DC-Build-Header: spades 3.13.1+dfsg-2 / 2020-02-25 12:20:16 +0000 DC-Task: type:rebuild-binarch-only source:spades version:3.13.1+dfsg-2 chroot:unstable esttime:1476 logfile:/tmp/spades_3.13.1+dfsg-2_unstable_clang8.log modes:clang8:binarch-only DC-Sbuild-call: su user42 -c 'sbuild -n --arch-any --apt-update -d unstable -v --no-run-lintian --chroot-setup-commands=/tmp/clang8 spades_3.13.1+dfsg-2' sbuild (Debian sbuild) 0.78.1 (09 February 2019) on ip-172-31-13-180.eu-central-1.compute.internal +==============================================================================+ | spades 3.13.1+dfsg-2 (amd64) Tue, 25 Feb 2020 12:20:17 +0000 | +==============================================================================+ Package: spades Version: 3.13.1+dfsg-2 Source Version: 3.13.1+dfsg-2 Distribution: unstable Machine Architecture: amd64 Host Architecture: amd64 Build Architecture: amd64 Build Type: binary I: NOTICE: Log filtering will replace 'var/run/schroot/mount/sid-amd64-sbuild-ba1160bb-6c90-46aa-a5f8-b86052e5e083' with '<>' +------------------------------------------------------------------------------+ | Chroot Setup Commands | +------------------------------------------------------------------------------+ /tmp/clang8 ----------- + echo 'Entering customization script...' Entering customization script... + CLANG_VERSION=8 + echo 'Install of clang-8' Install of clang-8 + apt-get update Get:1 http://127.0.0.1:12990/debian sid InRelease [142 kB] Get:2 http://127.0.0.1:12990/debian sid/main Sources.diff/Index [27.9 kB] Get:3 http://127.0.0.1:12990/debian sid/main amd64 Packages.diff/Index [27.9 kB] Get:4 http://127.0.0.1:12990/debian sid/main Sources 2020-02-24-0823.32.pdiff [11.0 kB] Get:5 http://127.0.0.1:12990/debian sid/main Sources 2020-02-24-1420.34.pdiff [30.2 kB] Get:6 http://127.0.0.1:12990/debian sid/main Sources 2020-02-24-2014.03.pdiff [16.9 kB] Get:7 http://127.0.0.1:12990/debian sid/main Sources 2020-02-25-0213.11.pdiff [23.2 kB] Get:8 http://127.0.0.1:12990/debian sid/main Sources 2020-02-25-0815.22.pdiff [9222 B] Get:9 http://127.0.0.1:12990/debian sid/main amd64 Packages 2020-02-24-0823.32.pdiff [15.5 kB] Get:10 http://127.0.0.1:12990/debian sid/main amd64 Packages 2020-02-24-1420.34.pdiff [27.5 kB] Get:11 http://127.0.0.1:12990/debian sid/main amd64 Packages 2020-02-24-2014.03.pdiff [21.6 kB] Get:12 http://127.0.0.1:12990/debian sid/main amd64 Packages 2020-02-25-0213.11.pdiff [35.0 kB] Get:8 http://127.0.0.1:12990/debian sid/main Sources 2020-02-25-0815.22.pdiff [9222 B] Get:13 http://127.0.0.1:12990/debian sid/main amd64 Packages 2020-02-25-0815.22.pdiff [20.1 kB] Get:13 http://127.0.0.1:12990/debian sid/main amd64 Packages 2020-02-25-0815.22.pdiff [20.1 kB] Get:14 http://127.0.0.1:12990/debian sid/main Translation-en [6195 kB] Fetched 6604 kB in 2s (3803 kB/s) Reading package lists... + apt-get install --yes --no-install-recommends --force-yes clang-8 libomp-8-dev libobjc-9-dev Reading package lists... Building dependency tree... The following additional packages will be installed: cpp-9 g++-9 gcc-8-base gcc-9 gcc-9-base lib32gcc-s1 lib32gcc1 lib32stdc++6 libasan5 libbsd0 libc6-i386 libclang-common-8-dev libclang1-8 libedit2 libgc1c2 libgcc-8-dev libgcc-9-dev libllvm8 libmpx2 libobjc-8-dev libobjc4 libomp5-8 libstdc++-8-dev libstdc++-9-dev Suggested packages: clang-8-doc gcc-9-locales g++-9-multilib gcc-9-doc gcc-9-multilib libomp-8-doc libstdc++-8-doc libstdc++-9-doc Recommended packages: llvm-8-dev python3 The following NEW packages will be installed: clang-8 gcc-8-base lib32gcc-s1 lib32gcc1 lib32stdc++6 libbsd0 libc6-i386 libclang-common-8-dev libclang1-8 libedit2 libgc1c2 libgcc-8-dev libllvm8 libmpx2 libobjc-8-dev libobjc-9-dev libobjc4 libomp-8-dev libomp5-8 libstdc++-8-dev The following packages will be upgraded: cpp-9 g++-9 gcc-9 gcc-9-base libasan5 libgcc-9-dev libstdc++-9-dev 7 upgraded, 20 newly installed, 0 to remove and 2 not upgraded. Need to get 74.9 MB of archives. After this operation, 223 MB of additional disk space will be used. Get:1 http://127.0.0.1:12990/debian sid/main amd64 libasan5 amd64 9.2.1-30 [389 kB] Get:2 http://127.0.0.1:12990/debian sid/main amd64 g++-9 amd64 9.2.1-30 [10.7 MB] Get:3 http://127.0.0.1:12990/debian sid/main amd64 gcc-9 amd64 9.2.1-30 [10.0 MB] Get:4 http://127.0.0.1:12990/debian sid/main amd64 libstdc++-9-dev amd64 9.2.1-30 [1697 kB] Get:5 http://127.0.0.1:12990/debian sid/main amd64 libgcc-9-dev amd64 9.2.1-30 [2349 kB] Get:6 http://127.0.0.1:12990/debian sid/main amd64 cpp-9 amd64 9.2.1-30 [9711 kB] Get:7 http://127.0.0.1:12990/debian sid/main amd64 gcc-9-base amd64 9.2.1-30 [196 kB] Get:8 http://127.0.0.1:12990/debian sid/main amd64 libbsd0 amd64 0.10.0-1 [107 kB] Get:9 http://127.0.0.1:12990/debian sid/main amd64 libedit2 amd64 3.1-20191231-1 [95.4 kB] Get:10 http://127.0.0.1:12990/debian sid/main amd64 libllvm8 amd64 1:8.0.1-7 [13.8 MB] Get:11 http://127.0.0.1:12990/debian sid/main amd64 gcc-8-base amd64 8.3.0-29 [194 kB] Get:12 http://127.0.0.1:12990/debian sid/main amd64 libmpx2 amd64 8.3.0-29 [11.4 kB] Get:13 http://127.0.0.1:12990/debian sid/main amd64 libgcc-8-dev amd64 8.3.0-29 [2297 kB] Get:14 http://127.0.0.1:12990/debian sid/main amd64 libstdc++-8-dev amd64 8.3.0-29 [1543 kB] Get:15 http://127.0.0.1:12990/debian sid/main amd64 libgc1c2 amd64 1:7.6.4-0.4 [224 kB] Get:16 http://127.0.0.1:12990/debian sid/main amd64 libobjc4 amd64 10-20200222-1 [41.6 kB] Get:17 http://127.0.0.1:12990/debian sid/main amd64 libobjc-8-dev amd64 8.3.0-29 [227 kB] Get:18 http://127.0.0.1:12990/debian sid/main amd64 libc6-i386 amd64 2.29-10 [2918 kB] Get:19 http://127.0.0.1:12990/debian sid/main amd64 lib32gcc-s1 amd64 10-20200222-1 [49.4 kB] Get:20 http://127.0.0.1:12990/debian sid/main amd64 lib32gcc1 amd64 1:10-20200222-1 [1104 B] Get:21 http://127.0.0.1:12990/debian sid/main amd64 lib32stdc++6 amd64 10-20200222-1 [510 kB] Get:22 http://127.0.0.1:12990/debian sid/main amd64 libclang-common-8-dev amd64 1:8.0.1-7 [2989 kB] Get:23 http://127.0.0.1:12990/debian sid/main amd64 libclang1-8 amd64 1:8.0.1-7 [6244 kB] Get:24 http://127.0.0.1:12990/debian sid/main amd64 clang-8 amd64 1:8.0.1-7 [8010 kB] Get:25 http://127.0.0.1:12990/debian sid/main amd64 libobjc-9-dev amd64 9.2.1-30 [219 kB] Get:26 http://127.0.0.1:12990/debian sid/main amd64 libomp5-8 amd64 1:8.0.1-7 [331 kB] Get:27 http://127.0.0.1:12990/debian sid/main amd64 libomp-8-dev amd64 1:8.0.1-7 [62.3 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 74.9 MB in 1s (96.1 MB/s) (Reading database ... (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 ... 12119 files and directories currently installed.) Preparing to unpack .../00-libasan5_9.2.1-30_amd64.deb ... Unpacking libasan5:amd64 (9.2.1-30) over (9.2.1-29) ... Preparing to unpack .../01-g++-9_9.2.1-30_amd64.deb ... Unpacking g++-9 (9.2.1-30) over (9.2.1-29) ... Preparing to unpack .../02-gcc-9_9.2.1-30_amd64.deb ... Unpacking gcc-9 (9.2.1-30) over (9.2.1-29) ... Preparing to unpack .../03-libstdc++-9-dev_9.2.1-30_amd64.deb ... 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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 8 9 10' + cd /usr/bin + for VERSION in $VERSIONS + rm -f g++-4.6 gcc-4.6 cpp-4.6 gcc + ln -s clang++-8 g++-4.6 + ln -s clang-8 gcc-4.6 + ln -s clang-8 cpp-4.6 + ln -s clang-8 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++-8 g++-4.7 + ln -s clang-8 gcc-4.7 + ln -s clang-8 cpp-4.7 + ln -s clang-8 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++-8 g++-4.8 + ln -s clang-8 gcc-4.8 + ln -s clang-8 cpp-4.8 + ln -s clang-8 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++-8 g++-4.9 + ln -s clang-8 gcc-4.9 + ln -s clang-8 cpp-4.9 + ln -s clang-8 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++-8 g++-5 + ln -s clang-8 gcc-5 + ln -s clang-8 cpp-5 + ln -s clang-8 gcc + echo 'gcc-5 hold' + dpkg --set-selections dpkg: warning: package not in status nor available database at line 1: gcc-5 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++-5 hold' + dpkg --set-selections dpkg: warning: package not in status nor available database at line 1: g++-5 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++-6 gcc-6 cpp-6 gcc + ln -s clang++-8 g++-6 + ln -s clang-8 gcc-6 + ln -s clang-8 cpp-6 + ln -s clang-8 gcc + echo 'gcc-6 hold' + dpkg --set-selections dpkg: warning: package not in status nor available database at line 1: gcc-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++-6 hold' + dpkg --set-selections dpkg: warning: package not in status nor available database at line 1: g++-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++-7 gcc-7 cpp-7 gcc + ln -s clang++-8 g++-7 + ln -s clang-8 gcc-7 + ln -s clang-8 cpp-7 + ln -s clang-8 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 + for VERSION in $VERSIONS + rm -f g++-8 gcc-8 cpp-8 gcc + ln -s clang++-8 g++-8 + ln -s clang-8 gcc-8 + ln -s clang-8 cpp-8 + ln -s clang-8 gcc + echo 'gcc-8 hold' + dpkg --set-selections dpkg: warning: package not in status nor available database at line 1: gcc-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++-8 hold' + dpkg --set-selections dpkg: warning: package not in status nor available database at line 1: g++-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++-9 gcc-9 cpp-9 gcc + ln -s clang++-8 g++-9 + ln -s clang-8 gcc-9 + ln -s clang-8 cpp-9 + ln -s clang-8 gcc + echo 'gcc-9 hold' + dpkg --set-selections + echo 'g++-9 hold' + dpkg --set-selections + for VERSION in $VERSIONS + rm -f g++-10 gcc-10 cpp-10 gcc + ln -s clang++-8 g++-10 + ln -s clang-8 gcc-10 + ln -s clang-8 cpp-10 + ln -s clang-8 gcc + echo 'gcc-10 hold' + dpkg --set-selections dpkg: warning: package not in status nor available database at line 1: gcc-10 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++-10 hold' + dpkg --set-selections dpkg: warning: package not in status nor available database at line 1: g++-10 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-NdrEb5 + 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/clang8'. Finished processing commands. -------------------------------------------------------------------------------- I: NOTICE: Log filtering will replace 'build/spades-NdrEb5/resolver-tsUnQK' with '<>' +------------------------------------------------------------------------------+ | Update chroot | +------------------------------------------------------------------------------+ Hit:1 http://127.0.0.1:12990/debian sid InRelease Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages will be upgraded: libgmp10 zlib1g 2 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 343 kB of archives. After this operation, 0 B of additional disk space will be used. Get:1 http://127.0.0.1:12990/debian sid/main amd64 libgmp10 amd64 2:6.2.0+dfsg-4 [253 kB] Get:2 http://127.0.0.1:12990/debian sid/main amd64 zlib1g amd64 1:1.2.11.dfsg-2 [90.4 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 343 kB in 0s (6464 kB/s) (Reading database ... (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 ... 13887 files and directories currently installed.) Preparing to unpack .../libgmp10_2%3a6.2.0+dfsg-4_amd64.deb ... Unpacking libgmp10:amd64 (2:6.2.0+dfsg-4) over (2:6.2.0+dfsg-3) ... Setting up libgmp10:amd64 (2:6.2.0+dfsg-4) ... (Reading database ... (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 ... 13887 files and directories currently installed.) Preparing to unpack .../zlib1g_1%3a1.2.11.dfsg-2_amd64.deb ... Unpacking zlib1g:amd64 (1:1.2.11.dfsg-2) over (1:1.2.11.dfsg-1.2) ... Setting up zlib1g:amd64 (1:1.2.11.dfsg-2) ... Processing triggers for libc-bin (2.29-10) ... +------------------------------------------------------------------------------+ | 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://salsa.debian.org/med-team/spades.git Please use: git clone https://salsa.debian.org/med-team/spades.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 3230 kB of source archives. Get:1 http://127.0.0.1:12990/debian sid/main spades 3.13.1+dfsg-2 (dsc) [2381 B] Get:2 http://127.0.0.1:12990/debian sid/main spades 3.13.1+dfsg-2 (tar) [3203 kB] Get:3 http://127.0.0.1:12990/debian sid/main spades 3.13.1+dfsg-2 (diff) [25.2 kB] Fetched 3230 kB in 0s (33.4 MB/s) Download complete and in download only mode I: NOTICE: Log filtering will replace 'build/spades-NdrEb5/spades-3.13.1+dfsg' with '<>' I: NOTICE: Log filtering will replace 'build/spades-NdrEb5' with '<>' +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper-compat (= 12), dh-python, cmake, python3-dev, zlib1g-dev, libbz2-dev, libboost-dev, libbam-dev, libbamtools-dev, libhat-trie-dev, libhts-dev, libnlopt-dev, libnlopt-cxx-dev, libssw-dev, python3-yaml, python3-joblib, asciidoctor (>= 1.5.3), bwa, libbwa-dev, lynx, build-essential, fakeroot Filtered Build-Depends: debhelper-compat (= 12), dh-python, cmake, python3-dev, zlib1g-dev, libbz2-dev, libboost-dev, libbam-dev, libbamtools-dev, libhat-trie-dev, libhts-dev, libnlopt-dev, libnlopt-cxx-dev, libssw-dev, python3-yaml, python3-joblib, asciidoctor (>= 1.5.3), bwa, libbwa-dev, lynx, build-essential, fakeroot dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/<>/apt_archive/sbuild-build-depends-main-dummy.deb'. Ign:1 copy:/<>/apt_archive ./ InRelease Get:2 copy:/<>/apt_archive ./ Release [957 B] Ign:3 copy:/<>/apt_archive ./ Release.gpg Get:4 copy:/<>/apt_archive ./ Sources [478 B] Get:5 copy:/<>/apt_archive ./ Packages [559 B] Fetched 1994 B in 0s (0 B/s) Reading package lists... Reading package lists... Install main 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-python dh-strip-nondeterminism dwz file gettext gettext-base groff-base intltool-debian libarchive-zip-perl libarchive13 libbam-dev libbamtools-dev libbamtools2.5.1 libboost-dev libboost1.67-dev libbrotli1 libbwa-dev libbz2-dev libcroco3 libcurl3-gnutls libcurl4 libdebhelper-perl libdeflate0 libelf1 libexpat1 libexpat1-dev libfile-stripnondeterminism-perl libglib2.0-0 libgssapi-krb5-2 libhat-trie-dev libhat-trie0 libhts-dev libhts3 libicu63 libidn11 libjsoncpp1 libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 libldap-2.4-2 libldap-common liblzma-dev libmagic-mgc libmagic1 libmpdec2 libncurses6 libnghttp2-14 libnlopt-cxx-dev libnlopt-cxx0 libnlopt-dev libnlopt0 libpipeline1 libprocps8 libpsl5 libpython3-dev libpython3-stdlib libpython3.7 libpython3.7-dev libpython3.7-minimal libpython3.7-stdlib libreadline8 librhash0 librtmp1 libruby2.5 libsasl2-2 libsasl2-modules-db libsigsegv2 libsqlite3-0 libssh2-1 libssl1.1 libssw-dev libssw0 libsub-override-perl libtool libuchardet0 libuv1 libxml2 libyaml-0-2 lynx lynx-common m4 man-db mime-support openssl po-debconf procps python3 python3-dev python3-distutils python3-joblib python3-lib2to3 python3-minimal python3-pkg-resources python3-yaml python3.7 python3.7-dev python3.7-minimal rake readline-common ruby ruby-asciidoctor ruby-did-you-mean ruby-minitest ruby-net-telnet ruby-power-assert ruby-test-unit ruby-xmlrpc ruby2.5 rubygems-integration sensible-utils zlib1g-dev Suggested packages: autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois vacation samtools cmake-doc ninja-build dh-make gettext-doc libasprintf-dev libgettextpo-dev groff lrzip libbamtools-doc libboost-doc libboost1.67-doc libboost-atomic1.67-dev libboost-chrono1.67-dev libboost-container1.67-dev libboost-context1.67-dev libboost-contract1.67-dev libboost-coroutine1.67-dev libboost-date-time1.67-dev libboost-exception1.67-dev libboost-fiber1.67-dev libboost-filesystem1.67-dev libboost-graph1.67-dev libboost-graph-parallel1.67-dev libboost-iostreams1.67-dev libboost-locale1.67-dev libboost-log1.67-dev libboost-math1.67-dev libboost-mpi1.67-dev libboost-mpi-python1.67-dev libboost-numpy1.67-dev libboost-program-options1.67-dev libboost-python1.67-dev libboost-random1.67-dev libboost-regex1.67-dev libboost-serialization1.67-dev libboost-signals1.67-dev libboost-stacktrace1.67-dev libboost-system1.67-dev libboost-test1.67-dev libboost-thread1.67-dev libboost-timer1.67-dev libboost-type-erasure1.67-dev libboost-wave1.67-dev libboost1.67-tools-dev libmpfrc++-dev libntl-dev krb5-doc krb5-user liblzma-doc libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc apparmor less libmail-box-perl python3-doc python3-tk python3-venv python3-setuptools python3.7-venv python3.7-doc binfmt-support readline-doc ri ruby-dev bundler Recommended packages: bzip2-doc libarchive-cpio-perl libglib2.0-data shared-mime-info xdg-user-dirs krb5-locales libgpm2 publicsuffix libsasl2-modules libltdl-dev libmail-sendmail-perl psmisc python3-numpy python3-pytest python3-simplejson python3-psutil 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-python dh-strip-nondeterminism dwz file gettext gettext-base groff-base intltool-debian libarchive-zip-perl libarchive13 libbam-dev libbamtools-dev libbamtools2.5.1 libboost-dev libboost1.67-dev libbrotli1 libbwa-dev libbz2-dev libcroco3 libcurl3-gnutls libcurl4 libdebhelper-perl libdeflate0 libelf1 libexpat1 libexpat1-dev libfile-stripnondeterminism-perl libglib2.0-0 libgssapi-krb5-2 libhat-trie-dev libhat-trie0 libhts-dev libhts3 libicu63 libidn11 libjsoncpp1 libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 