https://launchpad.net/ubuntu/+archive/test-rebuild-20181222-test/+build/16111743 RUN: /usr/share/launchpad-buildd/slavebin/slave-prep Forking launchpad-buildd slave process... Kernel version: Linux bos02-arm64-058 4.4.0-142-generic #168-Ubuntu SMP Wed Jan 16 21:00:53 UTC 2019 aarch64 Buildd toolchain package versions: launchpad-buildd_167 python-lpbuildd_167 sbuild_0.67.0-2ubuntu7.1 bzr-builder_0.7.3+bzr174~ppa13~ubuntu14.10.1 bzr_2.7.0-2ubuntu3.1 git-build-recipe_0.3.4~git201611291343.dcee459~ubuntu16.04.1 git_1:2.7.4-0ubuntu1.6 dpkg-dev_1.18.4ubuntu1.5 python-debian_0.1.27ubuntu2. Syncing the system clock with the buildd NTP service... 22 Feb 09:00:36 ntpdate[1841]: adjust time server 10.211.37.1 offset 0.017783 sec RUN: /usr/share/launchpad-buildd/slavebin/in-target unpack-chroot --backend=chroot --series=bionic --arch=armhf PACKAGEBUILD-16111743 --image-type chroot /home/buildd/filecache-default/fc6c56f66744d62233b3c844f67cb7d83d839bbc Creating target for build PACKAGEBUILD-16111743 RUN: /usr/share/launchpad-buildd/slavebin/in-target mount-chroot --backend=chroot --series=bionic --arch=armhf PACKAGEBUILD-16111743 Starting target for build PACKAGEBUILD-16111743 RUN: /usr/share/launchpad-buildd/slavebin/in-target override-sources-list --backend=chroot --series=bionic --arch=armhf PACKAGEBUILD-16111743 'deb http://ppa.launchpad.net/canonical-foundations/openjdk11-stage2/ubuntu bionic main' 'deb http://ppa.launchpad.net/canonical-foundations/openjdk11-stage1/ubuntu bionic main' 'deb http://ppa.launchpad.net/openjdk-r/ppa/ubuntu bionic main' 'deb http://ppa.launchpad.net/ubuntu-toolchain-r/ppa/ubuntu bionic main' 'deb http://ppa.launchpad.net/ci-train-ppa-service/3473/ubuntu bionic main' 'deb http://ftpmaster.internal/ubuntu bionic main restricted universe multiverse' 'deb http://ftpmaster.internal/ubuntu bionic-security main restricted universe multiverse' 'deb http://ftpmaster.internal/ubuntu bionic-updates main restricted universe multiverse' Overriding sources.list in build-PACKAGEBUILD-16111743 RUN: /usr/share/launchpad-buildd/slavebin/in-target add-trusted-keys --backend=chroot --series=bionic --arch=armhf PACKAGEBUILD-16111743 Adding trusted keys to build-PACKAGEBUILD-16111743 Warning: apt-key output should not be parsed (stdout is not a terminal) OK Warning: apt-key output should not be parsed (stdout is not a terminal) /etc/apt/trusted.gpg -------------------- pub rsa1024 2009-10-22 [SC] 60C3 1780 3A41 BA51 845E 371A 1E93 77A2 BA9E F27F uid [ unknown] Launchpad Toolchain builds pub rsa1024 2014-01-08 [SC] B4C3 96DF 0DD9 A0ED 00B2 1D28 8550 4128 ECF1 204C uid [ unknown] Launchpad PPA for CI Train PPA Service Team pub rsa1024 2012-12-04 [SC] CDE5 112B D410 4F97 5FC8 A53F D4C0 B668 FD4C 9139 uid [ unknown] Launchpad PPA for Canonical Foundations Team pub rsa1024 2010-04-12 [SC] DA1A 4A13 543B 4668 53BA F164 EB9B 1D88 86F4 4E2A uid [ unknown] Launchpad OpenJDK builds (all archs) /etc/apt/trusted.gpg.d/ubuntu-keyring-2012-archive.gpg ------------------------------------------------------ pub rsa4096 2012-05-11 [SC] 790B C727 7767 219C 42C8 6F93 3B4F E6AC C0B2 1F32 uid [ unknown] Ubuntu Archive Automatic Signing Key (2012) /etc/apt/trusted.gpg.d/ubuntu-keyring-2012-cdimage.gpg ------------------------------------------------------ pub rsa4096 2012-05-11 [SC] 8439 38DF 228D 22F7 B374 2BC0 D94A A3F0 EFE2 1092 uid [ unknown] Ubuntu CD Image Automatic Signing Key (2012) RUN: /usr/share/launchpad-buildd/slavebin/in-target update-debian-chroot --backend=chroot --series=bionic --arch=armhf PACKAGEBUILD-16111743 Updating target for build PACKAGEBUILD-16111743 Get:1 http://ppa.launchpad.net/canonical-foundations/openjdk11-stage2/ubuntu bionic InRelease [15.4 kB] Get:2 http://ftpmaster.internal/ubuntu bionic InRelease [242 kB] Get:3 http://ppa.launchpad.net/canonical-foundations/openjdk11-stage1/ubuntu bionic InRelease [15.4 kB] Get:4 http://ftpmaster.internal/ubuntu bionic-security InRelease [88.7 kB] Get:5 http://ppa.launchpad.net/openjdk-r/ppa/ubuntu bionic InRelease [15.4 kB] Get:6 http://ftpmaster.internal/ubuntu bionic-updates InRelease [88.7 kB] Get:7 http://ppa.launchpad.net/ubuntu-toolchain-r/ppa/ubuntu bionic InRelease [15.4 kB] Get:8 http://ppa.launchpad.net/ci-train-ppa-service/3473/ubuntu bionic InRelease [20.8 kB] Get:9 http://ftpmaster.internal/ubuntu bionic/main armhf Packages [968 kB] Get:10 http://ppa.launchpad.net/canonical-foundations/openjdk11-stage2/ubuntu bionic/main armhf Packages [680 B] Get:11 http://ppa.launchpad.net/canonical-foundations/openjdk11-stage2/ubuntu bionic/main Translation-en [632 B] Get:12 http://ppa.launchpad.net/canonical-foundations/openjdk11-stage1/ubuntu bionic/main armhf Packages [4080 B] Get:13 http://ftpmaster.internal/ubuntu bionic/main Translation-en [516 kB] Get:14 http://ppa.launchpad.net/canonical-foundations/openjdk11-stage1/ubuntu bionic/main Translation-en [3620 B] Get:15 http://ftpmaster.internal/ubuntu bionic/universe armhf Packages [8269 kB] Get:16 http://ppa.launchpad.net/openjdk-r/ppa/ubuntu bionic/main armhf Packages [4400 B] Get:17 http://ppa.launchpad.net/openjdk-r/ppa/ubuntu bionic/main Translation-en [1344 B] Get:18 http://ppa.launchpad.net/ubuntu-toolchain-r/ppa/ubuntu bionic/main armhf Packages [40.7 kB] Get:19 http://ppa.launchpad.net/ubuntu-toolchain-r/ppa/ubuntu bionic/main Translation-en [14.5 kB] Get:20 http://ppa.launchpad.net/ci-train-ppa-service/3473/ubuntu bionic/main armhf Packages [17.3 kB] Get:21 http://ppa.launchpad.net/ci-train-ppa-service/3473/ubuntu bionic/main Translation-en [7264 B] Get:22 http://ftpmaster.internal/ubuntu bionic/universe Translation-en [4941 kB] Get:23 http://ftpmaster.internal/ubuntu bionic/multiverse armhf Packages [129 kB] Get:24 http://ftpmaster.internal/ubuntu bionic-security/main armhf Packages [180 kB] Get:25 http://ftpmaster.internal/ubuntu bionic-security/main Translation-en [101 kB] Get:26 http://ftpmaster.internal/ubuntu bionic-security/universe armhf Packages [123 kB] Get:27 http://ftpmaster.internal/ubuntu bionic-security/universe Translation-en [71.2 kB] Get:28 http://ftpmaster.internal/ubuntu bionic-security/multiverse armhf Packages [1448 B] Get:29 http://ftpmaster.internal/ubuntu bionic-security/multiverse Translation-en [1848 B] Get:30 http://ftpmaster.internal/ubuntu bionic-updates/main armhf Packages [415 kB] Get:31 http://ftpmaster.internal/ubuntu bionic-updates/main Translation-en [196 kB] Get:32 http://ftpmaster.internal/ubuntu bionic-updates/restricted armhf Packages [6476 B] Get:33 http://ftpmaster.internal/ubuntu bionic-updates/restricted Translation-en [3076 B] Get:34 http://ftpmaster.internal/ubuntu bionic-updates/universe armhf Packages [588 kB] Get:35 http://ftpmaster.internal/ubuntu bionic-updates/universe Translation-en [189 kB] Get:36 http://ftpmaster.internal/ubuntu bionic-updates/multiverse armhf Packages [3360 B] Get:37 http://ftpmaster.internal/ubuntu bionic-updates/multiverse Translation-en [3452 B] Fetched 17.3 MB in 10s (1702 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages will be upgraded: apt base-files binutils binutils-arm-linux-gnueabihf binutils-common bsdutils cpp cpp-7 dpkg dpkg-dev e2fslibs e2fsprogs fdisk g++ g++-7 gcc gcc-7 gcc-7-base gcc-8-base gpg gpg-agent gpgconf gpgv libapparmor1 libapt-pkg5.0 libasan4 libatomic1 libbinutils libblkid1 libcc1-0 libcilkrts5 libcom-err2 libcomerr2 libcryptsetup12 libdpkg-perl libext2fs2 libfdisk1 libgcc-7-dev libgcc1 libgcrypt20 libgomp1 libkmod2 libmount1 libncurses5 libncursesw5 libperl5.26 libpng16-16 libprocps6 libsmartcols1 libss2 libssl1.1 libstdc++-7-dev libstdc++6 libsystemd0 libtinfo5 libubsan0 libudev1 libuuid1 linux-libc-dev mount ncurses-base ncurses-bin openssl perl perl-base perl-modules-5.26 pkgbinarymangler procps systemd systemd-sysv tar tzdata ubuntu-keyring util-linux 74 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 48.6 MB of archives. After this operation, 5330 kB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu bionic-updates/main armhf base-files armhf 10.1ubuntu2.4 [59.9 kB] Get:2 http://ppa.launchpad.net/ubuntu-toolchain-r/ppa/ubuntu bionic/main armhf libgomp1 armhf 8.2.0-14ubuntu1~18.04~ppa1 [66.6 kB] Get:3 http://ppa.launchpad.net/ubuntu-toolchain-r/ppa/ubuntu bionic/main armhf gcc-8-base armhf 8.2.0-14ubuntu1~18.04~ppa1 [18.6 kB] Get:4 http://ppa.launchpad.net/ubuntu-toolchain-r/ppa/ubuntu bionic/main armhf libgcc1 armhf 1:8.2.0-14ubuntu1~18.04~ppa1 [37.1 kB] Get:5 http://ppa.launchpad.net/ubuntu-toolchain-r/ppa/ubuntu bionic/main armhf libcc1-0 armhf 8.2.0-14ubuntu1~18.04~ppa1 [32.8 kB] Get:6 http://ftpmaster.internal/ubuntu bionic-updates/main armhf bsdutils armhf 1:2.31.1-0.4ubuntu3.3 [55.5 kB] Get:7 http://ppa.launchpad.net/ubuntu-toolchain-r/ppa/ubuntu bionic/main armhf libatomic1 armhf 8.2.0-14ubuntu1~18.04~ppa1 [7072 B] Get:8 http://ppa.launchpad.net/ubuntu-toolchain-r/ppa/ubuntu bionic/main armhf libstdc++6 armhf 8.2.0-14ubuntu1~18.04~ppa1 [350 kB] Get:9 http://ftpmaster.internal/ubuntu bionic-updates/main armhf tar armhf 1.29b-2ubuntu0.1 [209 kB] Get:10 http://ppa.launchpad.net/ubuntu-toolchain-r/ppa/ubuntu bionic/main armhf libasan4 armhf 7.4.0-3ubuntu2~18.04~ppa1 [327 kB] Get:11 http://ftpmaster.internal/ubuntu bionic-updates/main armhf dpkg armhf 1.19.0.5ubuntu2.1 [1094 kB] Get:12 http://ppa.launchpad.net/ubuntu-toolchain-r/ppa/ubuntu bionic/main armhf libubsan0 armhf 7.4.0-3ubuntu2~18.04~ppa1 [108 kB] Get:13 http://ppa.launchpad.net/ubuntu-toolchain-r/ppa/ubuntu bionic/main armhf libcilkrts5 armhf 7.4.0-3ubuntu2~18.04~ppa1 [35.9 kB] Get:14 http://ppa.launchpad.net/ubuntu-toolchain-r/ppa/ubuntu bionic/main armhf g++-7 armhf 7.4.0-3ubuntu2~18.04~ppa1 [7471 kB] Get:15 http://ftpmaster.internal/ubuntu bionic-updates/main armhf libext2fs2 armhf 1.44.1-1ubuntu1.1 [144 kB] Get:16 http://ftpmaster.internal/ubuntu bionic-updates/main armhf e2fsprogs armhf 1.44.1-1ubuntu1.1 [369 kB] Get:17 http://ftpmaster.internal/ubuntu bionic-updates/main armhf ncurses-bin armhf 6.1-1ubuntu1.18.04 [155 kB] Get:18 http://ftpmaster.internal/ubuntu bionic-security/main armhf libperl5.26 armhf 5.26.1-6ubuntu0.3 [2888 kB] Get:19 http://ftpmaster.internal/ubuntu bionic-security/main armhf perl armhf 5.26.1-6ubuntu0.3 [201 kB] Get:20 http://ftpmaster.internal/ubuntu bionic-security/main armhf perl-base armhf 5.26.1-6ubuntu0.3 [1291 kB] Get:21 http://ppa.launchpad.net/ubuntu-toolchain-r/ppa/ubuntu bionic/main armhf gcc-7 armhf 7.4.0-3ubuntu2~18.04~ppa1 [7245 kB] Get:22 http://ftpmaster.internal/ubuntu bionic-security/main armhf perl-modules-5.26 all 5.26.1-6ubuntu0.3 [2763 kB] Get:23 http://ftpmaster.internal/ubuntu bionic-updates/main armhf libuuid1 armhf 2.31.1-0.4ubuntu3.3 [19.5 kB] Get:24 http://ftpmaster.internal/ubuntu bionic-updates/main armhf libblkid1 armhf 2.31.1-0.4ubuntu3.3 [112 kB] Get:25 http://ftpmaster.internal/ubuntu bionic-updates/main armhf libfdisk1 armhf 2.31.1-0.4ubuntu3.3 [152 kB] Get:26 http://ftpmaster.internal/ubuntu bionic-updates/main armhf libmount1 armhf 2.31.1-0.4ubuntu3.3 [122 kB] Get:27 http://ftpmaster.internal/ubuntu bionic-updates/main armhf libncurses5 armhf 6.1-1ubuntu1.18.04 [74.8 kB] Get:28 http://ftpmaster.internal/ubuntu bionic-updates/main armhf libtinfo5 armhf 6.1-1ubuntu1.18.04 [68.2 kB] Get:29 http://ftpmaster.internal/ubuntu bionic-updates/main armhf libncursesw5 armhf 6.1-1ubuntu1.18.04 [95.3 kB] Get:30 http://ftpmaster.internal/ubuntu bionic-updates/main armhf libsmartcols1 armhf 2.31.1-0.4ubuntu3.3 [74.6 kB] Get:31 http://ftpmaster.internal/ubuntu bionic-updates/main armhf fdisk armhf 2.31.1-0.4ubuntu3.3 [97.5 kB] Get:32 http://ftpmaster.internal/ubuntu bionic-updates/main armhf util-linux armhf 2.31.1-0.4ubuntu3.3 [845 kB] Get:33 http://ppa.launchpad.net/ubuntu-toolchain-r/ppa/ubuntu bionic/main armhf libstdc++-7-dev armhf 7.4.0-3ubuntu2~18.04~ppa1 [1540 kB] Get:34 http://ftpmaster.internal/ubuntu bionic-updates/main armhf ncurses-base all 6.1-1ubuntu1.18.04 [17.8 kB] Get:35 http://ftpmaster.internal/ubuntu bionic-security/main armhf libudev1 armhf 237-3ubuntu10.13 [48.7 kB] Get:36 http://ftpmaster.internal/ubuntu bionic-updates/main armhf libapt-pkg5.0 armhf 1.6.8 [731 kB] Get:37 http://ftpmaster.internal/ubuntu bionic-security/main armhf libgcrypt20 armhf 1.8.1-4ubuntu1.1 [364 kB] Get:38 http://ppa.launchpad.net/ubuntu-toolchain-r/ppa/ubuntu bionic/main armhf libgcc-7-dev armhf 7.4.0-3ubuntu2~18.04~ppa1 [711 kB] Get:39 http://ppa.launchpad.net/ubuntu-toolchain-r/ppa/ubuntu bionic/main armhf cpp-7 armhf 7.4.0-3ubuntu2~18.04~ppa1 [6549 kB] Get:40 http://ftpmaster.internal/ubuntu bionic-security/main armhf gpgv armhf 2.2.4-1ubuntu1.2 [167 kB] Get:41 http://ftpmaster.internal/ubuntu bionic-updates/main armhf ubuntu-keyring all 2018.09.18.1~18.04.0 [22.4 kB] Get:42 http://ftpmaster.internal/ubuntu bionic-updates/main armhf apt armhf 1.6.8 [1121 kB] Get:43 http://ftpmaster.internal/ubuntu bionic-security/main armhf libapparmor1 armhf 2.12-4ubuntu5.1 [27.1 kB] Get:44 http://ftpmaster.internal/ubuntu bionic-updates/main armhf libcryptsetup12 armhf 2:2.0.2-1ubuntu1.1 [119 kB] Get:45 http://ftpmaster.internal/ubuntu bionic-updates/main armhf libkmod2 armhf 24-1ubuntu3.2 [34.3 kB] Get:46 http://ftpmaster.internal/ubuntu bionic-updates/main armhf mount armhf 2.31.1-0.4ubuntu3.3 [99.7 kB] Get:47 http://ftpmaster.internal/ubuntu bionic-security/main armhf libprocps6 armhf 2:3.3.12-3ubuntu1.1 [28.8 kB] Get:48 http://ftpmaster.internal/ubuntu bionic-security/main armhf procps armhf 2:3.3.12-3ubuntu1.1 [213 kB] Get:49 http://ftpmaster.internal/ubuntu bionic-security/main armhf systemd armhf 237-3ubuntu10.13 [2726 kB] Get:50 http://ftpmaster.internal/ubuntu bionic-security/main armhf libsystemd0 armhf 237-3ubuntu10.13 [186 kB] Get:51 http://ppa.launchpad.net/ubuntu-toolchain-r/ppa/ubuntu bionic/main armhf gcc-7-base armhf 7.4.0-3ubuntu2~18.04~ppa1 [18.8 kB] Get:52 http://ppa.launchpad.net/ci-train-ppa-service/3473/ubuntu bionic/main armhf libssl1.1 armhf 1.1.1-1ubuntu2.1~18.04.0 [1064 kB] Get:53 http://ftpmaster.internal/ubuntu bionic-security/main armhf systemd-sysv armhf 237-3ubuntu10.13 [12.0 kB] Get:54 http://ftpmaster.internal/ubuntu bionic-updates/main armhf libcom-err2 armhf 1.44.1-1ubuntu1.1 [8416 B] Get:55 http://ftpmaster.internal/ubuntu bionic-updates/main armhf libss2 armhf 1.44.1-1ubuntu1.1 [9392 B] Get:56 http://ftpmaster.internal/ubuntu bionic-updates/main armhf libbinutils armhf 2.30-21ubuntu1~18.04 [308 kB] Get:57 http://ftpmaster.internal/ubuntu bionic-updates/main armhf binutils-common armhf 2.30-21ubuntu1~18.04 [193 kB] Get:58 http://ftpmaster.internal/ubuntu bionic-updates/main armhf binutils armhf 2.30-21ubuntu1~18.04 [3356 B] Get:59 http://ftpmaster.internal/ubuntu bionic-updates/main armhf binutils-arm-linux-gnueabihf armhf 2.30-21ubuntu1~18.04 [2175 kB] Get:60 http://ppa.launchpad.net/ci-train-ppa-service/3473/ubuntu bionic/main armhf openssl armhf 1.1.1-1ubuntu2.1~18.04.0 [591 kB] Get:61 http://ftpmaster.internal/ubuntu bionic-security/main armhf tzdata all 2018i-0ubuntu0.18.04 [189 kB] Get:62 http://ftpmaster.internal/ubuntu bionic-security/main armhf libpng16-16 armhf 1.6.34-1ubuntu0.18.04.1 [159 kB] Get:63 http://ftpmaster.internal/ubuntu bionic-updates/main armhf cpp armhf 4:7.3.0-3ubuntu2.1 [27.6 kB] Get:64 http://ftpmaster.internal/ubuntu bionic-updates/main armhf dpkg-dev all 1.19.0.5ubuntu2.1 [608 kB] Get:65 http://ftpmaster.internal/ubuntu bionic-updates/main armhf libdpkg-perl all 1.19.0.5ubuntu2.1 [211 kB] Get:66 http://ftpmaster.internal/ubuntu bionic-updates/main armhf e2fslibs armhf 1.44.1-1ubuntu1.1 [2712 B] Get:67 http://ftpmaster.internal/ubuntu bionic-updates/main armhf gcc armhf 4:7.3.0-3ubuntu2.1 [5204 B] Get:68 http://ftpmaster.internal/ubuntu bionic-updates/main armhf g++ armhf 4:7.3.0-3ubuntu2.1 [1576 B] Get:69 http://ftpmaster.internal/ubuntu bionic-security/main armhf gpg armhf 2.2.4-1ubuntu1.2 [408 kB] Get:70 http://ftpmaster.internal/ubuntu bionic-security/main armhf gpgconf armhf 2.2.4-1ubuntu1.2 [105 kB] Get:71 http://ftpmaster.internal/ubuntu bionic-security/main armhf gpg-agent armhf 2.2.4-1ubuntu1.2 [188 kB] Get:72 http://ftpmaster.internal/ubuntu bionic-updates/main armhf libcomerr2 armhf 1.44.1-1ubuntu1.1 [2712 B] Get:73 http://ftpmaster.internal/ubuntu bionic-security/main armhf linux-libc-dev armhf 4.15.0-45.48 [981 kB] Get:74 http://ftpmaster.internal/ubuntu bionic-security/main armhf pkgbinarymangler all 138.18.04.0 [52.8 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 48.6 MB in 2s (29.2 MB/s) (Reading database ... 12378 files and directories currently installed.) Preparing to unpack .../base-files_10.1ubuntu2.4_armhf.deb ... Unpacking base-files (10.1ubuntu2.4) over (10.1ubuntu2) ... Setting up base-files (10.1ubuntu2.4) ... Installing new version of config file /etc/issue ... Installing new version of config file /etc/issue.net ... Installing new version of config file /etc/lsb-release ... Installing new version of config file /etc/update-motd.d/50-motd-news ... (Reading database ... 12380 files and directories currently installed.) Preparing to unpack .../bsdutils_1%3a2.31.1-0.4ubuntu3.3_armhf.deb ... Unpacking bsdutils (1:2.31.1-0.4ubuntu3.3) over (1:2.31.1-0.4ubuntu3) ... Setting up bsdutils (1:2.31.1-0.4ubuntu3.3) ... (Reading database ... 12380 files and directories currently installed.) Preparing to unpack .../tar_1.29b-2ubuntu0.1_armhf.deb ... Unpacking tar (1.29b-2ubuntu0.1) over (1.29b-2) ... Setting up tar (1.29b-2ubuntu0.1) ... (Reading database ... 12380 files and directories currently installed.) 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Preparing to unpack .../libperl5.26_5.26.1-6ubuntu0.3_armhf.deb ... Unpacking libperl5.26:armhf (5.26.1-6ubuntu0.3) over (5.26.1-6) ... Preparing to unpack .../perl_5.26.1-6ubuntu0.3_armhf.deb ... Unpacking perl (5.26.1-6ubuntu0.3) over (5.26.1-6) ... Preparing to unpack .../perl-base_5.26.1-6ubuntu0.3_armhf.deb ... Unpacking perl-base (5.26.1-6ubuntu0.3) over (5.26.1-6) ... Setting up perl-base (5.26.1-6ubuntu0.3) ... (Reading database ... 12380 files and directories currently installed.) Preparing to unpack .../perl-modules-5.26_5.26.1-6ubuntu0.3_all.deb ... Unpacking perl-modules-5.26 (5.26.1-6ubuntu0.3) over (5.26.1-6) ... Preparing to unpack .../libuuid1_2.31.1-0.4ubuntu3.3_armhf.deb ... Unpacking libuuid1:armhf (2.31.1-0.4ubuntu3.3) over (2.31.1-0.4ubuntu3) ... Setting up libuuid1:armhf (2.31.1-0.4ubuntu3.3) ... (Reading database ... 12380 files and directories currently installed.) Preparing to unpack .../libblkid1_2.31.1-0.4ubuntu3.3_armhf.deb ... 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Setting up libgcc-7-dev:armhf (7.4.0-3ubuntu2~18.04~ppa1) ... Setting up cpp-7 (7.4.0-3ubuntu2~18.04~ppa1) ... Setting up libstdc++-7-dev:armhf (7.4.0-3ubuntu2~18.04~ppa1) ... Setting up perl (5.26.1-6ubuntu0.3) ... Setting up binutils (2.30-21ubuntu1~18.04) ... Setting up cpp (4:7.3.0-3ubuntu2.1) ... Setting up gcc-7 (7.4.0-3ubuntu2~18.04~ppa1) ... Setting up g++-7 (7.4.0-3ubuntu2~18.04~ppa1) ... Setting up libdpkg-perl (1.19.0.5ubuntu2.1) ... Setting up gcc (4:7.3.0-3ubuntu2.1) ... Setting up dpkg-dev (1.19.0.5ubuntu2.1) ... Setting up g++ (4:7.3.0-3ubuntu2.1) ... Processing triggers for libc-bin (2.27-3ubuntu1) ... RUN: /usr/share/launchpad-buildd/slavebin/sbuild-package PACKAGEBUILD-16111743 armhf bionic -c chroot:build-PACKAGEBUILD-16111743 --arch=armhf --dist=bionic --nolog discosnp_1.2.6-2.dsc Initiating build PACKAGEBUILD-16111743 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 4.4.0-142-generic #168-Ubuntu SMP Wed Jan 16 21:00:53 UTC 2019 armv7l sbuild (Debian sbuild) 0.67.0 (26 Dec 2015) on bos02-arm64-058.buildd +==============================================================================+ | discosnp 1.2.6-2 (armhf) 22 Feb 2019 09:01 | +==============================================================================+ Package: discosnp Version: 1.2.6-2 Source Version: 1.2.6-2 Distribution: bionic Machine Architecture: arm64 Host Architecture: armhf Build Architecture: armhf I: NOTICE: Log filtering will replace 'build/discosnp-UDeoVI/discosnp-1.2.6' with '<>' I: NOTICE: Log filtering will replace 'build/discosnp-UDeoVI' with '<>' I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-16111743/chroot-autobuild' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- discosnp_1.2.6-2.