https://launchpad.net/ubuntu/+source/spades/3.13.0+dfsg-1/+build/15636794 RUN: /usr/share/launchpad-buildd/slavebin/slave-prep Forking launchpad-buildd slave process... Kernel version: Linux lcy01-amd64-024 4.4.0-140-generic #166-Ubuntu SMP Wed Nov 14 20:09:47 UTC 2018 x86_64 Buildd toolchain package versions: launchpad-buildd_165 python-lpbuildd_165 sbuild_0.67.0-2ubuntu7.1 bzr-builder_0.7.3+bzr174~ppa13~ubuntu14.10.1 bzr_2.7.0-2ubuntu3.1 git-build-recipe_0.3.4~git201611291343.dcee459~ubuntu16.04.1 git_1:2.7.4-0ubuntu1.6 dpkg-dev_1.18.4ubuntu1.5 python-debian_0.1.27ubuntu2. Syncing the system clock with the buildd NTP service... 8 Dec 12:29:57 ntpdate[1812]: adjust time server 10.211.37.1 offset 0.000698 sec RUN: /usr/share/launchpad-buildd/slavebin/in-target unpack-chroot --backend=chroot --series=disco --arch=amd64 PACKAGEBUILD-15636794 /home/buildd/filecache-default/b71572c9405b6ce6ff1d1ad001cf764bb07f52ae Creating target for build PACKAGEBUILD-15636794 RUN: /usr/share/launchpad-buildd/slavebin/in-target mount-chroot --backend=chroot --series=disco --arch=amd64 PACKAGEBUILD-15636794 Starting target for build PACKAGEBUILD-15636794 RUN: /usr/share/launchpad-buildd/slavebin/in-target override-sources-list --backend=chroot --series=disco --arch=amd64 PACKAGEBUILD-15636794 'deb http://ftpmaster.internal/ubuntu disco main universe' 'deb http://ftpmaster.internal/ubuntu disco-security main universe' 'deb http://ftpmaster.internal/ubuntu disco-updates main universe' 'deb http://ftpmaster.internal/ubuntu disco-proposed main universe' Overriding sources.list in build-PACKAGEBUILD-15636794 RUN: /usr/share/launchpad-buildd/slavebin/in-target update-debian-chroot --backend=chroot --series=disco --arch=amd64 PACKAGEBUILD-15636794 Updating target for build PACKAGEBUILD-15636794 Get:1 http://ftpmaster.internal/ubuntu disco InRelease [243 kB] Get:2 http://ftpmaster.internal/ubuntu disco-security InRelease [65.4 kB] Get:3 http://ftpmaster.internal/ubuntu disco-updates InRelease [65.4 kB] Get:4 http://ftpmaster.internal/ubuntu disco-proposed InRelease [93.2 kB] Get:5 http://ftpmaster.internal/ubuntu disco/main amd64 Packages [1006 kB] Get:6 http://ftpmaster.internal/ubuntu disco/main Translation-en [509 kB] Get:7 http://ftpmaster.internal/ubuntu disco/universe amd64 Packages [8944 kB] Get:8 http://ftpmaster.internal/ubuntu disco/universe Translation-en [5138 kB] Get:9 http://ftpmaster.internal/ubuntu disco-proposed/main amd64 Packages [118 kB] Get:10 http://ftpmaster.internal/ubuntu disco-proposed/main Translation-en [47.6 kB] Get:11 http://ftpmaster.internal/ubuntu disco-proposed/universe amd64 Packages [319 kB] Get:12 http://ftpmaster.internal/ubuntu disco-proposed/universe Translation-en [165 kB] Fetched 16.7 MB in 7s (2523 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages were automatically installed and are no longer required: libgdbm5 libperl5.26 perl-modules-5.26 Use 'sudo apt autoremove' to remove them. The following NEW packages will be installed: libgdbm6 libperl5.28 perl-modules-5.28 The following packages will be upgraded: apt base-files binutils binutils-common binutils-x86-64-linux-gnu cpp cpp-8 dash dmsetup dpkg dpkg-dev e2fslibs e2fsprogs fakeroot findutils g++ g++-8 gcc gcc-8 gcc-8-base grep hostname init init-system-helpers libapparmor1 libapt-pkg5.0 libasan5 libatomic1 libaudit-common libaudit1 libbinutils libcap-ng0 libcc1-0 libcom-err2 libcomerr2 libdb5.3 libdevmapper1.02.1 libdpkg-perl libext2fs2 libfakeroot libffi6 libgcc-8-dev libgcc1 libgcrypt20 libgdbm-compat4 libgmp10 libgnutls30 libgomp1 libgpg-error0 libhogweed4 libip4tc0 libitm1 libkmod2 liblsan0 libmpfr6 libmpx2 libnettle6 libquadmath0 libseccomp2 libselinux1 libsemanage-common libsemanage1 libsqlite3-0 libss2 libssl1.1 libstdc++-8-dev libstdc++6 libsystemd0 libtsan0 libubsan1 libudev1 linux-libc-dev lockfile-progs openssl perl perl-base sed systemd systemd-sysv tar tzdata 81 upgraded, 3 newly installed, 0 to remove and 0 not upgraded. Need to get 55.6 MB of archives. After this operation, 48.9 MB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu disco/main amd64 base-files amd64 10.1ubuntu8 [60.1 kB] Get:2 http://ftpmaster.internal/ubuntu disco/main amd64 tar amd64 1.30+dfsg-3 [242 kB] Get:3 http://ftpmaster.internal/ubuntu disco-proposed/main amd64 dpkg amd64 1.19.2ubuntu2 [1101 kB] Get:4 http://ftpmaster.internal/ubuntu disco/main amd64 dash amd64 0.5.10.2-1 [89.3 kB] Get:5 http://ftpmaster.internal/ubuntu disco/main amd64 findutils amd64 4.6.0+git+20181018-1 [295 kB] Get:6 http://ftpmaster.internal/ubuntu disco/main amd64 grep amd64 3.1-3 [152 kB] Get:7 http://ftpmaster.internal/ubuntu disco/main amd64 hostname amd64 3.21 [11.2 kB] Get:8 http://ftpmaster.internal/ubuntu disco-proposed/main amd64 perl-modules-5.28 all 5.28.1-3 [2812 kB] Get:9 http://ftpmaster.internal/ubuntu disco/main amd64 libgdbm6 amd64 1.18.1-2 [27.6 kB] Get:10 http://ftpmaster.internal/ubuntu disco/main amd64 libgdbm-compat4 amd64 1.18.1-2 [6152 B] Get:11 http://ftpmaster.internal/ubuntu disco-proposed/main amd64 libperl5.28 amd64 5.28.1-3 [3820 kB] Get:12 http://ftpmaster.internal/ubuntu disco-proposed/main amd64 perl amd64 5.28.1-3 [204 kB] Get:13 http://ftpmaster.internal/ubuntu disco-proposed/main amd64 perl-base amd64 5.28.1-3 [1513 kB] Get:14 http://ftpmaster.internal/ubuntu disco/main amd64 libdb5.3 amd64 5.3.28+dfsg1-0.2 [672 kB] Get:15 http://ftpmaster.internal/ubuntu disco/main amd64 sed amd64 4.5-2 [186 kB] Get:16 http://ftpmaster.internal/ubuntu disco/main amd64 init-system-helpers all 1.56 [38.8 kB] Get:17 http://ftpmaster.internal/ubuntu disco-proposed/main amd64 libquadmath0 amd64 8.2.0-11ubuntu1 [134 kB] Get:18 http://ftpmaster.internal/ubuntu disco-proposed/main amd64 libubsan1 amd64 8.2.0-11ubuntu1 [121 kB] Get:19 http://ftpmaster.internal/ubuntu disco-proposed/main amd64 gcc-8-base amd64 8.2.0-11ubuntu1 [18.6 kB] Get:20 http://ftpmaster.internal/ubuntu disco-proposed/main amd64 libgcc1 amd64 1:8.2.0-11ubuntu1 [40.8 kB] Get:21 http://ftpmaster.internal/ubuntu disco-proposed/main amd64 libitm1 amd64 8.2.0-11ubuntu1 [28.1 kB] Get:22 http://ftpmaster.internal/ubuntu disco-proposed/main amd64 libasan5 amd64 8.2.0-11ubuntu1 [364 kB] Get:23 http://ftpmaster.internal/ubuntu disco-proposed/main amd64 libgomp1 amd64 8.2.0-11ubuntu1 [76.4 kB] Get:24 http://ftpmaster.internal/ubuntu disco-proposed/main amd64 libatomic1 amd64 8.2.0-11ubuntu1 [9072 B] Get:25 http://ftpmaster.internal/ubuntu disco-proposed/main amd64 liblsan0 amd64 8.2.0-11ubuntu1 [132 kB] Get:26 http://ftpmaster.internal/ubuntu disco-proposed/main amd64 libtsan0 amd64 8.2.0-11ubuntu1 [288 kB] Get:27 http://ftpmaster.internal/ubuntu disco-proposed/main amd64 libmpx2 amd64 8.2.0-11ubuntu1 [11.7 kB] Get:28 http://ftpmaster.internal/ubuntu disco-proposed/main amd64 cpp-8 amd64 8.2.0-11ubuntu1 [7222 kB] Get:29 http://ftpmaster.internal/ubuntu disco-proposed/main amd64 libcc1-0 amd64 8.2.0-11ubuntu1 [39.5 kB] Get:30 http://ftpmaster.internal/ubuntu disco-proposed/main amd64 gcc-8 amd64 8.2.0-11ubuntu1 [8003 kB] Get:31 http://ftpmaster.internal/ubuntu disco-proposed/main amd64 g++-8 amd64 8.2.0-11ubuntu1 [8112 kB] Get:32 http://ftpmaster.internal/ubuntu disco-proposed/main amd64 libstdc++-8-dev amd64 8.2.0-11ubuntu1 [1539 kB] Get:33 http://ftpmaster.internal/ubuntu disco-proposed/main amd64 libgcc-8-dev amd64 8.2.0-11ubuntu1 [2304 kB] Get:34 http://ftpmaster.internal/ubuntu disco-proposed/main amd64 libstdc++6 amd64 8.2.0-11ubuntu1 [399 kB] Get:35 http://ftpmaster.internal/ubuntu disco/main amd64 libgmp10 amd64 2:6.1.2+dfsg-4 [236 kB] Get:36 http://ftpmaster.internal/ubuntu disco/main amd64 libmpfr6 amd64 4.0.1-2 [241 kB] Get:37 http://ftpmaster.internal/ubuntu disco/main amd64 libbinutils amd64 2.31.1-10ubuntu1 [482 kB] Get:38 http://ftpmaster.internal/ubuntu disco/main amd64 binutils-common amd64 2.31.1-10ubuntu1 [194 kB] Get:39 http://ftpmaster.internal/ubuntu disco/main amd64 binutils amd64 2.31.1-10ubuntu1 [3396 B] Get:40 http://ftpmaster.internal/ubuntu disco/main amd64 binutils-x86-64-linux-gnu amd64 2.31.1-10ubuntu1 [1830 kB] Get:41 http://ftpmaster.internal/ubuntu disco/main amd64 libudev1 amd64 239-7ubuntu15 [54.7 kB] Get:42 http://ftpmaster.internal/ubuntu disco/main amd64 libapt-pkg5.0 amd64 1.8.0~alpha2ubuntu1 [814 kB] Get:43 http://ftpmaster.internal/ubuntu disco/main amd64 libnettle6 amd64 3.4.1~rc1-1 [111 kB] Get:44 http://ftpmaster.internal/ubuntu disco/main amd64 libhogweed4 amd64 3.4.1~rc1-1 [140 kB] Get:45 http://ftpmaster.internal/ubuntu disco/main amd64 libgnutls30 amd64 3.6.4-2ubuntu2 [747 kB] Get:46 http://ftpmaster.internal/ubuntu disco/main amd64 libseccomp2 amd64 2.3.3-3ubuntu2 [38.9 kB] Get:47 http://ftpmaster.internal/ubuntu disco/main amd64 apt amd64 1.8.0~alpha2ubuntu1 [1182 kB] Get:48 http://ftpmaster.internal/ubuntu disco/main amd64 systemd-sysv amd64 239-7ubuntu15 [9396 B] Get:49 http://ftpmaster.internal/ubuntu disco/main amd64 libapparmor1 amd64 2.12-4ubuntu10 [29.9 kB] Get:50 http://ftpmaster.internal/ubuntu disco/main amd64 libaudit-common all 1:2.8.3-1ubuntu3 [4068 B] Get:51 http://ftpmaster.internal/ubuntu disco/main amd64 libcap-ng0 amd64 0.7.9-1build1 [10.9 kB] Get:52 http://ftpmaster.internal/ubuntu disco/main amd64 libaudit1 amd64 1:2.8.3-1ubuntu3 [38.8 kB] Get:53 http://ftpmaster.internal/ubuntu disco/main amd64 libgpg-error0 amd64 1.32-3 [56.0 kB] Get:54 http://ftpmaster.internal/ubuntu disco/main amd64 libkmod2 amd64 25-1ubuntu2 [41.7 kB] Get:55 http://ftpmaster.internal/ubuntu disco/main amd64 systemd amd64 239-7ubuntu15 [2971 kB] Get:56 http://ftpmaster.internal/ubuntu disco/main amd64 libsystemd0 amd64 239-7ubuntu15 [212 kB] Get:57 http://ftpmaster.internal/ubuntu disco/main amd64 libext2fs2 amd64 1.44.4-2ubuntu1 [159 kB] Get:58 http://ftpmaster.internal/ubuntu disco/main amd64 e2fsprogs amd64 1.44.4-2ubuntu1 [513 kB] Get:59 http://ftpmaster.internal/ubuntu disco/main amd64 init amd64 1.56 [6652 B] Get:60 http://ftpmaster.internal/ubuntu disco/main amd64 libgcrypt20 amd64 1.8.4-3ubuntu1 [420 kB] Get:61 http://ftpmaster.internal/ubuntu disco/main amd64 libselinux1 amd64 2.8-1build2 [68.6 kB] Get:62 http://ftpmaster.internal/ubuntu disco/main amd64 libsemanage-common all 2.8-1build2 [6892 B] Get:63 http://ftpmaster.internal/ubuntu disco/main amd64 libsemanage1 amd64 2.8-1build2 [85.1 kB] Get:64 http://ftpmaster.internal/ubuntu disco/main amd64 libffi6 amd64 3.2.1-9 [18.1 kB] Get:65 http://ftpmaster.internal/ubuntu disco/main amd64 libcom-err2 amd64 1.44.4-2ubuntu1 [8844 B] Get:66 http://ftpmaster.internal/ubuntu disco/main amd64 libss2 amd64 1.44.4-2ubuntu1 [11.1 kB] Get:67 http://ftpmaster.internal/ubuntu disco/main amd64 libdevmapper1.02.1 amd64 2:1.02.145-4.1ubuntu4 [127 kB] Get:68 http://ftpmaster.internal/ubuntu disco/main amd64 dmsetup amd64 2:1.02.145-4.1ubuntu4 [74.6 kB] Get:69 http://ftpmaster.internal/ubuntu disco-proposed/main amd64 libip4tc0 amd64 1.6.1-2ubuntu3 [19.7 kB] Get:70 http://ftpmaster.internal/ubuntu disco/main amd64 libsqlite3-0 amd64 3.26.0-2 [530 kB] Get:71 http://ftpmaster.internal/ubuntu disco/main amd64 libssl1.1 amd64 1.1.1a-1ubuntu2 [1297 kB] Get:72 http://ftpmaster.internal/ubuntu disco/main amd64 openssl amd64 1.1.1a-1ubuntu2 [618 kB] Get:73 http://ftpmaster.internal/ubuntu disco/main amd64 tzdata all 2018g-1 [188 kB] Get:74 http://ftpmaster.internal/ubuntu disco/main amd64 g++ amd64 4:8.2.0-2ubuntu2 [1608 B] Get:75 http://ftpmaster.internal/ubuntu disco/main amd64 gcc amd64 4:8.2.0-2ubuntu2 [5224 B] Get:76 http://ftpmaster.internal/ubuntu disco/main amd64 cpp amd64 4:8.2.0-2ubuntu2 [27.6 kB] Get:77 http://ftpmaster.internal/ubuntu disco-proposed/main amd64 dpkg-dev all 1.19.2ubuntu2 [549 kB] Get:78 http://ftpmaster.internal/ubuntu disco-proposed/main amd64 libdpkg-perl all 1.19.2ubuntu2 [227 kB] Get:79 http://ftpmaster.internal/ubuntu disco/main amd64 e2fslibs amd64 1.44.4-2ubuntu1 [2712 B] Get:80 http://ftpmaster.internal/ubuntu disco/main amd64 libfakeroot amd64 1.23-1 [25.3 kB] Get:81 http://ftpmaster.internal/ubuntu disco/main amd64 fakeroot amd64 1.23-1 [62.4 kB] Get:82 http://ftpmaster.internal/ubuntu disco/main amd64 libcomerr2 amd64 1.44.4-2ubuntu1 [2712 B] Get:83 http://ftpmaster.internal/ubuntu disco-proposed/main amd64 linux-libc-dev amd64 4.19.0-8.9 [1036 kB] Get:84 http://ftpmaster.internal/ubuntu disco/main amd64 lockfile-progs amd64 0.1.18 [9872 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 55.6 MB in 3s (18.4 MB/s) (Reading database ... 12650 files and directories currently installed.) 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Processing triggers for libc-bin (2.28-0ubuntu1) ... RUN: /usr/share/launchpad-buildd/slavebin/sbuild-package PACKAGEBUILD-15636794 amd64 disco-proposed -c chroot:build-PACKAGEBUILD-15636794 --arch=amd64 --dist=disco-proposed --nolog -A spades_3.13.0+dfsg-1.dsc Initiating build PACKAGEBUILD-15636794 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 4.4.0-140-generic #166-Ubuntu SMP Wed Nov 14 20:09:47 UTC 2018 x86_64 sbuild (Debian sbuild) 0.67.0 (26 Dec 2015) on lcy01-amd64-024.buildd +==============================================================================+ | spades 3.13.0+dfsg-1 (amd64) 08 Dec 2018 12:31 | +==============================================================================+ Package: spades Version: 3.13.0+dfsg-1 Source Version: 3.13.0+dfsg-1 Distribution: disco-proposed Machine Architecture: amd64 Host Architecture: amd64 Build Architecture: amd64 I: NOTICE: Log filtering will replace 'build/spades-3qnaY_/spades-3.13.0+dfsg' with '<>' I: NOTICE: Log filtering will replace 'build/spades-3qnaY_' with '<>' I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-15636794/chroot-autobuild' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- spades_3.13.0+dfsg-1.dsc exists in .; copying to chroot Check architectures ------------------- Check dependencies ------------------ Merged Build-Depends: build-essential, fakeroot Filtered Build-Depends: build-essential, fakeroot dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/<>/resolver-mwKo0a/apt_archive/sbuild-build-depends-core-dummy.deb'. Ign:1 copy:/<>/resolver-mwKo0a/apt_archive ./ InRelease Get:2 copy:/<>/resolver-mwKo0a/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-mwKo0a/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-mwKo0a/apt_archive ./ Sources [214 B] Get:5 copy:/<>/resolver-mwKo0a/apt_archive ./ Packages [528 B] Fetched 2861 B in 0s (121 kB/s) Reading package lists... Reading package lists... +------------------------------------------------------------------------------+ | Install core build dependencies (apt-based resolver) | +------------------------------------------------------------------------------+ Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following packages were automatically installed and are no longer required: libgdbm5 libperl5.26 perl-modules-5.26 Use 'apt autoremove' to remove them. The following NEW packages will be installed: sbuild-build-depends-core-dummy 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 852 B of archives. After this operation, 0 B of additional disk space will be used. Get:1 copy:/<>/resolver-mwKo0a/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [852 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 852 B in 0s (0 B/s) Selecting previously unselected package sbuild-build-depends-core-dummy. (Reading database ... 14507 files and directories currently installed.) Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_amd64.deb ... Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ... Setting up sbuild-build-depends-core-dummy (0.invalid.0) ... Merged Build-Depends: debhelper (>= 11~), dh-python, cmake, python-all-dev, zlib1g-dev, libbz2-dev, libboost-dev, libbam-dev, libbamtools-dev, libjemalloc-dev, libhat-trie-dev, libhts-dev, libnlopt-dev, libnlopt-cxx-dev, libssw-dev, python-yaml, python-joblib, asciidoctor (>= 1.5.3), bwa, libbwa-dev, lynx Filtered Build-Depends: debhelper (>= 11~), dh-python, cmake, python-all-dev, zlib1g-dev, libbz2-dev, libboost-dev, libbam-dev, libbamtools-dev, libjemalloc-dev, libhat-trie-dev, libhts-dev, libnlopt-dev, libnlopt-cxx-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-Q9hAib/apt_archive/sbuild-build-depends-spades-dummy.deb'. Ign:1 copy:/<>/resolver-Q9hAib/apt_archive ./ InRelease Get:2 copy:/<>/resolver-Q9hAib/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-Q9hAib/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-Q9hAib/apt_archive ./ Sources [322 B] Get:5 copy:/<>/resolver-Q9hAib/apt_archive ./ Packages [646 B] Fetched 3087 B in 0s (126 kB/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 packages were automatically installed and are no longer required: libgdbm5 libperl5.26 perl-modules-5.26 Use 'apt autoremove' to remove them. The following additional packages will be installed: asciidoctor autoconf automake autopoint autotools-dev bsdmainutils bwa cmake cmake-data debhelper dh-autoreconf dh-python dh-strip-nondeterminism dwz file gettext gettext-base groff-base intltool-debian libarchive-zip-perl libarchive13 libasn1-8-heimdal libbam-dev libbamtools-dev libbamtools2.5.1 libboost-dev libboost1.67-dev libbsd0 libbwa-dev libbz2-dev libcroco3 libcurl3-gnutls libcurl4 libelf1 libexpat1 libexpat1-dev libfile-stripnondeterminism-perl libglib2.0-0 libgssapi-krb5-2 libgssapi3-heimdal libhat-trie-dev libhat-trie0 libhcrypto4-heimdal libheimbase1-heimdal libheimntlm0-heimdal libhts-dev libhts2 libhx509-5-heimdal libicu63 libjemalloc-dev libjemalloc2 libjsoncpp1 libk5crypto3 libkeyutils1 libkrb5-26-heimdal libkrb5-3 libkrb5support0 libldap-2.4-2 libldap-common liblzma-dev liblzo2-2 libmagic-mgc libmagic1 libmpdec2 libnghttp2-14 libnlopt-cxx-dev libnlopt-cxx0 libnlopt-dev libnlopt0 libpipeline1 libpsl5 libpython-all-dev libpython-dev libpython-stdlib libpython2-dev libpython2-stdlib libpython2.7 libpython2.7-dev libpython2.7-minimal libpython2.7-stdlib libpython3-stdlib libpython3.7-minimal libpython3.7-stdlib librhash0 libroken18-heimdal librtmp1 libruby2.5 libsasl2-2 libsasl2-modules-db libsigsegv2 libssw-dev libssw0 libtool libuv1 libwind0-heimdal libxml2 libyaml-0-2 lynx lynx-common m4 man-db mime-support po-debconf python python-all python-all-dev python-dev python-joblib python-minimal python-yaml python2 python2-dev python2-minimal python2.7 python2.7-dev python2.7-minimal python3 python3-distutils python3-lib2to3 python3-minimal python3.7 python3.7-minimal rake ruby ruby-asciidoctor ruby-did-you-mean ruby-minitest ruby-net-telnet ruby-power-assert ruby-test-unit ruby-xmlrpc ruby2.5 rubygems-integration 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-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 python-doc python-tk python2-doc python2.7-doc binfmt-support python3-doc python3-tk python3-venv python3.7-venv python3.7-doc ri ruby-dev bundler Recommended packages: bzip2-doc libarchive-cpio-perl libglib2.0-data shared-mime-info xdg-user-dirs krb5-locales publicsuffix libsasl2-modules libltdl-dev libmail-sendmail-perl python-numpy python-pytest python-simplejson python-lz4 python-psutil zip fonts-lato libjs-jquery The following NEW packages will be installed: asciidoctor autoconf automake autopoint autotools-dev bsdmainutils bwa cmake cmake-data debhelper dh-autoreconf dh-python dh-strip-nondeterminism dwz file gettext gettext-base groff-base intltool-debian libarchive-zip-perl libarchive13 libasn1-8-heimdal libbam-dev libbamtools-dev libbamtools2.5.1 libboost-dev libboost1.67-dev libbsd0 libbwa-dev libbz2-dev libcroco3 libcurl3-gnutls libcurl4 libelf1 libexpat1 libexpat1-dev libfile-stripnondeterminism-perl libglib2.0-0 libgssapi-krb5-2 libgssapi3-heimdal libhat-trie-dev libhat-trie0 libhcrypto4-heimdal libheimbase1-heimdal libheimntlm0-heimdal libhts-dev libhts2 libhx509-5-heimdal libicu63 libjemalloc-dev libjemalloc2 libjsoncpp1 libk5crypto3 libkeyutils1 libkrb5-26-heimdal libkrb5-3 libkrb5support0 libldap-2.4-2 libldap-common liblzma-dev liblzo2-2 libmagic-mgc libmagic1 libmpdec2 libnghttp2-14 libnlopt-cxx-dev libnlopt-cxx0 libnlopt-dev libnlopt0 libpipeline1 libpsl5 libpython-all-dev libpython-dev libpython-stdlib libpython2-dev libpython2-stdlib libpython2.7 libpython2.7-dev libpython2.7-minimal libpython2.7-stdlib libpython3-stdlib libpython3.7-minimal libpython3.7-stdlib librhash0 libroken18-heimdal librtmp1 libruby2.5 libsasl2-2 libsasl2-modules-db libsigsegv2 libssw-dev libssw0 libtool libuv1 libwind0-heimdal libxml2 libyaml-0-2 lynx lynx-common m4 man-db mime-support po-debconf python python-all python-all-dev python-dev python-joblib python-minimal python-yaml python2 python2-dev python2-minimal python2.7 python2.7-dev python2.7-minimal python3 python3-distutils python3-lib2to3 python3-minimal python3.7 python3.7-minimal rake 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-spades-dummy zlib1g-dev 0 upgraded, 135 newly installed, 0 to remove and 0 not upgraded. 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http://ftpmaster.internal/ubuntu disco/main amd64 python-yaml amd64 3.13-1 [123 kB] Get:134 http://ftpmaster.internal/ubuntu disco/universe amd64 libjemalloc-dev amd64 5.1.0-1 [325 kB] Get:135 http://ftpmaster.internal/ubuntu disco/universe amd64 lynx amd64 2.8.9rel.1-2 [632 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 83.0 MB in 4s (19.3 MB/s) Selecting previously unselected package libpython3.7-minimal:amd64. 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Setting up ruby-xmlrpc (0.3.0-2) ... Setting up libarchive-zip-perl (1.64-1) ... Setting up libnghttp2-14:amd64 (1.35.0-1) ... Setting up mime-support (3.60ubuntu1) ... Setting up libicu63:amd64 (63.1-5) ... Setting up libsigsegv2:amd64 (2.12-2) ... Setting up libldap-common (2.4.46+dfsg-5ubuntu3) ... Setting up libssw0:amd64 (1.1-2) ... Setting up libuv1:amd64 (1.24.0-1) ... Setting up libpsl5:amd64 (0.20.2-2) ... Setting up libelf1:amd64 (0.175-1) ... Setting up groff-base (1.22.3-10) ... Setting up libglib2.0-0:amd64 (2.58.1-2) ... No schema files found: doing nothing. Setting up libsasl2-modules-db:amd64 (2.1.27~101-g0780600+dfsg-3ubuntu2) ... Setting up libnlopt-cxx0:amd64 (2.4.2+dfsg-8build1) ... Setting up libsasl2-2:amd64 (2.1.27~101-g0780600+dfsg-3ubuntu2) ... Setting up libssw-dev:amd64 (1.1-2) ... Setting up gettext-base (0.19.8.1-9) ... Setting up cmake-data (3.12.3-3) ... Setting up libpipeline1:amd64 (1.5.0-2) ... Setting up libroken18-heimdal:amd64 (7.5.0+dfsg-2.1) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2) ... Setting up m4 (1.4.18-2) ... Setting up libbsd0:amd64 (0.9.1-1) ... Setting up libkrb5support0:amd64 (1.16.1-1ubuntu1) ... Setting up libjemalloc-dev (5.1.0-1) ... Setting up libxml2:amd64 (2.9.4+dfsg1-7ubuntu3) ... Setting up libmagic-mgc (1:5.34-2) ... Setting up libmagic1:amd64 (1:5.34-2) ... Setting up librhash0:amd64 (1.3.6-3) ... Setting up libcroco3:amd64 (0.6.12-2) ... Setting up ruby-did-you-mean (1.2.1-1) ... Setting up libyaml-0-2:amd64 (0.2.1-1) ... Processing triggers for libc-bin (2.28-0ubuntu1) ... Setting up dwz (0.12-2) ... Setting up autotools-dev (20180224.1) ... Setting up libboost1.67-dev:amd64 (1.67.0-11) ... Setting up libheimbase1-heimdal:amd64 (7.5.0+dfsg-2.1) ... Setting up libbamtools2.5.1:amd64 (2.5.1+dfsg-3) ... Setting up ruby-net-telnet (0.1.1-2) ... Setting up libbam-dev (0.1.19-4) ... Setting up rubygems-integration (1.11) ... Setting up libexpat1-dev:amd64 (2.2.6-1) ... Setting up libbwa-dev (0.7.17-2) ... Setting up libboost-dev:amd64 (1.67.0.1) ... Setting up liblzma-dev:amd64 (5.2.2-1.3) ... Setting up libkeyutils1:amd64 (1.5.9-9.3) ... Setting up bsdmainutils (11.1.2ubuntu2) ... update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode Setting up ruby-minitest (5.11.3-1) ... Setting up lynx-common (2.8.9rel.1-2) ... Setting up libnlopt0:amd64 (2.4.2+dfsg-8build1) ... Setting up libpython2.7-stdlib:amd64 (2.7.15-5) ... Setting up autopoint (0.19.8.1-9) ... Setting up libmpdec2:amd64 (2.4.2-2) ... Setting up libhat-trie0:amd64 (0.1.2-1) ... Setting up liblzo2-2:amd64 (2.10-0.1) ... Setting up ruby-power-assert (1.1.1-1) ... Setting up lynx (2.8.9rel.1-2) ... update-alternatives: using /usr/bin/lynx to provide /usr/bin/www-browser (www-browser) in auto mode Setting up zlib1g-dev:amd64 (1:1.2.11.dfsg-0ubuntu2) ... Setting up libfile-stripnondeterminism-perl (1.0.0-1) ... Setting up libjsoncpp1:amd64 (1.7.4-3) ... Setting up libk5crypto3:amd64 (1.16.1-1ubuntu1) ... Setting up libpython3.7-stdlib:amd64 (3.7.1-1) ... Setting up libwind0-heimdal:amd64 (7.5.0+dfsg-2.1) ... Setting up ruby-test-unit (3.2.8-1) ... Setting up gettext (0.19.8.1-9) ... Setting up libarchive13:amd64 (3.2.2-5) ... Setting up libasn1-8-heimdal:amd64 (7.5.0+dfsg-2.1) ... Setting up libbamtools-dev:amd64 (2.5.1+dfsg-3) ... Setting up libhcrypto4-heimdal:amd64 (7.5.0+dfsg-2.1) ... Setting up python2.7 (2.7.15-5) ... Setting up python3.7 (3.7.1-1) ... Setting up autoconf (2.69-11) ... Setting up file (1:5.34-2) ... Setting up libhx509-5-heimdal:amd64 (7.5.0+dfsg-2.1) ... Setting up libhat-trie-dev:amd64 (0.1.2-1) ... Setting up intltool-debian (0.35.0+20060710.4) ... Setting up libnlopt-dev:amd64 (2.4.2+dfsg-8build1) ... Setting up libpython2.7:amd64 (2.7.15-5) ... 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 man-db (2.8.4-3) ... Not building database; man-db/auto-update is not 'true'. Setting up libpython2-stdlib:amd64 (2.7.15-3) ... Setting up libkrb5-3:amd64 (1.16.1-1ubuntu1) ... Setting up libpython2.7-dev:amd64 (2.7.15-5) ... Setting up libkrb5-26-heimdal:amd64 (7.5.0+dfsg-2.1) ... Setting up python2.7-dev (2.7.15-5) ... Setting up libheimntlm0-heimdal:amd64 (7.5.0+dfsg-2.1) ... Setting up libtool (2.4.6-6) ... Setting up libpython3-stdlib:amd64 (3.7.1-1ubuntu1) ... Setting up po-debconf (1.0.21) ... Setting up python3 (3.7.1-1ubuntu1) ... Setting up libnlopt-cxx-dev:amd64 (2.4.2+dfsg-8build1) ... Setting up python2 (2.7.15-3) ... Setting up libgssapi-krb5-2:amd64 (1.16.1-1ubuntu1) ... Setting up libpython2-dev:amd64 (2.7.15-3) ... Setting up libpython-stdlib:amd64 (2.7.15-3) ... Setting up python2-dev (2.7.15-3) ... Setting up libgssapi3-heimdal:amd64 (7.5.0+dfsg-2.1) ... Setting up python3-lib2to3 (3.7.1-1ubuntu4) ... Setting up python3-distutils (3.7.1-1ubuntu4) ... Setting up python (2.7.15-3) ... Setting up libpython-dev:amd64 (2.7.15-3) ... Setting up python-yaml (3.13-1) ... Setting up python-dev (2.7.15-3) ... Setting up python-joblib (0.13.0-1) ... Setting up libpython-all-dev:amd64 (2.7.15-3) ... Setting up libldap-2.4-2:amd64 (2.4.46+dfsg-5ubuntu3) ... Setting up dh-python (3.20180927ubuntu2) ... Setting up python-all (2.7.15-3) ... Setting up libcurl3-gnutls:amd64 (7.61.0-1ubuntu2.2) ... Setting up libcurl4:amd64 (7.61.0-1ubuntu2.2) ... Setting up python-all-dev (2.7.15-3) ... Setting up cmake (3.12.3-3) ... Setting up libhts2:amd64 (1.9-6) ... Setting up libhts-dev:amd64 (1.9-6) ... Setting up libruby2.5:amd64 (2.5.3-3ubuntu1) ... Setting up dh-autoreconf (19) ... Setting up dh-strip-nondeterminism (1.0.0-1) ... Setting up debhelper (11.5.3ubuntu1) ... Setting up ruby2.5 (2.5.3-3ubuntu1) ... Setting up ruby (1:2.5.1) ... Setting up rake (12.3.1-3) ... Setting up ruby-asciidoctor (1.5.8-1) ... Setting up asciidoctor (1.5.8-1) ... Setting up sbuild-build-depends-spades-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.28-0ubuntu1) ... +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 4.4.0-140-generic amd64 (x86_64) Toolchain package versions: binutils_2.31.1-10ubuntu1 dpkg-dev_1.19.2ubuntu2 g++-8_8.2.0-11ubuntu1 gcc-8_8.2.0-11ubuntu1 libc6-dev_2.28-0ubuntu1 libstdc++-8-dev_8.2.0-11ubuntu1 libstdc++6_8.2.0-11ubuntu1 linux-libc-dev_4.19.0-8.9 Package versions: adduser_3.117ubuntu1 advancecomp_2.1-1 apt_1.8.0~alpha2ubuntu1 asciidoctor_1.5.8-1 autoconf_2.69-11 automake_1:1.16.1-4 autopoint_0.19.8.1-9 autotools-dev_20180224.1 base-files_10.1ubuntu8 base-passwd_3.5.45 bash_4.4.18-2ubuntu3 binutils_2.31.1-10ubuntu1 binutils-common_2.31.1-10ubuntu1 binutils-x86-64-linux-gnu_2.31.1-10ubuntu1 bsdmainutils_11.1.2ubuntu2 bsdutils_1:2.32-0.1ubuntu2 build-essential_12.5ubuntu2 bwa_0.7.17-2 bzip2_1.0.6-9 ca-certificates_20180409 cmake_3.12.3-3 cmake-data_3.12.3-3 coreutils_8.28-1ubuntu2 cpp_4:8.2.0-2ubuntu2 cpp-8_8.2.0-11ubuntu1 dash_0.5.10.2-1 debconf_1.5.69 debhelper_11.5.3ubuntu1 debianutils_4.8.6 dh-autoreconf_19 dh-python_3.20180927ubuntu2 dh-strip-nondeterminism_1.0.0-1 diffutils_1:3.6-1 dmsetup_2:1.02.145-4.1ubuntu4 dpkg_1.19.2ubuntu2 dpkg-dev_1.19.2ubuntu2 dwz_0.12-2 e2fslibs_1.44.4-2ubuntu1 e2fsprogs_1.44.4-2ubuntu1 fakeroot_1.23-1 fdisk_2.32-0.1ubuntu2 file_1:5.34-2 findutils_4.6.0+git+20181018-1 g++_4:8.2.0-2ubuntu2 g++-8_8.2.0-11ubuntu1 gcc_4:8.2.0-2ubuntu2 gcc-8_8.2.0-11ubuntu1 gcc-8-base_8.2.0-11ubuntu1 gettext_0.19.8.1-9 gettext-base_0.19.8.1-9 gpg_2.2.8-3ubuntu1 gpg-agent_2.2.8-3ubuntu1 gpgconf_2.2.8-3ubuntu1 gpgv_2.2.8-3ubuntu1 grep_3.1-3 groff-base_1.22.3-10 gzip_1.6-5ubuntu2 hostname_3.21 init_1.56 init-system-helpers_1.56 initscripts_2.88dsf-59.3ubuntu2 insserv_1.14.0-5ubuntu3 intltool-debian_0.35.0+20060710.4 libacl1_2.2.52-3build1 libapparmor1_2.12-4ubuntu10 libapt-pkg5.0_1.8.0~alpha2ubuntu1 libarchive-zip-perl_1.64-1 libarchive13_3.2.2-5 libargon2-1_0~20171227-0.1 libasan5_8.2.0-11ubuntu1 libasn1-8-heimdal_7.5.0+dfsg-2.1 libassuan0_2.5.1-2 libatomic1_8.2.0-11ubuntu1 libattr1_1:2.4.47-2build1 libaudit-common_1:2.8.3-1ubuntu3 libaudit1_1:2.8.3-1ubuntu3 libbam-dev_0.1.19-4 libbamtools-dev_2.5.1+dfsg-3 libbamtools2.5.1_2.5.1+dfsg-3 libbinutils_2.31.1-10ubuntu1 libblkid1_2.32-0.1ubuntu2 libboost-dev_1.67.0.1 libboost1.67-dev_1.67.0-11 libbsd0_0.9.1-1 libbwa-dev_0.7.17-2 libbz2-1.0_1.0.6-9 libbz2-dev_1.0.6-9 libc-bin_2.28-0ubuntu1 libc-dev-bin_2.28-0ubuntu1 libc6_2.28-0ubuntu1 libc6-dev_2.28-0ubuntu1 libcap-ng0_0.7.9-1build1 libcap2_1:2.25-1.2 libcc1-0_8.2.0-11ubuntu1 libcom-err2_1.44.4-2ubuntu1 libcomerr2_1.44.4-2ubuntu1 libcroco3_0.6.12-2 libcryptsetup12_2:2.0.4-2ubuntu2 libcurl3-gnutls_7.61.0-1ubuntu2.2 libcurl4_7.61.0-1ubuntu2.2 libdb5.3_5.3.28+dfsg1-0.2 libdebconfclient0_0.244ubuntu1 libdevmapper1.02.1_2:1.02.145-4.1ubuntu4 libdpkg-perl_1.19.2ubuntu2 libelf1_0.175-1 libexpat1_2.2.6-1 libexpat1-dev_2.2.6-1 libext2fs2_1.44.4-2ubuntu1 libfakeroot_1.23-1 libfdisk1_2.32-0.1ubuntu2 libffi6_3.2.1-9 libfile-stripnondeterminism-perl_1.0.0-1 libgcc-8-dev_8.2.0-11ubuntu1 libgcc1_1:8.2.0-11ubuntu1 libgcrypt20_1.8.4-3ubuntu1 libgdbm-compat4_1.18.1-2 libgdbm5_1.14.1-6 libgdbm6_1.18.1-2 libglib2.0-0_2.58.1-2 libgmp10_2:6.1.2+dfsg-4 libgnutls30_3.6.4-2ubuntu2 libgomp1_8.2.0-11ubuntu1 libgpg-error0_1.32-3 libgssapi-krb5-2_1.16.1-1ubuntu1 libgssapi3-heimdal_7.5.0+dfsg-2.1 libhat-trie-dev_0.1.2-1 libhat-trie0_0.1.2-1 libhcrypto4-heimdal_7.5.0+dfsg-2.1 libheimbase1-heimdal_7.5.0+dfsg-2.1 libheimntlm0-heimdal_7.5.0+dfsg-2.1 libhogweed4_3.4.1~rc1-1 libhts-dev_1.9-6 libhts2_1.9-6 libhx509-5-heimdal_7.5.0+dfsg-2.1 libicu63_63.1-5 libidn11_1.33-2.2ubuntu1 libidn2-0_2.0.5-1 libip4tc0_1.6.1-2ubuntu3 libisl19_0.20-2 libitm1_8.2.0-11ubuntu1 libjemalloc-dev_5.1.0-1 libjemalloc2_5.1.0-1 libjson-c3_0.12.1-1.3 libjsoncpp1_1.7.4-3 libk5crypto3_1.16.1-1ubuntu1 libkeyutils1_1.5.9-9.3 libkmod2_25-1ubuntu2 libkrb5-26-heimdal_7.5.0+dfsg-2.1 libkrb5-3_1.16.1-1ubuntu1 libkrb5support0_1.16.1-1ubuntu1 libldap-2.4-2_2.4.46+dfsg-5ubuntu3 libldap-common_2.4.46+dfsg-5ubuntu3 liblockfile-bin_1.14-1.1 liblockfile1_1.14-1.1 liblsan0_8.2.0-11ubuntu1 liblz4-1_1.8.2-1ubuntu1 liblzma-dev_5.2.2-1.3 liblzma5_5.2.2-1.3 liblzo2-2_2.10-0.1 libmagic-mgc_1:5.34-2 libmagic1_1:5.34-2 libmount1_2.32-0.1ubuntu2 libmpc3_1.1.0-1 libmpdec2_2.4.2-2 libmpfr6_4.0.1-2 libmpx2_8.2.0-11ubuntu1 libncurses6_6.1+20180210-4ubuntu1 libncursesw6_6.1+20180210-4ubuntu1 libnettle6_3.4.1~rc1-1 libnghttp2-14_1.35.0-1 libnlopt-cxx-dev_2.4.2+dfsg-8build1 libnlopt-cxx0_2.4.2+dfsg-8build1 libnlopt-dev_2.4.2+dfsg-8build1 libnlopt0_2.4.2+dfsg-8build1 libnpth0_1.6-1 libp11-kit0_0.23.14-2 libpam-modules_1.1.8-3.6ubuntu2 libpam-modules-bin_1.1.8-3.6ubuntu2 libpam-runtime_1.1.8-3.6ubuntu2 libpam0g_1.1.8-3.6ubuntu2 libpcre3_2:8.39-11 libperl5.26_5.26.2-7 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libstdc++-8-dev_8.2.0-11ubuntu1 libstdc++6_8.2.0-11ubuntu1 libsystemd0_239-7ubuntu15 libtasn1-6_4.13-3 libtinfo6_6.1+20180210-4ubuntu1 libtool_2.4.6-6 libtsan0_8.2.0-11ubuntu1 libubsan1_8.2.0-11ubuntu1 libudev1_239-7ubuntu15 libunistring2_0.9.10-1ubuntu1 libusb-0.1-4_2:0.1.12-32 libuuid1_2.32-0.1ubuntu2 libuv1_1.24.0-1 libwind0-heimdal_7.5.0+dfsg-2.1 libxml2_2.9.4+dfsg1-7ubuntu3 libyaml-0-2_0.2.1-1 libzstd1_1.3.5+dfsg-1ubuntu1 linux-libc-dev_4.19.0-8.9 lockfile-progs_0.1.18 login_1:4.5-1ubuntu1 lsb-base_9.20170808ubuntu1 lynx_2.8.9rel.1-2 lynx-common_2.8.9rel.1-2 m4_1.4.18-2 make_4.2.1-1.2 man-db_2.8.4-3 mawk_1.3.3-17ubuntu3 mime-support_3.60ubuntu1 mount_2.32-0.1ubuntu2 multiarch-support_2.28-0ubuntu1 ncurses-base_6.1+20180210-4ubuntu1 ncurses-bin_6.1+20180210-4ubuntu1 openssl_1.1.1a-1ubuntu2 optipng_0.7.6-1.1 passwd_1:4.5-1ubuntu1 patch_2.7.6-3 perl_5.28.1-3 perl-base_5.28.1-3 perl-modules-5.26_5.26.2-7 perl-modules-5.28_5.28.1-3 pinentry-curses_1.1.0-1build2 pkgbinarymangler_143 po-debconf_1.0.21 policyrcd-script-zg2_0.1-3 procps_2:3.3.15-2ubuntu1 python_2.7.15-3 python-all_2.7.15-3 python-all-dev_2.7.15-3 python-dev_2.7.15-3 python-joblib_0.13.0-1 python-minimal_2.7.15-3 python-yaml_3.13-1 python2_2.7.15-3 python2-dev_2.7.15-3 python2-minimal_2.7.15-3 python2.7_2.7.15-5 python2.7-dev_2.7.15-5 python2.7-minimal_2.7.15-5 python3_3.7.1-1ubuntu1 python3-distutils_3.7.1-1ubuntu4 python3-lib2to3_3.7.1-1ubuntu4 python3-minimal_3.7.1-1ubuntu1 python3.7_3.7.1-1 python3.7-minimal_3.7.1-1 rake_12.3.1-3 readline-common_7.0-5 ruby_1:2.5.1 ruby-asciidoctor_1.5.8-1 ruby-did-you-mean_1.2.1-1 ruby-minitest_5.11.3-1 ruby-net-telnet_0.1.1-2 ruby-power-assert_1.1.1-1 ruby-test-unit_3.2.8-1 ruby-xmlrpc_0.3.0-2 ruby2.5_2.5.3-3ubuntu1 rubygems-integration_1.11 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-spades-dummy_0.invalid.0 sed_4.5-2 sensible-utils_0.0.12 systemd_239-7ubuntu15 systemd-sysv_239-7ubuntu15 sysv-rc_2.88dsf-59.3ubuntu2 sysvinit-utils_2.88dsf-59.10ubuntu2 tar_1.30+dfsg-3 tzdata_2018g-1 ubuntu-keyring_2018.09.18.1 util-linux_2.32-0.1ubuntu2 xz-utils_5.2.2-1.3 zlib1g_1:1.2.11.dfsg-0ubuntu2 zlib1g-dev_1:1.2.11.dfsg-0ubuntu2 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- gpgv: Signature made Tue Oct 16 20:28:48 2018 UTC gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./spades_3.13.0+dfsg-1.dsc dpkg-source: info: extracting spades in spades-3.13.0+dfsg dpkg-source: info: unpacking spades_3.13.0+dfsg.orig.tar.xz dpkg-source: info: unpacking spades_3.13.0+dfsg-1.