libldap-2.4-2 libldap-common liblzma-dev libmagic-mgc libmagic1 libmpdec2 libncurses6 libnghttp2-14 libnlopt-cxx-dev libnlopt-cxx0 libnlopt-dev libnlopt0 libpipeline1 libprocps8 libpsl5 libpython3-dev libpython3-stdlib libpython3.7 libpython3.7-dev libpython3.7-minimal libpython3.7-stdlib libreadline8 librhash0 librtmp1 libruby2.5 libsasl2-2 libsasl2-modules-db libsigsegv2 libsqlite3-0 libssh2-1 libssl1.1 libssw-dev libssw0 libsub-override-perl libtool libuchardet0 libuv1 libxml2 libyaml-0-2 lynx lynx-common m4 man-db mime-support openssl po-debconf procps python3 python3-dev python3-distutils python3-joblib python3-lib2to3 python3-minimal python3-pkg-resources python3-yaml python3.7 python3.7-dev python3.7-minimal rake readline-common ruby ruby-asciidoctor ruby-did-you-mean ruby-minitest ruby-net-telnet ruby-power-assert ruby-test-unit ruby-xmlrpc ruby2.5 rubygems-integration sbuild-build-depends-main-dummy sensible-utils zlib1g-dev 0 upgraded, 125 newly installed, 0 to remove and 0 not upgraded. Need to get 102 MB of archives. After this operation, 393 MB of additional disk space will be used. Get:1 copy:/<>/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [988 B] Get:2 http://127.0.0.1:12990/debian sid/main amd64 bsdmainutils amd64 11.1.2+b1 [191 kB] Get:3 http://127.0.0.1:12990/debian sid/main amd64 libuchardet0 amd64 0.0.6-3 [64.9 kB] Get:4 http://127.0.0.1:12990/debian sid/main amd64 groff-base amd64 1.22.4-4 [919 kB] Get:5 http://127.0.0.1:12990/debian sid/main amd64 libpipeline1 amd64 1.5.2-2 [33.9 kB] Get:6 http://127.0.0.1:12990/debian sid/main amd64 man-db amd64 2.9.0-2 [1307 kB] Get:7 http://127.0.0.1:12990/debian sid/main amd64 libssl1.1 amd64 1.1.1d-2 [1540 kB] Get:8 http://127.0.0.1:12990/debian sid/main amd64 libpython3.7-minimal amd64 3.7.6-1+b1 [591 kB] Get:9 http://127.0.0.1:12990/debian sid/main amd64 libexpat1 amd64 2.2.9-1 [94.3 kB] Get:10 http://127.0.0.1:12990/debian sid/main amd64 python3.7-minimal amd64 3.7.6-1+b1 [1813 kB] Get:11 http://127.0.0.1:12990/debian sid/main amd64 python3-minimal amd64 3.7.5-3 [36.8 kB] Get:12 http://127.0.0.1:12990/debian sid/main amd64 mime-support all 3.64 [37.8 kB] Get:13 http://127.0.0.1:12990/debian sid/main amd64 libmpdec2 amd64 2.4.2-2 [87.2 kB] Get:14 http://127.0.0.1:12990/debian sid/main amd64 readline-common all 8.0-3 [72.5 kB] Get:15 http://127.0.0.1:12990/debian sid/main amd64 libreadline8 amd64 8.0-3 [160 kB] Get:16 http://127.0.0.1:12990/debian sid/main amd64 libsqlite3-0 amd64 3.31.1-3 [661 kB] Get:17 http://127.0.0.1:12990/debian sid/main amd64 libpython3.7-stdlib amd64 3.7.6-1+b1 [1735 kB] Get:18 http://127.0.0.1:12990/debian sid/main amd64 python3.7 amd64 3.7.6-1+b1 [351 kB] Get:19 http://127.0.0.1:12990/debian sid/main amd64 libpython3-stdlib amd64 3.7.5-3 [20.2 kB] Get:20 http://127.0.0.1:12990/debian sid/main amd64 python3 amd64 3.7.5-3 [62.1 kB] Get:21 http://127.0.0.1:12990/debian sid/main amd64 libncurses6 amd64 6.1+20191019-1 [102 kB] Get:22 http://127.0.0.1:12990/debian sid/main amd64 libprocps8 amd64 2:3.3.16-1+b1 [62.8 kB] Get:23 http://127.0.0.1:12990/debian sid/main amd64 procps amd64 2:3.3.16-1+b1 [263 kB] Get:24 http://127.0.0.1:12990/debian sid/main amd64 sensible-utils all 0.0.12+nmu1 [16.0 kB] Get:25 http://127.0.0.1:12990/debian sid/main amd64 libmagic-mgc amd64 1:5.38-4 [262 kB] Get:26 http://127.0.0.1:12990/debian sid/main amd64 libmagic1 amd64 1:5.38-4 [120 kB] Get:27 http://127.0.0.1:12990/debian sid/main amd64 file amd64 1:5.38-4 [67.9 kB] Get:28 http://127.0.0.1:12990/debian sid/main amd64 gettext-base amd64 0.19.8.1-10 [123 kB] Get:29 http://127.0.0.1:12990/debian sid/main amd64 openssl amd64 1.1.1d-2 [840 kB] Get:30 http://127.0.0.1:12990/debian sid/main amd64 ca-certificates all 20190110 [157 kB] Get:31 http://127.0.0.1:12990/debian sid/main amd64 rubygems-integration all 1.16 [5632 B] Get:32 http://127.0.0.1:12990/debian sid/main amd64 rake all 13.0.1-2 [67.9 kB] Get:33 http://127.0.0.1:12990/debian sid/main amd64 ruby-did-you-mean all 1.2.1-1 [14.4 kB] Get:34 http://127.0.0.1:12990/debian sid/main amd64 ruby-minitest all 5.13.0-1 [57.3 kB] Get:35 http://127.0.0.1:12990/debian sid/main amd64 ruby-net-telnet all 0.1.1-2 [12.5 kB] Get:36 http://127.0.0.1:12990/debian sid/main amd64 ruby-power-assert all 1.1.5-1 [11.3 kB] Get:37 http://127.0.0.1:12990/debian sid/main amd64 ruby-test-unit all 3.3.4-1 [85.1 kB] Get:38 http://127.0.0.1:12990/debian sid/main amd64 ruby-xmlrpc all 0.3.0-2 [23.7 kB] Get:39 http://127.0.0.1:12990/debian sid/main amd64 libyaml-0-2 amd64 0.2.2-1 [49.6 kB] Get:40 http://127.0.0.1:12990/debian sid/main amd64 libruby2.5 amd64 2.5.7-1+b1 [3412 kB] Get:41 http://127.0.0.1:12990/debian sid/main amd64 ruby2.5 amd64 2.5.7-1+b1 [375 kB] Get:42 http://127.0.0.1:12990/debian sid/main amd64 ruby amd64 1:2.5.7.1 [11.7 kB] Get:43 http://127.0.0.1:12990/debian sid/main amd64 ruby-asciidoctor all 2.0.10-2 [201 kB] Get:44 http://127.0.0.1:12990/debian sid/main amd64 asciidoctor all 2.0.10-2 [77.7 kB] Get:45 http://127.0.0.1:12990/debian sid/main amd64 libsigsegv2 amd64 2.12-2 [32.8 kB] Get:46 http://127.0.0.1:12990/debian sid/main amd64 m4 amd64 1.4.18-4 [203 kB] Get:47 http://127.0.0.1:12990/debian sid/main amd64 autoconf all 2.69-11.1 [341 kB] Get:48 http://127.0.0.1:12990/debian sid/main amd64 autotools-dev all 20180224.1 [77.0 kB] Get:49 http://127.0.0.1:12990/debian sid/main amd64 automake all 1:1.16.1-4 [771 kB] Get:50 http://127.0.0.1:12990/debian sid/main amd64 autopoint all 0.19.8.1-10 [435 kB] Get:51 http://127.0.0.1:12990/debian sid/main amd64 bwa amd64 0.7.17-4 [220 kB] Get:52 http://127.0.0.1:12990/debian sid/main amd64 cmake-data all 3.16.3-1 [1628 kB] Get:53 http://127.0.0.1:12990/debian sid/main amd64 libicu63 amd64 63.2-2 [8301 kB] Get:54 http://127.0.0.1:12990/debian sid/main amd64 libxml2 amd64 2.9.10+dfsg-3 [709 kB] Get:55 http://127.0.0.1:12990/debian sid/main amd64 libarchive13 amd64 3.4.0-1+b1 [335 kB] Get:56 http://127.0.0.1:12990/debian sid/main amd64 libbrotli1 amd64 1.0.7-6 [266 kB] Get:57 http://127.0.0.1:12990/debian sid/main amd64 libkeyutils1 amd64 1.6.1-2 [15.4 kB] Get:58 http://127.0.0.1:12990/debian sid/main amd64 libkrb5support0 amd64 1.17-6 [64.6 kB] Get:59 http://127.0.0.1:12990/debian sid/main amd64 libk5crypto3 amd64 1.17-6 [116 kB] Get:60 http://127.0.0.1:12990/debian sid/main amd64 libkrb5-3 amd64 1.17-6 [366 kB] Get:61 http://127.0.0.1:12990/debian sid/main amd64 libgssapi-krb5-2 amd64 1.17-6 [156 kB] Get:62 http://127.0.0.1:12990/debian sid/main amd64 libsasl2-modules-db amd64 2.1.27+dfsg-2 [69.0 kB] Get:63 http://127.0.0.1:12990/debian sid/main amd64 libsasl2-2 amd64 2.1.27+dfsg-2 [106 kB] Get:64 http://127.0.0.1:12990/debian sid/main amd64 libldap-common all 2.4.49+dfsg-1 [91.9 kB] Get:65 http://127.0.0.1:12990/debian sid/main amd64 libldap-2.4-2 amd64 2.4.49+dfsg-1 [226 kB] Get:66 http://127.0.0.1:12990/debian sid/main amd64 libnghttp2-14 amd64 1.40.0-1 [85.0 kB] Get:67 http://127.0.0.1:12990/debian sid/main amd64 libpsl5 amd64 0.20.2-2 [53.7 kB] Get:68 http://127.0.0.1:12990/debian sid/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b1 [60.8 kB] Get:69 http://127.0.0.1:12990/debian sid/main amd64 libssh2-1 amd64 1.8.0-2.1 [140 kB] Get:70 http://127.0.0.1:12990/debian sid/main amd64 libcurl4 amd64 7.68.0-1 [321 kB] Get:71 http://127.0.0.1:12990/debian sid/main amd64 libjsoncpp1 amd64 1.7.4-3.1 [77.6 kB] Get:72 http://127.0.0.1:12990/debian sid/main amd64 librhash0 amd64 1.3.9-1 [123 kB] Get:73 http://127.0.0.1:12990/debian sid/main amd64 libuv1 amd64 1.34.2-1 [127 kB] Get:74 http://127.0.0.1:12990/debian sid/main amd64 cmake amd64 3.16.3-1 [3673 kB] Get:75 http://127.0.0.1:12990/debian sid/main amd64 libtool all 2.4.6-13 [513 kB] Get:76 http://127.0.0.1:12990/debian sid/main amd64 dh-autoreconf all 19 [16.9 kB] Get:77 http://127.0.0.1:12990/debian sid/main amd64 libdebhelper-perl all 12.9 [183 kB] Get:78 http://127.0.0.1:12990/debian sid/main amd64 libarchive-zip-perl all 1.67-1 [104 kB] Get:79 http://127.0.0.1:12990/debian sid/main amd64 libsub-override-perl all 0.09-2 [10.2 kB] Get:80 http://127.0.0.1:12990/debian sid/main amd64 libfile-stripnondeterminism-perl all 1.6.3-2 [23.7 kB] Get:81 http://127.0.0.1:12990/debian sid/main amd64 dh-strip-nondeterminism all 1.6.3-2 [14.7 kB] Get:82 http://127.0.0.1:12990/debian sid/main amd64 libelf1 amd64 0.176-1.1 [161 kB] Get:83 http://127.0.0.1:12990/debian sid/main amd64 dwz amd64 0.13-5 [151 kB] Get:84 http://127.0.0.1:12990/debian sid/main amd64 libglib2.0-0 amd64 2.62.4-2 [1319 