https://launchpad.net/ubuntu/+archive/test-rebuild-20191220-focal/+build/18355010 RUN: /usr/share/launchpad-buildd/bin/builder-prep Kernel version: Linux lcy01-amd64-028 4.4.0-170-generic #199-Ubuntu SMP Thu Nov 14 01:45:04 UTC 2019 x86_64 Buildd toolchain package versions: launchpad-buildd_183 python-lpbuildd_183 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_0.3.6~git201906051340.ff11471~ubuntu16.04.1 git_1:2.7.4-0ubuntu1.7 dpkg-dev_1.18.4ubuntu1.6 python-debian_0.1.27ubuntu2. Syncing the system clock with the buildd NTP service... 5 Jan 10:30:06 ntpdate[1912]: adjust time server 10.211.37.1 offset 0.006300 sec RUN: /usr/share/launchpad-buildd/bin/in-target unpack-chroot --backend=chroot --series=focal --arch=amd64 PACKAGEBUILD-18355010 --image-type chroot /home/buildd/filecache-default/e96c25c651525abc9f0cabeb95ea71010abf4ecb Creating target for build PACKAGEBUILD-18355010 RUN: /usr/share/launchpad-buildd/bin/in-target mount-chroot --backend=chroot --series=focal --arch=amd64 PACKAGEBUILD-18355010 Starting target for build PACKAGEBUILD-18355010 RUN: /usr/share/launchpad-buildd/bin/in-target override-sources-list --backend=chroot --series=focal --arch=amd64 PACKAGEBUILD-18355010 'deb http://ftpmaster.internal/ubuntu focal main restricted universe multiverse' Overriding sources.list in build-PACKAGEBUILD-18355010 RUN: /usr/share/launchpad-buildd/bin/in-target update-debian-chroot --backend=chroot --series=focal --arch=amd64 PACKAGEBUILD-18355010 Updating target for build PACKAGEBUILD-18355010 Get:1 http://ftpmaster.internal/ubuntu focal InRelease [255 kB] Get:2 http://ftpmaster.internal/ubuntu focal/main amd64 Packages [966 kB] Get:3 http://ftpmaster.internal/ubuntu focal/main Translation-en [499 kB] Get:4 http://ftpmaster.internal/ubuntu focal/restricted amd64 Packages [18.4 kB] Get:5 http://ftpmaster.internal/ubuntu focal/restricted Translation-en [5768 B] Get:6 http://ftpmaster.internal/ubuntu focal/universe amd64 Packages [8671 kB] Get:7 http://ftpmaster.internal/ubuntu focal/universe Translation-en [5195 kB] Get:8 http://ftpmaster.internal/ubuntu focal/multiverse amd64 Packages [152 kB] Get:9 http://ftpmaster.internal/ubuntu focal/multiverse Translation-en [110 kB] Fetched 15.9 MB in 4s (3884 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: libhogweed4 libisl21 libnettle6 libperl5.28 perl-modules-5.28 Use 'sudo apt autoremove' to remove them. The following NEW packages will be installed: libhogweed5 libisl22 libnettle7 libperl5.30 perl-modules-5.30 The following packages will be upgraded: apt base-files base-passwd bash binutils binutils-common binutils-x86-64-linux-gnu bsdutils bzip2 cpp-9 debianutils fdisk g++-9 gcc-9 gcc-9-base gpg gpg-agent gpgconf gpgv gzip hostname libacl1 libapparmor1 libapt-pkg5.90 libasan5 libatomic1 libattr1 libaudit-common libaudit1 libbinutils libblkid1 libbz2-1.0 libc-bin libc-dev-bin libc6 libc6-dev libcap-ng0 libcap2 libcc1-0 libcryptsetup12 libdebconfclient0 libdevmapper1.02.1 libfdisk1 libgcc-9-dev libgcc1 libgcrypt20 libgnutls30 libgomp1 libitm1 libjson-c4 libkmod2 liblockfile-bin liblockfile1 liblsan0 liblz4-1 libmount1 libncurses6 libncursesw6 libp11-kit0 libpam-modules libpam-modules-bin libpam-runtime libpam0g libpcre2-8-0 libquadmath0 libseccomp2 libselinux1 libsemanage-common libsemanage1 libsepol1 libsmartcols1 libsqlite3-0 libstdc++-9-dev libstdc++6 libsystemd0 libtasn1-6 libtinfo6 libtsan0 libubsan1 libudev1 libuuid1 libzstd1 linux-libc-dev lsb-base mount ncurses-base ncurses-bin perl perl-base sensible-utils systemd systemd-sysv sysvinit-utils util-linux 94 upgraded, 5 newly installed, 0 to remove and 0 not upgraded. Need to get 70.2 MB of archives. After this operation, 51.0 MB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu focal/main amd64 libc6-dev amd64 2.30-0ubuntu3 [2549 kB] Get:2 http://ftpmaster.internal/ubuntu focal/main amd64 libc-dev-bin amd64 2.30-0ubuntu3 [71.8 kB] Get:3 http://ftpmaster.internal/ubuntu focal/main amd64 linux-libc-dev amd64 5.3.0-24.26 [1096 kB] Get:4 http://ftpmaster.internal/ubuntu focal/main amd64 libisl22 amd64 0.22-2 [592 kB] Get:5 http://ftpmaster.internal/ubuntu focal/main amd64 libcc1-0 amd64 9.2.1-21ubuntu1 [49.0 kB] Get:6 http://ftpmaster.internal/ubuntu focal/main amd64 binutils-x86-64-linux-gnu amd64 2.33.1-6ubuntu3 [1639 kB] Get:7 http://ftpmaster.internal/ubuntu focal/main amd64 libbinutils amd64 2.33.1-6ubuntu3 [474 kB] Get:8 http://ftpmaster.internal/ubuntu focal/main amd64 binutils-common amd64 2.33.1-6ubuntu3 [203 kB] Get:9 http://ftpmaster.internal/ubuntu focal/main amd64 binutils amd64 2.33.1-6ubuntu3 [3400 B] Get:10 http://ftpmaster.internal/ubuntu focal/main amd64 gcc-9-base amd64 9.2.1-21ubuntu1 [19.1 kB] Get:11 http://ftpmaster.internal/ubuntu focal/main amd64 libgcc1 amd64 1:9.2.1-21ubuntu1 [40.8 kB] Get:12 http://ftpmaster.internal/ubuntu focal/main amd64 libgomp1 amd64 9.2.1-21ubuntu1 [89.3 kB] Get:13 http://ftpmaster.internal/ubuntu focal/main amd64 libitm1 amd64 9.2.1-21ubuntu1 [28.1 kB] Get:14 http://ftpmaster.internal/ubuntu focal/main amd64 libatomic1 amd64 9.2.1-21ubuntu1 [9236 B] Get:15 http://ftpmaster.internal/ubuntu focal/main amd64 libasan5 amd64 9.2.1-21ubuntu1 [395 kB] Get:16 http://ftpmaster.internal/ubuntu focal/main amd64 liblsan0 amd64 9.2.1-21ubuntu1 [139 kB] Get:17 http://ftpmaster.internal/ubuntu focal/main amd64 libtsan0 amd64 9.2.1-21ubuntu1 [301 kB] Get:18 http://ftpmaster.internal/ubuntu focal/main amd64 libubsan1 amd64 9.2.1-21ubuntu1 [130 kB] Get:19 http://ftpmaster.internal/ubuntu focal/main amd64 libquadmath0 amd64 9.2.1-21ubuntu1 [146 kB] Get:20 http://ftpmaster.internal/ubuntu focal/main amd64 g++-9 amd64 9.2.1-21ubuntu1 [11.0 MB] Get:21 http://ftpmaster.internal/ubuntu focal/main amd64 libstdc++-9-dev amd64 9.2.1-21ubuntu1 [1709 kB] Get:22 http://ftpmaster.internal/ubuntu focal/main amd64 libgcc-9-dev amd64 9.2.1-21ubuntu1 [2362 kB] Get:23 http://ftpmaster.internal/ubuntu focal/main amd64 gcc-9 amd64 9.2.1-21ubuntu1 [10.4 MB] Get:24 http://ftpmaster.internal/ubuntu focal/main amd64 cpp-9 amd64 9.2.1-21ubuntu1 [9729 kB] Get:25 http://ftpmaster.internal/ubuntu focal/main amd64 libstdc++6 amd64 9.2.1-21ubuntu1 [512 kB] Get:26 http://ftpmaster.internal/ubuntu focal/main amd64 libc6 amd64 2.30-0ubuntu3 [2725 kB] Get:27 http://ftpmaster.internal/ubuntu focal/main amd64 base-files amd64 11ubuntu2 [60.1 kB] Get:28 http://ftpmaster.internal/ubuntu focal/main amd64 debianutils amd64 4.9.1 [85.8 kB] Get:29 http://ftpmaster.internal/ubuntu focal/main amd64 bash amd64 5.0-5ubuntu1 [639 kB] Get:30 http://ftpmaster.internal/ubuntu focal/main amd64 bsdutils amd64 1:2.34-0.1ubuntu4 [63.8 kB] Get:31 http://ftpmaster.internal/ubuntu focal/main amd64 gzip amd64 1.10-0ubuntu4 [95.3 kB] Get:32 http://ftpmaster.internal/ubuntu focal/main amd64 hostname amd64 3.23 [11.4 kB] Get:33 http://ftpmaster.internal/ubuntu focal/main amd64 ncurses-bin amd64 6.1+20191019-1ubuntu1 [172 kB] Get:34 http://ftpmaster.internal/ubuntu focal/main amd64 perl-modules-5.30 all 5.30.0-9 [2739 kB] Get:35 http://ftpmaster.internal/ubuntu focal/main amd64 libperl5.30 amd64 5.30.0-9 [3950 kB] Get:36 http://ftpmaster.internal/ubuntu focal/main amd64 perl amd64 5.30.0-9 [224 kB] Get:37 http://ftpmaster.internal/ubuntu focal/main amd64 perl-base amd64 5.30.0-9 [1511 kB] Get:38 http://ftpmaster.internal/ubuntu focal/main amd64 bzip2 amd64 1.0.8-2 [34.1 kB] Get:39 http://ftpmaster.internal/ubuntu focal/main amd64 libbz2-1.0 amd64 1.0.8-2 [32.3 kB] Get:40 http://ftpmaster.internal/ubuntu focal/main amd64 libblkid1 amd64 2.34-0.1ubuntu4 [137 kB] Get:41 http://ftpmaster.internal/ubuntu focal/main amd64 libuuid1 amd64 2.34-0.1ubuntu4 [20.5 kB] Get:42 http://ftpmaster.internal/ubuntu focal/main amd64 libfdisk1 amd64 2.34-0.1ubuntu4 [175 kB] Get:43 http://ftpmaster.internal/ubuntu focal/main amd64 libpcre2-8-0 amd64 10.34-7 [197 kB] Get:44 http://ftpmaster.internal/ubuntu focal/main amd64 libselinux1 amd64 3.0-1 [68.7 kB] Get:45 http://ftpmaster.internal/ubuntu focal/main amd64 libmount1 amd64 2.34-0.1ubuntu4 [149 kB] Get:46 http://ftpmaster.internal/ubuntu focal/main amd64 libncurses6 amd64 6.1+20191019-1ubuntu1 [101 kB] Get:47 http://ftpmaster.internal/ubuntu focal/main amd64 libtinfo6 amd64 6.1+20191019-1ubuntu1 [85.9 kB] Get:48 http://ftpmaster.internal/ubuntu focal/main amd64 libncursesw6 amd64 6.1+20191019-1ubuntu1 [132 kB] Get:49 http://ftpmaster.internal/ubuntu focal/main amd64 libsmartcols1 amd64 2.34-0.1ubuntu4 [101 kB] Get:50 http://ftpmaster.internal/ubuntu focal/main amd64 fdisk amd64 2.34-0.1ubuntu4 [120 kB] Get:51 http://ftpmaster.internal/ubuntu focal/main amd64 util-linux amd64 2.34-0.1ubuntu4 [1022 kB] Get:52 http://ftpmaster.internal/ubuntu focal/main amd64 libdebconfclient0 amd64 0.250ubuntu2 [6336 B] Get:53 http://ftpmaster.internal/ubuntu focal/main amd64 base-passwd amd64 3.5.47 [47.7 kB] Get:54 http://ftpmaster.internal/ubuntu focal/main amd64 libc-bin amd64 2.30-0ubuntu3 [625 kB] Get:55 http://ftpmaster.internal/ubuntu focal/main amd64 ncurses-base all 6.1+20191019-1ubuntu1 [17.9 kB] Get:56 http://ftpmaster.internal/ubuntu focal/main amd64 lsb-base all 11.1.0ubuntu2 [12.1 kB] Get:57 http://ftpmaster.internal/ubuntu focal/main amd64 sysvinit-utils amd64 2.96-1ubuntu1 [20.8 kB] Get:58 http://ftpmaster.internal/ubuntu focal/main amd64 liblz4-1 amd64 1.9.2-2 [55.9 kB] Get:59 http://ftpmaster.internal/ubuntu focal/main amd64 systemd-sysv amd64 244-3ubuntu1 [9368 B] Get:60 http://ftpmaster.internal/ubuntu focal/main amd64 libacl1 amd64 2.2.53-5ubuntu1 [18.7 kB] Get:61 http://ftpmaster.internal/ubuntu focal/main amd64 libapparmor1 amd64 2.13.3-7ubuntu1 [34.3 kB] Get:62 http://ftpmaster.internal/ubuntu focal/main amd64 libaudit-common all 1:2.8.5-2ubuntu5 [4076 B] Get:63 http://ftpmaster.internal/ubuntu focal/main amd64 libcap-ng0 amd64 0.7.9-2.1 [11.1 kB] Get:64 http://ftpmaster.internal/ubuntu focal/main amd64 libaudit1 amd64 1:2.8.5-2ubuntu5 [39.1 kB] Get:65 http://ftpmaster.internal/ubuntu focal/main amd64 libcap2 amd64 1:2.27-1 [14.1 kB] Get:66 http://ftpmaster.internal/ubuntu focal/main amd64 libudev1 amd64 244-3ubuntu1 [76.3 kB] Get:67 http://ftpmaster.internal/ubuntu focal/main amd64 libdevmapper1.02.1 amd64 2:1.02.155-2ubuntu7 [127 kB] Get:68 http://ftpmaster.internal/ubuntu focal/main amd64 libjson-c4 amd64 0.13.1+dfsg-6 [29.2 kB] Get:69 http://ftpmaster.internal/ubuntu focal/main amd64 libcryptsetup12 amd64 2:2.2.2-1ubuntu1 [182 kB] Get:70 http://ftpmaster.internal/ubuntu focal/main amd64 libnettle7 amd64 3.5.1+really3.5.1-2 [114 kB] Get:71 http://ftpmaster.internal/ubuntu focal/main amd64 libhogweed5 amd64 3.5.1+really3.5.1-2 [138 kB] Get:72 http://ftpmaster.internal/ubuntu focal/main amd64 libp11-kit0 amd64 0.23.18.1-2 [189 kB] Get:73 http://ftpmaster.internal/ubuntu focal/main amd64 libtasn1-6 amd64 4.15.0-2 [37.7 kB] Get:74 http://ftpmaster.internal/ubuntu focal/main amd64 libgnutls30 amd64 3.6.11.1-2 [793 kB] Get:75 http://ftpmaster.internal/ubuntu focal/main amd64 libkmod2 amd64 26-3ubuntu1 [42.9 kB] Get:76 http://ftpmaster.internal/ubuntu focal/main amd64 libpam0g amd64 1.3.1-5ubuntu4 [55.4 kB] Get:77 http://ftpmaster.internal/ubuntu focal/main amd64 libseccomp2 amd64 2.4.2-2ubuntu1 [39.4 kB] Get:78 http://ftpmaster.internal/ubuntu focal/main amd64 mount amd64 2.34-0.1ubuntu4 [115 kB] Get:79 http://ftpmaster.internal/ubuntu focal/main amd64 systemd amd64 244-3ubuntu1 [3677 kB] Get:80 http://ftpmaster.internal/ubuntu focal/main amd64 libsystemd0 amd64 244-3ubuntu1 [260 kB] Get:81 http://ftpmaster.internal/ubuntu focal/main amd64 libzstd1 amd64 1.4.4+dfsg-1 [237 kB] Get:82 http://ftpmaster.internal/ubuntu focal/main amd64 libapt-pkg5.90 amd64 1.9.5 [851 kB] Get:83 http://ftpmaster.internal/ubuntu focal/main amd64 libgcrypt20 amd64 1.8.5-3ubuntu1 [419 kB] Get:84 http://ftpmaster.internal/ubuntu focal/main amd64 gpgv amd64 2.2.17-3ubuntu1 [200 kB] Get:85 http://ftpmaster.internal/ubuntu focal/main amd64 apt amd64 1.9.5 [1281 kB] Get:86 http://ftpmaster.internal/ubuntu focal/main amd64 libpam-modules-bin amd64 1.3.1-5ubuntu4 [37.7 kB] Get:87 http://ftpmaster.internal/ubuntu focal/main amd64 libpam-modules amd64 1.3.1-5ubuntu4 [250 kB] Get:88 http://ftpmaster.internal/ubuntu focal/main amd64 libattr1 amd64 1:2.4.48-5 [12.7 kB] Get:89 http://ftpmaster.internal/ubuntu focal/main amd64 libpam-runtime all 1.3.1-5ubuntu4 [37.3 kB] Get:90 http://ftpmaster.internal/ubuntu focal/main amd64 libsepol1 amd64 3.0-1 [252 kB] Get:91 http://ftpmaster.internal/ubuntu focal/main amd64 libsemanage-common all 3.0-1 [9880 B] Get:92 http://ftpmaster.internal/ubuntu focal/main amd64 libsemanage1 amd64 3.0-1 [85.3 kB] Get:93 http://ftpmaster.internal/ubuntu focal/main amd64 sensible-utils all 0.0.12+nmu1 [15.0 kB] Get:94 http://ftpmaster.internal/ubuntu focal/main amd64 libsqlite3-0 amd64 3.30.1-1ubuntu1 [540 kB] Get:95 http://ftpmaster.internal/ubuntu focal/main amd64 gpg amd64 2.2.17-3ubuntu1 [479 kB] Get:96 http://ftpmaster.internal/ubuntu focal/main amd64 gpgconf amd64 2.2.17-3ubuntu1 [124 kB] Get:97 http://ftpmaster.internal/ubuntu focal/main amd64 gpg-agent amd64 2.2.17-3ubuntu1 [232 kB] Get:98 http://ftpmaster.internal/ubuntu focal/main amd64 liblockfile-bin amd64 1.16-1.1 [11.7 kB] Get:99 http://ftpmaster.internal/ubuntu focal/main amd64 liblockfile1 amd64 1.16-1.1 [6680 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 70.2 MB in 3s (21.9 MB/s) (Reading database ... 