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 Check disc space ---------------- Sufficient free space for build User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf DEB_BUILD_OPTIONS=parallel=4 HOME=/sbuild-nonexistent LANG=C.UTF-8 LC_ALL=C.UTF-8 LOGNAME=buildd PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games SCHROOT_ALIAS_NAME=build-PACKAGEBUILD-15636794 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-15636794 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-15636794 SCHROOT_UID=2001 SCHROOT_USER=buildd SHELL=/bin/sh TERM=unknown USER=buildd V=1 dpkg-buildpackage ----------------- dpkg-buildpackage: info: source package spades dpkg-buildpackage: info: source version 3.13.0+dfsg-1 dpkg-buildpackage: info: source distribution unstable dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 fakeroot debian/rules clean dh clean --with python2 --sourcedirectory=src --buildsystem=cmake debian/rules override_dh_auto_clean make[1]: Entering directory '/<>/spades-3.13.0+dfsg' dh_auto_clean rm -rf build_spades rm -rf install_spades rm -rf spades_test find . -name "*.pyc" -delete rm -rf /<>/spades-3.13.0+dfsg/debian/man_src/*.html /<>/spades-3.13.0+dfsg/debian/man_src/*.? rm -rf /<>/spades-3.13.0+dfsg/debian/man make[1]: Leaving directory '/<>/spades-3.13.0+dfsg' dh_autoreconf_clean -O--sourcedirectory=src -O--buildsystem=cmake debian/rules override_dh_clean make[1]: Entering directory '/<>/spades-3.13.0+dfsg' dh_clean -X.orig make[1]: Leaving directory '/<>/spades-3.13.0+dfsg' debian/rules build dh build --with python2 --sourcedirectory=src --buildsystem=cmake dh_update_autotools_config -O--sourcedirectory=src -O--buildsystem=cmake dh_autoreconf -O--sourcedirectory=src -O--buildsystem=cmake debian/rules override_dh_auto_configure make[1]: Entering directory '/<>/spades-3.13.0+dfsg' echo "Simply use spades_compile.sh in auto_build" Simply use spades_compile.sh in auto_build make[1]: Leaving directory '/<>/spades-3.13.0+dfsg' debian/rules override_dh_auto_build make[1]: Entering directory '/<>/spades-3.13.0+dfsg' PREFIX=/<>/spades-3.13.0+dfsg/install_spades ./spades_compile.sh -- The C compiler identification is GNU 8.2.0 -- The CXX compiler identification is GNU 8.2.0 -- 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 -- Found OpenMP_C: -fopenmp (found version "4.5") -- Found OpenMP_CXX: -fopenmp (found version "4.5") -- Found OpenMP: TRUE (found version "4.5") -- 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 "1.0.6") -- Looking for BZ2_bzCompressInit -- Looking for BZ2_bzCompressInit - found -- Could NOT find readline (missing: READLINE_INCLUDE_DIR READLINE_LIBRARY) -- Boost version: 1.67.0 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-3.13.0+dfsg/build_spades make[2]: Entering directory '/<>/spades-3.13.0+dfsg/build_spades' /usr/bin/cmake -H/<>/spades-3.13.0+dfsg/src -B/<>/spades-3.13.0+dfsg/build_spades --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /<>/spades-3.13.0+dfsg/build_spades/CMakeFiles /<>/spades-3.13.0+dfsg/build_spades/CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[3]: Entering directory '/<>/spades-3.13.0+dfsg/build_spades' make -f ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/build.make ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/depend make[4]: Entering directory '/<>/spades-3.13.0+dfsg/build_spades' cd /<>/spades-3.13.0+dfsg/build_spades && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/spades-3.13.0+dfsg/src /<>/spades-3.13.0+dfsg/ext/src/ConsensusCore /<>/spades-3.13.0+dfsg/build_spades /<>/spades-3.13.0+dfsg/build_spades/ext/ConsensusCore /<>/spades-3.13.0+dfsg/build_spades/ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/DependInfo.cmake --color= Dependee "/<>/spades-3.13.0+dfsg/build_spades/ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/DependInfo.cmake" is newer than depender "/<>/spades-3.13.0+dfsg/build_spades/ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/depend.internal". Dependee "/<>/spades-3.13.0+dfsg/build_spades/ext/ConsensusCore/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/<>/spades-3.13.0+dfsg/build_spades/ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/depend.internal". Scanning dependencies of target ConsensusCore make[4]: Leaving directory '/<>/spades-3.13.0+dfsg/build_spades' make -f ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/build.make ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/build make[4]: Entering directory '/<>/spades-3.13.0+dfsg/build_spades' [ 1%] Building CXX object ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/AffineAlignment.cpp.o cd /<>/spades-3.13.0+dfsg/build_spades/ext/ConsensusCore && /usr/bin/c++ -DJEMALLOC_NO_DEMANGLE -DUSE_GLIBCXX_PARALLEL=1 -I/<>/spades-3.13.0+dfsg/build_spades/ext/ConsensusCore -I/<>/spades-3.13.0+dfsg/ext/src/ConsensusCore -I/<>/spades-3.13.0+dfsg/src/include -I/<>/spades-3.13.0+dfsg/build_spades/include -I/<>/spades-3.13.0+dfsg/src -I/<>/spades-3.13.0+dfsg/src/common -I/<>/spades-3.13.0+dfsg/src/../ext/include/ConsensusCore -isystem /<>/spades-3.13.0+dfsg/src/../ext/include -g -O2 -fdebug-prefix-map=/<>/spades-3.13.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -o CMakeFiles/ConsensusCore.dir/AffineAlignment.cpp.o -c /<>/spades-3.13.0+dfsg/ext/src/ConsensusCore/AffineAlignment.cpp [ 1%] Building CXX object ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/Coverage.cpp.o cd /<>/spades-3.13.0+dfsg/build_spades/ext/ConsensusCore && /usr/bin/c++ -DJEMALLOC_NO_DEMANGLE -DUSE_GLIBCXX_PARALLEL=1 -I/<>/spades-3.13.0+dfsg/build_spades/ext/ConsensusCore -I/<>/spades-3.13.0+dfsg/ext/src/ConsensusCore -I/<>/spades-3.13.0+dfsg/src/include -I/<>/spades-3.13.0+dfsg/build_spades/include -I/<>/spades-3.13.0+dfsg/src -I/<>/spades-3.13.0+dfsg/src/common -I/<>/spades-3.13.0+dfsg/src/../ext/include/ConsensusCore -isystem /<>/spades-3.13.0+dfsg/src/../ext/include -g -O2 -fdebug-prefix-map=/<>/spades-3.13.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -o CMakeFiles/ConsensusCore.dir/Coverage.cpp.o -c /<>/spades-3.13.0+dfsg/ext/src/ConsensusCore/Coverage.cpp [ 2%] Building CXX object ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/Mutation.cpp.o cd /<>/spades-3.13.0+dfsg/build_spades/ext/ConsensusCore && /usr/bin/c++ -DJEMALLOC_NO_DEMANGLE -DUSE_GLIBCXX_PARALLEL=1 -I/<>/spades-3.13.0+dfsg/build_spades/ext/ConsensusCore -I/<>/spades-3.13.0+dfsg/ext/src/ConsensusCore -I/<>/spades-3.13.0+dfsg/src/include -I/<>/spades-3.13.0+dfsg/build_spades/include -I/<>/spades-3.13.0+dfsg/src -I/<>/spades-3.13.0+dfsg/src/common -I/<>/spades-3.13.0+dfsg/src/../ext/include/ConsensusCore -isystem /<>/spades-3.13.0+dfsg/src/../ext/include -g -O2 -fdebug-prefix-map=/<>/spades-3.13.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -o CMakeFiles/ConsensusCore.dir/Mutation.cpp.o -c /<>/spades-3.13.0+dfsg/ext/src/ConsensusCore/Mutation.cpp [ 2%] Building CXX object ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/PairwiseAlignment.cpp.o cd /<>/spades-3.13.0+dfsg/build_spades/ext/ConsensusCore && /usr/bin/c++ -DJEMALLOC_NO_DEMANGLE -DUSE_GLIBCXX_PARALLEL=1 -I/<>/spades-3.13.0+dfsg/build_spades/ext/ConsensusCore -I/<>/spades-3.13.0+dfsg/ext/src/ConsensusCore -I/<>/spades-3.13.0+dfsg/src/include -I/<>/spades-3.13.0+dfsg/build_spades/include -I/<>/spades-3.13.0+dfsg/src -I/<>/spades-3.13.0+dfsg/src/common -I/<>/spades-3.13.0+dfsg/src/../ext/include/ConsensusCore -isystem /<>/spades-3.13.0+dfsg/src/../ext/include -g -O2 -fdebug-prefix-map=/<>/spades-3.13.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -o CMakeFiles/ConsensusCore.dir/PairwiseAlignment.cpp.o -c /<>/spades-3.13.0+dfsg/ext/src/ConsensusCore/PairwiseAlignment.cpp [ 2%] Building CXX object ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/Sequence.cpp.o cd /<>/spades-3.13.0+dfsg/build_spades/ext/ConsensusCore && /usr/bin/c++ -DJEMALLOC_NO_DEMANGLE -DUSE_GLIBCXX_PARALLEL=1 -I/<>/spades-3.13.0+dfsg/build_spades/ext/ConsensusCore -I/<>/spades-3.13.0+dfsg/ext/src/ConsensusCore -I/<>/spades-3.13.0+dfsg/src/include -I/<>/spades-3.13.0+dfsg/build_spades/include -I/<>/spades-3.13.0+dfsg/src -I/<>/spades-3.13.0+dfsg/src/common -I/<>/spades-3.13.0+dfsg/src/../ext/include/ConsensusCore -isystem /<>/spades-3.13.0+dfsg/src/../ext/include -g -O2 -fdebug-prefix-map=/<>/spades-3.13.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -o CMakeFiles/ConsensusCore.dir/Sequence.cpp.o -c /<>/spades-3.13.0+dfsg/ext/src/ConsensusCore/Sequence.cpp [ 3%] Building CXX object ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/Utils.cpp.o cd /<>/spades-3.13.0+dfsg/build_spades/ext/ConsensusCore && /usr/bin/c++ -DJEMALLOC_NO_DEMANGLE -DUSE_GLIBCXX_PARALLEL=1 -I/<>/spades-3.13.0+dfsg/build_spades/ext/ConsensusCore -I/<>/spades-3.13.0+dfsg/ext/src/ConsensusCore -I/<>/spades-3.13.0+dfsg/src/include -I/<>/spades-3.13.0+dfsg/build_spades/include -I/<>/spades-3.13.0+dfsg/src -I/<>/spades-3.13.0+dfsg/src/common -I/<>/spades-3.13.0+dfsg/src/../ext/include/ConsensusCore -isystem /<>/spades-3.13.0+dfsg/src/../ext/include -g -O2 -fdebug-prefix-map=/<>/spades-3.13.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -o CMakeFiles/ConsensusCore.dir/Utils.cpp.o -c /<>/spades-3.13.0+dfsg/ext/src/ConsensusCore/Utils.cpp [ 3%] Building CXX object ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/Version.cpp.o cd /<>/spades-3.13.0+dfsg/build_spades/ext/ConsensusCore && /usr/bin/c++ -DJEMALLOC_NO_DEMANGLE -DUSE_GLIBCXX_PARALLEL=1 -I/<>/spades-3.13.0+dfsg/build_spades/ext/ConsensusCore -I/<>/spades-3.13.0+dfsg/ext/src/ConsensusCore -I/<>/spades-3.13.0+dfsg/src/include -I/<>/spades-3.13.0+dfsg/build_spades/include -I/<>/spades-3.13.0+dfsg/src -I/<>/spades-3.13.0+dfsg/src/common -I/<>/spades-3.13.0+dfsg/src/../ext/include/ConsensusCore -isystem /<>/spades-3.13.0+dfsg/src/../ext/include -g -O2 -fdebug-prefix-map=/<>/spades-3.13.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -o CMakeFiles/ConsensusCore.dir/Version.cpp.o -c /<>/spades-3.13.0+dfsg/ext/src/ConsensusCore/Version.cpp [ 4%] Building CXX object ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/Matrix/DenseMatrix.cpp.o cd /<>/spades-3.13.0+dfsg/build_spades/ext/ConsensusCore && /usr/bin/c++ -DJEMALLOC_NO_DEMANGLE -DUSE_GLIBCXX_PARALLEL=1 -I/<>/spades-3.13.0+dfsg/build_spades/ext/ConsensusCore -I/<>/spades-3.13.0+dfsg/ext/src/ConsensusCore -I/<>/spades-3.13.0+dfsg/src/include -I/<>/spades-3.13.0+dfsg/build_spades/include -I/<>/spades-3.13.0+dfsg/src -I/<>/spades-3.13.0+dfsg/src/common -I/<>/spades-3.13.0+dfsg/src/../ext/include/ConsensusCore -isystem /<>/spades-3.13.0+dfsg/src/../ext/include -g -O2 -fdebug-prefix-map=/<>/spades-3.13.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -o CMakeFiles/ConsensusCore.dir/Matrix/DenseMatrix.cpp.o -c /<>/spades-3.13.0+dfsg/ext/src/ConsensusCore/Matrix/DenseMatrix.cpp [ 4%] Building CXX object ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/Matrix/SparseMatrix.cpp.o cd /<>/spades-3.13.0+dfsg/build_spades/ext/ConsensusCore && /usr/bin/c++ -DJEMALLOC_NO_DEMANGLE -DUSE_GLIBCXX_PARALLEL=1 -I/<>/spades-3.13.0+dfsg/build_spades/ext/ConsensusCore -I/<>/spades-3.13.0+dfsg/ext/src/ConsensusCore -I/<>/spades-3.13.0+dfsg/src/include -I/<>/spades-3.13.0+dfsg/build_spades/include -I/<>/spades-3.13.0+dfsg/src -I/<>/spades-3.13.0+dfsg/src/common -I/<>/spades-3.13.0+dfsg/src/../ext/include/ConsensusCore -isystem /<>/spades-3.13.0+dfsg/src/../ext/include -g -O2 -fdebug-prefix-map=/<>/spades-3.13.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -o CMakeFiles/ConsensusCore.dir/Matrix/SparseMatrix.cpp.o -c /<>/spades-3.13.0+dfsg/ext/src/ConsensusCore/Matrix/SparseMatrix.cpp [ 5%] Building CXX object ext/ConsensusCore/CMakeFiles/ConsensusCore.dir/Poa/PoaConfig.cpp.o cd /<>/spades-3.13.0+dfsg/build_spades/ext/ConsensusCore && /usr/bin/c++ -DJEMALLOC_NO_DEMANGLE -DUSE_GLIBCXX_PARALLEL=1 -I/<>/spades-3.13.0+dfsg/build_spades/ext/ConsensusCore -I/<>/spades-3.13.0+dfsg/ext/src/ConsensusCore -I/<>/spades-3.13.0+dfsg/src/include -I/<>/spades-3.13.0+dfsg/build_spades/include -I/<>/spades-3.13.0+dfsg/src -I/<>/spades-3.13.0+dfsg/src/common 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-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -o CMakeFiles/ConsensusCore.dir/Poa/PoaGraph.cpp.o -c /<>/spades-3.13.0+dfsg/ext/src/ConsensusCore/Poa/PoaGraph.cpp [ 6%] Linking CXX static library libConsensusCore.a cd /<>/spades-3.13.0+dfsg/build_spades/ext/ConsensusCore && /usr/bin/cmake -P CMakeFiles/ConsensusCore.dir/cmake_clean_target.cmake cd /<>/spades-3.13.0+dfsg/build_spades/ext/ConsensusCore && /usr/bin/cmake -E cmake_link_script CMakeFiles/ConsensusCore.dir/link.txt --verbose=1 /usr/bin/ar qc libConsensusCore.a CMakeFiles/ConsensusCore.dir/AffineAlignment.cpp.o CMakeFiles/ConsensusCore.dir/Coverage.cpp.o CMakeFiles/ConsensusCore.dir/Mutation.cpp.o CMakeFiles/ConsensusCore.dir/PairwiseAlignment.cpp.o CMakeFiles/ConsensusCore.dir/Sequence.cpp.o CMakeFiles/ConsensusCore.dir/Utils.cpp.o CMakeFiles/ConsensusCore.dir/Version.cpp.o 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/<>/spades-3.13.0+dfsg/ext/src/bamtools/api/SamSequence.cpp [ 11%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/SamSequenceDictionary.cpp.o cd /<>/spades-3.13.0+dfsg/build_spades/ext/bamtools/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DJEMALLOC_NO_DEMANGLE -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/<>/spades-3.13.0+dfsg/build_spades/ext/bamtools/api -I/<>/spades-3.13.0+dfsg/ext/src/bamtools/api -I/<>/spades-3.13.0+dfsg/src/include -I/<>/spades-3.13.0+dfsg/build_spades/include -I/<>/spades-3.13.0+dfsg/src -I/<>/spades-3.13.0+dfsg/src/common -I/<>/spades-3.13.0+dfsg/ext/src/bamtools -I/<>/spades-3.13.0+dfsg/ext/src/bamtools/src -isystem /<>/spades-3.13.0+dfsg/src/../ext/include -g -O2 -fdebug-prefix-map=/<>/spades-3.13.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -o CMakeFiles/BamTools.dir/SamSequenceDictionary.cpp.o -c /<>/spades-3.13.0+dfsg/ext/src/bamtools/api/SamSequenceDictionary.cpp [ 11%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/bam/BamHeader_p.cpp.o cd /<>/spades-3.13.0+dfsg/build_spades/ext/bamtools/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DJEMALLOC_NO_DEMANGLE -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/<>/spades-3.13.0+dfsg/build_spades/ext/bamtools/api -I/<>/spades-3.13.0+dfsg/ext/src/bamtools/api -I/<>/spades-3.13.0+dfsg/src/include -I/<>/spades-3.13.0+dfsg/build_spades/include -I/<>/spades-3.13.0+dfsg/src -I/<>/spades-3.13.0+dfsg/src/common -I/<>/spades-3.13.0+dfsg/ext/src/bamtools -I/<>/spades-3.13.0+dfsg/ext/src/bamtools/src -isystem /<>/spades-3.13.0+dfsg/src/../ext/include -g -O2 -fdebug-prefix-map=/<>/spades-3.13.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -o CMakeFiles/BamTools.dir/internal/bam/BamHeader_p.cpp.o -c 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-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -o CMakeFiles/BamTools.dir/internal/io/BamDeviceFactory_p.cpp.o -c /<>/spades-3.13.0+dfsg/ext/src/bamtools/api/internal/io/BamDeviceFactory_p.cpp [ 15%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/BamFile_p.cpp.o cd /<>/spades-3.13.0+dfsg/build_spades/ext/bamtools/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DJEMALLOC_NO_DEMANGLE -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/<>/spades-3.13.0+dfsg/build_spades/ext/bamtools/api -I/<>/spades-3.13.0+dfsg/ext/src/bamtools/api -I/<>/spades-3.13.0+dfsg/src/include -I/<>/spades-3.13.0+dfsg/build_spades/include -I/<>/spades-3.13.0+dfsg/src -I/<>/spades-3.13.0+dfsg/src/common -I/<>/spades-3.13.0+dfsg/ext/src/bamtools -I/<>/spades-3.13.0+dfsg/ext/src/bamtools/src -isystem /<>/spades-3.13.0+dfsg/src/../ext/include -g -O2 -fdebug-prefix-map=/<>/spades-3.13.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -o CMakeFiles/BamTools.dir/internal/io/BamFile_p.cpp.o -c /<>/spades-3.13.0+dfsg/ext/src/bamtools/api/internal/io/BamFile_p.cpp [ 16%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/BgzfStream_p.cpp.o cd /<>/spades-3.13.0+dfsg/build_spades/ext/bamtools/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DJEMALLOC_NO_DEMANGLE -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/<>/spades-3.13.0+dfsg/build_spades/ext/bamtools/api -I/<>/spades-3.13.0+dfsg/ext/src/bamtools/api -I/<>/spades-3.13.0+dfsg/src/include -I/<>/spades-3.13.0+dfsg/build_spades/include -I/<>/spades-3.13.0+dfsg/src -I/<>/spades-3.13.0+dfsg/src/common -I/<>/spades-3.13.0+dfsg/ext/src/bamtools -I/<>/spades-3.13.0+dfsg/ext/src/bamtools/src -isystem /<>/spades-3.13.0+dfsg/src/../ext/include -g -O2 -fdebug-prefix-map=/<>/spades-3.13.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -o CMakeFiles/BamTools.dir/internal/io/BgzfStream_p.cpp.o -c /<>/spades-3.13.0+dfsg/ext/src/bamtools/api/internal/io/BgzfStream_p.cpp [ 16%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/ByteArray_p.cpp.o cd /<>/spades-3.13.0+dfsg/build_spades/ext/bamtools/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DJEMALLOC_NO_DEMANGLE -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/<>/spades-3.13.0+dfsg/build_spades/ext/bamtools/api -I/<>/spades-3.13.0+dfsg/ext/src/bamtools/api -I/<>/spades-3.13.0+dfsg/src/include -I/<>/spades-3.13.0+dfsg/build_spades/include -I/<>/spades-3.13.0+dfsg/src -I/<>/spades-3.13.0+dfsg/src/common -I/<>/spades-3.13.0+dfsg/ext/src/bamtools -I/<>/spades-3.13.0+dfsg/ext/src/bamtools/src -isystem /<>/spades-3.13.0+dfsg/src/../ext/include -g -O2 -fdebug-prefix-map=/<>/spades-3.13.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -o CMakeFiles/BamTools.dir/internal/io/ByteArray_p.cpp.o -c /<>/spades-3.13.0+dfsg/ext/src/bamtools/api/internal/io/ByteArray_p.cpp [ 16%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/ILocalIODevice_p.cpp.o cd /<>/spades-3.13.0+dfsg/build_spades/ext/bamtools/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DJEMALLOC_NO_DEMANGLE -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/<>/spades-3.13.0+dfsg/build_spades/ext/bamtools/api -I/<>/spades-3.13.0+dfsg/ext/src/bamtools/api -I/<>/spades-3.13.0+dfsg/src/include -I/<>/spades-3.13.0+dfsg/build_spades/include -I/<>/spades-3.13.0+dfsg/src -I/<>/spades-3.13.0+dfsg/src/common -I/<>/spades-3.13.0+dfsg/ext/src/bamtools -I/<>/spades-3.13.0+dfsg/ext/src/bamtools/src -isystem /<>/spades-3.13.0+dfsg/src/../ext/include -g -O2 -fdebug-prefix-map=/<>/spades-3.13.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -o CMakeFiles/BamTools.dir/internal/io/ILocalIODevice_p.cpp.o -c /<>/spades-3.13.0+dfsg/ext/src/bamtools/api/internal/io/ILocalIODevice_p.cpp [ 17%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/ParallelBgzfStream_p.cpp.o cd /<>/spades-3.13.0+dfsg/build_spades/ext/bamtools/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DJEMALLOC_NO_DEMANGLE -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/<>/spades-3.13.0+dfsg/build_spades/ext/bamtools/api -I/<>/spades-3.13.0+dfsg/ext/src/bamtools/api -I/<>/spades-3.13.0+dfsg/src/include -I/<>/spades-3.13.0+dfsg/build_spades/include -I/<>/spades-3.13.0+dfsg/src -I/<>/spades-3.13.0+dfsg/src/common -I/<>/spades-3.13.0+dfsg/ext/src/bamtools -I/<>/spades-3.13.0+dfsg/ext/src/bamtools/src -isystem /<>/spades-3.13.0+dfsg/src/../ext/include -g -O2 -fdebug-prefix-map=/<>/spades-3.13.