [84.3 kB] Get:101 http://127.0.0.1:9999/debian unstable/main amd64 libijs-0.35 amd64 0.35-12 [18.4 kB] Get:102 http://127.0.0.1:9999/debian unstable/main amd64 libjbig2dec0 amd64 0.13-4.1 [60.1 kB] Get:103 http://127.0.0.1:9999/debian unstable/main amd64 libpaper1 amd64 1.1.24+nmu5 [21.6 kB] Get:104 http://127.0.0.1:9999/debian unstable/main amd64 libgs9-common all 9.21~dfsg-1 [5164 kB] Get:105 http://127.0.0.1:9999/debian unstable/main amd64 libgs9 amd64 9.21~dfsg-1 [2142 kB] Get:106 http://127.0.0.1:9999/debian unstable/main amd64 libharfbuzz0b amd64 1.4.2-1 [671 kB] Get:107 http://127.0.0.1:9999/debian unstable/main amd64 libharfbuzz-icu0 amd64 1.4.2-1 [466 kB] Get:108 http://127.0.0.1:9999/debian unstable/main amd64 x11-common all 1:7.7+19 [251 kB] Get:109 http://127.0.0.1:9999/debian unstable/main amd64 libice6 amd64 2:1.0.9-2 [58.7 kB] Get:110 http://127.0.0.1:9999/debian unstable/main amd64 libkpathsea6 amd64 2017.20170613.44572-2 [161 kB] Get:111 http://127.0.0.1:9999/debian unstable/main amd64 libnspr4 amd64 2:4.15-1 [117 kB] Get:112 http://127.0.0.1:9999/debian unstable/main amd64 libnss3 amd64 2:3.31-1 [1160 kB] Get:113 http://127.0.0.1:9999/debian unstable/main amd64 libpaper-utils amd64 1.1.24+nmu5 [17.6 kB] Get:114 http://127.0.0.1:9999/debian unstable/main amd64 libpoppler64 amd64 0.48.0-2 [1285 kB] Get:115 http://127.0.0.1:9999/debian unstable/main amd64 libpotrace0 amd64 1.14-2 [25.7 kB] Get:116 http://127.0.0.1:9999/debian unstable/main amd64 libptexenc1 amd64 2017.20170613.44572-2 [58.1 kB] Get:117 http://127.0.0.1:9999/debian unstable/main amd64 libsm6 amd64 2:1.2.2-1+b3 [33.3 kB] Get:118 http://127.0.0.1:9999/debian unstable/main amd64 libsynctex1 amd64 2017.20170613.44572-2 [65.1 kB] Get:119 http://127.0.0.1:9999/debian unstable/main amd64 libtexlua52 amd64 2017.20170613.44572-2 [111 kB] Get:120 http://127.0.0.1:9999/debian unstable/main amd64 libtexluajit2 amd64 2017.20170613.44572-2 [250 kB] Get:121 http://127.0.0.1:9999/debian unstable/main amd64 libxt6 amd64 1:1.1.5-1 [188 kB] Get:122 http://127.0.0.1:9999/debian unstable/main amd64 libxmu6 amd64 2:1.1.2-2 [60.3 kB] Get:123 http://127.0.0.1:9999/debian unstable/main amd64 libxpm4 amd64 1:3.5.12-1 [49.1 kB] Get:124 http://127.0.0.1:9999/debian unstable/main amd64 libxaw7 amd64 2:1.0.13-1+b2 [201 kB] Get:125 http://127.0.0.1:9999/debian unstable/main amd64 libxi6 amd64 2:1.7.9-1 [82.6 kB] Get:126 http://127.0.0.1:9999/debian unstable/main amd64 libzzip-0-13 amd64 0.13.62-3.1 [55.4 kB] Get:127 http://127.0.0.1:9999/debian unstable/main amd64 t1utils amd64 1.39-2 [59.0 kB] Get:128 http://127.0.0.1:9999/debian unstable/main amd64 texlive-binaries amd64 2017.20170613.44572-2 [8082 kB] Get:129 http://127.0.0.1:9999/debian unstable/main amd64 xdg-utils all 1.1.1-1 [71.1 kB] Get:130 http://127.0.0.1:9999/debian unstable/main amd64 texlive-base all 2017.20170629-1 [18.7 MB] Get:131 http://127.0.0.1:9999/debian unstable/main amd64 texlive-latex-base all 2017.20170629-1 [975 kB] Get:132 http://127.0.0.1:9999/debian unstable/main amd64 texlive-latex-recommended all 2017.20170629-1 [14.8 MB] debconf: delaying package configuration, since apt-utils is not installed Fetched 102 MB in 1s (88.0 MB/s) Selecting previously unselected package groff-base. 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Setting up libpng16-16:amd64 (1.6.29-3) ... Setting up libtimedate-perl (2.3000-2) ... Setting up liblcms2-2:amd64 (2.8-4) ... Setting up libjbig0:amd64 (2.1-3.1+b2) ... Setting up libsigsegv2:amd64 (2.11-1) ... Setting up libldap-common (2.4.44+dfsg-7) ... Setting up fonts-dejavu-core (2.37-1) ... Setting up poppler-data (0.4.7-8) ... Setting up libuv1:amd64 (1.9.1-3) ... Setting up libpsl5:amd64 (0.17.0-4+b1) ... Setting up groff-base (1.22.3-9) ... Setting up libglib2.0-0:amd64 (2.52.3-1) ... No schema files found: doing nothing. Setting up libsasl2-modules-db:amd64 (2.1.27~101-g0780600+dfsg-3) ... Setting up libsasl2-2:amd64 (2.1.27~101-g0780600+dfsg-3) ... Setting up libtiff5:amd64 (4.0.8-3) ... Setting up gettext-base (0.19.8.1-2+b1) ... Setting up cmake-data (3.7.2-1) ... Setting up libffindex0 (0.9.9.7-4) ... Setting up libpipeline1:amd64 (1.4.1-2) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-1+b1) ... Setting up m4 (1.4.18-1) ... Setting up libfftw3-double3:amd64 (3.3.6p2-1) ... Setting up libicu57:amd64 (57.1-6) ... Setting up libprocps6:amd64 (2:3.3.12-3) ... Setting up libnspr4:amd64 (2:4.15-1) ... Setting up ucf (3.0036) ... Setting up libxml2:amd64 (2.9.4+dfsg1-3) ... Setting up libfreetype6:amd64 (2.8-0.2) ... Setting up libmagic-mgc (1:5.30-1) ... Setting up libmagic1:amd64 (1:5.30-1) ... Setting up lsb-base (9.20161125) ... Setting up libgraphite2-3:amd64 (1.3.10-2) ... Setting up procps (2:3.3.12-3) ... update-alternatives: using /usr/bin/w.procps to provide /usr/bin/w (w) in auto mode Setting up libcroco3:amd64 (0.6.12-1) ... Setting up libssl1.0.2:amd64 (1.0.2l-2) ... Setting up liblqr-1-0:amd64 (0.4.2-2+b2) ... Setting up libjbig2dec0:amd64 (0.13-4.1) ... Setting up libpixman-1-0:amd64 (0.34.0-1) ... Setting up libssh2-1:amd64 (1.8.0-1) ... Processing triggers for libc-bin (2.24-12) ... Setting up autotools-dev (20161112.1) ... Setting up libldap-2.4-2:amd64 (2.4.44+dfsg-7) ... Setting up t1utils (1.39-2) ... Setting up libltdl7:amd64 (2.4.6-2) ... Setting up libijs-0.35:amd64 (0.35-12) ... Setting up libsqlite3-0:amd64 (3.16.2-5) ... Setting up liblocale-gettext-perl (1.07-3+b1) ... Setting up libpotrace0 (1.14-2) ... Setting up libxdmcp6:amd64 (1:1.1.2-3) ... Setting up libkeyutils1:amd64 (1.5.9-9) ... Setting up bsdmainutils (9.0.12+nmu1) ... 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 libzzip-0-13:amd64 (0.13.62-3.1) ... Setting up x11-common (1:7.7+19) ... update-rc.d: warning: start and stop actions are no longer supported; falling back to defaults invoke-rc.d: could not determine current runlevel All runlevel operations denied by policy invoke-rc.d: policy-rc.d denied execution of start. Setting up xdg-utils (1.1.1-1) ... Setting up hicolor-icon-theme (0.15-1) ... Setting up libtexluajit2:amd64 (2017.20170613.44572-2) ... Setting up libx11-data (2:1.6.4-3) ... Setting up libxau6:amd64 (1:1.0.8-1) ... Setting up autopoint (0.19.8.1-2) ... Setting up libidn11:amd64 (1.33-1) ... Setting up libdbus-1-3:amd64 (1.10.20-1) ... Setting up liblzo2-2:amd64 (2.08-1.2+b2) ... Setting up fonts-lmodern (2.004.5-3) ... Setting up libavahi-common-data:amd64 (0.6.32-2) ... Setting up libfile-stripnondeterminism-perl (0.035-2) ... Setting up libpaper1:amd64 (1.1.24+nmu5) ... Creating config file /etc/papersize with new version Setting up libpaper-utils (1.1.24+nmu5) ... Setting up fontconfig-config (2.12.3-0.1) ... Setting up tex-common (6.07) ... update-language: texlive-base not installed and configured, doing nothing! Setting up gettext (0.19.8.1-2+b1) ... Setting up libarchive13:amd64 (3.2.2-2) ... Setting up libffindex0-dev (0.9.9.7-4) ... Setting up libnss3:amd64 (2:3.31-1) ... Setting up libharfbuzz0b:amd64 (1.4.2-1) ... Setting up autoconf (2.69-10) ... Setting up file (1:5.30-1) ... Setting up libkrb5support0:amd64 (1.15-1) ... Setting up intltool-debian (0.35.0+20060710.4) ... Setting up automake (1:1.15.1-2) ... update-alternatives: using /usr/bin/automake-1.15 to provide /usr/bin/automake (automake) in auto mode Setting up help2man (1.47.4) ... Setting up libice6:amd64 (2:1.0.9-2) ... Setting up man-db (2.7.6.1-2) ... Not building database; man-db/auto-update is not 'true'. Setting up libavahi-common3:amd64 (0.6.32-2) ... Setting up libxcb1:amd64 (1.12-1) ... Setting up libtool (2.4.6-2) ... Setting up libfontconfig1:amd64 (2.12.3-0.1) ... Setting up libsm6:amd64 (2:1.2.2-1+b3) ... Setting up libk5crypto3:amd64 (1.15-1) ... Setting up libxcb-render0:amd64 (1.12-1) ... Setting up libharfbuzz-icu0:amd64 (1.4.2-1) ... Setting up po-debconf (1.0.20) ... Setting up libpoppler64:amd64 (0.48.0-2) ... Setting up libx11-6:amd64 (2:1.6.4-3) ... Setting up libxcb-shm0:amd64 (1.12-1) ... 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 (0.6.32-2) ... Setting up libkrb5-3:amd64 (1.15-1) ... Setting up libxext6:amd64 (2:1.3.3-1+b2) ... Setting up libxmu6:amd64 (2:1.1.2-2) ... Setting up libgssapi-krb5-2:amd64 (1.15-1) ... Setting up libcups2:amd64 (2.2.4-1) ... Setting up libxi6:amd64 (2:1.7.9-1) ... Setting up libxaw7:amd64 (2:1.0.13-1+b2) ... Setting up libcairo2:amd64 (1.14.10-1) ... Setting up libmagickcore-6.q16-3:amd64 (8:6.9.7.4+dfsg-11) ... Setting up libcurl3:amd64 (7.52.1-5) ... Setting up libcupsimage2:amd64 (2.2.4-1) ... Setting up libmagickwand-6.q16-3:amd64 (8:6.9.7.4+dfsg-11) ... Setting up cmake (3.7.2-1) ... Setting up libgs9:amd64 (9.21~dfsg-1) ... Setting up imagemagick-6.q16 (8:6.9.7.4+dfsg-11) ... 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 texlive-binaries (2017.20170613.44572-2) ... 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 imagemagick (8:6.9.7.4+dfsg-11) ... Setting up texlive-base (2017.20170629-1) ... /usr/bin/tl-paper: setting paper size for dvips to a4. /usr/bin/tl-paper: setting paper size for dvipdfmx to a4. /usr/bin/tl-paper: setting paper size for xdvi to a4. /usr/bin/tl-paper: setting paper size for pdftex to a4. Setting up texlive-latex-base (2017.20170629-1) ... Setting up texlive-latex-recommended (2017.20170629-1) ... Setting up dh-strip-nondeterminism (0.035-2) ... Setting up debhelper (10.6.2) ... Setting up dh-autoreconf (14) ... Setting up sbuild-build-depends-hhsuite-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.24-12) ... Processing triggers for tex-common (6.07) ... 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 4.9.0-2-amd64 amd64 (x86_64) Toolchain package versions: binutils_2.28-6 dpkg-dev_1.18.24 g++-6_6.4.0-1 gcc-6_6.4.0-1 libc6-dev_2.24-12 libstdc++-6-dev_6.4.0-1 libstdc++6_7.1.0-9 linux-libc-dev_4.11.6-1 Package versions: adduser_3.115 apt_1.5~beta1 autoconf_2.69-10 automake_1:1.15.1-2 autopoint_0.19.8.1-2 autotools-dev_20161112.1 base-files_10 base-passwd_3.5.43 bash_4.4-5 binutils_2.28-6 bsdmainutils_9.0.12+nmu1 bsdutils_1:2.29.2-1 build-essential_12.3 bzip2_1.0.6-8.1 clang-4.0_1:4.0.1-1 cmake_3.7.2-1 cmake-data_3.7.2-1 coreutils_8.26-3 cpp_4:6.3.0-4d1 cpp-6_6.4.0-1 dash_0.5.8-2.4 debconf_1.5.62 debfoster_2.7-2.1+b1 debhelper_10.6.2 debian-archive-keyring_2017.5 debianutils_4.8.1.1 dh-autoreconf_14 dh-strip-nondeterminism_0.035-2 diffutils_1:3.5-3 dpkg_1.18.24 dpkg-dev_1.18.24 e2fslibs_1.43.4-2 e2fsprogs_1.43.4-2 eatmydata_105-5 fakeroot_1.21-3.1 file_1:5.30-1 findutils_4.6.0+git+20170606-2 fontconfig-config_2.12.3-0.1 fonts-dejavu-core_2.37-1 fonts-lmodern_2.004.5-3 g++_4:6.3.0-4d1 g++-6_6.4.0-1 gcc_4:6.3.0-4d1 gcc-6_6.4.0-1 gcc-6-base_6.4.0-1 gcc-7-base_7.1.0-9 gettext_0.19.8.1-2+b1 gettext-base_0.19.8.1-2+b1 gpgv_2.1.18-8 grep_2.27-2 groff-base_1.22.3-9 gzip_1.6-5+b1 help2man_1.47.4 hicolor-icon-theme_0.15-1 hostname_3.18+b1 imagemagick_8:6.9.7.4+dfsg-11 imagemagick-6-common_8:6.9.7.4+dfsg-11 imagemagick-6.q16_8:6.9.7.4+dfsg-11 init-system-helpers_1.48 intltool-debian_0.35.0+20060710.4 libacl1_2.2.52-3+b1 libapt-pkg5.0_1.5~beta1 libarchive-zip-perl_1.59-1 libarchive13_3.2.2-2 libasan3_6.4.0-1 libatomic1_7.1.0-9 libattr1_1:2.4.47-2+b2 libaudit-common_1:2.7.7-1 libaudit1_1:2.7.7-1+b1 libavahi-client3_0.6.32-2 libavahi-common-data_0.6.32-2 libavahi-common3_0.6.32-2 libblkid1_2.29.2-1 libbsd0_0.8.5-1 libbz2-1.0_1.0.6-8.1 libc-bin_2.24-12 libc-dev-bin_2.24-12 libc6_2.24-12 libc6-dev_2.24-12 libcairo2_1.14.10-1 libcap-ng0_0.7.7-3+b1 libcc1-0_7.1.0-9 libcilkrts5_7.1.0-9 libclang-common-4.0-dev_1:4.0.1-1 libclang1-4.0_1:4.0.1-1 libcomerr2_1.43.4-2 libcroco3_0.6.12-1 libcups2_2.2.4-1 libcupsimage2_2.2.4-1 libcurl3_7.52.1-5 libdb5.3_5.3.28-12+b1 libdbus-1-3_1.10.20-1 libdebconfclient0_0.229 libdpkg-perl_1.18.24 libeatmydata1_105-5 libedit2_3.1-20170329-1 libexpat1_2.2.1-3 libfakeroot_1.21-3.1 libfdisk1_2.29.2-1 libffi6_3.2.1-6 libffindex0_0.9.9.7-4 libffindex0-dev_0.9.9.7-4 libfftw3-double3_3.3.6p2-1 libfile-stripnondeterminism-perl_0.035-2 libfontconfig1_2.12.3-0.1 libfreetype6_2.8-0.2 libgc1c2_1:7.4.2-8 libgcc-6-dev_6.4.0-1 libgcc1_1:7.1.0-9 libgcrypt20_1.7.8-1 libgdbm3_1.8.3-14 libglib2.0-0_2.52.3-1 libgmp10_2:6.1.2+dfsg-1 libgnutls30_3.5.13-2 libgomp1_7.1.0-9 libgpg-error0_1.27-3 libgraphite2-3_1.3.10-2 libgs9_9.21~dfsg-1 libgs9-common_9.21~dfsg-1 libgssapi-krb5-2_1.15-1 libharfbuzz-icu0_1.4.2-1 libharfbuzz0b_1.4.2-1 libhogweed4_3.3-1+b1 libice6_2:1.0.9-2 libicu57_57.1-6 libidn11_1.33-1 libidn2-0_0.16-1+b1 libijs-0.35_0.35-12 libisl15_0.18-1 libitm1_7.1.0-9 libjbig0_2.1-3.1+b2 libjbig2dec0_0.13-4.1 libjpeg62-turbo_1:1.5.1-2 libjsoncpp1_1.7.4-3 libk5crypto3_1.15-1 libkeyutils1_1.5.9-9 libkpathsea6_2017.20170613.44572-2 libkrb5-3_1.15-1 libkrb5support0_1.15-1 liblcms2-2_2.8-4 libldap-2.4-2_2.4.44+dfsg-7 libldap-common_2.4.44+dfsg-7 libllvm4.0_1:4.0.1-1 liblocale-gettext-perl_1.07-3+b1 liblqr-1-0_0.4.2-2+b2 liblsan0_7.1.0-9 libltdl7_2.4.6-2 liblz4-1_0.0~r131-2+b1 liblzma5_5.2.2-1.2+b1 liblzo2-2_2.08-1.2+b2 libmagic-mgc_1:5.30-1 libmagic1_1:5.30-1 libmagickcore-6.q16-3_8:6.9.7.4+dfsg-11 libmagickwand-6.q16-3_8:6.9.7.4+dfsg-11 libmount1_2.29.2-1 libmpc3_1.0.3-1+b2 libmpfr4_3.1.5-1 libmpx2_7.1.0-9 libncurses5_6.0+20161126-1 libncursesw5_6.0+20161126-1 libnettle6_3.3-1+b1 libnghttp2-14_1.24.0-1 libnspr4_2:4.15-1 libnss3_2:3.31-1 libobjc-6-dev_6.4.0-1 libobjc4_7.1.0-9 libopenjp2-7_2.1.2-1.1 libp11-kit0_0.23.7-2 libpam-modules_1.1.8-3.6 libpam-modules-bin_1.1.8-3.6 libpam-runtime_1.1.8-3.6 libpam0g_1.1.8-3.6 libpaper-utils_1.1.24+nmu5 libpaper1_1.1.24+nmu5 libpcre3_2:8.39-3 libperl5.24_5.24.1-6 libpipeline1_1.4.1-2 libpixman-1-0_0.34.0-1 libpng16-16_1.6.29-3 libpoppler64_0.48.0-2 libpotrace0_1.14-2 libprocps6_2:3.3.12-3 libpsl5_0.17.0-4+b1 libptexenc1_2017.20170613.44572-2 libquadmath0_7.1.0-9 librtmp1_2.4+20151223.gitfa8646d.1-1+b1 libsasl2-2_2.1.27~101-g0780600+dfsg-3 libsasl2-modules-db_2.1.27~101-g0780600+dfsg-3 libselinux1_2.6-3+b2 libsemanage-common_2.6-2 libsemanage1_2.6-2+b1 libsepol1_2.6-2 libsigsegv2_2.11-1 libsm6_2:1.2.2-1+b3 libsmartcols1_2.29.2-1 libsqlite3-0_3.16.2-5 libss2_1.43.4-2 libssh2-1_1.8.0-1 libssl1.0.2_1.0.2l-2 libstdc++-6-dev_6.4.0-1 libstdc++6_7.1.0-9 libsynctex1_2017.20170613.44572-2 libsystemd0_233-10 libtasn1-6_4.12-2 libtexlua52_2017.20170613.44572-2 libtexluajit2_2017.20170613.44572-2 libtiff5_4.0.8-3 libtimedate-perl_2.3000-2 libtinfo5_6.0+20161126-1 libtool_2.4.6-2 libtsan0_7.1.0-9 libubsan0_7.1.0-9 libudev1_233-10 libunistring2_0.9.7-2 libustr-1.0-1_1.0.4-6 libuuid1_2.29.2-1 libuv1_1.9.1-3 libx11-6_2:1.6.4-3 libx11-data_2:1.6.4-3 libxau6_1:1.0.8-1 libxaw7_2:1.0.13-1+b2 libxcb-render0_1.12-1 libxcb-shm0_1.12-1 libxcb1_1.12-1 libxdmcp6_1:1.1.2-3 libxext6_2:1.3.3-1+b2 libxi6_2:1.7.9-1 libxml2_2.9.4+dfsg1-3 libxmu6_2:1.1.2-2 libxpm4_1:3.5.12-1 libxrender1_1:0.9.10-1 libxt6_1:1.1.5-1 libzzip-0-13_0.13.62-3.1 linux-libc-dev_4.11.6-1 login_1:4.4-4.1 lsb-base_9.20161125 m4_1.4.18-1 make_4.1-9.1 man-db_2.7.6.1-2 mawk_1.3.3-17+b3 mount_2.29.2-1 multiarch-support_2.24-12 ncurses-base_6.0+20161126-1 ncurses-bin_6.0+20161126-1 passwd_1:4.4-4.1 patch_2.7.5-1+b2 perl_5.24.1-6 perl-base_5.24.1-6 perl-modules-5.24_5.24.1-6 po-debconf_1.0.20 poppler-data_0.4.7-8 procps_2:3.3.12-3 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-hhsuite-dummy_0.invalid.0 sed_4.4-1 sensible-utils_0.0.9 sysvinit-utils_2.88dsf-59.9 t1utils_1.39-2 tar_1.29b-1.1 tex-common_6.07 texlive-base_2017.20170629-1 texlive-binaries_2017.20170613.44572-2 texlive-latex-base_2017.20170629-1 texlive-latex-recommended_2017.20170629-1 ucf_3.0036 util-linux_2.29.2-1 x11-common_1:7.7+19 xdg-utils_1.1.1-1 xz-utils_5.2.2-1.2+b1 zlib1g_1:1.2.8.dfsg-5 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/sbuild-nonexistent/.gnupg/trustedkeys.kbx': General error gpgv: Signature made Wed Jan 18 15:57:31 2017 UTC gpgv: using RSA key 578A0494D1C646D1 gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./hhsuite_3.0~beta2+dfsg-3.dsc dpkg-source: info: extracting hhsuite in /<>/hhsuite-3.0~beta2+dfsg dpkg-source: info: unpacking hhsuite_3.0~beta2+dfsg.orig.tar.xz dpkg-source: info: unpacking hhsuite_3.0~beta2+dfsg-3.debian.tar.xz 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 spelling.patch dpkg-source: info: applying disable-ffindex-build.patch dpkg-source: info: applying fix-namespace.