12741 files and directories currently installed.) 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Setting up libtsan0:amd64 (9.2.1-21ubuntu1) ... Setting up gpg-agent (2.2.17-3ubuntu1) ... Installing new version of config file /etc/logcheck/ignore.d.server/gpg-agent ... Created symlink /etc/systemd/user/sockets.target.wants/gpg-agent-browser.socket -> /usr/lib/systemd/user/gpg-agent-browser.socket. Created symlink /etc/systemd/user/sockets.target.wants/gpg-agent-extra.socket -> /usr/lib/systemd/user/gpg-agent-extra.socket. Created symlink /etc/systemd/user/sockets.target.wants/gpg-agent-ssh.socket -> /usr/lib/systemd/user/gpg-agent-ssh.socket. Created symlink /etc/systemd/user/sockets.target.wants/gpg-agent.socket -> /usr/lib/systemd/user/gpg-agent.socket. Setting up binutils (2.33.1-6ubuntu3) ... Setting up libgcc-9-dev:amd64 (9.2.1-21ubuntu1) ... Setting up perl (5.30.0-9) ... Setting up cpp-9 (9.2.1-21ubuntu1) ... Setting up libc6-dev:amd64 (2.30-0ubuntu3) ... Setting up libcryptsetup12:amd64 (2:2.2.2-1ubuntu1) ... Setting up gcc-9 (9.2.1-21ubuntu1) ... Setting up libstdc++-9-dev:amd64 (9.2.1-21ubuntu1) ... Setting up systemd (244-3ubuntu1) ... Installing new version of config file /etc/dhcp/dhclient-enter-hooks.d/resolved ... Installing new version of config file /etc/systemd/networkd.conf ... Installing new version of config file /etc/systemd/system.conf ... Installing new version of config file /etc/systemd/user.conf ... Initializing machine ID from KVM UUID. Setting up g++-9 (9.2.1-21ubuntu1) ... Setting up systemd-sysv (244-3ubuntu1) ... Processing triggers for libc-bin (2.30-0ubuntu3) ... RUN: /usr/share/launchpad-buildd/bin/sbuild-package PACKAGEBUILD-18355010 amd64 focal -c chroot:build-PACKAGEBUILD-18355010 --arch=amd64 --dist=focal --nolog -A salmon_0.12.0+ds1-1.dsc Initiating build PACKAGEBUILD-18355010 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 4.4.0-170-generic #199-Ubuntu SMP Thu Nov 14 01:45:04 UTC 2019 x86_64 sbuild (Debian sbuild) 0.67.0 (26 Dec 2015) on lcy01-amd64-028.buildd +==============================================================================+ | salmon 0.12.0+ds1-1 (amd64) 05 Jan 2020 10:30 | +==============================================================================+ Package: salmon Version: 0.12.0+ds1-1 Source Version: 0.12.0+ds1-1 Distribution: focal Machine Architecture: amd64 Host Architecture: amd64 Build Architecture: amd64 I: NOTICE: Log filtering will replace 'build/salmon-DiMyQ4/salmon-0.12.0+ds1' with '<>' I: NOTICE: Log filtering will replace 'build/salmon-DiMyQ4' with '<>' I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-18355010/chroot-autobuild' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- salmon_0.12.0+ds1-1.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-ev6yho/apt_archive/sbuild-build-depends-core-dummy.deb'. Ign:1 copy:/<>/resolver-ev6yho/apt_archive ./ InRelease Get:2 copy:/<>/resolver-ev6yho/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-ev6yho/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-ev6yho/apt_archive ./ Sources [214 B] Get:5 copy:/<>/resolver-ev6yho/apt_archive ./ Packages [524 B] Fetched 2857 B in 0s (226 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: libhogweed4 libisl21 libnettle6 libperl5.28 perl-modules-5.28 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-ev6yho/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 ... 14652 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~), cmake, libboost-filesystem-dev, libboost-system-dev, libboost-iostreams-dev, libboost-thread-dev, libboost-program-options-dev, libboost-timer-dev, libjellyfish-2.0-dev (>> 2.2.3-2), libpthread-stubs0-dev, libsparsehash-dev, libdivsufsort-dev, libbwa-dev, pkg-config, libjemalloc-dev, libcereal-dev, libtbb-dev, libgff-dev, libstaden-read-dev, libspdlog-dev, libtclap-dev, help2man, sphinx-doc, python3-sphinx, python3-sphinx-rtd-theme, zlib1g-dev, libeigen3-dev, libbz2-dev, liblzma-dev, rapmap-dev (>= 0.12.0~) Filtered Build-Depends: debhelper (>= 11~), cmake, libboost-filesystem-dev, libboost-system-dev, libboost-iostreams-dev, libboost-thread-dev, libboost-program-options-dev, libboost-timer-dev, libjellyfish-2.0-dev (>> 2.2.3-2), libpthread-stubs0-dev, libsparsehash-dev, libdivsufsort-dev, libbwa-dev, pkg-config, libjemalloc-dev, libcereal-dev, libtbb-dev, libgff-dev, libstaden-read-dev, libspdlog-dev, libtclap-dev, help2man, sphinx-doc, python3-sphinx, python3-sphinx-rtd-theme, zlib1g-dev, libeigen3-dev, libbz2-dev, liblzma-dev, rapmap-dev (>= 0.12.0~) dpkg-deb: building package 'sbuild-build-depends-salmon-dummy' in '/<>/resolver-YKYAHw/apt_archive/sbuild-build-depends-salmon-dummy.deb'. Ign:1 copy:/<>/resolver-YKYAHw/apt_archive ./ InRelease Get:2 copy:/<>/resolver-YKYAHw/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-YKYAHw/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-YKYAHw/apt_archive ./ Sources [427 B] Get:5 copy:/<>/resolver-YKYAHw/apt_archive ./ Packages [755 B] Fetched 3301 B in 0s (227 kB/s) Reading package lists... Reading package lists... +------------------------------------------------------------------------------+ | Install salmon 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: libhogweed4 libisl21 libnettle6 libperl5.28 perl-modules-5.28 Use 'apt autoremove' to remove them. The following additional packages will be installed: autoconf automake autopoint autotools-dev bsdmainutils cmake cmake-data debhelper dh-autoreconf dh-strip-nondeterminism docutils-common docutils-doc dwz file fonts-font-awesome fonts-lato fonts-roboto-slab gettext gettext-base groff-base help2man icu-devtools intltool-debian libarchive-zip-perl libarchive13 libasn1-8-heimdal libboost-atomic1.67-dev libboost-atomic1.67.0 libboost-chrono1.67-dev libboost-chrono1.67.0 libboost-date-time1.67-dev libboost-date-time1.67.0 libboost-filesystem-dev libboost-filesystem1.67-dev libboost-filesystem1.67.0 libboost-iostreams-dev libboost-iostreams1.67-dev libboost-iostreams1.67.0 libboost-program-options-dev libboost-program-options1.67-dev libboost-program-options1.67.0 libboost-regex1.67-dev libboost-regex1.67.0 libboost-serialization1.67-dev libboost-serialization1.67.0 libboost-system-dev libboost-system1.67-dev libboost-system1.67.0 libboost-thread-dev libboost-thread1.67-dev libboost-thread1.67.0 libboost-timer-dev libboost-timer1.67-dev libboost-timer1.67.0 libboost1.67-dev libbrotli1 libbsd0 libbwa-dev libbz2-dev libcereal-dev libcroco3 libcurl3-gnutls libcurl4 libcurl4-gnutls-dev libdebhelper-perl libdivsufsort-dev libdivsufsort3 libeigen3-dev libelf1 libexpat1 libfile-stripnondeterminism-perl libgff-dev libglib2.0-0 libgssapi-krb5-2 libgssapi3-heimdal libhcrypto4-heimdal libheimbase1-heimdal libheimntlm0-heimdal libhx509-5-heimdal libicu-dev libicu63 libjellyfish-2.0-2 libjellyfish-2.0-dev libjemalloc-dev libjemalloc2 libjs-jquery libjs-modernizr libjs-sphinxdoc libjs-underscore libjsoncpp1 libk5crypto3 libkeyutils1 libkrb5-26-heimdal libkrb5-3 libkrb5support0 libldap-2.4-2 libldap-common liblocale-gettext-perl liblzma-dev libmagic-mgc libmagic1 libmpdec2 libnghttp2-14 libpipeline1 libpsl5 libpthread-stubs0-dev libpython3-stdlib libpython3.7-minimal libpython3.7-stdlib librhash0 libroken18-heimdal librtmp1 libsasl2-2 libsasl2-modules-db libsigsegv2 libsparsehash-dev libspdlog-dev libssh-4 libstaden-read-dev libstaden-read13 libsub-override-perl libtbb-dev libtbb2 libtclap-dev libtool libuchardet0 libuv1 libwind0-heimdal libxml2 m4 man-db mime-support pkg-config po-debconf python-babel-localedata python3 python3-alabaster python3-attr python3-babel python3-certifi python3-chardet python3-distutils python3-docutils python3-idna python3-imagesize python3-jinja2 python3-lib2to3 python3-markupsafe python3-minimal python3-packaging python3-pkg-resources python3-pygments python3-pyparsing python3-requests python3-roman python3-six python3-sphinx python3-sphinx-rtd-theme python3-tz python3-urllib3 python3.7 python3.7-minimal rapmap-dev sgml-base sphinx-common sphinx-doc sphinx-rtd-theme-common xml-core zlib1g-dev Suggested packages: autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois vacation cmake-doc ninja-build dh-make fonts-roboto gettext-doc libasprintf-dev libgettextpo-dev groff lrzip libboost1.67-doc libboost-container1.67-dev libboost-context1.67-dev libboost-contract1.67-dev libboost-coroutine1.67-dev libboost-exception1.67-dev libboost-fiber1.67-dev libboost-graph1.67-dev libboost-graph-parallel1.67-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-python1.67-dev libboost-random1.67-dev libboost-signals1.67-dev libboost-stacktrace1.67-dev libboost-test1.67-dev libboost-type-erasure1.67-dev libboost-wave1.67-dev libboost1.67-tools-dev libmpfrc++-dev libntl-dev samtools libcurl4-doc libgnutls28-dev libidn11-dev libkrb5-dev libldap2-dev librtmp-dev libssh2-1-dev libeigen3-doc krb5-doc krb5-user icu-doc liblzma-doc tbb-examples libtbb-doc libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc apparmor less www-browser libmail-box-perl python3-doc python3-tk python3-venv python-attr-doc fonts-linuxlibertine | ttf-linux-libertine texlive-lang-french texlive-latex-base texlive-latex-recommended python-jinja2-doc python3-setuptools python-pygments-doc ttf-bitstream-vera python-pyparsing-doc python3-cryptography python3-openssl python3-socks dvipng imagemagick-6.q16 latexmk libjs-mathjax python3-stemmer texlive-fonts-recommended texlive-latex-extra texlive-plain-generic python3.7-venv python3.7-doc binfmt-support sgml-base-doc Recommended packages: curl | wget | lynx bzip2-doc libarchive-cpio-perl libglib2.0-data shared-mime-info xdg-user-dirs javascript-common krb5-locales publicsuffix libsasl2-modules libltdl-dev libmail-sendmail-perl libpaper-utils python3-pil The following NEW packages will be installed: autoconf automake autopoint autotools-dev bsdmainutils cmake cmake-data debhelper dh-autoreconf dh-strip-nondeterminism docutils-common docutils-doc dwz file fonts-font-awesome fonts-lato fonts-roboto-slab gettext gettext-base groff-base help2man icu-devtools intltool-debian libarchive-zip-perl libarchive13 libasn1-8-heimdal libboost-atomic1.67-dev libboost-atomic1.67.0 libboost-chrono1.67-dev libboost-chrono1.67.0 libboost-date-time1.67-dev libboost-date-time1.67.0 libboost-filesystem-dev libboost-filesystem1.67-dev libboost-filesystem1.67.0 libboost-iostreams-dev libboost-iostreams1.67-dev libboost-iostreams1.67.0 libboost-program-options-dev libboost-program-options1.67-dev libboost-program-options1.67.0 libboost-regex1.67-dev libboost-regex1.67.0 libboost-serialization1.67-dev libboost-serialization1.67.0 libboost-system-dev libboost-system1.67-dev libboost-system1.67.0 libboost-thread-dev libboost-thread1.67-dev libboost-thread1.67.0 libboost-timer-dev libboost-timer1.67-dev libboost-timer1.67.0 libboost1.67-dev libbrotli1 libbsd0 libbwa-dev libbz2-dev libcereal-dev libcroco3 libcurl3-gnutls libcurl4 libcurl4-gnutls-dev libdebhelper-perl libdivsufsort-dev libdivsufsort3 libeigen3-dev libelf1 libexpat1 libfile-stripnondeterminism-perl libgff-dev libglib2.0-0 libgssapi-krb5-2 libgssapi3-heimdal libhcrypto4-heimdal libheimbase1-heimdal libheimntlm0-heimdal libhx509-5-heimdal libicu-dev libicu63 libjellyfish-2.0-2 libjellyfish-2.0-dev libjemalloc-dev libjemalloc2 libjs-jquery libjs-modernizr libjs-sphinxdoc libjs-underscore libjsoncpp1 libk5crypto3 libkeyutils1 libkrb5-26-heimdal libkrb5-3 libkrb5support0 libldap-2.4-2 libldap-common liblocale-gettext-perl liblzma-dev libmagic-mgc libmagic1 libmpdec2 libnghttp2-14 libpipeline1 libpsl5 libpthread-stubs0-dev libpython3-stdlib libpython3.7-minimal libpython3.7-stdlib librhash0 libroken18-heimdal librtmp1 libsasl2-2 libsasl2-modules-db libsigsegv2 libsparsehash-dev libspdlog-dev libssh-4 libstaden-read-dev libstaden-read13 libsub-override-perl libtbb-dev libtbb2 libtclap-dev libtool libuchardet0 libuv1 libwind0-heimdal libxml2 m4 man-db mime-support pkg-config po-debconf python-babel-localedata python3 python3-alabaster