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -o CMakeFiles/BamTools.dir/internal/io/ParallelBgzfStream_p.cpp.o -c /<>/spades-3.13.0+dfsg/ext/src/bamtools/api/internal/io/ParallelBgzfStream_p.cpp [ 17%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/RollingBuffer_p.cpp.o cd /<>/spades-3.13.0+dfsg/build_spades/ext/bamtools/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DJEMALLOC_NO_DEMANGLE -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/<>/spades-3.13.0+dfsg/build_spades/ext/bamtools/api -I/<>/spades-3.13.0+dfsg/ext/src/bamtools/api -I/<>/spades-3.13.0+dfsg/src/include -I/<>/spades-3.13.0+dfsg/build_spades/include -I/<>/spades-3.13.0+dfsg/src -I/<>/spades-3.13.0+dfsg/src/common -I/<>/spades-3.13.0+dfsg/ext/src/bamtools -I/<>/spades-3.13.0+dfsg/ext/src/bamtools/src -isystem /<>/spades-3.13.0+dfsg/src/../ext/include -g -O2 -fdebug-prefix-map=/<>/spades-3.13.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -o CMakeFiles/BamTools.dir/internal/io/RollingBuffer_p.cpp.o -c /<>/spades-3.13.0+dfsg/ext/src/bamtools/api/internal/io/RollingBuffer_p.cpp [ 18%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/SerialBgzfStream_p.cpp.o cd /<>/spades-3.13.0+dfsg/build_spades/ext/bamtools/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DJEMALLOC_NO_DEMANGLE -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/<>/spades-3.13.0+dfsg/build_spades/ext/bamtools/api -I/<>/spades-3.13.0+dfsg/ext/src/bamtools/api -I/<>/spades-3.13.0+dfsg/src/include -I/<>/spades-3.13.0+dfsg/build_spades/include -I/<>/spades-3.13.0+dfsg/src -I/<>/spades-3.13.0+dfsg/src/common -I/<>/spades-3.13.0+dfsg/ext/src/bamtools -I/<>/spades-3.13.0+dfsg/ext/src/bamtools/src -isystem /<>/spades-3.13.0+dfsg/src/../ext/include -g -O2 -fdebug-prefix-map=/<>/spades-3.13.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -o CMakeFiles/BamTools.dir/internal/io/SerialBgzfStream_p.cpp.o -c /<>/spades-3.13.0+dfsg/ext/src/bamtools/api/internal/io/SerialBgzfStream_p.cpp [ 18%] Building C object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/bgzf.c.o cd /<>/spades-3.13.0+dfsg/build_spades/ext/bamtools/api && /usr/bin/cc -DBAMTOOLS_API_LIBRARY -DJEMALLOC_NO_DEMANGLE -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/<>/spades-3.13.0+dfsg/build_spades/ext/bamtools/api -I/<>/spades-3.13.0+dfsg/ext/src/bamtools/api -I/<>/spades-3.13.0+dfsg/src/include -I/<>/spades-3.13.0+dfsg/build_spades/include -I/<>/spades-3.13.0+dfsg/src -I/<>/spades-3.13.0+dfsg/src/common -I/<>/spades-3.13.0+dfsg/ext/src/bamtools -I/<>/spades-3.13.0+dfsg/ext/src/bamtools/src -isystem /<>/spades-3.13.0+dfsg/src/../ext/include -g -O2 -fdebug-prefix-map=/<>/spades-3.13.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -o CMakeFiles/BamTools.dir/internal/io/pbgzf/bgzf.c.o -c /<>/spades-3.13.0+dfsg/ext/src/bamtools/api/internal/io/pbgzf/bgzf.c In file included from /<>/spades-3.13.0+dfsg/ext/src/bamtools/api/internal/io/pbgzf/bgzf.c:32: /<>/spades-3.13.0+dfsg/ext/src/bamtools/api/internal/io/pbgzf/bgzf.c: In function 'bgzf_check_EOF': /<>/spades-3.13.0+dfsg/ext/src/bamtools/api/internal/io/pbgzf/bgzf.h:73:34: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define _bgzf_read(fp, buf, len) fread(buf, 1, len, (_bgzf_file_t)fp) ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/spades-3.13.0+dfsg/ext/src/bamtools/api/internal/io/pbgzf/bgzf.c:578:2: note: in expansion of macro '_bgzf_read' _bgzf_read(fp->fp, buf, 28); ^~~~~~~~~~ [ 19%] Building C object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/knetfile.c.o cd /<>/spades-3.13.0+dfsg/build_spades/ext/bamtools/api && /usr/bin/cc -DBAMTOOLS_API_LIBRARY -DJEMALLOC_NO_DEMANGLE -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/<>/spades-3.13.0+dfsg/build_spades/ext/bamtools/api -I/<>/spades-3.13.0+dfsg/ext/src/bamtools/api -I/<>/spades-3.13.0+dfsg/src/include -I/<>/spades-3.13.0+dfsg/build_spades/include -I/<>/spades-3.13.0+dfsg/src -I/<>/spades-3.13.0+dfsg/src/common -I/<>/spades-3.13.0+dfsg/ext/src/bamtools -I/<>/spades-3.13.0+dfsg/ext/src/bamtools/src -isystem /<>/spades-3.13.0+dfsg/src/../ext/include -g -O2 -fdebug-prefix-map=/<>/spades-3.13.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -o CMakeFiles/BamTools.dir/internal/io/pbgzf/knetfile.c.o -c /<>/spades-3.13.0+dfsg/ext/src/bamtools/api/internal/io/pbgzf/knetfile.c In file included from /<>/spades-3.13.0+dfsg/ext/src/bamtools/api/internal/io/pbgzf/knetfile.c:46: /<>/spades-3.13.0+dfsg/ext/src/bamtools/api/internal/io/pbgzf/knetfile.c: In function 'kftp_send_cmd': /<>/spades-3.13.0+dfsg/ext/src/bamtools/api/internal/io/pbgzf/knetfile.h:9:32: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] #define netwrite(fd, ptr, len) write(fd, ptr, len) ^~~~~~~~~~~~~~~~~~~ /<>/spades-3.13.0+dfsg/ext/src/bamtools/api/internal/io/pbgzf/knetfile.c:236:2: note: in expansion of macro 'netwrite' netwrite(ftp->ctrl_fd, cmd, strlen(cmd)); ^~~~~~~~ /<>/spades-3.13.0+dfsg/ext/src/bamtools/api/internal/io/pbgzf/knetfile.c: In function 'khttp_connect_file': /<>/spades-3.13.0+dfsg/ext/src/bamtools/api/internal/io/pbgzf/knetfile.h:9:32: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] #define netwrite(fd, ptr, len) write(fd, ptr, len) ^~~~~~~~~~~~~~~~~~~ /<>/spades-3.13.0+dfsg/ext/src/bamtools/api/internal/io/pbgzf/knetfile.c:415:2: note: in expansion of macro 'netwrite' netwrite(fp->fd, buf, l); ^~~~~~~~ [ 19%] Building C object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/block.c.o cd /<>/spades-3.13.0+dfsg/build_spades/ext/bamtools/api && /usr/bin/cc -DBAMTOOLS_API_LIBRARY -DJEMALLOC_NO_DEMANGLE -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/<>/spades-3.13.0+dfsg/build_spades/ext/bamtools/api -I/<>/spades-3.13.0+dfsg/ext/src/bamtools/api -I/<>/spades-3.13.0+dfsg/src/include -I/<>/spades-3.13.0+dfsg/build_spades/include -I/<>/spades-3.13.0+dfsg/src -I/<>/spades-3.13.0+dfsg/src/common -I/<>/spades-3.13.0+dfsg/ext/src/bamtools -I/<>/spades-3.13.0+dfsg/ext/src/bamtools/src -isystem /<>/spades-3.13.0+dfsg/src/../ext/include -g -O2 -fdebug-prefix-map=/<>/spades-3.13.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -o CMakeFiles/BamTools.dir/internal/io/pbgzf/block.c.o -c /<>/spades-3.13.0+dfsg/ext/src/bamtools/api/internal/io/pbgzf/block.c In file included from /<>/spades-3.13.0+dfsg/ext/src/bamtools/api/internal/io/pbgzf/block.c:5: /<>/spades-3.13.0+dfsg/ext/src/bamtools/api/internal/io/pbgzf/util.h:8:1: warning: inline function 'safe_mutex_unlock' declared but never defined safe_mutex_unlock(pthread_mutex_t *mutex); ^~~~~~~~~~~~~~~~~ /<>/spades-3.13.0+dfsg/ext/src/bamtools/api/internal/io/pbgzf/util.h:5:1: warning: inline function 'safe_mutex_lock' declared but never defined safe_mutex_lock(pthread_mutex_t *mutex); ^~~~~~~~~~~~~~~ In file included from /<>/spades-3.13.0+dfsg/ext/src/bamtools/api/internal/io/pbgzf/block.c:4: /<>/spades-3.13.0+dfsg/ext/src/bamtools/api/internal/io/pbgzf/bgzf.h:240:11: warning: inline function 'unpackInt16' declared but never defined unpackInt16(const uint8_t* buffer); ^~~~~~~~~~~ [ 20%] Building C object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/consumer.c.o cd /<>/spades-3.13.0+dfsg/build_spades/ext/bamtools/api && /usr/bin/cc -DBAMTOOLS_API_LIBRARY -DJEMALLOC_NO_DEMANGLE -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/<>/spades-3.13.0+dfsg/build_spades/ext/bamtools/api -I/<>/spades-3.13.0+dfsg/ext/src/bamtools/api -I/<>/spades-3.13.0+dfsg/src/include -I/<>/spades-3.13.0+dfsg/build_spades/include -I/<>/spades-3.13.0+dfsg/src -I/<>/spades-3.13.0+dfsg/src/common -I/<>/spades-3.13.0+dfsg/ext/src/bamtools -I/<>/spades-3.13.0+dfsg/ext/src/bamtools/src -isystem /<>/spades-3.13.0+dfsg/src/../ext/include -g -O2 -fdebug-prefix-map=/<>/spades-3.13.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -o CMakeFiles/BamTools.dir/internal/io/pbgzf/consumer.c.o -c /<>/spades-3.13.0+dfsg/ext/src/bamtools/api/internal/io/pbgzf/consumer.c In file included from /<>/spades-3.13.0+dfsg/ext/src/bamtools/api/internal/io/pbgzf/consumer.c:12: /<>/spades-3.13.0+dfsg/ext/src/bamtools/api/internal/io/pbgzf/util.h:8:1: warning: inline function 'safe_mutex_unlock' declared but never defined safe_mutex_unlock(pthread_mutex_t *mutex); ^~~~~~~~~~~~~~~~~ /<>/spades-3.13.0+dfsg/ext/src/bamtools/api/internal/io/pbgzf/util.h:5:1: warning: inline function 'safe_mutex_lock' declared but never defined safe_mutex_lock(pthread_mutex_t *mutex); ^~~~~~~~~~~~~~~ In file included from /<>/spades-3.13.0+dfsg/ext/src/bamtools/api/internal/io/pbgzf/consumer.c:11: /<>/spades-3.13.0+dfsg/ext/src/bamtools/api/internal/io/pbgzf/bgzf.h:240:11: warning: inline function 'unpackInt16' declared but never defined unpackInt16(const uint8_t* buffer); ^~~~~~~~~~~ [ 20%] Building C object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/pbgzf.c.o cd /<>/spades-3.13.0+dfsg/build_spades/ext/bamtools/api && /usr/bin/cc -DBAMTOOLS_API_LIBRARY -DJEMALLOC_NO_DEMANGLE -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/<>/spades-3.13.0+dfsg/build_spades/ext/bamtools/api -I/<>/spades-3.13.0+dfsg/ext/src/bamtools/api -I/<>/spades-3.13.0+dfsg/src/include -I/<>/spades-3.13.0+dfsg/build_spades/include -I/<>/spades-3.13.0+dfsg/src -I/<>/spades-3.13.0+dfsg/src/common -I/<>/spades-3.13.0+dfsg/ext/src/bamtools -I/<>/spades-3.13.0+dfsg/ext/src/bamtools/src -isystem /<>/spades-3.13.0+dfsg/src/../ext/include -g -O2 -fdebug-prefix-map=/<>/spades-3.13.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -o CMakeFiles/BamTools.dir/internal/io/pbgzf/pbgzf.c.o -c /<>/spades-3.13.0+dfsg/ext/src/bamtools/api/internal/io/pbgzf/pbgzf.c In file included from /<>/spades-3.13.0+dfsg/ext/src/bamtools/api/internal/io/pbgzf/pbgzf.c:14: /<>/spades-3.13.0+dfsg/ext/src/bamtools/api/internal/io/pbgzf/util.h:8:1: warning: inline function 'safe_mutex_unlock' declared but never defined safe_mutex_unlock(pthread_mutex_t *mutex); ^~~~~~~~~~~~~~~~~ /<>/spades-3.13.0+dfsg/ext/src/bamtools/api/internal/io/pbgzf/util.h:5:1: warning: inline function 'safe_mutex_lock' declared but never defined safe_mutex_lock(pthread_mutex_t *mutex); ^~~~~~~~~~~~~~~ In file included from /<>/spades-3.13.0+dfsg/ext/src/bamtools/api/internal/io/pbgzf/pbgzf.c:13: /<>/spades-3.13.0+dfsg/ext/src/bamtools/api/internal/io/pbgzf/bgzf.h:240:11: warning: inline function 'unpackInt16' declared but never defined unpackInt16(const uint8_t* buffer); ^~~~~~~~~~~ [ 21%] Building C object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/queue.c.o cd /<>/spades-3.13.0+dfsg/build_spades/ext/bamtools/api && /usr/bin/cc -DBAMTOOLS_API_LIBRARY -DJEMALLOC_NO_DEMANGLE -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/<>/spades-3.13.0+dfsg/build_spades/ext/bamtools/api -I/<>/spades-3.13.0+dfsg/ext/src/bamtools/api -I/<>/spades-3.13.0+dfsg/src/include -I/<>/spades-3.13.0+dfsg/build_spades/include -I/<>/spades-3.13.0+dfsg/src -I/<>/spades-3.13.0+dfsg/src/common -I/<>/spades-3.13.0+dfsg/ext/src/bamtools -I/<>/spades-3.13.0+dfsg/ext/src/bamtools/src -isystem /<>/spades-3.13.0+dfsg/src/../ext/include -g -O2 -fdebug-prefix-map=/<>/spades-3.13.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -o CMakeFiles/BamTools.dir/internal/io/pbgzf/queue.c.o -c /<>/spades-3.13.0+dfsg/ext/src/bamtools/api/internal/io/pbgzf/queue.c /<>/spades-3.13.0+dfsg/ext/src/bamtools/api/internal/io/pbgzf/queue.c: In function 'queue_print_status': /<>/spades-3.13.0+dfsg/ext/src/bamtools/api/internal/io/pbgzf/queue.c:344:62: warning: format '%lld' expects argument of type 'long long int', but argument 8 has type 'int64_t' {aka 'long int'} [-Wformat=] fprintf(fp, "mem=%d head=%d tail=%d n=%d length=%d id=%lld ordered=%d num_adders=%d num_getters=%d\n", ~~~^ %ld q->mem, q->head, q->tail, q->n, q->length, q->id, q->ordered, q->num_adders, q->num_getters); ~~~~~ In file included from /<>/spades-3.13.0+dfsg/ext/src/bamtools/api/internal/io/pbgzf/queue.c:6: /<>/spades-3.13.0+dfsg/ext/src/bamtools/api/internal/io/pbgzf/queue.c: At top level: /<>/spades-3.13.0+dfsg/ext/src/bamtools/api/internal/io/pbgzf/util.h:8:1: warning: inline function 'safe_mutex_unlock' declared but never defined safe_mutex_unlock(pthread_mutex_t *mutex); ^~~~~~~~~~~~~~~~~ /<>/spades-3.13.0+dfsg/ext/src/bamtools/api/internal/io/pbgzf/util.h:5:1: warning: inline function 'safe_mutex_lock' declared but never defined safe_mutex_lock(pthread_mutex_t *mutex); ^~~~~~~~~~~~~~~ [ 21%] Building C object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/reader.c.o cd /<>/spades-3.13.0+dfsg/build_spades/ext/bamtools/api && /usr/bin/cc -DBAMTOOLS_API_LIBRARY -DJEMALLOC_NO_DEMANGLE -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/<>/spades-3.13.0+dfsg/build_spades/ext/bamtools/api -I/<>/spades-3.13.0+dfsg/ext/src/bamtools/api -I/<>/spades-3.13.0+dfsg/src/include -I/<>/spades-3.13.0+dfsg/build_spades/include -I/<>/spades-3.13.0+dfsg/src -I/<>/spades-3.13.0+dfsg/src/common -I/<>/spades-3.13.0+dfsg/ext/src/bamtools -I/<>/spades-3.13.0+dfsg/ext/src/bamtools/src -isystem /<>/spades-3.13.0+dfsg/src/../ext/include -g -O2 -fdebug-prefix-map=/<>/spades-3.13.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -o CMakeFiles/BamTools.dir/internal/io/pbgzf/reader.c.o -c /<>/spades-3.13.0+dfsg/ext/src/bamtools/api/internal/io/pbgzf/reader.c In file included from /<>/spades-3.13.0+dfsg/ext/src/bamtools/api/internal/io/pbgzf/reader.c:8: /<>/spades-3.13.0+dfsg/ext/src/bamtools/api/internal/io/pbgzf/util.h:8:1: warning: inline function 'safe_mutex_unlock' declared but never defined safe_mutex_unlock(pthread_mutex_t *mutex); ^~~~~~~~~~~~~~~~~ /<>/spades-3.13.0+dfsg/ext/src/bamtools/api/internal/io/pbgzf/util.h:5:1: warning: inline function 'safe_mutex_lock' declared but never defined safe_mutex_lock(pthread_mutex_t *mutex); ^~~~~~~~~~~~~~~ In file included from /<>/spades-3.13.0+dfsg/ext/src/bamtools/api/internal/io/pbgzf/reader.c:7: /<>/spades-3.13.0+dfsg/ext/src/bamtools/api/internal/io/pbgzf/bgzf.h:240:11: warning: inline function 'unpackInt16' declared but never defined unpackInt16(const uint8_t* buffer); ^~~~~~~~~~~ [ 21%] Building C object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/util.c.o cd /<>/spades-3.13.0+dfsg/build_spades/ext/bamtools/api && /usr/bin/cc -DBAMTOOLS_API_LIBRARY -DJEMALLOC_NO_DEMANGLE -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/<>/spades-3.13.0+dfsg/build_spades/ext/bamtools/api -I/<>/spades-3.13.0+dfsg/ext/src/bamtools/api -I/<>/spades-3.13.0+dfsg/src/include -I/<>/spades-3.13.0+dfsg/build_spades/include -I/<>/spades-3.13.0+dfsg/src -I/<>/spades-3.13.0+dfsg/src/common -I/<>/spades-3.13.0+dfsg/ext/src/bamtools -I/<>/spades-3.13.0+dfsg/ext/src/bamtools/src -isystem /<>/spades-3.13.0+dfsg/src/../ext/include -g -O2 -fdebug-prefix-map=/<>/spades-3.13.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -o CMakeFiles/BamTools.dir/internal/io/pbgzf/util.c.o -c /<>/spades-3.13.0+dfsg/ext/src/bamtools/api/internal/io/pbgzf/util.c [ 22%] Building C object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/io/pbgzf/writer.c.o cd /<>/spades-3.13.0+dfsg/build_spades/ext/bamtools/api && /usr/bin/cc -DBAMTOOLS_API_LIBRARY -DJEMALLOC_NO_DEMANGLE -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/<>/spades-3.13.0+dfsg/build_spades/ext/bamtools/api -I/<>/spades-3.13.0+dfsg/ext/src/bamtools/api -I/<>/spades-3.13.0+dfsg/src/include -I/<>/spades-3.13.0+dfsg/build_spades/include -I/<>/spades-3.13.0+dfsg/src -I/<>/spades-3.13.0+dfsg/src/common -I/<>/spades-3.13.0+dfsg/ext/src/bamtools -I/<>/spades-3.13.0+dfsg/ext/src/bamtools/src -isystem /<>/spades-3.13.0+dfsg/src/../ext/include -g -O2 -fdebug-prefix-map=/<>/spades-3.13.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -o CMakeFiles/BamTools.dir/internal/io/pbgzf/writer.c.o -c /<>/spades-3.13.0+dfsg/ext/src/bamtools/api/internal/io/pbgzf/writer.c In file included from /<>/spades-3.13.0+dfsg/ext/src/bamtools/api/internal/io/pbgzf/pbgzf.h:11, from /<>/spades-3.13.0+dfsg/ext/src/bamtools/api/internal/io/pbgzf/writer.c:10: /<>/spades-3.13.0+dfsg/ext/src/bamtools/api/internal/io/pbgzf/util.h:8:1: warning: inline function 'safe_mutex_unlock' declared but never defined safe_mutex_unlock(pthread_mutex_t *mutex); ^~~~~~~~~~~~~~~~~ /<>/spades-3.13.0+dfsg/ext/src/bamtools/api/internal/io/pbgzf/util.h:5:1: warning: inline function 'safe_mutex_lock' declared but never defined safe_mutex_lock(pthread_mutex_t *mutex); ^~~~~~~~~~~~~~~ In file included from /<>/spades-3.13.0+dfsg/ext/src/bamtools/api/internal/io/pbgzf/writer.c:7: /<>/spades-3.13.0+dfsg/ext/src/bamtools/api/internal/io/pbgzf/bgzf.h:240:11: warning: inline function 'unpackInt16' declared but never defined unpackInt16(const uint8_t* buffer); ^~~~~~~~~~~ [ 22%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/sam/SamFormatParser_p.cpp.o cd /<>/spades-3.13.0+dfsg/build_spades/ext/bamtools/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DJEMALLOC_NO_DEMANGLE -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/<>/spades-3.13.0+dfsg/build_spades/ext/bamtools/api -I/<>/spades-3.13.0+dfsg/ext/src/bamtools/api -I/<>/spades-3.13.0+dfsg/src/include -I/<>/spades-3.13.0+dfsg/build_spades/include -I/<>/spades-3.13.0+dfsg/src -I/<>/spades-3.13.0+dfsg/src/common -I/<>/spades-3.13.0+dfsg/ext/src/bamtools -I/<>/spades-3.13.0+dfsg/ext/src/bamtools/src -isystem /<>/spades-3.13.0+dfsg/src/../ext/include -g -O2 -fdebug-prefix-map=/<>/spades-3.13.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -o CMakeFiles/BamTools.dir/internal/sam/SamFormatParser_p.cpp.o -c /<>/spades-3.13.0+dfsg/ext/src/bamtools/api/internal/sam/SamFormatParser_p.cpp [ 23%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/sam/SamFormatPrinter_p.cpp.o cd /<>/spades-3.13.0+dfsg/build_spades/ext/bamtools/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DJEMALLOC_NO_DEMANGLE -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/<>/spades-3.13.0+dfsg/build_spades/ext/bamtools/api -I/<>/spades-3.13.0+dfsg/ext/src/bamtools/api -I/<>/spades-3.13.0+dfsg/src/include -I/<>/spades-3.13.0+dfsg/build_spades/include -I/<>/spades-3.13.0+dfsg/src -I/<>/spades-3.13.0+dfsg/src/common -I/<>/spades-3.13.0+dfsg/ext/src/bamtools -I/<>/spades-3.13.0+dfsg/ext/src/bamtools/src -isystem /<>/spades-3.13.0+dfsg/src/../ext/include -g -O2 -fdebug-prefix-map=/<>/spades-3.13.