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-r7LEzP/apt_archive/sbuild-build-depends-core-dummy.deb'. Ign:1 copy:/<>/resolver-r7LEzP/apt_archive ./ InRelease Get:2 copy:/<>/resolver-r7LEzP/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-r7LEzP/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-r7LEzP/apt_archive ./ Sources [214 B] Get:5 copy:/<>/resolver-r7LEzP/apt_archive ./ Packages [527 B] Fetched 2860 B in 0s (55.5 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 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-r7LEzP/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 (77.4 kB/s) Selecting previously unselected package sbuild-build-depends-core-dummy. (Reading database ... 12392 files and directories currently installed.) Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_armhf.deb ... Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ... Setting up sbuild-build-depends-core-dummy (0.invalid.0) ... Merged Build-Depends: debhelper (>= 10), bc, zlib1g-dev, help2man Filtered Build-Depends: debhelper (>= 10), bc, zlib1g-dev, help2man dpkg-deb: building package 'sbuild-build-depends-discosnp-dummy' in '/<>/resolver-SyG2Yx/apt_archive/sbuild-build-depends-discosnp-dummy.deb'. Ign:1 copy:/<>/resolver-SyG2Yx/apt_archive ./ InRelease Get:2 copy:/<>/resolver-SyG2Yx/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-SyG2Yx/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-SyG2Yx/apt_archive ./ Sources [228 B] Get:5 copy:/<>/resolver-SyG2Yx/apt_archive ./ Packages [545 B] Fetched 2892 B in 0s (40.7 kB/s) Reading package lists... Reading package lists... +------------------------------------------------------------------------------+ | Install discosnp build dependencies (apt-based resolver) | +------------------------------------------------------------------------------+ Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: autoconf automake autopoint autotools-dev bc bsdmainutils debhelper dh-autoreconf dh-strip-nondeterminism file gettext gettext-base groff-base help2man intltool-debian libarchive-zip-perl libbsd0 libcroco3 libfile-stripnondeterminism-perl libglib2.0-0 libicu60 liblocale-gettext-perl libmagic-mgc libmagic1 libpipeline1 libsigsegv2 libtimedate-perl libtool libxml2 m4 man-db po-debconf zlib1g-dev Suggested packages: autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois vacation dh-make dwz gettext-doc libasprintf-dev libgettextpo-dev groff libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc apparmor less www-browser libmail-box-perl Recommended packages: curl | wget | lynx libarchive-cpio-perl libglib2.0-data shared-mime-info xdg-user-dirs libltdl-dev libmail-sendmail-perl The following NEW packages will be installed: autoconf automake autopoint autotools-dev bc bsdmainutils debhelper dh-autoreconf dh-strip-nondeterminism file gettext gettext-base groff-base help2man intltool-debian libarchive-zip-perl libbsd0 libcroco3 libfile-stripnondeterminism-perl libglib2.0-0 libicu60 liblocale-gettext-perl libmagic-mgc libmagic1 libpipeline1 libsigsegv2 libtimedate-perl libtool libxml2 m4 man-db po-debconf sbuild-build-depends-discosnp-dummy zlib1g-dev 0 upgraded, 34 newly installed, 0 to remove and 0 not upgraded. Need to get 16.3 MB of archives. After this operation, 58.3 MB of additional disk space will be used. Get:1 copy:/<>/resolver-SyG2Yx/apt_archive ./ sbuild-build-depends-discosnp-dummy 0.invalid.0 [876 B] Get:2 http://ftpmaster.internal/ubuntu bionic/main armhf liblocale-gettext-perl armhf 1.07-3build2 [16.1 kB] Get:3 http://ftpmaster.internal/ubuntu bionic/main armhf libbsd0 armhf 0.8.7-1 [40.4 kB] Get:4 http://ftpmaster.internal/ubuntu bionic/main armhf bsdmainutils armhf 11.1.2ubuntu1 [177 kB] Get:5 http://ftpmaster.internal/ubuntu bionic/main armhf groff-base armhf 1.22.3-10 [1013 kB] Get:6 http://ftpmaster.internal/ubuntu bionic/main armhf libpipeline1 armhf 1.5.0-1 [21.1 kB] Get:7 http://ftpmaster.internal/ubuntu bionic-updates/main armhf man-db armhf 2.8.3-2ubuntu0.1 [993 kB] Get:8 http://ftpmaster.internal/ubuntu bionic-security/main armhf libmagic-mgc armhf 1:5.32-2ubuntu0.1 [184 kB] Get:9 http://ftpmaster.internal/ubuntu bionic-security/main armhf libmagic1 armhf 1:5.32-2ubuntu0.1 [62.7 kB] Get:10 http://ftpmaster.internal/ubuntu bionic-security/main armhf file armhf 1:5.32-2ubuntu0.1 [21.5 kB] Get:11 http://ftpmaster.internal/ubuntu bionic-updates/main armhf libglib2.0-0 armhf 2.56.3-0ubuntu0.18.04.1 [1016 kB] Get:12 http://ftpmaster.internal/ubuntu bionic/main armhf libicu60 armhf 60.2-3ubuntu3 [7797 kB] Get:13 http://ftpmaster.internal/ubuntu bionic-security/main armhf libxml2 armhf 2.9.4+dfsg1-6.1ubuntu1.2 [567 kB] Get:14 http://ftpmaster.internal/ubuntu bionic-security/main armhf gettext-base armhf 0.19.8.1-6ubuntu0.1 [46.4 kB] Get:15 http://ftpmaster.internal/ubuntu bionic/main armhf libsigsegv2 armhf 2.12-1 [14.0 kB] Get:16 http://ftpmaster.internal/ubuntu bionic/main armhf m4 armhf 1.4.18-1 [181 kB] Get:17 http://ftpmaster.internal/ubuntu bionic/main armhf autoconf all 2.69-11 [322 kB] Get:18 http://ftpmaster.internal/ubuntu bionic/main armhf autotools-dev all 20180224.1 [39.6 kB] Get:19 http://ftpmaster.internal/ubuntu bionic/main armhf automake all 1:1.15.1-3ubuntu2 [509 kB] Get:20 http://ftpmaster.internal/ubuntu bionic-security/main armhf autopoint all 0.19.8.1-6ubuntu0.1 [412 kB] Get:21 http://ftpmaster.internal/ubuntu bionic/main armhf bc armhf 1.07.1-2 [81.3 kB] Get:22 http://ftpmaster.internal/ubuntu bionic/main armhf libtool all 2.4.6-2 [194 kB] Get:23 http://ftpmaster.internal/ubuntu bionic/main armhf dh-autoreconf all 17 [15.8 kB] Get:24 http://ftpmaster.internal/ubuntu bionic-security/main armhf libarchive-zip-perl all 1.60-1ubuntu0.1 [84.6 kB] Get:25 http://ftpmaster.internal/ubuntu bionic/main armhf libfile-stripnondeterminism-perl all 0.040-1.1~build1 [13.8 kB] Get:26 http://ftpmaster.internal/ubuntu bionic/main armhf libtimedate-perl all 2.3000-2 [37.5 kB] Get:27 http://ftpmaster.internal/ubuntu bionic/main armhf dh-strip-nondeterminism all 0.040-1.1~build1 [5208 B] Get:28 http://ftpmaster.internal/ubuntu bionic/main armhf libcroco3 armhf 0.6.12-2 [69.4 kB] Get:29 http://ftpmaster.internal/ubuntu bionic-security/main armhf gettext armhf 0.19.8.1-6ubuntu0.1 [834 kB] Get:30 http://ftpmaster.internal/ubuntu bionic/main armhf intltool-debian all 0.35.0+20060710.4 [24.9 kB] Get:31 http://ftpmaster.internal/ubuntu bionic/main armhf po-debconf all 1.0.20 [232 kB] Get:32 http://ftpmaster.internal/ubuntu bionic-updates/main armhf debhelper all 11.1.6ubuntu2 [902 kB] Get:33 http://ftpmaster.internal/ubuntu bionic/universe armhf help2man armhf 1.47.6 [162 kB] Get:34 http://ftpmaster.internal/ubuntu bionic/main armhf zlib1g-dev armhf 1:1.2.11.dfsg-0ubuntu2 [168 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 16.3 MB in 1s (21.4 MB/s) Selecting previously unselected package liblocale-gettext-perl. (Reading database ... 12392 files and directories currently installed.) Preparing to unpack .../00-liblocale-gettext-perl_1.07-3build2_armhf.deb ... Unpacking liblocale-gettext-perl (1.07-3build2) ... Selecting previously unselected package libbsd0:armhf. Preparing to unpack .../01-libbsd0_0.8.7-1_armhf.deb ... Unpacking libbsd0:armhf (0.8.7-1) ... Selecting previously unselected package bsdmainutils. Preparing to unpack .../02-bsdmainutils_11.1.2ubuntu1_armhf.deb ... Unpacking bsdmainutils (11.1.2ubuntu1) ... Selecting previously unselected package groff-base. Preparing to unpack .../03-groff-base_1.22.3-10_armhf.deb ... Unpacking groff-base (1.22.3-10) ... Selecting previously unselected package libpipeline1:armhf. Preparing to unpack .../04-libpipeline1_1.5.0-1_armhf.deb ... Unpacking libpipeline1:armhf (1.5.0-1) ... Selecting previously unselected package man-db. Preparing to unpack .../05-man-db_2.8.3-2ubuntu0.1_armhf.deb ... Unpacking man-db (2.8.3-2ubuntu0.1) ... 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Setting up libglib2.0-0:armhf (2.56.3-0ubuntu0.18.04.1) ... No schema files found: doing nothing. Setting up gettext-base (0.19.8.1-6ubuntu0.1) ... Setting up libpipeline1:armhf (1.5.0-1) ... Setting up m4 (1.4.18-1) ... Setting up libbsd0:armhf (0.8.7-1) ... Setting up libxml2:armhf (2.9.4+dfsg1-6.1ubuntu1.2) ... Setting up libmagic-mgc (1:5.32-2ubuntu0.1) ... Setting up libmagic1:armhf (1:5.32-2ubuntu0.1) ... Setting up libcroco3:armhf (0.6.12-2) ... Processing triggers for libc-bin (2.27-3ubuntu1) ... Setting up autotools-dev (20180224.1) ... Setting up liblocale-gettext-perl (1.07-3build2) ... Setting up bsdmainutils (11.1.2ubuntu1) ... update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode Setting up bc (1.07.1-2) ... Setting up autopoint (0.19.8.1-6ubuntu0.1) ... Setting up zlib1g-dev:armhf (1:1.2.11.dfsg-0ubuntu2) ... Setting up libfile-stripnondeterminism-perl (0.040-1.1~build1) ... Setting up gettext (0.19.8.1-6ubuntu0.1) ... Setting up autoconf (2.69-11) ... Setting up file (1:5.32-2ubuntu0.1) ... Setting up intltool-debian (0.35.0+20060710.4) ... Setting up automake (1:1.15.1-3ubuntu2) ... update-alternatives: using /usr/bin/automake-1.15 to provide /usr/bin/automake (automake) in auto mode Setting up help2man (1.47.6) ... Setting up man-db (2.8.3-2ubuntu0.1) ... Not building database; man-db/auto-update is not 'true'. Setting up libtool (2.4.6-2) ... Setting up po-debconf (1.0.20) ... Setting up dh-autoreconf (17) ... Setting up dh-strip-nondeterminism (0.040-1.1~build1) ... Setting up debhelper (11.1.6ubuntu2) ... Setting up sbuild-build-depends-discosnp-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.27-3ubuntu1) ... +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 