DC-Build-Header: spades 3.10.1+dfsg-2 / 2017-07-06 18:14:59 +0000 DC-Task: type:rebuild-binarch-only source:spades version:3.10.1+dfsg-2 chroot:unstable esttime:735 logfile:/tmp/spades_3.10.1+dfsg-2_unstable_clang3.9.log modes:clang:binarch-only DC-Sbuild-call: su user42 -c 'sbuild -n --arch-any --apt-update -d unstable -v --chroot-setup-commands=/tmp/clang spades_3.10.1+dfsg-2' sbuild (Debian sbuild) 0.73.0 (23 Dec 2016) on ip-172-31-42-24.eu-central-1.compute.internal +==============================================================================+ | spades 3.10.1+dfsg-2 (amd64) Thu, 06 Jul 2017 18:14:59 +0000 | +==============================================================================+ Package: spades Version: 3.10.1+dfsg-2 Source Version: 3.10.1+dfsg-2 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-8ae1ff47-b1b1-4aef-a3e2-e5dba7785f79' with '<>' +------------------------------------------------------------------------------+ | Chroot Setup Commands | +------------------------------------------------------------------------------+ /tmp/clang ---------- + echo 'Entering customization script...' Entering customization script... + CLANG_VERSION=3.9 + echo 'Install of clang-3.9' Install of clang-3.9 + 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 (788 kB/s) Reading package lists... + apt-get install --yes --no-install-recommends --force-yes clang-3.9 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-3.9-dev libclang1-3.9 libedit2 libffi6 libgcc-6-dev libgcc1 libgomp1 libitm1 libjsoncpp1 libllvm3.9 liblsan0 libmpx2 libncurses5 libobjc-6-dev libobjc4 libquadmath0 libstdc++-6-dev libstdc++6 libtsan0 libubsan0 Suggested packages: gnustep gnustep-devel clang-3.9-doc 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-3.9-dev python libgpm2 The following NEW packages will be installed: clang-3.9 libbsd0 libclang-common-3.9-dev libclang1-3.9 libedit2 libffi6 libjsoncpp1 libllvm3.9 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 83.9 MB of archives. After this operation, 251 MB of additional disk space will be used. 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Preparing to unpack .../16-libclang-common-3.9-dev_1%3a3.9.1-10_amd64.deb ... Unpacking libclang-common-3.9-dev (1:3.9.1-10) ... Selecting previously unselected package clang-3.9. Preparing to unpack .../17-clang-3.9_1%3a3.9.1-10_amd64.deb ... Unpacking clang-3.9 (1:3.9.1-10) ... 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 libllvm3.9:amd64 (1:3.9.1-10) ... Setting up libclang-common-3.9-dev (1:3.9.1-10) ... Setting up gcc-6 (6.4.0-1) ... Setting up g++-6 (6.4.0-1) ... Setting up libobjc-6-dev:amd64 (6.4.0-1) ... Setting up libclang1-3.9:amd64 (1:3.9.1-10) ... Setting up clang-3.9 (1:3.9.1-10) ... 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++-3.9 g++-4.6 + ln -s clang-3.9 gcc-4.6 + ln -s clang-3.9 cpp-4.6 + ln -s clang-3.9 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++-3.9 g++-4.7 + ln -s clang-3.9 gcc-4.7 + ln -s clang-3.9 cpp-4.7 + ln -s clang-3.9 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++-3.9 g++-4.8 + ln -s clang-3.9 gcc-4.8 + ln -s clang-3.9 cpp-4.8 + ln -s clang-3.9 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++-3.9 g++-4.9 + ln -s clang-3.9 gcc-4.9 + ln -s clang-3.9 cpp-4.9 + ln -s clang-3.9 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++-3.9 g++-5 + ln -s clang-3.9 gcc-5 + ln -s clang-3.9 cpp-5 + ln -s clang-3.9 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++-3.9 g++-6 + ln -s clang-3.9 gcc-6 + ln -s clang-3.9 cpp-6 + ln -s clang-3.9 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++-3.9 g++-7 + ln -s clang-3.9 gcc-7 + ln -s clang-3.9 cpp-7 + ln -s clang-3.9 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/spades-Dayd7F + 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/clang'. 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 (87.8 MB/s) (Reading database ... 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(Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 10176 files and directories currently installed.) Preparing to unpack .../cpp_4%3a6.3.0-4d1_amd64.deb ... Unpacking cpp (4:6.3.0-4d1) over (4:6.3.0-4) ... Preparing to unpack .../gcc_4%3a6.3.0-4d1_amd64.deb ... Removing old gcc doc directory. Unpacking gcc (4:6.3.0-4d1) over (4:6.3.0-4) ... Preparing to unpack .../g++_4%3a6.3.0-4d1_amd64.deb ... Unpacking g++ (4:6.3.0-4d1) over (4:6.3.0-4) ... Setting up cpp (4:6.3.0-4d1) ... 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: 'spades' packaging is maintained in the 'Git' version control system at: https://anonscm.debian.org/git/debian-med/spades.git Please use: git clone https://anonscm.debian.org/git/debian-med/spades.