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -o CMakeFiles/BamTools.dir/internal/sam/SamFormatPrinter_p.cpp.o -c /<>/spades-3.13.0+dfsg/ext/src/bamtools/api/internal/sam/SamFormatPrinter_p.cpp [ 23%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/sam/SamHeaderValidator_p.cpp.o cd /<>/spades-3.13.0+dfsg/build_spades/ext/bamtools/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DJEMALLOC_NO_DEMANGLE -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/<>/spades-3.13.0+dfsg/build_spades/ext/bamtools/api -I/<>/spades-3.13.0+dfsg/ext/src/bamtools/api -I/<>/spades-3.13.0+dfsg/src/include -I/<>/spades-3.13.0+dfsg/build_spades/include -I/<>/spades-3.13.0+dfsg/src -I/<>/spades-3.13.0+dfsg/src/common -I/<>/spades-3.13.0+dfsg/ext/src/bamtools -I/<>/spades-3.13.0+dfsg/ext/src/bamtools/src -isystem /<>/spades-3.13.0+dfsg/src/../ext/include -g -O2 -fdebug-prefix-map=/<>/spades-3.13.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -o CMakeFiles/BamTools.dir/internal/sam/SamHeaderValidator_p.cpp.o -c /<>/spades-3.13.0+dfsg/ext/src/bamtools/api/internal/sam/SamHeaderValidator_p.cpp [ 24%] Building CXX object ext/bamtools/api/CMakeFiles/BamTools.dir/internal/utils/BamException_p.cpp.o cd /<>/spades-3.13.0+dfsg/build_spades/ext/bamtools/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DJEMALLOC_NO_DEMANGLE -DUSE_GLIBCXX_PARALLEL=1 -D_FILE_OFFSET_BITS=64 -I/<>/spades-3.13.0+dfsg/build_spades/ext/bamtools/api -I/<>/spades-3.13.0+dfsg/ext/src/bamtools/api -I/<>/spades-3.13.0+dfsg/src/include -I/<>/spades-3.13.0+dfsg/build_spades/include -I/<>/spades-3.13.0+dfsg/src -I/<>/spades-3.13.0+dfsg/src/common -I/<>/spades-3.13.0+dfsg/ext/src/bamtools -I/<>/spades-3.13.0+dfsg/ext/src/bamtools/src -isystem /<>/spades-3.13.0+dfsg/src/../ext/include -g -O2 -fdebug-prefix-map=/<>/spades-3.13.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -o CMakeFiles/BamTools.dir/internal/utils/BamException_p.cpp.o -c /<>/spades-3.13.0+dfsg/ext/src/bamtools/api/internal/utils/BamException_p.cpp [ 24%] Linking CXX static library libBamTools.a cd /<>/spades-3.13.0+dfsg/build_spades/ext/bamtools/api && /usr/bin/cmake -P CMakeFiles/BamTools.dir/cmake_clean_target.cmake cd /<>/spades-3.13.0+dfsg/build_spades/ext/bamtools/api && /usr/bin/cmake -E cmake_link_script CMakeFiles/BamTools.dir/link.txt --verbose=1 /usr/bin/ar qc libBamTools.a CMakeFiles/BamTools.dir/BamAlignment.cpp.o CMakeFiles/BamTools.dir/BamMultiReader.cpp.o CMakeFiles/BamTools.dir/BamReader.cpp.o CMakeFiles/BamTools.dir/BamWriter.cpp.o CMakeFiles/BamTools.dir/SamHeader.cpp.o CMakeFiles/BamTools.dir/SamProgram.cpp.o CMakeFiles/BamTools.dir/SamProgramChain.cpp.o CMakeFiles/BamTools.dir/SamReadGroup.cpp.o CMakeFiles/BamTools.dir/SamReadGroupDictionary.cpp.o CMakeFiles/BamTools.dir/SamSequence.cpp.o CMakeFiles/BamTools.dir/SamSequenceDictionary.cpp.o CMakeFiles/BamTools.dir/internal/bam/BamHeader_p.cpp.o CMakeFiles/BamTools.dir/internal/bam/BamMultiReader_p.cpp.o CMakeFiles/BamTools.dir/internal/bam/BamRandomAccessController_p.cpp.o CMakeFiles/BamTools.dir/internal/bam/BamReader_p.cpp.o CMakeFiles/BamTools.dir/internal/bam/BamWriter_p.cpp.o CMakeFiles/BamTools.dir/internal/index/BamIndexFactory_p.cpp.o CMakeFiles/BamTools.dir/internal/index/BamStandardIndex_p.cpp.o CMakeFiles/BamTools.dir/internal/index/BamToolsIndex_p.cpp.o CMakeFiles/BamTools.dir/internal/io/BamDeviceFactory_p.cpp.o CMakeFiles/BamTools.dir/internal/io/BamFile_p.cpp.o CMakeFiles/BamTools.dir/internal/io/BgzfStream_p.cpp.o CMakeFiles/BamTools.dir/internal/io/ByteArray_p.cpp.o CMakeFiles/BamTools.dir/internal/io/ILocalIODevice_p.cpp.o CMakeFiles/BamTools.dir/internal/io/ParallelBgzfStream_p.cpp.o CMakeFiles/BamTools.dir/internal/io/RollingBuffer_p.cpp.o CMakeFiles/BamTools.dir/internal/io/SerialBgzfStream_p.cpp.o CMakeFiles/BamTools.dir/internal/io/pbgzf/bgzf.c.o CMakeFiles/BamTools.dir/internal/io/pbgzf/knetfile.c.o CMakeFiles/BamTools.dir/internal/io/pbgzf/block.c.o CMakeFiles/BamTools.dir/internal/io/pbgzf/consumer.c.o CMakeFiles/BamTools.dir/internal/io/pbgzf/pbgzf.c.o CMakeFiles/BamTools.dir/internal/io/pbgzf/queue.c.o CMakeFiles/BamTools.dir/internal/io/pbgzf/reader.c.o CMakeFiles/BamTools.dir/internal/io/pbgzf/util.c.o CMakeFiles/BamTools.dir/internal/io/pbgzf/writer.c.o CMakeFiles/BamTools.dir/internal/sam/SamFormatParser_p.cpp.o CMakeFiles/BamTools.dir/internal/sam/SamFormatPrinter_p.cpp.o CMakeFiles/BamTools.dir/internal/sam/SamHeaderValidator_p.cpp.o CMakeFiles/BamTools.dir/internal/utils/BamException_p.cpp.o /usr/bin/ranlib libBamTools.a make[4]: Leaving directory '/<>/spades-3.13.0+dfsg/build_spades' [ 24%] Built target BamTools make -f ext/samtools/CMakeFiles/samtools.dir/build.make ext/samtools/CMakeFiles/samtools.dir/depend make[4]: Entering directory '/<>/spades-3.13.0+dfsg/build_spades' cd /<>/spades-3.13.0+dfsg/build_spades && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/spades-3.13.0+dfsg/src /<>/spades-3.13.0+dfsg/ext/src/samtools /<>/spades-3.13.0+dfsg/build_spades /<>/spades-3.13.0+dfsg/build_spades/ext/samtools /<>/spades-3.13.0+dfsg/build_spades/ext/samtools/CMakeFiles/samtools.dir/DependInfo.cmake --color= Dependee "/<>/spades-3.13.0+dfsg/build_spades/ext/samtools/CMakeFiles/samtools.dir/DependInfo.cmake" is newer than depender "/<>/spades-3.13.0+dfsg/build_spades/ext/samtools/CMakeFiles/samtools.dir/depend.internal". Dependee "/<>/spades-3.13.0+dfsg/build_spades/ext/samtools/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/<>/spades-3.13.0+dfsg/build_spades/ext/samtools/CMakeFiles/samtools.dir/depend.internal". Scanning dependencies of target samtools make[4]: Leaving directory '/<>/spades-3.13.0+dfsg/build_spades' make -f ext/samtools/CMakeFiles/samtools.dir/build.make ext/samtools/CMakeFiles/samtools.dir/build make[4]: Entering directory '/<>/spades-3.13.0+dfsg/build_spades' [ 25%] Building C object ext/samtools/CMakeFiles/samtools.dir/kstring.c.o cd /<>/spades-3.13.0+dfsg/build_spades/ext/samtools && /usr/bin/cc -DJEMALLOC_NO_DEMANGLE -DMD5SUM_MAIN -DUSE_GLIBCXX_PARALLEL=1 -D_CURSES_LIB=1 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -I/<>/spades-3.13.0+dfsg/build_spades/ext/samtools -I/<>/spades-3.13.0+dfsg/ext/src/samtools -I/<>/spades-3.13.0+dfsg/src/include -I/<>/spades-3.13.0+dfsg/build_spades/include -I/<>/spades-3.13.0+dfsg/src -I/<>/spades-3.13.0+dfsg/src/common -isystem /<>/spades-3.13.0+dfsg/src/../ext/include -g -O2 -fdebug-prefix-map=/<>/spades-3.13.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -o CMakeFiles/samtools.dir/kstring.c.o -c /<>/spades-3.13.0+dfsg/ext/src/samtools/kstring.c [ 25%] Building C object ext/samtools/CMakeFiles/samtools.dir/bam_aux.c.o cd /<>/spades-3.13.0+dfsg/build_spades/ext/samtools && /usr/bin/cc -DJEMALLOC_NO_DEMANGLE -DMD5SUM_MAIN -DUSE_GLIBCXX_PARALLEL=1 -D_CURSES_LIB=1 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -I/<>/spades-3.13.0+dfsg/build_spades/ext/samtools -I/<>/spades-3.13.0+dfsg/ext/src/samtools -I/<>/spades-3.13.0+dfsg/src/include -I/<>/spades-3.13.0+dfsg/build_spades/include -I/<>/spades-3.13.0+dfsg/src -I/<>/spades-3.13.0+dfsg/src/common -isystem /<>/spades-3.13.0+dfsg/src/../ext/include -g -O2 -fdebug-prefix-map=/<>/spades-3.13.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -o CMakeFiles/samtools.dir/bam_aux.c.o -c /<>/spades-3.13.0+dfsg/ext/src/samtools/bam_aux.c [ 26%] Building C object ext/samtools/CMakeFiles/samtools.dir/bam.c.o cd /<>/spades-3.13.0+dfsg/build_spades/ext/samtools && /usr/bin/cc -DJEMALLOC_NO_DEMANGLE -DMD5SUM_MAIN -DUSE_GLIBCXX_PARALLEL=1 -D_CURSES_LIB=1 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -I/<>/spades-3.13.0+dfsg/build_spades/ext/samtools -I/<>/spades-3.13.0+dfsg/ext/src/samtools -I/<>/spades-3.13.0+dfsg/src/include -I/<>/spades-3.13.0+dfsg/build_spades/include -I/<>/spades-3.13.0+dfsg/src -I/<>/spades-3.13.0+dfsg/src/common -isystem /<>/spades-3.13.0+dfsg/src/../ext/include -g -O2 -fdebug-prefix-map=/<>/spades-3.13.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -o CMakeFiles/samtools.dir/bam.c.o -c /<>/spades-3.13.0+dfsg/ext/src/samtools/bam.c [ 26%] Building C object ext/samtools/CMakeFiles/samtools.dir/bam_import.c.o cd /<>/spades-3.13.0+dfsg/build_spades/ext/samtools && /usr/bin/cc -DJEMALLOC_NO_DEMANGLE -DMD5SUM_MAIN -DUSE_GLIBCXX_PARALLEL=1 -D_CURSES_LIB=1 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -I/<>/spades-3.13.0+dfsg/build_spades/ext/samtools -I/<>/spades-3.13.0+dfsg/ext/src/samtools -I/<>/spades-3.13.0+dfsg/src/include -I/<>/spades-3.13.0+dfsg/build_spades/include -I/<>/spades-3.13.0+dfsg/src -I/<>/spades-3.13.0+dfsg/src/common -isystem /<>/spades-3.13.0+dfsg/src/../ext/include -g -O2 -fdebug-prefix-map=/<>/spades-3.13.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -o CMakeFiles/samtools.dir/bam_import.c.o -c /<>/spades-3.13.0+dfsg/ext/src/samtools/bam_import.c [ 27%] Building C object ext/samtools/CMakeFiles/samtools.dir/sam.c.o cd /<>/spades-3.13.0+dfsg/build_spades/ext/samtools && /usr/bin/cc -DJEMALLOC_NO_DEMANGLE -DMD5SUM_MAIN -DUSE_GLIBCXX_PARALLEL=1 -D_CURSES_LIB=1 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -I/<>/spades-3.13.0+dfsg/build_spades/ext/samtools -I/<>/spades-3.13.0+dfsg/ext/src/samtools -I/<>/spades-3.13.0+dfsg/src/include -I/<>/spades-3.13.0+dfsg/build_spades/include -I/<>/spades-3.13.0+dfsg/src -I/<>/spades-3.13.0+dfsg/src/common -isystem /<>/spades-3.13.0+dfsg/src/../ext/include -g -O2 -fdebug-prefix-map=/<>/spades-3.13.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -o CMakeFiles/samtools.dir/sam.c.o -c /<>/spades-3.13.0+dfsg/ext/src/samtools/sam.c [ 27%] Building C object ext/samtools/CMakeFiles/samtools.dir/bam_index.c.o cd /<>/spades-3.13.0+dfsg/build_spades/ext/samtools && /usr/bin/cc -DJEMALLOC_NO_DEMANGLE -DMD5SUM_MAIN -DUSE_GLIBCXX_PARALLEL=1 -D_CURSES_LIB=1 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -I/<>/spades-3.13.0+dfsg/build_spades/ext/samtools -I/<>/spades-3.13.0+dfsg/ext/src/samtools -I/<>/spades-3.13.0+dfsg/src/include -I/<>/spades-3.13.0+dfsg/build_spades/include -I/<>/spades-3.13.0+dfsg/src -I/<>/spades-3.13.0+dfsg/src/common -isystem /<>/spades-3.13.0+dfsg/src/../ext/include -g -O2 -fdebug-prefix-map=/<>/spades-3.13.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -o CMakeFiles/samtools.dir/bam_index.c.o -c /<>/spades-3.13.0+dfsg/ext/src/samtools/bam_index.c /<>/spades-3.13.0+dfsg/ext/src/samtools/bam_index.c: In function 'bam_index_load_core': /<>/spades-3.13.0+dfsg/ext/src/samtools/bam_index.c:335:2: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(magic, 1, 4, fp); ^~~~~~~~~~~~~~~~~~~~~~ /<>/spades-3.13.0+dfsg/ext/src/samtools/bam_index.c:342:2: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&idx->n, 4, 1, fp); ^~~~~~~~~~~~~~~~~~~~~~~~ /<>/spades-3.13.0+dfsg/ext/src/samtools/bam_index.c:355:3: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&size, 4, 1, fp); ^~~~~~~~~~~~~~~~~~~~~~ /<>/spades-3.13.0+dfsg/ext/src/samtools/bam_index.c:358:4: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&key, 4, 1, fp); ^~~~~~~~~~~~~~~~~~~~~ /<>/spades-3.13.0+dfsg/ext/src/samtools/bam_index.c:362:4: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&p->n, 4, 1, fp); ^~~~~~~~~~~~~~~~~~~~~~ /<>/spades-3.13.0+dfsg/ext/src/samtools/bam_index.c:366:4: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(p->list, 16, p->n, fp); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/spades-3.13.0+dfsg/ext/src/samtools/bam_index.c:376:3: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&index2->n, 4, 1, fp); ^~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/spades-3.13.0+dfsg/ext/src/samtools/bam_index.c:380:3: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(index2->offset, index2->n, 8, fp); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 28%] Building C object ext/samtools/CMakeFiles/samtools.dir/bam_pileup.c.o cd /<>/spades-3.13.0+dfsg/build_spades/ext/samtools && /usr/bin/cc -DJEMALLOC_NO_DEMANGLE -DMD5SUM_MAIN -DUSE_GLIBCXX_PARALLEL=1 -D_CURSES_LIB=1 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -I/<>/spades-3.13.0+dfsg/build_spades/ext/samtools -I/<>/spades-3.13.0+dfsg/ext/src/samtools -I/<>/spades-3.13.0+dfsg/src/include -I/<>/spades-3.13.0+dfsg/build_spades/include -I/<>/spades-3.13.0+dfsg/src -I/<>/spades-3.13.0+dfsg/src/common -isystem /<>/spades-3.13.0+dfsg/src/../ext/include -g -O2 -fdebug-prefix-map=/<>/spades-3.13.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -o CMakeFiles/samtools.dir/bam_pileup.c.o -c /<>/spades-3.13.0+dfsg/ext/src/samtools/bam_pileup.c [ 28%] Building C object ext/samtools/CMakeFiles/samtools.dir/bam_lpileup.c.o cd /<>/spades-3.13.0+dfsg/build_spades/ext/samtools && /usr/bin/cc -DJEMALLOC_NO_DEMANGLE -DMD5SUM_MAIN -DUSE_GLIBCXX_PARALLEL=1 -D_CURSES_LIB=1 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -I/<>/spades-3.13.0+dfsg/build_spades/ext/samtools -I/<>/spades-3.13.0+dfsg/ext/src/samtools -I/<>/spades-3.13.0+dfsg/src/include -I/<>/spades-3.13.0+dfsg/build_spades/include -I/<>/spades-3.13.0+dfsg/src -I/<>/spades-3.13.0+dfsg/src/common -isystem /<>/spades-3.13.0+dfsg/src/../ext/include -g -O2 -fdebug-prefix-map=/<>/spades-3.13.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -o CMakeFiles/samtools.dir/bam_lpileup.c.o -c /<>/spades-3.13.0+dfsg/ext/src/samtools/bam_lpileup.c [ 28%] Building C object ext/samtools/CMakeFiles/samtools.dir/bam_md.c.o cd /<>/spades-3.13.0+dfsg/build_spades/ext/samtools && /usr/bin/cc -DJEMALLOC_NO_DEMANGLE -DMD5SUM_MAIN -DUSE_GLIBCXX_PARALLEL=1 -D_CURSES_LIB=1 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -I/<>/spades-3.13.0+dfsg/build_spades/ext/samtools -I/<>/spades-3.13.0+dfsg/ext/src/samtools -I/<>/spades-3.13.0+dfsg/src/include -I/<>/spades-3.13.0+dfsg/build_spades/include -I/<>/spades-3.13.0+dfsg/src -I/<>/spades-3.13.0+dfsg/src/common -isystem /<>/spades-3.13.0+dfsg/src/../ext/include -g -O2 -fdebug-prefix-map=/<>/spades-3.13.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -o CMakeFiles/samtools.dir/bam_md.c.o -c /<>/spades-3.13.0+dfsg/ext/src/samtools/bam_md.c [ 29%] Building C object ext/samtools/CMakeFiles/samtools.dir/razf.c.o cd /<>/spades-3.13.0+dfsg/build_spades/ext/samtools && /usr/bin/cc -DJEMALLOC_NO_DEMANGLE -DMD5SUM_MAIN -DUSE_GLIBCXX_PARALLEL=1 -D_CURSES_LIB=1 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -I/<>/spades-3.13.0+dfsg/build_spades/ext/samtools -I/<>/spades-3.13.0+dfsg/ext/src/samtools -I/<>/spades-3.13.0+dfsg/src/include -I/<>/spades-3.13.0+dfsg/build_spades/include -I/<>/spades-3.13.0+dfsg/src -I/<>/spades-3.13.0+dfsg/src/common -isystem /<>/spades-3.13.0+dfsg/src/../ext/include -g -O2 -fdebug-prefix-map=/<>/spades-3.13.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -o CMakeFiles/samtools.dir/razf.c.o -c /<>/spades-3.13.0+dfsg/ext/src/samtools/razf.c /<>/spades-3.13.0+dfsg/ext/src/samtools/razf.c: In function 'razf_flush': /<>/spades-3.13.0+dfsg/ext/src/samtools/razf.c:221:3: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] write(rz->x.fpw, rz->outbuf, RZ_BUFFER_SIZE - rz->stream->avail_out); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/spades-3.13.0+dfsg/ext/src/samtools/razf.c:234:4: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] write(rz->x.fpw, rz->outbuf, RZ_BUFFER_SIZE - rz->stream->avail_out); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/spades-3.13.0+dfsg/ext/src/samtools/razf.c: In function '_razf_write': /<>/spades-3.13.0+dfsg/ext/src/samtools/razf.c:201:3: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] write(rz->x.fpw, rz->outbuf, RZ_BUFFER_SIZE - rz->stream->avail_out); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/spades-3.13.0+dfsg/ext/src/samtools/razf.c: In function 'razf_close': /<>/spades-3.13.0+dfsg/ext/src/samtools/razf.c:804:4: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] write(rz->x.fpw, &rz->in, sizeof(int64_t)); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/spades-3.13.0+dfsg/ext/src/samtools/razf.c:805:4: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] write(rz->x.fpw, &rz->out, sizeof(int64_t)); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/spades-3.13.0+dfsg/ext/src/samtools/razf.c:808:4: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] write(rz->x.fpw, &v64, sizeof(int64_t)); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/spades-3.13.0+dfsg/ext/src/samtools/razf.c:810:4: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] write(rz->x.fpw, &v64, sizeof(int64_t)); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/spades-3.13.0+dfsg/ext/src/samtools/razf.c: In function 'razf_end_flush': /<>/spades-3.13.0+dfsg/ext/src/samtools/razf.c:258:4: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] write(rz->x.fpw, rz->outbuf, RZ_BUFFER_SIZE - rz->stream->avail_out); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/spades-3.13.0+dfsg/ext/src/samtools/razf.c: In function 'save_zindex': /<>/spades-3.13.0+dfsg/ext/src/samtools/razf.c:96:12: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] if(is_be) write(fd, &rz->index->size, sizeof(int)); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/spades-3.13.0+dfsg/ext/src/samtools/razf.c:99:3: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] write(fd, &v32, sizeof(uint32_t)); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/spades-3.13.0+dfsg/ext/src/samtools/razf.c:106:2: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] write(fd, rz->index->bin_offsets, sizeof(int64_t) * v32); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/spades-3.13.0+dfsg/ext/src/samtools/razf.c:107:2: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] write(fd, rz->index->cell_offsets, sizeof(int32_t) * rz->index->size); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 29%] Building C object ext/samtools/CMakeFiles/samtools.dir/faidx.c.o cd /<>/spades-3.13.0+dfsg/build_spades/ext/samtools && /usr/bin/cc -DJEMALLOC_NO_DEMANGLE -DMD5SUM_MAIN -DUSE_GLIBCXX_PARALLEL=1 -D_CURSES_LIB=1 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -I/<>/spades-3.13.0+dfsg/build_spades/ext/samtools -I/<>/spades-3.13.0+dfsg/ext/src/samtools -I/<>/spades-3.13.0+dfsg/src/include -I/<>/spades-3.13.0+dfsg/build_spades/include -I/<>/spades-3.13.0+dfsg/src -I/<>/spades-3.13.0+dfsg/src/common -isystem /<>/spades-3.13.0+dfsg/src/../ext/include -g -O2 -fdebug-prefix-map=/<>/spades-3.13.