4.4.0-142-generic arm64 (armv7l) Toolchain package versions: binutils_2.30-21ubuntu1~18.04 dpkg-dev_1.19.0.5ubuntu2.1 g++-7_7.4.0-3ubuntu2~18.04~ppa1 gcc-7_7.4.0-3ubuntu2~18.04~ppa1 libc6-dev_2.27-3ubuntu1 libstdc++-7-dev_7.4.0-3ubuntu2~18.04~ppa1 libstdc++6_8.2.0-14ubuntu1~18.04~ppa1 linux-libc-dev_4.15.0-45.48 Package versions: adduser_3.116ubuntu1 advancecomp_2.1-1 apt_1.6.8 autoconf_2.69-11 automake_1:1.15.1-3ubuntu2 autopoint_0.19.8.1-6ubuntu0.1 autotools-dev_20180224.1 base-files_10.1ubuntu2.4 base-passwd_3.5.44 bash_4.4.18-2ubuntu1 bc_1.07.1-2 binutils_2.30-21ubuntu1~18.04 binutils-arm-linux-gnueabihf_2.30-21ubuntu1~18.04 binutils-common_2.30-21ubuntu1~18.04 bsdmainutils_11.1.2ubuntu1 bsdutils_1:2.31.1-0.4ubuntu3.3 build-essential_12.4ubuntu1 bzip2_1.0.6-8.1 ca-certificates_20180409 coreutils_8.28-1ubuntu1 cpp_4:7.3.0-3ubuntu2.1 cpp-7_7.4.0-3ubuntu2~18.04~ppa1 dash_0.5.8-2.10 debconf_1.5.66 debhelper_11.1.6ubuntu2 debianutils_4.8.4 dh-autoreconf_17 dh-strip-nondeterminism_0.040-1.1~build1 diffutils_1:3.6-1 dmsetup_2:1.02.145-4.1ubuntu3 dpkg_1.19.0.5ubuntu2.1 dpkg-dev_1.19.0.5ubuntu2.1 e2fslibs_1.44.1-1ubuntu1.1 e2fsprogs_1.44.1-1ubuntu1.1 fakeroot_1.22-2ubuntu1 fdisk_2.31.1-0.4ubuntu3.3 file_1:5.32-2ubuntu0.1 findutils_4.6.0+git+20170828-2 g++_4:7.3.0-3ubuntu2.1 g++-7_7.4.0-3ubuntu2~18.04~ppa1 gcc_4:7.3.0-3ubuntu2.1 gcc-7_7.4.0-3ubuntu2~18.04~ppa1 gcc-7-base_7.4.0-3ubuntu2~18.04~ppa1 gcc-8-base_8.2.0-14ubuntu1~18.04~ppa1 gettext_0.19.8.1-6ubuntu0.1 gettext-base_0.19.8.1-6ubuntu0.1 gpg_2.2.4-1ubuntu1.2 gpg-agent_2.2.4-1ubuntu1.2 gpgconf_2.2.4-1ubuntu1.2 gpgv_2.2.4-1ubuntu1.2 grep_3.1-2 groff-base_1.22.3-10 gzip_1.6-5ubuntu1 help2man_1.47.6 hostname_3.20 init_1.51 init-system-helpers_1.51 initscripts_2.88dsf-59.3ubuntu2 insserv_1.14.0-5ubuntu3 intltool-debian_0.35.0+20060710.4 libacl1_2.2.52-3build1 libapparmor1_2.12-4ubuntu5.1 libapt-pkg5.0_1.6.8 libarchive-zip-perl_1.60-1ubuntu0.1 libargon2-0_0~20161029-1.1 libasan4_7.4.0-3ubuntu2~18.04~ppa1 libassuan0_2.5.1-2 libatomic1_8.2.0-14ubuntu1~18.04~ppa1 libattr1_1:2.4.47-2build1 libaudit-common_1:2.8.2-1ubuntu1 libaudit1_1:2.8.2-1ubuntu1 libbinutils_2.30-21ubuntu1~18.04 libblkid1_2.31.1-0.4ubuntu3.3 libbsd0_0.8.7-1 libbz2-1.0_1.0.6-8.1 libc-bin_2.27-3ubuntu1 libc-dev-bin_2.27-3ubuntu1 libc6_2.27-3ubuntu1 libc6-dev_2.27-3ubuntu1 libcap-ng0_0.7.7-3.1 libcap2_1:2.25-1.2 libcc1-0_8.2.0-14ubuntu1~18.04~ppa1 libcilkrts5_7.4.0-3ubuntu2~18.04~ppa1 libcom-err2_1.44.1-1ubuntu1.1 libcomerr2_1.44.1-1ubuntu1.1 libcroco3_0.6.12-2 libcryptsetup12_2:2.0.2-1ubuntu1.1 libdb5.3_5.3.28-13.1ubuntu1 libdebconfclient0_0.213ubuntu1 libdevmapper1.02.1_2:1.02.145-4.1ubuntu3 libdpkg-perl_1.19.0.5ubuntu2.1 libext2fs2_1.44.1-1ubuntu1.1 libfakeroot_1.22-2ubuntu1 libfdisk1_2.31.1-0.4ubuntu3.3 libffi6_3.2.1-8 libfile-stripnondeterminism-perl_0.040-1.1~build1 libgcc-7-dev_7.4.0-3ubuntu2~18.04~ppa1 libgcc1_1:8.2.0-14ubuntu1~18.04~ppa1 libgcrypt20_1.8.1-4ubuntu1.1 libgdbm-compat4_1.14.1-6 libgdbm5_1.14.1-6 libglib2.0-0_2.56.3-0ubuntu0.18.04.1 libgmp10_2:6.1.2+dfsg-2 libgnutls30_3.5.18-1ubuntu1 libgomp1_8.2.0-14ubuntu1~18.04~ppa1 libgpg-error0_1.27-6 libhogweed4_3.4-1 libicu60_60.2-3ubuntu3 libidn11_1.33-2.1ubuntu1 libidn2-0_2.0.4-1.1build2 libip4tc0_1.6.1-2ubuntu2 libisl19_0.19-1 libjson-c3_0.12.1-1.3 libkmod2_24-1ubuntu3.2 liblocale-gettext-perl_1.07-3build2 liblockfile-bin_1.14-1.1 liblockfile1_1.14-1.1 liblz4-1_0.0~r131-2ubuntu3 liblzma5_5.2.2-1.3 libmagic-mgc_1:5.32-2ubuntu0.1 libmagic1_1:5.32-2ubuntu0.1 libmount1_2.31.1-0.4ubuntu3.3 libmpc3_1.1.0-1 libmpfr6_4.0.1-1 libncurses5_6.1-1ubuntu1.18.04 libncursesw5_6.1-1ubuntu1.18.04 libnettle6_3.4-1 libnpth0_1.5-3 libp11-kit0_0.23.9-2 libpam-modules_1.1.8-3.6ubuntu2 libpam-modules-bin_1.1.8-3.6ubuntu2 libpam-runtime_1.1.8-3.6ubuntu2 libpam0g_1.1.8-3.6ubuntu2 libpcre3_2:8.39-9 libperl5.26_5.26.1-6ubuntu0.3 libpipeline1_1.5.0-1 libpng16-16_1.6.34-1ubuntu0.18.04.1 libprocps6_2:3.3.12-3ubuntu1.1 libreadline7_7.0-3 libseccomp2_2.3.1-2.1ubuntu4 libselinux1_2.7-2build2 libsemanage-common_2.7-2build2 libsemanage1_2.7-2build2 libsepol1_2.7-1 libsigsegv2_2.12-1 libslang2_2.3.1a-3ubuntu1 libsmartcols1_2.31.1-0.4ubuntu3.3 libsqlite3-0_3.22.0-1 libss2_1.44.1-1ubuntu1.1 libssl1.1_1.1.1-1ubuntu2.1~18.04.0 libstdc++-7-dev_7.4.0-3ubuntu2~18.04~ppa1 libstdc++6_8.2.0-14ubuntu1~18.04~ppa1 libsystemd0_237-3ubuntu10.13 libtasn1-6_4.13-2 libtimedate-perl_2.3000-2 libtinfo5_6.1-1ubuntu1.18.04 libtool_2.4.6-2 libubsan0_7.4.0-3ubuntu2~18.04~ppa1 libudev1_237-3ubuntu10.13 libunistring2_0.9.9-0ubuntu1 libusb-0.1-4_2:0.1.12-31 libuuid1_2.31.1-0.4ubuntu3.3 libxml2_2.9.4+dfsg1-6.1ubuntu1.2 libzstd1_1.3.3+dfsg-2ubuntu1 linux-libc-dev_4.15.0-45.48 lockfile-progs_0.1.17build1 login_1:4.5-1ubuntu1 lsb-base_9.20170808ubuntu1 m4_1.4.18-1 make_4.1-9.1ubuntu1 man-db_2.8.3-2ubuntu0.1 mawk_1.3.3-17ubuntu3 mount_2.31.1-0.4ubuntu3.3 multiarch-support_2.27-3ubuntu1 ncurses-base_6.1-1ubuntu1.18.04 ncurses-bin_6.1-1ubuntu1.18.04 openssl_1.1.1-1ubuntu2.1~18.04.0 optipng_0.7.6-1.1 passwd_1:4.5-1ubuntu1 patch_2.7.6-2ubuntu1 perl_5.26.1-6ubuntu0.3 perl-base_5.26.1-6ubuntu0.3 perl-modules-5.26_5.26.1-6ubuntu0.3 pinentry-curses_1.1.0-1 pkgbinarymangler_138.18.04.0 po-debconf_1.0.20 policyrcd-script-zg2_0.1-3 procps_2:3.3.12-3ubuntu1.1 readline-common_7.0-3 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-discosnp-dummy_0.invalid.0 sed_4.4-2 sensible-utils_0.0.12 systemd_237-3ubuntu10.13 systemd-sysv_237-3ubuntu10.13 sysv-rc_2.88dsf-59.3ubuntu2 sysvinit-utils_2.88dsf-59.10ubuntu1 tar_1.29b-2ubuntu0.1 tzdata_2018i-0ubuntu0.18.04 ubuntu-keyring_2018.09.18.1~18.04.0 util-linux_2.31.1-0.4ubuntu3.3 xz-utils_5.2.2-1.3 zlib1g_1:1.2.11.dfsg-0ubuntu2 zlib1g-dev_1:1.2.11.dfsg-0ubuntu2 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- gpgv: Signature made Tue Nov 14 09:09:00 2017 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 ./discosnp_1.2.6-2.dsc dpkg-source: info: extracting discosnp in discosnp-1.2.6 dpkg-source: info: unpacking discosnp_1.2.6.orig.tar.gz dpkg-source: info: unpacking discosnp_1.2.6-2.debian.tar.xz dpkg-source: info: applying fix_build 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-16111743 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-16111743 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-16111743 SCHROOT_UID=2001 SCHROOT_USER=buildd SHELL=/bin/sh TERM=unknown USER=buildd V=1 dpkg-buildpackage ----------------- dpkg-buildpackage: info: source package discosnp dpkg-buildpackage: info: source version 1.2.6-2 dpkg-buildpackage: info: source distribution unstable dpkg-source --before-build discosnp-1.2.6 dpkg-buildpackage: info: host architecture armhf fakeroot debian/rules clean dh clean debian/rules override_dh_clean make[1]: Entering directory '/<>' cd minia && make clean make[2]: Entering directory '/<>/minia' rm -rf *.o make[2]: Leaving directory '/<>/minia' cd kissnp2 && make clean make[2]: Entering directory '/<>/kissnp2' rm -rf *.o ../minia/*.o make[2]: Leaving directory '/<>/kissnp2' cd kissreads && make clean make[2]: Entering directory '/<>/kissreads' rm -rf ./src/*.o kissreads make[2]: Leaving directory '/<>/kissreads' rm -f output_analyses/discoSnp_to_genotypes rm -f output_analyses/discoSnp_to_csv rm -f kissnp2/kissnp2 rm -f kissreads/kissreads rm -f kissreads.1 rm -f kissnp2.1 dh_clean make[1]: Leaving directory '/<>' debian/rules build-arch dh build-arch dh_update_autotools_config -a dh_autoreconf -a debian/rules override_dh_auto_build make[1]: Entering directory '/<>' dh_auto_build cd kissnp2 && make k=29 make[2]: Entering directory '/<>/kissnp2' g++ -o ../minia/Pool.o -c ../minia/Pool.cpp -g -O2 -fdebug-prefix-map=/<>/kissnp2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O4 -lz -DMINIA_IS_IN_PARENT_FOLDER g++ -o ../minia/Bank.o -c ../minia/Bank.cpp -g -O2 -fdebug-prefix-map=/<>/kissnp2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O4 -lz -DMINIA_IS_IN_PARENT_FOLDER ../minia/Bank.cpp: In member function ‘void Bank::init(char**, int)’: ../minia/Bank.cpp:279:19: warning: ignoring return value of ‘char* strerror_r(int, char*, size_t)’, declared with attribute warn_unused_result [-Wunused-result] strerror_r( errno, buffer, BUFSIZ ); // get string message from errno ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ ../minia/Bank.cpp: In member function ‘void BinaryBank::open(bool)’: ../minia/Bank.cpp:710:19: warning: ignoring return value of ‘char* strerror_r(int, char*, size_t)’, declared with attribute warn_unused_result [-Wunused-result] strerror_r( errno, buffer, BUFSIZ ); // get string message from errno ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ ../minia/Bank.cpp: In member function ‘void BinaryReads::open(bool)’: ../minia/Bank.cpp:795:19: warning: ignoring return value of ‘char* strerror_r(int, char*, size_t)’, declared with attribute warn_unused_result [-Wunused-result] strerror_r( errno, buffer, BUFSIZ ); // get string message from errno ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ ../minia/Bank.cpp: In member function ‘int KmersBuffer::readkmers()’: ../minia/Bank.cpp:985:14: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fread(buffer,sizeof( char),block_size, binary_read_file); // read a block of sequences into the buffer ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -o ../minia/Bloom.o -c ../minia/Bloom.cpp -g -O2 -fdebug-prefix-map=/<>/kissnp2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O4 -lz -DMINIA_IS_IN_PARENT_FOLDER ../minia/Bloom.cpp: In member function ‘void Bloom::load(char*)’: ../minia/Bloom.cpp:257:7: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fread(blooma, sizeof(unsigned char), nchar, file_data); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -o ../minia/Hash16.o -c ../minia/Hash16.cpp -g -O2 -fdebug-prefix-map=/<>/kissnp2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O4 -lz -DMINIA_IS_IN_PARENT_FOLDER g++ -o ../minia/Terminator.o -c ../minia/Terminator.cpp -g -O2 -fdebug-prefix-map=/<>/kissnp2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O4 -lz -DMINIA_IS_IN_PARENT_FOLDER ../minia/Terminator.cpp: In constructor ‘BranchingTerminator::BranchingTerminator(BinaryBank*, BinaryBank*, Bloom*, Set*)’: ../minia/Terminator.cpp:337:186: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 4 has type ‘unsigned int’ [-Wformat=] fprintf (stderr,"\nLoaded %lld branching kmers x %lu B = %.1f MB\n",nb_branching_kmers,sizeof(cell),((1<)*1.0)/1024.0/1024.0); ^ g++ -o ../minia/Kmer.o -c ../minia/Kmer.cpp -g -O2 -fdebug-prefix-map=/<>/kissnp2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O4 -lz -DMINIA_IS_IN_PARENT_FOLDER g++ -o ../minia/Traversal.o -c ../minia/Traversal.cpp -g -O2 -fdebug-prefix-map=/<>/kissnp2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O4 -lz -DMINIA_IS_IN_PARENT_FOLDER ../minia/Traversal.cpp: In member function ‘bool MonumentTraversal::find_starting_kmer(kmer_type, kmer_type&)’: ../minia/Traversal.cpp:352:252: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 5 has type ‘std::set::size_type {aka unsigned int}’ [-Wformat=] if (debug) printf("depth %d useless int %d and starting belongs %d nb involved nodes %lu\n",frontline.depth,useless_int,all_involved_extensions.find(starting_kmer) != all_involved_extensions.end(),all_involved_extensions.size()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^ ../minia/Traversal.cpp: In member function ‘bool MonumentTraversal::validate_consensuses(std::set >, char*, int&)’: ../minia/Traversal.cpp:820:101: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 4 has type ‘std::__cxx11::basic_string::size_type {aka unsigned int}’ [-Wformat=] if (debug) printf("bubble path %d: %s (len=%lu)\n",path_number,(*it).c_str(),(*it).length()); ~~~~~~~~~~~~~~^ ../minia/Traversal.cpp:841:87: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘std::set >::size_type {aka unsigned int}’ [-Wformat=] if (debug) printf("%lu-bubble mean %d, stdev %.1f\n",consensuses.size(),mean,stdev); ~~~~~~~~~~~~~~~~~~ ^ In file included from /usr/include/c++/7/deque:66:0, from /usr/include/c++/7/queue:60, from ../minia/Traversal.h:5, from ../minia/Traversal.cpp:3: /usr/include/c++/7/bits/deque.tcc: In function ‘std::_Deque_iterator<_Tp, _Tp&, _Tp*> std::copy(std::_Deque_iterator<_Tp, const _Tp&, const _Tp*>, std::_Deque_iterator<_Tp, const _Tp&, const _Tp*>, std::_Deque_iterator<_Tp, _Tp&, _Tp*>) [with _Tp = kmer_strand_nt]’: /usr/include/c++/7/bits/deque.tcc:985:5: note: parameter passing for argument of type ‘std::_Deque_iterator’ changed in GCC 7.1 copy(_Deque_iterator<_Tp, const _Tp&, const _Tp*> __first, ^~~~ /usr/include/c++/7/bits/deque.tcc:985:5: note: parameter passing for argument of type ‘std::_Deque_iterator’ changed in GCC 7.1 /usr/include/c++/7/bits/deque.tcc: In member function ‘void std::deque<_Tp, _Alloc>::_M_insert_aux(std::deque<_Tp, _Alloc>::iterator, _ForwardIterator, _ForwardIterator, std::deque<_Tp, _Alloc>::size_type) [with _ForwardIterator = std::_Deque_iterator; _Tp = kmer_strand_nt; _Alloc = std::allocator]’: /usr/include/c++/7/bits/deque.tcc:757:7: note: parameter passing for argument of type ‘std::_Deque_iterator’ changed in GCC 7.1 deque<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~ /usr/include/c++/7/bits/deque.tcc:757:7: note: parameter passing for argument of type ‘std::_Deque_iterator’ changed in GCC 7.1 /usr/include/c++/7/bits/deque.tcc:780:7: note: parameter passing for argument of type ‘std::_Deque_iterator’ changed in GCC 7.1 std::copy(__first, __last, __pos - difference_type(__n)); ^~~ /usr/include/c++/7/bits/deque.tcc:780:7: note: parameter passing for argument of type ‘std::_Deque_iterator’ changed in GCC 7.1 /usr/include/c++/7/bits/deque.tcc:780:7: note: parameter passing for argument of type ‘std::_Deque_iterator’ changed in GCC 7.1 /usr/include/c++/7/bits/deque.tcc:791:7: note: parameter passing for argument of type ‘std::_Deque_iterator’ changed in GCC 7.1 std::copy(__mid, __last, __old_start); ^~~ /usr/include/c++/7/bits/deque.tcc:791:7: note: parameter passing for argument of type ‘std::_Deque_iterator’ changed in GCC 7.1 /usr/include/c++/7/bits/deque.tcc:791:7: note: parameter passing for argument of type ‘std::_Deque_iterator’ changed in GCC 7.1 /usr/include/c++/7/bits/deque.tcc:820:5: note: parameter passing for argument of type ‘std::_Deque_iterator’ changed in GCC 7.1 std::copy(__first, __last, __pos); ^~~ /usr/include/c++/7/bits/deque.tcc:820:5: note: parameter passing for argument of type ‘std::_Deque_iterator’ changed in GCC 7.1 /usr/include/c++/7/bits/deque.tcc:820:5: note: parameter passing for argument of type ‘std::_Deque_iterator’ changed in GCC 7.1 /usr/include/c++/7/bits/deque.tcc:831:5: note: parameter passing for argument of type ‘std::_Deque_iterator’ changed in GCC 7.1 std::copy(__first, __mid, __pos); ^~~ /usr/include/c++/7/bits/deque.tcc:831:5: note: parameter passing for argument of type ‘std::_Deque_iterator’ changed in GCC 7.1 /usr/include/c++/7/bits/deque.tcc:831:5: note: parameter passing for argument of type ‘std::_Deque_iterator’ changed in GCC 7.1 /usr/include/c++/7/bits/deque.tcc: In member function ‘std::deque<_Tp, _Alloc>& std::deque<_Tp, _Alloc>::operator=(const std::deque<_Tp, _Alloc>&) [with _Tp = kmer_strand_nt; _Alloc = std::allocator]’: /usr/include/c++/7/bits/deque.tcc:116:21: note: parameter passing for argument of type ‘std::_Deque_iterator’ changed in GCC 7.1 _M_erase_at_end(std::copy(__x.begin(), __x.end(), ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ this->_M_impl._M_start)); ~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/7/bits/deque.tcc:116:21: note: parameter passing for argument of type ‘std::_Deque_iterator’ changed in GCC 7.1 /usr/include/c++/7/bits/deque.tcc:116:21: note: parameter passing for argument of type ‘std::_Deque_iterator’ changed in GCC 7.1 /usr/include/c++/7/bits/deque.tcc:121:8: note: parameter passing for argument of type ‘std::_Deque_iterator’ changed in GCC 7.1 std::copy(__x.begin(), __mid, this->_M_impl._M_start); ^~~ /usr/include/c++/7/bits/deque.tcc:121:8: note: parameter passing for argument of type ‘std::_Deque_iterator’ changed in GCC 7.1 /usr/include/c++/7/bits/deque.tcc:121:8: note: parameter passing for argument of type ‘std::deque >::const_iterator {aka std::_Deque_iterator}’ changed in GCC 7.1 g++ -o ../minia/LinearCounter.o -c ../minia/LinearCounter.cpp -g -O2 -fdebug-prefix-map=/<>/kissnp2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O4 -lz -DMINIA_IS_IN_PARENT_FOLDER g++ -o ../minia/Set.o -c ../minia/Set.cpp -g -O2 -fdebug-prefix-map=/<>/kissnp2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O4 -lz -DMINIA_IS_IN_PARENT_FOLDER ../minia/Set.cpp: In member function ‘void AssocSet::print_total_size()’: ../minia/Set.cpp:132:48: warning: format ‘%li’ expects argument of type ‘long int’, but argument 2 has type ‘std::vector::size_type {aka unsigned int}’ [-Wformat=] printf("Assoc set size: %li\n",liste.size()); ~~~~~~~~~~~~^ ../minia/Set.cpp:133:103: warning: format ‘%li’ expects argument of type ‘long int’, but argument 2 has type ‘std::vector::size_type {aka unsigned int}’ [-Wformat=] printf("Assoc set capacity: listekmer %li liste val%li\n",liste.capacity(),liste_value.capacity()); ~~~~~~~~~~~~~~~~ ^ ../minia/Set.cpp:133:103: warning: format ‘%li’ expects argument of type ‘long int’, but argument 3 has type ‘std::vector::size_type {aka unsigned int}’ [-Wformat=] ../minia/Set.cpp:136:11: warning: format ‘%li’ expects argument of type ‘long int’, but argument 2 has type ‘std::vector::size_type {aka unsigned int}’ [-Wformat=] ../minia/Set.cpp:134:48: printf("%li *%li + %li* %li = %li MB \n",liste.capacity(),sizeof(set_elem),liste_value.capacity(),sizeof(set_value_t), ~~~~~~~~~~~~~~~~ ../minia/Set.cpp:136:11: ); ^ ../minia/Set.cpp:136:11: warning: format ‘%li’ expects argument of type ‘long int’, but argument 3 has type ‘unsigned int’ [-Wformat=] ../minia/Set.cpp:136:11: warning: format ‘%li’ expects argument of type ‘long int’, but argument 4 has type ‘std::vector::size_type {aka unsigned int}’ [-Wformat=] ../minia/Set.cpp:136:11: warning: format ‘%li’ expects argument of type ‘long int’, but argument 5 has type ‘unsigned int’ [-Wformat=] ../minia/Set.cpp:136:11: warning: format ‘%li’ expects argument of type ‘long int’, but argument 6 has type ‘std::vector::size_type {aka unsigned int}’ [-Wformat=] ../minia/Set.cpp: In member function ‘void AssocPairedSet::print()’: ../minia/Set.cpp:242:45: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘std::vector::size_type {aka unsigned int}’ [-Wformat=] printf("print %lu elems \n",liste.size()); ~~~~~~~~~~~~^ ../minia/Set.cpp: In member function ‘void AssocPairedSet::print_total_size()’: ../minia/Set.cpp:298:55: warning: format ‘%li’ expects argument of type ‘long int’, but argument 2 has type ‘std::vector::size_type {aka unsigned int}’ [-Wformat=] printf("Assoc paired set size: %li\n",liste.size()); ~~~~~~~~~~~~^ ../minia/Set.cpp:299:110: warning: format ‘%li’ expects argument of type ‘long int’, but argument 2 has type ‘std::vector::size_type {aka unsigned int}’ [-Wformat=] printf("Assoc paired set capacity: listekmer %li liste val%li\n",liste.capacity(),liste_value.capacity()); ~~~~~~~~~~~~~~~~ ^ ../minia/Set.cpp:299:110: warning: format ‘%li’ expects argument of type ‘long int’, but argument 3 has type ‘std::vector::size_type {aka unsigned int}’ [-Wformat=] ../minia/Set.cpp:302:12: warning: format ‘%li’ expects argument of type ‘long int’, but argument 2 has type ‘std::vector::size_type {aka unsigned int}’ [-Wformat=] ../minia/Set.cpp:300:48: printf("%li *%li + %li* %li = %li MB \n",liste.capacity(),sizeof(set_elem),liste_value.capacity(),sizeof(set_value_t), ~~~~~~~~~~~~~~~~ ../minia/Set.cpp:302:12: ); ^ ../minia/Set.cpp:302:12: warning: format ‘%li’ expects argument of type ‘long int’, but argument 3 has type ‘unsigned int’ [-Wformat=] ../minia/Set.cpp:302:12: warning: format ‘%li’ expects argument of type ‘long int’, but argument 4 has type ‘std::vector::size_type {aka unsigned int}’ [-Wformat=] ../minia/Set.cpp:302:12: warning: format ‘%li’ expects argument of type ‘long int’, but argument 5 has type ‘unsigned int’ [-Wformat=] ../minia/Set.cpp:302:12: warning: format ‘%li’ expects argument of type ‘long int’, but argument 6 has type ‘std::vector::size_type {aka unsigned int}’ [-Wformat=] ../minia/Set.cpp: In member function ‘void AssocPairedSet::load(char*)’: ../minia/Set.cpp:290:10: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fread(&liste_value[0], sizeof(pair_nt_kmer_t), liste_value.size(), file_data); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/7/vector:69:0, from ../minia/Set.h:10, from ../minia/Set.cpp:1: /usr/include/c++/7/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const long long unsigned int&}; _Tp = long long unsigned int; _Alloc = std::allocator]’: /usr/include/c++/7/bits/vector.tcc:394:7: note: parameter passing for argument of type ‘std::vector::iterator {aka __gnu_cxx::__normal_iterator >}’ changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/7/vector:64:0, from ../minia/Set.h:10, from ../minia/Set.cpp:1: /usr/include/c++/7/bits/stl_vector.h: In member function ‘void AssocPairedSet::load_branching(BinaryBank*)’: /usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 _M_realloc_insert(end(), __x); ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /usr/include/c++/7/bits/stl_algo.h:61:0, from /usr/include/c++/7/algorithm:62, from ../minia/Pool.h:11, from ../minia/Hash16.h:12, from ../minia/Set.h:6, from ../minia/Set.cpp:1: /usr/include/c++/7/bits/stl_heap.h: In function ‘void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = long long unsigned int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’: /usr/include/c++/7/bits/stl_heap.h:214:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, ^~~~~~~~~~~~~ In file included from /usr/include/c++/7/algorithm:62:0, from ../minia/Pool.h:11, from ../minia/Hash16.h:12, from ../minia/Set.h:6, from ../minia/Set.cpp:1: /usr/include/c++/7/bits/stl_algo.h: In function ‘void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’: /usr/include/c++/7/bits/stl_algo.h:1940:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 __introsort_loop(_RandomAccessIterator __first, ^~~~~~~~~~~~~~~~ /usr/include/c++/7/bits/stl_algo.h:1940:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/include/c++/7/bits/stl_algo.h:1954:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 std::__introsort_loop(__cut, __last, __depth_limit, __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/7/bits/stl_algo.h: In member function ‘virtual void AssocPairedSet::finalize()’: /usr/include/c++/7/bits/stl_algo.h:1968:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 std::__introsort_loop(__first, __last, ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ std::__lg(__last - __first) * 2, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __comp); ~~~~~~~ /usr/include/c++/7/bits/stl_algo.h: In member function ‘virtual void ListSet::finalize()’: /usr/include/c++/7/bits/stl_algo.h:1968:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 std::__introsort_loop(__first, __last, ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ std::__lg(__last - __first) * 2, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __comp); ~~~~~~~ /usr/include/c++/7/bits/stl_algo.h: In member function ‘virtual void AssocSet::finalize()’: /usr/include/c++/7/bits/stl_algo.h:1968:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 std::__introsort_loop(__first, __last, ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ std::__lg(__last - __first) * 2, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __comp); ~~~~~~~ g++ -o ../minia/Utils.o -c ../minia/Utils.cpp -g -O2 -fdebug-prefix-map=/<>/kissnp2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O4 -lz -DMINIA_IS_IN_PARENT_FOLDER ../minia/Utils.cpp: In function ‘void end_kmer_count_partition(bool, Hash16*)’: ../minia/Utils.cpp:187:14: warning: ignoring return value of ‘int ftruncate(int, __off_t)’, declared with attribute warn_unused_result [-Wunused-result] ftruncate(fileno(F_kmercpt_write), 0); //erase previous file ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../minia/Utils.cpp:199:14: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fread(&cptk, sizeof(cptk), 1, F_kmercpt_read); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../minia/Utils.cpp:225:18: warning: ignoring return value of ‘int ftruncate(int, __off_t)’, declared with attribute warn_unused_result [-Wunused-result] ftruncate(fileno(F_kmercpt_read), 0); //erase previous file ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -o ../minia/SortingCount.o -c ../minia/SortingCount.cpp -g -O2 -fdebug-prefix-map=/<>/kissnp2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O4 -lz -DMINIA_IS_IN_PARENT_FOLDER ../minia/SortingCount.cpp: In function ‘void sorting_count(Bank*, char*, int, int, bool, int, bool)’: ../minia/SortingCount.cpp:56:15: warning: ignoring return value of ‘char* getcwd(char*, size_t)’, declared with attribute warn_unused_result [-Wunused-result] getcwd(current_path,sizeof(current_path)); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../minia/SortingCount.cpp:283:15: warning: ignoring return value of ‘int system(const char*)’, declared with attribute warn_unused_result [-Wunused-result] system("echo 3 > /proc/sys/vm/drop_caches"); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../minia/SortingCount.cpp:537:19: warning: ignoring return value of ‘int system(const char*)’, declared with attribute warn_unused_result [-Wunused-result] system("echo 3 > /proc/sys/vm/drop_caches"); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/7/vector:69:0, from ../minia/SortingCount.h:8, from ../minia/SortingCount.cpp:1: /usr/include/c++/7/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const long long unsigned int&}; _Tp = long long unsigned int; _Alloc = std::allocator]’: /usr/include/c++/7/bits/vector.tcc:394:7: note: parameter passing for argument of type ‘std::vector::iterator {aka __gnu_cxx::__normal_iterator >}’ changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/7/bits/stl_algo.h:61:0, from /usr/include/c++/7/algorithm:62, from ../minia/Utils.h:9, from ../minia/SortingCount.h:17, from ../minia/SortingCount.cpp:1: /usr/include/c++/7/bits/stl_heap.h: In function ‘void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = long long unsigned int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’: /usr/include/c++/7/bits/stl_heap.h:214:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, ^~~~~~~~~~~~~ In file included from /usr/include/c++/7/algorithm:62:0, from ../minia/Utils.h:9, from ../minia/SortingCount.h:17, from ../minia/SortingCount.cpp:1: /usr/include/c++/7/bits/stl_algo.h: In function ‘void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’: /usr/include/c++/7/bits/stl_algo.h:1940:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 __introsort_loop(_RandomAccessIterator __first, ^~~~~~~~~~~~~~~~ /usr/include/c++/7/bits/stl_algo.h:1940:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/include/c++/7/bits/stl_algo.h:1954:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 std::__introsort_loop(__cut, __last, __depth_limit, __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/7/vector:64:0, from ../minia/SortingCount.h:8, from ../minia/SortingCount.cpp:1: /usr/include/c++/7/bits/stl_vector.h: In function ‘void sorting_count(Bank*, char*, int, int, bool, int, bool)’: /usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 _M_realloc_insert(end(), __x); ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /usr/include/c++/7/algorithm:62:0, from ../minia/Utils.h:9, from ../minia/SortingCount.h:17, from ../minia/SortingCount.cpp:1: /usr/include/c++/7/bits/stl_algo.h:1968:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 std::__introsort_loop(__first, __last, ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ std::__lg(__last - __first) * 2, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __comp); ~~~~~~~ g++ -o ../minia/Debloom.o -c ../minia/Debloom.cpp -g -O2 -fdebug-prefix-map=/<>/kissnp2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O4 -lz -DMINIA_IS_IN_PARENT_FOLDER ../minia/Debloom.cpp: In function ‘void end_debloom_partition(bool)’: ../minia/Debloom.cpp:29:11: warning: ignoring return value of ‘int ftruncate(int, __off_t)’, declared with attribute warn_unused_result [-Wunused-result] ftruncate(fileno(F_debloom_write), 0); //erase previous file ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -o ../minia/OAHash.o -c ../minia/OAHash.cpp -g -O2 -fdebug-prefix-map=/<>/kissnp2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O4 -lz -DMINIA_IS_IN_PARENT_FOLDER g++ -o Kmer_for_kissnp2.o -c Kmer_for_kissnp2.cpp -g -O2 -fdebug-prefix-map=/<>/kissnp2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O4 -lz -DMINIA_IS_IN_PARENT_FOLDER g++ -o SNP.o -c SNP.cpp -g -O2 -fdebug-prefix-map=/<>/kissnp2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O4 -lz -DMINIA_IS_IN_PARENT_FOLDER SNP.cpp: In member function ‘void Bubble::find_bubbles(const char*, int, int)’: SNP.cpp:858:49: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘long unsigned int’ [-Wformat=] {printf("%c \t %llu %%",13,(nb*100)/nbel); ~~~~~~~~~~~~~^ g++ -o filter.o -c filter.cpp -g -O2 -fdebug-prefix-map=/<>/kissnp2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O4 -lz -DMINIA_IS_IN_PARENT_FOLDER g++ -o IterativeExtensions.o -c IterativeExtensions.cpp -g -O2 -fdebug-prefix-map=/<>/kissnp2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O4 -lz -DMINIA_IS_IN_PARENT_FOLDER IterativeExtensions.cpp: In static member function ‘static void IterativeExtensions::construct_linear_seqs(std::__cxx11::string, std::__cxx11::string, int, std::__cxx11::string, int, int, parcours_t, bool)’: IterativeExtensions.cpp:237:126: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘long long int’ [-Wformat=] printf("... XXX Stopped extending node %s because %d nodes reached. Was at depth %d.