kB] Get:85 http://127.0.0.1:12990/debian sid/main amd64 libcroco3 amd64 0.6.13-1 [146 kB] Get:86 http://127.0.0.1:12990/debian sid/main amd64 gettext amd64 0.19.8.1-10 [1303 kB] Get:87 http://127.0.0.1:12990/debian sid/main amd64 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get:88 http://127.0.0.1:12990/debian sid/main amd64 po-debconf all 1.0.21 [248 kB] Get:89 http://127.0.0.1:12990/debian sid/main amd64 debhelper all 12.9 [994 kB] Get:90 http://127.0.0.1:12990/debian sid/main amd64 python3-lib2to3 all 3.8.0-1 [78.3 kB] Get:91 http://127.0.0.1:12990/debian sid/main amd64 python3-distutils all 3.8.0-1 [145 kB] Get:92 http://127.0.0.1:12990/debian sid/main amd64 dh-python all 4.20191017 [94.4 kB] Get:93 http://127.0.0.1:12990/debian sid/main amd64 libbam-dev amd64 0.1.19-4 [125 kB] Get:94 http://127.0.0.1:12990/debian sid/main amd64 libbamtools2.5.1 amd64 2.5.1+dfsg-5 [161 kB] Get:95 http://127.0.0.1:12990/debian sid/main amd64 libbamtools-dev amd64 2.5.1+dfsg-5 [22.1 kB] Get:96 http://127.0.0.1:12990/debian sid/main amd64 libboost1.67-dev amd64 1.67.0-17 [8389 kB] Get:97 http://127.0.0.1:12990/debian sid/main amd64 libboost-dev amd64 1.67.0.2+b1 [4496 B] Get:98 http://127.0.0.1:12990/debian sid/main amd64 libbwa-dev amd64 0.7.17-4 [146 kB] Get:99 http://127.0.0.1:12990/debian sid/main amd64 libbz2-dev amd64 1.0.8-2 [30.1 kB] Get:100 http://127.0.0.1:12990/debian sid/main amd64 libcurl3-gnutls amd64 7.68.0-1 [319 kB] Get:101 http://127.0.0.1:12990/debian sid/main amd64 libdeflate0 amd64 1.5-3 [55.8 kB] Get:102 http://127.0.0.1:12990/debian sid/main amd64 libexpat1-dev amd64 2.2.9-1 [136 kB] Get:103 http://127.0.0.1:12990/debian sid/main amd64 libhat-trie0 amd64 0.1.2-2 [11.8 kB] Get:104 http://127.0.0.1:12990/debian sid/main amd64 libhat-trie-dev amd64 0.1.2-2 [19.9 kB] Get:105 http://127.0.0.1:12990/debian sid/main amd64 libhts3 amd64 1.10.2-3 [370 kB] Get:106 http://127.0.0.1:12990/debian sid/main amd64 liblzma-dev amd64 5.2.4-1+b1 [211 kB] Get:107 http://127.0.0.1:12990/debian sid/main amd64 zlib1g-dev amd64 1:1.2.11.dfsg-2 [190 kB] Get:108 http://127.0.0.1:12990/debian sid/main amd64 libhts-dev amd64 1.10.2-3 [4846 kB] Get:109 http://127.0.0.1:12990/debian sid/main amd64 libidn11 amd64 1.33-2.2 [116 kB] Get:110 http://127.0.0.1:12990/debian sid/main amd64 libnlopt0 amd64 2.6.1-8 [170 kB] Get:111 http://127.0.0.1:12990/debian sid/main amd64 libnlopt-dev amd64 2.6.1-8 [29.6 kB] Get:112 http://127.0.0.1:12990/debian sid/main amd64 libnlopt-cxx0 amd64 2.6.1-8 [197 kB] Get:113 http://127.0.0.1:12990/debian sid/main amd64 libnlopt-cxx-dev amd64 2.6.1-8 [14.6 kB] Get:114 http://127.0.0.1:12990/debian sid/main amd64 libpython3.7 amd64 3.7.6-1+b1 [1484 kB] Get:115 http://127.0.0.1:12990/debian sid/main amd64 libpython3.7-dev amd64 3.7.6-1+b1 [41.4 MB] Get:116 http://127.0.0.1:12990/debian sid/main amd64 libpython3-dev amd64 3.7.5-3 [20.3 kB] Get:117 http://127.0.0.1:12990/debian sid/main amd64 libssw0 amd64 1.1-9 [19.2 kB] Get:118 http://127.0.0.1:12990/debian sid/main amd64 libssw-dev amd64 1.1-9 [22.0 kB] Get:119 http://127.0.0.1:12990/debian sid/main amd64 lynx-common all 2.9.0dev.4-1 [1187 kB] Get:120 http://127.0.0.1:12990/debian sid/main amd64 lynx amd64 2.9.0dev.4-1 [642 kB] Get:121 http://127.0.0.1:12990/debian sid/main amd64 python3.7-dev amd64 3.7.6-1+b1 [518 kB] Get:122 http://127.0.0.1:12990/debian sid/main amd64 python3-dev amd64 3.7.5-3 [1260 B] Get:123 http://127.0.0.1:12990/debian sid/main amd64 python3-pkg-resources all 44.0.0-1 [155 kB] Get:124 http://127.0.0.1:12990/debian sid/main amd64 python3-joblib all 0.14.0-3 [203 kB] Get:125 http://127.0.0.1:12990/debian sid/main amd64 python3-yaml amd64 5.3-1 [209 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 102 MB in 1s (93.3 MB/s) Selecting previously unselected package bsdmainutils. 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Preparing to unpack .../106-sbuild-build-depends-main-dummy_0.invalid.0_amd64.deb ... Unpacking sbuild-build-depends-main-dummy (0.invalid.0) ... Setting up libboost1.67-dev:amd64 (1.67.0-17) ... Setting up libpipeline1:amd64 (1.5.2-2) ... Setting up libkeyutils1:amd64 (1.6.1-2) ... Setting up libpsl5:amd64 (0.20.2-2) ... Setting up mime-support (3.64) ... Setting up ruby-power-assert (1.1.5-1) ... Setting up libmagic-mgc (1:5.38-4) ... Setting up libarchive-zip-perl (1.67-1) ... Setting up libyaml-0-2:amd64 (0.2.2-1) ... Setting up libglib2.0-0:amd64 (2.62.4-2) ... No schema files found: doing nothing. Setting up bwa (0.7.17-4) ... Setting up libdebhelper-perl (12.9) ... Setting up libbrotli1:amd64 (1.0.7-6) ... Setting up libsqlite3-0:amd64 (3.31.1-3) ... Setting up libnghttp2-14:amd64 (1.40.0-1) ... Setting up libmagic1:amd64 (1:5.38-4) ... Setting up libdeflate0 (1.5-3) ... Setting up gettext-base (0.19.8.1-10) ... Setting up libnlopt0:amd64 (2.6.1-8) ... Setting up file (1:5.38-4) ... Setting up libldap-common (2.4.49+dfsg-1) ... Setting up libicu63:amd64 (63.2-2) ... Setting up libkrb5support0:amd64 (1.17-6) ... Setting up libsasl2-modules-db:amd64 (2.1.27+dfsg-2) ... Setting up ruby-minitest (5.13.0-1) ... Setting up autotools-dev (20180224.1) ... Setting up libuv1:amd64 (1.34.2-1) ... Setting up libhat-trie0:amd64 (0.1.2-2) ... Setting up libexpat1-dev:amd64 (2.2.9-1) ... Setting up ruby-test-unit (3.3.4-1) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b1) ... Setting up libidn11:amd64 (1.33-2.2) ... Setting up libncurses6:amd64 (6.1+20191019-1) ... Setting up ruby-net-telnet (0.1.1-2) ... Setting up libsigsegv2:amd64 (2.12-2) ... Setting up bsdmainutils (11.1.2+b1) ... 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 libbamtools2.5.1:amd64 (2.5.1+dfsg-5) ... Setting up autopoint (0.19.8.1-10) ... Setting up libbam-dev (0.1.19-4) ... Setting up libk5crypto3:amd64 (1.17-6) ... Setting up lynx-common (2.9.0dev.4-1) ... Setting up libsasl2-2:amd64 (2.1.27+dfsg-2) ... Setting up libbwa-dev (0.7.17-4) ... Setting up libnlopt-cxx0:amd64 (2.6.1-8) ... Setting up liblzma-dev:amd64 (5.2.4-1+b1) ... Setting up zlib1g-dev:amd64 (1:1.2.11.dfsg-2) ... Setting up sensible-utils (0.0.12+nmu1) ... Setting up libhat-trie-dev:amd64 (0.1.2-2) ... Setting up librhash0:amd64 (1.3.9-1) ... Setting up libuchardet0:amd64 (0.0.6-3) ... Setting up libsub-override-perl (0.09-2) ... Setting up libssh2-1:amd64 (1.8.0-2.1) ... Setting up cmake-data (3.16.3-1) ... Setting up libkrb5-3:amd64 (1.17-6) ... Setting up libboost-dev:amd64 (1.67.0.2+b1) ... Setting up libmpdec2:amd64 (2.4.2-2) ... Setting up lynx (2.9.0dev.4-1) ... update-alternatives: using /usr/bin/lynx to provide /usr/bin/www-browser (www-browser) in auto mode Setting up ruby-did-you-mean (1.2.1-1) ... Setting up libnlopt-dev:amd64 (2.6.1-8) ... Setting up openssl (1.1.1d-2) ... Setting up libelf1:amd64 (0.176-1.1) ... Setting up libssw0:amd64 (1.1-9) ... Setting up readline-common (8.0-3) ... Setting up ruby-xmlrpc (0.3.0-2) ... Setting up libxml2:amd64 (2.9.10+dfsg-3) ... Setting up libprocps8:amd64 (2:3.3.16-1+b1) ... Setting up libjsoncpp1:amd64 (1.7.4-3.1) ... Setting up libbz2-dev:amd64 (1.0.8-2) ... Setting up libfile-stripnondeterminism-perl (1.6.3-2) ... Setting up libssw-dev:amd64 (1.1-9) ... Setting up libtool (2.4.6-13) ... Setting up libarchive13:amd64 (3.4.0-1+b1) ... Setting up libreadline8:amd64 (8.0-3) ... Setting up libldap-2.4-2:amd64 (2.4.49+dfsg-1) ... Setting up m4 (1.4.18-4) ... Setting up ca-certificates (20190110) ... Updating certificates in /etc/ssl/certs... 