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -o CMakeFiles/samtools.dir/faidx.c.o -c /<>/spades-3.13.0+dfsg/ext/src/samtools/faidx.c [ 30%] Building C object ext/samtools/CMakeFiles/samtools.dir/bedidx.c.o cd /<>/spades-3.13.0+dfsg/build_spades/ext/samtools && /usr/bin/cc -DJEMALLOC_NO_DEMANGLE -DMD5SUM_MAIN -DUSE_GLIBCXX_PARALLEL=1 -D_CURSES_LIB=1 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -I/<>/spades-3.13.0+dfsg/build_spades/ext/samtools -I/<>/spades-3.13.0+dfsg/ext/src/samtools -I/<>/spades-3.13.0+dfsg/src/include -I/<>/spades-3.13.0+dfsg/build_spades/include -I/<>/spades-3.13.0+dfsg/src -I/<>/spades-3.13.0+dfsg/src/common -isystem /<>/spades-3.13.0+dfsg/src/../ext/include -g -O2 -fdebug-prefix-map=/<>/spades-3.13.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -o CMakeFiles/samtools.dir/bedidx.c.o -c /<>/spades-3.13.0+dfsg/ext/src/samtools/bedidx.c [ 30%] Building C object ext/samtools/CMakeFiles/samtools.dir/bam_sort.c.o cd /<>/spades-3.13.0+dfsg/build_spades/ext/samtools && /usr/bin/cc -DJEMALLOC_NO_DEMANGLE -DMD5SUM_MAIN -DUSE_GLIBCXX_PARALLEL=1 -D_CURSES_LIB=1 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -I/<>/spades-3.13.0+dfsg/build_spades/ext/samtools -I/<>/spades-3.13.0+dfsg/ext/src/samtools -I/<>/spades-3.13.0+dfsg/src/include -I/<>/spades-3.13.0+dfsg/build_spades/include -I/<>/spades-3.13.0+dfsg/src -I/<>/spades-3.13.0+dfsg/src/common -isystem /<>/spades-3.13.0+dfsg/src/../ext/include -g -O2 -fdebug-prefix-map=/<>/spades-3.13.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -o CMakeFiles/samtools.dir/bam_sort.c.o -c /<>/spades-3.13.0+dfsg/ext/src/samtools/bam_sort.c [ 31%] Building C object ext/samtools/CMakeFiles/samtools.dir/sam_header.c.o cd /<>/spades-3.13.0+dfsg/build_spades/ext/samtools && /usr/bin/cc -DJEMALLOC_NO_DEMANGLE -DMD5SUM_MAIN -DUSE_GLIBCXX_PARALLEL=1 -D_CURSES_LIB=1 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -I/<>/spades-3.13.0+dfsg/build_spades/ext/samtools -I/<>/spades-3.13.0+dfsg/ext/src/samtools -I/<>/spades-3.13.0+dfsg/src/include -I/<>/spades-3.13.0+dfsg/build_spades/include -I/<>/spades-3.13.0+dfsg/src -I/<>/spades-3.13.0+dfsg/src/common -isystem /<>/spades-3.13.0+dfsg/src/../ext/include -g -O2 -fdebug-prefix-map=/<>/spades-3.13.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -o CMakeFiles/samtools.dir/sam_header.c.o -c /<>/spades-3.13.0+dfsg/ext/src/samtools/sam_header.c [ 31%] Building C object ext/samtools/CMakeFiles/samtools.dir/bam_reheader.c.o cd /<>/spades-3.13.0+dfsg/build_spades/ext/samtools && /usr/bin/cc -DJEMALLOC_NO_DEMANGLE -DMD5SUM_MAIN -DUSE_GLIBCXX_PARALLEL=1 -D_CURSES_LIB=1 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -I/<>/spades-3.13.0+dfsg/build_spades/ext/samtools -I/<>/spades-3.13.0+dfsg/ext/src/samtools -I/<>/spades-3.13.0+dfsg/src/include -I/<>/spades-3.13.0+dfsg/build_spades/include -I/<>/spades-3.13.0+dfsg/src -I/<>/spades-3.13.0+dfsg/src/common -isystem /<>/spades-3.13.0+dfsg/src/../ext/include -g -O2 -fdebug-prefix-map=/<>/spades-3.13.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -o CMakeFiles/samtools.dir/bam_reheader.c.o -c /<>/spades-3.13.0+dfsg/ext/src/samtools/bam_reheader.c [ 32%] Building C object ext/samtools/CMakeFiles/samtools.dir/kprobaln.c.o cd /<>/spades-3.13.0+dfsg/build_spades/ext/samtools && /usr/bin/cc -DJEMALLOC_NO_DEMANGLE -DMD5SUM_MAIN -DUSE_GLIBCXX_PARALLEL=1 -D_CURSES_LIB=1 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -I/<>/spades-3.13.0+dfsg/build_spades/ext/samtools -I/<>/spades-3.13.0+dfsg/ext/src/samtools -I/<>/spades-3.13.0+dfsg/src/include -I/<>/spades-3.13.0+dfsg/build_spades/include -I/<>/spades-3.13.0+dfsg/src -I/<>/spades-3.13.0+dfsg/src/common -isystem /<>/spades-3.13.0+dfsg/src/../ext/include -g -O2 -fdebug-prefix-map=/<>/spades-3.13.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -o CMakeFiles/samtools.dir/kprobaln.c.o -c /<>/spades-3.13.0+dfsg/ext/src/samtools/kprobaln.c [ 32%] Building C object ext/samtools/CMakeFiles/samtools.dir/bam_cat.c.o cd /<>/spades-3.13.0+dfsg/build_spades/ext/samtools && /usr/bin/cc -DJEMALLOC_NO_DEMANGLE -DMD5SUM_MAIN -DUSE_GLIBCXX_PARALLEL=1 -D_CURSES_LIB=1 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -I/<>/spades-3.13.0+dfsg/build_spades/ext/samtools -I/<>/spades-3.13.0+dfsg/ext/src/samtools -I/<>/spades-3.13.0+dfsg/src/include -I/<>/spades-3.13.0+dfsg/build_spades/include -I/<>/spades-3.13.0+dfsg/src -I/<>/spades-3.13.0+dfsg/src/common -isystem /<>/spades-3.13.0+dfsg/src/../ext/include -g -O2 -fdebug-prefix-map=/<>/spades-3.13.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -o CMakeFiles/samtools.dir/bam_cat.c.o -c /<>/spades-3.13.0+dfsg/ext/src/samtools/bam_cat.c [ 33%] Linking CXX static library libsamtools.a cd /<>/spades-3.13.0+dfsg/build_spades/ext/samtools && /usr/bin/cmake -P CMakeFiles/samtools.dir/cmake_clean_target.cmake cd /<>/spades-3.13.0+dfsg/build_spades/ext/samtools && /usr/bin/cmake -E cmake_link_script CMakeFiles/samtools.dir/link.txt --verbose=1 /usr/bin/ar qc libsamtools.a CMakeFiles/samtools.dir/kstring.c.o CMakeFiles/samtools.dir/bam_aux.c.o CMakeFiles/samtools.dir/bam.c.o CMakeFiles/samtools.dir/bam_import.c.o CMakeFiles/samtools.dir/sam.c.o CMakeFiles/samtools.dir/bam_index.c.o CMakeFiles/samtools.dir/bam_pileup.c.o CMakeFiles/samtools.dir/bam_lpileup.c.o CMakeFiles/samtools.dir/bam_md.c.o CMakeFiles/samtools.dir/razf.c.o CMakeFiles/samtools.dir/faidx.c.o CMakeFiles/samtools.dir/bedidx.c.o CMakeFiles/samtools.dir/bam_sort.c.o CMakeFiles/samtools.dir/sam_header.c.o CMakeFiles/samtools.dir/bam_reheader.c.o CMakeFiles/samtools.dir/kprobaln.c.o CMakeFiles/samtools.dir/bam_cat.c.o /usr/bin/ranlib libsamtools.a make[4]: Leaving directory '/<>/spades-3.13.0+dfsg/build_spades' [ 33%] Built target samtools make -f ext/cppformat/CMakeFiles/format.dir/build.make ext/cppformat/CMakeFiles/format.dir/depend make[4]: Entering directory '/<>/spades-3.13.0+dfsg/build_spades' cd /<>/spades-3.13.0+dfsg/build_spades && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/spades-3.13.0+dfsg/src /<>/spades-3.13.0+dfsg/ext/src/cppformat /<>/spades-3.13.0+dfsg/build_spades /<>/spades-3.13.0+dfsg/build_spades/ext/cppformat /<>/spades-3.13.0+dfsg/build_spades/ext/cppformat/CMakeFiles/format.dir/DependInfo.cmake --color= Dependee "/<>/spades-3.13.0+dfsg/build_spades/ext/cppformat/CMakeFiles/format.dir/DependInfo.cmake" is newer than depender "/<>/spades-3.13.0+dfsg/build_spades/ext/cppformat/CMakeFiles/format.dir/depend.internal". 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Scanning dependencies of target format make[4]: Leaving directory '/<>/spades-3.13.0+dfsg/build_spades' make -f ext/cppformat/CMakeFiles/format.dir/build.make ext/cppformat/CMakeFiles/format.dir/build make[4]: Entering directory '/<>/spades-3.13.0+dfsg/build_spades' [ 34%] Building CXX object ext/cppformat/CMakeFiles/format.dir/format.cc.o cd /<>/spades-3.13.0+dfsg/build_spades/ext/cppformat && /usr/bin/c++ -DFMT_USE_FILE_DESCRIPTORS=1 -DJEMALLOC_NO_DEMANGLE -DUSE_GLIBCXX_PARALLEL=1 -I/<>/spades-3.13.0+dfsg/build_spades/ext/cppformat -I/<>/spades-3.13.0+dfsg/ext/src/cppformat -I/<>/spades-3.13.0+dfsg/src/include -I/<>/spades-3.13.0+dfsg/build_spades/include -I/<>/spades-3.13.0+dfsg/src -I/<>/spades-3.13.0+dfsg/src/common -isystem /<>/spades-3.13.0+dfsg/src/../ext/include -g -O2 -fdebug-prefix-map=/<>/spades-3.13.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wall -Wextra -pedantic -Wno-deprecated -g3 -O2 -o CMakeFiles/format.dir/format.cc.o -c /<>/spades-3.13.0+dfsg/ext/src/cppformat/format.cc [ 34%] Building CXX object ext/cppformat/CMakeFiles/format.dir/posix.cc.o cd /<>/spades-3.13.0+dfsg/build_spades/ext/cppformat && /usr/bin/c++ -DFMT_USE_FILE_DESCRIPTORS=1 -DJEMALLOC_NO_DEMANGLE -DUSE_GLIBCXX_PARALLEL=1 -I/<>/spades-3.13.0+dfsg/build_spades/ext/cppformat -I/<>/spades-3.13.0+dfsg/ext/src/cppformat -I/<>/spades-3.13.0+dfsg/src/include -I/<>/spades-3.13.0+dfsg/build_spades/include -I/<>/spades-3.13.0+dfsg/src -I/<>/spades-3.13.0+dfsg/src/common -isystem /<>/spades-3.13.0+dfsg/src/../ext/include -g -O2 -fdebug-prefix-map=/<>/spades-3.13.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wall -Wextra -pedantic -Wno-deprecated -g3 -O2 -o CMakeFiles/format.dir/posix.cc.o -c /<>/spades-3.13.0+dfsg/ext/src/cppformat/posix.cc [ 35%] Linking CXX static library libformat.a cd /<>/spades-3.13.0+dfsg/build_spades/ext/cppformat && /usr/bin/cmake -P CMakeFiles/format.dir/cmake_clean_target.cmake cd /<>/spades-3.13.0+dfsg/build_spades/ext/cppformat && /usr/bin/cmake -E cmake_link_script CMakeFiles/format.dir/link.txt --verbose=1 /usr/bin/ar qc libformat.a CMakeFiles/format.dir/format.cc.o CMakeFiles/format.dir/posix.cc.o /usr/bin/ranlib libformat.a make[4]: Leaving directory '/<>/spades-3.13.0+dfsg/build_spades' [ 35%] Built target format make -f ext/cityhash/CMakeFiles/cityhash.dir/build.make ext/cityhash/CMakeFiles/cityhash.dir/depend make[4]: Entering directory '/<>/spades-3.13.0+dfsg/build_spades' cd /<>/spades-3.13.0+dfsg/build_spades && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/spades-3.13.0+dfsg/src /<>/spades-3.13.0+dfsg/ext/src/cityhash /<>/spades-3.13.0+dfsg/build_spades /<>/spades-3.13.0+dfsg/build_spades/ext/cityhash /<>/spades-3.13.0+dfsg/build_spades/ext/cityhash/CMakeFiles/cityhash.dir/DependInfo.cmake --color= Dependee "/<>/spades-3.13.0+dfsg/build_spades/ext/cityhash/CMakeFiles/cityhash.dir/DependInfo.cmake" is newer than depender "/<>/spades-3.13.0+dfsg/build_spades/ext/cityhash/CMakeFiles/cityhash.dir/depend.internal". 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Scanning dependencies of target cityhash make[4]: Leaving directory '/<>/spades-3.13.0+dfsg/build_spades' make -f ext/cityhash/CMakeFiles/cityhash.dir/build.make ext/cityhash/CMakeFiles/cityhash.dir/build make[4]: Entering directory '/<>/spades-3.13.0+dfsg/build_spades' [ 35%] Building CXX object ext/cityhash/CMakeFiles/cityhash.dir/city.cc.o cd /<>/spades-3.13.0+dfsg/build_spades/ext/cityhash && /usr/bin/c++ -DJEMALLOC_NO_DEMANGLE -DUSE_GLIBCXX_PARALLEL=1 -I/<>/spades-3.13.0+dfsg/build_spades/ext/cityhash -I/<>/spades-3.13.0+dfsg/ext/src/cityhash -I/<>/spades-3.13.0+dfsg/src/include -I/<>/spades-3.13.0+dfsg/build_spades/include -I/<>/spades-3.13.0+dfsg/src -I/<>/spades-3.13.0+dfsg/src/common -isystem /<>/spades-3.13.0+dfsg/src/../ext/include -g -O2 -fdebug-prefix-map=/<>/spades-3.13.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -o CMakeFiles/cityhash.dir/city.cc.o -c /<>/spades-3.13.0+dfsg/ext/src/cityhash/city.cc [ 36%] Linking CXX static library libcityhash.a cd /<>/spades-3.13.0+dfsg/build_spades/ext/cityhash && /usr/bin/cmake -P CMakeFiles/cityhash.dir/cmake_clean_target.cmake cd /<>/spades-3.13.0+dfsg/build_spades/ext/cityhash && /usr/bin/cmake -E cmake_link_script CMakeFiles/cityhash.dir/link.txt --verbose=1 /usr/bin/ar qc libcityhash.a CMakeFiles/cityhash.dir/city.cc.o /usr/bin/ranlib libcityhash.a make[4]: Leaving directory '/<>/spades-3.13.0+dfsg/build_spades' [ 36%] Built target cityhash make -f ext/getopt_pp/CMakeFiles/getopt_pp.dir/build.make ext/getopt_pp/CMakeFiles/getopt_pp.dir/depend make[4]: Entering directory '/<>/spades-3.13.0+dfsg/build_spades' cd /<>/spades-3.13.0+dfsg/build_spades && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/spades-3.13.0+dfsg/src /<>/spades-3.13.0+dfsg/ext/src/getopt_pp /<>/spades-3.13.0+dfsg/build_spades /<>/spades-3.13.0+dfsg/build_spades/ext/getopt_pp /<>/spades-3.13.0+dfsg/build_spades/ext/getopt_pp/CMakeFiles/getopt_pp.dir/DependInfo.cmake --color= Dependee "/<>/spades-3.13.0+dfsg/build_spades/ext/getopt_pp/CMakeFiles/getopt_pp.dir/DependInfo.cmake" is newer than depender "/<>/spades-3.13.0+dfsg/build_spades/ext/getopt_pp/CMakeFiles/getopt_pp.dir/depend.internal". 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Scanning dependencies of target getopt_pp make[4]: Leaving directory '/<>/spades-3.13.0+dfsg/build_spades' make -f ext/getopt_pp/CMakeFiles/getopt_pp.dir/build.make ext/getopt_pp/CMakeFiles/getopt_pp.dir/build make[4]: Entering directory '/<>/spades-3.13.0+dfsg/build_spades' [ 36%] Building CXX object ext/getopt_pp/CMakeFiles/getopt_pp.dir/getopt_pp.cpp.o cd /<>/spades-3.13.0+dfsg/build_spades/ext/getopt_pp && /usr/bin/c++ -DJEMALLOC_NO_DEMANGLE -DUSE_GLIBCXX_PARALLEL=1 -I/<>/spades-3.13.0+dfsg/build_spades/ext/getopt_pp -I/<>/spades-3.13.0+dfsg/ext/src/getopt_pp -I/<>/spades-3.13.0+dfsg/src/include -I/<>/spades-3.13.0+dfsg/build_spades/include -I/<>/spades-3.13.0+dfsg/src -I/<>/spades-3.13.0+dfsg/src/common -isystem /<>/spades-3.13.0+dfsg/src/../ext/include -g -O2 -fdebug-prefix-map=/<>/spades-3.13.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -o CMakeFiles/getopt_pp.dir/getopt_pp.cpp.o -c /<>/spades-3.13.0+dfsg/ext/src/getopt_pp/getopt_pp.cpp [ 37%] Linking CXX static library libgetopt_pp.a cd /<>/spades-3.13.0+dfsg/build_spades/ext/getopt_pp && /usr/bin/cmake -P CMakeFiles/getopt_pp.dir/cmake_clean_target.cmake cd /<>/spades-3.13.0+dfsg/build_spades/ext/getopt_pp && /usr/bin/cmake -E cmake_link_script CMakeFiles/getopt_pp.dir/link.txt --verbose=1 /usr/bin/ar qc libgetopt_pp.a CMakeFiles/getopt_pp.dir/getopt_pp.cpp.o /usr/bin/ranlib libgetopt_pp.a make[4]: Leaving directory '/<>/spades-3.13.0+dfsg/build_spades' [ 37%] Built target getopt_pp make -f ext/llvm/CMakeFiles/llvm-support.dir/build.make ext/llvm/CMakeFiles/llvm-support.dir/depend make[4]: Entering directory '/<>/spades-3.13.0+dfsg/build_spades' cd /<>/spades-3.13.0+dfsg/build_spades && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/spades-3.13.0+dfsg/src /<>/spades-3.13.0+dfsg/ext/src/llvm /<>/spades-3.13.0+dfsg/build_spades /<>/spades-3.13.0+dfsg/build_spades/ext/llvm /<>/spades-3.13.0+dfsg/build_spades/ext/llvm/CMakeFiles/llvm-support.dir/DependInfo.cmake --color= Dependee "/<>/spades-3.13.0+dfsg/build_spades/ext/llvm/CMakeFiles/llvm-support.dir/DependInfo.cmake" is newer than depender "/<>/spades-3.13.0+dfsg/build_spades/ext/llvm/CMakeFiles/llvm-support.dir/depend.internal". 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Scanning dependencies of target llvm-support make[4]: Leaving directory '/<>/spades-3.13.0+dfsg/build_spades' make -f ext/llvm/CMakeFiles/llvm-support.dir/build.make ext/llvm/CMakeFiles/llvm-support.dir/build make[4]: Entering directory '/<>/spades-3.13.0+dfsg/build_spades' [ 38%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/Atomic.cpp.o cd /<>/spades-3.13.0+dfsg/build_spades/ext/llvm && /usr/bin/c++ -DJEMALLOC_NO_DEMANGLE -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/<>/spades-3.13.0+dfsg/build_spades/ext/llvm -I/<>/spades-3.13.0+dfsg/ext/src/llvm -I/<>/spades-3.13.0+dfsg/src/include -I/<>/spades-3.13.0+dfsg/build_spades/include -I/<>/spades-3.13.0+dfsg/src -I/<>/spades-3.13.0+dfsg/src/common -isystem /<>/spades-3.13.0+dfsg/src/../ext/include -g -O2 -fdebug-prefix-map=/<>/spades-3.13.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -o CMakeFiles/llvm-support.dir/Atomic.cpp.o -c /<>/spades-3.13.0+dfsg/ext/src/llvm/Atomic.cpp [ 38%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/ErrorHandling.cpp.o cd /<>/spades-3.13.0+dfsg/build_spades/ext/llvm && /usr/bin/c++ -DJEMALLOC_NO_DEMANGLE -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/<>/spades-3.13.0+dfsg/build_spades/ext/llvm -I/<>/spades-3.13.0+dfsg/ext/src/llvm -I/<>/spades-3.13.0+dfsg/src/include -I/<>/spades-3.13.0+dfsg/build_spades/include -I/<>/spades-3.13.0+dfsg/src -I/<>/spades-3.13.0+dfsg/src/common -isystem /<>/spades-3.13.0+dfsg/src/../ext/include -g -O2 -fdebug-prefix-map=/<>/spades-3.13.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -o CMakeFiles/llvm-support.dir/ErrorHandling.cpp.o -c /<>/spades-3.13.0+dfsg/ext/src/llvm/ErrorHandling.cpp [ 38%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/Hashing.cpp.o cd /<>/spades-3.13.0+dfsg/build_spades/ext/llvm && /usr/bin/c++ -DJEMALLOC_NO_DEMANGLE -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/<>/spades-3.13.0+dfsg/build_spades/ext/llvm -I/<>/spades-3.13.0+dfsg/ext/src/llvm -I/<>/spades-3.13.0+dfsg/src/include -I/<>/spades-3.13.0+dfsg/build_spades/include -I/<>/spades-3.13.0+dfsg/src -I/<>/spades-3.13.0+dfsg/src/common -isystem /<>/spades-3.13.0+dfsg/src/../ext/include -g -O2 -fdebug-prefix-map=/<>/spades-3.13.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -o CMakeFiles/llvm-support.dir/Hashing.cpp.o -c /<>/spades-3.13.0+dfsg/ext/src/llvm/Hashing.cpp [ 39%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/LineIterator.cpp.o cd /<>/spades-3.13.0+dfsg/build_spades/ext/llvm && /usr/bin/c++ -DJEMALLOC_NO_DEMANGLE -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/<>/spades-3.13.0+dfsg/build_spades/ext/llvm -I/<>/spades-3.13.0+dfsg/ext/src/llvm -I/<>/spades-3.13.0+dfsg/src/include -I/<>/spades-3.13.0+dfsg/build_spades/include -I/<>/spades-3.13.0+dfsg/src -I/<>/spades-3.13.0+dfsg/src/common -isystem /<>/spades-3.13.0+dfsg/src/../ext/include -g -O2 -fdebug-prefix-map=/<>/spades-3.13.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -o CMakeFiles/llvm-support.dir/LineIterator.cpp.o -c /<>/spades-3.13.0+dfsg/ext/src/llvm/LineIterator.cpp [ 39%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/MemoryBuffer.cpp.o cd /<>/spades-3.13.0+dfsg/build_spades/ext/llvm && /usr/bin/c++ -DJEMALLOC_NO_DEMANGLE -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/<>/spades-3.13.0+dfsg/build_spades/ext/llvm -I/<>/spades-3.13.0+dfsg/ext/src/llvm -I/<>/spades-3.13.0+dfsg/src/include -I/<>/spades-3.13.0+dfsg/build_spades/include -I/<>/spades-3.13.0+dfsg/src -I/<>/spades-3.13.0+dfsg/src/common -isystem /<>/spades-3.13.0+dfsg/src/../ext/include -g -O2 -fdebug-prefix-map=/<>/spades-3.13.