https://launchpad.net/ubuntu/+archive/test-rebuild-20190614/+build/16961252 RUN: /usr/share/launchpad-buildd/bin/builder-prep Kernel version: Linux bos02-s390x-004 4.4.0-151-generic #178-Ubuntu SMP Tue Jun 11 08:33:12 UTC 2019 s390x Buildd toolchain package versions: launchpad-buildd_176 python-lpbuildd_176 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 Jun 20:08:19 ntpdate[1839]: adjust time server 10.211.37.1 offset -0.000005 sec RUN: /usr/share/launchpad-buildd/bin/in-target unpack-chroot --backend=chroot --series=eoan --arch=s390x PACKAGEBUILD-16961252 --image-type chroot /home/buildd/filecache-default/5f92d5ecab7ce0d953bb2def2bd7e5fe5fb7c904 Creating target for build PACKAGEBUILD-16961252 RUN: /usr/share/launchpad-buildd/bin/in-target mount-chroot --backend=chroot --series=eoan --arch=s390x PACKAGEBUILD-16961252 Starting target for build PACKAGEBUILD-16961252 RUN: /usr/share/launchpad-buildd/bin/in-target override-sources-list --backend=chroot --series=eoan --arch=s390x PACKAGEBUILD-16961252 'deb http://ppa.launchpad.net/ubuntu-toolchain-r/ppa/ubuntu eoan main' 'deb http://ftpmaster.internal/ubuntu eoan main restricted universe multiverse' Overriding sources.list in build-PACKAGEBUILD-16961252 RUN: /usr/share/launchpad-buildd/bin/in-target add-trusted-keys --backend=chroot --series=eoan --arch=s390x PACKAGEBUILD-16961252 Adding trusted keys to build-PACKAGEBUILD-16961252 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 /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) /etc/apt/trusted.gpg.d/ubuntu-keyring-2018-archive.gpg ------------------------------------------------------ pub rsa4096 2018-09-17 [SC] F6EC B376 2474 EDA9 D21B 7022 8719 20D1 991B C93C uid [ unknown] Ubuntu Archive Automatic Signing Key (2018) RUN: /usr/share/launchpad-buildd/bin/in-target update-debian-chroot --backend=chroot --series=eoan --arch=s390x PACKAGEBUILD-16961252 Updating target for build PACKAGEBUILD-16961252 Get:1 http://ftpmaster.internal/ubuntu eoan InRelease [255 kB] Get:2 http://ppa.launchpad.net/ubuntu-toolchain-r/ppa/ubuntu eoan InRelease [20.7 kB] Get:3 http://ppa.launchpad.net/ubuntu-toolchain-r/ppa/ubuntu eoan/main s390x Packages [22.6 kB] Get:4 http://ftpmaster.internal/ubuntu eoan/main s390x Packages [922 kB] Get:5 http://ppa.launchpad.net/ubuntu-toolchain-r/ppa/ubuntu eoan/main Translation-en [12.9 kB] Get:6 http://ftpmaster.internal/ubuntu eoan/main Translation-en [503 kB] Get:7 http://ftpmaster.internal/ubuntu eoan/restricted s390x Packages [1196 B] Get:8 http://ftpmaster.internal/ubuntu eoan/restricted Translation-en [5528 B] Get:9 http://ftpmaster.internal/ubuntu eoan/universe s390x Packages [8649 kB] Get:10 http://ftpmaster.internal/ubuntu eoan/universe Translation-en [5283 kB] Get:11 http://ftpmaster.internal/ubuntu eoan/multiverse s390x Packages [120 kB] Get:12 http://ftpmaster.internal/ubuntu eoan/multiverse Translation-en [112 kB] Fetched 15.9 MB in 3s (4806 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: libisl19 libreadline7 Use 'sudo apt autoremove' to remove them. The following NEW packages will be installed: gcc-9-base libisl21 libpcre2-8-0 libreadline8 The following packages will be upgraded: adduser advancecomp apt base-files base-passwd bash binutils binutils-common binutils-s390x-linux-gnu bsdutils build-essential ca-certificates coreutils cpp cpp-8 dash debconf debianutils diffutils dmsetup dpkg dpkg-dev e2fslibs e2fsprogs fdisk findutils g++ g++-8 gcc gcc-8 gcc-8-base gpg gpg-agent gpgconf gpgv grep gzip init init-system-helpers libacl1 libapparmor1 libapt-pkg5.0 libargon2-1 libasan5 libassuan0 libatomic1 libattr1 libaudit-common libaudit1 libbinutils libblkid1 libc-bin libc-dev-bin libc6 libc6-dev libcap-ng0 libcap2 libcc1-0 libcom-err2 libcomerr2 libcryptsetup12 libdb5.3 libdebconfclient0 libdevmapper1.02.1 libdpkg-perl libext2fs2 libfdisk1 libgcc-8-dev libgcc1 libgcrypt20 libgdbm-compat4 libgdbm6 libgnutls30 libgomp1 libgpg-error0 libhogweed4 libidn11 libitm1 libjson-c3 libkmod2 liblz4-1 liblzma5 libmount1 libmpfr6 libncurses6 libncursesw6 libnettle6 libp11-kit0 libpam-modules libpam-modules-bin libpam-runtime libpam0g libpcre3 libperl5.28 libpng16-16 libprocps7 libseccomp2 libselinux1 libsemanage-common libsemanage1 libsepol1 libslang2 libsmartcols1 libsqlite3-0 libss2 libssl1.1 libstdc++-8-dev libstdc++6 libsystemd0 libtinfo6 libubsan1 libudev1 libunistring2 libuuid1 libzstd1 linux-libc-dev login lsb-base mount multiarch-support ncurses-base ncurses-bin openssl optipng passwd perl perl-base perl-modules-5.28 pinentry-curses pkgbinarymangler procps readline-common sed systemd systemd-sysv sysvinit-utils tar tzdata util-linux xz-utils zlib1g 141 upgraded, 4 newly installed, 0 to remove and 0 not upgraded. Need to get 67.3 MB of archives. After this operation, 13.5 MB of additional disk space will be used. Get:1 http://ppa.launchpad.net/ubuntu-toolchain-r/ppa/ubuntu eoan/main s390x gcc-9-base s390x 9.1.0-4ubuntu1 [18.0 kB] Get:2 http://ftpmaster.internal/ubuntu eoan/main s390x libc6-dev s390x 2.29-0ubuntu2 [2033 kB] Get:3 http://ppa.launchpad.net/ubuntu-toolchain-r/ppa/ubuntu eoan/main s390x libgcc1 s390x 1:9.1.0-4ubuntu1 [24.4 kB] Get:4 http://ppa.launchpad.net/ubuntu-toolchain-r/ppa/ubuntu eoan/main s390x libstdc++6 s390x 9.1.0-4ubuntu1 [497 kB] Get:5 http://ppa.launchpad.net/ubuntu-toolchain-r/ppa/ubuntu eoan/main s390x libgomp1 s390x 9.1.0-4ubuntu1 [81.9 kB] Get:6 http://ppa.launchpad.net/ubuntu-toolchain-r/ppa/ubuntu eoan/main s390x libitm1 s390x 9.1.0-4ubuntu1 [26.9 kB] Get:7 http://ppa.launchpad.net/ubuntu-toolchain-r/ppa/ubuntu eoan/main s390x libatomic1 s390x 9.1.0-4ubuntu1 [8408 B] Get:8 http://ppa.launchpad.net/ubuntu-toolchain-r/ppa/ubuntu eoan/main s390x libasan5 s390x 9.1.0-4ubuntu1 [349 kB] Get:9 http://ppa.launchpad.net/ubuntu-toolchain-r/ppa/ubuntu eoan/main s390x libubsan1 s390x 9.1.0-4ubuntu1 [123 kB] Get:10 http://ppa.launchpad.net/ubuntu-toolchain-r/ppa/ubuntu eoan/main s390x g++-8 s390x 8.3.0-14ubuntu1 [7951 kB] Get:11 http://ftpmaster.internal/ubuntu eoan/main s390x libc-dev-bin s390x 2.29-0ubuntu2 [62.1 kB] Get:12 http://ftpmaster.internal/ubuntu eoan/main s390x linux-libc-dev s390x 5.0.0-17.18 [1058 kB] Get:13 http://ftpmaster.internal/ubuntu eoan/main s390x libc6 s390x 2.29-0ubuntu2 [2249 kB] Get:14 http://ftpmaster.internal/ubuntu eoan/main s390x libc-bin s390x 2.29-0ubuntu2 [513 kB] Get:15 http://ftpmaster.internal/ubuntu eoan/main s390x base-files s390x 10.2ubuntu3 [60.3 kB] Get:16 http://ftpmaster.internal/ubuntu eoan/main s390x debianutils s390x 4.8.6.1 [85.0 kB] Get:17 http://ftpmaster.internal/ubuntu eoan/main s390x bash s390x 5.0-4ubuntu1 [602 kB] Get:18 http://ftpmaster.internal/ubuntu eoan/main s390x bsdutils s390x 1:2.33.1-0.1ubuntu2 [61.2 kB] Get:19 http://ftpmaster.internal/ubuntu eoan/main s390x coreutils s390x 8.30-3ubuntu1 [1221 kB] Get:20 http://ftpmaster.internal/ubuntu eoan/main s390x lsb-base all 10.2019051400ubuntu1 [12.4 kB] Get:21 http://ftpmaster.internal/ubuntu eoan/main s390x tar s390x 1.30+dfsg-6 [230 kB] Get:22 http://ftpmaster.internal/ubuntu eoan/main s390x dpkg s390x 1.19.6ubuntu1 [1110 kB] Get:23 http://ftpmaster.internal/ubuntu eoan/main s390x libperl5.28 s390x 5.28.1-6 [3669 kB] Get:24 http://ftpmaster.internal/ubuntu eoan/main s390x perl s390x 5.28.1-6 [204 kB] Get:25 http://ftpmaster.internal/ubuntu eoan/main s390x perl-base s390x 5.28.1-6 [1420 kB] Get:26 http://ftpmaster.internal/ubuntu eoan/main s390x perl-modules-5.28 all 5.28.1-6 [2818 kB] Get:27 http://ppa.launchpad.net/ubuntu-toolchain-r/ppa/ubuntu eoan/main s390x gcc-8 s390x 8.3.0-14ubuntu1 [7718 kB] Get:28 http://ftpmaster.internal/ubuntu eoan/main s390x libdb5.3 s390x 5.3.28+dfsg1-0.6ubuntu1 [608 kB] Get:29 http://ftpmaster.internal/ubuntu eoan/main s390x libgdbm6 s390x 1.18.1-4 [26.8 kB] Get:30 http://ftpmaster.internal/ubuntu eoan/main s390x libgdbm-compat4 s390x 1.18.1-4 [6260 B] Get:31 http://ftpmaster.internal/ubuntu eoan/main s390x zlib1g s390x 1:1.2.11.dfsg-1ubuntu2 [51.8 kB] Get:32 http://ftpmaster.internal/ubuntu eoan/main s390x debconf all 1.5.72 [122 kB] Get:33 http://ftpmaster.internal/ubuntu eoan/main s390x dash s390x 0.5.10.2-5 [83.6 kB] Get:34 http://ftpmaster.internal/ubuntu eoan/main s390x diffutils s390x 1:3.7-3 [194 kB] Get:35 http://ftpmaster.internal/ubuntu eoan/main s390x findutils s390x 4.6.0+git+20190209-2 [321 kB] Get:36 http://ftpmaster.internal/ubuntu eoan/main s390x grep s390x 3.3-1 [146 kB] Get:37 http://ftpmaster.internal/ubuntu eoan/main s390x gzip s390x 1.10-0ubuntu1 [92.9 kB] Get:38 http://ftpmaster.internal/ubuntu eoan/main s390x libsmartcols1 s390x 2.33.1-0.1ubuntu2 [85.8 kB] Get:39 http://ftpmaster.internal/ubuntu eoan/main s390x libuuid1 s390x 2.33.1-0.1ubuntu2 [21.0 kB] Get:40 http://ftpmaster.internal/ubuntu eoan/main s390x libblkid1 s390x 2.33.1-0.1ubuntu2 [123 kB] Get:41 http://ftpmaster.internal/ubuntu eoan/main s390x libfdisk1 s390x 2.33.1-0.1ubuntu2 [159 kB] Get:42 http://ftpmaster.internal/ubuntu eoan/main s390x libpcre2-8-0 s390x 10.32-5 [99.3 kB] Get:43 http://ftpmaster.internal/ubuntu eoan/main s390x libselinux1 s390x 2.9-1 [64.7 kB] Get:44 http://ftpmaster.internal/ubuntu eoan/main s390x libmount1 s390x 2.33.1-0.1ubuntu2 [133 kB] Get:45 http://ftpmaster.internal/ubuntu eoan/main s390x libncurses6 s390x 6.1+20181013-2ubuntu2 [94.4 kB] Get:46 http://ftpmaster.internal/ubuntu eoan/main s390x libtinfo6 s390x 6.1+20181013-2ubuntu2 [80.2 kB] Get:47 http://ftpmaster.internal/ubuntu eoan/main s390x libncursesw6 s390x 6.1+20181013-2ubuntu2 [120 kB] Get:48 http://ftpmaster.internal/ubuntu eoan/main s390x fdisk s390x 2.33.1-0.1ubuntu2 [111 kB] Get:49 http://ftpmaster.internal/ubuntu eoan/main s390x login s390x 