\n", node, nbNodes, depth); ^ In file included from /usr/include/c++/7/vector:69:0, from ../minia/Set.h:10, from ../minia/Terminator.h:13, from IterativeExtensions.h:42, from IterativeExtensions.cpp:37: /usr/include/c++/7/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const kmer_strand_depth&}; _Tp = kmer_strand_depth; _Alloc = std::allocator]’: /usr/include/c++/7/bits/vector.tcc:394:7: note: parameter passing for argument of type ‘std::vector::iterator {aka __gnu_cxx::__normal_iterator >}’ changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/7/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {kmer_strand_depth}; _Tp = kmer_strand_depth; _Alloc = std::allocator]’: /usr/include/c++/7/bits/vector.tcc:394:7: note: parameter passing for argument of type ‘std::vector::iterator {aka __gnu_cxx::__normal_iterator >}’ changed in GCC 7.1 In file included from /usr/include/c++/7/vector:64:0, from ../minia/Set.h:10, from ../minia/Terminator.h:13, from IterativeExtensions.h:42, from IterativeExtensions.cpp:37: /usr/include/c++/7/bits/stl_vector.h: In static member function ‘static void IterativeExtensions::construct_linear_seqs_paired(std::__cxx11::string, std::__cxx11::string, int, std::__cxx11::string, int, int)’: /usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 _M_realloc_insert(end(), __x); ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /usr/include/c++/7/vector:69:0, from ../minia/Set.h:10, from ../minia/Terminator.h:13, from IterativeExtensions.h:42, from IterativeExtensions.cpp:37: /usr/include/c++/7/bits/vector.tcc:105:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/7/bits/vector.tcc:105:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/7/vector:64:0, from ../minia/Set.h:10, from ../minia/Terminator.h:13, from IterativeExtensions.h:42, from IterativeExtensions.cpp:37: /usr/include/c++/7/bits/stl_vector.h: In static member function ‘static void IterativeExtensions::construct_linear_seqs(std::__cxx11::string, std::__cxx11::string, int, std::__cxx11::string, int, int, parcours_t, bool)’: /usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 _M_realloc_insert(end(), __x); ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /usr/include/c++/7/vector:69:0, from ../minia/Set.h:10, from ../minia/Terminator.h:13, from IterativeExtensions.h:42, from IterativeExtensions.cpp:37: /usr/include/c++/7/bits/vector.tcc:105:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/7/vector:64:0, from ../minia/Set.h:10, from ../minia/Terminator.h:13, from IterativeExtensions.h:42, from IterativeExtensions.cpp:37: /usr/include/c++/7/bits/stl_vector.h: In static member function ‘static void IterativeExtensions::construct_linear_seqs(std::__cxx11::string, int, std::__cxx11::string)’: /usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 _M_realloc_insert(end(), __x); ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /usr/include/c++/7/vector:69:0, from ../minia/Set.h:10, from ../minia/Terminator.h:13, from IterativeExtensions.h:42, from IterativeExtensions.cpp:37: /usr/include/c++/7/bits/vector.tcc:105:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -o commons.o -c commons.cpp -g -O2 -fdebug-prefix-map=/<>/kissnp2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O4 -lz -DMINIA_IS_IN_PARENT_FOLDER g++ -o kissnp2 ../minia/Pool.o ../minia/Bank.o ../minia/Bloom.o ../minia/Hash16.o ../minia/Terminator.o ../minia/Kmer.o ../minia/Traversal.o ../minia/LinearCounter.o ../minia/Set.o ../minia/Utils.o ../minia/SortingCount.o ../minia/Debloom.o ../minia/OAHash.o Kmer_for_kissnp2.o SNP.o filter.o IterativeExtensions.o commons.o kissnp2.cpp -g -O2 -fdebug-prefix-map=/<>/kissnp2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O4 -lz -DMINIA_IS_IN_PARENT_FOLDER -Wl,-Bsymbolic-functions -Wl,-z,relro kissnp2.cpp: In function ‘int main(int, char**)’: kissnp2.cpp:256:85: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 2 has type ‘unsigned int’ [-Wformat=] printf("Max kmer size on this compiled version is %lu\n",sizeof(kmer_type)*2); ^ make[2]: Leaving directory '/<>/kissnp2' cd kissreads && make k=29 make[2]: Entering directory '/<>/kissreads' gcc -o src/coherent_algorithm.o -c src/coherent_algorithm.c -g -O2 -fdebug-prefix-map=/<>/kissreads=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -lz -I./include/ gcc -o src/commons.o -c src/commons.c -g -O2 -fdebug-prefix-map=/<>/kissreads=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -lz -I./include/ gcc -o src/couple.o -c src/couple.c -g -O2 -fdebug-prefix-map=/<>/kissreads=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -lz -I./include/ gcc -o src/extension_algorithm.o -c src/extension_algorithm.c -g -O2 -fdebug-prefix-map=/<>/kissreads=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -lz -I./include/ src/extension_algorithm.c: In function ‘read_coherence’: src/extension_algorithm.c:312:23: warning: unused variable ‘j’ [-Wunused-variable] int read_len, i, ii, j, starter_id, pwi, stop, read_coherence; ^ gcc -o src/fragment_index.o -c src/fragment_index.c -g -O2 -fdebug-prefix-map=/<>/kissreads=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -lz -I./include/ src/fragment_index.c: In function ‘index_starters_from_input_file’: src/fragment_index.c:148:7: warning: unused variable ‘validSeed’ [-Wunused-variable] char validSeed; ^~~~~~~~~ src/fragment_index.c:147:8: warning: unused variable ‘j’ [-Wunused-variable] int i,j,z,stop; ^ gcc -o src/kissReads.o -c src/kissReads.c -g -O2 -fdebug-prefix-map=/<>/kissreads=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -lz -I./include/ gcc -o src/list.o -c src/list.c -g -O2 -fdebug-prefix-map=/<>/kissreads=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -lz -I./include/ gcc -o src/outputs.o -c src/outputs.c -g -O2 -fdebug-prefix-map=/<>/kissreads=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -lz -I./include/ gcc -o src/interface_libchash.o -c src/interface_libchash.c -g -O2 -fdebug-prefix-map=/<>/kissreads=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -lz -I./include/ gcc -o src/libchash.o -c src/libchash.c -g -O2 -fdebug-prefix-map=/<>/kissreads=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -lz -I./include/ In file included from src/libchash.c:126:0: src/libchash.c: In function ‘EntriesUpto’: src/libchash.c:468:14: warning: comparison with string literal results in unspecified behavior [-Waddress] assert("" == "word size is too big in EntriesUpto()"); ^ src/libchash.c:468:14: warning: comparison with string literal results in unspecified behavior [-Waddress] assert("" == "word size is too big in EntriesUpto()"); ^ src/libchash.c: In function ‘Delete’: src/libchash.c:165:7: warning: suggest explicit braces to avoid ambiguous ‘else’ [-Wdangling-else] if ( STORES_PTR(ht) && (ht)->fSaveKeys ) \ ^ ./include/libchash.h:165:40: note: in expansion of macro ‘FREE_KEY’ FREE_KEY(ht, (bck)->key); } while ( 0 ) ^~~~~~~~ src/libchash.c:1119:4: note: in expansion of macro ‘SET_BCK_DELETED’ SET_BCK_DELETED(ht, ht->posLastFind); /* find set this, how nice */ ^~~~~~~~~~~~~~~ src/libchash.c: In function ‘ClearHashTable’: src/libchash.c:165:7: warning: suggest explicit braces to avoid ambiguous ‘else’ [-Wdangling-else] if ( STORES_PTR(ht) && (ht)->fSaveKeys ) \ ^ src/libchash.c:1183:3: note: in expansion of macro ‘FREE_KEY’ FREE_KEY(ht, bck->key); ^~~~~~~~ src/libchash.c: In function ‘HashFirstBucket’: src/libchash.c:1289:10: warning: suggest explicit braces to avoid ambiguous ‘else’ [-Wdangling-else] if ( !IS_BCK_DELETED(retval) ) ^ src/libchash.c: In function ‘HashNextBucket’: src/libchash.c:1299:10: warning: suggest explicit braces to avoid ambiguous ‘else’ [-Wdangling-else] if ( !IS_BCK_DELETED(retval) ) ^ src/libchash.c: In function ‘HashDoLoad’: src/libchash.c:1431:10: warning: suggest explicit braces to avoid ambiguous ‘else’ [-Wdangling-else] if ( dataRead != NULL ) /* if it's null, we're done */ ^ src/libchash.c: In function ‘HashFind’: src/libchash.c:193:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(&_ul, sizeof(_ul), 1, (fp)); \ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/libchash.c:220:7: note: in expansion of macro ‘READ_UL’ READ_UL((ht)->fpData, cchData); \ ^~~~~~~ src/libchash.c:1221:4: note: in expansion of macro ‘LOAD_AND_RETURN’ LOAD_AND_RETURN(ht, Find(ht, KEY_TRUNC(ht, key), NULL)); ^~~~~~~~~~~~~~~ src/libchash.c: In function ‘HashFindLast’: src/libchash.c:193:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(&_ul, sizeof(_ul), 1, (fp)); \ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/libchash.c:220:7: note: in expansion of macro ‘READ_UL’ READ_UL((ht)->fpData, cchData); \ ^~~~~~~ src/libchash.c:1226:4: note: in expansion of macro ‘LOAD_AND_RETURN’ LOAD_AND_RETURN(ht, ht->posLastFind); ^~~~~~~~~~~~~~~ src/libchash.c: In function ‘HashFirstBucket’: src/libchash.c:193:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(&_ul, sizeof(_ul), 1, (fp)); \ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/libchash.c:220:7: note: in expansion of macro ‘READ_UL’ READ_UL((ht)->fpData, cchData); \ ^~~~~~~ src/libchash.c:1290:3: note: in expansion of macro ‘LOAD_AND_RETURN’ LOAD_AND_RETURN(ht, retval); ^~~~~~~~~~~~~~~ src/libchash.c: In function ‘HashNextBucket’: src/libchash.c:193:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(&_ul, sizeof(_ul), 1, (fp)); \ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/libchash.c:220:7: note: in expansion of macro ‘READ_UL’ READ_UL((ht)->fpData, cchData); \ ^~~~~~~ src/libchash.c:1300:3: note: in expansion of macro ‘LOAD_AND_RETURN’ LOAD_AND_RETURN(ht, retval); ^~~~~~~~~~~~~~~ src/libchash.c: In function ‘HashDoLoad’: src/libchash.c:1407:4: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(szMagicKey, 1, 4, fp); ^~~~~~~~~~~~~~~~~~~~~~~~~~~ src/libchash.c:193:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(&_ul, sizeof(_ul), 1, (fp)); \ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/libchash.c:1416:4: note: in expansion of macro ‘READ_UL’ READ_UL(fp, ht->cchKey); ^~~~~~~ src/libchash.c:193:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(&_ul, sizeof(_ul), 1, (fp)); \ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/libchash.c:1417:4: note: in expansion of macro ‘READ_UL’ READ_UL(fp, ht->cItems); ^~~~~~~ src/libchash.c:193:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(&_ul, sizeof(_ul), 1, (fp)); \ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/libchash.c:1418:4: note: in expansion of macro ‘READ_UL’ READ_UL(fp, ht->cDeletedItems); ^~~~~~~ src/libchash.c:193:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(&_ul, sizeof(_ul), 1, (fp)); \ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/libchash.c:1421:4: note: in expansion of macro ‘READ_UL’ READ_UL(fp, cchKey); ^~~~~~~ src/libchash.c:1423:4: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(rgchKeys, 1, cchKey, fp); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/libchash.c:193:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(&_ul, sizeof(_ul), 1, (fp)); \ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/libchash.c:1428:7: note: in expansion of macro ‘READ_UL’ READ_UL(fp, bck->data); /* all we need if dataRead is NULL */ ^~~~~~~ src/libchash.c: In function ‘SparseRead’: src/libchash.c:193:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(&_ul, sizeof(_ul), 1, (fp)); \ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/libchash.c:622:4: note: in expansion of macro ‘READ_UL’ READ_UL(fp, cBuckets); /* actually, cBuckets is stored */ ^~~~~~~ src/libchash.c:193:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(&_ul, sizeof(_ul), 1, (fp)); \ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/libchash.c:627:3: note: in expansion of macro ‘READ_UL’ READ_UL(fp, (*pbinSparse)[i].bmOccupied[j]); ^~~~~~~ At top level: src/libchash.c:789:14: warning: ‘DenseMemory’ defined but not used [-Wunused-function] static ulong DenseMemory(ulong cBuckets, ulong cOccupied) ^~~~~~~~~~~ src/libchash.c:767:14: warning: ‘DenseRead’ defined but not used [-Wunused-function] static ulong DenseRead(FILE *fp, DenseBin **pbin) ^~~~~~~~~ src/libchash.c:748:13: warning: ‘DenseWrite’ defined but not used [-Wunused-function] static void DenseWrite(FILE *fp, DenseBin *bin, ulong cBuckets) ^~~~~~~~~~ src/libchash.c:739:21: warning: ‘DenseFirstBucket’ defined but not used [-Wunused-function] static DenseBucket *DenseFirstBucket(DenseIterator *iter, ^~~~~~~~~~~~~~~~ src/libchash.c:710:21: warning: ‘DenseInsert’ defined but not used [-Wunused-function] static DenseBucket *DenseInsert(DenseBin *bin, DenseBucket *bckInsert, ^~~~~~~~~~~ src/libchash.c:691:18: warning: ‘DenseFree’ defined but not used [-Wunused-function] static DenseBin *DenseFree(DenseBin *bin, ulong cBuckets) ^~~~~~~~~ gcc -o kissreads src/coherent_algorithm.o src/commons.o src/couple.o src/extension_algorithm.o src/fragment_index.o src/kissReads.o src/list.o src/outputs.o src/interface_libchash.o src/libchash.o -g -O2 -fdebug-prefix-map=/<>/kissreads=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -lz -Wl,-Bsymbolic-functions -Wl,-z,relro -Wall -lm -O3 -lz ################# # Compilation OK# ################# make[2]: Leaving directory '/<>/kissreads' make[1]: Leaving directory '/<>' create-stamp debian/debhelper-build-stamp fakeroot debian/rules binary-arch dh binary-arch dh_testroot -a dh_prep -a debian/rules override_dh_install make[1]: Entering directory '/<>' cp output_analyses/discoSnp_to_genotypes.py output_analyses/discoSnp_to_genotypes cp output_analyses/discoSnp_to_csv.py output_analyses/discoSnp_to_csv help2man --help-option=-h --no-discard-stderr --version-string=1.2.6 kissnp2/kissnp2 > kissnp2.1 help2man --help-option=-h --no-discard-stderr --version-string=1.2.6 kissreads/kissreads > kissreads.1 dh_install make[1]: Leaving directory '/<>' dh_installdocs -a dh_installchangelogs -a dh_installman -a dh_perl -a dh_link -a dh_strip_nondeterminism -a dh_compress -a dh_fixperms -a dh_missing -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dh_installdeb -a dh_gencontrol -a dh_md5sums -a dh_builddeb -a INFO: pkgstriptranslations version 138.18.04.0 pkgstriptranslations: processing discosnp (in debian/discosnp); do_strip: , oemstrip: pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/discosnp/DEBIAN/control, package discosnp, directory debian/discosnp pkgstripfiles: Running PNG optimization (using 4 cpus) for package discosnp ... pkgstripfiles: No PNG files. dpkg-deb: building package 'discosnp' in '../discosnp_1.2.6-2_armhf.deb'. dpkg-genbuildinfo --build=any dpkg-genchanges --build=any -mLaunchpad Build Daemon >../discosnp_1.2.6-2_armhf.changes dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included) dpkg-source --after-build discosnp-1.2.6 dpkg-buildpackage: info: binary-only upload (no source included) -------------------------------------------------------------------------------- Build finished at 20190222-0903 Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Post Build Chroot | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ discosnp_1.2.6-2_armhf.changes: ------------------------------- Format: 1.8 Date: Tue, 14 Nov 2017 10:05:31 +0100 Source: discosnp Binary: discosnp Architecture: armhf Version: 1.2.6-2 Distribution: bionic Urgency: medium Maintainer: Launchpad Build Daemon Changed-By: Andreas Tille Description: discosnp - discovering Single Nucleotide Polymorphism from raw set(s) of rea Changes: discosnp (1.2.6-2) unstable; urgency=medium . * Secure URI in watch file * Mention that program is superseded by DiscoSnp++ * Moved packaging from SVN to Git * debhelper 10 * d/rules: do not parse d/changelog * Standards-Version: 4.1.1 * DEP5 * Remove unused lintian override Checksums-Sha1: 5d30df97120c5557486e42b63a6677be66853c26 5202 discosnp_1.2.6-2_armhf.buildinfo c9af87feef29f9bbb77c6a152687ccf0b5ab5e33 136832 discosnp_1.2.6-2_armhf.deb Checksums-Sha256: 4d0cd6fcf1ab298e9a0466d9cf0a371a29c365fa3ac6cf27914e69c44944f985 5202 discosnp_1.2.6-2_armhf.buildinfo 6b9c37149a2f7e2b8b703a6b603e3bcb6a4cfdab48abfceb66b5e6c1e0f8fc40 136832 discosnp_1.2.6-2_armhf.deb Files: a72d982acfd461698446c71686332344 5202 science optional discosnp_1.2.6-2_armhf.buildinfo 4de1fc5850e3f3bd074a424b8e8cb69b 136832 science optional discosnp_1.2.6-2_armhf.deb +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ discosnp_1.2.6-2_armhf.deb -------------------------- new debian package, version 2.0. size 136832 bytes: control archive=1324 bytes. 1175 bytes, 27 lines control 850 bytes, 12 lines md5sums Package: discosnp Version: 1.2.6-2 Architecture: armhf Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 247 Depends: libc6 (>= 2.27), libgcc1 (>= 1:3.5), libstdc++6 (>= 5.2), zlib1g (>= 1:1.2.3.4), bc, python Section: science Priority: optional Homepage: http://colibread.inria.fr/discosnp/ Description: discovering Single Nucleotide Polymorphism from raw set(s) of reads Software discoSnp is designed for discovering Single Nucleotide Polymorphism (SNP) from raw set(s) of reads obtained with Next Generation Sequencers (NGS). . Note that number of input read sets is not constrained, it can be one, two, or more. Note also that no other data as reference genome or annotations are needed. . The software is composed by two modules. First module, kissnp2, detects SNPs from read sets. A second module, kissreads, enhance the kissnp2 results by computing per read set and for each found SNP: . 1) its mean read coverage 2) the (phred) quality of reads generating the polymorphism. . This program is superseded by DiscoSnp++. drwxr-xr-x root/root 0 2017-11-14 09:05 ./ drwxr-xr-x root/root 0 2017-11-14 09:05 ./usr/ drwxr-xr-x root/root 0 2017-11-14 09:05 ./usr/bin/ -rwxr-xr-x root/root 1612 2017-11-14 09:05 ./usr/bin/discoSnp_to_csv -rwxr-xr-x root/root 2099 2017-11-14 09:05 ./usr/bin/discoSnp_to_genotypes -rwxr-xr-x root/root 124532 2017-11-14 09:05 ./usr/bin/kissnp2 -rwxr-xr-x root/root 46500 2017-11-14 09:05 ./usr/bin/kissreads drwxr-xr-x root/root 0 2017-11-14 09:05 ./usr/share/ drwxr-xr-x root/root 0 2017-11-14 09:05 ./usr/share/doc/ drwxr-xr-x root/root 0 2017-11-14 09:05 ./usr/share/doc/discosnp/ -rw-r--r-- root/root 465 2017-11-14 09:05 ./usr/share/doc/discosnp/README.Debian -rw-r--r-- root/root 4896 2014-07-28 15:18 ./usr/share/doc/discosnp/README.txt.gz -rw-r--r-- root/root 594 2017-11-14 09:05 ./usr/share/doc/discosnp/changelog.Debian.gz -rw-r--r-- root/root 25363 2017-11-14 09:05 ./usr/share/doc/discosnp/copyright drwxr-xr-x root/root 0 2017-11-14 09:05 ./usr/share/doc/discosnp/examples/ drwxr-xr-x root/root 0 2017-11-14 09:05 ./usr/share/doc/discosnp/examples/data_sample/ -rw-r--r-- root/root 12531 2013-10-14 18:51 ./usr/share/doc/discosnp/examples/data_sample/reads_sequence1.fasta.gz -rw-r--r-- root/root 13427 2017-11-14 09:05 ./usr/share/doc/discosnp/examples/data_sample/reads_sequence2.fasta.gz drwxr-xr-x root/root 0 2017-11-14 09:05 ./usr/share/man/ drwxr-xr-x root/root 0 2017-11-14 09:05 ./usr/share/man/man1/ -rw-r--r-- root/root 1273 2017-11-14 09:05 ./usr/share/man/man1/kissnp2.1.gz -rw-r--r-- root/root 1407 2017-11-14 09:05 ./usr/share/man/man1/kissreads.1.gz +------------------------------------------------------------------------------+ | Post Build | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not removing build depends: as requested +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: armhf Build-Space: 6916 Build-Time: 76 Distribution: bionic Host Architecture: armhf Install-Time: 23 Job: discosnp_1.2.6-2.dsc Machine Architecture: arm64 Package: discosnp Package-Time: 102 Source-Version: 1.2.6-2 Space: 6916 Status: successful Version: 1.2.6-2 -------------------------------------------------------------------------------- Finished at 20190222-0903 Build needed 00:01:42, 6916k disc space RUN: /usr/share/launchpad-buildd/slavebin/in-target scan-for-processes --backend=chroot --series=bionic --arch=armhf PACKAGEBUILD-16111743 Scanning for processes to kill in build PACKAGEBUILD-16111743