python3-attr python3-babel python3-certifi python3-chardet python3-distutils python3-docutils python3-idna python3-imagesize python3-jinja2 python3-lib2to3 python3-markupsafe python3-minimal python3-packaging python3-pkg-resources python3-pygments python3-pyparsing python3-requests python3-roman python3-six python3-sphinx python3-sphinx-rtd-theme python3-tz python3-urllib3 python3.7 python3.7-minimal rapmap-dev sbuild-build-depends-salmon-dummy sgml-base sphinx-common sphinx-doc sphinx-rtd-theme-common xml-core zlib1g-dev 0 upgraded, 170 newly installed, 0 to remove and 0 not upgraded. Need to get 72.7 MB of archives. After this operation, 454 MB of additional disk space will be used. Get:1 copy:/<>/resolver-YKYAHw/apt_archive ./ sbuild-build-depends-salmon-dummy 0.invalid.0 [1080 B] Get:2 http://ftpmaster.internal/ubuntu focal/main amd64 liblocale-gettext-perl amd64 1.07-4 [17.1 kB] Get:3 http://ftpmaster.internal/ubuntu focal/main amd64 libpython3.7-minimal amd64 3.7.5-2 [545 kB] Get:4 http://ftpmaster.internal/ubuntu focal/main amd64 libexpat1 amd64 2.2.9-1 [73.3 kB] Get:5 http://ftpmaster.internal/ubuntu focal/main amd64 python3.7-minimal amd64 3.7.5-2 [1766 kB] Get:6 http://ftpmaster.internal/ubuntu focal/main amd64 python3-minimal amd64 3.7.5-1ubuntu1 [23.3 kB] Get:7 http://ftpmaster.internal/ubuntu focal/main amd64 mime-support all 3.64ubuntu1 [30.6 kB] Get:8 http://ftpmaster.internal/ubuntu focal/main amd64 libmpdec2 amd64 2.4.2-2 [84.1 kB] Get:9 http://ftpmaster.internal/ubuntu focal/main amd64 libpython3.7-stdlib amd64 3.7.5-2 [1732 kB] Get:10 http://ftpmaster.internal/ubuntu focal/main amd64 python3.7 amd64 3.7.5-2 [301 kB] Get:11 http://ftpmaster.internal/ubuntu focal/main amd64 libpython3-stdlib amd64 3.7.5-1ubuntu1 [6844 B] Get:12 http://ftpmaster.internal/ubuntu focal/main amd64 python3 amd64 3.7.5-1ubuntu1 [47.2 kB] Get:13 http://ftpmaster.internal/ubuntu focal/main amd64 libbsd0 amd64 0.10.0-1 [45.4 kB] Get:14 http://ftpmaster.internal/ubuntu focal/main amd64 bsdmainutils amd64 11.1.2ubuntu2 [181 kB] Get:15 http://ftpmaster.internal/ubuntu focal/main amd64 libuchardet0 amd64 0.0.6-3 [64.9 kB] Get:16 http://ftpmaster.internal/ubuntu focal/main amd64 groff-base amd64 1.22.4-4 [865 kB] Get:17 http://ftpmaster.internal/ubuntu focal/main amd64 libpipeline1 amd64 1.5.1-3 [27.4 kB] Get:18 http://ftpmaster.internal/ubuntu focal/main amd64 man-db amd64 2.9.0-2 [1114 kB] Get:19 http://ftpmaster.internal/ubuntu focal/main amd64 fonts-lato all 2.0-2 [2698 kB] Get:20 http://ftpmaster.internal/ubuntu focal/main amd64 sgml-base all 1.29.1 [12.4 kB] Get:21 http://ftpmaster.internal/ubuntu focal/main amd64 libmagic-mgc amd64 1:5.37-6 [209 kB] Get:22 http://ftpmaster.internal/ubuntu focal/main amd64 libmagic1 amd64 1:5.37-6 [75.3 kB] Get:23 http://ftpmaster.internal/ubuntu focal/main amd64 file amd64 1:5.37-6 [23.2 kB] Get:24 http://ftpmaster.internal/ubuntu focal/main amd64 libelf1 amd64 0.176-1.1 [44.1 kB] Get:25 http://ftpmaster.internal/ubuntu focal/main amd64 libglib2.0-0 amd64 2.63.3-1 [1279 kB] Get:26 http://ftpmaster.internal/ubuntu focal/main amd64 libicu63 amd64 63.2-2 [8294 kB] Get:27 http://ftpmaster.internal/ubuntu focal/main amd64 libxml2 amd64 2.9.4+dfsg1-8ubuntu1 [648 kB] Get:28 http://ftpmaster.internal/ubuntu focal/main amd64 python3-pkg-resources all 41.4.0-1 [100 kB] Get:29 http://ftpmaster.internal/ubuntu focal/main amd64 python3-six all 1.12.0-2build1 [11.7 kB] Get:30 http://ftpmaster.internal/ubuntu focal/main amd64 gettext-base amd64 0.19.8.1-10 [50.2 kB] Get:31 http://ftpmaster.internal/ubuntu focal/main amd64 libkrb5support0 amd64 1.17-6 [31.4 kB] Get:32 http://ftpmaster.internal/ubuntu focal/main amd64 libk5crypto3 amd64 1.17-6 [80.2 kB] Get:33 http://ftpmaster.internal/ubuntu focal/main amd64 libkeyutils1 amd64 1.6-6ubuntu1 [10.2 kB] Get:34 http://ftpmaster.internal/ubuntu focal/main amd64 libkrb5-3 amd64 1.17-6 [330 kB] Get:35 http://ftpmaster.internal/ubuntu focal/main amd64 libgssapi-krb5-2 amd64 1.17-6 [121 kB] Get:36 http://ftpmaster.internal/ubuntu focal/main amd64 libpsl5 amd64 0.20.2-2 [50.0 kB] Get:37 http://ftpmaster.internal/ubuntu focal/main amd64 libsigsegv2 amd64 2.12-2 [13.9 kB] Get:38 http://ftpmaster.internal/ubuntu focal/main amd64 m4 amd64 1.4.18-4 [199 kB] Get:39 http://ftpmaster.internal/ubuntu focal/main amd64 autoconf all 2.69-11ubuntu1 [321 kB] Get:40 http://ftpmaster.internal/ubuntu focal/main amd64 autotools-dev all 20180224.1 [39.6 kB] Get:41 http://ftpmaster.internal/ubuntu focal/main amd64 automake all 1:1.16.1-4ubuntu3 [522 kB] Get:42 http://ftpmaster.internal/ubuntu focal/main amd64 autopoint all 0.19.8.1-10 [412 kB] Get:43 http://ftpmaster.internal/ubuntu focal/main amd64 cmake-data all 3.15.4-1ubuntu2 [1562 kB] Get:44 http://ftpmaster.internal/ubuntu focal/main amd64 libarchive13 amd64 3.4.0-1build1 [327 kB] Get:45 http://ftpmaster.internal/ubuntu focal/main amd64 libbrotli1 amd64 1.0.7-5 [265 kB] Get:46 http://ftpmaster.internal/ubuntu focal/main amd64 libroken18-heimdal amd64 7.7.0+dfsg-1 [41.9 kB] Get:47 http://ftpmaster.internal/ubuntu focal/main amd64 libasn1-8-heimdal amd64 7.7.0+dfsg-1 [181 kB] Get:48 http://ftpmaster.internal/ubuntu focal/main amd64 libheimbase1-heimdal amd64 7.7.0+dfsg-1 [29.7 kB] Get:49 http://ftpmaster.internal/ubuntu focal/main amd64 libhcrypto4-heimdal amd64 7.7.0+dfsg-1 [87.8 kB] Get:50 http://ftpmaster.internal/ubuntu focal/main amd64 libwind0-heimdal amd64 7.7.0+dfsg-1 [47.9 kB] Get:51 http://ftpmaster.internal/ubuntu focal/main amd64 libhx509-5-heimdal amd64 7.7.0+dfsg-1 [107 kB] Get:52 http://ftpmaster.internal/ubuntu focal/main amd64 libkrb5-26-heimdal amd64 7.7.0+dfsg-1 [207 kB] Get:53 http://ftpmaster.internal/ubuntu focal/main amd64 libheimntlm0-heimdal amd64 7.7.0+dfsg-1 [15.1 kB] Get:54 http://ftpmaster.internal/ubuntu focal/main amd64 libgssapi3-heimdal amd64 7.7.0+dfsg-1 [96.6 kB] Get:55 http://ftpmaster.internal/ubuntu focal/main amd64 libsasl2-modules-db amd64 2.1.27+dfsg-2 [14.9 kB] Get:56 http://ftpmaster.internal/ubuntu focal/main amd64 libsasl2-2 amd64 2.1.27+dfsg-2 [49.3 kB] Get:57 http://ftpmaster.internal/ubuntu focal/main amd64 libldap-common all 2.4.48+dfsg-1ubuntu3 [17.3 kB] Get:58 http://ftpmaster.internal/ubuntu focal/main amd64 libldap-2.4-2 amd64 2.4.48+dfsg-1ubuntu3 [155 kB] Get:59 http://ftpmaster.internal/ubuntu focal/main amd64 libnghttp2-14 amd64 1.40.0-1 [78.1 kB] Get:60 http://ftpmaster.internal/ubuntu focal/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2build1 [54.9 kB] Get:61 http://ftpmaster.internal/ubuntu focal/main amd64 libssh-4 amd64 0.9.0-1ubuntu5 [196 kB] Get:62 http://ftpmaster.internal/ubuntu focal/main amd64 libcurl4 amd64 7.66.0-1ubuntu1 [232 kB] Get:63 http://ftpmaster.internal/ubuntu focal/main amd64 libjsoncpp1 amd64 1.7.4-3 [73.6 kB] Get:64 http://ftpmaster.internal/ubuntu focal/main amd64 librhash0 amd64 1.3.9-1 [113 kB] Get:65 http://ftpmaster.internal/ubuntu focal/main amd64 libuv1 amd64 1.33.1-2 [80.1 kB] Get:66 http://ftpmaster.internal/ubuntu focal/main amd64 cmake amd64 3.15.4-1ubuntu2 [3607 kB] Get:67 http://ftpmaster.internal/ubuntu focal/main amd64 libtool all 2.4.6-11 [194 kB] Get:68 http://ftpmaster.internal/ubuntu focal/main amd64 dh-autoreconf all 19 [16.1 kB] Get:69 http://ftpmaster.internal/ubuntu focal/main amd64 libdebhelper-perl all 12.7.1ubuntu1 [52.0 kB] Get:70 http://ftpmaster.internal/ubuntu focal/main amd64 libarchive-zip-perl all 1.67-1 [90.4 kB] Get:71 http://ftpmaster.internal/ubuntu focal/main amd64 libsub-override-perl all 0.09-2 [9532 B] Get:72 http://ftpmaster.internal/ubuntu focal/main amd64 libfile-stripnondeterminism-perl all 1.6.3-1 [16.0 kB] Get:73 http://ftpmaster.internal/ubuntu focal/main amd64 dh-strip-nondeterminism all 1.6.3-1 [5224 B] Get:74 http://ftpmaster.internal/ubuntu focal/main amd64 dwz amd64 0.13-5 [151 kB] Get:75 http://ftpmaster.internal/ubuntu focal/main amd64 libcroco3 amd64 0.6.13-1 [82.5 kB] Get:76 http://ftpmaster.internal/ubuntu focal/main amd64 gettext amd64 0.19.8.1-10 [897 kB] Get:77 http://ftpmaster.internal/ubuntu focal/main amd64 intltool-debian all 0.35.0+20060710.5 [24.9 kB] Get:78 http://ftpmaster.internal/ubuntu focal/main amd64 po-debconf all 1.0.21 [233 kB] Get:79 http://ftpmaster.internal/ubuntu focal/main amd64 debhelper all 12.7.1ubuntu1 [875 kB] Get:80 http://ftpmaster.internal/ubuntu focal/main amd64 xml-core all 0.18+nmu1 [21.6 kB] Get:81 http://ftpmaster.internal/ubuntu focal/main amd64 docutils-common all 0.15.2+dfsg-1 [156 kB] Get:82 http://ftpmaster.internal/ubuntu focal/main amd64 docutils-doc all 0.15.2+dfsg-1 [917 kB] Get:83 http://ftpmaster.internal/ubuntu focal/main amd64 fonts-font-awesome all 5.0.10+really4.7.0~dfsg-1 [514 kB] Get:84 http://ftpmaster.internal/ubuntu focal/main amd64 fonts-roboto-slab all 1.100263+20170512-2 [166 kB] Get:85 http://ftpmaster.internal/ubuntu focal/universe amd64 help2man amd64 1.47.12 [172 kB] Get:86 http://ftpmaster.internal/ubuntu focal/main amd64 icu-devtools amd64 63.2-2 [180 kB] Get:87 http://ftpmaster.internal/ubuntu focal/main amd64 libboost1.67-dev amd64 1.67.0-13ubuntu2 [8365 kB] Get:88 http://ftpmaster.internal/ubuntu focal/main amd64 libboost-atomic1.67.0 amd64 1.67.0-13ubuntu2 [201 kB] Get:89 http://ftpmaster.internal/ubuntu focal/main amd64 libboost-atomic1.67-dev amd64 1.67.0-13ubuntu2 [199 kB] Get:90 http://ftpmaster.internal/ubuntu focal/main amd64 libboost-system1.67.0 amd64 1.67.0-13ubuntu2 [205 kB] Get:91 http://ftpmaster.internal/ubuntu focal/main amd64 libboost-chrono1.67.0 amd64 1.67.0-13ubuntu2 [208 kB] Get:92 http://ftpmaster.internal/ubuntu focal/main amd64 libboost-chrono1.67-dev amd64 1.67.0-13ubuntu2 [210 kB] Get:93 http://ftpmaster.internal/ubuntu focal/main amd64 libboost-date-time1.67.0 amd64 1.67.0-13ubuntu2 [215 kB] Get:94 http://ftpmaster.internal/ubuntu focal/main amd64 libboost-serialization1.67.0 amd64 1.67.0-13ubuntu2 [292 kB] Get:95 http://ftpmaster.internal/ubuntu focal/main amd64 libboost-serialization1.67-dev amd64 1.67.0-13ubuntu2 [331 kB] Get:96 http://ftpmaster.internal/ubuntu focal/main amd64 libboost-date-time1.67-dev amd64 1.67.0-13ubuntu2 [221 kB] Get:97 http://ftpmaster.internal/ubuntu focal/main amd64 libboost-filesystem1.67.0 amd64 1.67.0-13ubuntu2 [234 kB] Get:98 http://ftpmaster.internal/ubuntu focal/main amd64 libboost-system1.67-dev amd64 1.67.0-13ubuntu2 [206 kB] Get:99 http://ftpmaster.internal/ubuntu focal/main amd64 libboost-filesystem1.67-dev amd64 1.67.0-13ubuntu2 [243 kB] Get:100 http://ftpmaster.internal/ubuntu focal/main amd64 libboost-filesystem-dev amd64 1.67.0.2 [3372 B] Get:101 http://ftpmaster.internal/ubuntu focal/universe amd64 libboost-regex1.67.0 amd64 1.67.0-13ubuntu2 [487 kB] Get:102 http://ftpmaster.internal/ubuntu focal/main amd64 libicu-dev amd64 63.2-2 [9178 kB] Get:103 http://ftpmaster.internal/ubuntu focal/universe amd64 libboost-regex1.67-dev amd64 1.67.0-13ubuntu2 [541 kB] Get:104 http://ftpmaster.internal/ubuntu focal/main amd64 libboost-iostreams1.67.0 amd64 1.67.0-13ubuntu2 [225 kB] Get:105 http://ftpmaster.internal/ubuntu focal/universe amd64 libboost-iostreams1.67-dev amd64 1.67.0-13ubuntu2 [229 kB] Get:106 http://ftpmaster.internal/ubuntu focal/universe amd64 libboost-iostreams-dev amd64 1.67.0.2 [3328 B] Get:107 http://ftpmaster.internal/ubuntu focal/main amd64 libboost-program-options1.67.0 amd64 1.67.0-13ubuntu2 [331 kB] Get:108 http://ftpmaster.internal/ubuntu focal/main amd64 libboost-program-options1.67-dev amd64 1.67.0-13ubuntu2 [355 kB] Get:109 http://ftpmaster.internal/ubuntu focal/main amd64 libboost-program-options-dev amd64 1.67.0.2 [3352 B] Get:110 http://ftpmaster.internal/ubuntu focal/main amd64 libboost-system-dev amd64 1.67.0.2 [3476 B] Get:111 http://ftpmaster.internal/ubuntu focal/main amd64 libboost-thread1.67.0 amd64 1.67.0-13ubuntu2 [243 kB] Get:112 http://ftpmaster.internal/ubuntu focal/main amd64 libboost-thread1.67-dev amd64 1.67.0-13ubuntu2 [245 kB] Get:113 http://ftpmaster.internal/ubuntu focal/main amd64 libboost-thread-dev amd64 1.67.0.2 [3360 B] Get:114 http://ftpmaster.internal/ubuntu focal/universe amd64 libboost-timer1.67.0 amd64 1.67.0-13ubuntu2 [205 kB] Get:115 http://ftpmaster.internal/ubuntu focal/universe amd64 libboost-timer1.67-dev amd64 1.67.0-13ubuntu2 [205 kB] Get:116 http://ftpmaster.internal/ubuntu focal/universe amd64 libboost-timer-dev amd64 1.67.0.2 [3456 B] Get:117 http://ftpmaster.internal/ubuntu focal/universe amd64 libbwa-dev amd64 0.7.17-4 [130 kB] Get:118 http://ftpmaster.internal/ubuntu focal/main amd64 libbz2-dev amd64 1.0.8-2 [30.2 kB] Get:119 http://ftpmaster.internal/ubuntu focal/universe amd64 libcereal-dev amd64 1.3.0-2 [299 kB] Get:120 http://ftpmaster.internal/ubuntu focal/main