1:4.5-1.1ubuntu2 [262 kB] Get:50 http://ftpmaster.internal/ubuntu eoan/main s390x util-linux s390x 2.33.1-0.1ubuntu2 [960 kB] Get:51 http://ftpmaster.internal/ubuntu eoan/main s390x ncurses-bin s390x 6.1+20181013-2ubuntu2 [160 kB] Get:52 http://ftpmaster.internal/ubuntu eoan/main s390x sed s390x 4.7-1 [187 kB] Get:53 http://ftpmaster.internal/ubuntu eoan/main s390x libdebconfclient0 s390x 0.249ubuntu1 [6192 B] Get:54 http://ftpmaster.internal/ubuntu eoan/main s390x base-passwd s390x 3.5.46 [46.3 kB] Get:55 http://ftpmaster.internal/ubuntu eoan/main s390x init-system-helpers all 1.57 [38.3 kB] Get:56 http://ftpmaster.internal/ubuntu eoan/main s390x ncurses-base all 6.1+20181013-2ubuntu2 [17.9 kB] Get:57 http://ftpmaster.internal/ubuntu eoan/main s390x sysvinit-utils s390x 2.93-8ubuntu1 [19.0 kB] Get:58 http://ftpmaster.internal/ubuntu eoan/main s390x libnettle6 s390x 3.4.1-1 [121 kB] Get:59 http://ftpmaster.internal/ubuntu eoan/main s390x libhogweed4 s390x 3.4.1-1 [138 kB] Get:60 http://ftpmaster.internal/ubuntu eoan/main s390x libp11-kit0 s390x 0.23.15-2 [184 kB] Get:61 http://ftpmaster.internal/ubuntu eoan/main s390x libunistring2 s390x 0.9.10-1ubuntu2 [359 kB] Get:62 http://ftpmaster.internal/ubuntu eoan/main s390x libgnutls30 s390x 3.6.7-4ubuntu1 [672 kB] Get:63 http://ftpmaster.internal/ubuntu eoan/main s390x liblz4-1 s390x 1.8.3-1ubuntu1 [56.1 kB] Get:64 http://ftpmaster.internal/ubuntu eoan/main s390x liblzma5 s390x 5.2.4-1 [91.5 kB] Get:65 http://ftpmaster.internal/ubuntu eoan/main s390x systemd-sysv s390x 240-6ubuntu9 [9380 B] Get:66 http://ftpmaster.internal/ubuntu eoan/main s390x libacl1 s390x 2.2.53-4 [17.9 kB] Get:67 http://ftpmaster.internal/ubuntu eoan/main s390x libapparmor1 s390x 2.13.2-9ubuntu7 [32.9 kB] Get:68 http://ftpmaster.internal/ubuntu eoan/main s390x libaudit-common all 1:2.8.4-3ubuntu1 [4200 B] Get:69 http://ftpmaster.internal/ubuntu eoan/main s390x libcap-ng0 s390x 0.7.9-2 [10.6 kB] Get:70 http://ftpmaster.internal/ubuntu eoan/main s390x libaudit1 s390x 1:2.8.4-3ubuntu1 [37.2 kB] Get:71 http://ftpmaster.internal/ubuntu eoan/main s390x libcap2 s390x 1:2.25-2 [13.3 kB] Get:72 http://ftpmaster.internal/ubuntu eoan/main s390x libargon2-1 s390x 0~20171227-0.2 [35.7 kB] Get:73 http://ftpmaster.internal/ubuntu eoan/main s390x libudev1 s390x 240-6ubuntu9 [59.8 kB] Get:74 http://ftpmaster.internal/ubuntu eoan/main s390x libdevmapper1.02.1 s390x 2:1.02.155-2ubuntu4 [122 kB] Get:75 http://ftpmaster.internal/ubuntu eoan/main s390x libjson-c3 s390x 0.12.1+ds-2 [21.4 kB] Get:76 http://ftpmaster.internal/ubuntu eoan/main s390x libssl1.1 s390x 1.1.1c-1ubuntu3 [969 kB] Get:77 http://ftpmaster.internal/ubuntu eoan/main s390x libcryptsetup12 s390x 2:2.1.0-5ubuntu1 [131 kB] Get:78 http://ftpmaster.internal/ubuntu eoan/main s390x libgpg-error0 s390x 1.36-1 [54.0 kB] Get:79 http://ftpmaster.internal/ubuntu eoan/main s390x libidn11 s390x 1.33-2.2ubuntu2 [44.6 kB] Get:80 http://ftpmaster.internal/ubuntu eoan/main s390x libkmod2 s390x 26-1ubuntu1 [39.0 kB] Get:81 http://ftpmaster.internal/ubuntu eoan/main s390x libpam0g s390x 1.3.1-5ubuntu1 [53.9 kB] Get:82 http://ftpmaster.internal/ubuntu eoan/main s390x libseccomp2 s390x 2.4.1-0ubuntu0.19.10.3 [40.5 kB] Get:83 http://ftpmaster.internal/ubuntu eoan/main s390x mount s390x 2.33.1-0.1ubuntu2 [108 kB] Get:84 http://ftpmaster.internal/ubuntu eoan/main s390x libsepol1 s390x 2.9-1 [227 kB] Get:85 http://ftpmaster.internal/ubuntu eoan/main s390x libsemanage-common all 2.9-1 [9916 B] Get:86 http://ftpmaster.internal/ubuntu eoan/main s390x libsemanage1 s390x 2.9-1 [79.2 kB] Get:87 http://ftpmaster.internal/ubuntu eoan/main s390x libpam-modules-bin s390x 1.3.1-5ubuntu1 [35.8 kB] Get:88 http://ftpmaster.internal/ubuntu eoan/main s390x libpam-modules s390x 1.3.1-5ubuntu1 [238 kB] Get:89 http://ftpmaster.internal/ubuntu eoan/main s390x passwd s390x 1:4.5-1.1ubuntu2 [797 kB] Get:90 http://ftpmaster.internal/ubuntu eoan/main s390x adduser all 3.118ubuntu1 [163 kB] Get:91 http://ppa.launchpad.net/ubuntu-toolchain-r/ppa/ubuntu eoan/main s390x libstdc++-8-dev s390x 8.3.0-14ubuntu1 [1519 kB] Get:92 http://ftpmaster.internal/ubuntu eoan/main s390x systemd s390x 240-6ubuntu9 [2994 kB] Get:93 http://ftpmaster.internal/ubuntu eoan/main s390x libsystemd0 s390x 240-6ubuntu9 [221 kB] Get:94 http://ftpmaster.internal/ubuntu eoan/main s390x libzstd1 s390x 1.3.8+dfsg-3 [204 kB] Get:95 http://ftpmaster.internal/ubuntu eoan/main s390x libapt-pkg5.0 s390x 1.8.2+19.10 [750 kB] Get:96 http://ftpmaster.internal/ubuntu eoan/main s390x libgcrypt20 s390x 1.8.4-5ubuntu1 [352 kB] Get:97 http://ppa.launchpad.net/ubuntu-toolchain-r/ppa/ubuntu eoan/main s390x libgcc-8-dev s390x 8.3.0-14ubuntu1 [651 kB] Get:98 http://ftpmaster.internal/ubuntu eoan/main s390x gpgv s390x 2.2.12-1ubuntu3 [180 kB] Get:99 http://ftpmaster.internal/ubuntu eoan/main s390x apt s390x 1.8.2+19.10 [1229 kB] Get:100 http://ppa.launchpad.net/ubuntu-toolchain-r/ppa/ubuntu eoan/main s390x libcc1-0 s390x 9.1.0-4ubuntu1 [45.5 kB] Get:101 http://ppa.launchpad.net/ubuntu-toolchain-r/ppa/ubuntu eoan/main s390x binutils-s390x-linux-gnu s390x 2.32.51.20190614-0ubuntu1 [1728 kB] Get:102 http://ftpmaster.internal/ubuntu eoan/main s390x libext2fs2 s390x 1.45.1-1ubuntu1 [179 kB] Get:103 http://ftpmaster.internal/ubuntu eoan/main s390x e2fsprogs s390x 1.45.1-1ubuntu1 [507 kB] Get:104 http://ftpmaster.internal/ubuntu eoan/main s390x init s390x 1.57 [6088 B] Get:105 http://ftpmaster.internal/ubuntu eoan/main s390x libattr1 s390x 1:2.4.48-4 [12.0 kB] Get:106 http://ftpmaster.internal/ubuntu eoan/main s390x libpam-runtime all 1.3.1-5ubuntu1 [37.3 kB] Get:107 http://ftpmaster.internal/ubuntu eoan/main s390x libpcre3 s390x 2:8.39-12 [154 kB] Get:108 http://ftpmaster.internal/ubuntu eoan/main s390x libisl21 s390x 0.21-1 [529 kB] Get:109 http://ftpmaster.internal/ubuntu eoan/main s390x libmpfr6 s390x 4.0.2-1 [229 kB] Get:110 http://ftpmaster.internal/ubuntu eoan/main s390x libcom-err2 s390x 1.45.1-1ubuntu1 [10.1 kB] Get:111 http://ftpmaster.internal/ubuntu eoan/main s390x libprocps7 s390x 2:3.3.15-2ubuntu2 [30.9 kB] Get:112 http://ftpmaster.internal/ubuntu eoan/main s390x libss2 s390x 1.45.1-1ubuntu1 [10.6 kB] Get:113 http://ftpmaster.internal/ubuntu eoan/main s390x procps s390x 2:3.3.15-2ubuntu2 [220 kB] Get:114 http://ftpmaster.internal/ubuntu eoan/main s390x openssl s390x 1.1.1c-1ubuntu3 [605 kB] Get:115 http://ftpmaster.internal/ubuntu eoan/main s390x ca-certificates all 20190110 [146 kB] Get:116 http://ftpmaster.internal/ubuntu eoan/main s390x dmsetup s390x 2:1.02.155-2ubuntu4 [73.5 kB] Get:117 http://ftpmaster.internal/ubuntu eoan/main s390x readline-common all 8.0-1 [53.4 kB] Get:118 http://ftpmaster.internal/ubuntu eoan/main s390x libreadline8 s390x 8.0-1 [122 kB] Get:119 http://ftpmaster.internal/ubuntu eoan/main s390x libslang2 s390x 2.3.2-3 [415 kB] Get:120 http://ftpmaster.internal/ubuntu eoan/main s390x libsqlite3-0 s390x 3.27.2-3 [497 kB] Get:121 http://ppa.launchpad.net/ubuntu-toolchain-r/ppa/ubuntu eoan/main s390x libbinutils s390x 2.32.51.20190614-0ubuntu1 [298 kB] Get:122 http://ftpmaster.internal/ubuntu eoan/main s390x tzdata all 2019a-1 [187 kB] Get:123 http://ppa.launchpad.net/ubuntu-toolchain-r/ppa/ubuntu eoan/main s390x binutils s390x 2.32.51.20190614-0ubuntu1 [3336 B] Get:124 http://ppa.launchpad.net/ubuntu-toolchain-r/ppa/ubuntu eoan/main s390x binutils-common s390x 2.32.51.20190614-0ubuntu1 [202 kB] Get:125 http://ftpmaster.internal/ubuntu eoan/main s390x xz-utils s390x 5.2.4-1 [80.3 kB] Get:126 http://ftpmaster.internal/ubuntu eoan/main s390x libpng16-16 s390x 1.6.37-1~exp4 [173 kB] Get:127 http://ftpmaster.internal/ubuntu eoan/main s390x multiarch-support s390x 2.29-0ubuntu2 [6916 B] Get:128 http://ftpmaster.internal/ubuntu eoan/main s390x advancecomp s390x 2.1-2.1 [182 kB] Get:129 http://ftpmaster.internal/ubuntu eoan/main s390x g++ s390x 4:8.3.0-1ubuntu3 [1596 B] Get:130 http://ftpmaster.internal/ubuntu eoan/main s390x gcc s390x 4:8.3.0-1ubuntu3 [5204 B] Get:131 http://ppa.launchpad.net/ubuntu-toolchain-r/ppa/ubuntu eoan/main s390x cpp-8 s390x 8.3.0-14ubuntu1 [6880 kB] Get:132 http://ftpmaster.internal/ubuntu eoan/main s390x cpp s390x 4:8.3.0-1ubuntu3 [27.6 kB] Get:133 http://ftpmaster.internal/ubuntu eoan/main s390x dpkg-dev all 1.19.6ubuntu1 [675 kB] Get:134 http://ftpmaster.internal/ubuntu eoan/main s390x libdpkg-perl all 1.19.6ubuntu1 [230 kB] Get:135 http://ftpmaster.internal/ubuntu eoan/main s390x build-essential s390x 12.6ubuntu1 [4664 B] Get:136 http://ftpmaster.internal/ubuntu eoan/main s390x e2fslibs s390x 1.45.1-1ubuntu1 [2716 B] Get:137 http://ftpmaster.internal/ubuntu eoan/main s390x libassuan0 s390x 2.5.3-1 [32.4 kB] Get:138 http://ftpmaster.internal/ubuntu eoan/main s390x pinentry-curses s390x 1.1.0-2 [34.3 kB] Get:139 http://ftpmaster.internal/ubuntu eoan/main s390x gpg s390x 2.2.12-1ubuntu3 [431 kB] Get:140 http://ftpmaster.internal/ubuntu eoan/main s390x gpgconf s390x 2.2.12-1ubuntu3 [115 kB] Get:141 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Setting up libsqlite3-0:s390x (3.27.2-3) ... Setting up binutils-common:s390x (2.32.51.20190614-0ubuntu1) ... Setting up linux-libc-dev:s390x (5.0.0-17.18) ... Setting up libcom-err2:s390x (1.45.1-1ubuntu1) ... Setting up libassuan0:s390x (2.5.3-1) ... Setting up libgomp1:s390x (9.1.0-4ubuntu1) ... Setting up tzdata (2019a-1) ... Current default time zone: 'Etc/UTC' Local time is now: Sat Jun 22 20:08:42 UTC 2019. Universal Time is now: Sat Jun 22 20:08:42 UTC 2019. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libasan5:s390x (9.1.0-4ubuntu1) ... Setting up libslang2:s390x (2.3.2-3) ... Setting up multiarch-support (2.29-0ubuntu2) ... Setting up libmpfr6:s390x (4.0.2-1) ... Setting up libncurses6:s390x (6.1+20181013-2ubuntu2) ... Setting up xz-utils (5.2.4-1) ... Setting up libpng16-16:s390x (1.6.37-1~exp4) ... Setting up libatomic1:s390x (9.1.0-4ubuntu1) ... Setting up libss2:s390x (1.45.1-1ubuntu1) ... Setting up gcc-8-base:s390x (8.3.0-14ubuntu1) ... Setting up libubsan1:s390x (9.1.0-4ubuntu1) ... Setting up advancecomp (2.1-2.1) ... Setting up dmsetup (2:1.02.155-2ubuntu4) ... Setting up libcomerr2:s390x (1.45.1-1ubuntu1) ... Setting up procps (2:3.3.15-2ubuntu2) ... Installing new version of config file /etc/sysctl.d/10-network-security.conf ... Setting up libbinutils:s390x (2.32.51.20190614-0ubuntu1) ... Setting up cpp-8 (8.3.0-14ubuntu1) ... Setting up libc-dev-bin (2.29-0ubuntu2) ... Setting up openssl (1.1.1c-1ubuntu3) ... Installing new version of config file /etc/ssl/openssl.cnf ... Setting up readline-common (8.0-1) ... Setting up libcc1-0:s390x (9.1.0-4ubuntu1) ... Setting up libitm1:s390x (9.1.0-4ubuntu1) ... Setting up libgdbm6:s390x (1.18.1-4) ... Setting up pinentry-curses (1.1.0-2) ... Setting up binutils-s390x-linux-gnu (2.32.51.20190614-0ubuntu1) ... Setting up libreadline8:s390x (8.0-1) ... Setting up e2fsprogs (1.45.1-1ubuntu1) ... Installing new version of config file /etc/mke2fs.conf ... Created symlink /etc/systemd/system/timers.target.wants/e2scrub_all.timer -> /lib/systemd/system/e2scrub_all.timer. Created symlink /etc/systemd/system/default.target.wants/e2scrub_reap.service -> /lib/systemd/system/e2scrub_reap.service. Setting up binutils (2.32.51.20190614-0ubuntu1) ... Setting up ca-certificates (20190110) ... Updating certificates in /etc/ssl/certs... 2 added, 7 removed; done. Setting up optipng (0.7.7-1) ... Setting up libgdbm-compat4:s390x (1.18.1-4) ... Setting up libgcc-8-dev:s390x (8.3.0-14ubuntu1) ... Setting up libperl5.28:s390x (5.28.1-6) ... Setting up cpp (4:8.3.0-1ubuntu3) ... Setting up gpgconf (2.2.12-1ubuntu3) ... Setting up libc6-dev:s390x (2.29-0ubuntu2) ... Setting up gpg (2.2.12-1ubuntu3) ... Setting up libstdc++-8-dev:s390x (8.3.0-14ubuntu1) ... Setting up gcc-8 (8.3.0-14ubuntu1) ... Setting up gpg-agent (2.2.12-1ubuntu3) ... Setting up pkgbinarymangler (144) ... Setting up gcc (4:8.3.0-1ubuntu3) ... Setting up perl (5.28.1-6) ... Setting up libdpkg-perl (1.19.6ubuntu1) ... Setting up g++-8 (8.3.0-14ubuntu1) ... Setting up dpkg-dev (1.19.6ubuntu1) ... Setting up g++ (4:8.3.0-1ubuntu3) ... Setting up build-essential (12.6ubuntu1) ... Processing triggers for systemd (240-6ubuntu9) ... Processing triggers for libc-bin (2.29-0ubuntu2) ... Processing triggers for ca-certificates (20190110) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. RUN: /usr/share/launchpad-buildd/bin/sbuild-package PACKAGEBUILD-16961252 s390x eoan -c chroot:build-PACKAGEBUILD-16961252 --arch=s390x --dist=eoan --nolog cyvcf2_0.10.8-1.dsc Initiating build PACKAGEBUILD-16961252 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 4.4.0-151-generic #178-Ubuntu SMP Tue Jun 11 08:33:12 UTC 2019 s390x sbuild (Debian sbuild) 0.67.0 (26 Dec 2015) on bos02-s390x-004.buildd +==============================================================================+ | cyvcf2 0.10.8-1 (s390x) 22 Jun 2019 20:08 | +==============================================================================+ Package: cyvcf2 Version: 0.10.8-1 Source Version: 0.10.8-1 Distribution: eoan Machine Architecture: s390x Host Architecture: s390x Build Architecture: s390x I: NOTICE: Log filtering will replace 'build/cyvcf2-UKj4MB/cyvcf2-0.10.8' with '<>' I: NOTICE: Log filtering will replace 'build/cyvcf2-UKj4MB' with '<>' I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-16961252/chroot-autobuild' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- cyvcf2_0.10.8-1.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-IeP1c4/apt_archive/sbuild-build-depends-core-dummy.deb'. Ign:1 copy:/<>/resolver-IeP1c4/apt_archive ./ InRelease Get:2 copy:/<>/resolver-IeP1c4/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-IeP1c4/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-IeP1c4/apt_archive ./ Sources [214 B] Get:5 copy:/<>/resolver-IeP1c4/apt_archive ./ Packages [527 B] Fetched 2860 B in 0s (0 B/s) Reading package lists... Reading package lists... +------------------------------------------------------------------------------+ | Install core build dependencies (apt-based resolver) | +------------------------------------------------------------------------------+ Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following packages were automatically installed and are no longer required: libisl19 libreadline7 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-IeP1c4/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 ... 12615 files and directories currently installed.) Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_s390x.deb ... Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ... Setting up sbuild-build-depends-core-dummy (0.invalid.0) ... Merged Build-Depends: debhelper (>= 12~), dh-python, zlib1g-dev, cython, cython3, python-all-dev, python-setuptools, python3-setuptools, python3-all-dev, python-numpy, python3-numpy, python-coloredlogs, python3-coloredlogs, python-click, python3-click, python-nose, python3-nose, libssl-dev, libcurl4-gnutls-dev | libcurl4-openssl-dev, libhts-dev, libbz2-dev Filtered Build-Depends: debhelper (>= 12~), dh-python, zlib1g-dev, cython, cython3, python-all-dev, python-setuptools, python3-setuptools, python3-all-dev, python-numpy, python3-numpy, python-coloredlogs, python3-coloredlogs, python-click, python3-click, python-nose, python3-nose, libssl-dev, libcurl4-gnutls-dev | libcurl4-openssl-dev, libhts-dev, libbz2-dev dpkg-deb: building package 'sbuild-build-depends-cyvcf2-dummy' in '/<>/resolver-2Uojdk/apt_archive/sbuild-build-depends-cyvcf2-dummy.deb'. Ign:1 copy:/<>/resolver-2Uojdk/apt_archive ./ InRelease Get:2 copy:/<>/resolver-2Uojdk/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-2Uojdk/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-2Uojdk/apt_archive ./ Sources [325 B] Get:5 copy:/<>/resolver-2Uojdk/apt_archive ./ Packages [649 B] Fetched 3093 B in 0s (0 B/s) Reading package lists... Reading package lists... +------------------------------------------------------------------------------+ | Install cyvcf2 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: libisl19 libreadline7 Use 'apt autoremove' to remove them. The following additional packages will be installed: autoconf automake autopoint autotools-dev bsdmainutils cython cython3 debhelper dh-autoreconf dh-python dh-strip-nondeterminism dwz file gettext gettext-base groff-base intltool-debian libarchive-zip-perl libasn1-8-heimdal libblas3 libbsd0 libbz2-dev libcroco3 libcurl3-gnutls libcurl4-gnutls-dev libdeflate0 libelf1 libexpat1 libexpat1-dev libfile-stripnondeterminism-perl libgfortran5 libglib2.0-0 libgssapi-krb5-2 libgssapi3-heimdal libhcrypto4-heimdal libheimbase1-heimdal libheimntlm0-heimdal libhts-dev libhts2 libhx509-5-heimdal libicu63 libk5crypto3 libkeyutils1 libkrb5-26-heimdal libkrb5-3 libkrb5support0 liblapack3 libldap-2.4-2 libldap-common liblzma-dev libmagic-mgc libmagic1 libmpdec2 libnghttp2-14 libpipeline1 libpsl5 libpython-all-dev libpython-dev libpython-stdlib libpython2-dev libpython2-stdlib libpython2.7 libpython2.7-dev libpython2.7-minimal libpython2.7-stdlib libpython3-all-dev libpython3-dev libpython3-stdlib libpython3.7 libpython3.7-dev libpython3.7-minimal libpython3.7-stdlib libroken18-heimdal librtmp1 libsasl2-2 libsasl2-modules-db libsigsegv2 libssh-4 libssl-dev libtool libuchardet0 libwind0-heimdal libxml2 m4 man-db mime-support po-debconf python python-all python-all-dev python-click python-colorama python-coloredlogs python-dev python-humanfriendly python-minimal python-monotonic python-nose python-numpy python-pkg-resources python-setuptools python2 python2-dev python2-minimal python2.7 python2.7-dev python2.7-minimal python3 python3-all python3-all-dev python3-click python3-colorama python3-coloredlogs python3-dev python3-distutils python3-humanfriendly python3-lib2to3 python3-minimal python3-nose python3-numpy python3-pkg-resources python3-setuptools python3.7 python3.7-dev python3.7-minimal zlib1g-dev Suggested packages: autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois vacation cython-doc dh-make gettext-doc libasprintf-dev libgettextpo-dev groff libcurl4-doc libgnutls28-dev libidn11-dev libkrb5-dev libldap2-dev librtmp-dev libssh2-1-dev pkg-config krb5-doc krb5-user liblzma-doc libssl-doc libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc apparmor less www-browser libmail-box-perl python-doc python-tk python-coverage python-nose-doc gfortran python-pytest python-numpy-dbg python-numpy-doc python-setuptools-doc python2-doc python2.7-doc binfmt-support python3-doc python3-tk python3-venv python3-pytest python3-numpy-dbg python3.7-venv python3.7-doc Recommended packages: curl | wget | lynx bzip2-doc libarchive-cpio-perl libglib2.0-data shared-mime-info xdg-user-dirs krb5-locales publicsuffix libsasl2-modules libltdl-dev libmail-sendmail-perl The following NEW packages will be installed: autoconf automake autopoint autotools-dev bsdmainutils cython cython3 debhelper dh-autoreconf dh-python dh-strip-nondeterminism dwz file gettext gettext-base groff-base intltool-debian libarchive-zip-perl libasn1-8-heimdal libblas3 libbsd0 libbz2-dev libcroco3 libcurl3-gnutls libcurl4-gnutls-dev libdeflate0 libelf1 libexpat1 libexpat1-dev libfile-stripnondeterminism-perl libgfortran5 libglib2.0-0 libgssapi-krb5-2 libgssapi3-heimdal libhcrypto4-heimdal libheimbase1-heimdal libheimntlm0-heimdal libhts-dev libhts2 