128 added, 0 removed; done. Setting up libnlopt-cxx-dev:amd64 (2.6.1-8) ... Setting up libbamtools-dev:amd64 (2.5.1+dfsg-5) ... Setting up libgssapi-krb5-2:amd64 (1.17-6) ... Setting up libcroco3:amd64 (0.6.13-1) ... Setting up autoconf (2.69-11.1) ... Setting up dh-strip-nondeterminism (1.6.3-2) ... Setting up dwz (0.13-5) ... Setting up groff-base (1.22.4-4) ... Setting up procps (2:3.3.16-1+b1) ... update-alternatives: using /usr/bin/w.procps to provide /usr/bin/w (w) in auto mode Setting up libcurl4:amd64 (7.68.0-1) ... Setting up automake (1:1.16.1-4) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libpython3.7-stdlib:amd64 (3.7.6-1+b1) ... Setting up gettext (0.19.8.1-10) ... Setting up libpython3.7:amd64 (3.7.6-1+b1) ... Setting up libpython3.7-dev:amd64 (3.7.6-1+b1) ... Setting up libcurl3-gnutls:amd64 (7.68.0-1) ... Setting up rubygems-integration (1.16) ... Setting up man-db (2.9.0-2) ... Not building database; man-db/auto-update is not 'true'. Setting up intltool-debian (0.35.0+20060710.5) ... Setting up cmake (3.16.3-1) ... Setting up libpython3-stdlib:amd64 (3.7.5-3) ... Setting up python3.7 (3.7.6-1+b1) ... Setting up libhts3:amd64 (1.10.2-3) ... Setting up libpython3-dev:amd64 (3.7.5-3) ... Setting up po-debconf (1.0.21) ... Setting up libhts-dev:amd64 (1.10.2-3) ... Setting up python3 (3.7.5-3) ... Setting up python3.7-dev (3.7.6-1+b1) ... Setting up python3-lib2to3 (3.8.0-1) ... Setting up python3-pkg-resources (44.0.0-1) ... Setting up python3-distutils (3.8.0-1) ... Setting up dh-python (4.20191017) ... Setting up python3-joblib (0.14.0-3) ... Setting up python3-yaml (5.3-1) ... Setting up python3-dev (3.7.5-3) ... Setting up dh-autoreconf (19) ... Setting up rake (13.0.1-2) ... Setting up libruby2.5:amd64 (2.5.7-1+b1) ... Setting up debhelper (12.9) ... Setting up ruby2.5 (2.5.7-1+b1) ... Setting up ruby (1:2.5.7.1) ... Setting up ruby-asciidoctor (2.0.10-2) ... Setting up asciidoctor (2.0.10-2) ... Setting up sbuild-build-depends-main-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.29-10) ... Processing triggers for ca-certificates (20190110) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (amd64 included in any) +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 4.19.0-6-cloud-amd64 #1 SMP Debian 4.19.67-2+deb10u2 (2019-11-11) amd64 (x86_64) Toolchain package versions: binutils_2.34-3 dpkg-dev_1.19.7 g++-9_9.2.1-30 gcc-9_9.2.1-30 libc6-dev_2.29-10 libstdc++-8-dev_8.3.0-29 libstdc++-9-dev_9.2.1-30 libstdc++6_10-20200222-1 linux-libc-dev_5.4.19-1 Package versions: adduser_3.118 apt_1.8.4 asciidoctor_2.0.10-2 autoconf_2.69-11.1 automake_1:1.16.1-4 autopoint_0.19.8.1-10 autotools-dev_20180224.1 base-files_11 base-passwd_3.5.47 bash_5.0-5 binutils_2.34-3 binutils-common_2.34-3 binutils-x86-64-linux-gnu_2.34-3 bsdmainutils_11.1.2+b1 bsdutils_1:2.34-0.1 build-essential_12.8 bwa_0.7.17-4 bzip2_1.0.8-2 ca-certificates_20190110 clang-8_1:8.0.1-7 cmake_3.16.3-1 cmake-data_3.16.3-1 coreutils_8.30-3+b1 cpp_4:9.2.1-3.1 cpp-9_9.2.1-30 dash_0.5.10.2-6 debconf_1.5.73 debhelper_12.9 debian-archive-keyring_2019.1 debianutils_4.9.1 dh-autoreconf_19 dh-python_4.20191017 dh-strip-nondeterminism_1.6.3-2 diffutils_1:3.7-3 dpkg_1.19.7 dpkg-dev_1.19.7 dwz_0.13-5 e2fsprogs_1.45.5-2 fakeroot_1.24-1 fdisk_2.34-0.1 file_1:5.38-4 findutils_4.7.0-1 g++_4:9.2.1-3.1 g++-9_9.2.1-30 gcc_4:9.2.1-3.1 gcc-10-base_10-20200222-1 gcc-8-base_8.3.0-29 gcc-9_9.2.1-30 gcc-9-base_9.2.1-30 gettext_0.19.8.1-10 gettext-base_0.19.8.1-10 gpgv_2.2.19-1 grep_3.4-1 groff-base_1.22.4-4 gzip_1.9-3+b1 hostname_3.23 init-system-helpers_1.57 intltool-debian_0.35.0+20060710.5 lib32gcc-s1_10-20200222-1 lib32gcc1_1:10-20200222-1 lib32stdc++6_10-20200222-1 libacl1_2.2.53-5 libapt-pkg5.0_1.8.4 libarchive-zip-perl_1.67-1 libarchive13_3.4.0-1+b1 libasan5_9.2.1-30 libatomic1_10-20200222-1 libattr1_1:2.4.48-5 libaudit-common_1:2.8.5-2 libaudit1_1:2.8.5-2+b1 libbam-dev_0.1.19-4 libbamtools-dev_2.5.1+dfsg-5 libbamtools2.5.1_2.5.1+dfsg-5 libbinutils_2.34-3 libblkid1_2.34-0.1 libboost-dev_1.67.0.2+b1 libboost1.67-dev_1.67.0-17 libbrotli1_1.0.7-6 libbsd0_0.10.0-1 libbwa-dev_0.7.17-4 libbz2-1.0_1.0.8-2 libbz2-dev_1.0.8-2 libc-bin_2.29-10 libc-dev-bin_2.29-10 libc6_2.29-10 libc6-dev_2.29-10 libc6-i386_2.29-10 libcap-ng0_0.7.9-2.1+b1 libcc1-0_10-20200222-1 libclang-common-8-dev_1:8.0.1-7 libclang1-8_1:8.0.1-7 libcom-err2_1.45.5-2 libcroco3_0.6.13-1 libcrypt-dev_1:4.4.10-10 libcrypt1_1:4.4.10-10 libctf-nobfd0_2.34-3 libctf0_2.34-3 libcurl3-gnutls_7.68.0-1 libcurl4_7.68.0-1 libdb5.3_5.3.28+dfsg1-0.6 libdebconfclient0_0.251 libdebhelper-perl_12.9 libdeflate0_1.5-3 libdpkg-perl_1.19.7 libedit2_3.1-20191231-1 libelf1_0.176-1.1 libexpat1_2.2.9-1 libexpat1-dev_2.2.9-1 libext2fs2_1.45.5-2 libfakeroot_1.24-1 libfdisk1_2.34-0.1 libffi7_3.3-3 libfile-stripnondeterminism-perl_1.6.3-2 libgc1c2_1:7.6.4-0.4 libgcc-8-dev_8.3.0-29 libgcc-9-dev_9.2.1-30 libgcc-s1_10-20200222-1 libgcc1_1:10-20200222-1 libgcrypt20_1.8.5-5 libgdbm-compat4_1.18.1-5 libgdbm6_1.18.1-5 libglib2.0-0_2.62.4-2 libgmp10_2:6.2.0+dfsg-4 libgnutls30_3.6.12-2 libgomp1_10-20200222-1 libgpg-error0_1.37-1 libgssapi-krb5-2_1.17-6 libhat-trie-dev_0.1.2-2 libhat-trie0_0.1.2-2 libhogweed5_3.5.1+really3.5.1-2 libhts-dev_1.10.2-3 libhts3_1.10.2-3 libicu63_63.2-2 libidn11_1.33-2.2 libidn2-0_2.2.0-2 libisl22_0.22.1-1 libitm1_10-20200222-1 libjsoncpp1_1.7.4-3.1 libk5crypto3_1.17-6 libkeyutils1_1.6.1-2 libkrb5-3_1.17-6 libkrb5support0_1.17-6 libldap-2.4-2_2.4.49+dfsg-1 libldap-common_2.4.49+dfsg-1 libllvm8_1:8.0.1-7 liblsan0_10-20200222-1 liblz4-1_1.9.2-2 liblzma-dev_5.2.4-1+b1 liblzma5_5.2.4-1+b1 libmagic-mgc_1:5.38-4 libmagic1_1:5.38-4 libmount1_2.34-0.1 libmpc3_1.1.0-1 libmpdec2_2.4.2-2 libmpfr6_4.0.2-1 libmpx2_8.3.0-29 libncurses6_6.1+20191019-1 libncursesw6_6.1+20191019-1 libnettle7_3.5.1+really3.5.1-2 libnghttp2-14_1.40.0-1 libnlopt-cxx-dev_2.6.1-8 libnlopt-cxx0_2.6.1-8 libnlopt-dev_2.6.1-8 libnlopt0_2.6.1-8 libobjc-8-dev_8.3.0-29 libobjc-9-dev_9.2.1-30 libobjc4_10-20200222-1 libomp-8-dev_1:8.0.1-7 libomp5-8_1:8.0.1-7 libp11-kit0_0.23.20-1 libpam-modules_1.3.1-5 libpam-modules-bin_1.3.1-5 libpam-runtime_1.3.1-5 libpam0g_1.3.1-5 libpcre2-8-0_10.34-7 libpcre3_2:8.39-12+b1 libperl5.30_5.30.0-9 libpipeline1_1.5.2-2 libprocps8_2:3.3.16-1+b1 libpsl5_0.20.2-2 libpython3-dev_3.7.5-3 libpython3-stdlib_3.7.5-3 libpython3.7_3.7.6-1+b1 libpython3.7-dev_3.7.6-1+b1 libpython3.7-minimal_3.7.6-1+b1 libpython3.7-stdlib_3.7.6-1+b1 libquadmath0_10-20200222-1 libreadline8_8.0-3 librhash0_1.3.9-1 librtmp1_2.4+20151223.gitfa8646d.1-2+b1 libruby2.5_2.5.7-1+b1 libsasl2-2_2.1.27+dfsg-2 libsasl2-modules-db_2.1.27+dfsg-2 libseccomp2_2.4.2-2 libselinux1_3.0-1+b1 libsemanage-common_3.0-1 libsemanage1_3.0-1+b1 libsepol1_3.0-1 libsigsegv2_2.12-2 libsmartcols1_2.34-0.1 libsqlite3-0_3.31.1-3 libss2_1.45.5-2 libssh2-1_1.8.0-2.1 libssl1.1_1.1.1d-2 libssw-dev_1.1-9 libssw0_1.1-9 libstdc++-8-dev_8.3.0-29 libstdc++-9-dev_9.2.1-30 libstdc++6_10-20200222-1 libsub-override-perl_0.09-2 libsystemd0_244.3-1 libtasn1-6_4.16.0-2 libtinfo6_6.1+20191019-1 libtool_2.4.6-13 libtsan0_10-20200222-1 libubsan1_10-20200222-1 libuchardet0_0.0.6-3 libudev1_244.3-1 libunistring2_0.9.10-2 libuuid1_2.34-0.1 libuv1_1.34.2-1 libxml2_2.9.10+dfsg-3 libyaml-0-2_0.2.2-1 libzstd1_1.4.4+dfsg-3 linux-libc-dev_5.4.19-1 login_1:4.8.1-1 logsave_1.45.5-2 lsb-base_11.1.0 lynx_2.9.0dev.4-1 lynx-common_2.9.0dev.4-1 m4_1.4.18-4 make_4.2.1-1.2 man-db_2.9.0-2 mawk_1.3.4.20200120-2 mime-support_3.64 mount_2.34-0.1 ncurses-base_6.1+20191019-1 ncurses-bin_6.1+20191019-1 openssl_1.1.1d-2 passwd_1:4.8.1-1 patch_2.7.6-6 perl_5.30.0-9 perl-base_5.30.0-9 perl-modules-5.30_5.30.0-9 po-debconf_1.0.21 procps_2:3.3.16-1+b1 python3_3.7.5-3 python3-dev_3.7.5-3 python3-distutils_3.8.0-1 python3-joblib_0.14.0-3 python3-lib2to3_3.8.0-1 python3-minimal_3.7.5-3 python3-pkg-resources_44.0.0-1 python3-yaml_5.3-1 python3.7_3.7.6-1+b1 python3.7-dev_3.7.6-1+b1 python3.7-minimal_3.7.6-1+b1 rake_13.0.1-2 readline-common_8.0-3 ruby_1:2.5.7.1 ruby-asciidoctor_2.0.10-2 ruby-did-you-mean_1.2.1-1 ruby-minitest_5.13.0-1 ruby-net-telnet_0.1.1-2 ruby-power-assert_1.1.5-1 ruby-test-unit_3.3.4-1 ruby-xmlrpc_0.3.0-2 ruby2.5_2.5.7-1+b1 rubygems-integration_1.16 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.7-1 sensible-utils_0.0.12+nmu1 sysvinit-utils_2.96-2.1 tar_1.30+dfsg-6+b1 tzdata_2019c-3 util-linux_2.34-0.1 xz-utils_5.2.4-1+b1 zlib1g_1:1.2.11.dfsg-2 zlib1g-dev_1:1.2.11.dfsg-2 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 3.0 (quilt) Source: spades Binary: spades Architecture: any Version: 3.13.1+dfsg-2 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille , Sascha Steinbiss , Michael R. Crusoe , Alexandre Mestiashvili Homepage: http://cab.spbu.ru/software/spades/ Standards-Version: 4.4.1 Vcs-Browser: https://salsa.debian.org/med-team/spades Vcs-Git: https://salsa.debian.org/med-team/spades.git Testsuite: autopkgtest Testsuite-Triggers: bwa Build-Depends: debhelper-compat (= 12), dh-python, cmake, python3-dev, zlib1g-dev, libbz2-dev, libboost-dev, libbam-dev, libbamtools-dev, libhat-trie-dev, libhts-dev, libnlopt-dev, libnlopt-cxx-dev, libssw-dev, python3-yaml, python3-joblib, asciidoctor (>= 1.5.3), bwa, libbwa-dev, lynx Package-List: spades deb science optional arch=any Checksums-Sha1: aa60dc1801d228263308bbe922122a2f8f626fa0 3202920 spades_3.13.1+dfsg.orig.tar.xz b047ce53afb5be865de76bbd885817c017f96052 25176 spades_3.13.1+dfsg-2.debian.tar.xz Checksums-Sha256: 7d2daf3b02df7b1c83de4e86659cf54a0d754271e8cb8d9d934e2d3d0fcfbb52 3202920 spades_3.13.1+dfsg.orig.tar.xz ca19c4897b971cc3fe6537f4cfebf2b9323131c13fad5e50186896e33e6832cd 25176 spades_3.13.1+dfsg-2.debian.tar.xz Files: a0b3101b8c70cf9e7db5fba88ce1c737 3202920 spades_3.13.1+dfsg.orig.tar.xz 63afd9fc4b5255c7feed13dee1490530 25176 spades_3.13.1+dfsg-2.