amd64 libcurl3-gnutls amd64 7.66.0-1ubuntu1 [231 kB] Get:121 http://ftpmaster.internal/ubuntu focal/main amd64 libcurl4-gnutls-dev amd64 7.66.0-1ubuntu1 [317 kB] Get:122 http://ftpmaster.internal/ubuntu focal/universe amd64 libdivsufsort3 amd64 2.0.1-4 [42.4 kB] Get:123 http://ftpmaster.internal/ubuntu focal/universe amd64 libdivsufsort-dev amd64 2.0.1-4 [19.4 kB] Get:124 http://ftpmaster.internal/ubuntu focal/universe amd64 libgff-dev amd64 1.0-2 [138 kB] Get:125 http://ftpmaster.internal/ubuntu focal/universe amd64 libjellyfish-2.0-2 amd64 2.3.0-2 [60.7 kB] Get:126 http://ftpmaster.internal/ubuntu focal/universe amd64 libjellyfish-2.0-dev amd64 2.3.0-2 [130 kB] Get:127 http://ftpmaster.internal/ubuntu focal/universe amd64 libjemalloc2 amd64 5.2.1-1 [235 kB] Get:128 http://ftpmaster.internal/ubuntu focal/main amd64 libjs-jquery all 3.3.1~dfsg-3 [329 kB] Get:129 http://ftpmaster.internal/ubuntu focal/main amd64 libjs-underscore all 1.9.1~dfsg-1 [98.6 kB] Get:130 http://ftpmaster.internal/ubuntu focal/main amd64 libjs-sphinxdoc all 1.8.5-4 [96.7 kB] Get:131 http://ftpmaster.internal/ubuntu focal/main amd64 libpthread-stubs0-dev amd64 0.4-1 [5384 B] Get:132 http://ftpmaster.internal/ubuntu focal/universe amd64 libsparsehash-dev all 2.0.3-1 [71.9 kB] Get:133 http://ftpmaster.internal/ubuntu focal/universe amd64 libspdlog-dev amd64 1:1.3.1-1 [176 kB] Get:134 http://ftpmaster.internal/ubuntu focal/universe amd64 libstaden-read13 amd64 1.14.11-6 [248 kB] Get:135 http://ftpmaster.internal/ubuntu focal/main amd64 zlib1g-dev amd64 1:1.2.11.dfsg-1ubuntu3 [172 kB] Get:136 http://ftpmaster.internal/ubuntu focal/universe amd64 libstaden-read-dev amd64 1.14.11-6 [330 kB] Get:137 http://ftpmaster.internal/ubuntu focal/universe amd64 libtclap-dev amd64 1.2.2-1 [127 kB] Get:138 http://ftpmaster.internal/ubuntu focal/main amd64 pkg-config amd64 0.29.1-0ubuntu3 [45.2 kB] Get:139 http://ftpmaster.internal/ubuntu focal/main amd64 python-babel-localedata all 2.6.0+dfsg.1-1 [4071 kB] Get:140 http://ftpmaster.internal/ubuntu focal/main amd64 python3-attr all 18.2.0-1build1 [29.7 kB] Get:141 http://ftpmaster.internal/ubuntu focal/main amd64 python3-tz all 2019.3-1 [24.4 kB] Get:142 http://ftpmaster.internal/ubuntu focal/main amd64 python3-babel all 2.6.0+dfsg.1-1 [83.4 kB] Get:143 http://ftpmaster.internal/ubuntu focal/main amd64 python3-certifi all 2019.11.28-1 [149 kB] Get:144 http://ftpmaster.internal/ubuntu focal/main amd64 python3-chardet all 3.0.4-4 [80.6 kB] Get:145 http://ftpmaster.internal/ubuntu focal/main amd64 python3-lib2to3 all 3.8.0-1 [75.6 kB] Get:146 http://ftpmaster.internal/ubuntu focal/main amd64 python3-distutils all 3.8.0-1 [142 kB] Get:147 http://ftpmaster.internal/ubuntu focal/main amd64 python3-roman all 2.0.0-3build1 [8728 B] Get:148 http://ftpmaster.internal/ubuntu focal/main amd64 python3-docutils all 0.15.2+dfsg-1 [366 kB] Get:149 http://ftpmaster.internal/ubuntu focal/main amd64 python3-idna all 2.6-2build1 [32.8 kB] Get:150 http://ftpmaster.internal/ubuntu focal/main amd64 python3-imagesize all 1.2.0-1 [5808 B] Get:151 http://ftpmaster.internal/ubuntu focal/main amd64 python3-markupsafe amd64 1.1.0-1build1 [14.5 kB] Get:152 http://ftpmaster.internal/ubuntu focal/main amd64 python3-jinja2 all 2.10-2ubuntu2 [95.5 kB] Get:153 http://ftpmaster.internal/ubuntu focal/main amd64 python3-pyparsing all 2.4.2-1 [58.8 kB] Get:154 http://ftpmaster.internal/ubuntu focal/main amd64 python3-packaging all 19.1-2 [21.7 kB] Get:155 http://ftpmaster.internal/ubuntu focal/main amd64 python3-pygments all 2.3.1+dfsg-1ubuntu2 [579 kB] Get:156 http://ftpmaster.internal/ubuntu focal/main amd64 python3-urllib3 all 1.24.1-1ubuntu2 [83.9 kB] Get:157 http://ftpmaster.internal/ubuntu focal/main amd64 python3-requests all 2.21.0-1 [46.8 kB] Get:158 http://ftpmaster.internal/ubuntu focal/main amd64 sphinx-common all 1.8.5-4 [492 kB] Get:159 http://ftpmaster.internal/ubuntu focal/main amd64 python3-alabaster all 0.7.8-1build1 [18.7 kB] Get:160 http://ftpmaster.internal/ubuntu focal/main amd64 python3-sphinx all 1.8.5-4 [482 kB] Get:161 http://ftpmaster.internal/ubuntu focal/main amd64 libjs-modernizr all 2.6.2+ds1-3ubuntu1 [46.2 kB] Get:162 http://ftpmaster.internal/ubuntu focal/main amd64 sphinx-rtd-theme-common all 0.4.3+dfsg-1 [1019 kB] Get:163 http://ftpmaster.internal/ubuntu focal/universe amd64 python3-sphinx-rtd-theme all 0.4.3+dfsg-1 [5324 B] Get:164 http://ftpmaster.internal/ubuntu focal/universe amd64 rapmap-dev all 0.14.1+dfsg-2 [194 kB] Get:165 http://ftpmaster.internal/ubuntu focal/main amd64 sphinx-doc all 1.8.5-4 [1103 kB] Get:166 http://ftpmaster.internal/ubuntu focal/universe amd64 libeigen3-dev all 3.3.7-1 [814 kB] Get:167 http://ftpmaster.internal/ubuntu focal/universe amd64 libjemalloc-dev amd64 5.2.1-1 [424 kB] Get:168 http://ftpmaster.internal/ubuntu focal/main amd64 liblzma-dev amd64 5.2.4-1 [145 kB] Get:169 http://ftpmaster.internal/ubuntu focal/universe amd64 libtbb2 amd64 2019~U9-2 [118 kB] Get:170 http://ftpmaster.internal/ubuntu focal/universe amd64 libtbb-dev amd64 2019~U9-2 [276 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 72.7 MB in 2s (40.3 MB/s) Selecting previously unselected package liblocale-gettext-perl. (Reading database ... 14652 files and directories currently installed.) Preparing to unpack .../liblocale-gettext-perl_1.07-4_amd64.deb ... Unpacking liblocale-gettext-perl (1.07-4) ... Selecting previously unselected package libpython3.7-minimal:amd64. Preparing to unpack .../libpython3.7-minimal_3.7.5-2_amd64.deb ... Unpacking libpython3.7-minimal:amd64 (3.7.5-2) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../libexpat1_2.2.9-1_amd64.deb ... Unpacking libexpat1:amd64 (2.2.9-1) ... Selecting previously unselected package python3.7-minimal. Preparing to unpack .../python3.7-minimal_3.7.5-2_amd64.deb ... Unpacking python3.7-minimal (3.7.5-2) ... Setting up libpython3.7-minimal:amd64 (3.7.5-2) ... Setting up libexpat1:amd64 (2.2.9-1) ... Setting up python3.7-minimal (3.7.5-2) ... Selecting previously unselected package python3-minimal. (Reading database ... 14915 files and directories currently installed.) 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Setting up sbuild-build-depends-salmon-dummy (0.invalid.0) ... +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 4.4.0-170-generic amd64 (x86_64) Toolchain package versions: binutils_2.33.1-6ubuntu3 dpkg-dev_1.19.7ubuntu2 g++-9_9.2.1-21ubuntu1 gcc-9_9.2.1-21ubuntu1 libc6-dev_2.30-0ubuntu3 libstdc++-9-dev_9.2.1-21ubuntu1 libstdc++6_9.2.1-21ubuntu1 linux-libc-dev_5.3.0-24.26 Package versions: adduser_3.118ubuntu1 advancecomp_2.1-2.1 apt_1.9.5 autoconf_2.69-11ubuntu1 automake_1:1.16.1-4ubuntu3 autopoint_0.19.8.1-10 autotools-dev_20180224.1 base-files_11ubuntu2 base-passwd_3.5.47 bash_5.0-5ubuntu1 binutils_2.33.1-6ubuntu3 binutils-common_2.33.1-6ubuntu3 binutils-x86-64-linux-gnu_2.33.1-6ubuntu3 bsdmainutils_11.1.2ubuntu2 bsdutils_1:2.34-0.1ubuntu4 build-essential_12.8ubuntu1 bzip2_1.0.8-2 ca-certificates_20190110 cmake_3.15.4-1ubuntu2 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libcurl4-gnutls-dev_7.66.0-1ubuntu1 libdb5.3_5.3.28+dfsg1-0.6ubuntu1 libdebconfclient0_0.250ubuntu2 libdebhelper-perl_12.7.1ubuntu1 libdevmapper1.02.1_2:1.02.155-2ubuntu7 libdivsufsort-dev_2.0.1-4 libdivsufsort3_2.0.1-4 libdpkg-perl_1.19.7ubuntu2 libeigen3-dev_3.3.7-1 libelf1_0.176-1.1 libexpat1_2.2.9-1 libext2fs2_1.45.3-4ubuntu2 libfakeroot_1.24-1 libfdisk1_2.34-0.1ubuntu4 libffi6_3.2.1-9 libfile-stripnondeterminism-perl_1.6.3-1 libgcc-9-dev_9.2.1-21ubuntu1 libgcc1_1:9.2.1-21ubuntu1 libgcrypt20_1.8.5-3ubuntu1 libgdbm-compat4_1.18.1-5 libgdbm6_1.18.1-5 libgff-dev_1.0-2 libglib2.0-0_2.63.3-1 libgmp10_2:6.1.2+dfsg-4 libgnutls30_3.6.11.1-2 libgomp1_9.2.1-21ubuntu1 libgpg-error0_1.36-7 libgssapi-krb5-2_1.17-6 libgssapi3-heimdal_7.7.0+dfsg-1 libhcrypto4-heimdal_7.7.0+dfsg-1 libheimbase1-heimdal_7.7.0+dfsg-1 libheimntlm0-heimdal_7.7.0+dfsg-1 libhogweed4_3.4.1-1 libhogweed5_3.5.1+really3.5.1-2 libhx509-5-heimdal_7.7.0+dfsg-1 libicu-dev_63.2-2 libicu63_63.2-2 libidn2-0_2.2.0-2 libip4tc2_1.8.3-2ubuntu5 libisl21_0.21-2 libisl22_0.22-2 libitm1_9.2.1-21ubuntu1 libjellyfish-2.0-2_2.3.0-2 libjellyfish-2.0-dev_2.3.0-2 libjemalloc-dev_5.2.1-1 libjemalloc2_5.2.1-1 libjs-jquery_3.3.1~dfsg-3 libjs-modernizr_2.6.2+ds1-3ubuntu1 libjs-sphinxdoc_1.8.5-4 libjs-underscore_1.9.1~dfsg-1 libjson-c4_0.13.1+dfsg-6 libjsoncpp1_1.7.4-3 libk5crypto3_1.17-6 libkeyutils1_1.6-6ubuntu1 libkmod2_26-3ubuntu1 libkrb5-26-heimdal_7.7.0+dfsg-1 libkrb5-3_1.17-6 libkrb5support0_1.17-6 libldap-2.4-2_2.4.48+dfsg-1ubuntu3 libldap-common_2.4.48+dfsg-1ubuntu3 liblocale-gettext-perl_1.07-4 liblockfile-bin_1.16-1.1 liblockfile1_1.16-1.1 liblsan0_9.2.1-21ubuntu1 liblz4-1_1.9.2-2 liblzma-dev_5.2.4-1 liblzma5_5.2.4-1 libmagic-mgc_1:5.37-6 libmagic1_1:5.37-6 libmount1_2.34-0.1ubuntu4 libmpc3_1.1.0-1 libmpdec2_2.4.2-2 libmpfr6_4.0.2-1 libncurses6_6.1+20191019-1ubuntu1 libncursesw6_6.1+20191019-1ubuntu1 libnettle6_3.4.1-1 libnettle7_3.5.1+really3.5.1-2 libnghttp2-14_1.40.0-1 libnpth0_1.6-1 libp11-kit0_0.23.18.1-2 libpam-modules_1.3.1-5ubuntu4 libpam-modules-bin_1.3.1-5ubuntu4 libpam-runtime_1.3.1-5ubuntu4 libpam0g_1.3.1-5ubuntu4 libpcre2-8-0_10.34-7 libpcre3_2:8.39-12 libperl5.28_5.28.1-6build1 libperl5.30_5.30.0-9 libpipeline1_1.5.1-3 libpng16-16_1.6.37-1 libprocps7_2:3.3.15-2ubuntu3 libpsl5_0.20.2-2 libpthread-stubs0-dev_0.4-1 libpython3-stdlib_3.7.5-1ubuntu1 libpython3.7-minimal_3.7.5-2 libpython3.7-stdlib_3.7.5-2 libquadmath0_9.2.1-21ubuntu1 libreadline8_8.0-3 librhash0_1.3.9-1 libroken18-heimdal_7.7.0+dfsg-1 librtmp1_2.4+20151223.gitfa8646d.1-2build1 libsasl2-2_2.1.27+dfsg-2 libsasl2-modules-db_2.1.27+dfsg-2 libseccomp2_2.4.2-2ubuntu1 libselinux1_3.0-1 libsemanage-common_3.0-1 libsemanage1_3.0-1 libsepol1_3.0-1 libsigsegv2_2.12-2 libsmartcols1_2.34-0.1ubuntu4 libsparsehash-dev_2.0.3-1 libspdlog-dev_1:1.3.1-1 libsqlite3-0_3.30.1-1ubuntu1 libss2_1.45.3-4ubuntu2 libssh-4_0.9.0-1ubuntu5 libssl1.1_1.1.1c-1ubuntu4 libstaden-read-dev_1.14.11-6 libstaden-read13_1.14.11-6 libstdc++-9-dev_9.2.1-21ubuntu1 libstdc++6_9.2.1-21ubuntu1 libsub-override-perl_0.09-2 libsystemd0_244-3ubuntu1 libtasn1-6_4.15.0-2 libtbb-dev_2019~U9-2 libtbb2_2019~U9-2 libtclap-dev_1.2.2-1 libtinfo6_6.1+20191019-1ubuntu1 libtool_2.4.6-11 libtsan0_9.2.1-21ubuntu1 libubsan1_9.2.1-21ubuntu1 libuchardet0_0.0.6-3 libudev1_244-3ubuntu1 libunistring2_0.9.10-2 libuuid1_2.34-0.1ubuntu4 libuv1_1.33.1-2 libwind0-heimdal_7.7.0+dfsg-1 libxml2_2.9.4+dfsg1-8ubuntu1 libzstd1_1.4.4+dfsg-1 linux-libc-dev_5.3.0-24.26 lockfile-progs_0.1.18 login_1:4.5-1.1ubuntu4 logsave_1.45.3-4ubuntu2 lsb-base_11.1.0ubuntu2 m4_1.4.18-4 make_4.2.1-1.2 man-db_2.9.0-2 mawk_1.3.3-17ubuntu3 mime-support_3.64ubuntu1 mount_2.34-0.1ubuntu4 ncurses-base_6.1+20191019-1ubuntu1 ncurses-bin_6.1+20191019-1ubuntu1 openssl_1.1.1c-1ubuntu4 optipng_0.7.7-1 passwd_1:4.5-1.1ubuntu4 patch_2.7.6-6 perl_5.30.0-9 perl-base_5.30.0-9 perl-modules-5.28_5.28.1-6build1 perl-modules-5.30_5.30.0-9 pinentry-curses_1.1.0-3 pkg-config_0.29.1-0ubuntu3 pkgbinarymangler_144 po-debconf_1.0.21 policyrcd-script-zg2_0.1-3 procps_2:3.3.15-2ubuntu3 python-babel-localedata_2.6.0+dfsg.1-1 python3_3.7.5-1ubuntu1 python3-alabaster_0.7.8-1build1 python3-attr_18.2.0-1build1 python3-babel_2.6.0+dfsg.1-1 python3-certifi_2019.11.28-1 python3-chardet_3.0.4-4 python3-distutils_3.8.0-1 python3-docutils_0.15.2+dfsg-1 python3-idna_2.6-2build1 python3-imagesize_1.2.0-1 python3-jinja2_2.10-2ubuntu2 python3-lib2to3_3.8.0-1 python3-markupsafe_1.1.0-1build1 python3-minimal_3.7.5-1ubuntu1 python3-packaging_19.1-2 python3-pkg-resources_41.4.0-1 python3-pygments_2.3.1+dfsg-1ubuntu2 python3-pyparsing_2.4.2-1 python3-requests_2.21.0-1 python3-roman_2.0.0-3build1 python3-six_1.12.0-2build1 python3-sphinx_1.8.5-4 python3-sphinx-rtd-theme_0.4.3+dfsg-1 python3-tz_2019.3-1 python3-urllib3_1.24.1-1ubuntu2 python3.7_3.7.5-2 python3.7-minimal_3.7.5-2 rapmap-dev_0.14.1+dfsg-2 readline-common_8.0-3 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-salmon-dummy_0.invalid.0 sed_4.7-1 sensible-utils_0.0.12+nmu1 sgml-base_1.29.1 sphinx-common_1.8.5-4 sphinx-doc_1.8.5-4 sphinx-rtd-theme-common_0.4.3+dfsg-1 systemd_244-3ubuntu1 systemd-sysv_244-3ubuntu1 sysvinit-utils_2.96-1ubuntu1 tar_1.30+dfsg-6 tzdata_2019c-3 ubuntu-keyring_2018.09.18.1 util-linux_2.34-0.1ubuntu4 xml-core_0.18+nmu1 xz-utils_5.2.4-1 zlib1g_1:1.2.11.dfsg-1ubuntu3 zlib1g-dev_1:1.2.11.dfsg-1ubuntu3 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- gpgv: Signature made Thu Dec 13 18:44:54 2018 UTC gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./salmon_0.12.0+ds1-1.dsc dpkg-source: info: extracting salmon in salmon-0.12.0+ds1 dpkg-source: info: unpacking