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 2049 kB of source archives. Get:1 http://127.0.0.1:9999/debian unstable/main spades 3.10.1+dfsg-2 (dsc) [1982 B] Get:2 http://127.0.0.1:9999/debian unstable/main spades 3.10.1+dfsg-2 (tar) [2028 kB] Get:3 http://127.0.0.1:9999/debian unstable/main spades 3.10.1+dfsg-2 (diff) [19.8 kB] Fetched 2049 kB in 0s (13.7 MB/s) Download complete and in download only mode I: NOTICE: Log filtering will replace 'build/spades-Dayd7F/spades-3.10.1+dfsg' with '<>' I: NOTICE: Log filtering will replace 'build/spades-Dayd7F' 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-6NYnzc/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-6NYnzc/apt_archive ./ InRelease Get:2 copy:/<>/resolver-6NYnzc/apt_archive ./ Release [957 B] Ign:3 copy:/<>/resolver-6NYnzc/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-6NYnzc/apt_archive ./ Sources [349 B] Get:5 copy:/<>/resolver-6NYnzc/apt_archive ./ Packages [430 B] Fetched 1736 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 782 B of archives. After this operation, 0 B of additional disk space will be used. Get:1 copy:/<>/resolver-6NYnzc/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [782 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 782 B in 0s (0 B/s) Selecting previously unselected package sbuild-build-depends-core-dummy. (Reading database ... 10178 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 any) +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper (>= 9), cmake, python-all-dev, zlib1g-dev, libbz2-dev, libboost-dev, libbam-dev, libbamtools-dev, libjemalloc-dev, libhat-trie-dev, libhts-dev, libnlopt-dev, libssw-dev, python-yaml, python-joblib, asciidoctor (>= 1.5.3), bwa, libbwa-dev, lynx Filtered Build-Depends: debhelper (>= 9), cmake, python-all-dev, zlib1g-dev, libbz2-dev, libboost-dev, libbam-dev, libbamtools-dev, libjemalloc-dev, libhat-trie-dev, libhts-dev, libnlopt-dev, libssw-dev, python-yaml, python-joblib, asciidoctor (>= 1.5.3), bwa, libbwa-dev, lynx dpkg-deb: building package 'sbuild-build-depends-spades-dummy' in '/<>/resolver-6NYnzc/apt_archive/sbuild-build-depends-spades-dummy.deb'. dpkg-scanpackages: warning: Packages in archive but missing from override file: dpkg-scanpackages: warning: sbuild-build-depends-core-dummy sbuild-build-depends-spades-dummy dpkg-scanpackages: info: Wrote 2 entries to output Packages file. Ign:1 copy:/<>/resolver-6NYnzc/apt_archive ./ InRelease Get:2 copy:/<>/resolver-6NYnzc/apt_archive ./ Release [963 B] Ign:3 copy:/<>/resolver-6NYnzc/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-6NYnzc/apt_archive ./ Sources [594 B] Get:5 copy:/<>/resolver-6NYnzc/apt_archive ./ Packages [669 B] Fetched 2226 B in 0s (0 B/s) Reading package lists... Reading package lists... Install spades build dependencies (apt-based resolver) ------------------------------------------------------ Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: asciidoctor autoconf automake autopoint autotools-dev bsdmainutils bwa ca-certificates cmake cmake-data debhelper dh-autoreconf dh-strip-nondeterminism file gettext gettext-base groff-base intltool-debian libarchive-zip-perl libarchive13 libbam-dev libbamtools-dev libbamtools2.4.0 libboost-dev libboost1.62-dev libbwa-dev libbz2-dev libcroco3 libcurl3 libcurl3-gnutls libexpat1 libexpat1-dev libfile-stripnondeterminism-perl libglib2.0-0 libgssapi-krb5-2 libhat-trie-dev libhat-trie0 libhts-dev libhts2 libicu57 libidn11 libjemalloc-dev libjemalloc1 libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 libldap-2.4-2 libldap-common liblzo2-2 libmagic-mgc libmagic1 libnghttp2-14 libnlopt-dev libnlopt0 libpipeline1 libprocps6 libpsl5 libpython-all-dev libpython-dev libpython-stdlib libpython2.7 libpython2.7-dev libpython2.7-minimal libpython2.7-stdlib libreadline7 librtmp1 libruby2.3 libsasl2-2 libsasl2-modules-db libsigsegv2 libsqlite3-0 libssh2-1 libssl1.0.2 libssl1.1 libssw-dev libssw0 libtimedate-perl libtool libuv1 libxml2 libyaml-0-2 lsb-base lynx lynx-common m4 man-db mime-support openssl po-debconf procps python python-all python-all-dev python-dev python-joblib python-minimal python-yaml python2.7 python2.7-dev python2.7-minimal rake readline-common ruby ruby-did-you-mean ruby-minitest ruby-net-telnet ruby-power-assert ruby-test-unit ruby2.3 rubygems-integration zlib1g-dev Suggested packages: autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois vacation samtools codeblocks eclipse ninja-build dh-make gettext-doc libasprintf-dev libgettextpo-dev groff lrzip libbamtools-doc libboost-doc libboost1.62-doc libboost-atomic1.62-dev libboost-chrono1.62-dev libboost-context1.62-dev libboost-coroutine1.62-dev libboost-date-time1.62-dev libboost-exception1.62-dev libboost-fiber1.62-dev libboost-filesystem1.62-dev libboost-graph1.62-dev libboost-graph-parallel1.62-dev libboost-iostreams1.62-dev libboost-locale1.62-dev libboost-log1.62-dev libboost-math1.62-dev libboost-mpi1.62-dev libboost-mpi-python1.62-dev libboost-program-options1.62-dev libboost-python1.62-dev libboost-random1.62-dev libboost-regex1.62-dev libboost-serialization1.62-dev libboost-signals1.62-dev libboost-system1.62-dev libboost-test1.62-dev libboost-thread1.62-dev libboost-timer1.62-dev libboost-type-erasure1.62-dev libboost-wave1.62-dev libboost1.62-tools-dev libmpfrc++-dev libntl-dev krb5-doc krb5-user libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc less libmail-box-perl python-doc python-tk python2.7-doc binfmt-support readline-doc ri