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -o CMakeFiles/llvm-support.dir/MemoryBuffer.cpp.o -c /<>/spades-3.13.0+dfsg/ext/src/llvm/MemoryBuffer.cpp [ 40%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/Mutex.cpp.o cd /<>/spades-3.13.0+dfsg/build_spades/ext/llvm && /usr/bin/c++ -DJEMALLOC_NO_DEMANGLE -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/<>/spades-3.13.0+dfsg/build_spades/ext/llvm -I/<>/spades-3.13.0+dfsg/ext/src/llvm -I/<>/spades-3.13.0+dfsg/src/include -I/<>/spades-3.13.0+dfsg/build_spades/include -I/<>/spades-3.13.0+dfsg/src -I/<>/spades-3.13.0+dfsg/src/common -isystem /<>/spades-3.13.0+dfsg/src/../ext/include -g -O2 -fdebug-prefix-map=/<>/spades-3.13.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -o CMakeFiles/llvm-support.dir/Mutex.cpp.o -c /<>/spades-3.13.0+dfsg/ext/src/llvm/Mutex.cpp [ 40%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/Path.cpp.o cd /<>/spades-3.13.0+dfsg/build_spades/ext/llvm && /usr/bin/c++ -DJEMALLOC_NO_DEMANGLE -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/<>/spades-3.13.0+dfsg/build_spades/ext/llvm -I/<>/spades-3.13.0+dfsg/ext/src/llvm -I/<>/spades-3.13.0+dfsg/src/include -I/<>/spades-3.13.0+dfsg/build_spades/include -I/<>/spades-3.13.0+dfsg/src -I/<>/spades-3.13.0+dfsg/src/common -isystem /<>/spades-3.13.0+dfsg/src/../ext/include -g -O2 -fdebug-prefix-map=/<>/spades-3.13.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -o CMakeFiles/llvm-support.dir/Path.cpp.o -c /<>/spades-3.13.0+dfsg/ext/src/llvm/Path.cpp [ 41%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/Regex.cpp.o cd /<>/spades-3.13.0+dfsg/build_spades/ext/llvm && /usr/bin/c++ -DJEMALLOC_NO_DEMANGLE -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/<>/spades-3.13.0+dfsg/build_spades/ext/llvm -I/<>/spades-3.13.0+dfsg/ext/src/llvm -I/<>/spades-3.13.0+dfsg/src/include -I/<>/spades-3.13.0+dfsg/build_spades/include -I/<>/spades-3.13.0+dfsg/src -I/<>/spades-3.13.0+dfsg/src/common -isystem /<>/spades-3.13.0+dfsg/src/../ext/include -g -O2 -fdebug-prefix-map=/<>/spades-3.13.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -o CMakeFiles/llvm-support.dir/Regex.cpp.o -c /<>/spades-3.13.0+dfsg/ext/src/llvm/Regex.cpp [ 41%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/Signals.cpp.o cd /<>/spades-3.13.0+dfsg/build_spades/ext/llvm && /usr/bin/c++ -DJEMALLOC_NO_DEMANGLE -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/<>/spades-3.13.0+dfsg/build_spades/ext/llvm -I/<>/spades-3.13.0+dfsg/ext/src/llvm -I/<>/spades-3.13.0+dfsg/src/include -I/<>/spades-3.13.0+dfsg/build_spades/include -I/<>/spades-3.13.0+dfsg/src -I/<>/spades-3.13.0+dfsg/src/common -isystem /<>/spades-3.13.0+dfsg/src/../ext/include -g -O2 -fdebug-prefix-map=/<>/spades-3.13.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -o CMakeFiles/llvm-support.dir/Signals.cpp.o -c /<>/spades-3.13.0+dfsg/ext/src/llvm/Signals.cpp [ 42%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/SmallVector.cpp.o cd /<>/spades-3.13.0+dfsg/build_spades/ext/llvm && /usr/bin/c++ -DJEMALLOC_NO_DEMANGLE -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/<>/spades-3.13.0+dfsg/build_spades/ext/llvm -I/<>/spades-3.13.0+dfsg/ext/src/llvm -I/<>/spades-3.13.0+dfsg/src/include -I/<>/spades-3.13.0+dfsg/build_spades/include -I/<>/spades-3.13.0+dfsg/src -I/<>/spades-3.13.0+dfsg/src/common -isystem /<>/spades-3.13.0+dfsg/src/../ext/include -g -O2 -fdebug-prefix-map=/<>/spades-3.13.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -o CMakeFiles/llvm-support.dir/SmallVector.cpp.o -c /<>/spades-3.13.0+dfsg/ext/src/llvm/SmallVector.cpp [ 42%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/SourceMgr.cpp.o cd /<>/spades-3.13.0+dfsg/build_spades/ext/llvm && /usr/bin/c++ -DJEMALLOC_NO_DEMANGLE -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/<>/spades-3.13.0+dfsg/build_spades/ext/llvm -I/<>/spades-3.13.0+dfsg/ext/src/llvm -I/<>/spades-3.13.0+dfsg/src/include -I/<>/spades-3.13.0+dfsg/build_spades/include -I/<>/spades-3.13.0+dfsg/src -I/<>/spades-3.13.0+dfsg/src/common -isystem /<>/spades-3.13.0+dfsg/src/../ext/include -g -O2 -fdebug-prefix-map=/<>/spades-3.13.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -o CMakeFiles/llvm-support.dir/SourceMgr.cpp.o -c /<>/spades-3.13.0+dfsg/ext/src/llvm/SourceMgr.cpp [ 43%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/StringMap.cpp.o cd /<>/spades-3.13.0+dfsg/build_spades/ext/llvm && /usr/bin/c++ -DJEMALLOC_NO_DEMANGLE -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/<>/spades-3.13.0+dfsg/build_spades/ext/llvm -I/<>/spades-3.13.0+dfsg/ext/src/llvm -I/<>/spades-3.13.0+dfsg/src/include -I/<>/spades-3.13.0+dfsg/build_spades/include -I/<>/spades-3.13.0+dfsg/src -I/<>/spades-3.13.0+dfsg/src/common -isystem /<>/spades-3.13.0+dfsg/src/../ext/include -g -O2 -fdebug-prefix-map=/<>/spades-3.13.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -o CMakeFiles/llvm-support.dir/StringMap.cpp.o -c /<>/spades-3.13.0+dfsg/ext/src/llvm/StringMap.cpp [ 43%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/StringRef.cpp.o cd /<>/spades-3.13.0+dfsg/build_spades/ext/llvm && /usr/bin/c++ -DJEMALLOC_NO_DEMANGLE -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/<>/spades-3.13.0+dfsg/build_spades/ext/llvm -I/<>/spades-3.13.0+dfsg/ext/src/llvm -I/<>/spades-3.13.0+dfsg/src/include -I/<>/spades-3.13.0+dfsg/build_spades/include -I/<>/spades-3.13.0+dfsg/src -I/<>/spades-3.13.0+dfsg/src/common -isystem /<>/spades-3.13.0+dfsg/src/../ext/include -g -O2 -fdebug-prefix-map=/<>/spades-3.13.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -o CMakeFiles/llvm-support.dir/StringRef.cpp.o -c /<>/spades-3.13.0+dfsg/ext/src/llvm/StringRef.cpp [ 43%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/Twine.cpp.o cd /<>/spades-3.13.0+dfsg/build_spades/ext/llvm && /usr/bin/c++ -DJEMALLOC_NO_DEMANGLE -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/<>/spades-3.13.0+dfsg/build_spades/ext/llvm -I/<>/spades-3.13.0+dfsg/ext/src/llvm -I/<>/spades-3.13.0+dfsg/src/include -I/<>/spades-3.13.0+dfsg/build_spades/include -I/<>/spades-3.13.0+dfsg/src -I/<>/spades-3.13.0+dfsg/src/common -isystem /<>/spades-3.13.0+dfsg/src/../ext/include -g -O2 -fdebug-prefix-map=/<>/spades-3.13.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -o CMakeFiles/llvm-support.dir/Twine.cpp.o -c /<>/spades-3.13.0+dfsg/ext/src/llvm/Twine.cpp [ 44%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/YAMLParser.cpp.o cd /<>/spades-3.13.0+dfsg/build_spades/ext/llvm && /usr/bin/c++ -DJEMALLOC_NO_DEMANGLE -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/<>/spades-3.13.0+dfsg/build_spades/ext/llvm -I/<>/spades-3.13.0+dfsg/ext/src/llvm -I/<>/spades-3.13.0+dfsg/src/include -I/<>/spades-3.13.0+dfsg/build_spades/include -I/<>/spades-3.13.0+dfsg/src -I/<>/spades-3.13.0+dfsg/src/common -isystem /<>/spades-3.13.0+dfsg/src/../ext/include -g -O2 -fdebug-prefix-map=/<>/spades-3.13.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -o CMakeFiles/llvm-support.dir/YAMLParser.cpp.o -c /<>/spades-3.13.0+dfsg/ext/src/llvm/YAMLParser.cpp [ 44%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/YAMLTraits.cpp.o cd /<>/spades-3.13.0+dfsg/build_spades/ext/llvm && /usr/bin/c++ -DJEMALLOC_NO_DEMANGLE -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/<>/spades-3.13.0+dfsg/build_spades/ext/llvm -I/<>/spades-3.13.0+dfsg/ext/src/llvm -I/<>/spades-3.13.0+dfsg/src/include -I/<>/spades-3.13.0+dfsg/build_spades/include -I/<>/spades-3.13.0+dfsg/src -I/<>/spades-3.13.0+dfsg/src/common -isystem /<>/spades-3.13.0+dfsg/src/../ext/include -g -O2 -fdebug-prefix-map=/<>/spades-3.13.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -o CMakeFiles/llvm-support.dir/YAMLTraits.cpp.o -c /<>/spades-3.13.0+dfsg/ext/src/llvm/YAMLTraits.cpp [ 45%] Building CXX object ext/llvm/CMakeFiles/llvm-support.dir/raw_ostream.cpp.o cd /<>/spades-3.13.0+dfsg/build_spades/ext/llvm && /usr/bin/c++ -DJEMALLOC_NO_DEMANGLE -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/<>/spades-3.13.0+dfsg/build_spades/ext/llvm -I/<>/spades-3.13.0+dfsg/ext/src/llvm -I/<>/spades-3.13.0+dfsg/src/include -I/<>/spades-3.13.0+dfsg/build_spades/include -I/<>/spades-3.13.0+dfsg/src -I/<>/spades-3.13.0+dfsg/src/common -isystem /<>/spades-3.13.0+dfsg/src/../ext/include -g -O2 -fdebug-prefix-map=/<>/spades-3.13.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -o CMakeFiles/llvm-support.dir/raw_ostream.cpp.o -c /<>/spades-3.13.0+dfsg/ext/src/llvm/raw_ostream.cpp [ 45%] Building C object ext/llvm/CMakeFiles/llvm-support.dir/regcomp.c.o cd /<>/spades-3.13.0+dfsg/build_spades/ext/llvm && /usr/bin/cc -DJEMALLOC_NO_DEMANGLE -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/<>/spades-3.13.0+dfsg/build_spades/ext/llvm -I/<>/spades-3.13.0+dfsg/ext/src/llvm -I/<>/spades-3.13.0+dfsg/src/include -I/<>/spades-3.13.0+dfsg/build_spades/include -I/<>/spades-3.13.0+dfsg/src -I/<>/spades-3.13.0+dfsg/src/common -isystem /<>/spades-3.13.0+dfsg/src/../ext/include -g -O2 -fdebug-prefix-map=/<>/spades-3.13.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -o CMakeFiles/llvm-support.dir/regcomp.c.o -c /<>/spades-3.13.0+dfsg/ext/src/llvm/regcomp.c [ 46%] Building C object ext/llvm/CMakeFiles/llvm-support.dir/regerror.c.o cd /<>/spades-3.13.0+dfsg/build_spades/ext/llvm && /usr/bin/cc -DJEMALLOC_NO_DEMANGLE -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/<>/spades-3.13.0+dfsg/build_spades/ext/llvm -I/<>/spades-3.13.0+dfsg/ext/src/llvm -I/<>/spades-3.13.0+dfsg/src/include -I/<>/spades-3.13.0+dfsg/build_spades/include -I/<>/spades-3.13.0+dfsg/src -I/<>/spades-3.13.0+dfsg/src/common -isystem /<>/spades-3.13.0+dfsg/src/../ext/include -g -O2 -fdebug-prefix-map=/<>/spades-3.13.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -o CMakeFiles/llvm-support.dir/regerror.c.o -c /<>/spades-3.13.0+dfsg/ext/src/llvm/regerror.c [ 46%] Building C object ext/llvm/CMakeFiles/llvm-support.dir/regexec.c.o cd /<>/spades-3.13.0+dfsg/build_spades/ext/llvm && /usr/bin/cc -DJEMALLOC_NO_DEMANGLE -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/<>/spades-3.13.0+dfsg/build_spades/ext/llvm -I/<>/spades-3.13.0+dfsg/ext/src/llvm -I/<>/spades-3.13.0+dfsg/src/include -I/<>/spades-3.13.0+dfsg/build_spades/include -I/<>/spades-3.13.0+dfsg/src -I/<>/spades-3.13.0+dfsg/src/common -isystem /<>/spades-3.13.0+dfsg/src/../ext/include -g -O2 -fdebug-prefix-map=/<>/spades-3.13.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -o CMakeFiles/llvm-support.dir/regexec.c.o -c /<>/spades-3.13.0+dfsg/ext/src/llvm/regexec.c [ 47%] Building C object ext/llvm/CMakeFiles/llvm-support.dir/regfree.c.o cd /<>/spades-3.13.0+dfsg/build_spades/ext/llvm && /usr/bin/cc -DJEMALLOC_NO_DEMANGLE -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/<>/spades-3.13.0+dfsg/build_spades/ext/llvm -I/<>/spades-3.13.0+dfsg/ext/src/llvm -I/<>/spades-3.13.0+dfsg/src/include -I/<>/spades-3.13.0+dfsg/build_spades/include -I/<>/spades-3.13.0+dfsg/src -I/<>/spades-3.13.0+dfsg/src/common -isystem /<>/spades-3.13.0+dfsg/src/../ext/include -g -O2 -fdebug-prefix-map=/<>/spades-3.13.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -o CMakeFiles/llvm-support.dir/regfree.c.o -c /<>/spades-3.13.0+dfsg/ext/src/llvm/regfree.c [ 47%] Building C object ext/llvm/CMakeFiles/llvm-support.dir/regstrlcpy.c.o cd /<>/spades-3.13.0+dfsg/build_spades/ext/llvm && /usr/bin/cc -DJEMALLOC_NO_DEMANGLE -DUSE_GLIBCXX_PARALLEL=1 -D__STDC_CONSTANT_MACROS -D__STDC_LIMIT_MACROS -I/<>/spades-3.13.0+dfsg/build_spades/ext/llvm -I/<>/spades-3.13.0+dfsg/ext/src/llvm -I/<>/spades-3.13.0+dfsg/src/include -I/<>/spades-3.13.0+dfsg/build_spades/include -I/<>/spades-3.13.0+dfsg/src -I/<>/spades-3.13.0+dfsg/src/common -isystem /<>/spades-3.13.0+dfsg/src/../ext/include -g -O2 -fdebug-prefix-map=/<>/spades-3.13.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -o CMakeFiles/llvm-support.dir/regstrlcpy.c.o -c /<>/spades-3.13.0+dfsg/ext/src/llvm/regstrlcpy.c [ 48%] Linking CXX static library libllvm-support.a cd /<>/spades-3.13.0+dfsg/build_spades/ext/llvm && /usr/bin/cmake -P CMakeFiles/llvm-support.dir/cmake_clean_target.cmake cd /<>/spades-3.13.0+dfsg/build_spades/ext/llvm && /usr/bin/cmake -E cmake_link_script CMakeFiles/llvm-support.dir/link.txt --verbose=1 /usr/bin/ar qc libllvm-support.a CMakeFiles/llvm-support.dir/Atomic.cpp.o CMakeFiles/llvm-support.dir/ErrorHandling.cpp.o CMakeFiles/llvm-support.dir/Hashing.cpp.o CMakeFiles/llvm-support.dir/LineIterator.cpp.o CMakeFiles/llvm-support.dir/MemoryBuffer.cpp.o CMakeFiles/llvm-support.dir/Mutex.cpp.o CMakeFiles/llvm-support.dir/Path.cpp.o CMakeFiles/llvm-support.dir/Regex.cpp.o CMakeFiles/llvm-support.dir/Signals.cpp.o CMakeFiles/llvm-support.dir/SmallVector.cpp.o CMakeFiles/llvm-support.dir/SourceMgr.cpp.o CMakeFiles/llvm-support.dir/StringMap.cpp.o CMakeFiles/llvm-support.dir/StringRef.cpp.o CMakeFiles/llvm-support.dir/Twine.cpp.o CMakeFiles/llvm-support.dir/YAMLParser.cpp.o CMakeFiles/llvm-support.dir/YAMLTraits.cpp.o CMakeFiles/llvm-support.dir/raw_ostream.cpp.o CMakeFiles/llvm-support.dir/regcomp.c.o CMakeFiles/llvm-support.dir/regerror.c.o CMakeFiles/llvm-support.dir/regexec.c.o CMakeFiles/llvm-support.dir/regfree.c.o CMakeFiles/llvm-support.dir/regstrlcpy.c.o /usr/bin/ranlib libllvm-support.a make[4]: Leaving directory '/<>/spades-3.13.0+dfsg/build_spades' [ 48%] Built target llvm-support make -f ext/gqf/CMakeFiles/gqf.dir/build.make ext/gqf/CMakeFiles/gqf.dir/depend make[4]: Entering directory '/<>/spades-3.13.0+dfsg/build_spades' cd /<>/spades-3.13.0+dfsg/build_spades && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/spades-3.13.0+dfsg/src /<>/spades-3.13.0+dfsg/ext/src/gqf /<>/spades-3.13.0+dfsg/build_spades /<>/spades-3.13.0+dfsg/build_spades/ext/gqf /<>/spades-3.13.0+dfsg/build_spades/ext/gqf/CMakeFiles/gqf.dir/DependInfo.cmake --color= Dependee "/<>/spades-3.13.0+dfsg/build_spades/ext/gqf/CMakeFiles/gqf.dir/DependInfo.cmake" is newer than depender "/<>/spades-3.13.0+dfsg/build_spades/ext/gqf/CMakeFiles/gqf.dir/depend.internal". Dependee "/<>/spades-3.13.0+dfsg/build_spades/ext/gqf/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/<>/spades-3.13.0+dfsg/build_spades/ext/gqf/CMakeFiles/gqf.dir/depend.internal". Scanning dependencies of target gqf make[4]: Leaving directory '/<>/spades-3.13.0+dfsg/build_spades' make -f ext/gqf/CMakeFiles/gqf.dir/build.make ext/gqf/CMakeFiles/gqf.dir/build make[4]: Entering directory '/<>/spades-3.13.0+dfsg/build_spades' [ 48%] Building C object ext/gqf/CMakeFiles/gqf.dir/gqf.c.o cd /<>/spades-3.13.0+dfsg/build_spades/ext/gqf && /usr/bin/cc -DJEMALLOC_NO_DEMANGLE -DUSE_GLIBCXX_PARALLEL=1 -I/<>/spades-3.13.0+dfsg/build_spades/ext/gqf -I/<>/spades-3.13.0+dfsg/ext/src/gqf -I/<>/spades-3.13.0+dfsg/src/include -I/<>/spades-3.13.0+dfsg/build_spades/include -I/<>/spades-3.13.0+dfsg/src -I/<>/spades-3.13.0+dfsg/src/common -isystem /<>/spades-3.13.0+dfsg/src/../ext/include -g -O2 -fdebug-prefix-map=/<>/spades-3.13.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -o CMakeFiles/gqf.dir/gqf.c.o -c /<>/spades-3.13.0+dfsg/ext/src/gqf/gqf.c /<>/spades-3.13.0+dfsg/ext/src/gqf/gqf.c: In function 'qf_dump_block': /<>/spades-3.13.0+dfsg/ext/src/gqf/gqf.c:614:16: warning: format '%llx' expects argument of type 'long long unsigned int', but argument 2 has type 'uint64_t' {aka 'long unsigned int'} [-Wformat=] printf("%02llx ", j); ~~~~~^ ~ %02lx /<>/spades-3.13.0+dfsg/ext/src/gqf/gqf.c: In function 'qf_dump': /<>/spades-3.13.0+dfsg/ext/src/gqf/gqf.c:645:13: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 2 has type 'uint64_t' {aka 'long unsigned int'} [-Wformat=] printf("%llu %llu %llu\n", ~~~^ %lu qf->metadata->nblocks, ~~~~~~~~~~~~~~~~~~~~~ /<>/spades-3.13.0+dfsg/ext/src/gqf/gqf.c:645:18: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'uint64_t' {aka 'long unsigned int'} [-Wformat=] printf("%llu %llu %llu\n", ~~~^ %lu /<>/spades-3.13.0+dfsg/ext/src/gqf/gqf.c:647:6: qf->metadata->ndistinct_elts, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/spades-3.13.0+dfsg/ext/src/gqf/gqf.c:645:23: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'uint64_t' {aka 'long unsigned int'} [-Wformat=] printf("%llu %llu %llu\n", ~~~^ %lu /<>/spades-3.13.0+dfsg/ext/src/gqf/gqf.c:648:6: qf->metadata->nelts); ~~~~~~~~~~~~~~~~~~~ /<>/spades-3.13.0+dfsg/ext/src/gqf/gqf.c: In function 'qf_init': /<>/spades-3.13.0+dfsg/ext/src/gqf/gqf.c:1451:22: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'uint64_t' {aka 'long unsigned int'} [-Wformat=] fprintf(stderr, "%llu %llu %llu\n", key_bits, key_remainder_bits, value_bits); ~~~^ ~~~~~~~~ %lu /<>/spades-3.13.0+dfsg/ext/src/gqf/gqf.c:1451:27: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'uint64_t' {aka 'long unsigned int'} [-Wformat=] fprintf(stderr, "%llu %llu %llu\n", key_bits, key_remainder_bits, value_bits); ~~~^ ~~~~~~~~~~~~~~~~~~ %lu /<>/spades-3.13.0+dfsg/ext/src/gqf/gqf.c:1451:32: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'uint64_t' {aka 'long unsigned int'} [-Wformat=] fprintf(stderr, "%llu %llu %llu\n", key_bits, key_remainder_bits, value_bits); ~~~^ ~~~~~~~~~~ %lu /<>/spades-3.13.0+dfsg/ext/src/gqf/gqf.c:1477:31: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'uint64_t' {aka 'long unsigned int'} [-Wformat=] fprintf(stderr, "nslots: %llu\n", qf->metadata->range); ~~~^ ~~~~~~~~~~~~~~~~~~~ %lu /<>/spades-3.13.0+dfsg/ext/src/gqf/gqf.c:1479:44: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'uint64_t' {aka 'long unsigned int'} [-Wformat=] fprintf(stderr, "bits per slot: %llu range: %016llx\n", qf->metadata->bits_per_slot, (uint64_t)qf->metadata->range); ~~~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~ %lu /<>/spades-3.13.0+dfsg/ext/src/gqf/gqf.c:1479:59: warning: format '%llx' expects argument of type 'long long unsigned int', but argument 4 has type 'long unsigned int' [-Wformat=] fprintf(stderr, "bits per slot: %llu range: %016llx\n", qf->metadata->bits_per_slot, (uint64_t)qf->metadata->range); ~~~~~~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ %016lx /<>/spades-3.13.0+dfsg/ext/include/gqf/gqf.h: In function 'qf_deserialize': /<>/spades-3.13.0+dfsg/ext/src/gqf/gqf.c:1610:2: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(qf->metadata, sizeof(qfmetadata), 1, fin); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /<>/spades-3.13.0+dfsg/ext/src/gqf/gqf.c:1619:2: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(qf->blocks, qf->metadata->size, 1, fin); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 48%] Linking C static library libgqf.a cd /<>/spades-3.13.0+dfsg/build_spades/ext/gqf && /usr/bin/cmake -P CMakeFiles/gqf.dir/cmake_clean_target.cmake cd /<>/spades-3.13.0+dfsg/build_spades/ext/gqf && /usr/bin/cmake -E cmake_link_script CMakeFiles/gqf.dir/link.txt --verbose=1 /usr/bin/ar qc libgqf.a CMakeFiles/gqf.dir/gqf.c.o /usr/bin/ranlib libgqf.a make[4]: Leaving directory '/<>/spades-3.13.0+dfsg/build_spades' [ 48%] Built target gqf make -f ext/edlib/CMakeFiles/edlib.dir/build.make ext/edlib/CMakeFiles/edlib.dir/depend make[4]: Entering directory '/<>/spades-3.13.0+dfsg/build_spades' cd /<>/spades-3.13.0+dfsg/build_spades && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/spades-3.13.0+dfsg/src /<>/spades-3.13.0+dfsg/ext/src/edlib /<>/spades-3.13.0+dfsg/build_spades /<>/spades-3.13.0+dfsg/build_spades/ext/edlib /<>/spades-3.13.0+dfsg/build_spades/ext/edlib/CMakeFiles/edlib.dir/DependInfo.cmake --color= Dependee "/<>/spades-3.13.0+dfsg/build_spades/ext/edlib/CMakeFiles/edlib.dir/DependInfo.cmake" is newer than depender "/<>/spades-3.13.0+dfsg/build_spades/ext/edlib/CMakeFiles/edlib.dir/depend.internal". Dependee "/<>/spades-3.13.0+dfsg/build_spades/ext/edlib/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/<>/spades-3.13.0+dfsg/build_spades/ext/edlib/CMakeFiles/edlib.dir/depend.internal". Scanning dependencies of target edlib make[4]: Leaving directory '/<>/spades-3.13.0+dfsg/build_spades' make -f ext/edlib/CMakeFiles/edlib.dir/build.make ext/edlib/CMakeFiles/edlib.dir/build make[4]: Entering directory '/<>/spades-3.13.0+dfsg/build_spades' [ 49%] Building CXX object ext/edlib/CMakeFiles/edlib.dir/edlib.cpp.o cd /<>/spades-3.13.0+dfsg/build_spades/ext/edlib && /usr/bin/c++ -DJEMALLOC_NO_DEMANGLE -DUSE_GLIBCXX_PARALLEL=1 -I/<>/spades-3.13.0+dfsg/build_spades/ext/edlib -I/<>/spades-3.13.0+dfsg/ext/src/edlib -I/<>/spades-3.13.0+dfsg/src/include -I/<>/spades-3.13.0+dfsg/build_spades/include -I/<>/spades-3.13.0+dfsg/src -I/<>/spades-3.13.0+dfsg/src/common -isystem /<>/spades-3.13.0+dfsg/src/../ext/include -g -O2 -fdebug-prefix-map=/<>/spades-3.13.