salmon_0.12.0+ds1.orig.tar.xz dpkg-source: info: unpacking salmon_0.12.0+ds1-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying use_debian_packaged_libs.patch dpkg-source: info: applying disable-version-check.patch Check disc space ---------------- Sufficient free space for build User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf DEB_BUILD_OPTIONS=noautodbgsym parallel=4 HOME=/sbuild-nonexistent LANG=C.UTF-8 LC_ALL=C.UTF-8 LOGNAME=buildd PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games SCHROOT_ALIAS_NAME=build-PACKAGEBUILD-18355010 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-18355010 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-18355010 SCHROOT_UID=2001 SCHROOT_USER=buildd SHELL=/bin/sh TERM=unknown USER=buildd V=1 dpkg-buildpackage ----------------- dpkg-buildpackage: info: source package salmon dpkg-buildpackage: info: source version 0.12.0+ds1-1 dpkg-buildpackage: info: source distribution unstable dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 fakeroot debian/rules clean dh clean --with sphinxdoc debian/rules override_dh_auto_clean make[1]: Entering directory '/<>/salmon-0.12.0+ds1' dh_auto_clean rm -rf external rm -f debian/*.1 rm -Rf sample_data cd doc && /usr/bin/make clean make[2]: Entering directory '/<>/salmon-0.12.0+ds1/doc' rm -rf build/* make[2]: Leaving directory '/<>/salmon-0.12.0+ds1/doc' make[1]: Leaving directory '/<>/salmon-0.12.0+ds1' dh_clean debian/rules build dh build --with sphinxdoc dh_update_autotools_config dh_autoreconf debian/rules override_dh_auto_configure make[1]: Entering directory '/<>/salmon-0.12.0+ds1' # See here # https://github.com/COMBINE-lab/salmon/issues/87 # for a discussion with upstream why it is necessary to include rapmap source mkdir -p /<>/salmon-0.12.0+ds1/external/install/src/rapmap cp -av /usr/share/rapmap/src/* /<>/salmon-0.12.0+ds1/external/install/src/rapmap '/usr/share/rapmap/src/HitManager.cpp' -> '/<>/salmon-0.12.0+ds1/external/install/src/rapmap/HitManager.cpp' '/usr/share/rapmap/src/RapMapFileSystem.cpp' -> '/<>/salmon-0.12.0+ds1/external/install/src/rapmap/RapMapFileSystem.cpp' '/usr/share/rapmap/src/RapMapSAIndex.cpp' -> '/<>/salmon-0.12.0+ds1/external/install/src/rapmap/RapMapSAIndex.cpp' '/usr/share/rapmap/src/RapMapSAIndexer.cpp' -> '/<>/salmon-0.12.0+ds1/external/install/src/rapmap/RapMapSAIndexer.cpp' '/usr/share/rapmap/src/RapMapUtils.cpp' -> '/<>/salmon-0.12.0+ds1/external/install/src/rapmap/RapMapUtils.cpp' '/usr/share/rapmap/src/bit_array.c' -> '/<>/salmon-0.12.0+ds1/external/install/src/rapmap/bit_array.c' '/usr/share/rapmap/src/rank9b.cpp' -> '/<>/salmon-0.12.0+ds1/external/install/src/rapmap/rank9b.cpp' dh_auto_configure -- -DDEBIAN_BUILD=1 -DCONDA_BUILD=1 -DFETCHED_RAPMAP=1 -DBZIP2_LIBRARIES=-lbz2 -DBZIP2_INCLUDE_DIR=/usr/include -DLIBLZMA_INCLUDE_DIR=/usr/include/ -DLIBLZMA_LIBRARY=lzma -DLIBLZMA_HAS_AUTO_DECODER=1 -DLIBLZMA_HAS_EASY_ENCODER=1 -DLIBLZMA_HAS_LZMA_PRESET=1 -DCMAKE_MODULE_PATH=/usr/share/cmake/Modules -DTBB_WILL_RECONFIGURE=FALSE -DBOOST_WILL_RECONFIGURE=FALSE cd obj-x86_64-linux-gnu && cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=None -DCMAKE_INSTALL_SYSCONFDIR=/etc -DCMAKE_INSTALL_LOCALSTATEDIR=/var -DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/x86_64-linux-gnu -DDEBIAN_BUILD=1 -DCONDA_BUILD=1 -DFETCHED_RAPMAP=1 -DBZIP2_LIBRARIES=-lbz2 -DBZIP2_INCLUDE_DIR=/usr/include -DLIBLZMA_INCLUDE_DIR=/usr/include/ -DLIBLZMA_LIBRARY=lzma -DLIBLZMA_HAS_AUTO_DECODER=1 -DLIBLZMA_HAS_EASY_ENCODER=1 -DLIBLZMA_HAS_LZMA_PRESET=1 -DCMAKE_MODULE_PATH=/usr/share/cmake/Modules -DTBB_WILL_RECONFIGURE=FALSE -DBOOST_WILL_RECONFIGURE=FALSE .. CC: gcc CC version: -- The C compiler identification is GNU 9.2.1 -- The CXX compiler identification is GNU 9.2.1 -- Check for working C compiler: /usr/bin/cc -- Check for working C compiler: /usr/bin/cc -- works -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Detecting C compile features -- Detecting C compile features - done -- Check for working CXX compiler: /usr/bin/c++ -- Check for working CXX compiler: /usr/bin/c++ -- works -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Detecting CXX compile features -- Detecting CXX compile features - done version: 0.12.0 -- Looking for pthread.h -- Looking for pthread.h - found -- Performing Test CMAKE_HAVE_LIBC_PTHREAD -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Failed -- Check if compiler accepts -pthread -- Check if compiler accepts -pthread - yes -- Found Threads: TRUE Building with CONDA_BUILD flag Making Default build type -- Found ZLIB: /usr/lib/x86_64-linux-gnu/libz.a (found version "1.2.11") -- Found LibLZMA: /<>/salmon-0.12.0+ds1/obj-x86_64-linux-gnu/lzma (found version "5.2.4") Found liblzma library: /<>/salmon-0.12.0+ds1/obj-x86_64-linux-gnu/lzma =========================================== -- Found BZip2: -lbz2 (found version "1.0.8") -- Looking for BZ2_bzCompressInit -- Looking for BZ2_bzCompressInit - found Found libbz2 library: -lbz2 =========================================== -- Found Boost: /usr/include (found suitable version "1.67.0", minimum required is "1.59.0") found components: iostreams filesystem system timer chrono program_options regex BOOST_INCLUDEDIR = BOOST_LIBRARYDIR = Boost_FOUND = TRUE BOOST ROOT = BOOST INCLUDE DIR = /usr/include BOOST INCLUDE DIRS = /usr/include BOOST LIB DIR = /usr/lib/x86_64-linux-gnu BOOST LIBRARIES = /usr/lib/x86_64-linux-gnu/libboost_iostreams.a;/usr/lib/x86_64-linux-gnu/libboost_filesystem.a;/usr/lib/x86_64-linux-gnu/libboost_system.a;/usr/lib/x86_64-linux-gnu/libboost_timer.a;/usr/lib/x86_64-linux-gnu/libboost_chrono.a;/usr/lib/x86_64-linux-gnu/libboost_program_options.a;/usr/lib/x86_64-linux-gnu/libboost_regex.a Use Debian packaged libdivsufsort ================================= -- Performing Test TBB_without_pthread -- Performing Test TBB_without_pthread - Failed -- Performing Test TBB_with_pthread -- Performing Test TBB_with_pthread - Success -- Found Intel TBB TBB_LIBRARIES = optimized;/usr/lib/x86_64-linux-gnu/libtbb.so;debug;/usr/lib/x86_64-linux-gnu/libtbb.so;optimized;/usr/lib/x86_64-linux-gnu/libtbbmalloc.so;debug;/usr/lib/x86_64-linux-gnu/libtbbmalloc.so;general;-pthread Use Debian packaged Staden IOLib ================================ -- Found PkgConfig: /usr/bin/pkg-config (found version "0.29.1") -- Found Jemalloc: /usr/lib/x86_64-linux-gnu/libjemalloc.a (found version "5.2.1-0-gea6b3e973b477b8061e0076bb257dbd7f3faa756") Found Jemalloc library --- using this memory allocator CPACK_SOURCE_IGNORE_FILES = /src/PCA.cpp;/src/PCAUtils.cpp;/build/;/scripts/AggregateToGeneLevel.py;/scripts/ExpressionTools.py;/scripts/GenerateExpressionFiles.sh;/scripts/ParseSoftFile.py;/scripts/PlotCorrelation.py;/scripts/junk;/scripts/sfstrace.log;/scripts/SFPipeline.py;/bin/;/lib/;/sample_data/;PublishREADMEToWebsite.sh;/external/;/src/obsolete/;/include/obsolete/;WebsiteHeader.txt;/experimental_configs/;.git/ TBB_LIBRARIES = optimized;/usr/lib/x86_64-linux-gnu/libtbb.so;debug;/usr/lib/x86_64-linux-gnu/libtbb.so;optimized;/usr/lib/x86_64-linux-gnu/libtbbmalloc.so;debug;/usr/lib/x86_64-linux-gnu/libtbbmalloc.so;general;-pthread -- Configuring done -- Generating done CMake Warning: Manually-specified variables were not used by the project: CMAKE_EXPORT_NO_PACKAGE_REGISTRY CMAKE_INSTALL_LIBDIR CMAKE_INSTALL_LOCALSTATEDIR CMAKE_INSTALL_RUNSTATEDIR CMAKE_INSTALL_SYSCONFDIR DEBIAN_BUILD -- Build files have been written to: /<>/salmon-0.12.0+ds1/obj-x86_64-linux-gnu make[1]: Leaving directory '/<>/salmon-0.12.0+ds1' debian/rules override_dh_auto_build make[1]: Entering directory '/<>/salmon-0.12.0+ds1' dh_auto_build cd obj-x86_64-linux-gnu && make -j4 "INSTALL=install --strip-program=true" make[2]: Entering directory '/<>/salmon-0.12.0+ds1/obj-x86_64-linux-gnu' /usr/bin/cmake -S/<>/salmon-0.12.0+ds1 -B/<>/salmon-0.12.0+ds1/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /<>/salmon-0.12.0+ds1/obj-x86_64-linux-gnu/CMakeFiles /<>/salmon-0.12.0+ds1/obj-x86_64-linux-gnu/CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[3]: Entering directory '/<>/salmon-0.12.0+ds1/obj-x86_64-linux-gnu' make -f CMakeFiles/libstadenio.dir/build.make CMakeFiles/libstadenio.dir/depend make -f CMakeFiles/libcereal.dir/build.make CMakeFiles/libcereal.dir/depend make[4]: Entering directory '/<>/salmon-0.12.0+ds1/obj-x86_64-linux-gnu' cd /<>/salmon-0.12.0+ds1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/salmon-0.12.0+ds1 /<>/salmon-0.12.0+ds1 /<>/salmon-0.12.0+ds1/obj-x86_64-linux-gnu /<>/salmon-0.12.0+ds1/obj-x86_64-linux-gnu /<>/salmon-0.12.0+ds1/obj-x86_64-linux-gnu/CMakeFiles/libstadenio.dir/DependInfo.cmake --color= make[4]: Entering directory '/<>/salmon-0.12.0+ds1/obj-x86_64-linux-gnu' make -f CMakeFiles/libdivsufsort.dir/build.make CMakeFiles/libdivsufsort.dir/depend cd /<>/salmon-0.12.0+ds1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/salmon-0.12.0+ds1 /<>/salmon-0.12.0+ds1 /<>/salmon-0.12.0+ds1/obj-x86_64-linux-gnu /<>/salmon-0.12.0+ds1/obj-x86_64-linux-gnu /<>/salmon-0.12.0+ds1/obj-x86_64-linux-gnu/CMakeFiles/libcereal.dir/DependInfo.cmake --color= make -f CMakeFiles/libgff.dir/build.make CMakeFiles/libgff.dir/depend make[4]: Entering directory '/<>/salmon-0.12.0+ds1/obj-x86_64-linux-gnu' cd /<>/salmon-0.12.0+ds1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/salmon-0.12.0+ds1 /<>/salmon-0.12.0+ds1 /<>/salmon-0.12.0+ds1/obj-x86_64-linux-gnu /<>/salmon-0.12.0+ds1/obj-x86_64-linux-gnu /<>/salmon-0.12.0+ds1/obj-x86_64-linux-gnu/CMakeFiles/libdivsufsort.dir/DependInfo.cmake --color= make[4]: Entering directory '/<>/salmon-0.12.0+ds1/obj-x86_64-linux-gnu' cd /<>/salmon-0.12.0+ds1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/salmon-0.12.0+ds1 /<>/salmon-0.12.0+ds1 /<>/salmon-0.12.0+ds1/obj-x86_64-linux-gnu /<>/salmon-0.12.0+ds1/obj-x86_64-linux-gnu /<>/salmon-0.12.0+ds1/obj-x86_64-linux-gnu/CMakeFiles/libgff.dir/DependInfo.cmake --color= Scanning dependencies of target libcereal make[4]: Leaving directory '/<>/salmon-0.12.0+ds1/obj-x86_64-linux-gnu' make -f CMakeFiles/libcereal.dir/build.make CMakeFiles/libcereal.dir/build Scanning dependencies of target libdivsufsort Scanning dependencies of target libstadenio make[4]: Leaving directory '/<>/salmon-0.12.0+ds1/obj-x86_64-linux-gnu' make[4]: Leaving directory '/<>/salmon-0.12.0+ds1/obj-x86_64-linux-gnu' make -f CMakeFiles/libdivsufsort.dir/build.make CMakeFiles/libdivsufsort.dir/build make[4]: Entering directory '/<>/salmon-0.12.0+ds1/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'CMakeFiles/libcereal.dir/build'. make[4]: Leaving directory '/<>/salmon-0.12.0+ds1/obj-x86_64-linux-gnu' make -f CMakeFiles/libstadenio.dir/build.make CMakeFiles/libstadenio.dir/build make[4]: Entering directory '/<>/salmon-0.12.0+ds1/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'CMakeFiles/libdivsufsort.dir/build'. make[4]: Entering directory '/<>/salmon-0.12.0+ds1/obj-x86_64-linux-gnu' make[4]: Leaving directory '/<>/salmon-0.12.0+ds1/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'CMakeFiles/libstadenio.dir/build'. make[4]: Leaving directory '/<>/salmon-0.12.0+ds1/obj-x86_64-linux-gnu' Scanning dependencies of target libgff make[4]: Leaving directory '/<>/salmon-0.12.0+ds1/obj-x86_64-linux-gnu' make -f CMakeFiles/libgff.dir/build.make CMakeFiles/libgff.dir/build make[4]: Entering directory '/<>/salmon-0.12.0+ds1/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'CMakeFiles/libgff.dir/build'. make[4]: Leaving directory '/<>/salmon-0.12.0+ds1/obj-x86_64-linux-gnu' [ 0%] Built target libcereal [ 0%] Built target libdivsufsort make -f src/CMakeFiles/ksw2pp_basic.dir/build.make src/CMakeFiles/ksw2pp_basic.dir/depend make -f src/CMakeFiles/ksw2pp_sse2.dir/build.make src/CMakeFiles/ksw2pp_sse2.dir/depend make[4]: Entering directory '/<>/salmon-0.12.0+ds1/obj-x86_64-linux-gnu' cd /<>/salmon-0.12.0+ds1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/salmon-0.12.0+ds1 /<>/salmon-0.12.0+ds1/src /<>/salmon-0.12.0+ds1/obj-x86_64-linux-gnu /<>/salmon-0.12.0+ds1/obj-x86_64-linux-gnu/src /<>/salmon-0.12.0+ds1/obj-x86_64-linux-gnu/src/CMakeFiles/ksw2pp_basic.dir/DependInfo.cmake --color= [ 0%] Built target libstadenio make -f src/CMakeFiles/ksw2pp_sse4.dir/build.make src/CMakeFiles/ksw2pp_sse4.dir/depend [ 0%] Built target libgff make[4]: Entering directory '/<>/salmon-0.12.0+ds1/obj-x86_64-linux-gnu' cd /<>/salmon-0.12.0+ds1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/salmon-0.12.0+ds1 /<>/salmon-0.12.0+ds1/src /<>/salmon-0.12.0+ds1/obj-x86_64-linux-gnu /<>/salmon-0.12.0+ds1/obj-x86_64-linux-gnu/src /<>/salmon-0.12.0+ds1/obj-x86_64-linux-gnu/src/CMakeFiles/ksw2pp_sse2.dir/DependInfo.cmake --color= make -f src/CMakeFiles/alevin_core.dir/build.make src/CMakeFiles/alevin_core.dir/depend make[4]: Entering directory '/<>/salmon-0.12.0+ds1/obj-x86_64-linux-gnu' cd /<>/salmon-0.12.0+ds1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/salmon-0.12.0+ds1 /<>/salmon-0.12.0+ds1/src /<>/salmon-0.12.0+ds1/obj-x86_64-linux-gnu /<>/salmon-0.12.0+ds1/obj-x86_64-linux-gnu/src /<>/salmon-0.12.0+ds1/obj-x86_64-linux-gnu/src/CMakeFiles/ksw2pp_sse4.dir/DependInfo.cmake --color= make[4]: Entering directory '/<>/salmon-0.12.0+ds1/obj-x86_64-linux-gnu' cd /<>/salmon-0.12.0+ds1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/salmon-0.12.0+ds1 /<>/salmon-0.12.0+ds1/src /<>/salmon-0.12.0+ds1/obj-x86_64-linux-gnu /<>/salmon-0.12.0+ds1/obj-x86_64-linux-gnu/src /<>/salmon-0.12.0+ds1/obj-x86_64-linux-gnu/src/CMakeFiles/alevin_core.dir/DependInfo.cmake --color= Scanning dependencies of target ksw2pp_basic make[4]: Leaving directory '/<>/salmon-0.12.0+ds1/obj-x86_64-linux-gnu' make -f src/CMakeFiles/ksw2pp_basic.dir/build.make src/CMakeFiles/ksw2pp_basic.dir/build make[4]: Entering directory '/<>/salmon-0.12.0+ds1/obj-x86_64-linux-gnu' Scanning dependencies of target ksw2pp_sse2 make[4]: Leaving directory '/<>/salmon-0.12.0+ds1/obj-x86_64-linux-gnu' make -f src/CMakeFiles/ksw2pp_sse2.dir/build.make src/CMakeFiles/ksw2pp_sse2.dir/build make[4]: Entering directory '/<>/salmon-0.12.0+ds1/obj-x86_64-linux-gnu' Scanning dependencies of target ksw2pp_sse4 [ 1%] Building C object src/CMakeFiles/ksw2pp_basic.dir/ksw2pp/kalloc.c.o cd /<>/salmon-0.12.0+ds1/obj-x86_64-linux-gnu/src && /usr/bin/cc -DHAVE_KALLOC -DKSW_CPU_DISPATCH -I/<>/salmon-0.12.0+ds1/include -g -O2 -fdebug-prefix-map=/<>/salmon-0.12.