ruby-dev bundler Recommended packages: curl | wget | lynx-cur bzip2-doc libarchive-cpio-perl libglib2.0-data shared-mime-info xdg-user-dirs krb5-locales publicsuffix libsasl2-modules libltdl-dev xml-core libmail-sendmail-perl psmisc python-numpy python-pytest python-simplejson zip fonts-lato libjs-jquery The following NEW packages will be installed: asciidoctor autoconf automake autopoint autotools-dev bsdmainutils bwa ca-certificates cmake cmake-data debhelper dh-autoreconf dh-strip-nondeterminism file gettext gettext-base groff-base intltool-debian libarchive-zip-perl libarchive13 libbam-dev libbamtools-dev libbamtools2.4.0 libboost-dev libboost1.62-dev libbwa-dev libbz2-dev libcroco3 libcurl3 libcurl3-gnutls libexpat1 libexpat1-dev libfile-stripnondeterminism-perl libglib2.0-0 libgssapi-krb5-2 libhat-trie-dev libhat-trie0 libhts-dev libhts2 libicu57 libidn11 libjemalloc-dev libjemalloc1 libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 libldap-2.4-2 libldap-common liblzo2-2 libmagic-mgc libmagic1 libnghttp2-14 libnlopt-dev libnlopt0 libpipeline1 libprocps6 libpsl5 libpython-all-dev libpython-dev libpython-stdlib libpython2.7 libpython2.7-dev libpython2.7-minimal libpython2.7-stdlib libreadline7 librtmp1 libruby2.3 libsasl2-2 libsasl2-modules-db libsigsegv2 libsqlite3-0 libssh2-1 libssl1.0.2 libssl1.1 libssw-dev libssw0 libtimedate-perl libtool libuv1 libxml2 libyaml-0-2 lsb-base lynx lynx-common m4 man-db mime-support openssl po-debconf procps python python-all python-all-dev python-dev python-joblib python-minimal python-yaml python2.7 python2.7-dev python2.7-minimal rake readline-common ruby ruby-did-you-mean ruby-minitest ruby-net-telnet ruby-power-assert ruby-test-unit ruby2.3 rubygems-integration sbuild-build-depends-spades-dummy zlib1g-dev 0 upgraded, 113 newly installed, 0 to remove and 0 not upgraded. Need to get 80.1 MB of archives. After this operation, 318 MB of additional disk space will be used. Get:1 copy:/<>/resolver-6NYnzc/apt_archive ./ sbuild-build-depends-spades-dummy 0.invalid.0 [886 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 libpython2.7-minimal amd64 2.7.13-2 [389 kB] Get:7 http://127.0.0.1:9999/debian unstable/main amd64 python2.7-minimal amd64 2.7.13-2 [1383 kB] Get:8 http://127.0.0.1:9999/debian unstable/main amd64 python-minimal amd64 2.7.13-2 [40.5 kB] Get:9 http://127.0.0.1:9999/debian unstable/main amd64 mime-support all 3.60 [36.7 kB] Get:10 http://127.0.0.1:9999/debian unstable/main amd64 libexpat1 amd64 2.2.1-3 [85.6 kB] Get:11 http://127.0.0.1:9999/debian unstable/main amd64 readline-common all 7.0-3 [70.4 kB] Get:12 http://127.0.0.1:9999/debian unstable/main amd64 libreadline7 amd64 7.0-3 [151 kB] Get:13 http://127.0.0.1:9999/debian unstable/main amd64 libsqlite3-0 amd64 3.16.2-5 [572 kB] Get:14 http://127.0.0.1:9999/debian unstable/main amd64 libssl1.1 amd64 1.1.0f-3 [1342 kB] Get:15 http://127.0.0.1:9999/debian unstable/main amd64 libpython2.7-stdlib amd64 2.7.13-2 [1895 kB] Get:16 http://127.0.0.1:9999/debian unstable/main amd64 python2.7 amd64 2.7.13-2 [285 kB] Get:17 http://127.0.0.1:9999/debian unstable/main amd64 libpython-stdlib amd64 2.7.13-2 [20.0 kB] Get:18 http://127.0.0.1:9999/debian unstable/main amd64 python amd64 2.7.13-2 [154 kB] Get:19 http://127.0.0.1:9999/debian unstable/main amd64 cmake-data all 3.7.2-1 [1216 kB] Get:20 http://127.0.0.1:9999/debian unstable/main amd64 libprocps6 amd64 2:3.3.12-3 [58.1 kB] Get:21 http://127.0.0.1:9999/debian unstable/main amd64 lsb-base all 9.20161125 [27.9 kB] Get:22 http://127.0.0.1:9999/debian unstable/main amd64 procps amd64 2:3.3.12-3 [249 kB] Get:23 http://127.0.0.1:9999/debian unstable/main amd64 liblzo2-2 amd64 2.08-1.2+b2 [55.0 kB] Get:24 http://127.0.0.1:9999/debian unstable/main amd64 libicu57 amd64 57.1-6 [7701 kB] Get:25 http://127.0.0.1:9999/debian unstable/main amd64 libxml2 amd64 2.9.4+dfsg1-3 [715 kB] Get:26 http://127.0.0.1:9999/debian unstable/main amd64 libarchive13 amd64 3.2.2-2 [294 kB] Get:27 http://127.0.0.1:9999/debian unstable/main amd64 libkeyutils1 amd64 1.5.9-9 [12.4 kB] Get:28 http://127.0.0.1:9999/debian unstable/main amd64 libkrb5support0 amd64 1.15-1 [61.7 kB] Get:29 http://127.0.0.1:9999/debian unstable/main amd64 libk5crypto3 amd64 1.15-1 [119 kB] Get:30 http://127.0.0.1:9999/debian unstable/main amd64 libkrb5-3 amd64 1.15-1 [311 kB] Get:31 http://127.0.0.1:9999/debian unstable/main amd64 libgssapi-krb5-2 amd64 1.15-1 [154 kB] Get:32 http://127.0.0.1:9999/debian unstable/main amd64 libsasl2-modules-db amd64 2.1.27~101-g0780600+dfsg-3 [68.2 kB] 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unstable/main amd64 cmake amd64 3.7.2-1 [3038 kB] Get:44 http://127.0.0.1:9999/debian unstable/main amd64 libmagic-mgc amd64 1:5.30-1 [222 kB] Get:45 http://127.0.0.1:9999/debian unstable/main amd64 libmagic1 amd64 1:5.30-1 [111 kB] Get:46 http://127.0.0.1:9999/debian unstable/main amd64 file amd64 1:5.30-1 [63.9 kB] Get:47 http://127.0.0.1:9999/debian unstable/main amd64 gettext-base amd64 0.19.8.1-2+b1 [122 kB] Get:48 http://127.0.0.1:9999/debian unstable/main amd64 libidn11 