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 dpkg-source: info: applying fix_type_mismatch_in_printf.patch Check disk space ---------------- Sufficient free space for build User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf HOME=/sbuild-nonexistent LANG=en_US.UTF-8 LC_ALL=POSIX LOGNAME=user42 PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games SCHROOT_ALIAS_NAME=unstable-amd64-sbuild SCHROOT_CHROOT_NAME=unstable-amd64-sbuild SCHROOT_COMMAND=env SCHROOT_GID=1001 SCHROOT_GROUP=user42 SCHROOT_SESSION_ID=unstable-amd64-sbuild-68f3b218-256a-4a67-bffa-b39c6dddb910 SCHROOT_UID=1001 SCHROOT_USER=user42 SHELL=/bin/sh USER=user42 dpkg-buildpackage ----------------- dpkg-buildpackage: info: source package hhsuite dpkg-buildpackage: info: source version 3.0~beta2+dfsg-3 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build hhsuite-3.0~beta2+dfsg dpkg-buildpackage: info: host architecture amd64 fakeroot debian/rules clean dh clean --builddirectory=mybuild dh_testdir -O--builddirectory=mybuild dh_auto_clean -O--builddirectory=mybuild dh_autoreconf_clean -O--builddirectory=mybuild debian/rules override_dh_clean make[1]: Entering directory '/<>/hhsuite-3.0~beta2+dfsg' rm -f hhalign.1 hhblits.1 hhblits_omp.1 hhconsensus.1 hhfilter.1 hhmake.1 hhsearch.1 dh_clean make[1]: Leaving directory '/<>/hhsuite-3.0~beta2+dfsg' debian/rules build-arch dh build-arch --builddirectory=mybuild dh_testdir -a -O--builddirectory=mybuild dh_update_autotools_config -a -O--builddirectory=mybuild dh_autoreconf -a -O--builddirectory=mybuild dh_auto_configure -a -O--builddirectory=mybuild cmake .. -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_BUILD_TYPE=None -DCMAKE_INSTALL_SYSCONFDIR=/etc -DCMAKE_INSTALL_LOCALSTATEDIR=/var -- The CXX compiler identification is Clang 4.0.1 -- 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 clang(++) -- 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: -msse4.2 -mfpmath=sse -- Try OpenMP CXX flag = [-fopenmp=libomp] -- Performing Test OpenMP_FLAG_DETECTED -- Performing Test OpenMP_FLAG_DETECTED - Failed -- Try OpenMP CXX flag = [ ] -- Performing Test OpenMP_FLAG_DETECTED -- Performing Test OpenMP_FLAG_DETECTED - Failed -- Try OpenMP CXX flag = [-fopenmp] -- Performing Test OpenMP_FLAG_DETECTED -- Performing Test OpenMP_FLAG_DETECTED - Failed -- Try OpenMP CXX flag = [/openmp] -- Performing Test OpenMP_FLAG_DETECTED -- Performing Test OpenMP_FLAG_DETECTED - Failed -- Try OpenMP CXX flag = [-Qopenmp] -- Performing Test OpenMP_FLAG_DETECTED -- Performing Test OpenMP_FLAG_DETECTED - Failed -- Try OpenMP CXX flag = [-openmp] -- Performing Test OpenMP_FLAG_DETECTED -- Performing Test OpenMP_FLAG_DETECTED - Failed -- Try OpenMP CXX flag = [-xopenmp] -- Performing Test OpenMP_FLAG_DETECTED -- Performing Test OpenMP_FLAG_DETECTED - Failed -- Try OpenMP CXX flag = [+Oopenmp] -- Performing Test OpenMP_FLAG_DETECTED -- Performing Test OpenMP_FLAG_DETECTED - Failed -- Try OpenMP CXX flag = [-qsmp] -- Performing Test OpenMP_FLAG_DETECTED -- Performing Test OpenMP_FLAG_DETECTED - Failed -- Try OpenMP CXX flag = [-mp] -- Performing Test OpenMP_FLAG_DETECTED -- Performing Test OpenMP_FLAG_DETECTED - Failed -- Could NOT find OpenMP (missing: OpenMP_CXX_FLAGS) -- 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_INSTALL_LOCALSTATEDIR CMAKE_INSTALL_SYSCONFDIR -- Build files have been written to: /<>/hhsuite-3.0~beta2+dfsg/mybuild debian/rules override_dh_auto_build make[1]: Entering directory '/<>/hhsuite-3.0~beta2+dfsg' dh_auto_build -- NO_PNG=1 make -j16 NO_PNG=1 make[2]: Entering directory '/<>/hhsuite-3.0~beta2+dfsg/mybuild' /usr/bin/cmake -H"/<>/hhsuite-3.0~beta2+dfsg" -B"/<>/hhsuite-3.0~beta2+dfsg/mybuild" --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start "/<>/hhsuite-3.0~beta2+dfsg/mybuild/CMakeFiles" "/<>/hhsuite-3.0~beta2+dfsg/mybuild/CMakeFiles/progress.marks" make -f CMakeFiles/Makefile2 all make[3]: Entering directory '/<>/hhsuite-3.0~beta2+dfsg/mybuild' make -f src/CMakeFiles/A3M_COMPRESS_OBJECT.dir/build.make src/CMakeFiles/A3M_COMPRESS_OBJECT.dir/depend make -f src/CMakeFiles/HH_OBJECTS.dir/build.make src/CMakeFiles/HH_OBJECTS.dir/depend make -f src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/build.make src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/depend make -f src/CMakeFiles/CS_OBJECTS.dir/build.make src/CMakeFiles/CS_OBJECTS.dir/depend 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/hhviterbialgorithm_and_ss.dir/build.make src/CMakeFiles/hhviterbialgorithm_and_ss.dir/depend make[4]: Entering directory '/<>/hhsuite-3.0~beta2+dfsg/mybuild' cd "/<>/hhsuite-3.0~beta2+dfsg/mybuild" && /usr/bin/cmake -E cmake_depends "Unix Makefiles" "/<>/hhsuite-3.0~beta2+dfsg" "/<>/hhsuite-3.0~beta2+dfsg/src" "/<>/hhsuite-3.0~beta2+dfsg/mybuild" "/<>/hhsuite-3.0~beta2+dfsg/mybuild/src" "/<>/hhsuite-3.0~beta2+dfsg/mybuild/src/CMakeFiles/A3M_COMPRESS_OBJECT.dir/DependInfo.cmake" --color= make -f doc/CMakeFiles/pdf.dir/build.make doc/CMakeFiles/pdf.dir/depend make[4]: Entering directory '/<>/hhsuite-3.0~beta2+dfsg/mybuild' cd "/<>/hhsuite-3.0~beta2+dfsg/mybuild" && /usr/bin/cmake -E cmake_depends "Unix Makefiles" "/<>/hhsuite-3.0~beta2+dfsg" "/<>/hhsuite-3.0~beta2+dfsg/doc" "/<>/hhsuite-3.0~beta2+dfsg/mybuild" "/<>/hhsuite-3.0~beta2+dfsg/mybuild/doc" "/<>/hhsuite-3.0~beta2+dfsg/mybuild/doc/CMakeFiles/pdf.dir/DependInfo.cmake" --color= make[4]: Entering directory '/<>/hhsuite-3.0~beta2+dfsg/mybuild' cd "/<>/hhsuite-3.0~beta2+dfsg/mybuild" && /usr/bin/cmake -E cmake_depends "Unix Makefiles" "/<>/hhsuite-3.0~beta2+dfsg" "/<>/hhsuite-3.0~beta2+dfsg/src" "/<>/hhsuite-3.0~beta2+dfsg/mybuild" "/<>/hhsuite-3.0~beta2+dfsg/mybuild/src" "/<>/hhsuite-3.0~beta2+dfsg/mybuild/src/CMakeFiles/HH_OBJECTS.dir/DependInfo.cmake" --color= make[4]: Entering directory '/<>/hhsuite-3.0~beta2+dfsg/mybuild' cd "/<>/hhsuite-3.0~beta2+dfsg/mybuild" && /usr/bin/cmake -E cmake_depends "Unix Makefiles" "/<>/hhsuite-3.0~beta2+dfsg" "/<>/hhsuite-3.0~beta2+dfsg/src" "/<>/hhsuite-3.0~beta2+dfsg/mybuild" "/<>/hhsuite-3.0~beta2+dfsg/mybuild/src" "/<>/hhsuite-3.0~beta2+dfsg/mybuild/src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/DependInfo.cmake" --color= make[4]: Entering directory '/<>/hhsuite-3.0~beta2+dfsg/mybuild' cd "/<>/hhsuite-3.0~beta2+dfsg/mybuild" && /usr/bin/cmake -E cmake_depends "Unix Makefiles" "/<>/hhsuite-3.0~beta2+dfsg" "/<>/hhsuite-3.0~beta2+dfsg/src" "/<>/hhsuite-3.0~beta2+dfsg/mybuild" "/<>/hhsuite-3.0~beta2+dfsg/mybuild/src" "/<>/hhsuite-3.0~beta2+dfsg/mybuild/src/CMakeFiles/CS_OBJECTS.dir/DependInfo.cmake" --color= make[4]: Entering directory '/<>/hhsuite-3.0~beta2+dfsg/mybuild' cd "/<>/hhsuite-3.0~beta2+dfsg/mybuild" && /usr/bin/cmake -E cmake_depends "Unix Makefiles" "/<>/hhsuite-3.0~beta2+dfsg" "/<>/hhsuite-3.0~beta2+dfsg/src" "/<>/hhsuite-3.0~beta2+dfsg/mybuild" "/<>/hhsuite-3.0~beta2+dfsg/mybuild/src" "/<>/hhsuite-3.0~beta2+dfsg/mybuild/src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/DependInfo.cmake" --color= make[4]: Entering directory '/<>/hhsuite-3.0~beta2+dfsg/mybuild' cd "/<>/hhsuite-3.0~beta2+dfsg/mybuild" && /usr/bin/cmake -E cmake_depends "Unix Makefiles" "/<>/hhsuite-3.0~beta2+dfsg" "/<>/hhsuite-3.0~beta2+dfsg/src" "/<>/hhsuite-3.0~beta2+dfsg/mybuild" "/<>/hhsuite-3.0~beta2+dfsg/mybuild/src" "/<>/hhsuite-3.0~beta2+dfsg/mybuild/src/CMakeFiles/hhviterbialgorithm_and_ss.dir/DependInfo.cmake" --color= Scanning dependencies of target pdf Scanning dependencies of target A3M_COMPRESS_OBJECT make[4]: Leaving directory '/<>/hhsuite-3.0~beta2+dfsg/mybuild' make -f doc/CMakeFiles/pdf.dir/build.make doc/CMakeFiles/pdf.dir/build make[4]: Leaving directory '/<>/hhsuite-3.0~beta2+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~beta2+dfsg/mybuild' make[4]: Entering directory '/<>/hhsuite-3.0~beta2+dfsg/mybuild' Scanning dependencies of target CS_OBJECTS Scanning dependencies of target hhviterbialgorithm_with_celloff make[4]: Leaving directory '/<>/hhsuite-3.0~beta2+dfsg/mybuild' make -f src/CMakeFiles/CS_OBJECTS.dir/build.make src/CMakeFiles/CS_OBJECTS.dir/build make[4]: Leaving directory '/<>/hhsuite-3.0~beta2+dfsg/mybuild' make -f src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/build.make src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/build Scanning dependencies of target hhviterbialgorithm_with_celloff_and_ss make[4]: Leaving directory '/<>/hhsuite-3.0~beta2+dfsg/mybuild' make -f src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/build.make src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/build Scanning dependencies of target hhviterbialgorithm_and_ss make[4]: Entering directory '/<>/hhsuite-3.0~beta2+dfsg/mybuild' make[4]: Entering directory '/<>/hhsuite-3.0~beta2+dfsg/mybuild' make[4]: Leaving directory '/<>/hhsuite-3.0~beta2+dfsg/mybuild' make -f src/CMakeFiles/hhviterbialgorithm_and_ss.dir/build.make src/CMakeFiles/hhviterbialgorithm_and_ss.dir/build make[4]: Entering directory '/<>/hhsuite-3.0~beta2+dfsg/mybuild' make[4]: Entering directory '/<>/hhsuite-3.0~beta2+dfsg/mybuild' [ 1%] Generating hhblits-hhsearch.png [ 2%] Generating hhsuite-userguide.tex cd "/<>/hhsuite-3.0~beta2+dfsg/mybuild/doc" && /usr/bin/cmake -E copy /<>/hhsuite-3.0~beta2+dfsg/doc/hhblits-hhsearch.png /<>/hhsuite-3.0~beta2+dfsg/mybuild/doc/hhblits-hhsearch.png cd "/<>/hhsuite-3.0~beta2+dfsg/mybuild/doc" && /usr/bin/cmake -E copy /<>/hhsuite-3.0~beta2+dfsg/doc/hhsuite-userguide.tex /<>/hhsuite-3.0~beta2+dfsg/mybuild/doc/hhsuite-userguide.tex [ 4%] Building CXX object src/CMakeFiles/A3M_COMPRESS_OBJECT.dir/a3m_compress.cpp.o cd "/<>/hhsuite-3.0~beta2+dfsg/mybuild/src" && /usr/bin/c++ 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(/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' v2.7a, with DG/SPQR fixes, and firstline=lastline fix <2008/02/07> (tvz)) (/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.def) (/usr/share/texlive/texmf-dist/tex/latex/latexconfig/hyperref.cfg)) Package hyperref Message: Driver (autodetected): hpdftex. 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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 429. [9] LaTeX Warning: Reference `installation' on page 10 undefined on input line 433. 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[12] Underfull \hbox (badness 10000) in paragraph at lines 572--573 [13] Overfull \hbox (7.67062pt too wide) in paragraph at lines 621--621 []\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 621--621 []\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 655--655 []\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 655--655 []\OT1/cmtt/m/n/10.95 $ ffindex_order sorting.dat _a3m.ff{data,index} _ a3m_ordered.ff{data,index}[] [14] Overfull \hbox (36.41406pt too wide) in paragraph at lines 670--670 []\OT1/cmtt/m/n/10.95 $ hhsuitedb.py -o --cpu 1 --ia3m= --ics219 = --ihhm=[] [15] LaTeX Warning: Citation `Todd:2001' on page 16 undefined on input line 687. LaTeX Warning: Citation `Pawlowski:2000' on page 16 undefined on input line 687 . LaTeX Warning: Citation `Rychlewski:1998' on page 16 undefined on input line 68 7. LaTeX Warning: Citation `Kinch:2002' on page 16 undefined on input line 687. LaTeX Warning: Citation `Soding:2006a' on page 16 undefined on input line 687. LaTeX Warning: Citation `Alva:2010' on page 16 undefined on input line 687. LaTeX Warning: Citation `Chothia:1986' on page 16 undefined on input line 690. LaTeX Warning: Citation `Todd:2001' on page 16 undefined on input line 690. LaTeX Warning: Citation `Alva:2010' on page 16 undefined on input line 690. LaTeX Warning: Citation `Remmert:2010' on page 16 undefined on input line 690. [16] LaTeX Warning: Citation `Soding:2006b' on page 17 undefined on input line 721. LaTeX Warning: Citation `Mariani:2011' on page 17 undefined on input line 725. LaTeX Warning: Citation `Battey:2007' on page 17 undefined on input line 725. [17] LaTeX Warning: Citation `Durbin:2008' on page 18 undefined on input line 735. LaTeX Warning: Citation `Biegert:2008' on page 18 undefined on input line 735. LaTeX Warning: Citation `Soding:2005b' on page 18 undefined on input line 747. LaTeX Warning: Citation `Hildebrand:2009' on page 18 undefined on input line 74 7. LaTeX Warning: Reference `hhmformat' on page 18 undefined on input line 778. [18] LaTeX Warning: Reference `aliblocksformat' on page 19 undefined on input line 7 93. LaTeX Warning: Reference `Neff' on page 19 undefined on input line 795. LaTeX Warning: Reference `hhmformat' on page 19 undefined on input line 795. [19] LaTeX Warning: Citation `Sadreyev:2008' on page 20 undefined on input line 799. [20] LaTeX Warning: Citation `Remmert:2011' on page 21 undefined on input line 838. [21][ 29%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhsearch.cpp.o cd "/<>/hhsuite-3.0~beta2+dfsg/mybuild/src" && /usr/bin/c++ -DSSE -I"/<>/hhsuite-3.0~beta2+dfsg/src" -I"/<>/hhsuite-3.0~beta2+dfsg/src/cs" -I"/<>/hhsuite-3.0~beta2+dfsg/mybuild" -g -O2 -fdebug-prefix-map=/<>/hhsuite-3.0~beta2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse4.2 -mfpmath=sse -fno-strict-aliasing -o CMakeFiles/HH_OBJECTS.dir/hhsearch.cpp.o -c "/<>/hhsuite-3.0~beta2+dfsg/src/hhsearch.cpp" LaTeX Warning: Reference `report-bug' on page 22 undefined on input line 855. LaTeX Warning: Reference `msa_hhblits' on page 22 undefined on input line 869. [22] [23] [24] [25] [26] [27] Overfull \hbox (3.64589pt too wide) in paragraph at lines 1234--1234 [][]\OT1/cmr/bx/n/10.95 Secondary struc-ture in-for-ma-tion in A3M/A2M or FASTA MSAs for HH-search/HHblits [28] LaTeX Warning: Reference `msa_hhblits' on page 29 undefined on input line 1306. Overfull \hbox (16.43517pt too wide) in paragraph at lines 1302--1307 \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 [29] [30] LaTeX Warning: Reference `transformation' on page 31 undefined on input line 13 90. LaTeX Warning: Reference `transformation' on page 31 undefined on input line 13 90. LaTeX Warning: Reference `transformation' on page 31 undefined on input line 13 90. [31] Overfull \hbox (8.27538pt too wide) in paragraph at lines 1584--1584 [] \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 1584--1584 [] \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 1584--1584 [] \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 1584--1584 [] \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 1584--1584 [] \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 1584--1584 [] \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 1584--1584 [] \OT1/cmtt/m/n/10 -pre_score_offset offset on sequence profile scores in prefilter S-W alignment (default=50)[] [32] Overfull \hbox (45.02505pt too wide) in paragraph at lines 1584--1584 [] \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 1584--1584 [] \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 1584--1584 [] \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 1584--1584 [] \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 1584--1584 [] \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 1584--1584 [] \OT1/cmtt/m/n/10 -pc_hhm_nocontxt_mode {0,..,3} position dependence of pc admixture 'tau' (pc mode, default=2)[] Overfull \hbox (60.77492pt too wide) in paragraph at lines 1584--1584 [] \OT1/cmtt/m/n/10 -pc_prefilter_contxt_mode {0,..,3} position dependence o f pc admixture 'tau' (pc mode, default=3)[] [33] Overfull \hbox (71.27483pt too wide) in paragraph at lines 1584--1584 [] \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 1584--1584 [] \OT1/cmtt/m/n/10 -contxt context file for computing context-specific pseudocounts (default=${HHLIB}/data/context_data.crf)[] [34] Overfull \hbox (8.27538pt too wide) in paragraph at lines 1715--1715 [] \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 1715--1715 [] \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 1715--1715 [] \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 1715--1715 [] \OT1/cmtt/m/n/10 -ssa [0,1] SS substitution matrix = (1-ssa)*I + ss a*full-SS-substition-matrix [def=1.00)[] [35][ 31%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhalign.cpp.o cd "/<>/hhsuite-3.0~beta2+dfsg/mybuild/src" && /usr/bin/c++ -DSSE -I"/<>/hhsuite-3.0~beta2+dfsg/src" -I"/<>/hhsuite-3.0~beta2+dfsg/src/cs" -I"/<>/hhsuite-3.0~beta2+dfsg/mybuild" -g -O2 -fdebug-prefix-map=/<>/hhsuite-3.0~beta2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse4.2 -mfpmath=sse -fno-strict-aliasing -o CMakeFiles/HH_OBJECTS.dir/hhalign.cpp.o -c "/<>/hhsuite-3.0~beta2+dfsg/src/hhalign.cpp" Overfull \hbox (29.27519pt too wide) in paragraph at lines 1715--1715 [] \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 1715--1715 [] \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 1715--1715 [] \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 1715--1715 [] \OT1/cmtt/m/n/10 -contxt context file for computing context-specific pseudocounts (default=${HHLIB}/data/context_data.crf)[] [36][ 32%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhhitlist.cpp.o cd "/<>/hhsuite-3.0~beta2+dfsg/mybuild/src" && /usr/bin/c++ -DSSE -I"/<>/hhsuite-3.0~beta2+dfsg/src" -I"/<>/hhsuite-3.0~beta2+dfsg/src/cs" -I"/<>/hhsuite-3.0~beta2+dfsg/mybuild" -g -O2 -fdebug-prefix-map=/<>/hhsuite-3.0~beta2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse4.2 -mfpmath=sse -fno-strict-aliasing -o CMakeFiles/HH_OBJECTS.dir/hhhitlist.cpp.o -c "/<>/hhsuite-3.0~beta2+dfsg/src/hhhitlist.cpp" Overfull \hbox (29.27519pt too wide) in paragraph at lines 1814--1814 [] \OT1/cmtt/m/n/10 -pc_hhm_contxt_mode {0,..,3} position dependence of pc a dmixture 'tau' (pc mode, default=0)[] [37] Overfull \hbox (92.27464pt too wide) in paragraph at lines 1814--1814 [] \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 1814--1814 [] \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 1814--1814 [] \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 1875--1875 [] \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 1875--1875 [] \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 1875--1875 [] \OT1/cmtt/m/n/10 -add_cons generate consensus sequence as master sequen ce of query MSA (default=don't)[] [38] [39][ 34%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhposteriordecoder.cpp.o cd "/<>/hhsuite-3.0~beta2+dfsg/mybuild/src" && /usr/bin/c++ -DSSE -I"/<>/hhsuite-3.0~beta2+dfsg/src" -I"/<>/hhsuite-3.0~beta2+dfsg/src/cs" -I"/<>/hhsuite-3.0~beta2+dfsg/mybuild" -g -O2 -fdebug-prefix-map=/<>/hhsuite-3.0~beta2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse4.2 -mfpmath=sse -fno-strict-aliasing -o CMakeFiles/HH_OBJECTS.dir/hhposteriordecoder.cpp.o -c "/<>/hhsuite-3.0~beta2+dfsg/src/hhposteriordecoder.cpp" LaTeX Warning: Citation `Sali:1993' on page 40 undefined on input line 1969. [40] [41] Overfull \hbox (50.27501pt too wide) in paragraph at lines 2057--2057 []\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 2079--2079 [] \OT1/cmtt/m/n/10 The program reads an input sequence in FASTA/A3M which must have a SCOP domain, PDB chain, or DALI[] Overfull \hbox (50.27501pt too wide) in paragraph at lines 2079--2079 [] \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 2079--2079 [] \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 2079--2079 [] \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 2079--2079 [] \OT1/cmtt/m/n/10 (HETATM records for MSE (selenomethionine) will be interpre ted as ATOM records for MET in the[] [42] Overfull \hbox (170.34192pt too wide) in paragraph at lines 2147--2149 []\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 . [43] LaTeX Warning: Citation `Remmert:2011' on page 44 undefined on input line 2176. [44]In file included from /<>/hhsuite-3.0~beta2+dfsg/src/hhdecl.cpp:1: In file included from /<>/hhsuite-3.0~beta2+dfsg/src/hhdecl.h:18: In file included from /<>/hhsuite-3.0~beta2+dfsg/src/cs/crf.h:24: In file included from /<>/hhsuite-3.0~beta2+dfsg/src/cs/context_profile-inl.h:23: In file included from /<>/hhsuite-3.0~beta2+dfsg/src/cs/context_profile.h:24: In file included from /<>/hhsuite-3.0~beta2+dfsg/src/cs/count_profile-inl.h:25: /<>/hhsuite-3.0~beta2+dfsg/src/cs/alignment-inl.h:674:15: warning: comparison of constant -1 with expression of type 'uint8_t' (aka 'unsigned char') is always false [-Wtautological-constant-out-of-range-compare] if (c == EOF) break; ~ ^ ~~~ [45]In file included from /<>/hhsuite-3.0~beta2+dfsg/src/hhviterbialgorithm.cpp:7: In file included from /<>/hhsuite-3.0~beta2+dfsg/src/hhviterbi.h:11: In file included from /<>/hhsuite-3.0~beta2+dfsg/src/hhhit.h:20: In file included from /<>/hhsuite-3.0~beta2+dfsg/src/hhhmm.h:16: In file included from /<>/hhsuite-3.0~beta2+dfsg/src/hhdecl.h:18: In file included from /<>/hhsuite-3.0~beta2+dfsg/src/cs/crf.h:24: In file included from /<>/hhsuite-3.0~beta2+dfsg/src/cs/context_profile-inl.h:23: In file included from /<>/hhsuite-3.0~beta2+dfsg/src/cs/context_profile.h:24: In file included from /<>/hhsuite-3.0~beta2+dfsg/src/cs/count_profile-inl.h:25: /<>/hhsuite-3.0~beta2+dfsg/src/cs/alignment-inl.h:674:15: warning: comparison of constant -1 with expression of type 'uint8_t' (aka 'unsigned char') is always false [-Wtautological-constant-out-of-range-compare] if (c == EOF) break; ~ ^ ~~~ /<>/hhsuite-3.0~beta2+dfsg/src/cs/alignment-inl.h:846:21: warning: add explicit braces to avoid dangling else [-Wdangling-else] else ^ LaTeX Warning: Citation `Farrar:2007' on page 46 undefined on input line 2338. [46]/<>/hhsuite-3.0~beta2+dfsg/src/cs/alignment-inl.h:846:21: warning: add explicit braces to avoid dangling else [-Wdangling-else] else ^ Underfull \hbox (badness 10000) in paragraph at lines 2363--2371 No file hhsuite-userguide.bbl. [47] (./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)>/hhsuite-3.0~beta2+dfsg/src/hhmatrices.cpp:3: In file included from /<>/hhsuite-3.0~beta2+dfsg/src/hhmatrices.h:11: In file included from /<>/hhsuite-3.0~beta2+dfsg/src/hhdecl.h:18: In file included from /<>/hhsuite-3.0~beta2+dfsg/src/cs/crf.h:24: In file included from /<>/hhsuite-3.0~beta2+dfsg/src/cs/context_profile-inl.h:23: In file included from /<>/hhsuite-3.0~beta2+dfsg/src/cs/context_profile.h:24: In file included from /<>/hhsuite-3.0~beta2+dfsg/src/cs/count_profile-inl.h:25: /<>/hhsuite-3.0~beta2+dfsg/src/cs/alignment-inl.h:674:15: warning: comparison of constant -1 with expression of type 'uint8_t' (aka 'unsigned char') is always false [-Wtautological-constant-out-of-range-compare] if (c == EOF) break; ~ ^ ~~~ >>/hhsuite-3.0~beta2+dfsg/src/cs/alignment-inl.h>:846:21: warning: add explicit braces to avoid dangling else [-Wdangling-else] else ^ >/hhsuite-3.0~beta2+dfsg/src/hhviterbialgorithm.cpp:7: In file included from /<>/hhsuite-3.0~beta2+dfsg/src/hhviterbi.h:11: In file included from /<>/hhsuite-3.0~beta2+dfsg/src/hhhit.h:20: In file included from /<>/hhsuite-3.0~beta2+dfsg/src/hhhmm.h:16: In file included from /<>/hhsuite-3.0~beta2+dfsg/src/hhdecl.h:18: In file included from /<>/hhsuite-3.0~beta2+dfsg/src/cs/crf.h:24: In file included from /<>/hhsuite-3.0~beta2+dfsg/src/cs/context_profile-inl.h:23: In file included from /<>/hhsuite-3.0~beta2+dfsg/src/cs/context_profile.h:24: In file included from /<>/hhsuite-3.0~beta2+dfsg/src/cs/count_profile-inl.h:25: /<>/hhsuite-3.0~beta2+dfsg/src/cs/alignment-inl.h:674:15: warning: comparison of constant -1 with expression of type 'uint8_t' (aka 'unsigned char') is always false [-Wtautological-constant-out-of-range-compare] if (c == EOF) break; ~ ^ ~~~ > /<>/hhsuite-3.0~beta2+dfsg/src/cs/alignment-inl.h:846:21: warning: add explicit braces to avoid dangling else [-Wdangling-else] else ^ Output written on hhsuite-userguide.pdf (47 pages, 329529 bytes). Transcript written on hhsuite-userguide.log. cd "/<>/hhsuite-3.0~beta2+dfsg/mybuild/doc" && /usr/bin/cmake -E chdir /<>/hhsuite-3.0~beta2+dfsg/mybuild/doc /usr/bin/bibtex hhsuite-userguide In file included from /<>/hhsuite-3.0~beta2+dfsg/src/hhviterbialgorithm.cpp:7: In file included from /<>/hhsuite-3.0~beta2+dfsg/src/hhviterbi.h:11: In file included from /<>/hhsuite-3.0~beta2+dfsg/src/hhhit.h:20: In file included from /<>/hhsuite-3.0~beta2+dfsg/src/hhhmm.h:16: In file included from /<>/hhsuite-3.0~beta2+dfsg/src/hhdecl.h:18: In file included from /<>/hhsuite-3.0~beta2+dfsg/src/cs/crf.h:24: In file included from /<>/hhsuite-3.0~beta2+dfsg/src/cs/context_profile-inl.h:23: In file included from /<>/hhsuite-3.0~beta2+dfsg/src/cs/context_profile.h:24: In file included from /<>/hhsuite-3.0~beta2+dfsg/src/cs/count_profile-inl.h:25: /<>/hhsuite-3.0~beta2+dfsg/src/cs/alignment-inl.h:674:15: warning: comparison of constant -1 with expression of type 'uint8_t' (aka 'unsigned char') is always false [-Wtautological-constant-out-of-range-compare] if (c == EOF) break; ~ ^ ~~~ /<>/hhsuite-3.0~beta2+dfsg/src/cs/alignment-inl.h:846:21: warning: add explicit braces to avoid dangling else [-Wdangling-else] else ^ In file included from /<>/hhsuite-3.0~beta2+dfsg/src/hhhit.cpp:3: In file included from /<>/hhsuite-3.0~beta2+dfsg/src/hhhit.h:20: In file included from /<>/hhsuite-3.0~beta2+dfsg/src/hhhmm.h:16: In file included from /<>/hhsuite-3.0~beta2+dfsg/src/hhdecl.h:18: In file included from /<>/hhsuite-3.0~beta2+dfsg/src/cs/crf.h:24: In file included from /<>/hhsuite-3.0~beta2+dfsg/src/cs/context_profile-inl.h:23: In file included from /<>/hhsuite-3.0~beta2+dfsg/src/cs/context_profile.h:24: In file included from /<>/hhsuite-3.0~beta2+dfsg/src/cs/count_profile-inl.h:25: /<>/hhsuite-3.0~beta2+dfsg/src/cs/alignment-inl.h:674:15: warning: comparison of constant -1 with expression of type 'uint8_t' (aka 'unsigned char') is always false [-Wtautological-constant-out-of-range-compare] if (c == EOF) break; ~ ^ ~~~ /<>/hhsuite-3.0~beta2+dfsg/src/cs/alignment-inl.h:846:21: warning: add explicit braces to avoid dangling else [-Wdangling-else] else ^ This is BibTeX, Version 0.99d (TeX Live 2017/Debian) The top-level auxiliary file: hhsuite-userguide.aux The style file: unsrt.bst Database file #1: hhsuite-userguide.bib.bib cd "/<>/hhsuite-3.0~beta2+dfsg/mybuild/doc" && /usr/bin/cmake -E chdir /<>/hhsuite-3.0~beta2+dfsg/mybuild/doc /usr/bin/pdflatex -interaction=nonstopmode hhsuite-userguide.tex This is pdfTeX, Version 3.14159265-2.6-1.40.18 (TeX Live 2017/Debian) (preloaded format=pdflatex) restricted \write18 enabled. In file included from /<>/hhsuite-3.0~beta2+dfsg/src/hhblits.cpp:8: In file included from /<>/hhsuite-3.0~beta2+dfsg/src/hhblits.h:51: In file included from /<>/hhsuite-3.0~beta2+dfsg/src/cs/context_library.h:25: In file included from /<>/hhsuite-3.0~beta2+dfsg/src/cs/context_profile.h:24: In file included from /<>/hhsuite-3.0~beta2+dfsg/src/cs/count_profile-inl.h:25: /<>/hhsuite-3.0~beta2+dfsg/src/cs/alignment-inl.h:674:15: warning: comparison of constant -1 with expression of type 'uint8_t' (aka 'unsigned char') is always false [-Wtautological-constant-out-of-range-compare] if (c == EOF) break; ~ ^ ~~~ /<>/hhsuite-3.0~beta2+dfsg/src/cs/alignment-inl.h:846:21: warning: add explicit braces to avoid dangling else [-Wdangling-else] else ^ entering extended mode (./hhsuite-userguide.tex LaTeX2e <2017-04-15> Babel <3.11> and hyphenation patterns for 3 language(s) loaded. (/usr/share/texlive/texmf-dist/tex/latex/base/article.cls Document Class: article 2014/09/29 v1.4h 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' v2.7a, with DG/SPQR fixes, and firstline=lastline fix <2008/02/07> (tvz)) (/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.def) (/usr/share/texlive/texmf-dist/tex/latex/latexconfig/hyperref.cfg)) Package hyperref Message: Driver (autodetected): hpdftex. (/usr/share/texlive/texmf-dist/tex/latex/hyperref/hpdftex.def (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/rerunfilecheck.sty)) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/bkm-pdftex.def/<>/hhsuite-3.0~beta2+dfsg/src/hhdecl.cpp:32:7: warning: comparison of array 'program_path' not equal to a null pointer is always true [-Wtautological-pointer-compare] if (program_path != NULL) { ^~~~~~~~~~~~ ~~~~ )) (/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/graphics/color.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/color.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[ 35%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhutil.cpp.o cd "/<>/hhsuite-3.0~beta2+dfsg/mybuild/src" && /usr/bin/c++ -DSSE -I"/<>/hhsuite-3.0~beta2+dfsg/src" -I"/<>/hhsuite-3.0~beta2+dfsg/src/cs" -I"/<>/hhsuite-3.0~beta2+dfsg/mybuild" -g -O2 -fdebug-prefix-map=/<>/hhsuite-3.0~beta2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse4.2 -mfpmath=sse -fno-strict-aliasing -o CMakeFiles/HH_OBJECTS.dir/hhutil.cpp.o -c "/<>/hhsuite-3.0~beta2+dfsg/src/hhutil.cpp" ]) [3] LaTeX Warning: Citation `Durbin:2008' on page 4 undefined on input line 98. 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[8] [9] [10] [11 <./hhblits-hhsearch.png2 warnings generated. make[4]: Leaving directory '/<>/hhsuite-3.0~beta2+dfsg/mybuild' [ 35%] Built target hhviterbialgorithm_with_celloff [ 37%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/util.cpp.o cd "/<>/hhsuite-3.0~beta2+dfsg/mybuild/src" && /usr/bin/c++ -DSSE -I"/<>/hhsuite-3.0~beta2+dfsg/src" -I"/<>/hhsuite-3.0~beta2+dfsg/src/cs" -I"/<>/hhsuite-3.0~beta2+dfsg/mybuild" -g -O2 -fdebug-prefix-map=/<>/hhsuite-3.0~beta2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse4.2 -mfpmath=sse -fno-strict-aliasing -o CMakeFiles/HH_OBJECTS.dir/util.cpp.o -c "/<>/hhsuite-3.0~beta2+dfsg/src/util.cpp" 2 warnings generated. 2 warnings generated. make[4]: Leaving directory '/<>/hhsuite-3.0~beta2+dfsg/mybuild' make[4]: Leaving directory '/<>/hhsuite-3.0~beta2+dfsg/mybuild' 2 warnings generated. [ 37%] Built target hhviterbialgorithm_with_celloff_and_ss [ 37%] Built target A3M_COMPRESS_OBJECT [ 38%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhalignment.cpp.o make -f src/CMakeFiles/a3m_database_filter.dir/build.make src/CMakeFiles/a3m_database_filter.dir/depend cd "/<>/hhsuite-3.0~beta2+dfsg/mybuild/src" && /usr/bin/c++ -DSSE -I"/<>/hhsuite-3.0~beta2+dfsg/src" -I"/<>/hhsuite-3.0~beta2+dfsg/src/cs" -I"/<>/hhsuite-3.0~beta2+dfsg/mybuild" -g -O2 -fdebug-prefix-map=/<>/hhsuite-3.0~beta2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse4.2 -mfpmath=sse -fno-strict-aliasing -o CMakeFiles/HH_OBJECTS.dir/hhalignment.cpp.o -c "/<>/hhsuite-3.0~beta2+dfsg/src/hhalignment.cpp" make[4]: Leaving directory '/<>/hhsuite-3.0~beta2+dfsg/mybuild' make[4]: Entering directory '/<>/hhsuite-3.0~beta2+dfsg/mybuild' cd "/<>/hhsuite-3.0~beta2+dfsg/mybuild" && /usr/bin/cmake -E cmake_depends "Unix Makefiles" "/<>/hhsuite-3.0~beta2+dfsg" "/<>/hhsuite-3.0~beta2+dfsg/src" "/<>/hhsuite-3.0~beta2+dfsg/mybuild" "/<>/hhsuite-3.0~beta2+dfsg/mybuild/src" "/<>/hhsuite-3.0~beta2+dfsg/mybuild/src/CMakeFiles/a3m_database_filter.dir/DependInfo.cmake" --color= [ 40%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhforwardalgorithm.cpp.o cd "/<>/hhsuite-3.0~beta2+dfsg/mybuild/src" && /usr/bin/c++ -DSSE -I"/<>/hhsuite-3.0~beta2+dfsg/src" -I"/<>/hhsuite-3.0~beta2+dfsg/src/cs" -I"/<>/hhsuite-3.0~beta2+dfsg/mybuild" -g -O2 -fdebug-prefix-map=/<>/hhsuite-3.0~beta2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse4.2 -mfpmath=sse -fno-strict-aliasing -o CMakeFiles/HH_OBJECTS.dir/hhforwardalgorithm.cpp.o -c "/<>/hhsuite-3.0~beta2+dfsg/src/hhforwardalgorithm.cpp" Scanning dependencies of target a3m_database_filter make[4]: Leaving directory '/<>/hhsuite-3.0~beta2+dfsg/mybuild' make -f src/CMakeFiles/a3m_database_filter.dir/build.make src/CMakeFiles/a3m_database_filter.dir/build make[4]: Entering directory '/<>/hhsuite-3.0~beta2+dfsg/mybuild' [ 40%] Built target hhviterbialgorithm_and_ss make -f src/CMakeFiles/a3m_database_reduce.dir/build.make src/CMakeFiles/a3m_database_reduce.dir/depend make[4]: Entering directory '/<>/hhsuite-3.0~beta2+dfsg/mybuild' cd "/<>/hhsuite-3.0~beta2+dfsg/mybuild" && /usr/bin/cmake -E cmake_depends "Unix Makefiles" "/<>/hhsuite-3.0~beta2+dfsg" "/<>/hhsuite-3.0~beta2+dfsg/src" "/<>/hhsuite-3.0~beta2+dfsg/mybuild" "/<>/hhsuite-3.0~beta2+dfsg/mybuild/src" "/<>/hhsuite-3.0~beta2+dfsg/mybuild/src/CMakeFiles/a3m_database_reduce.dir/DependInfo.cmake" --color= [ 41%] Building CXX object src/CMakeFiles/a3m_database_filter.dir/a3m_database_filter.cpp.o cd "/<>/hhsuite-3.0~beta2+dfsg/mybuild/src" && /usr/bin/c++ -DSSE -I"/<>/hhsuite-3.0~beta2+dfsg/src" -I"/<>/hhsuite-3.0~beta2+dfsg/src/cs" -I"/<>/hhsuite-3.0~beta2+dfsg/mybuild" -g -O2 -fdebug-prefix-map=/<>/hhsuite-3.0~beta2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security 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CMakeFiles/a3m_database_reduce.dir/a3m_database_reduce.cpp.o -c "/<>/hhsuite-3.0~beta2+dfsg/src/a3m_database_reduce.cpp" 3 warnings generated. make -f src/CMakeFiles/a3m_database_extract.dir/build.make src/CMakeFiles/a3m_database_extract.dir/depend make[4]: Entering directory '/<>/hhsuite-3.0~beta2+dfsg/mybuild' cd "/<>/hhsuite-3.0~beta2+dfsg/mybuild" && /usr/bin/cmake -E cmake_depends "Unix Makefiles" "/<>/hhsuite-3.0~beta2+dfsg" "/<>/hhsuite-3.0~beta2+dfsg/src" "/<>/hhsuite-3.0~beta2+dfsg/mybuild" "/<>/hhsuite-3.0~beta2+dfsg/mybuild/src" "/<>/hhsuite-3.0~beta2+dfsg/mybuild/src/CMakeFiles/a3m_database_extract.dir/DependInfo.cmake" --color= [ 44%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhhmm.cpp.o cd "/<>/hhsuite-3.0~beta2+dfsg/mybuild/src" && /usr/bin/c++ -DSSE -I"/<>/hhsuite-3.0~beta2+dfsg/src" -I"/<>/hhsuite-3.0~beta2+dfsg/src/cs" -I"/<>/hhsuite-3.0~beta2+dfsg/mybuild" -g -O2 -fdebug-prefix-map=/<>/hhsuite-3.0~beta2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse4.2 -mfpmath=sse -fno-strict-aliasing -o CMakeFiles/HH_OBJECTS.dir/hhhmm.cpp.o -c "/<>/hhsuite-3.0~beta2+dfsg/src/hhhmm.cpp" Scanning dependencies of target a3m_database_extract make[4]: Leaving directory '/<>/hhsuite-3.0~beta2+dfsg/mybuild' make -f src/CMakeFiles/a3m_database_extract.dir/build.make src/CMakeFiles/a3m_database_extract.dir/build make[4]: Entering directory '/<>/hhsuite-3.0~beta2+dfsg/mybuild' [ 46%] Building CXX object src/CMakeFiles/a3m_database_extract.dir/a3m_database_extract.cpp.o cd "/<>/hhsuite-3.0~beta2+dfsg/mybuild/src" && /usr/bin/c++ -DSSE -I"/<>/hhsuite-3.0~beta2+dfsg/src" -I"/<>/hhsuite-3.0~beta2+dfsg/src/cs" -I"/<>/hhsuite-3.0~beta2+dfsg/mybuild" -g -O2 -fdebug-prefix-map=/<>/hhsuite-3.0~beta2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse4.2 -mfpmath=sse -fno-strict-aliasing -o CMakeFiles/a3m_database_extract.dir/a3m_database_extract.cpp.o -c "/<>/hhsuite-3.0~beta2+dfsg/src/a3m_database_extract.cpp" make[4]: Leaving directory '/<>/hhsuite-3.0~beta2+dfsg/mybuild' [ 46%] Built target CS_OBJECTS make -f src/CMakeFiles/a3m_reduce.dir/build.make src/CMakeFiles/a3m_reduce.dir/depend make[4]: Entering directory '/<>/hhsuite-3.0~beta2+dfsg/mybuild' cd "/<>/hhsuite-3.0~beta2+dfsg/mybuild" && /usr/bin/cmake -E cmake_depends "Unix Makefiles" "/<>/hhsuite-3.0~beta2+dfsg" "/<>/hhsuite-3.0~beta2+dfsg/src" "/<>/hhsuite-3.0~beta2+dfsg/mybuild" "/<>/hhsuite-3.0~beta2+dfsg/mybuild/src" "/<>/hhsuite-3.0~beta2+dfsg/mybuild/src/CMakeFiles/a3m_reduce.dir/DependInfo.cmake" --color= Scanning dependencies of target a3m_reduce make[4]: Leaving directory '/<>/hhsuite-3.0~beta2+dfsg/mybuild' make -f src/CMakeFiles/a3m_reduce.dir/build.make src/CMakeFiles/a3m_reduce.dir/build make[4]: Entering directory '/<>/hhsuite-3.0~beta2+dfsg/mybuild' >] [12][ 47%] Building CXX object src/CMakeFiles/a3m_reduce.dir/a3m_reduce.cpp.o cd "/<>/hhsuite-3.0~beta2+dfsg/mybuild/src" && /usr/bin/c++ -DSSE -I"/<>/hhsuite-3.0~beta2+dfsg/src" -I"/<>/hhsuite-3.0~beta2+dfsg/src/cs" -I"/<>/hhsuite-3.0~beta2+dfsg/mybuild" -g -O2 -fdebug-prefix-map=/<>/hhsuite-3.0~beta2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse4.2 -mfpmath=sse -fno-strict-aliasing -o CMakeFiles/a3m_reduce.dir/a3m_reduce.cpp.o -c "/<>/hhsuite-3.0~beta2+dfsg/src/a3m_reduce.cpp" LaTeX Warning: Citation `Gonzalez:2010' on page 13 undefined on input line 532. [13] Underfull \hbox (badness 10000) in paragraph at lines 572--573 [14] Overfull \hbox (7.67062pt too wide) in paragraph at lines 621--621 []\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 621--621 []\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 655--655 []\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 655--655 []\OT1/cmtt/m/n/10.95 $ ffindex_order sorting.dat _a3m.ff{data,index} _ a3m_ordered.ff{data,index}[] [15] Overfull \hbox (36.41406pt too wide) in paragraph at lines 670--670 []\OT1/cmtt/m/n/10.95 $ hhsuitedb.py -o --cpu 1 --ia3m= --ics219 = --ihhm=[] [16] LaTeX Warning: Citation `Todd:2001' on page 17 undefined on input line 687. LaTeX Warning: Citation `Pawlowski:2000' on page 17 undefined on input line 687 . LaTeX Warning: Citation `Rychlewski:1998' on page 17 undefined on input line 68 7. LaTeX Warning: Citation `Kinch:2002' on page 17 undefined on input line 687. LaTeX Warning: Citation `Soding:2006a' on page 17 undefined on input line 687. LaTeX Warning: Citation `Alva:2010' on page 17 undefined on input line 687. LaTeX Warning: Citation `Chothia:1986' on page 17 undefined on input line 690. LaTeX Warning: Citation `Todd:2001' on page 17 undefined on input line 690. LaTeX Warning: Citation `Alva:2010' on page 17 undefined on input line 690. LaTeX Warning: Citation `Remmert:2010' on page 17 undefined on input line 690. [17] LaTeX Warning: Citation `Soding:2006b' on page 18 undefined on input line 721. LaTeX Warning: Citation `Mariani:2011' on page 18 undefined on input line 725. LaTeX Warning: Citation `Battey:2007' on page 18 undefined on input line 725. [18]In file included from /<>/hhsuite-3.0~beta2+dfsg/src/hhsearch.cpp:3: In file included from /<>/hhsuite-3.0~beta2+dfsg/src/hhsearch.h:34: In file included from /<>/hhsuite-3.0~beta2+dfsg/src/hhblits.h:51: In file included from /<>/hhsuite-3.0~beta2+dfsg/src/cs/context_library.h:25: In file included from /<>/hhsuite-3.0~beta2+dfsg/src/cs/context_profile.h:24: In file included from /<>/hhsuite-3.0~beta2+dfsg/src/cs/count_profile-inl.h:25: /<>/hhsuite-3.0~beta2+dfsg/src/cs/alignment-inl.h:674:15: warning: comparison of constant -1 with expression of type 'uint8_t' (aka 'unsigned char') is always false [-Wtautological-constant-out-of-range-compare] if (c == EOF) break; ~ ^ ~~~ In file included from /<>/hhsuite-3.0~beta2+dfsg/src/hhalign.cpp:30: In file included from /<>/hhsuite-3.0~beta2+dfsg/src/hhalign.h:38: In file included from /<>/hhsuite-3.0~beta2+dfsg/src/cs/context_library.h:25: In file included from /<>/hhsuite-3.0~beta2+dfsg/src/cs/context_profile.h:24: In file included from /<>/hhsuite-3.0~beta2+dfsg/src/cs/count_profile-inl.h:25: /<>/hhsuite-3.0~beta2+dfsg/src/cs/alignment-inl.h:674:15: warning: comparison of constant -1 with expression of type 'uint8_t' (aka 'unsigned char') is always false [-Wtautological-constant-out-of-range-compare] if (c == EOF) break; ~ ^ ~~~ LaTeX Warning: Citation `Durbin:2008' on page 19 undefined on input line 735. LaTeX Warning: Citation `Biegert:2008' on page 19 undefined on input line 735. LaTeX Warning: Citation `Soding:2005b' on page 19 undefined on input line 747. LaTeX Warning: Citation `Hildebrand:2009' on page 19 undefined on input line 74 7. [19]/<>/hhsuite-3.0~beta2+dfsg/src/cs/alignment-inl.h:846:21: warning: add explicit braces to avoid dangling else [-Wdangling-else] else ^ /<>/hhsuite-3.0~beta2+dfsg/src/cs/alignment-inl.h:846:21: warning: add explicit braces to avoid dangling else [-Wdangling-else] else ^ [20] LaTeX Warning: Citation `Sadreyev:2008' on page 21 undefined on input line 799. [21] LaTeX Warning: Citation `Remmert:2011' on page 22 undefined on input line 838. [22] [23] [24] [25] [26] [27] [28] Overfull \hbox (3.64589pt too wide) in paragraph at lines 1234--1234 [][]\OT1/cmr/bx/n/10.95 Secondary struc-ture in-for-ma-tion in A3M/A2M or FASTA MSAs for HH-search/HHblits [29] Overfull \hbox (16.43517pt too wide) in paragraph at lines 1302--1307 \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 [30] [31] [32] Overfull \hbox (8.27538pt too wide) in paragraph at lines 1584--1584 [] \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 1584--1584 [] \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 1584--1584 [] \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 1584--1584 [] \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 1584--1584 [] \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 1584--1584 [] \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 1584--1584 [] \OT1/cmtt/m/n/10 -pre_score_offset offset on sequence profile scores in prefilter S-W alignment (default=50)[] [33] Overfull \hbox (45.02505pt too wide) in paragraph at lines 1584--1584 [] \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 1584--1584 [] \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 1584--1584 [] \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 1584--1584 [] \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 1584--1584 [] \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 1584--1584 [] \OT1/cmtt/m/n/10 -pc_hhm_nocontxt_mode {0,..,3} position dependence of pc admixture 'tau' (pc mode, default=2)[] Overfull \hbox (60.77492pt too wide) in paragraph at lines 1584--1584 [] \OT1/cmtt/m/n/10 -pc_prefilter_contxt_mode {0,..,3} position dependence o f pc admixture 'tau' (pc mode, default=3)[] [34] Overfull \hbox (71.27483pt too wide) in paragraph at lines 1584--1584 [] \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 1584--1584 [] \OT1/cmtt/m/n/10 -contxt context file for computing context-specific pseudocounts (default=${HHLIB}/data/context_data.crf)[] [35]In file included from /<>/hhsuite-3.0~beta2+dfsg/src/hhhitlist.cpp:9: Overfull \hbox (8.27538pt too wide) in paragraph at lines 1715--1715 [] \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 1715--1715 [] \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 1715--1715 [] \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 1715--1715 [] \OT1/cmtt/m/n/10 -ssa [0,1] SS substitution matrix = (1-ssa)*I + ss a*full-SS-substition-matrix [def=1.00)[] [36In file included from /<>/hhsuite-3.0~beta2+dfsg/src/hhhitlist.h:17: In file included from /<>/hhsuite-3.0~beta2+dfsg/src/hhhit.h:20: In file included from /<>/hhsuite-3.0~beta2+dfsg/src/hhhmm.h:16: In file included from /<>/hhsuite-3.0~beta2+dfsg/src/hhdecl.h:18: In file included from /<>/hhsuite-3.0~beta2+dfsg/src/cs/crf.h:24: In file included from /<>/hhsuite-3.0~beta2+dfsg/src/cs/context_profile-inl.h:23: In file included from /<>/hhsuite-3.0~beta2+dfsg/src/cs/context_profile.h:24: In file included from /<>/hhsuite-3.0~beta2+dfsg/src/cs/count_profile-inl.h:25: /<>/hhsuite-3.0~beta2+dfsg/src/cs/alignment-inl.h:674:15: warning: comparison of constant -1 with expression of type 'uint8_t' (aka 'unsigned char') is always false [-Wtautological-constant-out-of-range-compare] if (c == EOF) break; ~ ^ ~~~ ] Overfull \hbox (29.27519pt too wide) in paragraph at lines 1715--1715 [] \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 1715--1715 [] \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 1715--1715 [] \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 1715--1715 [] \OT1/cmtt/m/n/10 -contxt context file for computing context-specific pseudocounts (default=${HHLIB}/data/context_data.crf)[] [37/<>/hhsuite-3.0~beta2+dfsg/src/cs/alignment-inl.h:846]:21: warning: add explicit braces to avoid dangling else [-Wdangling-else] else ^ Overfull \hbox (29.27519pt too wide) in paragraph at lines 1814--1814 [] \OT1/cmtt/m/n/10 -pc_hhm_contxt_mode {0,..,3} position dependence of pc a dmixture 'tau' (pc mode, default=0)[] [38]In file included from /<>/hhsuite-3.0~beta2+dfsg/src/hhposteriordecoder.cpp:29: In file included from /<>/hhsuite-3.0~beta2+dfsg/src/hhposteriordecoder.h:36: In file included from /<>/hhsuite-3.0~beta2+dfsg/src/hhhmmsimd.h:5: In file included from /<>/hhsuite-3.0~beta2+dfsg/src/hhhmm.h:16: In file included from /<>/hhsuite-3.0~beta2+dfsg/src/hhdecl.h:18: In file included from /<>/hhsuite-3.0~beta2+dfsg/src/cs/crf.h:24: In file included from /<>/hhsuite-3.0~beta2+dfsg/src/cs/context_profile-inl.h:23: In file included from /<>/hhsuite-3.0~beta2+dfsg/src/cs/context_profile.h:24: In file included from /<>/hhsuite-3.0~beta2+dfsg/src/cs/count_profile-inl.h:25: /<>/hhsuite-3.0~beta2+dfsg/src/cs/alignment-inl.h:674:15: warning: comparison of constant -1 with expression of type 'uint8_t' (aka 'unsigned char') is always false [-Wtautological-constant-out-of-range-compare] if (c == EOF) break; ~ ^ ~~~ Overfull \hbox (92.27464pt too wide) in paragraph at lines 1814--1814 [] \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 1814--1814 [] \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 1814--1814 [] \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 1875--1875 [] \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 1875--1875 [] \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 1875--1875 [] \OT1/cmtt/m/n/10 -add_cons generate consensus sequence as master sequen ce of query MSA (default=don't)[] [39]/<>/hhsuite-3.0~beta2+dfsg/src/cs/alignment-inl.h:846:21: warning: add explicit braces to avoid dangling else [-Wdangling-else] else ^ [40] LaTeX Warning: Citation `Sali:1993' on page 41 undefined on input line 1969. [41] [42] Overfull \hbox (50.27501pt too wide) in paragraph at lines 2057--2057 []\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 2079--2079 [] \OT1/cmtt/m/n/10 The program reads an input sequence in FASTA/A3M which must have a SCOP domain, PDB chain, or DALI[] Overfull \hbox (50.27501pt too wide) in paragraph at lines 2079--2079 [] \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 2079--2079 [] \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 2079--2079 [] \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 2079--2079 [] \OT1/cmtt/m/n/10 (HETATM records for MSE (selenomethionine) will be interpre ted as ATOM records for MET in the[] [43] Overfull \hbox (170.34192pt too wide) in paragraph at lines 2147--2149 []\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 . [44] LaTeX Warning: Citation `Remmert:2011' on page 45 undefined on input line 2176. [45] [46] LaTeX Warning: Citation `Farrar:2007' on page 47 undefined on input line 2338. [47] Underfull \hbox (badness 10000) in paragraph at lines 2363--2371 (./hhsuite-userguide.bbl [48] [49]) [50] (./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 (50 pages, 343311 bytes). Transcript written on hhsuite-userguide.log. cd "/<>/hhsuite-3.0~beta2+dfsg/mybuild/doc" && /usr/bin/cmake -E chdir /<>/hhsuite-3.0~beta2+dfsg/mybuild/doc /usr/bin/pdflatex -interaction=nonstopmode hhsuite-userguide.tex This is pdfTeX, Version 3.14159265-2.6-1.40.18 (TeX Live 2017/Debian) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./hhsuite-userguide.tex LaTeX2e <2017-04-15> Babel <3.11> and hyphenation patterns for 3 language(s) loaded. (/usr/share/texlive/texmf-dist/tex/latex/base/article.cls Document Class: article 2014/09/29 v1.4h 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' v2.7a, with DG/SPQR fixes, and firstline=lastline fix <2008/02/07> (tvz)) (/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))In file included from /<>/hhsuite-3.0~beta2+dfsg/src/hhutil.cpp:1: In file included from /<>/hhsuite-3.0~beta2+dfsg/src/hhutil.h:12: In file included from /<>/hhsuite-3.0~beta2+dfsg/src/hhdecl.h:18: (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/auxhook.styIn file included from /<>/hhsuite-3.0~beta2+dfsg/src/cs/crf.h:24: In file included from /<>/hhsuite-3.0~beta2+dfsg/src/cs/context_profile-inl.h:23: In file included from /<>/hhsuite-3.0~beta2+dfsg/src/cs/context_profile.h:)24: In file included from /<>/hhsuite-3.0~beta2+dfsg/src/cs/count_profile-inl.h:25: /<>/hhsuite-3.0~beta2+dfsg/src/cs/alignment-inl.h:674:15: warning: comparison of constant -1 with expression of type 'uint8_t' (aka 'unsigned char') is always false [-Wtautological-constant-out-of-range-compare] if (c == EOF) break; ~ ^ ~~~ (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/kvoptions.sty) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/pd1enc.def/<>/hhsuite-3.0~beta2+dfsg/src/cs/alignment-inl.h:846:21: warning: add explicit braces to avoid dangling else [-Wdangling-else] else ^ ) (/usr/share/texlive/texmf-dist/tex/latex/latexconfig/hyperref.cfg)) Package hyperref Message: Driver (autodetected): hpdftex. 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[ 49%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhposteriordecoderrunner.cpp.o cd "/<>/hhsuite-3.0~beta2+dfsg/mybuild/src" && /usr/bin/c++ -DSSE -I"/<>/hhsuite-3.0~beta2+dfsg/src" -I"/<>/hhsuite-3.0~beta2+dfsg/src/cs" -I"/<>/hhsuite-3.0~beta2+dfsg/mybuild" -g -O2 -fdebug-prefix-map=/<>/hhsuite-3.0~beta2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse4.2 -mfpmath=sse -fno-strict-aliasing -o CMakeFiles/HH_OBJECTS.dir/hhposteriordecoderrunner.cpp.o -c "/<>/hhsuite-3.0~beta2+dfsg/src/hhposteriordecoderrunner.cpp" ) (./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/graphics/color.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/color.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]In file included from /<>/hhsuite-3.0~beta2+dfsg/src/hhalignment.cpp:8: In file included from /<>/hhsuite-3.0~beta2+dfsg/src/hhalignment.h:15: In file included from /<>/hhsuite-3.0~beta2+dfsg/src/hhdecl.h:18: In file included from /<>/hhsuite-3.0~beta2+dfsg/src/cs/crf.h:24: In file included from /<>/hhsuite-3.0~beta2+dfsg/src/cs/context_profile-inl.h:23: In file included from /<>/hhsuite-3.0~beta2+dfsg/src/cs/context_profile.h:24: In file included from /<>/hhsuite-3.0~beta2+dfsg/src/cs/count_profile-inl.h:25: /<>/hhsuite-3.0~beta2+dfsg/src/cs/alignment-inl.h:674:15: warning: comparison of constant -1 with expression of type 'uint8_t' (aka 'unsigned char') is always false [-Wtautological-constant-out-of-range-compare] if (c == EOF) break; ~ ^ ~~~ 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]/<>/hhsuite-3.0~beta2+dfsg/src/cs/alignment-inl.h:846:21: warning: add explicit braces to avoid dangling else [-Wdangling-else] else ^ [9] [10] [11 <./hhblits-hhsearch.png[ 50%] Linking CXX executable ../bin/a3m_database_reduce cd "/<>/hhsuite-3.0~beta2+dfsg/mybuild/src" && /usr/bin/cmake -E cmake_link_script CMakeFiles/a3m_database_reduce.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/<>/hhsuite-3.0~beta2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse4.2 -mfpmath=sse -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now CMakeFiles/a3m_database_reduce.dir/a3m_database_reduce.cpp.o CMakeFiles/A3M_COMPRESS_OBJECT.dir/a3m_compress.cpp.o -o ../bin/a3m_database_reduce -rdynamic -lffindex In file included from /<>/hhsuite-3.0~beta2+dfsg/src/hhhmm.cpp:3: In file included from /<>/hhsuite-3.0~beta2+dfsg/src/hhhmm.h:16: In file included from /<>/hhsuite-3.0~beta2+dfsg/src/hhdecl.h:18: In file included from /<>/hhsuite-3.0~beta2+dfsg/src/cs/crf.h:24: In file included from /<>/hhsuite-3.0~beta2+dfsg/src/cs/context_profile-inl.h:23: In file included from /<>/hhsuite-3.0~beta2+dfsg/src/cs/context_profile.h:24: In file included from /<>/hhsuite-3.0~beta2+dfsg/src/cs/count_profile-inl.h:25: /<>/hhsuite-3.0~beta2+dfsg/src/cs/alignment-inl.h:674:15: warning: comparison of constant -1 with expression of type 'uint8_t' (aka 'unsigned char') is always false [-Wtautological-constant-out-of-range-compare] if (c == EOF) break; ~ ^ ~~~ /<>/hhsuite-3.0~beta2+dfsg/src/cs/alignment-inl.h:846:21: warning: add explicit braces to avoid dangling else [-Wdangling-else] else ^ [ 53%] Linking CXX executable ../bin/a3m_database_extract [ 53%] Linking CXX executable ../bin/a3m_reduce cd "/<>/hhsuite-3.0~beta2+dfsg/mybuild/src" && /usr/bin/cmake -E cmake_link_script CMakeFiles/a3m_reduce.dir/link.txt --verbose=1 cd "/<>/hhsuite-3.0~beta2+dfsg/mybuild/src" && /usr/bin/cmake -E cmake_link_script CMakeFiles/a3m_database_extract.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/<>/hhsuite-3.0~beta2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse4.2 -mfpmath=sse -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now CMakeFiles/a3m_database_extract.dir/a3m_database_extract.cpp.o CMakeFiles/A3M_COMPRESS_OBJECT.dir/a3m_compress.cpp.o -o ../bin/a3m_database_extract -rdynamic -lffindex /usr/bin/c++ -g -O2 -fdebug-prefix-map=/<>/hhsuite-3.0~beta2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse4.2 -mfpmath=sse -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now CMakeFiles/a3m_reduce.dir/a3m_reduce.cpp.o CMakeFiles/A3M_COMPRESS_OBJECT.dir/a3m_compress.cpp.o -o ../bin/a3m_reduce -rdynamic -lffindex make[4]: Leaving directory '/<>/hhsuite-3.0~beta2+dfsg/mybuild' In file included from /<>/hhsuite-3.0~beta2+dfsg/src/hhforwardalgorithm.cpp:8: In file included from /<>/hhsuite-3.0~beta2+dfsg/src/hhposteriordecoder.h:36: In file included from /<>/hhsuite-3.0~beta2+dfsg/src/hhhmmsimd.h:5: In file included from /<>/hhsuite-3.0~beta2+dfsg/src/hhhmm.h:16: In file included from /<>/hhsuite-3.0~beta2+dfsg/src/hhdecl.h:18: In file included from /<>/hhsuite-3.0~beta2+dfsg/src/cs/crf.h:24: In file included from /<>/hhsuite-3.0~beta2+dfsg/src/cs/context_profile-inl.h:23: In file included from /<>/hhsuite-3.0~beta2+dfsg/src/cs/context_profile.h:24: In file included from /<>/hhsuite-3.0~beta2+dfsg/src/cs/count_profile-inl.h:25: /<>/hhsuite-3.0~beta2+dfsg/src/cs/alignment-inl.h:674:15: warning: comparison of constant -1 with expression of type 'uint8_t' (aka 'unsigned char') is always false [-Wtautological-constant-out-of-range-compare] if (c == EOF) break; ~ ^ ~~~ /<>/hhsuite-3.0~beta2+dfsg/src/cs/alignment-inl.h:846:21: warning: add explicit braces to avoid dangling else [-Wdangling-else] else ^ [ 53%] Built target a3m_database_reduce make -f src/CMakeFiles/a3m_extract.dir/build.make src/CMakeFiles/a3m_extract.dir/depend make[4]: Entering directory '/<>/hhsuite-3.0~beta2+dfsg/mybuild' cd "/<>/hhsuite-3.0~beta2+dfsg/mybuild" && /usr/bin/cmake -E cmake_depends "Unix Makefiles" "/<>/hhsuite-3.0~beta2+dfsg" "/<>/hhsuite-3.0~beta2+dfsg/src" "/<>/hhsuite-3.0~beta2+dfsg/mybuild" "/<>/hhsuite-3.0~beta2+dfsg/mybuild/src" "/<>/hhsuite-3.0~beta2+dfsg/mybuild/src/CMakeFiles/a3m_extract.dir/DependInfo.cmake" --color= Scanning dependencies of target a3m_extract make[4]: Leaving directory '/<>/hhsuite-3.0~beta2+dfsg/mybuild' make -f src/CMakeFiles/a3m_extract.dir/build.make src/CMakeFiles/a3m_extract.dir/build make[4]: Entering directory '/<>/hhsuite-3.0~beta2+dfsg/mybuild' [ 55%] Building CXX object src/CMakeFiles/a3m_extract.dir/a3m_extract.cpp.o cd "/<>/hhsuite-3.0~beta2+dfsg/mybuild/src" && /usr/bin/c++ -DSSE -I"/<>/hhsuite-3.0~beta2+dfsg/src" -I"/<>/hhsuite-3.0~beta2+dfsg/src/cs" -I"/<>/hhsuite-3.0~beta2+dfsg/mybuild" -g -O2 -fdebug-prefix-map=/<>/hhsuite-3.0~beta2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse4.2 -mfpmath=sse -fno-strict-aliasing -o CMakeFiles/a3m_extract.dir/a3m_extract.cpp.o -c "/<>/hhsuite-3.0~beta2+dfsg/src/a3m_extract.cpp" make[4]: Leaving directory '/<>/hhsuite-3.0~beta2+dfsg/mybuild' make[4]: Leaving directory '/<>/hhsuite-3.0~beta2+dfsg/mybuild' 2 warnings generated. [ 55%] Built target a3m_database_extract [ 55%] Built target a3m_reduce [ 56%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhviterbialgorithm.cpp.o cd "/<>/hhsuite-3.0~beta2+dfsg/mybuild/src" && /usr/bin/c++ -DSSE -I"/<>/hhsuite-3.0~beta2+dfsg/src" -I"/<>/hhsuite-3.0~beta2+dfsg/src/cs" -I"/<>/hhsuite-3.0~beta2+dfsg/mybuild" -g -O2 -fdebug-prefix-map=/<>/hhsuite-3.0~beta2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse4.2 -mfpmath=sse -fno-strict-aliasing -o CMakeFiles/HH_OBJECTS.dir/hhviterbialgorithm.cpp.o -c "/<>/hhsuite-3.0~beta2+dfsg/src/hhviterbialgorithm.cpp" [ 58%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhhmmsimd.cpp.o [ 59%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhfullalignment.cpp.o cd "/<>/hhsuite-3.0~beta2+dfsg/mybuild/src" && /usr/bin/c++ -DSSE -I"/<>/hhsuite-3.0~beta2+dfsg/src" -I"/<>/hhsuite-3.0~beta2+dfsg/src/cs" -I"/<>/hhsuite-3.0~beta2+dfsg/mybuild" -g -O2 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Secondary struc-ture in-for-ma-tion in A3M/A2M or FASTA MSAs for HH-search/HHblits [29] Overfull \hbox (16.43517pt too wide) in paragraph at lines 1302--1307 \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 [30] [31] [32] Overfull \hbox (8.27538pt too wide) in paragraph at lines 1584--1584 [] \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 1584--1584 [] \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 1584--1584 [] \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 1584--1584 [] \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 1584--1584 [] \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 1584--1584 [] \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 1584--1584 [] \OT1/cmtt/m/n/10 -pre_score_offset offset on sequence profile scores in prefilter S-W alignment (default=50)[] [33] Overfull \hbox (45.02505pt too wide) in paragraph at lines 1584--1584 [] \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 1584--1584 [] \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 1584--1584 [] \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 1584--1584 [] \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 1584--1584 [] \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 1584--1584 [] \OT1/cmtt/m/n/10 -pc_hhm_nocontxt_mode {0,..,3} position dependence of pc admixture 'tau' (pc mode, default=2)[] Overfull \hbox (60.77492pt too wide) in paragraph at lines 1584--1584 [] \OT1/cmtt/m/n/10 -pc_prefilter_contxt_mode {0,..,3} position dependence o f pc admixture 'tau' (pc mode, default=3)[] [34] Overfull \hbox (71.27483pt too wide) in paragraph at lines 1584--1584 [] \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 1584--1584 [] \OT1/cmtt/m/n/10 -contxt context file for computing context-specific pseudocounts (default=${HHLIB}/data/context_data.crf)[] [35] Overfull \hbox (8.27538pt too wide) in paragraph at lines 1715--1715 [] \OT1/cmtt/m/n/10 -add_cons generate consensus sequence as master sequen ce of query MSA (default=don't)[] Overfull \hbox (39.7751pt too wide) in paragraph at lines 1715--1715 [] \OT1/cmtt/m/n/10 -ovlp banded alignment: forbid largest diagonals |i-j| of DP matrix (def=0)[] Overfull \hbox (18.77528pt too wide) in paragraph at lines 1715--1715 [] \OT1/cmtt/m/n/10 -alt show up to this many alternative alignm ents with raw score > smin(def=4)[] Overfull \hbox (45.02505pt too wide) in paragraph at lines 1715--1715 [] \OT1/cmtt/m/n/10 -ssa [0,1] SS substitution matrix = (1-ssa)*I + ss a*full-SS-substition-matrix [def=1.00)[] [36] Overfull \hbox (29.27519pt too wide) in paragraph at lines 1715--1715 [] \OT1/cmtt/m/n/10 -pc_hhm_contxt_mode {0,..,3} position dependence of pc a dmixture 'tau' (pc mode, default=2)[] Overfull \hbox (92.27464pt too wide) in paragraph at lines 1715--1715 [] \OT1/cmtt/m/n/10 Context independent hhm pseudocounts (used for templates; u sed for query if contxt file is not available):[] Overfull \hbox (39.7751pt too wide) in paragraph at lines 1715--1715 [] \OT1/cmtt/m/n/10 -pc_hhm_nocontxt_mode {0,..,3} position dependence of pc admixture 'tau' (pc mode, default=2)[] Overfull \hbox (129.02432pt too wide) in paragraph at lines 1715--1715 [] \OT1/cmtt/m/n/10 -contxt context file for computing context-specific pseudocounts (default=${HHLIB}/data/context_data.crf)[] [37] Overfull \hbox (29.27519pt too wide) in paragraph at lines 1814--1814 [] \OT1/cmtt/m/n/10 -pc_hhm_contxt_mode {0,..,3} position dependence of pc a dmixture 'tau' (pc mode, default=0)[] [38]make[4]: Leaving directory '/<>/hhsuite-3.0~beta2+dfsg/mybuild' Overfull \hbox (92.27464pt too wide) in paragraph at lines 1814--1814 [] \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 1814--1814 [] \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 1814--1814 [] \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 1875--1875 [] \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 1875--1875 [] \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 1875--1875 [] \OT1/cmtt/m/n/10 -add_cons generate consensus sequence as master sequen ce of query MSA (default=don't)[] [39] [40/<>/hhsuite-3.0~beta2+dfsg/src/hhalignment.cpp:2399:11: warning: add explicit braces to avoid dangling else [-Wdangling-else] HH_LOG(WARNING) << "Maximum number " << q->maxseqdis << " of sequences for display of alignment exceeded" << std::endl; ^ /<>/hhsuite-3.0~beta2+dfsg/src/log.h:116:5: note: ]expanded from macro 'HH_LOG' else Log().Get(level) ^ [ 62%] Built target a3m_database_filter [41][ 64%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhviterbi.cpp.o cd "/<>/hhsuite-3.0~beta2+dfsg/mybuild/src" && /usr/bin/c++ -DSSE -I"/<>/hhsuite-3.0~beta2+dfsg/src" -I"/<>/hhsuite-3.0~beta2+dfsg/src/cs" -I"/<>/hhsuite-3.0~beta2+dfsg/mybuild" -g -O2 -fdebug-prefix-map=/<>/hhsuite-3.0~beta2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse4.2 -mfpmath=sse -fno-strict-aliasing -o CMakeFiles/HH_OBJECTS.dir/hhviterbi.cpp.o -c "/<>/hhsuite-3.0~beta2+dfsg/src/hhviterbi.cpp" [42] Overfull \hbox (50.27501pt too wide) in paragraph at lines 2057--2057 []\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 2079--2079 [] \OT1/cmtt/m/n/10 The program reads an input sequence in FASTA/A3M which must have a SCOP domain, PDB chain, or DALI[] Overfull \hbox (50.27501pt too wide) in paragraph at lines 2079--2079 [] \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 2079--2079 [] \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 2079--2079 [] \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 2079--2079 [] \OT1/cmtt/m/n/10 (HETATM records for MSE (selenomethionine) will be interpre ted as ATOM records for MET in the[] [43] Overfull \hbox (170.34192pt too wide) in paragraph at lines 2147--2149 []\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 . [44] [45/<>/hhsuite-3.0~beta2+dfsg/src/hhalignment.cpp:3172:13: warning: add explicit braces to avoid dangling else [-Wdangling-else] else ^ ] [46] [47]/<>/hhsuite-3.0~beta2+dfsg/src/hhalignment.cpp:3377:13: warning: add explicit braces to avoid dangling else [-Wdangling-else] else ^ Underfull \hbox (badness 10000) in paragraph at lines 2363--2371 (./hhsuite-userguide.bbl [48] [49]) [50] (./hhsuite-userguide.aux) ) (see the transcript file for additional information) Output written on hhsuite-userguide.pdf (50 pages, 344309 bytes). Transcript written on hhsuite-userguide.log. make[4]: Leaving directory '/<>/hhsuite-3.0~beta2+dfsg/mybuild' [ 64%] Built target pdf 2 warnings generated. [ 65%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhbacktracemac.cpp.o cd "/<>/hhsuite-3.0~beta2+dfsg/mybuild/src" && /usr/bin/c++ -DSSE -I"/<>/hhsuite-3.0~beta2+dfsg/src" -I"/<>/hhsuite-3.0~beta2+dfsg/src/cs" -I"/<>/hhsuite-3.0~beta2+dfsg/mybuild" -g -O2 -fdebug-prefix-map=/<>/hhsuite-3.0~beta2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse4.2 -mfpmath=sse -fno-strict-aliasing -o CMakeFiles/HH_OBJECTS.dir/hhbacktracemac.cpp.o -c "/<>/hhsuite-3.0~beta2+dfsg/src/hhbacktracemac.cpp" [ 67%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhmacalgorithm.cpp.o cd "/<>/hhsuite-3.0~beta2+dfsg/mybuild/src" && /usr/bin/c++ -DSSE -I"/<>/hhsuite-3.0~beta2+dfsg/src" -I"/<>/hhsuite-3.0~beta2+dfsg/src/cs" -I"/<>/hhsuite-3.0~beta2+dfsg/mybuild" -g -O2 -fdebug-prefix-map=/<>/hhsuite-3.0~beta2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse4.2 -mfpmath=sse -fno-strict-aliasing -o CMakeFiles/HH_OBJECTS.dir/hhmacalgorithm.cpp.o -c "/<>/hhsuite-3.0~beta2+dfsg/src/hhmacalgorithm.cpp" 2 warnings generated. [ 68%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhprefilter.cpp.o cd "/<>/hhsuite-3.0~beta2+dfsg/mybuild/src" && /usr/bin/c++ -DSSE -I"/<>/hhsuite-3.0~beta2+dfsg/src" -I"/<>/hhsuite-3.0~beta2+dfsg/src/cs" -I"/<>/hhsuite-3.0~beta2+dfsg/mybuild" -g -O2 -fdebug-prefix-map=/<>/hhsuite-3.0~beta2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse4.2 -mfpmath=sse -fno-strict-aliasing -o CMakeFiles/HH_OBJECTS.dir/hhprefilter.cpp.o -c "/<>/hhsuite-3.0~beta2+dfsg/src/hhprefilter.cpp" In file included from /<>/hhsuite-3.0~beta2+dfsg/src/hhposteriordecoderrunner.cpp:17: In file included from /<>/hhsuite-3.0~beta2+dfsg/src/hhposteriordecoderrunner.h:8: In file included from /<>/hhsuite-3.0~beta2+dfsg/src/hhposteriordecoder.h:36: In file included from /<>/hhsuite-3.0~beta2+dfsg/src/hhhmmsimd.h:5: In file included from /<>/hhsuite-3.0~beta2+dfsg/src/hhhmm.h:16: In file included from /<>/hhsuite-3.0~beta2+dfsg/src/hhdecl.h:18: In file included from /<>/hhsuite-3.0~beta2+dfsg/src/cs/crf.h:24: In file included from /<>/hhsuite-3.0~beta2+dfsg/src/cs/context_profile-inl.h:23: In file included from /<>/hhsuite-3.0~beta2+dfsg/src/cs/context_profile.h:24: In file included from /<>/hhsuite-3.0~beta2+dfsg/src/cs/count_profile-inl.h:25: /<>/hhsuite-3.0~beta2+dfsg/src/cs/alignment-inl.h:674:15: warning: comparison of constant -1 with expression of type 'uint8_t' (aka 'unsigned char') is always false [-Wtautological-constant-out-of-range-compare] if (c == EOF) break; ~ ^ ~~~ /<>/hhsuite-3.0~beta2+dfsg/src/cs/alignment-inl.h:846:21: warning: add explicit braces to avoid dangling else [-Wdangling-else] else ^ [ 70%] Linking CXX executable ../bin/a3m_extract cd "/<>/hhsuite-3.0~beta2+dfsg/mybuild/src" && /usr/bin/cmake -E cmake_link_script CMakeFiles/a3m_extract.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/<>/hhsuite-3.0~beta2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse4.2 -mfpmath=sse -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now CMakeFiles/a3m_extract.dir/a3m_extract.cpp.o CMakeFiles/A3M_COMPRESS_OBJECT.dir/a3m_compress.cpp.o -o ../bin/a3m_extract -rdynamic -lffindex 2 warnings generated. 2 warnings generated. make[4]: Leaving directory '/<>/hhsuite-3.0~beta2+dfsg/mybuild' [ 70%] Built target a3m_extract [ 71%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhviterbimatrix.cpp.o [ 73%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhbackwardalgorithm.cpp.o cd "/<>/hhsuite-3.0~beta2+dfsg/mybuild/src" && /usr/bin/c++ -DSSE -I"/<>/hhsuite-3.0~beta2+dfsg/src" -I"/<>/hhsuite-3.0~beta2+dfsg/src/cs" -I"/<>/hhsuite-3.0~beta2+dfsg/mybuild" -g -O2 -fdebug-prefix-map=/<>/hhsuite-3.0~beta2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse4.2 -mfpmath=sse -fno-strict-aliasing -o CMakeFiles/HH_OBJECTS.dir/hhviterbimatrix.cpp.o -c "/<>/hhsuite-3.0~beta2+dfsg/src/hhviterbimatrix.cpp" cd "/<>/hhsuite-3.0~beta2+dfsg/mybuild/src" && /usr/bin/c++ -DSSE -I"/<>/hhsuite-3.0~beta2+dfsg/src" -I"/<>/hhsuite-3.0~beta2+dfsg/src/cs" -I"/<>/hhsuite-3.0~beta2+dfsg/mybuild" -g -O2 -fdebug-prefix-map=/<>/hhsuite-3.0~beta2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse4.2 -mfpmath=sse -fno-strict-aliasing -o CMakeFiles/HH_OBJECTS.dir/hhbackwardalgorithm.cpp.o -c "/<>/hhsuite-3.0~beta2+dfsg/src/hhbackwardalgorithm.cpp" [ 74%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhdatabase.cpp.o cd "/<>/hhsuite-3.0~beta2+dfsg/mybuild/src" && /usr/bin/c++ -DSSE -I"/<>/hhsuite-3.0~beta2+dfsg/src" -I"/<>/hhsuite-3.0~beta2+dfsg/src/cs" -I"/<>/hhsuite-3.0~beta2+dfsg/mybuild" -g -O2 -fdebug-prefix-map=/<>/hhsuite-3.0~beta2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse4.2 -mfpmath=sse -fno-strict-aliasing -o CMakeFiles/HH_OBJECTS.dir/hhdatabase.cpp.o -c "/<>/hhsuite-3.0~beta2+dfsg/src/hhdatabase.cpp" In file included from /<>/hhsuite-3.0~beta2+dfsg/src/hhviterbialgorithm.cpp:7: In file included from /<>/hhsuite-3.0~beta2+dfsg/src/hhviterbi.h:11: In file included from /<>/hhsuite-3.0~beta2+dfsg/src/hhhit.h:20: In file included from /<>/hhsuite-3.0~beta2+dfsg/src/hhhmm.h:16: In file included from /<>/hhsuite-3.0~beta2+dfsg/src/hhdecl.h:18: In file included from /<>/hhsuite-3.0~beta2+dfsg/src/cs/crf.h:24: In file included from /<>/hhsuite-3.0~beta2+dfsg/src/cs/context_profile-inl.h:23: In file included from /<>/hhsuite-3.0~beta2+dfsg/src/cs/context_profile.h:24: In file included from /<>/hhsuite-3.0~beta2+dfsg/src/cs/count_profile-inl.h:25: /<>/hhsuite-3.0~beta2+dfsg/src/cs/alignment-inl.h:674:15: warning: comparison of constant -1 with expression of type 'uint8_t' (aka 'unsigned char') is always false [-Wtautological-constant-out-of-range-compare] if (c == EOF) break; ~ ^ ~~~ /<>/hhsuite-3.0~beta2+dfsg/src/cs/alignment-inl.h:846:21: warning: add explicit braces to avoid dangling else [-Wdangling-else] else ^ In file included from /<>/hhsuite-3.0~beta2+dfsg/src/hhhmmsimd.cpp:10: In file included from /<>/hhsuite-3.0~beta2+dfsg/src/hhhmmsimd.h:5: In file included from /<>/hhsuite-3.0~beta2+dfsg/src/hhhmm.h:16: In file included from /<>/hhsuite-3.0~beta2+dfsg/src/hhdecl.h:18: In file included from /<>/hhsuite-3.0~beta2+dfsg/src/cs/crf.h:24: In file included from /<>/hhsuite-3.0~beta2+dfsg/src/cs/context_profile-inl.h:23: In file included from /<>/hhsuite-3.0~beta2+dfsg/src/cs/context_profile.h:24: In file included from /<>/hhsuite-3.0~beta2+dfsg/src/cs/count_profile-inl.h:25: /<>/hhsuite-3.0~beta2+dfsg/src/cs/alignment-inl.h:674:15: warning: comparison of constant -1 with expression of type 'uint8_t' (aka 'unsigned char') is always false [-Wtautological-constant-out-of-range-compare] if (c == EOF) break; ~ ^ ~~~ In file included from /<>/hhsuite-3.0~beta2+dfsg/src/hhposteriormatrix.cpp:8: In file included from /<>/hhsuite-3.0~beta2+dfsg/src/hhposteriormatrix.h:12: In file included from /<>/hhsuite-3.0~beta2+dfsg/src/hhhmmsimd.h:5: In file included from /<>/hhsuite-3.0~beta2+dfsg/src/hhhmm.h:16: In file included from /<>/hhsuite-3.0~beta2+dfsg/src/hhdecl.h:18: In file included from /<>/hhsuite-3.0~beta2+dfsg/src/cs/crf.h:24: In file included from /<>/hhsuite-3.0~beta2+dfsg/src/cs/context_profile-inl.h:23: In file included from /<>/hhsuite-3.0~beta2+dfsg/src/cs/context_profile.h:24: In file included from /<>/hhsuite-3.0~beta2+dfsg/src/cs/count_profile-inl.h:25: /<>/hhsuite-3.0~beta2+dfsg/src/cs/alignment-inl.h:674:15: warning: comparison of constant -1 with expression of type 'uint8_t' (aka 'unsigned char') is always false [-Wtautological-constant-out-of-range-compare] if (c == EOF) break; ~ ^ ~~~ /<>/hhsuite-3.0~beta2+dfsg/src/cs/alignment-inl.h:846:21: warning: add explicit braces to avoid dangling else [-Wdangling-else] else ^ /<>/hhsuite-3.0~beta2+dfsg/src/cs/alignment-inl.h:846:21: warning: add explicit braces to avoid dangling else [-Wdangling-else] else ^ In file included from /<>/hhsuite-3.0~beta2+dfsg/src/hhfullalignment.cpp:3: In file included from /<>/hhsuite-3.0~beta2+dfsg/src/hhfullalignment.h:5: In file included from /<>/hhsuite-3.0~beta2+dfsg/src/hhhalfalignment.h:6: In file included from /<>/hhsuite-3.0~beta2+dfsg/src/hhhit.h:20: In file included from /<>/hhsuite-3.0~beta2+dfsg/src/hhhmm.h:16: In file included from /<>/hhsuite-3.0~beta2+dfsg/src/hhdecl.h:18: In file included from /<>/hhsuite-3.0~beta2+dfsg/src/cs/crf.h:24: In file included from /<>/hhsuite-3.0~beta2+dfsg/src/cs/context_profile-inl.h:23: In file included from /<>/hhsuite-3.0~beta2+dfsg/src/cs/context_profile.h:24: In file included from /<>/hhsuite-3.0~beta2+dfsg/src/cs/count_profile-inl.h:25: /<>/hhsuite-3.0~beta2+dfsg/src/cs/alignment-inl.h:674:15: warning: comparison of constant -1 with expression of type 'uint8_t' (aka 'unsigned char') is always false [-Wtautological-constant-out-of-range-compare] if (c == EOF) break; ~ ^ ~~~ /<>/hhsuite-3.0~beta2+dfsg/src/cs/alignment-inl.h:846:21: warning: add explicit braces to avoid dangling else [-Wdangling-else] else ^ In file included from /<>/hhsuite-3.0~beta2+dfsg/src/hhviterbi.cpp:8: In file included from /<>/hhsuite-3.0~beta2+dfsg/src/hhviterbi.h:11: In file included from /<>/hhsuite-3.0~beta2+dfsg/src/hhhit.h:20: In file included from /<>/hhsuite-3.0~beta2+dfsg/src/hhhmm.h:16: In file included from /<>/hhsuite-3.0~beta2+dfsg/src/hhdecl.h:18: In file included from /<>/hhsuite-3.0~beta2+dfsg/src/cs/crf.h:24: In file included from /<>/hhsuite-3.0~beta2+dfsg/src/cs/context_profile-inl.h:23: In file included from /<>/hhsuite-3.0~beta2+dfsg/src/cs/context_profile.h:24: In file included from /<>/hhsuite-3.0~beta2+dfsg/src/cs/count_profile-inl.h:25: /<>/hhsuite-3.0~beta2+dfsg/src/cs/alignment-inl.h:674:15: warning: comparison of constant -1 with expression of type 'uint8_t' (aka 'unsigned char') is always false [-Wtautological-constant-out-of-range-compare] if (c == EOF) break; ~ ^ ~~~ /<>/hhsuite-3.0~beta2+dfsg/src/cs/alignment-inl.h:846:21: warning: add explicit braces to avoid dangling else [-Wdangling-else] else ^ 2 warnings generated. [ 76%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhhalfalignment.cpp.o cd "/<>/hhsuite-3.0~beta2+dfsg/mybuild/src" && /usr/bin/c++ -DSSE -I"/<>/hhsuite-3.0~beta2+dfsg/src" -I"/<>/hhsuite-3.0~beta2+dfsg/src/cs" -I"/<>/hhsuite-3.0~beta2+dfsg/mybuild" -g -O2 -fdebug-prefix-map=/<>/hhsuite-3.0~beta2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse4.2 -mfpmath=sse -fno-strict-aliasing -o CMakeFiles/HH_OBJECTS.dir/hhhalfalignment.cpp.o -c "/<>/hhsuite-3.0~beta2+dfsg/src/hhhalfalignment.cpp" In file included from /<>/hhsuite-3.0~beta2+dfsg/src/hhbacktracemac.cpp:8: In file included from /<>/hhsuite-3.0~beta2+dfsg/src/hhposteriordecoder.h:36: In file included from /<>/hhsuite-3.0~beta2+dfsg/src/hhhmmsimd.h:5: In file included from /<>/hhsuite-3.0~beta2+dfsg/src/hhhmm.h:16: In file included from /<>/hhsuite-3.0~beta2+dfsg/src/hhdecl.h:18: In file included from /<>/hhsuite-3.0~beta2+dfsg/src/cs/crf.h:24: In file included from /<>/hhsuite-3.0~beta2+dfsg/src/cs/context_profile-inl.h:23: In file included from /<>/hhsuite-3.0~beta2+dfsg/src/cs/context_profile.h:24: In file included from /<>/hhsuite-3.0~beta2+dfsg/src/cs/count_profile-inl.h:25: /<>/hhsuite-3.0~beta2+dfsg/src/cs/alignment-inl.h:674:15: warning: comparison of constant -1 with expression of type 'uint8_t' (aka 'unsigned char') is always false [-Wtautological-constant-out-of-range-compare] if (c == EOF) break; ~ ^ ~~~ /<>/hhsuite-3.0~beta2+dfsg/src/cs/alignment-inl.h:846:21: warning: add explicit braces to avoid dangling else [-Wdangling-else] else ^ In file included from /<>/hhsuite-3.0~beta2+dfsg/src/hhmacalgorithm.cpp:8: In file included from /<>/hhsuite-3.0~beta2+dfsg/src/hhposteriordecoder.h:36: In file included from /<>/hhsuite-3.0~beta2+dfsg/src/hhhmmsimd.h:5: In file included from /<>/hhsuite-3.0~beta2+dfsg/src/hhhmm.h:16: In file included from /<>/hhsuite-3.0~beta2+dfsg/src/hhdecl.h:18: In file included from /<>/hhsuite-3.0~beta2+dfsg/src/cs/crf.h:24: In file included from /<>/hhsuite-3.0~beta2+dfsg/src/cs/context_profile-inl.h:23: In file included from /<>/hhsuite-3.0~beta2+dfsg/src/cs/context_profile.h:24: In file included from /<>/hhsuite-3.0~beta2+dfsg/src/cs/count_profile-inl.h:25: /<>/hhsuite-3.0~beta2+dfsg/src/cs/alignment-inl.h:674:15: warning: comparison of constant -1 with expression of type 'uint8_t' (aka 'unsigned char') is always false [-Wtautological-constant-out-of-range-compare] if (c == EOF) break; ~ ^ ~~~ /<>/hhsuite-3.0~beta2+dfsg/src/cs/alignment-inl.h:846:21: warning: add explicit braces to avoid dangling else [-Wdangling-else] else ^ 2 warnings generated. 