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/ksw2pp_basic.dir/ksw2pp/kalloc.c.o -c /<>/salmon-0.12.0+ds1/src/ksw2pp/kalloc.c make[4]: Leaving directory '/<>/salmon-0.12.0+ds1/obj-x86_64-linux-gnu' make -f src/CMakeFiles/ksw2pp_sse4.dir/build.make src/CMakeFiles/ksw2pp_sse4.dir/build [ 2%] Building C object src/CMakeFiles/ksw2pp_sse2.dir/ksw2pp/ksw2_extd2_sse.c.o cd /<>/salmon-0.12.0+ds1/obj-x86_64-linux-gnu/src && /usr/bin/cc -DHAVE_KALLOC -DKSW_CPU_DISPATCH -DKSW_SSE2_ONLY -I/<>/salmon-0.12.0+ds1/include -I/usr/include/eigen3 -I/<>/salmon-0.12.0+ds1/external -I/<>/salmon-0.12.0+ds1/external/cereal/include -I/<>/salmon-0.12.0+ds1/external/install/include -I/usr/include/rapmap -I/usr/include/rapmap/digestpp -g -O2 -fdebug-prefix-map=/<>/salmon-0.12.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -msse2 -mno-sse4.1 -o CMakeFiles/ksw2pp_sse2.dir/ksw2pp/ksw2_extd2_sse.c.o -c /<>/salmon-0.12.0+ds1/src/ksw2pp/ksw2_extd2_sse.c make[4]: Entering directory '/<>/salmon-0.12.0+ds1/obj-x86_64-linux-gnu' [ 4%] Building C object src/CMakeFiles/ksw2pp_sse4.dir/ksw2pp/ksw2_extd2_sse.c.o cd /<>/salmon-0.12.0+ds1/obj-x86_64-linux-gnu/src && /usr/bin/cc -DHAVE_KALLOC -DKSW_CPU_DISPATCH -I/<>/salmon-0.12.0+ds1/include -g -O2 -fdebug-prefix-map=/<>/salmon-0.12.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -msse4.1 -o CMakeFiles/ksw2pp_sse4.dir/ksw2pp/ksw2_extd2_sse.c.o -c /<>/salmon-0.12.0+ds1/src/ksw2pp/ksw2_extd2_sse.c Scanning dependencies of target alevin_core make[4]: Leaving directory '/<>/salmon-0.12.0+ds1/obj-x86_64-linux-gnu' make -f src/CMakeFiles/alevin_core.dir/build.make src/CMakeFiles/alevin_core.dir/build make[4]: Entering directory '/<>/salmon-0.12.0+ds1/obj-x86_64-linux-gnu' [ 5%] Building CXX object src/CMakeFiles/alevin_core.dir/edlib.cpp.o cd /<>/salmon-0.12.0+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DRAPMAP_SALMON_SUPPORT=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/<>/salmon-0.12.0+ds1/include -I/usr/include/eigen3 -I/<>/salmon-0.12.0+ds1/external -I/<>/salmon-0.12.0+ds1/external/cereal/include -I/<>/salmon-0.12.0+ds1/external/install/include -I/usr/include/rapmap -I/usr/include/rapmap/digestpp -g -O2 -fdebug-prefix-map=/<>/salmon-0.12.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -o CMakeFiles/alevin_core.dir/edlib.cpp.o -c /<>/salmon-0.12.0+ds1/src/edlib.cpp [ 7%] Building C object src/CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_extd.c.o cd /<>/salmon-0.12.0+ds1/obj-x86_64-linux-gnu/src && /usr/bin/cc -DHAVE_KALLOC -DKSW_CPU_DISPATCH -I/<>/salmon-0.12.0+ds1/include -g -O2 -fdebug-prefix-map=/<>/salmon-0.12.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_extd.c.o -c /<>/salmon-0.12.0+ds1/src/ksw2pp/ksw2_extd.c [ 8%] Building C object src/CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_extz.c.o cd /<>/salmon-0.12.0+ds1/obj-x86_64-linux-gnu/src && /usr/bin/cc -DHAVE_KALLOC -DKSW_CPU_DISPATCH -I/<>/salmon-0.12.0+ds1/include -g -O2 -fdebug-prefix-map=/<>/salmon-0.12.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_extz.c.o -c /<>/salmon-0.12.0+ds1/src/ksw2pp/ksw2_extz.c [ 10%] Building C object src/CMakeFiles/ksw2pp_sse4.dir/ksw2pp/ksw2_extf2_sse.c.o cd /<>/salmon-0.12.0+ds1/obj-x86_64-linux-gnu/src && /usr/bin/cc -DHAVE_KALLOC -DKSW_CPU_DISPATCH -I/<>/salmon-0.12.0+ds1/include -g -O2 -fdebug-prefix-map=/<>/salmon-0.12.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -msse4.1 -o CMakeFiles/ksw2pp_sse4.dir/ksw2pp/ksw2_extf2_sse.c.o -c /<>/salmon-0.12.0+ds1/src/ksw2pp/ksw2_extf2_sse.c [ 11%] Building C object src/CMakeFiles/ksw2pp_sse2.dir/ksw2pp/ksw2_extf2_sse.c.o cd /<>/salmon-0.12.0+ds1/obj-x86_64-linux-gnu/src && /usr/bin/cc -DHAVE_KALLOC -DKSW_CPU_DISPATCH -DKSW_SSE2_ONLY -I/<>/salmon-0.12.0+ds1/include -I/usr/include/eigen3 -I/<>/salmon-0.12.0+ds1/external -I/<>/salmon-0.12.0+ds1/external/cereal/include -I/<>/salmon-0.12.0+ds1/external/install/include -I/usr/include/rapmap -I/usr/include/rapmap/digestpp -g -O2 -fdebug-prefix-map=/<>/salmon-0.12.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -msse2 -mno-sse4.1 -o CMakeFiles/ksw2pp_sse2.dir/ksw2pp/ksw2_extf2_sse.c.o -c /<>/salmon-0.12.0+ds1/src/ksw2pp/ksw2_extf2_sse.c [ 13%] Building C object src/CMakeFiles/ksw2pp_sse2.dir/ksw2pp/ksw2_extz2_sse.c.o cd /<>/salmon-0.12.0+ds1/obj-x86_64-linux-gnu/src && /usr/bin/cc -DHAVE_KALLOC -DKSW_CPU_DISPATCH -DKSW_SSE2_ONLY -I/<>/salmon-0.12.0+ds1/include -I/usr/include/eigen3 -I/<>/salmon-0.12.0+ds1/external -I/<>/salmon-0.12.0+ds1/external/cereal/include -I/<>/salmon-0.12.0+ds1/external/install/include -I/usr/include/rapmap -I/usr/include/rapmap/digestpp -g -O2 -fdebug-prefix-map=/<>/salmon-0.12.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -msse2 -mno-sse4.1 -o CMakeFiles/ksw2pp_sse2.dir/ksw2pp/ksw2_extz2_sse.c.o -c /<>/salmon-0.12.0+ds1/src/ksw2pp/ksw2_extz2_sse.c [ 14%] Building C object src/CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg.c.o cd /<>/salmon-0.12.0+ds1/obj-x86_64-linux-gnu/src && /usr/bin/cc -DHAVE_KALLOC -DKSW_CPU_DISPATCH -I/<>/salmon-0.12.0+ds1/include -g -O2 -fdebug-prefix-map=/<>/salmon-0.12.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg.c.o -c /<>/salmon-0.12.0+ds1/src/ksw2pp/ksw2_gg.c [ 15%] Building C object src/CMakeFiles/ksw2pp_sse4.dir/ksw2pp/ksw2_extz2_sse.c.o cd /<>/salmon-0.12.0+ds1/obj-x86_64-linux-gnu/src && /usr/bin/cc -DHAVE_KALLOC -DKSW_CPU_DISPATCH -I/<>/salmon-0.12.0+ds1/include -g -O2 -fdebug-prefix-map=/<>/salmon-0.12.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -msse4.1 -o CMakeFiles/ksw2pp_sse4.dir/ksw2pp/ksw2_extz2_sse.c.o -c /<>/salmon-0.12.0+ds1/src/ksw2pp/ksw2_extz2_sse.c [ 17%] Building C object src/CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg2.c.o cd /<>/salmon-0.12.0+ds1/obj-x86_64-linux-gnu/src && /usr/bin/cc -DHAVE_KALLOC -DKSW_CPU_DISPATCH -I/<>/salmon-0.12.0+ds1/include -g -O2 -fdebug-prefix-map=/<>/salmon-0.12.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg2.c.o -c /<>/salmon-0.12.0+ds1/src/ksw2pp/ksw2_gg2.c [ 18%] Building C object src/CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg2_sse.c.o cd /<>/salmon-0.12.0+ds1/obj-x86_64-linux-gnu/src && /usr/bin/cc -DHAVE_KALLOC -DKSW_CPU_DISPATCH -I/<>/salmon-0.12.0+ds1/include -g -O2 -fdebug-prefix-map=/<>/salmon-0.12.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg2_sse.c.o -c /<>/salmon-0.12.0+ds1/src/ksw2pp/ksw2_gg2_sse.c make[4]: Leaving directory '/<>/salmon-0.12.0+ds1/obj-x86_64-linux-gnu' [ 18%] Built target ksw2pp_sse2 make -f src/CMakeFiles/salmon_core.dir/build.make src/CMakeFiles/salmon_core.dir/depend make[4]: Entering directory '/<>/salmon-0.12.0+ds1/obj-x86_64-linux-gnu' cd /<>/salmon-0.12.0+ds1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/salmon-0.12.0+ds1 /<>/salmon-0.12.0+ds1/src /<>/salmon-0.12.0+ds1/obj-x86_64-linux-gnu /<>/salmon-0.12.0+ds1/obj-x86_64-linux-gnu/src /<>/salmon-0.12.0+ds1/obj-x86_64-linux-gnu/src/CMakeFiles/salmon_core.dir/DependInfo.cmake --color= make[4]: Leaving directory '/<>/salmon-0.12.0+ds1/obj-x86_64-linux-gnu' [ 18%] Built target ksw2pp_sse4 Scanning dependencies of target salmon_core make[4]: Leaving directory '/<>/salmon-0.12.0+ds1/obj-x86_64-linux-gnu' make -f src/CMakeFiles/salmon_core.dir/build.make src/CMakeFiles/salmon_core.dir/build make[4]: Entering directory '/<>/salmon-0.12.0+ds1/obj-x86_64-linux-gnu' [ 20%] Building CXX object src/CMakeFiles/ksw2pp_basic.dir/ksw2pp/KSW2Aligner.cpp.o cd /<>/salmon-0.12.0+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_KALLOC -DKSW_CPU_DISPATCH -I/<>/salmon-0.12.0+ds1/include -g -O2 -fdebug-prefix-map=/<>/salmon-0.12.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -o CMakeFiles/ksw2pp_basic.dir/ksw2pp/KSW2Aligner.cpp.o -c /<>/salmon-0.12.0+ds1/src/ksw2pp/KSW2Aligner.cpp [ 21%] Building CXX object src/CMakeFiles/salmon_core.dir/jellyfish/mer_dna.cc.o cd /<>/salmon-0.12.0+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DRAPMAP_SALMON_SUPPORT=1 -I/<>/salmon-0.12.0+ds1/include -I/usr/include/eigen3 -I/<>/salmon-0.12.0+ds1/external -I/<>/salmon-0.12.0+ds1/external/cereal/include -I/<>/salmon-0.12.0+ds1/external/install/include -I/usr/include/rapmap -I/usr/include/rapmap/digestpp -g -O2 -fdebug-prefix-map=/<>/salmon-0.12.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -o CMakeFiles/salmon_core.dir/jellyfish/mer_dna.cc.o -c /<>/salmon-0.12.0+ds1/src/jellyfish/mer_dna.cc [ 23%] Building C object src/CMakeFiles/salmon_core.dir/xxhash.c.o cd /<>/salmon-0.12.0+ds1/obj-x86_64-linux-gnu/src && /usr/bin/cc -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DRAPMAP_SALMON_SUPPORT=1 -I/<>/salmon-0.12.0+ds1/include -I/usr/include/eigen3 -I/<>/salmon-0.12.0+ds1/external -I/<>/salmon-0.12.0+ds1/external/cereal/include -I/<>/salmon-0.12.0+ds1/external/install/include -I/usr/include/rapmap -I/usr/include/rapmap/digestpp -g -O2 -fdebug-prefix-map=/<>/salmon-0.12.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o CMakeFiles/salmon_core.dir/xxhash.c.o -c /<>/salmon-0.12.0+ds1/src/xxhash.c [ 24%] Building CXX object src/CMakeFiles/salmon_core.dir/TranscriptGroup.cpp.o cd /<>/salmon-0.12.0+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DRAPMAP_SALMON_SUPPORT=1 -I/<>/salmon-0.12.0+ds1/include -I/usr/include/eigen3 -I/<>/salmon-0.12.0+ds1/external -I/<>/salmon-0.12.0+ds1/external/cereal/include -I/<>/salmon-0.12.0+ds1/external/install/include -I/usr/include/rapmap -I/usr/include/rapmap/digestpp -g -O2 -fdebug-prefix-map=/<>/salmon-0.12.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -o CMakeFiles/salmon_core.dir/TranscriptGroup.cpp.o -c /<>/salmon-0.12.0+ds1/src/TranscriptGroup.cpp [ 26%] Building CXX object src/CMakeFiles/alevin_core.dir/AlevinUtils.cpp.o cd /<>/salmon-0.12.0+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DRAPMAP_SALMON_SUPPORT=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/<>/salmon-0.12.0+ds1/include -I/usr/include/eigen3 -I/<>/salmon-0.12.0+ds1/external -I/<>/salmon-0.12.0+ds1/external/cereal/include -I/<>/salmon-0.12.0+ds1/external/install/include -I/usr/include/rapmap -I/usr/include/rapmap/digestpp -g -O2 -fdebug-prefix-map=/<>/salmon-0.12.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -o CMakeFiles/alevin_core.dir/AlevinUtils.cpp.o -c /<>/salmon-0.12.0+ds1/src/AlevinUtils.cpp [ 27%] Building CXX object src/CMakeFiles/salmon_core.dir/EffectiveLengthStats.cpp.o cd /<>/salmon-0.12.0+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DRAPMAP_SALMON_SUPPORT=1 -I/<>/salmon-0.12.0+ds1/include -I/usr/include/eigen3 -I/<>/salmon-0.12.0+ds1/external -I/<>/salmon-0.12.0+ds1/external/cereal/include -I/<>/salmon-0.12.0+ds1/external/install/include -I/usr/include/rapmap -I/usr/include/rapmap/digestpp -g -O2 -fdebug-prefix-map=/<>/salmon-0.12.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -o CMakeFiles/salmon_core.dir/EffectiveLengthStats.cpp.o -c /<>/salmon-0.12.0+ds1/src/EffectiveLengthStats.cpp make[4]: Leaving directory '/<>/salmon-0.12.0+ds1/obj-x86_64-linux-gnu' [ 27%] Built target ksw2pp_basic [ 28%] Building CXX object src/CMakeFiles/salmon_core.dir/LibraryFormat.cpp.o cd /<>/salmon-0.12.0+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DRAPMAP_SALMON_SUPPORT=1 -I/<>/salmon-0.12.0+ds1/include -I/usr/include/eigen3 -I/<>/salmon-0.12.0+ds1/external -I/<>/salmon-0.12.0+ds1/external/cereal/include -I/<>/salmon-0.12.0+ds1/external/install/include -I/usr/include/rapmap -I/usr/include/rapmap/digestpp -g -O2 -fdebug-prefix-map=/<>/salmon-0.12.