amd64 1.33-1 [115 kB] Get:49 http://127.0.0.1:9999/debian unstable/main amd64 openssl amd64 1.1.0f-3 [725 kB] Get:50 http://127.0.0.1:9999/debian unstable/main amd64 ca-certificates all 20161130+nmu1 [196 kB] Get:51 http://127.0.0.1:9999/debian unstable/main amd64 rubygems-integration all 1.11 [4994 B] Get:52 http://127.0.0.1:9999/debian unstable/main amd64 rake all 12.0.0-1 [45.7 kB] Get:53 http://127.0.0.1:9999/debian unstable/main amd64 ruby-did-you-mean all 1.0.0-2 [11.2 kB] Get:54 http://127.0.0.1:9999/debian unstable/main amd64 ruby-minitest all 5.10.2-1 [52.2 kB] Get:55 http://127.0.0.1:9999/debian unstable/main amd64 ruby-net-telnet all 0.1.1-2 [12.5 kB] Get:56 http://127.0.0.1:9999/debian unstable/main amd64 ruby-power-assert all 0.3.0-1 [7902 B] Get:57 http://127.0.0.1:9999/debian unstable/main amd64 ruby-test-unit all 3.2.5-1 [71.7 kB] Get:58 http://127.0.0.1:9999/debian unstable/main amd64 libyaml-0-2 amd64 0.1.7-2 [47.6 kB] Get:59 http://127.0.0.1:9999/debian unstable/main amd64 libruby2.3 amd64 2.3.3-1 [3104 kB] Get:60 http://127.0.0.1:9999/debian unstable/main amd64 ruby2.3 amd64 2.3.3-1 [186 kB] Get:61 http://127.0.0.1:9999/debian unstable/main amd64 ruby amd64 1:2.3.3 [10.8 kB] Get:62 http://127.0.0.1:9999/debian unstable/main amd64 asciidoctor all 1.5.5-1 [183 kB] Get:63 http://127.0.0.1:9999/debian unstable/main amd64 libsigsegv2 amd64 2.11-1 [29.9 kB] Get:64 http://127.0.0.1:9999/debian unstable/main amd64 m4 amd64 1.4.18-1 [202 kB] Get:65 http://127.0.0.1:9999/debian unstable/main amd64 autoconf all 2.69-10 [338 kB] Get:66 http://127.0.0.1:9999/debian unstable/main amd64 autotools-dev all 20161112.1 [73.4 kB] Get:67 http://127.0.0.1:9999/debian unstable/main amd64 automake all 1:1.15.1-2 [736 kB] Get:68 http://127.0.0.1:9999/debian unstable/main amd64 autopoint all 0.19.8.1-2 [433 kB] Get:69 http://127.0.0.1:9999/debian unstable/main amd64 bwa amd64 0.7.15-3 [193 kB] Get:70 http://127.0.0.1:9999/debian unstable/main amd64 libtool all 2.4.6-2 [545 kB] Get:71 http://127.0.0.1:9999/debian unstable/main amd64 dh-autoreconf all 14 [15.9 kB] Get:72 http://127.0.0.1:9999/debian unstable/main amd64 libarchive-zip-perl all 1.59-1 [95.5 kB] Get:73 http://127.0.0.1:9999/debian unstable/main amd64 libfile-stripnondeterminism-perl all 0.035-2 [17.0 kB] Get:74 http://127.0.0.1:9999/debian unstable/main amd64 libtimedate-perl all 2.3000-2 [42.2 kB] Get:75 http://127.0.0.1:9999/debian unstable/main amd64 dh-strip-nondeterminism all 0.035-2 [10.7 kB] Get:76 http://127.0.0.1:9999/debian unstable/main amd64 libglib2.0-0 amd64 2.52.3-1 [2742 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 libbam-dev amd64 0.1.19-2 [123 kB] Get:83 http://127.0.0.1:9999/debian unstable/main amd64 libbamtools2.4.0 amd64 2.4.1+dfsg-1 [190 kB] Get:84 http://127.0.0.1:9999/debian unstable/main amd64 zlib1g-dev amd64 1:1.2.8.dfsg-5 [205 kB] Get:85 http://127.0.0.1:9999/debian unstable/main amd64 libbamtools-dev amd64 2.4.1+dfsg-1 [229 kB] Get:86 http://127.0.0.1:9999/debian unstable/main amd64 libboost1.62-dev amd64 1.62.0+dfsg-4+b1 [7053 kB] Get:87 http://127.0.0.1:9999/debian unstable/main amd64 libboost-dev amd64 1.62.0.1 [3632 B] Get:88 http://127.0.0.1:9999/debian unstable/main amd64 libbwa-dev amd64 0.7.15-3 [129 kB] Get:89 http://127.0.0.1:9999/debian unstable/main amd64 libbz2-dev amd64 1.0.6-8.1 [29.4 kB] Get:90 http://127.0.0.1:9999/debian unstable/main amd64 libcurl3-gnutls amd64 7.52.1-5 [289 kB] Get:91 http://127.0.0.1:9999/debian unstable/main amd64 libexpat1-dev amd64 2.2.1-3 [137 kB] Get:92 http://127.0.0.1:9999/debian unstable/main amd64 libhat-trie0 amd64 0.1.2-1 [11.5 kB] Get:93 http://127.0.0.1:9999/debian unstable/main amd64 libhat-trie-dev amd64 0.1.2-1 [19.7 kB] Get:94 http://127.0.0.1:9999/debian unstable/main amd64 libhts2 amd64 1.4.1-2 [294 kB] Get:95 http://127.0.0.1:9999/debian unstable/main amd64 libhts-dev amd64 1.4.1-2 [398 kB] Get:96 http://127.0.0.1:9999/debian unstable/main amd64 libjemalloc1 amd64 3.6.0-9.1 [89.8 kB] Get:97 http://127.0.0.1:9999/debian unstable/main amd64 libjemalloc-dev amd64 3.6.0-9.1 [167 kB] Get:98 http://127.0.0.1:9999/debian unstable/main amd64 libnlopt0 amd64 2.4.2+dfsg-2+b3 [162 kB] Get:99 http://127.0.0.1:9999/debian unstable/main amd64 libnlopt-dev amd64 2.4.2+dfsg-2+b3 [171 kB] Get:100 http://127.0.0.1:9999/debian unstable/main amd64 libpython2.7 amd64 2.7.13-2 [1072 kB] Get:101 http://127.0.0.1:9999/debian unstable/main amd64 libpython2.7-dev amd64 2.7.13-2 [28.2 MB] Get:102 http://127.0.0.1:9999/debian unstable/main amd64 libpython-dev amd64 2.7.13-2 [20.1 kB] Get:103 http://127.0.0.1:9999/debian unstable/main amd64 libpython-all-dev amd64 2.7.13-2 [960 B] Get:104 http://127.0.0.1:9999/debian unstable/main amd64 libssw0 amd64 1.1-1+b1 [16.5 kB] Get:105 http://127.0.0.1:9999/debian unstable/main amd64 libssw-dev amd64 1.1-1+b1 [19.4 kB] Get:106 http://127.0.0.1:9999/debian unstable/main amd64 lynx-common all 2.8.9dev15-1 [1103 kB] Get:107 http://127.0.0.1:9999/debian unstable/main amd64 lynx amd64 2.8.9dev15-1 [632 kB] Get:108 http://127.0.0.1:9999/debian unstable/main amd64 python-all amd64 2.7.13-2 [942 B] Get:109 http://127.0.0.1:9999/debian unstable/main amd64 python2.7-dev amd64 2.7.13-2 [281 kB] Get:110 http://127.0.0.1:9999/debian unstable/main amd64 python-dev amd64 2.7.13-2 [1126 B] Get:111 http://127.0.0.1:9999/debian unstable/main amd64 python-all-dev amd64 2.7.13-2 [962 B] Get:112 http://127.0.0.1:9999/debian unstable/main amd64 python-joblib all 0.10.3+git55-g660fe5d-1 [115 kB] Get:113 http://127.0.0.1:9999/debian unstable/main amd64 python-yaml amd64 3.12-1+b1 [123 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 80.1 MB in 0s (84.8 MB/s) Selecting previously unselected package groff-base. (Reading database ... 