2 warnings generated. [ 77%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhviterbirunner.cpp.o cd "/<>/hhsuite-3.0~beta2+dfsg/mybuild/src" && /usr/bin/c++ -DSSE -I"/<>/hhsuite-3.0~beta2+dfsg/src" -I"/<>/hhsuite-3.0~beta2+dfsg/src/cs" -I"/<>/hhsuite-3.0~beta2+dfsg/mybuild" -g -O2 -fdebug-prefix-map=/<>/hhsuite-3.0~beta2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse4.2 -mfpmath=sse -fno-strict-aliasing -o CMakeFiles/HH_OBJECTS.dir/hhviterbirunner.cpp.o -c "/<>/hhsuite-3.0~beta2+dfsg/src/hhviterbirunner.cpp" [ 79%] Building CXX object src/CMakeFiles/HH_OBJECTS.dir/hhfunc.cpp.o cd "/<>/hhsuite-3.0~beta2+dfsg/mybuild/src" && /usr/bin/c++ -DSSE -I"/<>/hhsuite-3.0~beta2+dfsg/src" -I"/<>/hhsuite-3.0~beta2+dfsg/src/cs" -I"/<>/hhsuite-3.0~beta2+dfsg/mybuild" -g -O2 -fdebug-prefix-map=/<>/hhsuite-3.0~beta2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse4.2 -mfpmath=sse -fno-strict-aliasing -o CMakeFiles/HH_OBJECTS.dir/hhfunc.cpp.o -c "/<>/hhsuite-3.0~beta2+dfsg/src/hhfunc.cpp" In file included from /<>/hhsuite-3.0~beta2+dfsg/src/hhprefilter.cpp:8: In file included from /<>/hhsuite-3.0~beta2+dfsg/src/hhprefilter.h:19: In file included from /<>/hhsuite-3.0~beta2+dfsg/src/hhhmm.h:16: In file included from /<>/hhsuite-3.0~beta2+dfsg/src/hhdecl.h:18: In file included from /<>/hhsuite-3.0~beta2+dfsg/src/cs/crf.h:24: In file included from /<>/hhsuite-3.0~beta2+dfsg/src/cs/context_profile-inl.h:23: In file included from /<>/hhsuite-3.0~beta2+dfsg/src/cs/context_profile.h:24: In file included from /<>/hhsuite-3.0~beta2+dfsg/src/cs/count_profile-inl.h:25: /<>/hhsuite-3.0~beta2+dfsg/src/cs/alignment-inl.h:674:15: warning: comparison of constant -1 with expression of type 'uint8_t' (aka 'unsigned char') is always false [-Wtautological-constant-out-of-range-compare] if (c == EOF) break; ~ ^ ~~~ /<>/hhsuite-3.0~beta2+dfsg/src/cs/alignment-inl.h:846:21: warning: add explicit braces to avoid dangling else [-Wdangling-else] else ^ 2 warnings generated. In file included from /<>/hhsuite-3.0~beta2+dfsg/src/hhdatabase.cpp:8: In file included from /<>/hhsuite-3.0~beta2+dfsg/src/hhdatabase.h:22: In file included from /<>/hhsuite-3.0~beta2+dfsg/src/hhutil.h:12: In file included from /<>/hhsuite-3.0~beta2+dfsg/src/hhdecl.h:18: In file included from /<>/hhsuite-3.0~beta2+dfsg/src/cs/crf.h:24: In file included from /<>/hhsuite-3.0~beta2+dfsg/src/cs/context_profile-inl.h:23: In file included from /<>/hhsuite-3.0~beta2+dfsg/src/cs/context_profile.h:24: In file included from /<>/hhsuite-3.0~beta2+dfsg/src/cs/count_profile-inl.h:25: /<>/hhsuite-3.0~beta2+dfsg/src/cs/alignment-inl.h:674:15: warning: comparison of constant -1 with expression of type 'uint8_t' (aka 'unsigned char') is always false [-Wtautological-constant-out-of-range-compare] if (c == EOF) break; ~ ^ ~~~ In file included from /<>/hhsuite-3.0~beta2+dfsg/src/hhviterbimatrix.cpp:11: In file included from /<>/hhsuite-3.0~beta2+dfsg/src/hhviterbimatrix.h:11: In file included from /<>/hhsuite-3.0~beta2+dfsg/src/hhutil.h:12: In file included from /<>/hhsuite-3.0~beta2+dfsg/src/hhdecl.h:18: In file included from /<>/hhsuite-3.0~beta2+dfsg/src/cs/crf.h:24: In file included from /<>/hhsuite-3.0~beta2+dfsg/src/cs/context_profile-inl.h:23: In file included from /<>/hhsuite-3.0~beta2+dfsg/src/cs/context_profile.h:24: In file included from /<>/hhsuite-3.0~beta2+dfsg/src/cs/count_profile-inl.h:25: /<>/hhsuite-3.0~beta2+dfsg/src/cs/alignment-inl.h:674:15: warning: comparison of constant -1 with expression of type 'uint8_t' (aka 'unsigned char') is always false [-Wtautological-constant-out-of-range-compare] if (c == EOF) break; ~ ^ ~~~ /<>/hhsuite-3.0~beta2+dfsg/src/cs/alignment-inl.h:846:21: warning: add explicit braces to avoid dangling else [-Wdangling-else] else ^ /<>/hhsuite-3.0~beta2+dfsg/src/cs/alignment-inl.h:846:21: warning: add explicit braces to avoid dangling else [-Wdangling-else] else ^ 2 warnings generated. In file included from /<>/hhsuite-3.0~beta2+dfsg/src/hhbackwardalgorithm.cpp:8: In file included from /<>/hhsuite-3.0~beta2+dfsg/src/hhposteriordecoder.h:36: In file included from /<>/hhsuite-3.0~beta2+dfsg/src/hhhmmsimd.h:5: In file included from /<>/hhsuite-3.0~beta2+dfsg/src/hhhmm.h:16: In file included from /<>/hhsuite-3.0~beta2+dfsg/src/hhdecl.h:18: In file included from /<>/hhsuite-3.0~beta2+dfsg/src/cs/crf.h:24: In file included from /<>/hhsuite-3.0~beta2+dfsg/src/cs/context_profile-inl.h:23: In file included from /<>/hhsuite-3.0~beta2+dfsg/src/cs/context_profile.h:24: In file included from /<>/hhsuite-3.0~beta2+dfsg/src/cs/count_profile-inl.h:25: /<>/hhsuite-3.0~beta2+dfsg/src/cs/alignment-inl.h:674:15: warning: comparison of constant -1 with expression of type 'uint8_t' (aka 'unsigned char') is always false [-Wtautological-constant-out-of-range-compare] if (c == EOF) break; ~ ^ ~~~ /<>/hhsuite-3.0~beta2+dfsg/src/cs/alignment-inl.h:846:21: warning: add explicit braces to avoid dangling else [-Wdangling-else] else ^ 2 warnings generated. In file included from /<>/hhsuite-3.0~beta2+dfsg/src/hhhalfalignment.cpp:3: In file included from /<>/hhsuite-3.0~beta2+dfsg/src/hhhalfalignment.h:6: In file included from /<>/hhsuite-3.0~beta2+dfsg/src/hhhit.h:20: In file included from /<>/hhsuite-3.0~beta2+dfsg/src/hhhmm.h:16: In file included from /<>/hhsuite-3.0~beta2+dfsg/src/hhdecl.h:18: In file included from /<>/hhsuite-3.0~beta2+dfsg/src/cs/crf.h:24: In file included from /<>/hhsuite-3.0~beta2+dfsg/src/cs/context_profile-inl.h:23: In file included from /<>/hhsuite-3.0~beta2+dfsg/src/cs/context_profile.h:24: In file included from /<>/hhsuite-3.0~beta2+dfsg/src/cs/count_profile-inl.h:25: /<>/hhsuite-3.0~beta2+dfsg/src/cs/alignment-inl.h:674:15: warning: comparison of constant -1 with expression of type 'uint8_t' (aka 'unsigned char') is always false [-Wtautological-constant-out-of-range-compare] if (c == EOF) break; ~ ^ ~~~ /<>/hhsuite-3.0~beta2+dfsg/src/cs/alignment-inl.h:846:21: warning: add explicit braces to avoid dangling else [-Wdangling-else] else ^ 2 warnings generated. 2 warnings generated. 2 warnings generated. 2 warnings generated. In file included from /<>/hhsuite-3.0~beta2+dfsg/src/hhfunc.cpp:3: In file included from /<>/hhsuite-3.0~beta2+dfsg/src/hhfunc.h:13: In file included from /<>/hhsuite-3.0~beta2+dfsg/src/hhhmm.h:16: In file included from /<>/hhsuite-3.0~beta2+dfsg/src/hhdecl.h:18: In file included from /<>/hhsuite-3.0~beta2+dfsg/src/cs/crf.h:24: In file included from /<>/hhsuite-3.0~beta2+dfsg/src/cs/context_profile-inl.h:23: In file included from /<>/hhsuite-3.0~beta2+dfsg/src/cs/context_profile.h:24: In file included from /<>/hhsuite-3.0~beta2+dfsg/src/cs/count_profile-inl.h:25: /<>/hhsuite-3.0~beta2+dfsg/src/cs/alignment-inl.h:674:15: warning: comparison of constant -1 with expression of type 'uint8_t' (aka 'unsigned char') is always false [-Wtautological-constant-out-of-range-compare] if (c == EOF) break; ~ ^ ~~~ /<>/hhsuite-3.0~beta2+dfsg/src/cs/alignment-inl.h:846:21: warning: add explicit braces to avoid dangling else [-Wdangling-else] else ^ 2 warnings generated. In file included from /<>/hhsuite-3.0~beta2+dfsg/src/hhviterbirunner.cpp:1: In file included from /<>/hhsuite-3.0~beta2+dfsg/src/hhviterbirunner.h:4: In file included from /<>/hhsuite-3.0~beta2+dfsg/src/hhhmmsimd.h:5: In file included from /<>/hhsuite-3.0~beta2+dfsg/src/hhhmm.h:16: In file included from /<>/hhsuite-3.0~beta2+dfsg/src/hhdecl.h:18: In file included from /<>/hhsuite-3.0~beta2+dfsg/src/cs/crf.h:24: In file included from /<>/hhsuite-3.0~beta2+dfsg/src/cs/context_profile-inl.h:23: In file included from /<>/hhsuite-3.0~beta2+dfsg/src/cs/context_profile.h:24: In file included from /<>/hhsuite-3.0~beta2+dfsg/src/cs/count_profile-inl.h:25: /<>/hhsuite-3.0~beta2+dfsg/src/cs/alignment-inl.h:674:15: warning: comparison of constant -1 with expression of type 'uint8_t' (aka 'unsigned char') is always false [-Wtautological-constant-out-of-range-compare] if (c == EOF) break; ~ ^ ~~~ /<>/hhsuite-3.0~beta2+dfsg/src/cs/alignment-inl.h:846:21: warning: add explicit braces to avoid dangling else [-Wdangling-else] else ^ 2 warnings generated. 2 warnings generated. 2 warnings generated. 2 warnings generated. 2 warnings generated. 2 warnings generated. 5 warnings generated. 2 warnings generated. make[4]: Leaving directory '/<>/hhsuite-3.0~beta2+dfsg/mybuild' [ 79%] Built target HH_OBJECTS make -f src/CMakeFiles/hhblits.dir/build.make src/CMakeFiles/hhblits.dir/depend make -f src/CMakeFiles/cstranslate.dir/build.make src/CMakeFiles/cstranslate.dir/depend make -f src/CMakeFiles/hhsearch.dir/build.make src/CMakeFiles/hhsearch.dir/depend make -f src/CMakeFiles/hhalign.dir/build.make src/CMakeFiles/hhalign.dir/depend make -f src/CMakeFiles/hhmake.dir/build.make src/CMakeFiles/hhmake.dir/depend make -f src/CMakeFiles/hhfilter.dir/build.make src/CMakeFiles/hhfilter.dir/depend make -f src/CMakeFiles/hhconsensus.dir/build.make src/CMakeFiles/hhconsensus.dir/depend make[4]: Entering directory '/<>/hhsuite-3.0~beta2+dfsg/mybuild' cd "/<>/hhsuite-3.0~beta2+dfsg/mybuild" && /usr/bin/cmake -E cmake_depends "Unix Makefiles" "/<>/hhsuite-3.0~beta2+dfsg" "/<>/hhsuite-3.0~beta2+dfsg/src" "/<>/hhsuite-3.0~beta2+dfsg/mybuild" "/<>/hhsuite-3.0~beta2+dfsg/mybuild/src" "/<>/hhsuite-3.0~beta2+dfsg/mybuild/src/CMakeFiles/hhblits.dir/DependInfo.cmake" --color= make[4]: Entering directory '/<>/hhsuite-3.0~beta2+dfsg/mybuild' cd "/<>/hhsuite-3.0~beta2+dfsg/mybuild" && /usr/bin/cmake -E cmake_depends "Unix Makefiles" "/<>/hhsuite-3.0~beta2+dfsg" "/<>/hhsuite-3.0~beta2+dfsg/src" "/<>/hhsuite-3.0~beta2+dfsg/mybuild" "/<>/hhsuite-3.0~beta2+dfsg/mybuild/src" "/<>/hhsuite-3.0~beta2+dfsg/mybuild/src/CMakeFiles/hhconsensus.dir/DependInfo.cmake" --color= make[4]: Entering directory '/<>/hhsuite-3.0~beta2+dfsg/mybuild' cd "/<>/hhsuite-3.0~beta2+dfsg/mybuild" && /usr/bin/cmake -E cmake_depends "Unix Makefiles" "/<>/hhsuite-3.0~beta2+dfsg" "/<>/hhsuite-3.0~beta2+dfsg/src" "/<>/hhsuite-3.0~beta2+dfsg/mybuild" "/<>/hhsuite-3.0~beta2+dfsg/mybuild/src" "/<>/hhsuite-3.0~beta2+dfsg/mybuild/src/CMakeFiles/cstranslate.dir/DependInfo.cmake" --color= make[4]: Entering directory '/<>/hhsuite-3.0~beta2+dfsg/mybuild' cd "/<>/hhsuite-3.0~beta2+dfsg/mybuild" && /usr/bin/cmake -E cmake_depends "Unix Makefiles" "/<>/hhsuite-3.0~beta2+dfsg" "/<>/hhsuite-3.0~beta2+dfsg/src" "/<>/hhsuite-3.0~beta2+dfsg/mybuild" "/<>/hhsuite-3.0~beta2+dfsg/mybuild/src" "/<>/hhsuite-3.0~beta2+dfsg/mybuild/src/CMakeFiles/hhfilter.dir/DependInfo.cmake" --color= make[4]: Entering directory '/<>/hhsuite-3.0~beta2+dfsg/mybuild' cd "/<>/hhsuite-3.0~beta2+dfsg/mybuild" && /usr/bin/cmake -E cmake_depends "Unix Makefiles" "/<>/hhsuite-3.0~beta2+dfsg" "/<>/hhsuite-3.0~beta2+dfsg/src" "/<>/hhsuite-3.0~beta2+dfsg/mybuild" "/<>/hhsuite-3.0~beta2+dfsg/mybuild/src" "/<>/hhsuite-3.0~beta2+dfsg/mybuild/src/CMakeFiles/hhmake.dir/DependInfo.cmake" --color= make[4]: Entering directory '/<>/hhsuite-3.0~beta2+dfsg/mybuild' cd "/<>/hhsuite-3.0~beta2+dfsg/mybuild" && /usr/bin/cmake -E cmake_depends "Unix Makefiles" "/<>/hhsuite-3.0~beta2+dfsg" "/<>/hhsuite-3.0~beta2+dfsg/src" "/<>/hhsuite-3.0~beta2+dfsg/mybuild" "/<>/hhsuite-3.0~beta2+dfsg/mybuild/src" "/<>/hhsuite-3.0~beta2+dfsg/mybuild/src/CMakeFiles/hhalign.dir/DependInfo.cmake" --color= make[4]: Entering directory '/<>/hhsuite-3.0~beta2+dfsg/mybuild' cd "/<>/hhsuite-3.0~beta2+dfsg/mybuild" && /usr/bin/cmake -E cmake_depends "Unix Makefiles" "/<>/hhsuite-3.0~beta2+dfsg" "/<>/hhsuite-3.0~beta2+dfsg/src" "/<>/hhsuite-3.0~beta2+dfsg/mybuild" "/<>/hhsuite-3.0~beta2+dfsg/mybuild/src" "/<>/hhsuite-3.0~beta2+dfsg/mybuild/src/CMakeFiles/hhsearch.dir/DependInfo.cmake" --color= Scanning dependencies of target hhblits Scanning dependencies of target hhconsensus make[4]: Leaving directory '/<>/hhsuite-3.0~beta2+dfsg/mybuild' Scanning dependencies of target cstranslate make[4]: Leaving directory '/<>/hhsuite-3.0~beta2+dfsg/mybuild' make -f src/CMakeFiles/hhconsensus.dir/build.make src/CMakeFiles/hhconsensus.dir/build make -f src/CMakeFiles/hhblits.dir/build.make src/CMakeFiles/hhblits.dir/build make[4]: Leaving directory '/<>/hhsuite-3.0~beta2+dfsg/mybuild' make -f src/CMakeFiles/cstranslate.dir/build.make src/CMakeFiles/cstranslate.dir/build Scanning dependencies of target hhfilter Scanning dependencies of target hhmake make[4]: Leaving directory '/<>/hhsuite-3.0~beta2+dfsg/mybuild' Scanning dependencies of target hhsearch make[4]: Leaving directory '/<>/hhsuite-3.0~beta2+dfsg/mybuild' make -f src/CMakeFiles/hhfilter.dir/build.make src/CMakeFiles/hhfilter.dir/build make[4]: Entering directory '/<>/hhsuite-3.0~beta2+dfsg/mybuild' make -f src/CMakeFiles/hhmake.dir/build.make src/CMakeFiles/hhmake.dir/build make[4]: Entering directory '/<>/hhsuite-3.0~beta2+dfsg/mybuild' make[4]: Leaving directory '/<>/hhsuite-3.0~beta2+dfsg/mybuild' make -f src/CMakeFiles/hhsearch.dir/build.make src/CMakeFiles/hhsearch.dir/build make[4]: Entering directory '/<>/hhsuite-3.0~beta2+dfsg/mybuild' make[4]: Entering directory '/<>/hhsuite-3.0~beta2+dfsg/mybuild' Scanning dependencies of target hhalign make[4]: Entering directory '/<>/hhsuite-3.0~beta2+dfsg/mybuild' make[4]: Leaving directory '/<>/hhsuite-3.0~beta2+dfsg/mybuild' make -f src/CMakeFiles/hhalign.dir/build.make src/CMakeFiles/hhalign.dir/build make[4]: Entering directory '/<>/hhsuite-3.0~beta2+dfsg/mybuild' make[4]: Entering directory '/<>/hhsuite-3.0~beta2+dfsg/mybuild' [ 80%] Building CXX object src/CMakeFiles/hhconsensus.dir/hhconsensus.cpp.o [ 82%] Building CXX object src/CMakeFiles/hhfilter.dir/hhfilter.cpp.o [ 83%] Building CXX object src/CMakeFiles/hhblits.dir/hhblits_app.cpp.o [ 85%] Building CXX object src/CMakeFiles/cstranslate.dir/cs/cstranslate_app.cc.o [ 86%] Building CXX object src/CMakeFiles/hhsearch.dir/hhsearch_app.cpp.o cd "/<>/hhsuite-3.0~beta2+dfsg/mybuild/src" && /usr/bin/c++ -DSSE -I"/<>/hhsuite-3.0~beta2+dfsg/src" -I"/<>/hhsuite-3.0~beta2+dfsg/src/cs" -I"/<>/hhsuite-3.0~beta2+dfsg/mybuild" -g -O2 -fdebug-prefix-map=/<>/hhsuite-3.0~beta2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse4.2 -mfpmath=sse -fno-strict-aliasing -o CMakeFiles/hhconsensus.dir/hhconsensus.cpp.o -c "/<>/hhsuite-3.0~beta2+dfsg/src/hhconsensus.cpp" cd "/<>/hhsuite-3.0~beta2+dfsg/mybuild/src" && /usr/bin/c++ -DSSE -I"/<>/hhsuite-3.0~beta2+dfsg/src" -I"/<>/hhsuite-3.0~beta2+dfsg/src/cs" -I"/<>/hhsuite-3.0~beta2+dfsg/mybuild" -g -O2 -fdebug-prefix-map=/<>/hhsuite-3.0~beta2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse4.2 -mfpmath=sse -fno-strict-aliasing -o CMakeFiles/hhfilter.dir/hhfilter.cpp.o -c "/<>/hhsuite-3.0~beta2+dfsg/src/hhfilter.cpp" cd "/<>/hhsuite-3.0~beta2+dfsg/mybuild/src" && /usr/bin/c++ -DSSE -I"/<>/hhsuite-3.0~beta2+dfsg/src" -I"/<>/hhsuite-3.0~beta2+dfsg/src/cs" -I"/<>/hhsuite-3.0~beta2+dfsg/mybuild" -g -O2 -fdebug-prefix-map=/<>/hhsuite-3.0~beta2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse4.2 -mfpmath=sse -fno-strict-aliasing -o CMakeFiles/hhblits.dir/hhblits_app.cpp.o -c "/<>/hhsuite-3.0~beta2+dfsg/src/hhblits_app.cpp" cd "/<>/hhsuite-3.0~beta2+dfsg/mybuild/src" && /usr/bin/c++ -DSSE -I"/<>/hhsuite-3.0~beta2+dfsg/src" -I"/<>/hhsuite-3.0~beta2+dfsg/src/cs" -I"/<>/hhsuite-3.0~beta2+dfsg/mybuild" -g -O2 -fdebug-prefix-map=/<>/hhsuite-3.0~beta2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse4.2 -mfpmath=sse -fno-strict-aliasing -o CMakeFiles/cstranslate.dir/cs/cstranslate_app.cc.o -c "/<>/hhsuite-3.0~beta2+dfsg/src/cs/cstranslate_app.cc" cd "/<>/hhsuite-3.0~beta2+dfsg/mybuild/src" && /usr/bin/c++ -DSSE -I"/<>/hhsuite-3.0~beta2+dfsg/src" -I"/<>/hhsuite-3.0~beta2+dfsg/src/cs" -I"/<>/hhsuite-3.0~beta2+dfsg/mybuild" -g -O2 -fdebug-prefix-map=/<>/hhsuite-3.0~beta2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse4.2 -mfpmath=sse -fno-strict-aliasing -o CMakeFiles/hhsearch.dir/hhsearch_app.cpp.o -c "/<>/hhsuite-3.0~beta2+dfsg/src/hhsearch_app.cpp" [ 88%] Building CXX object src/CMakeFiles/hhmake.dir/hhmake.cpp.o cd "/<>/hhsuite-3.0~beta2+dfsg/mybuild/src" && /usr/bin/c++ -DSSE -I"/<>/hhsuite-3.0~beta2+dfsg/src" -I"/<>/hhsuite-3.0~beta2+dfsg/src/cs" -I"/<>/hhsuite-3.0~beta2+dfsg/mybuild" -g -O2 -fdebug-prefix-map=/<>/hhsuite-3.0~beta2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse4.2 -mfpmath=sse -fno-strict-aliasing -o CMakeFiles/hhmake.dir/hhmake.cpp.o -c "/<>/hhsuite-3.0~beta2+dfsg/src/hhmake.cpp" [ 89%] Building CXX object src/CMakeFiles/hhalign.dir/hhalign_app.cpp.o cd "/<>/hhsuite-3.0~beta2+dfsg/mybuild/src" && /usr/bin/c++ -DSSE -I"/<>/hhsuite-3.0~beta2+dfsg/src" -I"/<>/hhsuite-3.0~beta2+dfsg/src/cs" -I"/<>/hhsuite-3.0~beta2+dfsg/mybuild" -g -O2 -fdebug-prefix-map=/<>/hhsuite-3.0~beta2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse4.2 -mfpmath=sse -fno-strict-aliasing -o CMakeFiles/hhalign.dir/hhalign_app.cpp.o -c "/<>/hhsuite-3.0~beta2+dfsg/src/hhalign_app.cpp" In file included from /<>/hhsuite-3.0~beta2+dfsg/src/cs/cstranslate_app.cc:20: In file included from /<>/hhsuite-3.0~beta2+dfsg/src/cs/cstranslate_app.h:21: /<>/hhsuite-3.0~beta2+dfsg/src/cs/alignment-inl.h:674:15: warning: comparison of constant -1 with expression of type 'uint8_t' (aka 'unsigned char') is always false [-Wtautological-constant-out-of-range-compare] if (c == EOF) break; ~ ^ ~~~ /<>/hhsuite-3.0~beta2+dfsg/src/cs/alignment-inl.h:846:21: warning: add explicit braces to avoid dangling else [-Wdangling-else] else ^ In file included from /<>/hhsuite-3.0~beta2+dfsg/src/hhalign_app.cpp:9: In file included from /<>/hhsuite-3.0~beta2+dfsg/src/hhalign.h:38: In file included from /<>/hhsuite-3.0~beta2+dfsg/src/cs/context_library.h:25: In file included from /<>/hhsuite-3.0~beta2+dfsg/src/cs/context_profile.h:24: In file included from /<>/hhsuite-3.0~beta2+dfsg/src/cs/count_profile-inl.h:25: /<>/hhsuite-3.0~beta2+dfsg/src/cs/alignment-inl.h:674:15: warning: comparison of constant -1 with expression of type 'uint8_t' (aka 'unsigned char') is always false [-Wtautological-constant-out-of-range-compare] if (c == EOF) break; ~ ^ ~~~ In file included from /<>/hhsuite-3.0~beta2+dfsg/src/hhconsensus.cpp:20: In file included from /<>/hhsuite-3.0~beta2+dfsg/src/cs/context_library.h:25: In file included from /<>/hhsuite-3.0~beta2+dfsg/src/cs/context_profile.h:24: In file included from /<>/hhsuite-3.0~beta2+dfsg/src/cs/count_profile-inl.h:25: /<>/hhsuite-3.0~beta2+dfsg/src/cs/alignment-inl.h:674:15: warning: comparison of constant -1 with expression of type 'uint8_t' (aka 'unsigned char') is always false [-Wtautological-constant-out-of-range-compare] if (c == EOF) break; ~ ^ ~~~ /<>/hhsuite-3.0~beta2+dfsg/src/cs/alignment-inl.h:846:21: warning: add explicit braces to avoid dangling else [-Wdangling-else] else ^ /<>/hhsuite-3.0~beta2+dfsg/src/cs/alignment-inl.h:846:21: warning: add explicit braces to avoid dangling else [-Wdangling-else] else ^ In file included from /<>/hhsuite-3.0~beta2+dfsg/src/hhfilter.cpp:40: In file included from /<>/hhsuite-3.0~beta2+dfsg/src/cs/context_library.h:25: In file included from /<>/hhsuite-3.0~beta2+dfsg/src/cs/context_profile.h:24: In file included from /<>/hhsuite-3.0~beta2+dfsg/src/cs/count_profile-inl.h:25: /<>/hhsuite-3.0~beta2+dfsg/src/cs/alignment-inl.h:674:15: warning: comparison of constant -1 with expression of type 'uint8_t' (aka 'unsigned char') is always false [-Wtautological-constant-out-of-range-compare] if (c == EOF) break; ~ ^ ~~~ /<>/hhsuite-3.0~beta2+dfsg/src/cs/alignment-inl.h:846:21: warning: add explicit braces to avoid dangling else [-Wdangling-else] else ^ In file included from /<>/hhsuite-3.0~beta2+dfsg/src/hhmake.cpp:40: In file included from /<>/hhsuite-3.0~beta2+dfsg/src/cs/context_library.h:25: In file included from /<>/hhsuite-3.0~beta2+dfsg/src/cs/context_profile.h:24: In file included from /<>/hhsuite-3.0~beta2+dfsg/src/cs/count_profile-inl.h:25: /<>/hhsuite-3.0~beta2+dfsg/src/cs/alignment-inl.h:674:15: warning: comparison of constant -1 with expression of type 'uint8_t' (aka 'unsigned char') is always false [-Wtautological-constant-out-of-range-compare] if (c == EOF) break; ~ ^ ~~~ /<>/hhsuite-3.0~beta2+dfsg/src/cs/alignment-inl.h:846:21: warning: add explicit braces to avoid dangling else [-Wdangling-else] else ^ In file included from /<>/hhsuite-3.0~beta2+dfsg/src/hhblits_app.cpp:56: In file included from /<>/hhsuite-3.0~beta2+dfsg/src/hhblits.h:51: In file included from /<>/hhsuite-3.0~beta2+dfsg/src/cs/context_library.h:25: In file included from /<>/hhsuite-3.0~beta2+dfsg/src/cs/context_profile.h:24: In file included from /<>/hhsuite-3.0~beta2+dfsg/src/cs/count_profile-inl.h:25: /<>/hhsuite-3.0~beta2+dfsg/src/cs/alignment-inl.h:674:15: warning: comparison of constant -1 with expression of type 'uint8_t' (aka 'unsigned char') is always false [-Wtautological-constant-out-of-range-compare] if (c == EOF) break; ~ ^ ~~~ /<>/hhsuite-3.0~beta2+dfsg/src/cs/alignment-inl.h:846:21: warning: add explicit braces to avoid dangling else [-Wdangling-else] else ^ In file included from /<>/hhsuite-3.0~beta2+dfsg/src/hhsearch_app.cpp:8: In file included from /<>/hhsuite-3.0~beta2+dfsg/src/hhsearch.h:34: In file included from /<>/hhsuite-3.0~beta2+dfsg/src/hhblits.h:51: In file included from /<>/hhsuite-3.0~beta2+dfsg/src/cs/context_library.h:25: In file included from /<>/hhsuite-3.0~beta2+dfsg/src/cs/context_profile.h:24: In file included from /<>/hhsuite-3.0~beta2+dfsg/src/cs/count_profile-inl.h:25: /<>/hhsuite-3.0~beta2+dfsg/src/cs/alignment-inl.h:674:15: warning: comparison of constant -1 with expression of type 'uint8_t' (aka 'unsigned char') is always false [-Wtautological-constant-out-of-range-compare] if (c == EOF) break; ~ ^ ~~~ /<>/hhsuite-3.0~beta2+dfsg/src/cs/alignment-inl.h:846:21: warning: add explicit braces to avoid dangling else [-Wdangling-else] else ^ 2 warnings generated. [ 91%] Linking CXX executable ../bin/hhalign cd "/<>/hhsuite-3.0~beta2+dfsg/mybuild/src" && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhalign.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/<>/hhsuite-3.0~beta2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse4.2 -mfpmath=sse -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now CMakeFiles/hhalign.dir/hhalign_app.cpp.o CMakeFiles/CS_OBJECTS.dir/cs/aa.cc.o CMakeFiles/CS_OBJECTS.dir/cs/as.cc.o CMakeFiles/CS_OBJECTS.dir/cs/assert_helpers.cc.o CMakeFiles/CS_OBJECTS.dir/cs/blosum_matrix.cc.o CMakeFiles/CS_OBJECTS.dir/cs/getopt_pp.cc.o CMakeFiles/CS_OBJECTS.dir/cs/log.cc.o CMakeFiles/CS_OBJECTS.dir/cs/application.cc.o CMakeFiles/HH_OBJECTS.dir/hhblits.cpp.o CMakeFiles/HH_OBJECTS.dir/hhdecl.cpp.o CMakeFiles/HH_OBJECTS.dir/hhhit.cpp.o CMakeFiles/HH_OBJECTS.dir/hhmatrices.cpp.o CMakeFiles/HH_OBJECTS.dir/hhsearch.cpp.o CMakeFiles/HH_OBJECTS.dir/hhalign.cpp.o CMakeFiles/HH_OBJECTS.dir/hhhitlist.cpp.o CMakeFiles/HH_OBJECTS.dir/hhposteriordecoder.cpp.o CMakeFiles/HH_OBJECTS.dir/hhutil.cpp.o CMakeFiles/HH_OBJECTS.dir/util.cpp.o CMakeFiles/HH_OBJECTS.dir/hhalignment.cpp.o CMakeFiles/HH_OBJECTS.dir/hhforwardalgorithm.cpp.o CMakeFiles/HH_OBJECTS.dir/hhhmm.cpp.o CMakeFiles/HH_OBJECTS.dir/hhposteriordecoderrunner.cpp.o CMakeFiles/HH_OBJECTS.dir/hhviterbialgorithm.cpp.o CMakeFiles/HH_OBJECTS.dir/hhfullalignment.cpp.o CMakeFiles/HH_OBJECTS.dir/hhhmmsimd.cpp.o CMakeFiles/HH_OBJECTS.dir/hhposteriormatrix.cpp.o CMakeFiles/HH_OBJECTS.dir/hhviterbi.cpp.o CMakeFiles/HH_OBJECTS.dir/hhbacktracemac.cpp.o CMakeFiles/HH_OBJECTS.dir/hhmacalgorithm.cpp.o CMakeFiles/HH_OBJECTS.dir/hhprefilter.cpp.o CMakeFiles/HH_OBJECTS.dir/hhviterbimatrix.cpp.o CMakeFiles/HH_OBJECTS.dir/hhbackwardalgorithm.cpp.o CMakeFiles/HH_OBJECTS.dir/hhdatabase.cpp.o CMakeFiles/HH_OBJECTS.dir/hhhalfalignment.cpp.o CMakeFiles/HH_OBJECTS.dir/hhviterbirunner.cpp.o CMakeFiles/HH_OBJECTS.dir/hhfunc.cpp.o CMakeFiles/hhviterbialgorithm_with_celloff.dir/hhviterbialgorithm.cpp.o CMakeFiles/hhviterbialgorithm_and_ss.dir/hhviterbialgorithm.cpp.o CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/hhviterbialgorithm.cpp.o -o ../bin/hhalign -rdynamic -lffindex 2 warnings generated. [ 92%] Linking CXX executable ../bin/hhblits cd "/<>/hhsuite-3.0~beta2+dfsg/mybuild/src" && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhblits.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/<>/hhsuite-3.0~beta2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse4.2 -mfpmath=sse -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now CMakeFiles/hhblits.dir/hhblits_app.cpp.o CMakeFiles/CS_OBJECTS.dir/cs/aa.cc.o CMakeFiles/CS_OBJECTS.dir/cs/as.cc.o CMakeFiles/CS_OBJECTS.dir/cs/assert_helpers.cc.o CMakeFiles/CS_OBJECTS.dir/cs/blosum_matrix.cc.o CMakeFiles/CS_OBJECTS.dir/cs/getopt_pp.cc.o CMakeFiles/CS_OBJECTS.dir/cs/log.cc.o CMakeFiles/CS_OBJECTS.dir/cs/application.cc.o CMakeFiles/HH_OBJECTS.dir/hhblits.cpp.o CMakeFiles/HH_OBJECTS.dir/hhdecl.cpp.o CMakeFiles/HH_OBJECTS.dir/hhhit.cpp.o CMakeFiles/HH_OBJECTS.dir/hhmatrices.cpp.o CMakeFiles/HH_OBJECTS.dir/hhsearch.cpp.o CMakeFiles/HH_OBJECTS.dir/hhalign.cpp.o CMakeFiles/HH_OBJECTS.dir/hhhitlist.cpp.o CMakeFiles/HH_OBJECTS.dir/hhposteriordecoder.cpp.o CMakeFiles/HH_OBJECTS.dir/hhutil.cpp.o CMakeFiles/HH_OBJECTS.dir/util.cpp.o CMakeFiles/HH_OBJECTS.dir/hhalignment.cpp.o CMakeFiles/HH_OBJECTS.dir/hhforwardalgorithm.cpp.o CMakeFiles/HH_OBJECTS.dir/hhhmm.cpp.o CMakeFiles/HH_OBJECTS.dir/hhposteriordecoderrunner.cpp.o CMakeFiles/HH_OBJECTS.dir/hhviterbialgorithm.cpp.o CMakeFiles/HH_OBJECTS.dir/hhfullalignment.cpp.o CMakeFiles/HH_OBJECTS.dir/hhhmmsimd.cpp.o CMakeFiles/HH_OBJECTS.dir/hhposteriormatrix.cpp.o CMakeFiles/HH_OBJECTS.dir/hhviterbi.cpp.o CMakeFiles/HH_OBJECTS.dir/hhbacktracemac.cpp.o CMakeFiles/HH_OBJECTS.dir/hhmacalgorithm.cpp.o CMakeFiles/HH_OBJECTS.dir/hhprefilter.cpp.o CMakeFiles/HH_OBJECTS.dir/hhviterbimatrix.cpp.o CMakeFiles/HH_OBJECTS.dir/hhbackwardalgorithm.cpp.o CMakeFiles/HH_OBJECTS.dir/hhdatabase.cpp.o CMakeFiles/HH_OBJECTS.dir/hhhalfalignment.cpp.o CMakeFiles/HH_OBJECTS.dir/hhviterbirunner.cpp.o CMakeFiles/HH_OBJECTS.dir/hhfunc.cpp.o CMakeFiles/hhviterbialgorithm_with_celloff.dir/hhviterbialgorithm.cpp.o CMakeFiles/hhviterbialgorithm_and_ss.dir/hhviterbialgorithm.cpp.o CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/hhviterbialgorithm.cpp.o -o ../bin/hhblits -rdynamic -lffindex 2 warnings generated. [ 94%] Linking CXX executable ../bin/hhsearch cd "/<>/hhsuite-3.0~beta2+dfsg/mybuild/src" && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhsearch.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/<>/hhsuite-3.0~beta2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse4.2 -mfpmath=sse -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now CMakeFiles/hhsearch.dir/hhsearch_app.cpp.o CMakeFiles/CS_OBJECTS.dir/cs/aa.cc.o CMakeFiles/CS_OBJECTS.dir/cs/as.cc.o CMakeFiles/CS_OBJECTS.dir/cs/assert_helpers.cc.o CMakeFiles/CS_OBJECTS.dir/cs/blosum_matrix.cc.o CMakeFiles/CS_OBJECTS.dir/cs/getopt_pp.cc.o CMakeFiles/CS_OBJECTS.dir/cs/log.cc.o CMakeFiles/CS_OBJECTS.dir/cs/application.cc.o CMakeFiles/HH_OBJECTS.dir/hhblits.cpp.o CMakeFiles/HH_OBJECTS.dir/hhdecl.cpp.o CMakeFiles/HH_OBJECTS.dir/hhhit.cpp.o CMakeFiles/HH_OBJECTS.dir/hhmatrices.cpp.o CMakeFiles/HH_OBJECTS.dir/hhsearch.cpp.o CMakeFiles/HH_OBJECTS.dir/hhalign.cpp.o CMakeFiles/HH_OBJECTS.dir/hhhitlist.cpp.o CMakeFiles/HH_OBJECTS.dir/hhposteriordecoder.cpp.o CMakeFiles/HH_OBJECTS.dir/hhutil.cpp.o CMakeFiles/HH_OBJECTS.dir/util.cpp.o CMakeFiles/HH_OBJECTS.dir/hhalignment.cpp.o CMakeFiles/HH_OBJECTS.dir/hhforwardalgorithm.cpp.o CMakeFiles/HH_OBJECTS.dir/hhhmm.cpp.o CMakeFiles/HH_OBJECTS.dir/hhposteriordecoderrunner.cpp.o CMakeFiles/HH_OBJECTS.dir/hhviterbialgorithm.cpp.o CMakeFiles/HH_OBJECTS.dir/hhfullalignment.cpp.o CMakeFiles/HH_OBJECTS.dir/hhhmmsimd.cpp.o CMakeFiles/HH_OBJECTS.dir/hhposteriormatrix.cpp.o CMakeFiles/HH_OBJECTS.dir/hhviterbi.cpp.o CMakeFiles/HH_OBJECTS.dir/hhbacktracemac.cpp.o CMakeFiles/HH_OBJECTS.dir/hhmacalgorithm.cpp.o CMakeFiles/HH_OBJECTS.dir/hhprefilter.cpp.o CMakeFiles/HH_OBJECTS.dir/hhviterbimatrix.cpp.o CMakeFiles/HH_OBJECTS.dir/hhbackwardalgorithm.cpp.o CMakeFiles/HH_OBJECTS.dir/hhdatabase.cpp.o CMakeFiles/HH_OBJECTS.dir/hhhalfalignment.cpp.o CMakeFiles/HH_OBJECTS.dir/hhviterbirunner.cpp.o CMakeFiles/HH_OBJECTS.dir/hhfunc.cpp.o CMakeFiles/hhviterbialgorithm_with_celloff.dir/hhviterbialgorithm.cpp.o CMakeFiles/hhviterbialgorithm_and_ss.dir/hhviterbialgorithm.cpp.o CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/hhviterbialgorithm.cpp.o -o ../bin/hhsearch -rdynamic -lffindex 2 warnings generated. [ 95%] Linking CXX executable ../bin/hhfilter cd "/<>/hhsuite-3.0~beta2+dfsg/mybuild/src" && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhfilter.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/<>/hhsuite-3.0~beta2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse4.2 -mfpmath=sse -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now CMakeFiles/hhfilter.dir/hhfilter.cpp.o CMakeFiles/CS_OBJECTS.dir/cs/aa.cc.o CMakeFiles/CS_OBJECTS.dir/cs/as.cc.o CMakeFiles/CS_OBJECTS.dir/cs/assert_helpers.cc.o CMakeFiles/CS_OBJECTS.dir/cs/blosum_matrix.cc.o CMakeFiles/CS_OBJECTS.dir/cs/getopt_pp.cc.o CMakeFiles/CS_OBJECTS.dir/cs/log.cc.o CMakeFiles/CS_OBJECTS.dir/cs/application.cc.o CMakeFiles/HH_OBJECTS.dir/hhblits.cpp.o CMakeFiles/HH_OBJECTS.dir/hhdecl.cpp.o CMakeFiles/HH_OBJECTS.dir/hhhit.cpp.o CMakeFiles/HH_OBJECTS.dir/hhmatrices.cpp.o CMakeFiles/HH_OBJECTS.dir/hhsearch.cpp.o CMakeFiles/HH_OBJECTS.dir/hhalign.cpp.o CMakeFiles/HH_OBJECTS.dir/hhhitlist.cpp.o CMakeFiles/HH_OBJECTS.dir/hhposteriordecoder.cpp.o CMakeFiles/HH_OBJECTS.dir/hhutil.cpp.o CMakeFiles/HH_OBJECTS.dir/util.cpp.o CMakeFiles/HH_OBJECTS.dir/hhalignment.cpp.o CMakeFiles/HH_OBJECTS.dir/hhforwardalgorithm.cpp.o CMakeFiles/HH_OBJECTS.dir/hhhmm.cpp.o CMakeFiles/HH_OBJECTS.dir/hhposteriordecoderrunner.cpp.o CMakeFiles/HH_OBJECTS.dir/hhviterbialgorithm.cpp.o CMakeFiles/HH_OBJECTS.dir/hhfullalignment.cpp.o CMakeFiles/HH_OBJECTS.dir/hhhmmsimd.cpp.o CMakeFiles/HH_OBJECTS.dir/hhposteriormatrix.cpp.o CMakeFiles/HH_OBJECTS.dir/hhviterbi.cpp.o CMakeFiles/HH_OBJECTS.dir/hhbacktracemac.cpp.o CMakeFiles/HH_OBJECTS.dir/hhmacalgorithm.cpp.o CMakeFiles/HH_OBJECTS.dir/hhprefilter.cpp.o CMakeFiles/HH_OBJECTS.dir/hhviterbimatrix.cpp.o CMakeFiles/HH_OBJECTS.dir/hhbackwardalgorithm.cpp.o CMakeFiles/HH_OBJECTS.dir/hhdatabase.cpp.o CMakeFiles/HH_OBJECTS.dir/hhhalfalignment.cpp.o CMakeFiles/HH_OBJECTS.dir/hhviterbirunner.cpp.o CMakeFiles/HH_OBJECTS.dir/hhfunc.cpp.o CMakeFiles/hhviterbialgorithm_with_celloff.dir/hhviterbialgorithm.cpp.o CMakeFiles/hhviterbialgorithm_and_ss.dir/hhviterbialgorithm.cpp.o CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/hhviterbialgorithm.cpp.o -o ../bin/hhfilter -rdynamic -lffindex make[4]: Leaving directory '/<>/hhsuite-3.0~beta2+dfsg/mybuild' [ 95%] Built target hhalign 2 warnings generated. 2 warnings generated. make[4]: Leaving directory '/<>/hhsuite-3.0~beta2+dfsg/mybuild' [ 97%] Linking CXX executable ../bin/hhconsensus cd "/<>/hhsuite-3.0~beta2+dfsg/mybuild/src" && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhconsensus.dir/link.txt --verbose=1 [ 97%] Built target hhblits [ 98%] Linking CXX executable ../bin/hhmake cd "/<>/hhsuite-3.0~beta2+dfsg/mybuild/src" && /usr/bin/cmake -E cmake_link_script CMakeFiles/hhmake.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/<>/hhsuite-3.0~beta2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse4.2 -mfpmath=sse -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now CMakeFiles/hhconsensus.dir/hhconsensus.cpp.o CMakeFiles/CS_OBJECTS.dir/cs/aa.cc.o CMakeFiles/CS_OBJECTS.dir/cs/as.cc.o CMakeFiles/CS_OBJECTS.dir/cs/assert_helpers.cc.o CMakeFiles/CS_OBJECTS.dir/cs/blosum_matrix.cc.o CMakeFiles/CS_OBJECTS.dir/cs/getopt_pp.cc.o CMakeFiles/CS_OBJECTS.dir/cs/log.cc.o CMakeFiles/CS_OBJECTS.dir/cs/application.cc.o CMakeFiles/HH_OBJECTS.dir/hhblits.cpp.o CMakeFiles/HH_OBJECTS.dir/hhdecl.cpp.o CMakeFiles/HH_OBJECTS.dir/hhhit.cpp.o CMakeFiles/HH_OBJECTS.dir/hhmatrices.cpp.o CMakeFiles/HH_OBJECTS.dir/hhsearch.cpp.o CMakeFiles/HH_OBJECTS.dir/hhalign.cpp.o CMakeFiles/HH_OBJECTS.dir/hhhitlist.cpp.o CMakeFiles/HH_OBJECTS.dir/hhposteriordecoder.cpp.o CMakeFiles/HH_OBJECTS.dir/hhutil.cpp.o CMakeFiles/HH_OBJECTS.dir/util.cpp.o CMakeFiles/HH_OBJECTS.dir/hhalignment.cpp.o CMakeFiles/HH_OBJECTS.dir/hhforwardalgorithm.cpp.o CMakeFiles/HH_OBJECTS.dir/hhhmm.cpp.o 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[100%] Linking CXX executable ../bin/cstranslate cd "/<>/hhsuite-3.0~beta2+dfsg/mybuild/src" && /usr/bin/cmake -E cmake_link_script CMakeFiles/cstranslate.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/<>/hhsuite-3.0~beta2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse4.2 -mfpmath=sse -fno-strict-aliasing -Wl,-z,relro -Wl,-z,now CMakeFiles/cstranslate.dir/cs/cstranslate_app.cc.o CMakeFiles/CS_OBJECTS.dir/cs/aa.cc.o CMakeFiles/CS_OBJECTS.dir/cs/as.cc.o CMakeFiles/CS_OBJECTS.dir/cs/assert_helpers.cc.o CMakeFiles/CS_OBJECTS.dir/cs/blosum_matrix.cc.o CMakeFiles/CS_OBJECTS.dir/cs/getopt_pp.cc.o CMakeFiles/CS_OBJECTS.dir/cs/log.cc.o CMakeFiles/CS_OBJECTS.dir/cs/application.cc.o CMakeFiles/HH_OBJECTS.dir/hhblits.cpp.o CMakeFiles/HH_OBJECTS.dir/hhdecl.cpp.o CMakeFiles/HH_OBJECTS.dir/hhhit.cpp.o CMakeFiles/HH_OBJECTS.dir/hhmatrices.cpp.o CMakeFiles/HH_OBJECTS.dir/hhsearch.cpp.o CMakeFiles/HH_OBJECTS.dir/hhalign.cpp.o CMakeFiles/HH_OBJECTS.dir/hhhitlist.cpp.o CMakeFiles/HH_OBJECTS.dir/hhposteriordecoder.cpp.o CMakeFiles/HH_OBJECTS.dir/hhutil.cpp.o CMakeFiles/HH_OBJECTS.dir/util.cpp.o CMakeFiles/HH_OBJECTS.dir/hhalignment.cpp.o CMakeFiles/HH_OBJECTS.dir/hhforwardalgorithm.cpp.o CMakeFiles/HH_OBJECTS.dir/hhhmm.cpp.o CMakeFiles/HH_OBJECTS.dir/hhposteriordecoderrunner.cpp.o CMakeFiles/HH_OBJECTS.dir/hhviterbialgorithm.cpp.o CMakeFiles/HH_OBJECTS.dir/hhfullalignment.cpp.o CMakeFiles/HH_OBJECTS.dir/hhhmmsimd.cpp.o CMakeFiles/HH_OBJECTS.dir/hhposteriormatrix.cpp.o CMakeFiles/HH_OBJECTS.dir/hhviterbi.cpp.o CMakeFiles/HH_OBJECTS.dir/hhbacktracemac.cpp.o CMakeFiles/HH_OBJECTS.dir/hhmacalgorithm.cpp.o CMakeFiles/HH_OBJECTS.dir/hhprefilter.cpp.o CMakeFiles/HH_OBJECTS.dir/hhviterbimatrix.cpp.o CMakeFiles/HH_OBJECTS.dir/hhbackwardalgorithm.cpp.o CMakeFiles/HH_OBJECTS.dir/hhdatabase.cpp.o CMakeFiles/HH_OBJECTS.dir/hhhalfalignment.cpp.o CMakeFiles/HH_OBJECTS.dir/hhviterbirunner.cpp.o CMakeFiles/HH_OBJECTS.dir/hhfunc.cpp.o CMakeFiles/hhviterbialgorithm_with_celloff.dir/hhviterbialgorithm.cpp.o CMakeFiles/hhviterbialgorithm_and_ss.dir/hhviterbialgorithm.cpp.o CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/hhviterbialgorithm.cpp.o CMakeFiles/A3M_COMPRESS_OBJECT.dir/a3m_compress.cpp.o -o ../bin/cstranslate -rdynamic -lffindex make[4]: Leaving directory '/<>/hhsuite-3.0~beta2+dfsg/mybuild' [100%] Built target cstranslate make[3]: Leaving directory '/<>/hhsuite-3.0~beta2+dfsg/mybuild' /usr/bin/cmake -E cmake_progress_start "/<>/hhsuite-3.0~beta2+dfsg/mybuild/CMakeFiles" 0 make[2]: Leaving directory '/<>/hhsuite-3.0~beta2+dfsg/mybuild' make[1]: Leaving directory '/<>/hhsuite-3.0~beta2+dfsg' dh_auto_test -a -O--builddirectory=mybuild make -j16 test ARGS\+=-j16 make[1]: Entering directory '/<>/hhsuite-3.0~beta2+dfsg/mybuild' Running tests... /usr/bin/ctest --force-new-ctest-process -j16 Test project /<>/hhsuite-3.0~beta2+dfsg/mybuild Start 1: hhblits Start 2: hhsearch Start 3: hhalign 1/3 Test #1: hhblits .......................... 