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -o CMakeFiles/salmon_core.dir/LibraryFormat.cpp.o -c /<>/salmon-0.12.0+ds1/src/LibraryFormat.cpp [ 30%] Building CXX object src/CMakeFiles/salmon_core.dir/GenomicFeature.cpp.o cd /<>/salmon-0.12.0+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DRAPMAP_SALMON_SUPPORT=1 -I/<>/salmon-0.12.0+ds1/include -I/usr/include/eigen3 -I/<>/salmon-0.12.0+ds1/external -I/<>/salmon-0.12.0+ds1/external/cereal/include -I/<>/salmon-0.12.0+ds1/external/install/include -I/usr/include/rapmap -I/usr/include/rapmap/digestpp -g -O2 -fdebug-prefix-map=/<>/salmon-0.12.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time 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-DRAPMAP_SALMON_SUPPORT=1 -I/<>/salmon-0.12.0+ds1/include -I/usr/include/eigen3 -I/<>/salmon-0.12.0+ds1/external -I/<>/salmon-0.12.0+ds1/external/cereal/include -I/<>/salmon-0.12.0+ds1/external/install/include -I/usr/include/rapmap -I/usr/include/rapmap/digestpp -g -O2 -fdebug-prefix-map=/<>/salmon-0.12.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -o CMakeFiles/salmon_core.dir/SBModel.cpp.o -c /<>/salmon-0.12.0+ds1/src/SBModel.cpp [ 34%] Building CXX object src/CMakeFiles/salmon_core.dir/FastxParser.cpp.o cd /<>/salmon-0.12.0+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DRAPMAP_SALMON_SUPPORT=1 -I/<>/salmon-0.12.0+ds1/include -I/usr/include/eigen3 -I/<>/salmon-0.12.0+ds1/external -I/<>/salmon-0.12.0+ds1/external/cereal/include -I/<>/salmon-0.12.0+ds1/external/install/include -I/usr/include/rapmap -I/usr/include/rapmap/digestpp -g -O2 -fdebug-prefix-map=/<>/salmon-0.12.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -o CMakeFiles/salmon_core.dir/FastxParser.cpp.o -c /<>/salmon-0.12.0+ds1/src/FastxParser.cpp make -f src/CMakeFiles/ksw2pp.dir/build.make src/CMakeFiles/ksw2pp.dir/depend make[4]: Entering directory '/<>/salmon-0.12.0+ds1/obj-x86_64-linux-gnu' cd /<>/salmon-0.12.0+ds1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/salmon-0.12.0+ds1 /<>/salmon-0.12.0+ds1/src /<>/salmon-0.12.0+ds1/obj-x86_64-linux-gnu /<>/salmon-0.12.0+ds1/obj-x86_64-linux-gnu/src /<>/salmon-0.12.0+ds1/obj-x86_64-linux-gnu/src/CMakeFiles/ksw2pp.dir/DependInfo.cmake --color= Scanning dependencies of target ksw2pp make[4]: Leaving directory '/<>/salmon-0.12.0+ds1/obj-x86_64-linux-gnu' make -f src/CMakeFiles/ksw2pp.dir/build.make src/CMakeFiles/ksw2pp.dir/build make[4]: Entering directory '/<>/salmon-0.12.0+ds1/obj-x86_64-linux-gnu' [ 36%] Linking CXX static library libksw2pp.a cd /<>/salmon-0.12.0+ds1/obj-x86_64-linux-gnu/src && /usr/bin/cmake -P CMakeFiles/ksw2pp.dir/cmake_clean_target.cmake cd /<>/salmon-0.12.0+ds1/obj-x86_64-linux-gnu/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ksw2pp.dir/link.txt --verbose=1 /usr/bin/ar qc libksw2pp.a CMakeFiles/ksw2pp_sse2.dir/ksw2pp/ksw2_extd2_sse.c.o CMakeFiles/ksw2pp_sse2.dir/ksw2pp/ksw2_extf2_sse.c.o CMakeFiles/ksw2pp_sse2.dir/ksw2pp/ksw2_extz2_sse.c.o CMakeFiles/ksw2pp_sse4.dir/ksw2pp/ksw2_extd2_sse.c.o CMakeFiles/ksw2pp_sse4.dir/ksw2pp/ksw2_extf2_sse.c.o CMakeFiles/ksw2pp_sse4.dir/ksw2pp/ksw2_extz2_sse.c.o CMakeFiles/ksw2pp_basic.dir/ksw2pp/kalloc.c.o CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_extd.c.o CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_extz.c.o CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg.c.o CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg2.c.o CMakeFiles/ksw2pp_basic.dir/ksw2pp/ksw2_gg2_sse.c.o CMakeFiles/ksw2pp_basic.dir/ksw2pp/KSW2Aligner.cpp.o /usr/bin/ranlib libksw2pp.a make[4]: Leaving directory '/<>/salmon-0.12.0+ds1/obj-x86_64-linux-gnu' [ 36%] Built target ksw2pp [ 37%] Building CXX object src/CMakeFiles/salmon_core.dir/StadenUtils.cpp.o cd /<>/salmon-0.12.0+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DRAPMAP_SALMON_SUPPORT=1 -I/<>/salmon-0.12.0+ds1/include -I/usr/include/eigen3 -I/<>/salmon-0.12.0+ds1/external -I/<>/salmon-0.12.0+ds1/external/cereal/include -I/<>/salmon-0.12.0+ds1/external/install/include -I/usr/include/rapmap -I/usr/include/rapmap/digestpp -g -O2 -fdebug-prefix-map=/<>/salmon-0.12.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -o CMakeFiles/salmon_core.dir/StadenUtils.cpp.o -c /<>/salmon-0.12.0+ds1/src/StadenUtils.cpp [ 39%] Building CXX object src/CMakeFiles/salmon_core.dir/SalmonUtils.cpp.o cd /<>/salmon-0.12.0+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DRAPMAP_SALMON_SUPPORT=1 -I/<>/salmon-0.12.0+ds1/include -I/usr/include/eigen3 -I/<>/salmon-0.12.0+ds1/external -I/<>/salmon-0.12.0+ds1/external/cereal/include -I/<>/salmon-0.12.0+ds1/external/install/include -I/usr/include/rapmap -I/usr/include/rapmap/digestpp -g -O2 -fdebug-prefix-map=/<>/salmon-0.12.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -o CMakeFiles/salmon_core.dir/SalmonUtils.cpp.o -c /<>/salmon-0.12.0+ds1/src/SalmonUtils.cpp [ 40%] Building CXX object src/CMakeFiles/salmon_core.dir/DistributionUtils.cpp.o cd /<>/salmon-0.12.0+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DRAPMAP_SALMON_SUPPORT=1 -I/<>/salmon-0.12.0+ds1/include -I/usr/include/eigen3 -I/<>/salmon-0.12.0+ds1/external -I/<>/salmon-0.12.0+ds1/external/cereal/include -I/<>/salmon-0.12.0+ds1/external/install/include -I/usr/include/rapmap -I/usr/include/rapmap/digestpp -g -O2 -fdebug-prefix-map=/<>/salmon-0.12.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -o CMakeFiles/salmon_core.dir/DistributionUtils.cpp.o -c /<>/salmon-0.12.0+ds1/src/DistributionUtils.cpp [ 42%] Building CXX object src/CMakeFiles/salmon_core.dir/SalmonExceptions.cpp.o cd /<>/salmon-0.12.0+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DRAPMAP_SALMON_SUPPORT=1 -I/<>/salmon-0.12.0+ds1/include -I/usr/include/eigen3 -I/<>/salmon-0.12.0+ds1/external -I/<>/salmon-0.12.0+ds1/external/cereal/include -I/<>/salmon-0.12.0+ds1/external/install/include -I/usr/include/rapmap -I/usr/include/rapmap/digestpp -g -O2 -fdebug-prefix-map=/<>/salmon-0.12.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -o CMakeFiles/salmon_core.dir/SalmonExceptions.cpp.o -c /<>/salmon-0.12.0+ds1/src/SalmonExceptions.cpp [ 43%] Building CXX object src/CMakeFiles/salmon_core.dir/SalmonStringUtils.cpp.o cd /<>/salmon-0.12.0+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DRAPMAP_SALMON_SUPPORT=1 -I/<>/salmon-0.12.0+ds1/include -I/usr/include/eigen3 -I/<>/salmon-0.12.0+ds1/external -I/<>/salmon-0.12.0+ds1/external/cereal/include -I/<>/salmon-0.12.0+ds1/external/install/include -I/usr/include/rapmap -I/usr/include/rapmap/digestpp -g -O2 -fdebug-prefix-map=/<>/salmon-0.12.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -o CMakeFiles/salmon_core.dir/SalmonStringUtils.cpp.o -c /<>/salmon-0.12.0+ds1/src/SalmonStringUtils.cpp [ 44%] Building CXX object src/CMakeFiles/salmon_core.dir/SimplePosBias.cpp.o cd /<>/salmon-0.12.0+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DRAPMAP_SALMON_SUPPORT=1 -I/<>/salmon-0.12.0+ds1/include -I/usr/include/eigen3 -I/<>/salmon-0.12.0+ds1/external -I/<>/salmon-0.12.0+ds1/external/cereal/include -I/<>/salmon-0.12.0+ds1/external/install/include -I/usr/include/rapmap -I/usr/include/rapmap/digestpp -g -O2 -fdebug-prefix-map=/<>/salmon-0.12.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -o CMakeFiles/salmon_core.dir/SimplePosBias.cpp.o -c /<>/salmon-0.12.0+ds1/src/SimplePosBias.cpp [ 46%] Building CXX object src/CMakeFiles/salmon_core.dir/SGSmooth.cpp.o cd /<>/salmon-0.12.0+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DRAPMAP_SALMON_SUPPORT=1 -I/<>/salmon-0.12.0+ds1/include -I/usr/include/eigen3 -I/<>/salmon-0.12.0+ds1/external -I/<>/salmon-0.12.0+ds1/external/cereal/include -I/<>/salmon-0.12.0+ds1/external/install/include -I/usr/include/rapmap -I/usr/include/rapmap/digestpp -g -O2 -fdebug-prefix-map=/<>/salmon-0.12.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -o CMakeFiles/salmon_core.dir/SGSmooth.cpp.o -c /<>/salmon-0.12.0+ds1/src/SGSmooth.cpp [ 47%] Building CXX object src/CMakeFiles/salmon_core.dir/metro/metrohash64.cpp.o cd /<>/salmon-0.12.0+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DRAPMAP_SALMON_SUPPORT=1 -I/<>/salmon-0.12.0+ds1/include -I/usr/include/eigen3 -I/<>/salmon-0.12.0+ds1/external -I/<>/salmon-0.12.0+ds1/external/cereal/include -I/<>/salmon-0.12.0+ds1/external/install/include -I/usr/include/rapmap -I/usr/include/rapmap/digestpp -g -O2 -fdebug-prefix-map=/<>/salmon-0.12.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -o CMakeFiles/salmon_core.dir/metro/metrohash64.cpp.o -c /<>/salmon-0.12.0+ds1/src/metro/metrohash64.cpp [ 49%] Linking CXX static library libalevin_core.a cd /<>/salmon-0.12.0+ds1/obj-x86_64-linux-gnu/src && /usr/bin/cmake -P CMakeFiles/alevin_core.dir/cmake_clean_target.cmake cd /<>/salmon-0.12.0+ds1/obj-x86_64-linux-gnu/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/alevin_core.dir/link.txt --verbose=1 /usr/bin/ar qc libalevin_core.a CMakeFiles/alevin_core.dir/edlib.cpp.o CMakeFiles/alevin_core.dir/AlevinUtils.cpp.o /usr/bin/ranlib libalevin_core.a make[4]: Leaving directory '/<>/salmon-0.12.0+ds1/obj-x86_64-linux-gnu' [ 49%] Built target alevin_core [ 50%] Linking CXX static library libsalmon_core.a cd /<>/salmon-0.12.0+ds1/obj-x86_64-linux-gnu/src && /usr/bin/cmake -P CMakeFiles/salmon_core.dir/cmake_clean_target.cmake cd /<>/salmon-0.12.0+ds1/obj-x86_64-linux-gnu/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/salmon_core.dir/link.txt --verbose=1 /usr/bin/ar qc libsalmon_core.a CMakeFiles/salmon_core.dir/jellyfish/mer_dna.cc.o CMakeFiles/salmon_core.dir/xxhash.c.o CMakeFiles/salmon_core.dir/TranscriptGroup.cpp.o CMakeFiles/salmon_core.dir/EffectiveLengthStats.cpp.o CMakeFiles/salmon_core.dir/LibraryFormat.cpp.o CMakeFiles/salmon_core.dir/GenomicFeature.cpp.o CMakeFiles/salmon_core.dir/VersionChecker.cpp.o CMakeFiles/salmon_core.dir/SBModel.cpp.o CMakeFiles/salmon_core.dir/FastxParser.cpp.o CMakeFiles/salmon_core.dir/StadenUtils.cpp.o CMakeFiles/salmon_core.dir/SalmonUtils.cpp.o CMakeFiles/salmon_core.dir/DistributionUtils.cpp.o CMakeFiles/salmon_core.dir/SalmonExceptions.cpp.o CMakeFiles/salmon_core.dir/SalmonStringUtils.cpp.o CMakeFiles/salmon_core.dir/SimplePosBias.cpp.o CMakeFiles/salmon_core.dir/SGSmooth.cpp.o CMakeFiles/salmon_core.dir/metro/metrohash64.cpp.o /usr/bin/ranlib libsalmon_core.a make[4]: Leaving directory '/<>/salmon-0.12.0+ds1/obj-x86_64-linux-gnu' [ 50%] Built target salmon_core make -f src/CMakeFiles/unitTests.dir/build.make src/CMakeFiles/unitTests.dir/depend make[4]: Entering directory '/<>/salmon-0.12.0+ds1/obj-x86_64-linux-gnu' cd /<>/salmon-0.12.0+ds1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/salmon-0.12.0+ds1 /<>/salmon-0.12.0+ds1/src /<>/salmon-0.12.0+ds1/obj-x86_64-linux-gnu /<>/salmon-0.12.0+ds1/obj-x86_64-linux-gnu/src /<>/salmon-0.12.0+ds1/obj-x86_64-linux-gnu/src/CMakeFiles/unitTests.dir/DependInfo.cmake --color= Scanning dependencies of target unitTests make[4]: Leaving directory '/<>/salmon-0.12.0+ds1/obj-x86_64-linux-gnu' make -f src/CMakeFiles/unitTests.dir/build.make src/CMakeFiles/unitTests.dir/build make[4]: Entering directory '/<>/salmon-0.12.0+ds1/obj-x86_64-linux-gnu' [ 52%] Building CXX object src/CMakeFiles/unitTests.dir/FragmentLengthDistribution.cpp.o [ 53%] Building CXX object src/CMakeFiles/unitTests.dir/__/external/install/src/rapmap/rank9b.cpp.o [ 55%] Building CXX object src/CMakeFiles/unitTests.dir/__/tests/UnitTests.cpp.o cd /<>/salmon-0.12.0+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DRAPMAP_SALMON_SUPPORT=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/<>/salmon-0.12.0+ds1/include -I/usr/include/eigen3 -I/<>/salmon-0.12.0+ds1/external -I/<>/salmon-0.12.0+ds1/external/cereal/include -I/<>/salmon-0.12.0+ds1/external/install/include -I/usr/include/rapmap -I/usr/include/rapmap/digestpp -g -O2 -fdebug-prefix-map=/<>/salmon-0.12.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -std=c++14 -o CMakeFiles/unitTests.dir/__/external/install/src/rapmap/rank9b.cpp.o -c /<>/salmon-0.12.0+ds1/external/install/src/rapmap/rank9b.cpp cd /<>/salmon-0.12.0+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DRAPMAP_SALMON_SUPPORT=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/<>/salmon-0.12.0+ds1/include -I/usr/include/eigen3 -I/<>/salmon-0.12.0+ds1/external -I/<>/salmon-0.12.0+ds1/external/cereal/include -I/<>/salmon-0.12.0+ds1/external/install/include -I/usr/include/rapmap -I/usr/include/rapmap/digestpp -g -O2 -fdebug-prefix-map=/<>/salmon-0.12.