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJCBAEBCAAsFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAl3XrzIOHHRpbGxlYUBy a2kuZGUACgkQV4oElNHGRtFn1g/+NQ5Q5Id/wMAscYIsVUNF+SiolFiL2+brB1oQ ob5vicQLgNv6dFVx4rL/b2nApEI4hz3aBHoXNnA7b56v/smS03+EZ/wFmwTkC6t3 fV6I0UwFRlnNPbgoriHOReYUzaaZD8O5T3muIroRzPrX/nSmxGlBgqr++gnu9uVC rqm6x6KgZuMNEbZuM5oWQ0aMlOZLPYKpoFY/Dj3Esq6Mj4NX+fksXhRMh1/sF64a EwsMTkcEHM9s4ru7ACeyoZA7bvks4efhIIt9wopGDOh7iru8cbzqzJJgIWbcvbgP iZNI+ZWzS/jSTn+cvjMNYXEUMbpJM8qMF3ay1zTM4XY4dT3U4FUbyZAN6bcHeGH9 z5P2rDxIDzvjlbO8/6LAhcQJg2ZkDZFADWsERfHHtCRujbFDNbcAQ2mMMlmjdLfm T1qjsDPUAVjsR0HL8oOw54QSPGELKlrr0NJ9tSk4mjztGEc5BjnxpG/8jAzQ/Taw J49psfmRFugtxWp5oNWt0k0aPeOfjLuBRHVegqxM1rv9ATEkzQZm8M70faGIMZ/G XZJYclCBmyfEMXNTMH4gWdurX5l7FFetq/dPGTGiTBMe78QcD1mUb2VJJNj+VYbA ArQSBXKz8CqBeebDSwzAEwQnUP/8vo7P1HKI4tafGH8HUdRFmXoypnuinp5Xltju +ETJ1Ak= =DpSK -----END PGP SIGNATURE----- gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/sbuild-nonexistent/.gnupg/trustedkeys.kbx': General error gpgv: Signature made Fri Nov 22 09:49:38 2019 UTC gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tillea@rki.de" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./spades_3.13.1+dfsg-2.dsc dpkg-source: info: extracting spades in /<> dpkg-source: info: unpacking spades_3.13.1+dfsg.orig.tar.xz dpkg-source: info: unpacking spades_3.13.1+dfsg-2.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series 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 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 0118_adjust_spades_home_again.patch dpkg-source: info: applying fix-bool-cast dpkg-source: info: applying spelling dpkg-source: info: applying gcc7.patch dpkg-source: info: applying python3.patch dpkg-source: info: applying yaml_load.patch Check disk space ---------------- Sufficient free space for build User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf HOME=/sbuild-nonexistent LANG=C.UTF-8 LC_ALL=C.UTF-8 LOGNAME=user42 PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games SCHROOT_ALIAS_NAME=unstable SCHROOT_CHROOT_NAME=sid-amd64-sbuild SCHROOT_COMMAND=env SCHROOT_GID=1001 SCHROOT_GROUP=user42 SCHROOT_SESSION_ID=sid-amd64-sbuild-ba1160bb-6c90-46aa-a5f8-b86052e5e083 SCHROOT_UID=1001 SCHROOT_USER=user42 SHELL=/bin/sh USER=user42 dpkg-buildpackage ----------------- Command: dpkg-buildpackage -us -uc -b -rfakeroot dpkg-buildpackage: info: source package spades dpkg-buildpackage: info: source version 3.13.1+dfsg-2 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 fakeroot debian/rules clean dh clean --with python3 --sourcedirectory=assembler/src --buildsystem=cmake debian/rules override_dh_auto_clean make[1]: Entering directory '/<>' dh_auto_clean rm -rf build_spades rm -rf install_spades rm -rf spades_test find . -name "*.pyc" -delete rm -rf /<>/debian/man_src/*.html /<>/debian/man_src/*.? rm -rf /<>/debian/man make[1]: Leaving directory '/<>' dh_autoreconf_clean -O--sourcedirectory=assembler/src -O--buildsystem=cmake debian/rules override_dh_clean make[1]: Entering directory '/<>' dh_clean -X.orig make[1]: Leaving directory '/<>' debian/rules build dh build --with python3 --sourcedirectory=assembler/src --buildsystem=cmake dh_update_autotools_config -O--sourcedirectory=assembler/src -O--buildsystem=cmake dh_autoreconf -O--sourcedirectory=assembler/src -O--buildsystem=cmake debian/rules override_dh_auto_configure make[1]: Entering directory '/<>' echo "Simply use spades_compile.sh in auto_build" Simply use spades_compile.sh in auto_build make[1]: Leaving directory '/<>' debian/rules override_dh_auto_build make[1]: Entering directory '/<>' cd assembler && PREFIX=/<>/install_spades ./spades_compile.sh CMake Warning (dev) in CMakeLists.txt: No project() command is present. The top-level CMakeLists.txt file must contain a literal, direct call to the project() command. Add a line of code such as project(ProjectName) near the top of the file, but after cmake_minimum_required(). CMake is pretending there is a "project(Project)" command on the first line. This warning is for project developers. Use -Wno-dev to suppress it. -- The C compiler identification is Clang 8.0.1 -- The CXX compiler identification is Clang 8.0.1 -- 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 CMake Warning (dev) at cmake/options.cmake:56 (set): implicitly converting 'INTEGER' to 'STRING' type. Call Stack (most recent call first): CMakeLists.txt:38 (include) This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at cmake/options.cmake:57 (set): implicitly converting 'INTEGER' to 'STRING' type. Call Stack (most recent call first): CMakeLists.txt:38 (include) This warning is for project developers. Use -Wno-dev to suppress it. -- Found OpenMP_C: -fopenmp=libomp (found version "3.1") -- Found OpenMP_CXX: -fopenmp=libomp (found version "3.1") -- Found OpenMP: TRUE (found version "3.1") -- Found ZLIB: /usr/lib/x86_64-linux-gnu/libz.so (found version "1.2.11") -- Found BZip2: /usr/lib/x86_64-linux-gnu/libbz2.so (found version "1.0.8") -- Looking for BZ2_bzCompressInit -- Looking for BZ2_bzCompressInit - found -- Could NOT find readline (missing: READLINE_INCLUDE_DIR READLINE_LIBRARY) -- Found Boost: /usr/include (found version "1.67.0") Making Release Configuration... Building SPAdes from N/A, sha: N/A -- Looking for include file features.h -- Looking for include file features.h - found -- Looking for include file sys/cdefs.h -- Looking for include file sys/cdefs.h - found -- Looking for atomic_fetchadd_long -- Looking for atomic_fetchadd_long - not found -- Looking for OSAtomicAdd64 -- Looking for OSAtomicAdd64 - not found -- Looking for OSSpinLockLock -- Looking for OSSpinLockLock - not found -- Looking for _malloc_thread_cleanup -- Looking for _malloc_thread_cleanup - not found -- Looking for _pthread_mutex_init_calloc_cb, -- Looking for _pthread_mutex_init_calloc_cb, - not found -- Looking for sbrk -- Looking for sbrk - found -- Performing Test JEMALLOC_TLS_MODEL_SUPPORTED -- Performing Test JEMALLOC_TLS_MODEL_SUPPORTED - Success -- Looking for sys/types.h -- Looking for sys/types.h - found -- Looking for stdint.h -- Looking for stdint.h - found -- Looking for stddef.h -- Looking for stddef.h - found -- Check size of void* -- Check size of void* - done -- Performing Test JEMALLOC_TLS -- Performing Test JEMALLOC_TLS - Success -- Looking for memalign -- Looking for memalign - found -- Looking for valloc -- Looking for valloc - found -- Check size of int -- Check size of int - done -- Check size of long -- Check size of long - done -- Check size of intmax_t -- Check size of intmax_t - done -- 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: /<>/assembler/build_spades make[2]: Entering directory '/<>/assembler/build_spades' /usr/bin/cmake -S/<>/assembler/src -B/<>/assembler/build_spades --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /<>/assembler/build_spades/CMakeFiles /<>/assembler/build_spades/CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[3]: Entering directory '/<>/assembler/build_spades' make -f ext/jemalloc/CMakeFiles/jemalloc.dir/build.make ext/jemalloc/CMakeFiles/jemalloc.dir/depend make[4]: Entering directory '/<>/assembler/build_spades' cd /<>/assembler/build_spades && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/assembler/src /<>/assembler/ext/src/jemalloc /<>/assembler/build_spades /<>/assembler/build_spades/ext/jemalloc /<>/assembler/build_spades/ext/jemalloc/CMakeFiles/jemalloc.dir/DependInfo.cmake --color= Dependee "/<>/assembler/build_spades/ext/jemalloc/CMakeFiles/jemalloc.dir/DependInfo.cmake" is newer than depender "/<>/assembler/build_spades/ext/jemalloc/CMakeFiles/jemalloc.dir/depend.internal". Dependee "/<>/assembler/build_spades/ext/jemalloc/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/<>/assembler/build_spades/ext/jemalloc/CMakeFiles/jemalloc.dir/depend.internal". Scanning dependencies of target jemalloc make[4]: Leaving directory '/<>/assembler/build_spades' make -f ext/jemalloc/CMakeFiles/jemalloc.dir/build.make ext/jemalloc/CMakeFiles/jemalloc.dir/build make[4]: Entering directory '/<>/assembler/build_spades' [ 1%] Building C object ext/jemalloc/CMakeFiles/jemalloc.dir/arena.c.o cd /<>/assembler/build_spades/ext/jemalloc && /usr/bin/cc -DUSE_GLIBCXX_PARALLEL=1 -D_GNU_SOURCE -D_REENTRANT -I/<>/assembler/build_spades/ext/jemalloc -I/<>/assembler/ext/src/jemalloc -I/<>/assembler/src/include -I/<>/assembler/build_spades/include -I/<>/assembler/src -I/<>/assembler/src/common -isystem /<>/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp=libomp -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -O3 -funroll-loops -o CMakeFiles/jemalloc.dir/arena.c.o -c /<>/assembler/ext/src/jemalloc/arena.c [ 1%] Building C object ext/jemalloc/CMakeFiles/jemalloc.dir/base.c.o cd /<>/assembler/build_spades/ext/jemalloc && /usr/bin/cc -DUSE_GLIBCXX_PARALLEL=1 -D_GNU_SOURCE -D_REENTRANT -I/<>/assembler/build_spades/ext/jemalloc -I/<>/assembler/ext/src/jemalloc -I/<>/assembler/src/include -I/<>/assembler/build_spades/include -I/<>/assembler/src -I/<>/assembler/src/common -isystem /<>/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp=libomp -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -O3 -funroll-loops -o CMakeFiles/jemalloc.dir/base.c.o -c /<>/assembler/ext/src/jemalloc/base.c [ 1%] Building C object ext/jemalloc/CMakeFiles/jemalloc.dir/chunk.c.o cd /<>/assembler/build_spades/ext/jemalloc && /usr/bin/cc -DUSE_GLIBCXX_PARALLEL=1 -D_GNU_SOURCE -D_REENTRANT -I/<>/assembler/build_spades/ext/jemalloc -I/<>/assembler/ext/src/jemalloc -I/<>/assembler/src/include -I/<>/assembler/build_spades/include -I/<>/assembler/src -I/<>/assembler/src/common -isystem /<>/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp=libomp -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -O3 -funroll-loops -o CMakeFiles/jemalloc.dir/chunk.c.o -c /<>/assembler/ext/src/jemalloc/chunk.c [ 2%] Building C object ext/jemalloc/CMakeFiles/jemalloc.dir/chunk_mmap.c.o cd /<>/assembler/build_spades/ext/jemalloc && /usr/bin/cc -DUSE_GLIBCXX_PARALLEL=1 -D_GNU_SOURCE -D_REENTRANT -I/<>/assembler/build_spades/ext/jemalloc -I/<>/assembler/ext/src/jemalloc -I/<>/assembler/src/include -I/<>/assembler/build_spades/include -I/<>/assembler/src -I/<>/assembler/src/common -isystem /<>/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp=libomp -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -O3 -funroll-loops -o CMakeFiles/jemalloc.dir/chunk_mmap.c.o -c /<>/assembler/ext/src/jemalloc/chunk_mmap.c [ 2%] Building C object ext/jemalloc/CMakeFiles/jemalloc.dir/ctl.c.o cd /<>/assembler/build_spades/ext/jemalloc && /usr/bin/cc -DUSE_GLIBCXX_PARALLEL=1 -D_GNU_SOURCE -D_REENTRANT -I/<>/assembler/build_spades/ext/jemalloc -I/<>/assembler/ext/src/jemalloc -I/<>/assembler/src/include -I/<>/assembler/build_spades/include -I/<>/assembler/src -I/<>/assembler/src/common -isystem /<>/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp=libomp -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -O3 -funroll-loops -o CMakeFiles/jemalloc.dir/ctl.c.o -c /<>/assembler/ext/src/jemalloc/ctl.c [ 2%] Building C object ext/jemalloc/CMakeFiles/jemalloc.dir/hash.c.o cd /<>/assembler/build_spades/ext/jemalloc && /usr/bin/cc -DUSE_GLIBCXX_PARALLEL=1 -D_GNU_SOURCE -D_REENTRANT -I/<>/assembler/build_spades/ext/jemalloc -I/<>/assembler/ext/src/jemalloc -I/<>/assembler/src/include -I/<>/assembler/build_spades/include -I/<>/assembler/src -I/<>/assembler/src/common -isystem /<>/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp=libomp -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -O3 -funroll-loops -o CMakeFiles/jemalloc.dir/hash.c.o -c /<>/assembler/ext/src/jemalloc/hash.c [ 3%] Building C object ext/jemalloc/CMakeFiles/jemalloc.dir/jemalloc.c.o cd /<>/assembler/build_spades/ext/jemalloc && /usr/bin/cc -DUSE_GLIBCXX_PARALLEL=1 -D_GNU_SOURCE -D_REENTRANT -I/<>/assembler/build_spades/ext/jemalloc -I/<>/assembler/ext/src/jemalloc -I/<>/assembler/src/include -I/<>/assembler/build_spades/include -I/<>/assembler/src -I/<>/assembler/src/common -isystem /<>/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp=libomp -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -O3 -funroll-loops -o CMakeFiles/jemalloc.dir/jemalloc.c.o -c /<>/assembler/ext/src/jemalloc/jemalloc.c [ 3%] Building C object ext/jemalloc/CMakeFiles/jemalloc.dir/mutex.c.o cd /<>/assembler/build_spades/ext/jemalloc && /usr/bin/cc -DUSE_GLIBCXX_PARALLEL=1 -D_GNU_SOURCE -D_REENTRANT -I/<>/assembler/build_spades/ext/jemalloc -I/<>/assembler/ext/src/jemalloc -I/<>/assembler/src/include -I/<>/assembler/build_spades/include -I/<>/assembler/src -I/<>/assembler/src/common -isystem /<>/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp=libomp -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -O3 -funroll-loops -o CMakeFiles/jemalloc.dir/mutex.c.o -c /<>/assembler/ext/src/jemalloc/mutex.c [ 3%] Building C object ext/jemalloc/CMakeFiles/jemalloc.dir/quarantine.c.o cd /<>/assembler/build_spades/ext/jemalloc && /usr/bin/cc -DUSE_GLIBCXX_PARALLEL=1 -D_GNU_SOURCE -D_REENTRANT -I/<>/assembler/build_spades/ext/jemalloc -I/<>/assembler/ext/src/jemalloc -I/<>/assembler/src/include -I/<>/assembler/build_spades/include -I/<>/assembler/src -I/<>/assembler/src/common -isystem /<>/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp=libomp -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -O3 -funroll-loops -o CMakeFiles/jemalloc.dir/quarantine.c.o -c /<>/assembler/ext/src/jemalloc/quarantine.c [ 4%] Building C object ext/jemalloc/CMakeFiles/jemalloc.dir/stats.c.o cd /<>/assembler/build_spades/ext/jemalloc && /usr/bin/cc -DUSE_GLIBCXX_PARALLEL=1 -D_GNU_SOURCE -D_REENTRANT -I/<>/assembler/build_spades/ext/jemalloc -I/<>/assembler/ext/src/jemalloc -I/<>/assembler/src/include -I/<>/assembler/build_spades/include -I/<>/assembler/src -I/<>/assembler/src/common -isystem /<>/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp=libomp -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -O3 -funroll-loops -o CMakeFiles/jemalloc.dir/stats.c.o -c /<>/assembler/ext/src/jemalloc/stats.c [ 4%] Building C object ext/jemalloc/CMakeFiles/jemalloc.dir/tsd.c.o cd /<>/assembler/build_spades/ext/jemalloc && /usr/bin/cc -DUSE_GLIBCXX_PARALLEL=1 -D_GNU_SOURCE -D_REENTRANT -I/<>/assembler/build_spades/ext/jemalloc -I/<>/assembler/ext/src/jemalloc -I/<>/assembler/src/include -I/<>/assembler/build_spades/include -I/<>/assembler/src -I/<>/assembler/src/common -isystem /<>/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp=libomp -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -O3 -funroll-loops -o CMakeFiles/jemalloc.dir/tsd.c.o -c /<>/assembler/ext/src/jemalloc/tsd.c [ 5%] Building C object ext/jemalloc/CMakeFiles/jemalloc.dir/atomic.c.o cd /<>/assembler/build_spades/ext/jemalloc && /usr/bin/cc -DUSE_GLIBCXX_PARALLEL=1 -D_GNU_SOURCE -D_REENTRANT -I/<>/assembler/build_spades/ext/jemalloc -I/<>/assembler/ext/src/jemalloc -I/<>/assembler/src/include -I/<>/assembler/build_spades/include -I/<>/assembler/src -I/<>/assembler/src/common -isystem /<>/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp=libomp -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -O3 -funroll-loops -o CMakeFiles/jemalloc.dir/atomic.c.o -c /<>/assembler/ext/src/jemalloc/atomic.c [ 5%] Building C object ext/jemalloc/CMakeFiles/jemalloc.dir/bitmap.c.o cd /<>/assembler/build_spades/ext/jemalloc && /usr/bin/cc -DUSE_GLIBCXX_PARALLEL=1 -D_GNU_SOURCE -D_REENTRANT -I/<>/assembler/build_spades/ext/jemalloc -I/<>/assembler/ext/src/jemalloc 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-DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -O3 -funroll-loops -o CMakeFiles/jemalloc.dir/chunk_dss.c.o -c /<>/assembler/ext/src/jemalloc/chunk_dss.c [ 7%] Building C object ext/jemalloc/CMakeFiles/jemalloc.dir/ckh.c.o cd /<>/assembler/build_spades/ext/jemalloc && /usr/bin/cc -DUSE_GLIBCXX_PARALLEL=1 -D_GNU_SOURCE -D_REENTRANT -I/<>/assembler/build_spades/ext/jemalloc -I/<>/assembler/ext/src/jemalloc -I/<>/assembler/src/include -I/<>/assembler/build_spades/include -I/<>/assembler/src -I/<>/assembler/src/common -isystem /<>/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp=libomp -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -O3 -funroll-loops -o CMakeFiles/jemalloc.dir/ckh.c.o -c /<>/assembler/ext/src/jemalloc/ckh.c [ 7%] Building C object ext/jemalloc/CMakeFiles/jemalloc.dir/extent.c.o cd /<>/assembler/build_spades/ext/jemalloc && /usr/bin/cc -DUSE_GLIBCXX_PARALLEL=1 -D_GNU_SOURCE -D_REENTRANT -I/<>/assembler/build_spades/ext/jemalloc -I/<>/assembler/ext/src/jemalloc -I/<>/assembler/src/include -I/<>/assembler/build_spades/include -I/<>/assembler/src -I/<>/assembler/src/common -isystem /<>/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp=libomp -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -O3 -funroll-loops -o CMakeFiles/jemalloc.dir/extent.c.o -c /<>/assembler/ext/src/jemalloc/extent.c [ 7%] Building C object