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -o CMakeFiles/edlib.dir/edlib.cpp.o -c /<>/spades-3.13.0+dfsg/ext/src/edlib/edlib.cpp [ 49%] Linking CXX static library libedlib.a cd /<>/spades-3.13.0+dfsg/build_spades/ext/edlib && /usr/bin/cmake -P CMakeFiles/edlib.dir/cmake_clean_target.cmake cd /<>/spades-3.13.0+dfsg/build_spades/ext/edlib && /usr/bin/cmake -E cmake_link_script CMakeFiles/edlib.dir/link.txt --verbose=1 /usr/bin/ar qc libedlib.a CMakeFiles/edlib.dir/edlib.cpp.o /usr/bin/ranlib libedlib.a make[4]: Leaving directory '/<>/spades-3.13.0+dfsg/build_spades' [ 49%] Built target edlib make -f ext/gfa1/CMakeFiles/gfa1.dir/build.make ext/gfa1/CMakeFiles/gfa1.dir/depend make[4]: Entering directory '/<>/spades-3.13.0+dfsg/build_spades' cd /<>/spades-3.13.0+dfsg/build_spades && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/spades-3.13.0+dfsg/src /<>/spades-3.13.0+dfsg/ext/src/gfa1 /<>/spades-3.13.0+dfsg/build_spades /<>/spades-3.13.0+dfsg/build_spades/ext/gfa1 /<>/spades-3.13.0+dfsg/build_spades/ext/gfa1/CMakeFiles/gfa1.dir/DependInfo.cmake --color= Dependee "/<>/spades-3.13.0+dfsg/build_spades/ext/gfa1/CMakeFiles/gfa1.dir/DependInfo.cmake" is newer than depender "/<>/spades-3.13.0+dfsg/build_spades/ext/gfa1/CMakeFiles/gfa1.dir/depend.internal". Dependee "/<>/spades-3.13.0+dfsg/build_spades/ext/gfa1/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/<>/spades-3.13.0+dfsg/build_spades/ext/gfa1/CMakeFiles/gfa1.dir/depend.internal". Scanning dependencies of target gfa1 make[4]: Leaving directory '/<>/spades-3.13.0+dfsg/build_spades' make -f ext/gfa1/CMakeFiles/gfa1.dir/build.make ext/gfa1/CMakeFiles/gfa1.dir/build make[4]: Entering directory '/<>/spades-3.13.0+dfsg/build_spades' [ 49%] Building C object ext/gfa1/CMakeFiles/gfa1.dir/gfa.c.o cd /<>/spades-3.13.0+dfsg/build_spades/ext/gfa1 && /usr/bin/cc -DJEMALLOC_NO_DEMANGLE -DUSE_GLIBCXX_PARALLEL=1 -I/<>/spades-3.13.0+dfsg/build_spades/ext/gfa1 -I/<>/spades-3.13.0+dfsg/ext/src/gfa1 -I/<>/spades-3.13.0+dfsg/src/include -I/<>/spades-3.13.0+dfsg/build_spades/include -I/<>/spades-3.13.0+dfsg/src -I/<>/spades-3.13.0+dfsg/src/common -isystem /<>/spades-3.13.0+dfsg/src/../ext/include -g -O2 -fdebug-prefix-map=/<>/spades-3.13.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -o CMakeFiles/gfa1.dir/gfa.c.o -c /<>/spades-3.13.0+dfsg/ext/src/gfa1/gfa.c [ 50%] Linking C static library libgfa1.a cd /<>/spades-3.13.0+dfsg/build_spades/ext/gfa1 && /usr/bin/cmake -P CMakeFiles/gfa1.dir/cmake_clean_target.cmake cd /<>/spades-3.13.0+dfsg/build_spades/ext/gfa1 && /usr/bin/cmake -E cmake_link_script CMakeFiles/gfa1.dir/link.txt --verbose=1 /usr/bin/ar qc libgfa1.a CMakeFiles/gfa1.dir/gfa.c.o /usr/bin/ranlib libgfa1.a make[4]: Leaving directory '/<>/spades-3.13.0+dfsg/build_spades' [ 50%] Built target gfa1 make -f common/modules/coverage_model/CMakeFiles/coverage_model.dir/build.make common/modules/coverage_model/CMakeFiles/coverage_model.dir/depend make[4]: Entering directory '/<>/spades-3.13.0+dfsg/build_spades' cd /<>/spades-3.13.0+dfsg/build_spades && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/spades-3.13.0+dfsg/src /<>/spades-3.13.0+dfsg/src/common/modules/coverage_model /<>/spades-3.13.0+dfsg/build_spades /<>/spades-3.13.0+dfsg/build_spades/common/modules/coverage_model /<>/spades-3.13.0+dfsg/build_spades/common/modules/coverage_model/CMakeFiles/coverage_model.dir/DependInfo.cmake --color= Dependee "/<>/spades-3.13.0+dfsg/build_spades/common/modules/coverage_model/CMakeFiles/coverage_model.dir/DependInfo.cmake" is newer than depender "/<>/spades-3.13.0+dfsg/build_spades/common/modules/coverage_model/CMakeFiles/coverage_model.dir/depend.internal". Dependee "/<>/spades-3.13.0+dfsg/build_spades/common/modules/coverage_model/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/<>/spades-3.13.0+dfsg/build_spades/common/modules/coverage_model/CMakeFiles/coverage_model.dir/depend.internal". Scanning dependencies of target coverage_model make[4]: Leaving directory '/<>/spades-3.13.0+dfsg/build_spades' make -f common/modules/coverage_model/CMakeFiles/coverage_model.dir/build.make common/modules/coverage_model/CMakeFiles/coverage_model.dir/build make[4]: Entering directory '/<>/spades-3.13.0+dfsg/build_spades' [ 50%] Building CXX object common/modules/coverage_model/CMakeFiles/coverage_model.dir/kmer_coverage_model.cpp.o cd /<>/spades-3.13.0+dfsg/build_spades/common/modules/coverage_model && /usr/bin/c++ -DJEMALLOC_NO_DEMANGLE -DUSE_GLIBCXX_PARALLEL=1 -I/<>/spades-3.13.0+dfsg/build_spades/common/modules/coverage_model -I/<>/spades-3.13.0+dfsg/src/common/modules/coverage_model -I/<>/spades-3.13.0+dfsg/src/include -I/<>/spades-3.13.0+dfsg/build_spades/include -I/<>/spades-3.13.0+dfsg/src -I/<>/spades-3.13.0+dfsg/src/common -isystem /<>/spades-3.13.0+dfsg/src/../ext/include -g -O2 -fdebug-prefix-map=/<>/spades-3.13.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -o CMakeFiles/coverage_model.dir/kmer_coverage_model.cpp.o -c /<>/spades-3.13.0+dfsg/src/common/modules/coverage_model/kmer_coverage_model.cpp /<>/spades-3.13.0+dfsg/src/common/modules/coverage_model/kmer_coverage_model.cpp: In member function 'void coverage_model::KMerCoverageModel::Fit()': /<>/spades-3.13.0+dfsg/src/common/modules/coverage_model/kmer_coverage_model.cpp:325:23: warning: conversion from 'size_t' {aka 'long unsigned int'} to '__gnu_cxx::__alloc_traits, double>::value_type' {aka 'double'} may change value [-Wconversion] if (converged_ && Valley_ > x[2] && x[2] > 2) { ^~~~~~~ /<>/spades-3.13.0+dfsg/src/common/modules/coverage_model/kmer_coverage_model.cpp:359:28: warning: conversion from 'size_t' {aka 'long unsigned int'} to 'double' may change value [-Wconversion] ErrorThreshold_ = (Valley_ < mean_coverage_ ? ^~~~~~~ [ 50%] Linking CXX static library libcoverage_model.a cd /<>/spades-3.13.0+dfsg/build_spades/common/modules/coverage_model && /usr/bin/cmake -P CMakeFiles/coverage_model.dir/cmake_clean_target.cmake cd /<>/spades-3.13.0+dfsg/build_spades/common/modules/coverage_model && /usr/bin/cmake -E cmake_link_script CMakeFiles/coverage_model.dir/link.txt --verbose=1 /usr/bin/ar qc libcoverage_model.a CMakeFiles/coverage_model.dir/kmer_coverage_model.cpp.o /usr/bin/ranlib libcoverage_model.a make[4]: Leaving directory '/<>/spades-3.13.0+dfsg/build_spades' [ 50%] Built target coverage_model make -f common/io/CMakeFiles/input.dir/build.make common/io/CMakeFiles/input.dir/depend make[4]: Entering directory '/<>/spades-3.13.0+dfsg/build_spades' cd /<>/spades-3.13.0+dfsg/build_spades && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/spades-3.13.0+dfsg/src /<>/spades-3.13.0+dfsg/src/common/io /<>/spades-3.13.0+dfsg/build_spades /<>/spades-3.13.0+dfsg/build_spades/common/io /<>/spades-3.13.0+dfsg/build_spades/common/io/CMakeFiles/input.dir/DependInfo.cmake --color= Dependee "/<>/spades-3.13.0+dfsg/build_spades/common/io/CMakeFiles/input.dir/DependInfo.cmake" is newer than depender "/<>/spades-3.13.0+dfsg/build_spades/common/io/CMakeFiles/input.dir/depend.internal". Dependee "/<>/spades-3.13.0+dfsg/build_spades/common/io/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/<>/spades-3.13.0+dfsg/build_spades/common/io/CMakeFiles/input.dir/depend.internal". Scanning dependencies of target input make[4]: Leaving directory '/<>/spades-3.13.0+dfsg/build_spades' make -f common/io/CMakeFiles/input.dir/build.make common/io/CMakeFiles/input.dir/build make[4]: Entering directory '/<>/spades-3.13.0+dfsg/build_spades' [ 51%] Building CXX object common/io/CMakeFiles/input.dir/reads/parser.cpp.o cd /<>/spades-3.13.0+dfsg/build_spades/common/io && /usr/bin/c++ -DJEMALLOC_NO_DEMANGLE -DUSE_GLIBCXX_PARALLEL=1 -I/<>/spades-3.13.0+dfsg/build_spades/common/io -I/<>/spades-3.13.0+dfsg/src/common/io -I/<>/spades-3.13.0+dfsg/src/include -I/<>/spades-3.13.0+dfsg/build_spades/include -I/<>/spades-3.13.0+dfsg/src -I/<>/spades-3.13.0+dfsg/src/common -isystem /<>/spades-3.13.0+dfsg/src/../ext/include -g -O2 -fdebug-prefix-map=/<>/spades-3.13.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -o CMakeFiles/input.dir/reads/parser.cpp.o -c /<>/spades-3.13.0+dfsg/src/common/io/reads/parser.cpp [ 51%] Building CXX object common/io/CMakeFiles/input.dir/sam/read.cpp.o cd /<>/spades-3.13.0+dfsg/build_spades/common/io && /usr/bin/c++ -DJEMALLOC_NO_DEMANGLE -DUSE_GLIBCXX_PARALLEL=1 -I/<>/spades-3.13.0+dfsg/build_spades/common/io -I/<>/spades-3.13.0+dfsg/src/common/io -I/<>/spades-3.13.0+dfsg/src/include -I/<>/spades-3.13.0+dfsg/build_spades/include -I/<>/spades-3.13.0+dfsg/src -I/<>/spades-3.13.0+dfsg/src/common -isystem /<>/spades-3.13.0+dfsg/src/../ext/include -g -O2 -fdebug-prefix-map=/<>/spades-3.13.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -o CMakeFiles/input.dir/sam/read.cpp.o -c /<>/spades-3.13.0+dfsg/src/common/io/sam/read.cpp [ 52%] Building CXX object common/io/CMakeFiles/input.dir/sam/sam_reader.cpp.o cd /<>/spades-3.13.0+dfsg/build_spades/common/io && /usr/bin/c++ -DJEMALLOC_NO_DEMANGLE -DUSE_GLIBCXX_PARALLEL=1 -I/<>/spades-3.13.0+dfsg/build_spades/common/io -I/<>/spades-3.13.0+dfsg/src/common/io -I/<>/spades-3.13.0+dfsg/src/include -I/<>/spades-3.13.0+dfsg/build_spades/include -I/<>/spades-3.13.0+dfsg/src -I/<>/spades-3.13.0+dfsg/src/common -isystem /<>/spades-3.13.0+dfsg/src/../ext/include -g -O2 -fdebug-prefix-map=/<>/spades-3.13.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -o CMakeFiles/input.dir/sam/sam_reader.cpp.o -c /<>/spades-3.13.0+dfsg/src/common/io/sam/sam_reader.cpp [ 52%] Linking CXX static library libinput.a cd /<>/spades-3.13.0+dfsg/build_spades/common/io && /usr/bin/cmake -P CMakeFiles/input.dir/cmake_clean_target.cmake cd /<>/spades-3.13.0+dfsg/build_spades/common/io && /usr/bin/cmake -E cmake_link_script CMakeFiles/input.dir/link.txt --verbose=1 /usr/bin/ar qc libinput.a CMakeFiles/input.dir/reads/parser.cpp.o CMakeFiles/input.dir/sam/read.cpp.o CMakeFiles/input.dir/sam/sam_reader.cpp.o /usr/bin/ranlib libinput.a make[4]: Leaving directory '/<>/spades-3.13.0+dfsg/build_spades' [ 52%] Built target input make -f common/pipeline/CMakeFiles/pipeline.dir/build.make common/pipeline/CMakeFiles/pipeline.dir/depend make[4]: Entering directory '/<>/spades-3.13.0+dfsg/build_spades' cd /<>/spades-3.13.0+dfsg/build_spades && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/spades-3.13.0+dfsg/src /<>/spades-3.13.0+dfsg/src/common/pipeline /<>/spades-3.13.0+dfsg/build_spades /<>/spades-3.13.0+dfsg/build_spades/common/pipeline /<>/spades-3.13.0+dfsg/build_spades/common/pipeline/CMakeFiles/pipeline.dir/DependInfo.cmake --color= Dependee "/<>/spades-3.13.0+dfsg/build_spades/common/pipeline/CMakeFiles/pipeline.dir/DependInfo.cmake" is newer than depender "/<>/spades-3.13.0+dfsg/build_spades/common/pipeline/CMakeFiles/pipeline.dir/depend.internal". Dependee "/<>/spades-3.13.0+dfsg/build_spades/common/pipeline/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/<>/spades-3.13.0+dfsg/build_spades/common/pipeline/CMakeFiles/pipeline.dir/depend.internal". Scanning dependencies of target pipeline make[4]: Leaving directory '/<>/spades-3.13.0+dfsg/build_spades' make -f common/pipeline/CMakeFiles/pipeline.dir/build.make common/pipeline/CMakeFiles/pipeline.dir/build make[4]: Entering directory '/<>/spades-3.13.0+dfsg/build_spades' [ 53%] Building CXX object common/pipeline/CMakeFiles/pipeline.dir/stage.cpp.o cd /<>/spades-3.13.0+dfsg/build_spades/common/pipeline && /usr/bin/c++ -DJEMALLOC_NO_DEMANGLE -DUSE_GLIBCXX_PARALLEL=1 -I/<>/spades-3.13.0+dfsg/build_spades/common/pipeline -I/<>/spades-3.13.0+dfsg/src/common/pipeline -I/<>/spades-3.13.0+dfsg/src/include -I/<>/spades-3.13.0+dfsg/build_spades/include -I/<>/spades-3.13.0+dfsg/src -I/<>/spades-3.13.0+dfsg/src/common -isystem /<>/spades-3.13.0+dfsg/src/../ext/include -g -O2 -fdebug-prefix-map=/<>/spades-3.13.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -o CMakeFiles/pipeline.dir/stage.cpp.o -c /<>/spades-3.13.0+dfsg/src/common/pipeline/stage.cpp In file included from /<>/spades-3.13.0+dfsg/src/common/modules/alignment/kmer_mapper.hpp:11, from /<>/spades-3.13.0+dfsg/src/common/modules/alignment/sequence_mapper.hpp:16, from /<>/spades-3.13.0+dfsg/src/common/assembly_graph/graph_support/genomic_quality.hpp:12, from /<>/spades-3.13.0+dfsg/src/common/pipeline/graph_pack.hpp:19, from /<>/spades-3.13.0+dfsg/src/common/pipeline/stage.hpp:11, from /<>/spades-3.13.0+dfsg/src/common/pipeline/stage.cpp:8: /<>/spades-3.13.0+dfsg/src/common/adt/kmer_vector.hpp: In member function 'adt::KMerVector::ElTy* adt::KMerVector::realloc()': /<>/spades-3.13.0+dfsg/src/common/adt/kmer_vector.hpp:31:89: error: 'ALLOCM_NO_MOVE' was not declared in this scope je_rallocm((void **) &storage_, NULL, sizeof(ElTy) * capacity_ * el_sz_, 0, ALLOCM_NO_MOVE) == ^~~~~~~~~~~~~~ /<>/spades-3.13.0+dfsg/src/common/adt/kmer_vector.hpp:31:89: note: suggested alternative: 'SPLICE_F_MOVE' je_rallocm((void **) &storage_, NULL, sizeof(ElTy) * capacity_ * el_sz_, 0, ALLOCM_NO_MOVE) == ^~~~~~~~~~~~~~ SPLICE_F_MOVE /<>/spades-3.13.0+dfsg/src/common/adt/kmer_vector.hpp:31:13: error: there are no arguments to 'je_rallocm' that depend on a template parameter, so a declaration of 'je_rallocm' must be available [-fpermissive] je_rallocm((void **) &storage_, NULL, sizeof(ElTy) * capacity_ * el_sz_, 0, ALLOCM_NO_MOVE) == ^~~~~~~~~~ /<>/spades-3.13.0+dfsg/src/common/adt/kmer_vector.hpp:31:13: note: (if you use '-fpermissive', G++ will accept your code, but allowing the use of an undeclared name is deprecated) /<>/spades-3.13.0+dfsg/src/common/adt/kmer_vector.hpp:32:13: error: 'ALLOCM_SUCCESS' was not declared in this scope ALLOCM_SUCCESS) ^~~~~~~~~~~~~~ /<>/spades-3.13.0+dfsg/src/common/adt/kmer_vector.hpp:32:13: note: suggested alternative: 'EXIT_SUCCESS' ALLOCM_SUCCESS) ^~~~~~~~~~~~~~ EXIT_SUCCESS make[4]: *** [common/pipeline/CMakeFiles/pipeline.dir/build.make:63: common/pipeline/CMakeFiles/pipeline.dir/stage.cpp.o] Error 1 make[4]: Leaving directory '/<>/spades-3.13.0+dfsg/build_spades' make[3]: *** [CMakeFiles/Makefile2:1000: common/pipeline/CMakeFiles/pipeline.dir/all] Error 2 make[3]: Leaving directory '/<>/spades-3.13.0+dfsg/build_spades' make[2]: *** [Makefile:152: all] Error 2 make[2]: Leaving directory '/<>/spades-3.13.0+dfsg/build_spades' make[1]: *** [debian/rules:42: override_dh_auto_build] Error 2 make[1]: Leaving directory '/<>/spades-3.13.0+dfsg' make: *** [debian/rules:24: build] Error 2 dpkg-buildpackage: error: debian/rules build subprocess returned exit status 2 -------------------------------------------------------------------------------- Build finished at 20181208-1239 Finished -------- E: Build failure (dpkg-buildpackage died) +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not removing build depends: as requested +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: amd64 Build-Space: 200384 Build-Time: 423 Distribution: disco-proposed Fail-Stage: build Host Architecture: amd64 Install-Time: 75 Job: spades_3.13.0+dfsg-1.dsc Machine Architecture: amd64 Package: spades Package-Time: 503 Source-Version: 3.13.0+dfsg-1 Space: 200384 Status: attempted Version: 3.13.0+dfsg-1 -------------------------------------------------------------------------------- Finished at 20181208-1239 Build needed 00:08:23, 200384k disc space RUN: /usr/share/launchpad-buildd/slavebin/in-target scan-for-processes --backend=chroot --series=disco --arch=amd64 PACKAGEBUILD-15636794 Scanning for processes to kill in build PACKAGEBUILD-15636794