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -std=c++14 -o CMakeFiles/unitTests.dir/__/tests/UnitTests.cpp.o -c 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-I/<>/salmon-0.12.0+ds1/include -I/usr/include/eigen3 -I/<>/salmon-0.12.0+ds1/external -I/<>/salmon-0.12.0+ds1/external/cereal/include -I/<>/salmon-0.12.0+ds1/external/install/include -I/usr/include/rapmap -I/usr/include/rapmap/digestpp -g -O2 -fdebug-prefix-map=/<>/salmon-0.12.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -o CMakeFiles/unitTests.dir/__/external/install/src/rapmap/bit_array.c.o -c /<>/salmon-0.12.0+ds1/external/install/src/rapmap/bit_array.c [ 57%] Linking CXX executable unitTests cd /<>/salmon-0.12.0+ds1/obj-x86_64-linux-gnu/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/unitTests.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/<>/salmon-0.12.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now CMakeFiles/unitTests.dir/__/tests/UnitTests.cpp.o CMakeFiles/unitTests.dir/FragmentLengthDistribution.cpp.o CMakeFiles/unitTests.dir/__/external/install/src/rapmap/rank9b.cpp.o CMakeFiles/unitTests.dir/__/external/install/src/rapmap/bit_array.c.o -o unitTests -L/<>/salmon-0.12.0+ds1/lib -L/<>/salmon-0.12.0+ds1/external/install/lib -Wl,-rpath,"\$ORIGIN/../lib:\$ORIGIN/../../lib:\$ORIGIN/:\$ORIGIN/../../external/install/lib" libsalmon_core.a libalevin_core.a -lgff -lboost_iostreams -lboost_filesystem -lboost_system -lboost_timer -lboost_chrono -lboost_program_options -lboost_regex -lstaden-read -lz -ldivsufsort -ldivsufsort64 -lm -llzma -lbz2 -ltbb -ltbbmalloc -lgomp -lrt -ldl -pthread Copying unitTests cd /<>/salmon-0.12.0+ds1/obj-x86_64-linux-gnu/src && /usr/bin/cmake -E copy /<>/salmon-0.12.0+ds1/obj-x86_64-linux-gnu/src/unitTests /<>/salmon-0.12.0+ds1/tests/unitTests make[4]: Leaving directory '/<>/salmon-0.12.0+ds1/obj-x86_64-linux-gnu' [ 57%] Built target unitTests make -f src/CMakeFiles/salmon.dir/build.make src/CMakeFiles/salmon.dir/depend make[4]: Entering directory '/<>/salmon-0.12.0+ds1/obj-x86_64-linux-gnu' cd /<>/salmon-0.12.0+ds1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<>/salmon-0.12.0+ds1 /<>/salmon-0.12.0+ds1/src /<>/salmon-0.12.0+ds1/obj-x86_64-linux-gnu /<>/salmon-0.12.0+ds1/obj-x86_64-linux-gnu/src /<>/salmon-0.12.0+ds1/obj-x86_64-linux-gnu/src/CMakeFiles/salmon.dir/DependInfo.cmake --color= Scanning dependencies of target salmon make[4]: Leaving directory '/<>/salmon-0.12.0+ds1/obj-x86_64-linux-gnu' make -f src/CMakeFiles/salmon.dir/build.make src/CMakeFiles/salmon.dir/build make[4]: Entering directory '/<>/salmon-0.12.0+ds1/obj-x86_64-linux-gnu' [ 59%] Building CXX object src/CMakeFiles/salmon.dir/__/external/install/src/rapmap/RapMapFileSystem.cpp.o cd /<>/salmon-0.12.0+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DRAPMAP_SALMON_SUPPORT=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/<>/salmon-0.12.0+ds1/include 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-I/<>/salmon-0.12.0+ds1/external/install/include -I/usr/include/rapmap -I/usr/include/rapmap/digestpp -g -O2 -fdebug-prefix-map=/<>/salmon-0.12.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -o CMakeFiles/salmon.dir/__/external/install/src/rapmap/bit_array.c.o -c /<>/salmon-0.12.0+ds1/external/install/src/rapmap/bit_array.c [ 69%] Building CXX object src/CMakeFiles/salmon.dir/EMUtils.cpp.o cd /<>/salmon-0.12.0+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DRAPMAP_SALMON_SUPPORT=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/<>/salmon-0.12.0+ds1/include -I/usr/include/eigen3 -I/<>/salmon-0.12.0+ds1/external -I/<>/salmon-0.12.0+ds1/external/cereal/include -I/<>/salmon-0.12.0+ds1/external/install/include -I/usr/include/rapmap -I/usr/include/rapmap/digestpp -g -O2 -fdebug-prefix-map=/<>/salmon-0.12.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 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-DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DRAPMAP_SALMON_SUPPORT=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/<>/salmon-0.12.0+ds1/include -I/usr/include/eigen3 -I/<>/salmon-0.12.0+ds1/external -I/<>/salmon-0.12.0+ds1/external/cereal/include -I/<>/salmon-0.12.0+ds1/external/install/include -I/usr/include/rapmap -I/usr/include/rapmap/digestpp -g -O2 -fdebug-prefix-map=/<>/salmon-0.12.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -std=c++14 -o CMakeFiles/salmon.dir/CollapsedCellOptimizer.cpp.o -c /<>/salmon-0.12.0+ds1/src/CollapsedCellOptimizer.cpp [ 73%] Building CXX object src/CMakeFiles/salmon.dir/CollapsedGibbsSampler.cpp.o cd /<>/salmon-0.12.0+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DRAPMAP_SALMON_SUPPORT=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/<>/salmon-0.12.0+ds1/include -I/usr/include/eigen3 -I/<>/salmon-0.12.0+ds1/external -I/<>/salmon-0.12.0+ds1/external/cereal/include -I/<>/salmon-0.12.0+ds1/external/install/include -I/usr/include/rapmap -I/usr/include/rapmap/digestpp -g -O2 -fdebug-prefix-map=/<>/salmon-0.12.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -std=c++14 -o CMakeFiles/salmon.dir/CollapsedGibbsSampler.cpp.o -c /<>/salmon-0.12.0+ds1/src/CollapsedGibbsSampler.cpp In file included from /<>/salmon-0.12.0+ds1/include/pcg_random.hpp:104, from /<>/salmon-0.12.0+ds1/src/CollapsedGibbsSampler.cpp:22: /<>/salmon-0.12.0+ds1/include/pcg_extras.hpp:563:51: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 563 | fnv(IntType(2166136261U ^ sizeof(IntType)), __DATE__ __TIME__ __FILE__); | ^~~~~~~~ /<>/salmon-0.12.0+ds1/include/pcg_extras.hpp:563:60: warning: macro "__TIME__" might prevent reproducible builds [-Wdate-time] 563 | fnv(IntType(2166136261U ^ sizeof(IntType)), __DATE__ __TIME__ __FILE__); | ^~~~~~~~ [ 75%] Building CXX object src/CMakeFiles/salmon.dir/Salmon.cpp.o cd /<>/salmon-0.12.0+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DRAPMAP_SALMON_SUPPORT=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/<>/salmon-0.12.0+ds1/include -I/usr/include/eigen3 -I/<>/salmon-0.12.0+ds1/external -I/<>/salmon-0.12.0+ds1/external/cereal/include -I/<>/salmon-0.12.0+ds1/external/install/include -I/usr/include/rapmap -I/usr/include/rapmap/digestpp -g -O2 -fdebug-prefix-map=/<>/salmon-0.12.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -std=c++14 -o CMakeFiles/salmon.dir/Salmon.cpp.o -c /<>/salmon-0.12.0+ds1/src/Salmon.cpp [ 76%] Building CXX object src/CMakeFiles/salmon.dir/BuildSalmonIndex.cpp.o cd /<>/salmon-0.12.0+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DRAPMAP_SALMON_SUPPORT=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/<>/salmon-0.12.0+ds1/include -I/usr/include/eigen3 -I/<>/salmon-0.12.0+ds1/external -I/<>/salmon-0.12.0+ds1/external/cereal/include -I/<>/salmon-0.12.0+ds1/external/install/include -I/usr/include/rapmap -I/usr/include/rapmap/digestpp -g -O2 -fdebug-prefix-map=/<>/salmon-0.12.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -std=c++14 -o CMakeFiles/salmon.dir/BuildSalmonIndex.cpp.o -c /<>/salmon-0.12.0+ds1/src/BuildSalmonIndex.cpp [ 78%] Building CXX object src/CMakeFiles/salmon.dir/Graph.cpp.o cd /<>/salmon-0.12.0+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DRAPMAP_SALMON_SUPPORT=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/<>/salmon-0.12.0+ds1/include -I/usr/include/eigen3 -I/<>/salmon-0.12.0+ds1/external -I/<>/salmon-0.12.0+ds1/external/cereal/include -I/<>/salmon-0.12.0+ds1/external/install/include -I/usr/include/rapmap -I/usr/include/rapmap/digestpp -g -O2 -fdebug-prefix-map=/<>/salmon-0.12.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -std=c++14 -o CMakeFiles/salmon.dir/Graph.cpp.o -c /<>/salmon-0.12.0+ds1/src/Graph.cpp [ 79%] Building CXX object src/CMakeFiles/salmon.dir/DedupUMI.cpp.o cd /<>/salmon-0.12.0+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DRAPMAP_SALMON_SUPPORT=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/<>/salmon-0.12.0+ds1/include -I/usr/include/eigen3 -I/<>/salmon-0.12.0+ds1/external -I/<>/salmon-0.12.0+ds1/external/cereal/include -I/<>/salmon-0.12.0+ds1/external/install/include -I/usr/include/rapmap -I/usr/include/rapmap/digestpp -g -O2 -fdebug-prefix-map=/<>/salmon-0.12.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -std=c++14 -o CMakeFiles/salmon.dir/DedupUMI.cpp.o -c /<>/salmon-0.12.0+ds1/src/DedupUMI.cpp [ 81%] Building CXX object src/CMakeFiles/salmon.dir/Alevin.cpp.o cd /<>/salmon-0.12.0+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DRAPMAP_SALMON_SUPPORT=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/<>/salmon-0.12.0+ds1/include -I/usr/include/eigen3 -I/<>/salmon-0.12.0+ds1/external -I/<>/salmon-0.12.0+ds1/external/cereal/include -I/<>/salmon-0.12.0+ds1/external/install/include -I/usr/include/rapmap -I/usr/include/rapmap/digestpp -g -O2 -fdebug-prefix-map=/<>/salmon-0.12.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -std=c++14 -o CMakeFiles/salmon.dir/Alevin.cpp.o -c /<>/salmon-0.12.0+ds1/src/Alevin.cpp [ 82%] Building CXX object src/CMakeFiles/salmon.dir/SalmonAlevin.cpp.o cd /<>/salmon-0.12.0+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DRAPMAP_SALMON_SUPPORT=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/<>/salmon-0.12.0+ds1/include -I/usr/include/eigen3 -I/<>/salmon-0.12.0+ds1/external -I/<>/salmon-0.12.0+ds1/external/cereal/include -I/<>/salmon-0.12.0+ds1/external/install/include -I/usr/include/rapmap -I/usr/include/rapmap/digestpp -g -O2 -fdebug-prefix-map=/<>/salmon-0.12.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -std=c++14 -o CMakeFiles/salmon.dir/SalmonAlevin.cpp.o -c /<>/salmon-0.12.0+ds1/src/SalmonAlevin.cpp [ 84%] Building CXX object src/CMakeFiles/salmon.dir/WhiteList.cpp.o cd /<>/salmon-0.12.0+ds1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DHAVE_ANSI_TERM=1 -DHAVE_SSTREAM=1 -DRAPMAP_SALMON_SUPPORT=1 -Dspan_FEATURE_MAKE_SPAN_TO_STD=14 -I/<>/salmon-0.12.0+ds1/include -I/usr/include/eigen3 -I/<>/salmon-0.12.0+ds1/external -I/<>/salmon-0.12.0+ds1/external/cereal/include -I/<>/salmon-0.12.0+ds1/external/install/include -I/usr/include/rapmap -I/usr/include/rapmap/digestpp -g -O2 -fdebug-prefix-map=/<>/salmon-0.12.0+ds1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -std=c++14 -o CMakeFiles/salmon.dir/WhiteList.cpp.o -c /<>/salmon-0.12.0+ds1/src/WhiteList.cpp /<>/salmon-0.12.0+ds1/src/SalmonAlevin.cpp: In function ‘void processReadsQuasi(alevin::paired_parser*, ReadExperimentT&, ReadLibrary&, alevin::AlnGroupVec&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, std::atomic&, RapMapIndexT*, std::vector&, ForgettingMassCalculator&, ClusterForest&, FragmentLengthDistribution&, BiasParams&, SalmonOpts&, std::mutex&, bool, std::atomic&, volatile bool&, AlevinOpts&, SoftMapT&, spp::sparse_hash_map, unsigned int>&)’: /<>/salmon-0.12.0+ds1/src/SalmonAlevin.cpp:780:6: error: ‘class rapmap::utils::MappingConfig’ has no member named ‘maxSlack’ 780 | mc.maxSlack = salmonOpts.consensusSlack; | ^~~~~~~~ make[4]: *** [src/CMakeFiles/salmon.dir/build.make:274: src/CMakeFiles/salmon.dir/SalmonAlevin.cpp.o] Error 1 make[4]: *** Waiting for unfinished jobs.... make[4]: Leaving directory '/<>/salmon-0.12.0+ds1/obj-x86_64-linux-gnu' make[3]: *** [CMakeFiles/Makefile2:423: src/CMakeFiles/salmon.dir/all] Error 2 make[3]: Leaving directory '/<>/salmon-0.12.0+ds1/obj-x86_64-linux-gnu' make[2]: *** [Makefile:166: all] Error 2 make[2]: Leaving directory '/<>/salmon-0.12.0+ds1/obj-x86_64-linux-gnu' dh_auto_build: cd obj-x86_64-linux-gnu && make -j4 "INSTALL=install --strip-program=true" returned exit code 2 make[1]: *** [debian/rules:36: override_dh_auto_build] Error 255 make[1]: Leaving directory '/<>/salmon-0.12.0+ds1' make: *** [debian/rules:25: build] Error 2 dpkg-buildpackage: error: debian/rules build subprocess returned exit status 2 -------------------------------------------------------------------------------- Build finished at 20200105-1036 Finished -------- E: Build failure (dpkg-buildpackage died) +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not removing build depends: as requested +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: amd64 Build-Space: 515604 Build-Time: 284 Distribution: focal Fail-Stage: build Host Architecture: amd64 Install-Time: 46 Job: salmon_0.12.0+ds1-1.dsc Machine Architecture: amd64 Package: salmon Package-Time: 332 Source-Version: 0.12.0+ds1-1 Space: 515604 Status: attempted Version: 0.12.0+ds1-1 -------------------------------------------------------------------------------- Finished at 20200105-1036 Build needed 00:05:32, 515604k disc space RUN: /usr/share/launchpad-buildd/bin/in-target scan-for-processes --backend=chroot --series=focal --arch=amd64 PACKAGEBUILD-18355010 Scanning for processes to kill in build PACKAGEBUILD-18355010