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"/<>/hhsuite-3.0~beta2+dfsg/mybuild/src" "/<>/hhsuite-3.0~beta2+dfsg/mybuild/src/CMakeFiles/hhviterbialgorithm_and_ss.dir/DependInfo.cmake" --color= make[3]: Entering directory '/<>/hhsuite-3.0~beta2+dfsg/mybuild' cd "/<>/hhsuite-3.0~beta2+dfsg/mybuild" && /usr/bin/cmake -E cmake_depends "Unix Makefiles" "/<>/hhsuite-3.0~beta2+dfsg" "/<>/hhsuite-3.0~beta2+dfsg/src" "/<>/hhsuite-3.0~beta2+dfsg/mybuild" "/<>/hhsuite-3.0~beta2+dfsg/mybuild/src" "/<>/hhsuite-3.0~beta2+dfsg/mybuild/src/CMakeFiles/HH_OBJECTS.dir/DependInfo.cmake" --color= make[3]: Leaving directory '/<>/hhsuite-3.0~beta2+dfsg/mybuild' make -f src/CMakeFiles/A3M_COMPRESS_OBJECT.dir/build.make src/CMakeFiles/A3M_COMPRESS_OBJECT.dir/build make[3]: Leaving directory '/<>/hhsuite-3.0~beta2+dfsg/mybuild' make -f doc/CMakeFiles/pdf.dir/build.make doc/CMakeFiles/pdf.dir/build make[3]: Entering directory '/<>/hhsuite-3.0~beta2+dfsg/mybuild' make[3]: Nothing to be done for 'src/CMakeFiles/A3M_COMPRESS_OBJECT.dir/build'. make[3]: 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"/<>/hhsuite-3.0~beta2+dfsg/mybuild/src/CMakeFiles/a3m_database_extract.dir/DependInfo.cmake" --color= make[3]: Entering directory '/<>/hhsuite-3.0~beta2+dfsg/mybuild' cd "/<>/hhsuite-3.0~beta2+dfsg/mybuild" && /usr/bin/cmake -E cmake_depends "Unix Makefiles" "/<>/hhsuite-3.0~beta2+dfsg" "/<>/hhsuite-3.0~beta2+dfsg/src" "/<>/hhsuite-3.0~beta2+dfsg/mybuild" "/<>/hhsuite-3.0~beta2+dfsg/mybuild/src" "/<>/hhsuite-3.0~beta2+dfsg/mybuild/src/CMakeFiles/a3m_reduce.dir/DependInfo.cmake" --color= make[3]: Entering directory '/<>/hhsuite-3.0~beta2+dfsg/mybuild' cd "/<>/hhsuite-3.0~beta2+dfsg/mybuild" && /usr/bin/cmake -E cmake_depends "Unix Makefiles" "/<>/hhsuite-3.0~beta2+dfsg" "/<>/hhsuite-3.0~beta2+dfsg/src" "/<>/hhsuite-3.0~beta2+dfsg/mybuild" "/<>/hhsuite-3.0~beta2+dfsg/mybuild/src" "/<>/hhsuite-3.0~beta2+dfsg/mybuild/src/CMakeFiles/a3m_extract.dir/DependInfo.cmake" --color= make[3]: Leaving directory '/<>/hhsuite-3.0~beta2+dfsg/mybuild' make -f src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/build.make src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/build make[3]: Leaving directory '/<>/hhsuite-3.0~beta2+dfsg/mybuild' make -f src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/build.make src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/build make[3]: Leaving directory '/<>/hhsuite-3.0~beta2+dfsg/mybuild' make -f src/CMakeFiles/hhviterbialgorithm_and_ss.dir/build.make src/CMakeFiles/hhviterbialgorithm_and_ss.dir/build make[3]: Leaving directory '/<>/hhsuite-3.0~beta2+dfsg/mybuild' make -f src/CMakeFiles/a3m_database_filter.dir/build.make src/CMakeFiles/a3m_database_filter.dir/build make[3]: Leaving directory '/<>/hhsuite-3.0~beta2+dfsg/mybuild' make -f src/CMakeFiles/a3m_database_reduce.dir/build.make src/CMakeFiles/a3m_database_reduce.dir/build make[3]: Leaving directory '/<>/hhsuite-3.0~beta2+dfsg/mybuild' make -f src/CMakeFiles/a3m_database_extract.dir/build.make src/CMakeFiles/a3m_database_extract.dir/build make[3]: Leaving directory '/<>/hhsuite-3.0~beta2+dfsg/mybuild' make -f src/CMakeFiles/a3m_reduce.dir/build.make src/CMakeFiles/a3m_reduce.dir/build make[3]: Leaving directory '/<>/hhsuite-3.0~beta2+dfsg/mybuild' make -f src/CMakeFiles/a3m_extract.dir/build.make src/CMakeFiles/a3m_extract.dir/build make[3]: Entering directory '/<>/hhsuite-3.0~beta2+dfsg/mybuild' make[3]: Nothing to be done for 'src/CMakeFiles/a3m_database_filter.dir/build'. make[3]: Leaving directory '/<>/hhsuite-3.0~beta2+dfsg/mybuild' make[3]: Entering directory '/<>/hhsuite-3.0~beta2+dfsg/mybuild' make[3]: Nothing to be done for 'src/CMakeFiles/a3m_database_reduce.dir/build'. make[3]: Leaving directory '/<>/hhsuite-3.0~beta2+dfsg/mybuild' make[3]: Entering directory '/<>/hhsuite-3.0~beta2+dfsg/mybuild' make[3]: Nothing to be done for 'src/CMakeFiles/a3m_database_extract.dir/build'. make[3]: Leaving directory '/<>/hhsuite-3.0~beta2+dfsg/mybuild' make[3]: Entering directory '/<>/hhsuite-3.0~beta2+dfsg/mybuild' make[3]: Nothing to be done for 'src/CMakeFiles/hhviterbialgorithm_with_celloff.dir/build'. make[3]: Leaving directory '/<>/hhsuite-3.0~beta2+dfsg/mybuild' make[3]: Leaving directory '/<>/hhsuite-3.0~beta2+dfsg/mybuild' make -f src/CMakeFiles/CS_OBJECTS.dir/build.make src/CMakeFiles/CS_OBJECTS.dir/build make[3]: Entering directory '/<>/hhsuite-3.0~beta2+dfsg/mybuild' make[3]: Nothing to be done for 'src/CMakeFiles/a3m_reduce.dir/build'. make[3]: Leaving directory '/<>/hhsuite-3.0~beta2+dfsg/mybuild' make[3]: Entering directory '/<>/hhsuite-3.0~beta2+dfsg/mybuild' make[3]: Nothing to be done for 'src/CMakeFiles/a3m_extract.dir/build'. make[3]: Leaving directory '/<>/hhsuite-3.0~beta2+dfsg/mybuild' make[3]: Entering directory '/<>/hhsuite-3.0~beta2+dfsg/mybuild' make[3]: Nothing to be done for 'src/CMakeFiles/hhviterbialgorithm_with_celloff_and_ss.dir/build'. make[3]: Leaving directory '/<>/hhsuite-3.0~beta2+dfsg/mybuild' make[3]: Entering directory '/<>/hhsuite-3.0~beta2+dfsg/mybuild' make[3]: Nothing to be done for 'src/CMakeFiles/hhviterbialgorithm_and_ss.dir/build'. make[3]: Leaving directory '/<>/hhsuite-3.0~beta2+dfsg/mybuild' [ 10%] Built target a3m_database_filter [ 13%] Built target a3m_database_reduce make[3]: Entering directory '/<>/hhsuite-3.0~beta2+dfsg/mybuild' make[3]: Nothing to be done for 'src/CMakeFiles/CS_OBJECTS.dir/build'. make[3]: Leaving directory '/<>/hhsuite-3.0~beta2+dfsg/mybuild' [ 14%] Built target hhviterbialgorithm_with_celloff [ 17%] Built target a3m_database_extract [ 20%] Built target a3m_extract [ 23%] Built target a3m_reduce [ 25%] Built target hhviterbialgorithm_and_ss [ 26%] Built target hhviterbialgorithm_with_celloff_and_ss [ 37%] Built target CS_OBJECTS make[3]: Leaving directory '/<>/hhsuite-3.0~beta2+dfsg/mybuild' make -f src/CMakeFiles/HH_OBJECTS.dir/build.make src/CMakeFiles/HH_OBJECTS.dir/build make[3]: Entering directory '/<>/hhsuite-3.0~beta2+dfsg/mybuild' make[3]: Nothing to be done for 'src/CMakeFiles/HH_OBJECTS.dir/build'. make[3]: Leaving directory '/<>/hhsuite-3.0~beta2+dfsg/mybuild' [ 79%] Built target HH_OBJECTS make -f src/CMakeFiles/hhblits.dir/build.make src/CMakeFiles/hhblits.dir/depend make -f src/CMakeFiles/cstranslate.dir/build.make src/CMakeFiles/cstranslate.dir/depend make -f src/CMakeFiles/hhsearch.dir/build.make src/CMakeFiles/hhsearch.dir/depend make -f src/CMakeFiles/hhalign.dir/build.make src/CMakeFiles/hhalign.dir/depend make -f src/CMakeFiles/hhmake.dir/build.make src/CMakeFiles/hhmake.dir/depend make -f src/CMakeFiles/hhfilter.dir/build.make src/CMakeFiles/hhfilter.dir/depend make -f src/CMakeFiles/hhconsensus.dir/build.make src/CMakeFiles/hhconsensus.dir/depend make[3]: Entering directory '/<>/hhsuite-3.0~beta2+dfsg/mybuild' cd "/<>/hhsuite-3.0~beta2+dfsg/mybuild" && /usr/bin/cmake -E cmake_depends "Unix Makefiles" "/<>/hhsuite-3.0~beta2+dfsg" "/<>/hhsuite-3.0~beta2+dfsg/src" "/<>/hhsuite-3.0~beta2+dfsg/mybuild" "/<>/hhsuite-3.0~beta2+dfsg/mybuild/src" "/<>/hhsuite-3.0~beta2+dfsg/mybuild/src/CMakeFiles/hhblits.dir/DependInfo.cmake" --color= make[3]: Entering directory '/<>/hhsuite-3.0~beta2+dfsg/mybuild' cd "/<>/hhsuite-3.0~beta2+dfsg/mybuild" && /usr/bin/cmake -E cmake_depends "Unix Makefiles" "/<>/hhsuite-3.0~beta2+dfsg" "/<>/hhsuite-3.0~beta2+dfsg/src" "/<>/hhsuite-3.0~beta2+dfsg/mybuild" "/<>/hhsuite-3.0~beta2+dfsg/mybuild/src" "/<>/hhsuite-3.0~beta2+dfsg/mybuild/src/CMakeFiles/cstranslate.dir/DependInfo.cmake" --color= make[3]: Entering directory '/<>/hhsuite-3.0~beta2+dfsg/mybuild' cd "/<>/hhsuite-3.0~beta2+dfsg/mybuild" && /usr/bin/cmake -E cmake_depends "Unix Makefiles" "/<>/hhsuite-3.0~beta2+dfsg" "/<>/hhsuite-3.0~beta2+dfsg/src" "/<>/hhsuite-3.0~beta2+dfsg/mybuild" "/<>/hhsuite-3.0~beta2+dfsg/mybuild/src" "/<>/hhsuite-3.0~beta2+dfsg/mybuild/src/CMakeFiles/hhsearch.dir/DependInfo.cmake" --color= make[3]: Entering directory '/<>/hhsuite-3.0~beta2+dfsg/mybuild' cd "/<>/hhsuite-3.0~beta2+dfsg/mybuild" && /usr/bin/cmake -E cmake_depends "Unix Makefiles" "/<>/hhsuite-3.0~beta2+dfsg" "/<>/hhsuite-3.0~beta2+dfsg/src" "/<>/hhsuite-3.0~beta2+dfsg/mybuild" "/<>/hhsuite-3.0~beta2+dfsg/mybuild/src" "/<>/hhsuite-3.0~beta2+dfsg/mybuild/src/CMakeFiles/hhmake.dir/DependInfo.cmake" --color= make[3]: Entering directory '/<>/hhsuite-3.0~beta2+dfsg/mybuild' cd "/<>/hhsuite-3.0~beta2+dfsg/mybuild" && /usr/bin/cmake -E cmake_depends "Unix Makefiles" "/<>/hhsuite-3.0~beta2+dfsg" "/<>/hhsuite-3.0~beta2+dfsg/src" "/<>/hhsuite-3.0~beta2+dfsg/mybuild" "/<>/hhsuite-3.0~beta2+dfsg/mybuild/src" "/<>/hhsuite-3.0~beta2+dfsg/mybuild/src/CMakeFiles/hhalign.dir/DependInfo.cmake" --color= make[3]: Entering directory '/<>/hhsuite-3.0~beta2+dfsg/mybuild' cd "/<>/hhsuite-3.0~beta2+dfsg/mybuild" && /usr/bin/cmake -E cmake_depends "Unix Makefiles" "/<>/hhsuite-3.0~beta2+dfsg" "/<>/hhsuite-3.0~beta2+dfsg/src" "/<>/hhsuite-3.0~beta2+dfsg/mybuild" "/<>/hhsuite-3.0~beta2+dfsg/mybuild/src" "/<>/hhsuite-3.0~beta2+dfsg/mybuild/src/CMakeFiles/hhfilter.dir/DependInfo.cmake" --color= make[3]: Entering directory '/<>/hhsuite-3.0~beta2+dfsg/mybuild' cd "/<>/hhsuite-3.0~beta2+dfsg/mybuild" && /usr/bin/cmake -E cmake_depends "Unix Makefiles" "/<>/hhsuite-3.0~beta2+dfsg" "/<>/hhsuite-3.0~beta2+dfsg/src" "/<>/hhsuite-3.0~beta2+dfsg/mybuild" "/<>/hhsuite-3.0~beta2+dfsg/mybuild/src" "/<>/hhsuite-3.0~beta2+dfsg/mybuild/src/CMakeFiles/hhconsensus.dir/DependInfo.cmake" --color= make[3]: Leaving directory '/<>/hhsuite-3.0~beta2+dfsg/mybuild' make -f src/CMakeFiles/hhblits.dir/build.make src/CMakeFiles/hhblits.dir/build make[3]: Leaving directory '/<>/hhsuite-3.0~beta2+dfsg/mybuild' make[3]: Leaving directory '/<>/hhsuite-3.0~beta2+dfsg/mybuild' make -f src/CMakeFiles/cstranslate.dir/build.make src/CMakeFiles/cstranslate.dir/build make -f src/CMakeFiles/hhmake.dir/build.make src/CMakeFiles/hhmake.dir/build make[3]: Leaving directory '/<>/hhsuite-3.0~beta2+dfsg/mybuild' make[3]: Leaving directory '/<>/hhsuite-3.0~beta2+dfsg/mybuild' make -f src/CMakeFiles/hhfilter.dir/build.make src/CMakeFiles/hhfilter.dir/build make -f src/CMakeFiles/hhconsensus.dir/build.make src/CMakeFiles/hhconsensus.dir/build make[3]: Leaving directory '/<>/hhsuite-3.0~beta2+dfsg/mybuild' make -f src/CMakeFiles/hhsearch.dir/build.make src/CMakeFiles/hhsearch.dir/build make[3]: Leaving directory '/<>/hhsuite-3.0~beta2+dfsg/mybuild' make -f src/CMakeFiles/hhalign.dir/build.make src/CMakeFiles/hhalign.dir/build make[3]: Entering directory '/<>/hhsuite-3.0~beta2+dfsg/mybuild' make[3]: Nothing to be done for 'src/CMakeFiles/cstranslate.dir/build'. make[3]: Leaving directory '/<>/hhsuite-3.0~beta2+dfsg/mybuild' make[3]: Entering directory '/<>/hhsuite-3.0~beta2+dfsg/mybuild' make[3]: Nothing to be done for 'src/CMakeFiles/hhblits.dir/build'. make[3]: Leaving directory '/<>/hhsuite-3.0~beta2+dfsg/mybuild' make[3]: Entering directory '/<>/hhsuite-3.0~beta2+dfsg/mybuild' make[3]: Nothing to be done for 'src/CMakeFiles/hhmake.dir/build'. make[3]: Leaving directory '/<>/hhsuite-3.0~beta2+dfsg/mybuild' make[3]: Entering directory '/<>/hhsuite-3.0~beta2+dfsg/mybuild' make[3]: Nothing to be done for 'src/CMakeFiles/hhfilter.dir/build'. make[3]: Leaving directory '/<>/hhsuite-3.0~beta2+dfsg/mybuild' make[3]: Entering directory '/<>/hhsuite-3.0~beta2+dfsg/mybuild' make[3]: Nothing to be done for 'src/CMakeFiles/hhconsensus.dir/build'. make[3]: Leaving directory '/<>/hhsuite-3.0~beta2+dfsg/mybuild' make[3]: Entering directory '/<>/hhsuite-3.0~beta2+dfsg/mybuild' make[3]: Nothing to be done for 'src/CMakeFiles/hhsearch.dir/build'. make[3]: Leaving directory '/<>/hhsuite-3.0~beta2+dfsg/mybuild' make[3]: Entering directory '/<>/hhsuite-3.0~beta2+dfsg/mybuild' make[3]: Nothing to be done for 'src/CMakeFiles/hhalign.dir/build'. make[3]: Leaving directory '/<>/hhsuite-3.0~beta2+dfsg/mybuild' [ 82%] Built target cstranslate [ 85%] Built target hhmake [ 88%] Built target hhblits [ 91%] Built target hhfilter [ 94%] Built target hhconsensus [ 97%] Built target hhsearch [100%] Built target hhalign make[2]: Leaving directory '/<>/hhsuite-3.0~beta2+dfsg/mybuild' /usr/bin/cmake -E cmake_progress_start "/<>/hhsuite-3.0~beta2+dfsg/mybuild/CMakeFiles" 0 make -f CMakeFiles/Makefile2 preinstall make[2]: Entering directory '/<>/hhsuite-3.0~beta2+dfsg/mybuild' make[2]: Nothing to be done for 'preinstall'. make[2]: Leaving directory '/<>/hhsuite-3.0~beta2+dfsg/mybuild' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "None" -- Installing: /<>/hhsuite-3.0~beta2+dfsg/debian/tmp/usr/./LICENSE -- Installing: /<>/hhsuite-3.0~beta2+dfsg/debian/tmp/usr/./README -- Installing: /<>/hhsuite-3.0~beta2+dfsg/debian/tmp/usr/bin/hhblits -- Installing: /<>/hhsuite-3.0~beta2+dfsg/debian/tmp/usr/bin/hhmake -- Installing: /<>/hhsuite-3.0~beta2+dfsg/debian/tmp/usr/bin/hhfilter -- Installing: /<>/hhsuite-3.0~beta2+dfsg/debian/tmp/usr/bin/hhsearch -- Installing: /<>/hhsuite-3.0~beta2+dfsg/debian/tmp/usr/bin/hhalign -- Installing: /<>/hhsuite-3.0~beta2+dfsg/debian/tmp/usr/bin/hhconsensus -- Installing: /<>/hhsuite-3.0~beta2+dfsg/debian/tmp/usr/bin/a3m_extract -- Installing: /<>/hhsuite-3.0~beta2+dfsg/debian/tmp/usr/bin/a3m_database_reduce -- Installing: /<>/hhsuite-3.0~beta2+dfsg/debian/tmp/usr/bin/a3m_database_extract -- Installing: /<>/hhsuite-3.0~beta2+dfsg/debian/tmp/usr/bin/a3m_database_filter -- Installing: /<>/hhsuite-3.0~beta2+dfsg/debian/tmp/usr/bin/cstranslate -- Installing: /<>/hhsuite-3.0~beta2+dfsg/debian/tmp/usr/data/context_data.crf -- Installing: /<>/hhsuite-3.0~beta2+dfsg/debian/tmp/usr/data/context_data.lib -- Installing: /<>/hhsuite-3.0~beta2+dfsg/debian/tmp/usr/data/cs219.lib -- Installing: /<>/hhsuite-3.0~beta2+dfsg/debian/tmp/usr/data/do_not_delete -- Installing: /<>/hhsuite-3.0~beta2+dfsg/debian/tmp/usr/data/do_not_delete.phr -- Installing: /<>/hhsuite-3.0~beta2+dfsg/debian/tmp/usr/data/do_not_delete.pin -- Installing: /<>/hhsuite-3.0~beta2+dfsg/debian/tmp/usr/data/do_not_delete.psq -- Installing: /<>/hhsuite-3.0~beta2+dfsg/debian/tmp/usr/scripts/Align.pm -- Installing: /<>/hhsuite-3.0~beta2+dfsg/debian/tmp/usr/scripts/HHPaths.pm -- Installing: /<>/hhsuite-3.0~beta2+dfsg/debian/tmp/usr/scripts/addss.pl -- Installing: /<>/hhsuite-3.0~beta2+dfsg/debian/tmp/usr/scripts/create_profile_from_hhm.pl -- Installing: /<>/hhsuite-3.0~beta2+dfsg/debian/tmp/usr/scripts/hhmakemodel.pl -- Installing: /<>/hhsuite-3.0~beta2+dfsg/debian/tmp/usr/scripts/hhsuitedb.py -- Installing: /<>/hhsuite-3.0~beta2+dfsg/debian/tmp/usr/scripts/mergeali.pl -- Installing: /<>/hhsuite-3.0~beta2+dfsg/debian/tmp/usr/scripts/multithread.pl -- Installing: /<>/hhsuite-3.0~beta2+dfsg/debian/tmp/usr/scripts/pdbfilter.pl -- Installing: /<>/hhsuite-3.0~beta2+dfsg/debian/tmp/usr/scripts/renumberpdb.pl -- Installing: /<>/hhsuite-3.0~beta2+dfsg/debian/tmp/usr/scripts/create_profile_from_hmmer.pl -- Installing: /<>/hhsuite-3.0~beta2+dfsg/debian/tmp/usr/scripts/pdb2fasta.pl -- Installing: /<>/hhsuite-3.0~beta2+dfsg/debian/tmp/usr/scripts/reformat.pl -- Installing: /<>/hhsuite-3.0~beta2+dfsg/debian/tmp/usr/scripts/splitfasta.pl -- Installing: /<>/hhsuite-3.0~beta2+dfsg/debian/tmp/usr/scripts/check_a3m.py -- Installing: /<>/hhsuite-3.0~beta2+dfsg/debian/tmp/usr/scripts/ffindex.py -- Installing: /<>/hhsuite-3.0~beta2+dfsg/debian/tmp/usr/scripts/a3m.py -- Installing: /<>/hhsuite-3.0~beta2+dfsg/debian/tmp/usr/scripts/get_a3m_size.py -- Installing: /<>/hhsuite-3.0~beta2+dfsg/debian/tmp/usr/scripts/is_huge_a3m.py make[1]: Leaving directory '/<>/hhsuite-3.0~beta2+dfsg/mybuild' dh_install -a -O--builddirectory=mybuild dh_installdocs -a -O--builddirectory=mybuild dh_installchangelogs -a -O--builddirectory=mybuild dh_installexamples -a -O--builddirectory=mybuild debian/rules override_dh_installman make[1]: Entering directory '/<>/hhsuite-3.0~beta2+dfsg' unset LD_PRELOAD && export LD_LIBRARY_PATH=debian/tmp/usr/lib && export HHLIB=. && help2man --no-info --help-option '-h all' --version-string 3.0~beta2 -n "$n_hhalign" 'debian/tmp/usr/bin/hhalign' | sed -e 's/\(^\|[^\]\)-/\1\\-/g;' > 'hhalign.1' unset LD_PRELOAD && export LD_LIBRARY_PATH=debian/tmp/usr/lib && export HHLIB=. && help2man --no-info --help-option '-h all' --version-string 3.0~beta2 -n "$n_hhblits" 'debian/tmp/usr/bin/hhblits' | sed -e 's/\(^\|[^\]\)-/\1\\-/g;' > 'hhblits.1' dh debian/tmp/usr/bin/hhblits_omp --builddirectory=mybuild dh: Unknown sequence debian/tmp/usr/bin/hhblits_omp (choose from: binary binary-arch binary-indep build build-arch build-indep clean install install-arch install-indep) debian/rules:38: recipe for target 'debian/tmp/usr/bin/hhblits_omp' failed make[1]: *** [debian/tmp/usr/bin/hhblits_omp] Error 255 make[1]: Leaving directory '/<>/hhsuite-3.0~beta2+dfsg' debian/rules:38: recipe for target 'binary-arch' failed make: *** [binary-arch] Error 2 dpkg-buildpackage: error: fakeroot debian/rules binary-arch gave error exit status 2 -------------------------------------------------------------------------------- Build finished at 2017-07-06T20:55:46Z Finished -------- +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not cleaning session: cloned chroot in use E: Build failure (dpkg-buildpackage died) +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: amd64 Build Type: any Build-Space: 147612 Build-Time: 16 Distribution: unstable Fail-Stage: build Host Architecture: amd64 Install-Time: 20 Job: hhsuite_3.0~beta2+dfsg-3 Machine Architecture: amd64 Package: hhsuite Package-Time: 58 Source-Version: 3.0~beta2+dfsg-3 Space: 147612 Status: attempted Version: 3.0~beta2+dfsg-3 -------------------------------------------------------------------------------- Finished at 2017-07-06T20:55:46Z Build needed 00:00:58, 147612k disk space E: Build failure (dpkg-buildpackage died) DC-Status: Failed 59.377938793s