libhx509-5-heimdal libicu63 libk5crypto3 libkeyutils1 libkrb5-26-heimdal libkrb5-3 libkrb5support0 liblapack3 libldap-2.4-2 libldap-common liblzma-dev libmagic-mgc libmagic1 libmpdec2 libnghttp2-14 libpipeline1 libpsl5 libpython-all-dev libpython-dev libpython-stdlib libpython2-dev libpython2-stdlib libpython2.7 libpython2.7-dev libpython2.7-minimal libpython2.7-stdlib libpython3-all-dev libpython3-dev libpython3-stdlib libpython3.7 libpython3.7-dev libpython3.7-minimal libpython3.7-stdlib libroken18-heimdal librtmp1 libsasl2-2 libsasl2-modules-db libsigsegv2 libssh-4 libssl-dev libtool libuchardet0 libwind0-heimdal libxml2 m4 man-db mime-support po-debconf python python-all python-all-dev python-click python-colorama python-coloredlogs python-dev python-humanfriendly python-minimal python-monotonic python-nose python-numpy python-pkg-resources python-setuptools python2 python2-dev python2-minimal python2.7 python2.7-dev python2.7-minimal python3 python3-all python3-all-dev python3-click python3-colorama python3-coloredlogs python3-dev python3-distutils python3-humanfriendly python3-lib2to3 python3-minimal python3-nose python3-numpy python3-pkg-resources python3-setuptools python3.7 python3.7-dev python3.7-minimal sbuild-build-depends-cyvcf2-dummy zlib1g-dev 0 upgraded, 127 newly installed, 0 to remove and 0 not upgraded. Need to get 125 MB of archives. After this operation, 333 MB of additional disk space will be used. Get:1 copy:/<>/resolver-2Uojdk/apt_archive ./ sbuild-build-depends-cyvcf2-dummy 0.invalid.0 [972 B] Get:2 http://ppa.launchpad.net/ubuntu-toolchain-r/ppa/ubuntu eoan/main s390x libgfortran5 s390x 9.1.0-4ubuntu1 [335 kB] Get:3 http://ftpmaster.internal/ubuntu eoan/main s390x libpython3.7-minimal s390x 3.7.4~rc1-1 [544 kB] Get:4 http://ftpmaster.internal/ubuntu eoan/main s390x libexpat1 s390x 2.2.6-1 [82.9 kB] Get:5 http://ftpmaster.internal/ubuntu eoan/main s390x python3.7-minimal s390x 3.7.4~rc1-1 [1561 kB] Get:6 http://ftpmaster.internal/ubuntu eoan/main s390x python3-minimal s390x 3.7.3-1 [23.4 kB] Get:7 http://ftpmaster.internal/ubuntu eoan/main s390x mime-support all 3.62ubuntu1 [30.6 kB] Get:8 http://ftpmaster.internal/ubuntu eoan/main s390x libmpdec2 s390x 2.4.2-2 [80.6 kB] Get:9 http://ftpmaster.internal/ubuntu eoan/main s390x libpython3.7-stdlib s390x 3.7.4~rc1-1 [1696 kB] Get:10 http://ftpmaster.internal/ubuntu eoan/main s390x python3.7 s390x 3.7.4~rc1-1 [293 kB] Get:11 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Get:74 http://ftpmaster.internal/ubuntu eoan/main s390x libkrb5-26-heimdal s390x 7.5.0+dfsg-3 [189 kB] Get:75 http://ftpmaster.internal/ubuntu eoan/main s390x libheimntlm0-heimdal s390x 7.5.0+dfsg-3 [14.1 kB] Get:76 http://ftpmaster.internal/ubuntu eoan/main s390x libgssapi3-heimdal s390x 7.5.0+dfsg-3 [86.9 kB] Get:77 http://ftpmaster.internal/ubuntu eoan/main s390x libsasl2-modules-db s390x 2.1.27+dfsg-1 [14.0 kB] Get:78 http://ftpmaster.internal/ubuntu eoan/main s390x libsasl2-2 s390x 2.1.27+dfsg-1 [46.4 kB] Get:79 http://ftpmaster.internal/ubuntu eoan/main s390x libldap-common all 2.4.47+dfsg-3ubuntu2 [16.6 kB] Get:80 http://ftpmaster.internal/ubuntu eoan/main s390x libldap-2.4-2 s390x 2.4.47+dfsg-3ubuntu2 [143 kB] Get:81 http://ftpmaster.internal/ubuntu eoan/main s390x libnghttp2-14 s390x 1.37.0-1 [75.1 kB] Get:82 http://ftpmaster.internal/ubuntu eoan/main s390x librtmp1 s390x 2.4+20151223.gitfa8646d.1-2 [51.1 kB] Get:83 http://ftpmaster.internal/ubuntu eoan/main s390x libssh-4 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http://ftpmaster.internal/ubuntu eoan/universe s390x python3-coloredlogs all 7.3-1 [27.8 kB] Get:125 http://ftpmaster.internal/ubuntu eoan/universe s390x python3-nose all 1.3.7-4 [116 kB] Get:126 http://ftpmaster.internal/ubuntu eoan/main s390x python3-numpy s390x 1:1.16.2-1ubuntu1 [1942 kB] Get:127 http://ftpmaster.internal/ubuntu eoan/main s390x python3-setuptools all 40.8.0-1 [252 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 125 MB in 2s (60.8 MB/s) Selecting previously unselected package libpython3.7-minimal:s390x. 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Setting up libmagic1:s390x (1:5.35-4) ... Setting up libdeflate0:s390x (1.2-1) ... Setting up gettext-base (0.19.8.1-9) ... Setting up file (1:5.35-4) ... Setting up libldap-common (2.4.47+dfsg-3ubuntu2) ... Setting up libicu63:s390x (63.2-2) ... Setting up libkrb5support0:s390x (1.17-3) ... Setting up libsasl2-modules-db:s390x (2.1.27+dfsg-1) ... Setting up libpython2.7-stdlib:s390x (2.7.16-2) ... Setting up autotools-dev (20180224.1) ... Setting up libblas3:s390x (3.8.0-2) ... update-alternatives: using /usr/lib/s390x-linux-gnu/blas/libblas.so.3 to provide /usr/lib/s390x-linux-gnu/libblas.so.3 (libblas.so.3-s390x-linux-gnu) in auto mode Setting up libexpat1-dev:s390x (2.2.6-1) ... Setting up librtmp1:s390x (2.4+20151223.gitfa8646d.1-2) ... Setting up libsigsegv2:s390x (2.12-2) ... Setting up libssl-dev:s390x (1.1.1c-1ubuntu3) ... Setting up autopoint (0.19.8.1-9) ... Setting up libk5crypto3:s390x (1.17-3) ... Setting up libsasl2-2:s390x (2.1.27+dfsg-1) ... Setting up libgfortran5:s390x (9.1.0-4ubuntu1) ... Setting up libroken18-heimdal:s390x (7.5.0+dfsg-3) ... Setting up liblzma-dev:s390x (5.2.4-1) ... Setting up zlib1g-dev:s390x (1:1.2.11.dfsg-1ubuntu2) ... Setting up libuchardet0:s390x (0.0.6-3) ... Setting up libkrb5-3:s390x (1.17-3) ... Setting up libmpdec2:s390x (2.4.2-2) ... Setting up libbsd0:s390x (0.9.1-2) ... Setting up libelf1:s390x (0.176-1.1) ... Setting up libxml2:s390x (2.9.4+dfsg1-7ubuntu3) ... Setting up libheimbase1-heimdal:s390x (7.5.0+dfsg-3) ... Setting up libbz2-dev:s390x (1.0.6-9) ... Setting up libfile-stripnondeterminism-perl (1.1.2-1) ... Setting up libpython3.7-stdlib:s390x (3.7.4~rc1-1) ... Setting up libpython2.7:s390x (2.7.16-2) ... Setting up liblapack3:s390x (3.8.0-2) ... update-alternatives: using /usr/lib/s390x-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/s390x-linux-gnu/liblapack.so.3 (liblapack.so.3-s390x-linux-gnu) in auto mode Setting up libpython2.7-dev:s390x (2.7.16-2) ... Setting up python2.7 (2.7.16-2) ... Setting up libpython3.7:s390x (3.7.4~rc1-1) ... Setting up libtool (2.4.6-10) ... Setting up libpython2-stdlib:s390x (2.7.16-1) ... Setting up libpython3.7-dev:s390x (3.7.4~rc1-1) ... Setting up libasn1-8-heimdal:s390x (7.5.0+dfsg-3) ... Setting up m4 (1.4.18-2) ... Setting up libhcrypto4-heimdal:s390x (7.5.0+dfsg-3) ... Setting up python2 (2.7.16-1) ... Setting up libpython-stdlib:s390x (2.7.16-1) ... Setting up libwind0-heimdal:s390x (7.5.0+dfsg-3) ... Setting up bsdmainutils (11.1.2ubuntu2) ... update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode Setting up libgssapi-krb5-2:s390x (1.17-3) ... Setting up libcroco3:s390x (0.6.12-3) ... Setting up libssh-4:s390x (0.8.7-1) ... Setting up autoconf (2.69-11) ... Setting up dwz (0.12-3) ... Setting up groff-base (1.22.4-3) ... Setting up libpython2-dev:s390x (2.7.16-1) ... Setting up python (2.7.16-1) ... Setting up libpython3-stdlib:s390x (3.7.3-1) ... Setting up python-monotonic (1.5-0ubuntu1) ... Setting up python2.7-dev (2.7.16-2) ... Setting up automake (1:1.16.1-4ubuntu3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up python3.7 (3.7.4~rc1-1) ... Setting up cython (0.29.2-2build1) ... Setting up gettext (0.19.8.1-9) ... Setting up python-colorama (0.3.7-1) ... Setting up libpython3-dev:s390x (3.7.3-1) ... Setting up python2-dev (2.7.16-1) ... Setting up python-pkg-resources (40.8.0-1) ... Setting up libhx509-5-heimdal:s390x (7.5.0+dfsg-3) ... Setting up python3 (3.7.3-1) ... Setting up python-all (2.7.16-1) ... Setting up man-db (2.8.5-2) ... Not building database; man-db/auto-update is not 'true'. Created symlink /etc/systemd/system/timers.target.wants/man-db.timer → /lib/systemd/system/man-db.timer. Setting up python3.7-dev (3.7.4~rc1-1) ... Setting up intltool-debian (0.35.0+20060710.5) ... Setting up libpython-dev:s390x (2.7.16-1) ... Setting up python-humanfriendly (4.18-1) ... Setting up python-click (7.0-1) ... Setting up python3-humanfriendly (4.18-1) ... Setting up libpython3-all-dev:s390x (3.7.3-1) ... Setting up cython3 (0.29.2-2build1) ... Setting up python-setuptools (40.8.0-1) ... Setting up python3-lib2to3 (3.7.3-1ubuntu1) ... Setting up python3-coloredlogs (7.3-1) ... Setting up python-coloredlogs (7.3-1) ... Setting up python-dev (2.7.16-1) ... Setting up libkrb5-26-heimdal:s390x (7.5.0+dfsg-3) ... Setting up python3-pkg-resources (40.8.0-1) ... Setting up python3-distutils (3.7.3-1ubuntu1) ... Setting up dh-python (3.20190308) ... Setting up python3-setuptools (40.8.0-1) ... Setting up libpython-all-dev:s390x (2.7.16-1) ... Setting up python-numpy (1:1.16.2-1ubuntu1) ... Setting up python3-colorama (0.3.7-1) ... Setting up python-nose (1.3.7-4) ... Setting up po-debconf (1.0.21) ... Setting up python3-all (3.7.3-1) ... Setting up python3-click (7.0-1) ... Setting up python3-nose (1.3.7-4) ... Setting up libheimntlm0-heimdal:s390x (7.5.0+dfsg-3) ... Setting up libgssapi3-heimdal:s390x (7.5.0+dfsg-3) ... Setting up python3-dev (3.7.3-1) ... Setting up python3-numpy (1:1.16.2-1ubuntu1) ... Setting up python-all-dev (2.7.16-1) ... Setting up python3-all-dev (3.7.3-1) ... Setting up libldap-2.4-2:s390x (2.4.47+dfsg-3ubuntu2) ... Setting up libcurl3-gnutls:s390x (7.64.0-4ubuntu1) ... Setting up libcurl4-gnutls-dev:s390x (7.64.0-4ubuntu1) ... Setting up libhts2:s390x (1.9-10) ... Setting up libhts-dev:s390x (1.9-10) ... Setting up debhelper (12.1.1ubuntu1) ... Setting up dh-autoreconf (19) ... Setting up dh-strip-nondeterminism (1.1.2-1) ... Setting up sbuild-build-depends-cyvcf2-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.29-0ubuntu2) ... +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 