10178 files and directories currently installed.) Preparing to unpack .../00-groff-base_1.22.3-9_amd64.deb ... Unpacking groff-base (1.22.3-9) ... Selecting previously unselected package bsdmainutils. Preparing to unpack .../01-bsdmainutils_9.0.12+nmu1_amd64.deb ... Unpacking bsdmainutils (9.0.12+nmu1) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../02-libpipeline1_1.4.1-2_amd64.deb ... Unpacking libpipeline1:amd64 (1.4.1-2) ... Selecting previously unselected package man-db. Preparing to unpack .../03-man-db_2.7.6.1-2_amd64.deb ... Unpacking man-db (2.7.6.1-2) ... Selecting previously unselected package libpython2.7-minimal:amd64. Preparing to unpack .../04-libpython2.7-minimal_2.7.13-2_amd64.deb ... Unpacking libpython2.7-minimal:amd64 (2.7.13-2) ... Selecting previously unselected package python2.7-minimal. Preparing to unpack .../05-python2.7-minimal_2.7.13-2_amd64.deb ... Unpacking python2.7-minimal (2.7.13-2) ... 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Setting up readline-common (7.0-3) ... Setting up libexpat1:amd64 (2.2.1-3) ... Setting up bwa (0.7.15-3) ... Setting up libbz2-dev:amd64 (1.0.6-8.1) ... Setting up libarchive-zip-perl (1.59-1) ... Setting up libnghttp2-14:amd64 (1.24.0-1) ... Setting up mime-support (3.60) ... Setting up libboost1.62-dev:amd64 (1.62.0+dfsg-4+b1) ... Setting up libjemalloc1 (3.6.0-9.1) ... Setting up libtimedate-perl (2.3000-2) ... Setting up libsigsegv2:amd64 (2.11-1) ... Setting up libldap-common (2.4.44+dfsg-7) ... Setting up libbamtools2.4.0 (2.4.1+dfsg-1) ... Setting up libssw0:amd64 (1.1-1+b1) ... Setting up libuv1:amd64 (1.9.1-3) ... Setting up libreadline7:amd64 (7.0-3) ... 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 libssw-dev:amd64 (1.1-1+b1) ... Setting up gettext-base (0.19.8.1-2+b1) ... Setting up cmake-data (3.7.2-1) ... 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 libicu57:amd64 (57.1-6) ... Setting up libjemalloc-dev (3.6.0-9.1) ... Setting up libprocps6:amd64 (2:3.3.12-3) ... Setting up libxml2:amd64 (2.9.4+dfsg1-3) ... Setting up libmagic-mgc (1:5.30-1) ... Setting up libmagic1:amd64 (1:5.30-1) ... Setting up lsb-base (9.20161125) ... 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 ruby-did-you-mean (1.0.0-2) ... Setting up libyaml-0-2:amd64 (0.1.7-2) ... 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 libssl1.1:amd64 (1.1.0f-3) ... Setting up openssl (1.1.0f-3) ... Setting up ruby-net-telnet (0.1.1-2) ... Setting up libbam-dev (0.1.19-2) ... Setting up libsqlite3-0:amd64 (3.16.2-5) ... Setting up libexpat1-dev:amd64 (2.2.1-3) ... Setting up libbwa-dev (0.7.15-3) ... Setting up libboost-dev:amd64 (1.62.0.1) ... 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 ruby-minitest (5.10.2-1) ... Setting up lynx-common (2.8.9dev15-1) ... Setting up ca-certificates (20161130+nmu1) ... Updating certificates in /etc/ssl/certs... 166 added, 0 removed; done. Setting up libnlopt0:amd64 (2.4.2+dfsg-2+b3) ... Setting up libpython2.7-stdlib:amd64 (2.7.13-2) ... Setting up autopoint (0.19.8.1-2) ... Setting up libidn11:amd64 (1.33-1) ... Setting up libhat-trie0:amd64 (0.1.2-1) ... Setting up liblzo2-2:amd64 (2.08-1.2+b2) ... Setting up ruby-power-assert (0.3.0-1) ... Setting up lynx (2.8.9dev15-1) ... update-alternatives: using /usr/bin/lynx to provide /usr/bin/www-browser (www-browser) in auto mode Setting up zlib1g-dev:amd64 (1:1.2.8.dfsg-5) ... Setting up libfile-stripnondeterminism-perl (0.035-2) ... Setting up gettext (0.19.8.1-2+b1) ... Setting up libarchive13:amd64 (3.2.2-2) ... Setting up libbamtools-dev (2.4.1+dfsg-1) ... Setting up python2.7 (2.7.13-2) ... Setting up autoconf (2.69-10) ... Setting up file (1:5.30-1) ... Setting up libkrb5support0:amd64 (1.15-1) ... Setting up libhat-trie-dev:amd64 (0.1.2-1) ... Setting up libpython-stdlib:amd64 (2.7.13-2) ... Setting up intltool-debian (0.35.0+20060710.4) ... Setting up libnlopt-dev (2.4.2+dfsg-2+b3) ... Setting up libpython2.7:amd64 (2.7.13-2) ... 