ext/jemalloc/CMakeFiles/jemalloc.dir/huge.c.o cd /<>/assembler/build_spades/ext/jemalloc && /usr/bin/cc -DUSE_GLIBCXX_PARALLEL=1 -D_GNU_SOURCE -D_REENTRANT -I/<>/assembler/build_spades/ext/jemalloc -I/<>/assembler/ext/src/jemalloc -I/<>/assembler/src/include -I/<>/assembler/build_spades/include -I/<>/assembler/src -I/<>/assembler/src/common -isystem /<>/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp=libomp -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -O3 -funroll-loops -o CMakeFiles/jemalloc.dir/huge.c.o -c /<>/assembler/ext/src/jemalloc/huge.c [ 8%] Building C object ext/jemalloc/CMakeFiles/jemalloc.dir/mb.c.o cd /<>/assembler/build_spades/ext/jemalloc && /usr/bin/cc -DUSE_GLIBCXX_PARALLEL=1 -D_GNU_SOURCE -D_REENTRANT -I/<>/assembler/build_spades/ext/jemalloc -I/<>/assembler/ext/src/jemalloc -I/<>/assembler/src/include -I/<>/assembler/build_spades/include -I/<>/assembler/src -I/<>/assembler/src/common -isystem /<>/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp=libomp -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -O3 -funroll-loops -o CMakeFiles/jemalloc.dir/mb.c.o -c /<>/assembler/ext/src/jemalloc/mb.c [ 8%] Building C object ext/jemalloc/CMakeFiles/jemalloc.dir/prof.c.o cd /<>/assembler/build_spades/ext/jemalloc && /usr/bin/cc -DUSE_GLIBCXX_PARALLEL=1 -D_GNU_SOURCE -D_REENTRANT -I/<>/assembler/build_spades/ext/jemalloc -I/<>/assembler/ext/src/jemalloc -I/<>/assembler/src/include -I/<>/assembler/build_spades/include -I/<>/assembler/src -I/<>/assembler/src/common -isystem /<>/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp=libomp -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -O3 -funroll-loops -o CMakeFiles/jemalloc.dir/prof.c.o -c /<>/assembler/ext/src/jemalloc/prof.c [ 8%] Building C object ext/jemalloc/CMakeFiles/jemalloc.dir/rtree.c.o cd /<>/assembler/build_spades/ext/jemalloc && /usr/bin/cc -DUSE_GLIBCXX_PARALLEL=1 -D_GNU_SOURCE -D_REENTRANT -I/<>/assembler/build_spades/ext/jemalloc -I/<>/assembler/ext/src/jemalloc -I/<>/assembler/src/include -I/<>/assembler/build_spades/include -I/<>/assembler/src -I/<>/assembler/src/common -isystem /<>/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp=libomp -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -O3 -funroll-loops -o CMakeFiles/jemalloc.dir/rtree.c.o -c /<>/assembler/ext/src/jemalloc/rtree.c [ 9%] Building C object ext/jemalloc/CMakeFiles/jemalloc.dir/tcache.c.o cd /<>/assembler/build_spades/ext/jemalloc && /usr/bin/cc -DUSE_GLIBCXX_PARALLEL=1 -D_GNU_SOURCE -D_REENTRANT -I/<>/assembler/build_spades/ext/jemalloc -I/<>/assembler/ext/src/jemalloc -I/<>/assembler/src/include -I/<>/assembler/build_spades/include -I/<>/assembler/src -I/<>/assembler/src/common -isystem /<>/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp=libomp -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -O3 -funroll-loops -o CMakeFiles/jemalloc.dir/tcache.c.o -c /<>/assembler/ext/src/jemalloc/tcache.c [ 9%] Building C object ext/jemalloc/CMakeFiles/jemalloc.dir/util.c.o cd /<>/assembler/build_spades/ext/jemalloc && /usr/bin/cc -DUSE_GLIBCXX_PARALLEL=1 -D_GNU_SOURCE -D_REENTRANT -I/<>/assembler/build_spades/ext/jemalloc -I/<>/assembler/ext/src/jemalloc -I/<>/assembler/src/include -I/<>/assembler/build_spades/include -I/<>/assembler/src -I/<>/assembler/src/common -isystem /<>/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp=libomp -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -O3 -funroll-loops -o CMakeFiles/jemalloc.dir/util.c.o -c /<>/assembler/ext/src/jemalloc/util.c [ 9%] Linking C static library libjemalloc.a cd /<>/assembler/build_spades/ext/jemalloc && /usr/bin/cmake -P CMakeFiles/jemalloc.dir/cmake_clean_target.cmake cd /<>/assembler/build_spades/ext/jemalloc && /usr/bin/cmake -E cmake_link_script CMakeFiles/jemalloc.dir/link.txt --verbose=1 /usr/bin/ar qc libjemalloc.a CMakeFiles/jemalloc.dir/arena.c.o CMakeFiles/jemalloc.dir/base.c.o CMakeFiles/jemalloc.dir/chunk.c.o CMakeFiles/jemalloc.dir/chunk_mmap.c.o CMakeFiles/jemalloc.dir/ctl.c.o CMakeFiles/jemalloc.dir/hash.c.o CMakeFiles/jemalloc.dir/jemalloc.c.o CMakeFiles/jemalloc.dir/mutex.c.o CMakeFiles/jemalloc.dir/quarantine.c.o CMakeFiles/jemalloc.dir/stats.c.o CMakeFiles/jemalloc.dir/tsd.c.o CMakeFiles/jemalloc.dir/atomic.c.o CMakeFiles/jemalloc.dir/bitmap.c.o CMakeFiles/jemalloc.dir/chunk_dss.c.o CMakeFiles/jemalloc.dir/ckh.c.o CMakeFiles/jemalloc.dir/extent.c.o CMakeFiles/jemalloc.dir/huge.c.o CMakeFiles/jemalloc.dir/mb.c.o CMakeFiles/jemalloc.dir/prof.c.o CMakeFiles/jemalloc.dir/rtree.c.o CMakeFiles/jemalloc.dir/tcache.c.o CMakeFiles/jemalloc.dir/util.c.o /usr/bin/ranlib libjemalloc.a make[4]: Leaving directory '/<>/assembler/build_spades' [ 9%] Built target jemalloc make -f ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/build.make ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/depend make[4]: Entering directory '/<>/assembler/build_spades' cd /<>/assembler/build_spades && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/assembler/src /<>/assembler/ext/src/ConsensusCore /<>/assembler/build_spades /<>/assembler/build_spades/ext/ConsensusCore /<>/assembler/build_spades/ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/DependInfo.cmake --color= Dependee "/<>/assembler/build_spades/ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/DependInfo.cmake" is newer than depender "/<>/assembler/build_spades/ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/depend.internal". Dependee "/<>/assembler/build_spades/ext/ConsensusCore/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/<>/assembler/build_spades/ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/depend.internal". Scanning dependencies of target ConsensusCore make[4]: Leaving directory '/<>/assembler/build_spades' make -f ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/build.make ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/build make[4]: Entering directory '/<>/assembler/build_spades' [ 9%] Building CXX object ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/AffineAlignment.cpp.o cd /<>/assembler/build_spades/ext/ConsensusCore && /usr/bin/c++ -DUSE_GLIBCXX_PARALLEL=1 -I/<>/assembler/build_spades/ext/ConsensusCore -I/<>/assembler/ext/src/ConsensusCore -I/<>/assembler/src/include -I/<>/assembler/build_spades/include -I/<>/assembler/src -I/<>/assembler/src/common -I/<>/assembler/src/../ext/include/ConsensusCore -isystem /<>/assembler/src/../ext/include -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp=libomp -std=c++14 -stdlib=libc++ -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -o CMakeFiles/ConsensusCore.dir/AffineAlignment.cpp.o -c /<>/assembler/ext/src/ConsensusCore/AffineAlignment.cpp In file included from /<>/assembler/ext/src/ConsensusCore/AffineAlignment.cpp:38: /<>/assembler/src/../ext/include/ConsensusCore/AffineAlignment.hpp:44:10: fatal error: 'string' file not found #include ^~~~~~~~ 1 error generated. make[4]: *** [ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/build.make:63: ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/AffineAlignment.cpp.o] Error 1 make[4]: Leaving directory '/<>/assembler/build_spades' make[3]: *** [CMakeFiles/Makefile2:1164: ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/all] Error 2 make[3]: Leaving directory '/<>/assembler/build_spades' make[2]: *** [Makefile:152: all] Error 2 make[2]: Leaving directory '/<>/assembler/build_spades' make[1]: *** [debian/rules:42: override_dh_auto_build] Error 2 make[1]: Leaving directory '/<>' make: *** [debian/rules:24: build] Error 2 dpkg-buildpackage: error: debian/rules build subprocess returned exit status 2 -------------------------------------------------------------------------------- Build finished at 2020-02-25T12:21:04Z Finished -------- +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not cleaning session: cloned chroot in use E: Build failure (dpkg-buildpackage died) +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: amd64 Build Type: binary Build-Space: 30852 Build-Time: 13 Distribution: unstable Fail-Stage: build Host Architecture: amd64 Install-Time: 18 Job: spades_3.13.1+dfsg-2 Machine Architecture: amd64 Package: spades Package-Time: 47 Source-Version: 3.13.1+dfsg-2 Space: 30852 Status: attempted Version: 3.13.1+dfsg-2 -------------------------------------------------------------------------------- Finished at 2020-02-25T12:21:04Z Build needed 00:00:47, 30852k disk space E: Build failure (dpkg-buildpackage died) DC-Status: Failed 48.279186436s DC-Time-Estimation: 48.279186436 versus expected 1476 (r/m: 29.572180456201753 ; m: 48.279186436)