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 rubygems-integration (1.11) ... Setting up man-db (2.7.6.1-2) ... Not building database; man-db/auto-update is not 'true'. Setting up libpython2.7-dev:amd64 (2.7.13-2) ... Setting up python2.7-dev (2.7.13-2) ... Setting up python (2.7.13-2) ... Setting up libtool (2.4.6-2) ... Setting up libpython-dev:amd64 (2.7.13-2) ... Setting up libk5crypto3:amd64 (1.15-1) ... Setting up python-yaml (3.12-1+b1) ... Setting up po-debconf (1.0.20) ... Setting up python-dev (2.7.13-2) ... Setting up python-joblib (0.10.3+git55-g660fe5d-1) ... Setting up libpython-all-dev:amd64 (2.7.13-2) ... Setting up libkrb5-3:amd64 (1.15-1) ... Setting up python-all (2.7.13-2) ... Setting up libgssapi-krb5-2:amd64 (1.15-1) ... Setting up python-all-dev (2.7.13-2) ... Setting up libcurl3:amd64 (7.52.1-5) ... Setting up libcurl3-gnutls:amd64 (7.52.1-5) ... Setting up cmake (3.7.2-1) ... Setting up libhts2:amd64 (1.4.1-2) ... Setting up libhts-dev:amd64 (1.4.1-2) ... Setting up dh-autoreconf (14) ... Setting up ruby-test-unit (3.2.5-1) ... Setting up dh-strip-nondeterminism (0.035-2) ... Setting up libruby2.3:amd64 (2.3.3-1) ... Setting up debhelper (10.6.2) ... Setting up ruby2.3 (2.3.3-1) ... Setting up ruby (1:2.3.3) ... Setting up asciidoctor (1.5.5-1) ... Setting up sbuild-build-depends-spades-dummy (0.invalid.0) ... Setting up rake (12.0.0-1) ... Processing triggers for libc-bin (2.24-12) ... Processing triggers for ca-certificates (20161130+nmu1) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... 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 asciidoctor_1.5.5-1 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 bwa_0.7.15-3 bzip2_1.0.6-8.1 ca-certificates_20161130+nmu1 clang-3.9_1:3.9.1-10 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 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 hostname_3.18+b1 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 libbam-dev_0.1.19-2 libbamtools-dev_2.4.1+dfsg-1 libbamtools2.4.0_2.4.1+dfsg-1 libblkid1_2.29.2-1 libboost-dev_1.62.0.1 libboost1.62-dev_1.62.0+dfsg-4+b1 libbsd0_0.8.5-1 libbwa-dev_0.7.15-3 libbz2-1.0_1.0.6-8.1 libbz2-dev_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 libcap-ng0_0.7.7-3+b1 libcc1-0_7.1.0-9 libcilkrts5_7.1.0-9 libclang-common-3.9-dev_1:3.9.1-10 libclang1-3.9_1:3.9.1-10 libcomerr2_1.43.4-2 libcroco3_0.6.12-1 libcurl3_7.52.1-5 libcurl3-gnutls_7.52.1-5 libdb5.3_5.3.28-12+b1 libdebconfclient0_0.229 libdpkg-perl_1.18.24 libeatmydata1_105-5 libedit2_3.1-20170329-1 libexpat1_2.2.1-3 libexpat1-dev_2.2.1-3 libfakeroot_1.21-3.1 libfdisk1_2.29.2-1 libffi6_3.2.1-6 libfile-stripnondeterminism-perl_0.035-2 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 libgssapi-krb5-2_1.15-1 libhat-trie-dev_0.1.2-1 libhat-trie0_0.1.2-1 libhogweed4_3.3-1+b1 libhts-dev_1.4.1-2 libhts2_1.4.1-2 libicu57_57.1-6 libidn11_1.33-1 libidn2-0_0.16-1+b1 libisl15_0.18-1 libitm1_7.1.0-9 libjemalloc-dev_3.6.0-9.1 libjemalloc1_3.6.0-9.1 libjsoncpp1_1.7.4-3 libk5crypto3_1.15-1 libkeyutils1_1.5.9-9 libkrb5-3_1.15-1 libkrb5support0_1.15-1 libldap-2.4-2_2.4.44+dfsg-7 libldap-common_2.4.44+dfsg-7 libllvm3.9_1:3.9.1-10 liblsan0_7.1.0-9 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 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 libnlopt-dev_2.4.2+dfsg-2+b3 libnlopt0_2.4.2+dfsg-2+b3 libobjc-6-dev_6.4.0-1 libobjc4_7.1.0-9 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 libpcre3_2:8.39-3 libperl5.24_5.24.1-6 libpipeline1_1.4.1-2 libprocps6_2:3.3.12-3 libpsl5_0.17.0-4+b1 libpython-all-dev_2.7.13-2 libpython-dev_2.7.13-2 libpython-stdlib_2.7.13-2 libpython2.7_2.7.13-2 libpython2.7-dev_2.7.13-2 libpython2.7-minimal_2.7.13-2 libpython2.7-stdlib_2.7.13-2 libquadmath0_7.1.0-9 libreadline7_7.0-3 librtmp1_2.4+20151223.gitfa8646d.1-1+b1 libruby2.3_2.3.3-1 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 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 libssl1.1_1.1.0f-3 libssw-dev_1.1-1+b1 libssw0_1.1-1+b1 libstdc++-6-dev_6.4.0-1 libstdc++6_7.1.0-9 libsystemd0_233-10 libtasn1-6_4.12-2 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 libxml2_2.9.4+dfsg1-3 libyaml-0-2_0.1.7-2 linux-libc-dev_4.11.6-1 login_1:4.4-4.1 lsb-base_9.20161125 lynx_2.8.9dev15-1 lynx-common_2.8.9dev15-1 m4_1.4.18-1 make_4.1-9.1 man-db_2.7.6.1-2 mawk_1.3.3-17+b3 mime-support_3.60 mount_2.29.2-1 multiarch-support_2.24-12 ncurses-base_6.0+20161126-1 ncurses-bin_6.0+20161126-1 openssl_1.1.0f-3 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 procps_2:3.3.12-3 python_2.7.13-2 python-all_2.7.13-2 python-all-dev_2.7.13-2 python-dev_2.7.13-2 python-joblib_0.10.3+git55-g660fe5d-1 python-minimal_2.7.13-2 python-yaml_3.12-1+b1 python2.7_2.7.13-2 python2.7-dev_2.7.13-2 python2.7-minimal_2.7.13-2 rake_12.0.0-1 readline-common_7.0-3 ruby_1:2.3.3 ruby-did-you-mean_1.0.0-2 ruby-minitest_5.10.2-1 ruby-net-telnet_0.1.1-2 ruby-power-assert_0.3.0-1 ruby-test-unit_3.2.5-1 ruby2.3_2.3.3-1 rubygems-integration_1.11 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-spades-dummy_0.invalid.0 sed_4.4-1 sensible-utils_0.0.9 sysvinit-utils_2.88dsf-59.9 tar_1.29b-1.1 util-linux_2.29.2-1 xz-utils_5.2.2-1.2+b1 zlib1g_1:1.2.8.dfsg-5 zlib1g-dev_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 Sun Jun 18 16:52:21 2017 UTC gpgv: using RSA key 8451F9178172E7E2DC73F79551F84A8FECCA7E09 gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./spades_3.10.1+dfsg-2.dsc dpkg-source: info: extracting spades in /<>/spades-3.10.1+dfsg dpkg-source: info: unpacking spades_3.10.1+dfsg.orig.tar.xz dpkg-source: info: unpacking spades_3.10.1+dfsg-2.debian.tar.xz dpkg-source: info: applying 0002_use_debian_packaged_python-joblib.patch dpkg-source: info: applying 0003_accept-system-bwa.patch dpkg-source: info: applying 0101_cmake_ignore_removed_python-yaml.patch dpkg-source: info: applying 0102_cmake_ignore_removed_python-joblib.patch dpkg-source: info: applying 0103_use-debian-packaged-bwa.patch dpkg-source: info: applying 0110_build_single_thread.patch dpkg-source: info: applying 0113_adjust_paths.patch dpkg-source: info: applying 0114_use_debian_provided_libs.patch dpkg-source: info: applying 0115_enable_compiler_messages.patch dpkg-source: info: applying 0111_use_full_config_dirs.patch dpkg-source: info: applying 0116_stable_link_order.patch dpkg-source: info: applying 0117_build_with_debug.patch dpkg-source: info: applying fix-bool-cast dpkg-source: info: applying spelling 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-8ae1ff47-b1b1-4aef-a3e2-e5dba7785f79 SCHROOT_UID=1001 SCHROOT_USER=user42 SHELL=/bin/sh USER=user42 dpkg-buildpackage ----------------- dpkg-buildpackage: info: source package spades dpkg-buildpackage: info: source version 3.10.1+dfsg-2 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Sascha Steinbiss dpkg-source --before-build spades-3.10.1+dfsg dpkg-buildpackage: info: host architecture amd64 fakeroot debian/rules clean dh clean --with python2 --sourcedirectory=src --buildsystem=cmake dh_testdir -O--sourcedirectory=src -O--buildsystem=cmake debian/rules override_dh_auto_clean make[1]: Entering directory '/<>/spades-3.10.1+dfsg' dh_auto_clean rm -rf build_spades rm -rf install_spades rm -rf spades_test find . -name "*.pyc" -delete rm -rf /<>/spades-3.10.1+dfsg/debian/man_src/*.html /<>/spades-3.10.1+dfsg/debian/man_src/*.? rm -rf /<>/spades-3.10.1+dfsg/debian/man make[1]: Leaving directory '/<>/spades-3.10.1+dfsg' debian/rules override_dh_clean make[1]: Entering directory '/<>/spades-3.10.1+dfsg' dh_clean -X.orig make[1]: Leaving directory '/<>/spades-3.10.1+dfsg' debian/rules build-arch dh build-arch --with python2 --sourcedirectory=src --buildsystem=cmake dh_testdir -a -O--sourcedirectory=src -O--buildsystem=cmake dh_update_autotools_config -a -O--sourcedirectory=src -O--buildsystem=cmake debian/rules override_dh_auto_configure make[1]: Entering directory '/<>/spades-3.10.1+dfsg' echo "Simply use spades_compile.sh in auto_build" Simply use spades_compile.sh in auto_build make[1]: Leaving directory '/<>/spades-3.10.1+dfsg' debian/rules override_dh_auto_build make[1]: Entering directory '/<>/spades-3.10.1+dfsg' PREFIX=/<>/spades-3.10.1+dfsg/install_spades ./spades_compile.sh -- The C compiler identification is Clang 3.9.1 -- The CXX compiler identification is Clang 3.9.1 -- Check for working C compiler: /usr/bin/cc -- Check for working C compiler: /usr/bin/cc -- works -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Detecting C compile features -- Detecting C compile features - done -- 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 -- Try OpenMP C flag = [-fopenmp=libomp] -- Performing Test OpenMP_FLAG_DETECTED -- Performing Test OpenMP_FLAG_DETECTED - Failed -- Try OpenMP C flag = [ ] -- Performing Test OpenMP_FLAG_DETECTED -- Performing Test OpenMP_FLAG_DETECTED - Failed -- Try OpenMP C flag = [-fopenmp] -- Performing Test OpenMP_FLAG_DETECTED -- Performing Test OpenMP_FLAG_DETECTED - Failed -- Try OpenMP C flag = [/openmp] -- Performing Test OpenMP_FLAG_DETECTED -- Performing Test OpenMP_FLAG_DETECTED - Failed -- Try OpenMP C flag = [-Qopenmp] -- Performing Test OpenMP_FLAG_DETECTED -- Performing Test OpenMP_FLAG_DETECTED - Failed -- Try OpenMP C flag = [-openmp] -- Performing Test OpenMP_FLAG_DETECTED -- Performing Test OpenMP_FLAG_DETECTED - Failed -- Try OpenMP C flag = [-xopenmp] -- Performing Test OpenMP_FLAG_DETECTED -- Performing Test OpenMP_FLAG_DETECTED - Failed -- Try OpenMP C flag = [+Oopenmp] -- Performing Test OpenMP_FLAG_DETECTED -- Performing Test OpenMP_FLAG_DETECTED - Failed -- Try OpenMP C flag = [-qsmp] -- Performing Test OpenMP_FLAG_DETECTED -- Performing Test OpenMP_FLAG_DETECTED - Failed -- Try OpenMP C flag = [-mp] -- Performing Test OpenMP_FLAG_DETECTED -- Performing Test OpenMP_FLAG_DETECTED - Failed -- 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_C_FLAGS OpenMP_CXX_FLAGS) -- Found ZLIB: /usr/lib/x86_64-linux-gnu/libz.so (found version "1.2.8") -- Found BZip2: /usr/lib/x86_64-linux-gnu/libbz2.so (found version "1.0.6") -- Looking for BZ2_bzCompressInit -- Looking for BZ2_bzCompressInit - found -- Could NOT find readline (missing: READLINE_INCLUDE_DIR READLINE_LIBRARY) -- Boost version: 1.62.0 Making Release Configuration... Building SPAdes from N/A, sha: N/A -- Looking for open -- Looking for open - found -- Looking for include file execinfo.h -- Looking for include file execinfo.h - found -- Looking for include file signal.h -- Looking for include file signal.h - found -- Looking for include file sys/stat.h -- Looking for include file sys/stat.h - found -- Looking for include file cxxabi.h -- Looking for include file cxxabi.h - not found -- Looking for include file dlfcn.h -- Looking for include file dlfcn.h - found -- Looking for include file mach/mach.h -- Looking for include file mach/mach.h - not found -- Looking for include file link.h -- Looking for include file link.h - found -- Looking for backtrace -- Looking for backtrace - found -- Configuring done -- Generating done -- Build files have been written to: /<>/spades-3.10.1+dfsg/build_spades make[2]: Entering directory '/<>/spades-3.10.1+dfsg/build_spades' /usr/bin/cmake -H/<>/spades-3.10.1+dfsg/src -B/<>/spades-3.10.1+dfsg/build_spades --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /<>/spades-3.10.1+dfsg/build_spades/CMakeFiles /<>/spades-3.10.1+dfsg/build_spades/CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[3]: Entering directory '/<>/spades-3.10.1+dfsg/build_spades' make -f ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/build.make ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/depend make[4]: Entering directory '/<>/spades-3.10.1+dfsg/build_spades' cd /<>/spades-3.10.1+dfsg/build_spades && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/spades-3.10.1+dfsg/src /<>/spades-3.10.1+dfsg/ext/src/ConsensusCore /<>/spades-3.10.1+dfsg/build_spades /<>/spades-3.10.1+dfsg/build_spades/ext/ConsensusCore /<>/spades-3.10.1+dfsg/build_spades/ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/DependInfo.cmake --color= Dependee "/<>/spades-3.10.1+dfsg/build_spades/ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/DependInfo.cmake" is newer than depender "/<>/spades-3.10.1+dfsg/build_spades/ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/depend.internal". Dependee "/<>/spades-3.10.1+dfsg/build_spades/ext/ConsensusCore/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/<>/spades-3.10.1+dfsg/build_spades/ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/depend.internal". Scanning dependencies of target ConsensusCore make[4]: Leaving directory '/<>/spades-3.10.1+dfsg/build_spades' make -f ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/build.make ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/build make[4]: Entering directory '/<>/spades-3.10.1+dfsg/build_spades' [ 0%] Building CXX object ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/AffineAlignment.cpp.o cd /<>/spades-3.10.1+dfsg/build_spades/ext/ConsensusCore && /usr/bin/c++ -DJEMALLOC_NO_DEMANGLE -I/<>/spades-3.10.1+dfsg/build_spades/ext/ConsensusCore -I/<>/spades-3.10.1+dfsg/ext/src/ConsensusCore -I/<>/spades-3.10.1+dfsg/src/include -I/<>/spades-3.10.1+dfsg/build_spades/include -I/<>/spades-3.10.1+dfsg/src -I/<>/spades-3.10.1+dfsg/src/common -isystem /<>/spades-3.10.1+dfsg/src/../ext/include -I/<>/spades-3.10.1+dfsg/src/../ext/include/ConsensusCore -g -O2 -fdebug-prefix-map=/<>/spades-3.10.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -stdlib=libc++ -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -o CMakeFiles/ConsensusCore.dir/AffineAlignment.cpp.o -c /<>/spades-3.10.1+dfsg/ext/src/ConsensusCore/AffineAlignment.cpp In file included from /<>/spades-3.10.1+dfsg/ext/src/ConsensusCore/AffineAlignment.cpp:38: /<>/spades-3.10.1+dfsg/src/../ext/include/ConsensusCore/AffineAlignment.hpp:44:10: fatal error: 'string' file not found #include ^ 1 error generated. ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/build.make:62: recipe for target 'ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/AffineAlignment.cpp.o' failed make[4]: *** [ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/AffineAlignment.cpp.o] Error 1 make[4]: Leaving directory '/<>/spades-3.10.1+dfsg/build_spades' CMakeFiles/Makefile2:153: recipe for target 'ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/all' failed make[3]: *** [ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/all] Error 2 make[3]: Leaving directory '/<>/spades-3.10.1+dfsg/build_spades' Makefile:149: recipe for target 'all' failed make[2]: *** [all] Error 2 make[2]: Leaving directory '/<>/spades-3.10.1+dfsg/build_spades' debian/rules:41: recipe for target 'override_dh_auto_build' failed make[1]: *** [override_dh_auto_build] Error 2 make[1]: Leaving directory '/<>/spades-3.10.1+dfsg' debian/rules:23: recipe for target 'build-arch' failed make: *** [build-arch] Error 2 dpkg-buildpackage: error: debian/rules build-arch gave error exit status 2 -------------------------------------------------------------------------------- Build finished at 2017-07-06T18:15:44Z 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: 16776 Build-Time: 7 Distribution: unstable Fail-Stage: build Host Architecture: amd64 Install-Time: 18 Job: spades_3.10.1+dfsg-2 Machine Architecture: amd64 Package: spades Package-Time: 45 Source-Version: 3.10.1+dfsg-2 Space: 16776 Status: attempted Version: 3.10.1+dfsg-2 -------------------------------------------------------------------------------- Finished at 2017-07-06T18:15:44Z Build needed 00:00:45, 16776k disk space E: Build failure (dpkg-buildpackage died) DC-Status: Failed 45.982961005s DC-Time-Estimation: 45.982961005 versus expected 735 (r/m: 14.984181617188138 ; m: 45.982961005)