4.4.0-151-generic s390x (s390x) Toolchain package versions: binutils_2.32.51.20190614-0ubuntu1 dpkg-dev_1.19.6ubuntu1 g++-8_8.3.0-14ubuntu1 gcc-8_8.3.0-14ubuntu1 libc6-dev_2.29-0ubuntu2 libstdc++-8-dev_8.3.0-14ubuntu1 libstdc++6_9.1.0-4ubuntu1 linux-libc-dev_5.0.0-17.18 Package versions: adduser_3.118ubuntu1 advancecomp_2.1-2.1 apt_1.8.2+19.10 autoconf_2.69-11 automake_1:1.16.1-4ubuntu3 autopoint_0.19.8.1-9 autotools-dev_20180224.1 base-files_10.2ubuntu3 base-passwd_3.5.46 bash_5.0-4ubuntu1 binutils_2.32.51.20190614-0ubuntu1 binutils-common_2.32.51.20190614-0ubuntu1 binutils-s390x-linux-gnu_2.32.51.20190614-0ubuntu1 bsdmainutils_11.1.2ubuntu2 bsdutils_1:2.33.1-0.1ubuntu2 build-essential_12.6ubuntu1 bzip2_1.0.6-9 ca-certificates_20190110 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lockfile-progs_0.1.18 login_1:4.5-1.1ubuntu2 lsb-base_10.2019051400ubuntu1 m4_1.4.18-2 make_4.2.1-1.2 man-db_2.8.5-2 mawk_1.3.3-17ubuntu3 mime-support_3.62ubuntu1 mount_2.33.1-0.1ubuntu2 multiarch-support_2.29-0ubuntu2 ncurses-base_6.1+20181013-2ubuntu2 ncurses-bin_6.1+20181013-2ubuntu2 openssl_1.1.1c-1ubuntu3 optipng_0.7.7-1 passwd_1:4.5-1.1ubuntu2 patch_2.7.6-3 perl_5.28.1-6 perl-base_5.28.1-6 perl-modules-5.28_5.28.1-6 pinentry-curses_1.1.0-2 pkgbinarymangler_144 po-debconf_1.0.21 policyrcd-script-zg2_0.1-3 procps_2:3.3.15-2ubuntu2 python_2.7.16-1 python-all_2.7.16-1 python-all-dev_2.7.16-1 python-click_7.0-1 python-colorama_0.3.7-1 python-coloredlogs_7.3-1 python-dev_2.7.16-1 python-humanfriendly_4.18-1 python-minimal_2.7.16-1 python-monotonic_1.5-0ubuntu1 python-nose_1.3.7-4 python-numpy_1:1.16.2-1ubuntu1 python-pkg-resources_40.8.0-1 python-setuptools_40.8.0-1 python2_2.7.16-1 python2-dev_2.7.16-1 python2-minimal_2.7.16-1 python2.7_2.7.16-2 python2.7-dev_2.7.16-2 python2.7-minimal_2.7.16-2 python3_3.7.3-1 python3-all_3.7.3-1 python3-all-dev_3.7.3-1 python3-click_7.0-1 python3-colorama_0.3.7-1 python3-coloredlogs_7.3-1 python3-dev_3.7.3-1 python3-distutils_3.7.3-1ubuntu1 python3-humanfriendly_4.18-1 python3-lib2to3_3.7.3-1ubuntu1 python3-minimal_3.7.3-1 python3-nose_1.3.7-4 python3-numpy_1:1.16.2-1ubuntu1 python3-pkg-resources_40.8.0-1 python3-setuptools_40.8.0-1 python3.7_3.7.4~rc1-1 python3.7-dev_3.7.4~rc1-1 python3.7-minimal_3.7.4~rc1-1 readline-common_8.0-1 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-cyvcf2-dummy_0.invalid.0 sed_4.7-1 sensible-utils_0.0.12 systemd_240-6ubuntu9 systemd-sysv_240-6ubuntu9 sysv-rc_2.88dsf-59.3ubuntu2 sysvinit-utils_2.93-8ubuntu1 tar_1.30+dfsg-6 tzdata_2019a-1 ubuntu-keyring_2018.09.18.1 util-linux_2.33.1-0.1ubuntu2 xz-utils_5.2.4-1 zlib1g_1:1.2.11.dfsg-1ubuntu2 zlib1g-dev_1:1.2.11.dfsg-1ubuntu2 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- gpgv: Signature made Tue Feb 12 21:19:03 2019 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 ./cyvcf2_0.10.8-1.dsc dpkg-source: info: extracting cyvcf2 in cyvcf2-0.10.8 dpkg-source: info: unpacking cyvcf2_0.10.8.orig.tar.gz dpkg-source: info: unpacking cyvcf2_0.10.8-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying add_htslib_link_dependency.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-16961252 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-16961252 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-16961252 SCHROOT_UID=2001 SCHROOT_USER=buildd SHELL=/bin/sh TERM=unknown USER=buildd V=1 dpkg-buildpackage ----------------- dpkg-buildpackage: info: source package cyvcf2 dpkg-buildpackage: info: source version 0.10.8-1 dpkg-buildpackage: info: source distribution unstable dpkg-source --before-build . dpkg-buildpackage: info: host architecture s390x dpkg-source: info: using options from cyvcf2-0.10.8/debian/source/options: --extend-diff-ignore=^[^/]*[.]egg-info/ fakeroot debian/rules clean dh clean --with python2,python3 --buildsystem=pybuild dh_auto_clean -O--buildsystem=pybuild I: pybuild base:217: python2.7 setup.py clean running clean removing '/<>/.pybuild/cpython2_2.7_cyvcf2/build' (and everything under it) 'build/bdist.linux-s390x' does not exist -- can't clean it 'build/scripts-2.7' does not exist -- can't clean it I: pybuild base:217: python3.7 setup.py clean running clean removing '/<>/.pybuild/cpython3_3.7_cyvcf2/build' (and everything under it) 'build/bdist.linux-s390x' does not exist -- can't clean it 'build/scripts-3.7' does not exist -- can't clean it dh_autoreconf_clean -O--buildsystem=pybuild debian/rules override_dh_clean make[1]: Entering directory '/<>' dh_clean rm -rf cyvcf2.egg-info cyvcf2/cyvcf2.c __o.vcf find . -name "*.so" -delete make[1]: Leaving directory '/<>' debian/rules build-arch dh build-arch --with python2,python3 --buildsystem=pybuild dh_update_autotools_config -a -O--buildsystem=pybuild dh_autoreconf -a -O--buildsystem=pybuild dh_auto_configure -a -O--buildsystem=pybuild I: pybuild base:217: python2.7 setup.py config running config I: pybuild base:217: python3.7 setup.py config running config dh_auto_build -a -O--buildsystem=pybuild I: pybuild base:217: /usr/bin/python setup.py build running build running build_py creating /<>/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2 copying cyvcf2/__init__.py -> /<>/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2 copying cyvcf2/__main__.py -> /<>/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2 copying cyvcf2/cli.py -> /<>/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2 creating /<>/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/test_hemi.py -> /<>/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/__init__.py -> /<>/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/test_reader.py -> /<>/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/test_cli.py -> /<>/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2/tests running egg_info creating cyvcf2.egg-info writing requirements to cyvcf2.egg-info/requires.txt writing cyvcf2.egg-info/PKG-INFO writing top-level names to cyvcf2.egg-info/top_level.txt writing dependency_links to cyvcf2.egg-info/dependency_links.txt writing entry points to cyvcf2.egg-info/entry_points.txt writing manifest file 'cyvcf2.egg-info/SOURCES.txt' reading manifest file 'cyvcf2.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no files found matching 'htslib/*.c' warning: no files found matching 'htslib/*.h' warning: no files found matching 'htslib/htslib/*.h' warning: no files found matching 'htslib/cram/*.c' warning: no files found matching 'htslib/cram/*.h' writing manifest file 'cyvcf2.egg-info/SOURCES.txt' copying cyvcf2/cyvcf2.pxd -> /<>/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2 copying cyvcf2/cyvcf2.pyx -> /<>/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2 copying cyvcf2/helpers.c -> /<>/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2 copying cyvcf2/helpers.h -> /<>/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2 copying cyvcf2/relatedness.h -> /<>/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2 copying cyvcf2/tests/bug.vcf.gz -> /<>/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/decomposed.vcf -> /<>/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/empty.vcf -> /<>/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/issue_44.vcf -> /<>/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/o.vcf.gz -> /<>/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/seg.vcf.gz -> /<>/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/test-alt-repr.vcf -> /<>/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/test-format-string.vcf -> /<>/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/test-haploidX.vcf -> /<>/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/test-hemi.vcf -> /<>/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/test-multiallelic-homozygous-alt.vcf.gz -> /<>/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/test-multiallelic-homozygous-alt.vcf.gz.tbi -> /<>/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/test-strict-gt-option-flag.vcf.gz -> /<>/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/test-strict-gt-option-flag.vcf.gz.tbi -> /<>/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/test.comp_het.3.vcf -> /<>/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/test.snpeff.bcf -> /<>/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/test.snpeff.bcf.csi -> /<>/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/test.snpeff.vcf -> /<>/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/test.vcf.gz -> /<>/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/test.vcf.gz.tbi -> /<>/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/test_gt_alt_freqs.vcf -> /<>/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/test_gt_bases.vcf.gz -> /<>/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2/tests running build_ext cythoning cyvcf2/cyvcf2.pyx to cyvcf2/cyvcf2.c /usr/lib/python2.7/dist-packages/Cython/Compiler/Main.py:367: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /<>/cyvcf2/cyvcf2.pxd tree = Parsing.p_module(s, pxd, full_module_name) warning: cyvcf2/cyvcf2.pxd:26:16: Declarations should not be declared inline. warning: cyvcf2/cyvcf2.pxd:188:14: 'BCF_HT_FLAG' redeclared warning: cyvcf2/cyvcf2.pxd:279:30: Declarations should not be declared inline. building 'cyvcf2.cyvcf2' extension creating build creating build/temp.linux-s390x-2.7 creating build/temp.linux-s390x-2.7/cyvcf2 s390x-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ihtslib -Icyvcf2 -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include/python2.7 -c cyvcf2/cyvcf2.c -o build/temp.linux-s390x-2.7/cyvcf2/cyvcf2.o In file included from /usr/lib/python2.7/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1822, from /usr/lib/python2.7/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /usr/lib/python2.7/dist-packages/numpy/core/include/numpy/arrayobject.h:4, from cyvcf2/cyvcf2.c:614: /usr/lib/python2.7/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] #warning "Using deprecated NumPy API, disable it with " \ ^~~~~~~ cyvcf2/cyvcf2.c: In function ‘__pyx_pf_6cyvcf2_6cyvcf2_3VCF_4add_to_header’: cyvcf2/cyvcf2.c:7883:44: warning: passing argument 1 of ‘bcf_hdr_append’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] __pyx_v_ret = bcf_hdr_append(__pyx_v_self->hdr, __pyx_t_2); ~~~~~~~~~~~~^~~~~ In file included from cyvcf2/helpers.h:1, from cyvcf2/cyvcf2.c:617: /usr/include/htslib/vcf.h:443:35: note: expected ‘bcf_hdr_t *’ {aka ‘struct *’} but argument is of type ‘const bcf_hdr_t *’ {aka ‘const struct *’} int bcf_hdr_append(bcf_hdr_t *h, const char *line); ~~~~~~~~~~~^ cyvcf2/cyvcf2.c:7925:42: warning: passing argument 1 of ‘bcf_hdr_sync’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] __pyx_v_ret = bcf_hdr_sync(__pyx_v_self->hdr); ~~~~~~~~~~~~^~~~~ In file included from cyvcf2/helpers.h:1, from cyvcf2/cyvcf2.c:617: /usr/include/htslib/vcf.h:479:33: note: expected ‘bcf_hdr_t *’ {aka ‘struct *’} but argument is of type ‘const bcf_hdr_t *’ {aka ‘const struct *’} int bcf_hdr_sync(bcf_hdr_t *h); ~~~~~~~~~~~^ cyvcf2/cyvcf2.c: In function ‘__pyx_pf_6cyvcf2_6cyvcf2_3VCF_12set_samples’: cyvcf2/cyvcf2.c:8441:49: warning: passing argument 1 of ‘bcf_hdr_set_samples’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] __pyx_v_ret = bcf_hdr_set_samples(__pyx_v_self->hdr, ((char const *)__pyx_t_6), 0); ~~~~~~~~~~~~^~~~~ In file included from cyvcf2/helpers.h:1, from cyvcf2/cyvcf2.c:617: /usr/include/htslib/vcf.h:315:40: note: expected ‘bcf_hdr_t *’ {aka ‘struct *’} but argument is of type ‘const bcf_hdr_t *’ {aka ‘const struct *’} int bcf_hdr_set_samples(bcf_hdr_t *hdr, const char *samples, int is_file); ~~~~~~~~~~~^~~ cyvcf2/cyvcf2.c: In function ‘__pyx_pf_6cyvcf2_6cyvcf2_3VCF_14update’: cyvcf2/cyvcf2.c:8739:44: warning: passing argument 1 of ‘bcf_hdr_append’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] __pyx_v_ret = bcf_hdr_append(__pyx_v_self->hdr, __pyx_t_4); ~~~~~~~~~~~~^~~~~ In file included from cyvcf2/helpers.h:1, from cyvcf2/cyvcf2.c:617: /usr/include/htslib/vcf.h:443:35: note: expected ‘bcf_hdr_t *’ {aka ‘struct *’} but argument is of type ‘const bcf_hdr_t *’ {aka ‘const struct *’} int bcf_hdr_append(bcf_hdr_t *h, const char *line); ~~~~~~~~~~~^ cyvcf2/cyvcf2.c:8792:42: warning: passing argument 1 of ‘bcf_hdr_sync’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] __pyx_v_ret = bcf_hdr_sync(__pyx_v_self->hdr); ~~~~~~~~~~~~^~~~~ In file included from cyvcf2/helpers.h:1, from cyvcf2/cyvcf2.c:617: /usr/include/htslib/vcf.h:479:33: note: expected ‘bcf_hdr_t *’ {aka ‘struct *’} but argument is of type ‘const bcf_hdr_t *’ {aka ‘const struct *’} int bcf_hdr_sync(bcf_hdr_t *h); ~~~~~~~~~~~^ cyvcf2/cyvcf2.c: In function ‘__pyx_gb_6cyvcf2_6cyvcf2_3VCF_18generator’: cyvcf2/cyvcf2.c:9001:115: warning: passing argument 4 of ‘hts_itr_querys’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] __pyx_cur_scope->__pyx_v_itr = bcf_itr_querys(__pyx_cur_scope->__pyx_v_self->hidx, __pyx_cur_scope->__pyx_v_self->hdr, __pyx_t_2); ^ In file included from /usr/include/htslib/vcf.h:39, from cyvcf2/helpers.h:1, from cyvcf2/cyvcf2.c:617: /usr/include/htslib/hts.h:675:16: note: expected ‘void *’ but argument is of type ‘const bcf_hdr_t *’ {aka ‘const struct *’} hts_itr_t *hts_itr_querys(const hts_idx_t *idx, const char *reg, hts_name2id_f getid, void *hdr, hts_itr_query_func *itr_query, hts_readrec_func *readrec); ^~~~~~~~~~~~~~ cyvcf2/cyvcf2.c: In function ‘__pyx_gb_6cyvcf2_6cyvcf2_3VCF_24generator2’: cyvcf2/cyvcf2.c:10286:163: warning: passing argument 2 of ‘__pyx_f_6cyvcf2_6cyvcf2_newHREC’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] __pyx_t_4 = ((PyObject *)__pyx_f_6cyvcf2_6cyvcf2_newHREC((__pyx_cur_scope->__pyx_v_self->hdr->hrec[__pyx_cur_scope->__pyx_v_i]), __pyx_cur_scope->__pyx_v_self->hdr)); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 408, __pyx_L1_error) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ cyvcf2/cyvcf2.c:2896:61: note: expected ‘bcf_hdr_t *’ {aka ‘struct *’} but argument is of type ‘const bcf_hdr_t *’ {aka ‘const struct *’} static CYTHON_INLINE struct __pyx_obj_6cyvcf2_6cyvcf2_HREC *__pyx_f_6cyvcf2_6cyvcf2_newHREC(bcf_hrec_t *, bcf_hdr_t *); /*proto*/ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cyvcf2/cyvcf2.c: In function ‘__pyx_pf_6cyvcf2_6cyvcf2_3VCF_35__dealloc__’: cyvcf2/cyvcf2.c:11943:33: warning: passing argument 1 of ‘bcf_hdr_destroy’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] bcf_hdr_destroy(__pyx_v_self->hdr); ~~~~~~~~~~~~^~~~~ In file included from cyvcf2/helpers.h:1, from cyvcf2/cyvcf2.c:617: /usr/include/htslib/vcf.h:261:37: note: expected ‘bcf_hdr_t *’ {aka ‘struct *’} but argument is of type ‘const bcf_hdr_t *’ {aka ‘const struct *’} void bcf_hdr_destroy(bcf_hdr_t *h); ~~~~~~~~~~~^ cyvcf2/cyvcf2.c: In function ‘__pyx_pf_6cyvcf2_6cyvcf2_3VCF_10raw_header___get__’: cyvcf2/cyvcf2.c:12424:3: warning: ‘bcf_hdr_fmt_text’ is deprecated: use bcf_hdr_format() instead [-Wdeprecated-declarations] __pyx_v_s = bcf_hdr_fmt_text(__pyx_v_self->hdr, 0, (&__pyx_v_hlen)); ^~~~~~~~~ In file included from cyvcf2/helpers.h:1, from cyvcf2/cyvcf2.c:617: /usr/include/htslib/vcf.h:439:11: note: declared here char *bcf_hdr_fmt_text(const bcf_hdr_t *hdr, int is_bcf, int *len) ^~~~~~~~~~~~~~~~ cyvcf2/cyvcf2.c: In function ‘__pyx_pf_6cyvcf2_6cyvcf2_3VCF_8seqnames___get__’: cyvcf2/cyvcf2.c:12677:18: warning: assignment to ‘char **’ from incompatible pointer type ‘const char **’ [-Wincompatible-pointer-types] __pyx_v_cnames = bcf_hdr_seqnames(__pyx_v_self->hdr, (&__pyx_v_n)); ^ In file included from cyvcf2/helpers.h:1, from cyvcf2/cyvcf2.c:617: cyvcf2/cyvcf2.c:12786:75: warning: passing argument 4 of ‘hts_idx_seqnames’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] __pyx_v_cnames = bcf_index_seqnames(__pyx_v_self->hidx, __pyx_v_self->hdr, (&__pyx_v_n)); ^ In file included from /usr/include/htslib/vcf.h:39, from cyvcf2/helpers.h:1, from cyvcf2/cyvcf2.c:617: /usr/include/htslib/hts.h:677:18: note: expected ‘void *’ but argument is of type ‘const bcf_hdr_t *’ {aka ‘const struct *’} const char **hts_idx_seqnames(const hts_idx_t *idx, int *n, hts_id2name_f getid, void *hdr); // free only the array, not the values ^~~~~~~~~~~~~~~~ cyvcf2/cyvcf2.c:12786:22: warning: assignment to ‘char **’ from incompatible pointer type ‘const char **’ [-Wincompatible-pointer-types] __pyx_v_cnames = bcf_index_seqnames(__pyx_v_self->hidx, __pyx_v_self->hdr, (&__pyx_v_n)); ^ cyvcf2/cyvcf2.c:12869:22: warning: assignment to ‘char **’ from incompatible pointer type ‘const char **’ [-Wincompatible-pointer-types] __pyx_v_cnames = tbx_seqnames(__pyx_v_self->idx, (&__pyx_v_n)); ^ cyvcf2/cyvcf2.c: In function ‘__pyx_pf_6cyvcf2_6cyvcf2_7Variant_6FORMAT___get__’: cyvcf2/cyvcf2.c:25686:17: warning: assignment discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] __pyx_v_key = bcf_hdr_int2id(__pyx_v_self->vcf->hdr, BCF_DT_ID, __pyx_v_fmt.id); ^ cyvcf2/cyvcf2.c: In function ‘__pyx_pf_6cyvcf2_6cyvcf2_7Variant_6FILTER_2__set__’: cyvcf2/cyvcf2.c:35895:13: warning: assignment discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] __pyx_v_h = __pyx_t_6; ^ cyvcf2/cyvcf2.c: In function ‘__pyx_pf_6cyvcf2_6cyvcf2_4INFO_12__next__’: cyvcf2/cyvcf2.c:38938:16: warning: assignment discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] __pyx_v_name = bcf_hdr_int2id(__pyx_v_self->hdr, BCF_DT_ID, __pyx_v_info->key); ^ cyvcf2/cyvcf2.c: In function ‘__pyx_f_6cyvcf2_6cyvcf2_newVariant’: cyvcf2/cyvcf2.c:39921:18: warning: assignment discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] __pyx_v_i->hdr = __pyx_t_4; ^ cyvcf2/cyvcf2.c: In function ‘__pyx_pf_6cyvcf2_6cyvcf2_6Writer___init__’: cyvcf2/cyvcf2.c:40575:35: warning: passing argument 1 of ‘bcf_hdr_sync’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] (void)(bcf_hdr_sync(__pyx_v_tmpl->hdr)); ~~~~~~~~~~~~^~~~~ In file included from cyvcf2/helpers.h:1, from cyvcf2/cyvcf2.c:617: /usr/include/htslib/vcf.h:479:33: note: expected ‘bcf_hdr_t *’ {aka ‘struct *’} but argument is of type ‘const bcf_hdr_t *’ {aka ‘const struct *’} int bcf_hdr_sync(bcf_hdr_t *h); ~~~~~~~~~~~^ cyvcf2/cyvcf2.c:40603:47: warning: passing argument 1 of ‘bcf_hdr_sync’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] (void)(bcf_hdr_sync(__pyx_v_self->__pyx_base.hdr)); ~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from cyvcf2/helpers.h:1, from cyvcf2/cyvcf2.c:617: /usr/include/htslib/vcf.h:479:33: note: expected ‘bcf_hdr_t *’ {aka ‘struct *’} but argument is of type ‘const bcf_hdr_t *’ {aka ‘const struct *’} int bcf_hdr_sync(bcf_hdr_t *h); ~~~~~~~~~~~^ cyvcf2/cyvcf2.c: In function ‘__pyx_pf_6cyvcf2_6cyvcf2_6Writer_2write_header’: cyvcf2/cyvcf2.c:40671:78: warning: passing argument 2 of ‘bcf_hdr_write’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] (void)(bcf_hdr_write(__pyx_v_self->__pyx_base.hts, __pyx_v_self->__pyx_base.hdr)); ~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from cyvcf2/helpers.h:1, from cyvcf2/cyvcf2.c:617: /usr/include/htslib/vcf.h:320:47: note: expected ‘bcf_hdr_t *’ {aka ‘struct *’} but argument is of type ‘const bcf_hdr_t *’ {aka ‘const struct *’} int bcf_hdr_write(htsFile *fp, bcf_hdr_t *h); ~~~~~~~~~~~^ cyvcf2/cyvcf2.c: In function ‘__pyx_pf_6cyvcf2_6cyvcf2_6Writer_4write_record’: cyvcf2/cyvcf2.c:40843:60: warning: passing argument 1 of ‘bcf_hdr_add_hrec’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] __pyx_t_1 = ((bcf_hdr_add_hrec(__pyx_v_self->__pyx_base.hdr, __pyx_v_h) < 0) != 0); ~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from cyvcf2/helpers.h:1, from cyvcf2/cyvcf2.c:617: /usr/include/htslib/vcf.h:482:37: note: expected ‘bcf_hdr_t *’ {aka ‘struct *’} but argument is of type ‘const bcf_hdr_t *’ {aka ‘const struct *’} int bcf_hdr_add_hrec(bcf_hdr_t *hdr, bcf_hrec_t *hrec); ~~~~~~~~~~~^~~ cyvcf2/cyvcf2.c:40881:49: warning: passing argument 1 of ‘bcf_hdr_sync’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] (void)(bcf_hdr_sync(__pyx_v_self->__pyx_base.hdr)); ~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from cyvcf2/helpers.h:1, from cyvcf2/cyvcf2.c:617: /usr/include/htslib/vcf.h:479:33: note: expected ‘bcf_hdr_t *’ {aka ‘struct *’} but argument is of type ‘const bcf_hdr_t *’ {aka ‘const struct *’} int bcf_hdr_sync(bcf_hdr_t *h); ~~~~~~~~~~~^ cyvcf2/cyvcf2.c:40940:100: warning: passing argument 2 of ‘bcf_write’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] __pyx_t_2 = __Pyx_PyInt_From_int(bcf_write(__pyx_v_self->__pyx_base.hts, __pyx_v_self->__pyx_base.hdr, __pyx_v_var->b)); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 2168, __pyx_L1_error) ~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from cyvcf2/helpers.h:1, from cyvcf2/cyvcf2.c:617: /usr/include/htslib/vcf.h:370:43: note: expected ‘bcf_hdr_t *’ {aka ‘struct *’} but argument is of type ‘const bcf_hdr_t *’ {aka ‘const struct *’} int bcf_write(htsFile *fp, bcf_hdr_t *h, bcf1_t *v); ~~~~~~~~~~~^ At top level: cyvcf2/cyvcf2.c:6567:18: warning: ‘__pyx_f_6cyvcf2_6cyvcf2_xstr’ defined but not used [-Wunused-function] static PyObject *__pyx_f_6cyvcf2_6cyvcf2_xstr(PyObject *__pyx_v_s) { ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ s390x-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ihtslib -Icyvcf2 -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include/python2.7 -c cyvcf2/helpers.c -o build/temp.linux-s390x-2.7/cyvcf2/helpers.o s390x-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -Wdate-time -D_FORTIFY_SOURCE=2 -g -fdebug-prefix-map=/build/python2.7-R0y9EA/python2.7-2.7.16=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-s390x-2.7/cyvcf2/cyvcf2.o build/temp.linux-s390x-2.7/cyvcf2/helpers.o -lz -lbz2 -llzma -lcurl -lssl -lhts -lcrypt -o /<>/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2/cyvcf2.so I: pybuild base:217: /usr/bin/python3 setup.py build running build running build_py creating /<>/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2 copying cyvcf2/__init__.py -> /<>/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2 copying cyvcf2/__main__.py -> /<>/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2 copying cyvcf2/cli.py -> /<>/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2 creating /<>/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/test_hemi.py -> /<>/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/__init__.py -> /<>/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/test_reader.py -> /<>/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/test_cli.py -> /<>/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2/tests running egg_info writing cyvcf2.egg-info/PKG-INFO writing dependency_links to cyvcf2.egg-info/dependency_links.txt writing entry points to cyvcf2.egg-info/entry_points.txt writing requirements to cyvcf2.egg-info/requires.txt writing top-level names to cyvcf2.egg-info/top_level.txt reading manifest file 'cyvcf2.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no files found matching 'htslib/*.c' warning: no files found matching 'htslib/*.h' warning: no files found matching 'htslib/htslib/*.h' warning: no files found matching 'htslib/cram/*.c' warning: no files found matching 'htslib/cram/*.h' writing manifest file 'cyvcf2.egg-info/SOURCES.txt' copying cyvcf2/cyvcf2.c -> /<>/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2 copying cyvcf2/cyvcf2.pxd -> /<>/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2 copying cyvcf2/cyvcf2.pyx -> /<>/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2 copying cyvcf2/helpers.c -> /<>/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2 copying cyvcf2/helpers.h -> /<>/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2 copying cyvcf2/relatedness.h -> /<>/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2 copying cyvcf2/tests/bug.vcf.gz -> /<>/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/decomposed.vcf -> /<>/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/empty.vcf -> /<>/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/issue_44.vcf -> /<>/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/o.vcf.gz -> /<>/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/seg.vcf.gz -> /<>/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/test-alt-repr.vcf -> /<>/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/test-format-string.vcf -> /<>/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/test-haploidX.vcf -> /<>/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/test-hemi.vcf -> /<>/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/test-multiallelic-homozygous-alt.vcf.gz -> /<>/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/test-multiallelic-homozygous-alt.vcf.gz.tbi -> /<>/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/test-strict-gt-option-flag.vcf.gz -> /<>/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/test-strict-gt-option-flag.vcf.gz.tbi -> /<>/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/test.comp_het.3.vcf -> /<>/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/test.snpeff.bcf -> /<>/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/test.snpeff.bcf.csi -> /<>/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/test.snpeff.vcf -> /<>/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/test.vcf.gz -> /<>/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/test.vcf.gz.tbi -> /<>/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/test_gt_alt_freqs.vcf -> /<>/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/test_gt_bases.vcf.gz -> /<>/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2/tests running build_ext skipping 'cyvcf2/cyvcf2.c' Cython extension (up-to-date) building 'cyvcf2.cyvcf2' extension creating build/temp.linux-s390x-3.7 creating build/temp.linux-s390x-3.7/cyvcf2 s390x-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ihtslib -Icyvcf2 -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.7m -c cyvcf2/cyvcf2.c -o build/temp.linux-s390x-3.7/cyvcf2/cyvcf2.o In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1822, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:4, from cyvcf2/cyvcf2.c:614: /usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] #warning "Using deprecated NumPy API, disable it with " \ ^~~~~~~ cyvcf2/cyvcf2.c: In function ‘__pyx_pf_6cyvcf2_6cyvcf2_3VCF_4add_to_header’: cyvcf2/cyvcf2.c:7883:44: warning: passing argument 1 of ‘bcf_hdr_append’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] __pyx_v_ret = bcf_hdr_append(__pyx_v_self->hdr, __pyx_t_2); ~~~~~~~~~~~~^~~~~ In file included from cyvcf2/helpers.h:1, from cyvcf2/cyvcf2.c:617: /usr/include/htslib/vcf.h:443:35: note: expected ‘bcf_hdr_t *’ {aka ‘struct *’} but argument is of type ‘const bcf_hdr_t *’ {aka ‘const struct *’} int bcf_hdr_append(bcf_hdr_t *h, const char *line); ~~~~~~~~~~~^ cyvcf2/cyvcf2.c:7925:42: warning: passing argument 1 of ‘bcf_hdr_sync’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] __pyx_v_ret = bcf_hdr_sync(__pyx_v_self->hdr); ~~~~~~~~~~~~^~~~~ In file included from cyvcf2/helpers.h:1, from cyvcf2/cyvcf2.c:617: /usr/include/htslib/vcf.h:479:33: note: expected ‘bcf_hdr_t *’ {aka ‘struct *’} but argument is of type ‘const bcf_hdr_t *’ {aka ‘const struct *’} int bcf_hdr_sync(bcf_hdr_t *h); ~~~~~~~~~~~^ cyvcf2/cyvcf2.c: In function ‘__pyx_pf_6cyvcf2_6cyvcf2_3VCF_12set_samples’: cyvcf2/cyvcf2.c:8441:49: warning: passing argument 1 of ‘bcf_hdr_set_samples’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] __pyx_v_ret = bcf_hdr_set_samples(__pyx_v_self->hdr, ((char const *)__pyx_t_6), 0); ~~~~~~~~~~~~^~~~~ In file included from cyvcf2/helpers.h:1, from cyvcf2/cyvcf2.c:617: /usr/include/htslib/vcf.h:315:40: note: expected ‘bcf_hdr_t *’ {aka ‘struct *’} but argument is of type ‘const bcf_hdr_t *’ {aka ‘const struct *’} int bcf_hdr_set_samples(bcf_hdr_t *hdr, const char *samples, int is_file); ~~~~~~~~~~~^~~ cyvcf2/cyvcf2.c: In function ‘__pyx_pf_6cyvcf2_6cyvcf2_3VCF_14update’: cyvcf2/cyvcf2.c:8739:44: warning: passing argument 1 of ‘bcf_hdr_append’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] __pyx_v_ret = bcf_hdr_append(__pyx_v_self->hdr, __pyx_t_4); ~~~~~~~~~~~~^~~~~ In file included from cyvcf2/helpers.h:1, from cyvcf2/cyvcf2.c:617: /usr/include/htslib/vcf.h:443:35: note: expected ‘bcf_hdr_t *’ {aka ‘struct *’} but argument is of type ‘const bcf_hdr_t *’ {aka ‘const struct *’} int bcf_hdr_append(bcf_hdr_t *h, const char *line); ~~~~~~~~~~~^ cyvcf2/cyvcf2.c:8792:42: warning: passing argument 1 of ‘bcf_hdr_sync’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] __pyx_v_ret = bcf_hdr_sync(__pyx_v_self->hdr); ~~~~~~~~~~~~^~~~~ In file included from cyvcf2/helpers.h:1, from cyvcf2/cyvcf2.c:617: /usr/include/htslib/vcf.h:479:33: note: expected ‘bcf_hdr_t *’ {aka ‘struct *’} but argument is of type ‘const bcf_hdr_t *’ {aka ‘const struct *’} int bcf_hdr_sync(bcf_hdr_t *h); ~~~~~~~~~~~^ cyvcf2/cyvcf2.c: In function ‘__pyx_gb_6cyvcf2_6cyvcf2_3VCF_18generator’: cyvcf2/cyvcf2.c:9001:115: warning: passing argument 4 of ‘hts_itr_querys’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] __pyx_cur_scope->__pyx_v_itr = bcf_itr_querys(__pyx_cur_scope->__pyx_v_self->hidx, __pyx_cur_scope->__pyx_v_self->hdr, __pyx_t_2); ^ In file included from /usr/include/htslib/vcf.h:39, from cyvcf2/helpers.h:1, from cyvcf2/cyvcf2.c:617: /usr/include/htslib/hts.h:675:16: note: expected ‘void *’ but argument is of type ‘const bcf_hdr_t *’ {aka ‘const struct *’} hts_itr_t *hts_itr_querys(const hts_idx_t *idx, const char *reg, hts_name2id_f getid, void *hdr, hts_itr_query_func *itr_query, hts_readrec_func *readrec); ^~~~~~~~~~~~~~ cyvcf2/cyvcf2.c: In function ‘__pyx_gb_6cyvcf2_6cyvcf2_3VCF_24generator2’: cyvcf2/cyvcf2.c:10286:163: warning: passing argument 2 of ‘__pyx_f_6cyvcf2_6cyvcf2_newHREC’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] __pyx_t_4 = ((PyObject *)__pyx_f_6cyvcf2_6cyvcf2_newHREC((__pyx_cur_scope->__pyx_v_self->hdr->hrec[__pyx_cur_scope->__pyx_v_i]), __pyx_cur_scope->__pyx_v_self->hdr)); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 408, __pyx_L1_error) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ cyvcf2/cyvcf2.c:2896:61: note: expected ‘bcf_hdr_t *’ {aka ‘struct *’} but argument is of type ‘const bcf_hdr_t *’ {aka ‘const struct *’} static CYTHON_INLINE struct __pyx_obj_6cyvcf2_6cyvcf2_HREC *__pyx_f_6cyvcf2_6cyvcf2_newHREC(bcf_hrec_t *, bcf_hdr_t *); /*proto*/ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cyvcf2/cyvcf2.c: In function ‘__pyx_pf_6cyvcf2_6cyvcf2_3VCF_35__dealloc__’: cyvcf2/cyvcf2.c:11943:33: warning: passing argument 1 of ‘bcf_hdr_destroy’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] bcf_hdr_destroy(__pyx_v_self->hdr); ~~~~~~~~~~~~^~~~~ In file included from cyvcf2/helpers.h:1, from cyvcf2/cyvcf2.c:617: /usr/include/htslib/vcf.h:261:37: note: expected ‘bcf_hdr_t *’ {aka ‘struct *’} but argument is of type ‘const bcf_hdr_t *’ {aka ‘const struct *’} void bcf_hdr_destroy(bcf_hdr_t *h); ~~~~~~~~~~~^ cyvcf2/cyvcf2.c: In function ‘__pyx_pf_6cyvcf2_6cyvcf2_3VCF_10raw_header___get__’: cyvcf2/cyvcf2.c:12424:3: warning: ‘bcf_hdr_fmt_text’ is deprecated: use bcf_hdr_format() instead [-Wdeprecated-declarations] __pyx_v_s = bcf_hdr_fmt_text(__pyx_v_self->hdr, 0, (&__pyx_v_hlen)); ^~~~~~~~~ In file included from cyvcf2/helpers.h:1, from cyvcf2/cyvcf2.c:617: /usr/include/htslib/vcf.h:439:11: note: declared here char *bcf_hdr_fmt_text(const bcf_hdr_t *hdr, int is_bcf, int *len) ^~~~~~~~~~~~~~~~ cyvcf2/cyvcf2.c: In function ‘__pyx_pf_6cyvcf2_6cyvcf2_3VCF_8seqnames___get__’: cyvcf2/cyvcf2.c:12677:18: warning: assignment to ‘char **’ from incompatible pointer type ‘const char **’ [-Wincompatible-pointer-types] __pyx_v_cnames = bcf_hdr_seqnames(__pyx_v_self->hdr, (&__pyx_v_n)); ^ In file included from cyvcf2/helpers.h:1, from cyvcf2/cyvcf2.c:617: cyvcf2/cyvcf2.c:12786:75: warning: passing argument 4 of ‘hts_idx_seqnames’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] __pyx_v_cnames = bcf_index_seqnames(__pyx_v_self->hidx, __pyx_v_self->hdr, (&__pyx_v_n)); ^ In file included from /usr/include/htslib/vcf.h:39, from cyvcf2/helpers.h:1, from cyvcf2/cyvcf2.c:617: /usr/include/htslib/hts.h:677:18: note: expected ‘void *’ but argument is of type ‘const bcf_hdr_t *’ {aka ‘const struct *’} const char **hts_idx_seqnames(const hts_idx_t *idx, int *n, hts_id2name_f getid, void *hdr); // free only the array, not the values ^~~~~~~~~~~~~~~~ cyvcf2/cyvcf2.c:12786:22: warning: assignment to ‘char **’ from incompatible pointer type ‘const char **’ [-Wincompatible-pointer-types] __pyx_v_cnames = bcf_index_seqnames(__pyx_v_self->hidx, __pyx_v_self->hdr, (&__pyx_v_n)); ^ cyvcf2/cyvcf2.c:12869:22: warning: assignment to ‘char **’ from incompatible pointer type ‘const char **’ [-Wincompatible-pointer-types] __pyx_v_cnames = tbx_seqnames(__pyx_v_self->idx, (&__pyx_v_n)); ^ cyvcf2/cyvcf2.c: In function ‘__pyx_pf_6cyvcf2_6cyvcf2_7Variant_6FORMAT___get__’: cyvcf2/cyvcf2.c:25686:17: warning: assignment discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] __pyx_v_key = bcf_hdr_int2id(__pyx_v_self->vcf->hdr, BCF_DT_ID, __pyx_v_fmt.id); ^ cyvcf2/cyvcf2.c: In function ‘__pyx_pf_6cyvcf2_6cyvcf2_7Variant_6FILTER_2__set__’: cyvcf2/cyvcf2.c:35895:13: warning: assignment discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] __pyx_v_h = __pyx_t_6; ^ cyvcf2/cyvcf2.c: In function ‘__pyx_pf_6cyvcf2_6cyvcf2_4INFO_12__next__’: cyvcf2/cyvcf2.c:38938:16: warning: assignment discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] __pyx_v_name = bcf_hdr_int2id(__pyx_v_self->hdr, BCF_DT_ID, __pyx_v_info->key); ^ cyvcf2/cyvcf2.c: In function ‘__pyx_f_6cyvcf2_6cyvcf2_newVariant’: cyvcf2/cyvcf2.c:39921:18: warning: assignment discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] __pyx_v_i->hdr = __pyx_t_4; ^ cyvcf2/cyvcf2.c: In function ‘__pyx_pf_6cyvcf2_6cyvcf2_6Writer___init__’: cyvcf2/cyvcf2.c:40575:35: warning: passing argument 1 of ‘bcf_hdr_sync’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] (void)(bcf_hdr_sync(__pyx_v_tmpl->hdr)); ~~~~~~~~~~~~^~~~~ In file included from cyvcf2/helpers.h:1, from cyvcf2/cyvcf2.c:617: /usr/include/htslib/vcf.h:479:33: note: expected ‘bcf_hdr_t *’ {aka ‘struct *’} but argument is of type ‘const bcf_hdr_t *’ {aka ‘const struct *’} int bcf_hdr_sync(bcf_hdr_t *h); ~~~~~~~~~~~^ cyvcf2/cyvcf2.c:40603:47: warning: passing argument 1 of ‘bcf_hdr_sync’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] (void)(bcf_hdr_sync(__pyx_v_self->__pyx_base.hdr)); ~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from cyvcf2/helpers.h:1, from cyvcf2/cyvcf2.c:617: /usr/include/htslib/vcf.h:479:33: note: expected ‘bcf_hdr_t *’ {aka ‘struct *’} but argument is of type ‘const bcf_hdr_t *’ {aka ‘const struct *’} int bcf_hdr_sync(bcf_hdr_t *h); ~~~~~~~~~~~^ cyvcf2/cyvcf2.c: In function ‘__pyx_pf_6cyvcf2_6cyvcf2_6Writer_2write_header’: cyvcf2/cyvcf2.c:40671:78: warning: passing argument 2 of ‘bcf_hdr_write’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] (void)(bcf_hdr_write(__pyx_v_self->__pyx_base.hts, __pyx_v_self->__pyx_base.hdr)); ~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from cyvcf2/helpers.h:1, from cyvcf2/cyvcf2.c:617: /usr/include/htslib/vcf.h:320:47: note: expected ‘bcf_hdr_t *’ {aka ‘struct *’} but argument is of type ‘const bcf_hdr_t *’ {aka ‘const struct *’} int bcf_hdr_write(htsFile *fp, bcf_hdr_t *h); ~~~~~~~~~~~^ cyvcf2/cyvcf2.c: In function ‘__pyx_pf_6cyvcf2_6cyvcf2_6Writer_4write_record’: cyvcf2/cyvcf2.c:40843:60: warning: passing argument 1 of ‘bcf_hdr_add_hrec’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] __pyx_t_1 = ((bcf_hdr_add_hrec(__pyx_v_self->__pyx_base.hdr, __pyx_v_h) < 0) != 0); ~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from cyvcf2/helpers.h:1, from cyvcf2/cyvcf2.c:617: /usr/include/htslib/vcf.h:482:37: note: expected ‘bcf_hdr_t *’ {aka ‘struct *’} but argument is of type ‘const bcf_hdr_t *’ {aka ‘const struct *’} int bcf_hdr_add_hrec(bcf_hdr_t *hdr, bcf_hrec_t *hrec); ~~~~~~~~~~~^~~ cyvcf2/cyvcf2.c:40881:49: warning: passing argument 1 of ‘bcf_hdr_sync’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] (void)(bcf_hdr_sync(__pyx_v_self->__pyx_base.hdr)); ~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from cyvcf2/helpers.h:1, from cyvcf2/cyvcf2.c:617: /usr/include/htslib/vcf.h:479:33: note: expected ‘bcf_hdr_t *’ {aka ‘struct *’} but argument is of type ‘const bcf_hdr_t *’ {aka ‘const struct *’} int bcf_hdr_sync(bcf_hdr_t *h); ~~~~~~~~~~~^ cyvcf2/cyvcf2.c:40940:100: warning: passing argument 2 of ‘bcf_write’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] __pyx_t_2 = __Pyx_PyInt_From_int(bcf_write(__pyx_v_self->__pyx_base.hts, __pyx_v_self->__pyx_base.hdr, __pyx_v_var->b)); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 2168, __pyx_L1_error) ~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from cyvcf2/helpers.h:1, from cyvcf2/cyvcf2.c:617: /usr/include/htslib/vcf.h:370:43: note: expected ‘bcf_hdr_t *’ {aka ‘struct *’} but argument is of type ‘const bcf_hdr_t *’ {aka ‘const struct *’} int bcf_write(htsFile *fp, bcf_hdr_t *h, bcf1_t *v); ~~~~~~~~~~~^ At top level: cyvcf2/cyvcf2.c:6567:18: warning: ‘__pyx_f_6cyvcf2_6cyvcf2_xstr’ defined but not used [-Wunused-function] static PyObject *__pyx_f_6cyvcf2_6cyvcf2_xstr(PyObject *__pyx_v_s) { ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ s390x-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ihtslib -Icyvcf2 -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.7m -c cyvcf2/helpers.c -o build/temp.linux-s390x-3.7/cyvcf2/helpers.o s390x-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-s390x-3.7/cyvcf2/cyvcf2.o build/temp.linux-s390x-3.7/cyvcf2/helpers.o -lz -lbz2 -llzma -lcurl -lssl -lhts -lcrypt -o /<>/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2/cyvcf2.cpython-37m-s390x-linux-gnu.so dh_auto_test -a -O--buildsystem=pybuild I: pybuild base:217: cd /<>/.pybuild/cpython2_2.7_cyvcf2/build; python2.7 -m nose -v cyvcf2.tests.test_cli.test_version ... Segmentation fault (core dumped) E: pybuild pybuild:341: test: plugin distutils failed with: exit code=139: cd /<>/.pybuild/cpython2_2.7_cyvcf2/build; python2.7 -m nose -v dh_auto_test: pybuild --test --test-nose -i python{version} -p 2.7 returned exit code 13 make: *** [debian/rules:12: build-arch] Error 25 dpkg-buildpackage: error: debian/rules build-arch subprocess returned exit status 2 -------------------------------------------------------------------------------- Build finished at 20190622-2009 Finished -------- E: Build failure (dpkg-buildpackage died) +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not removing build depends: as requested +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: s390x Build-Space: 35364 Build-Time: 41 Distribution: eoan Fail-Stage: build Host Architecture: s390x Install-Time: 25 Job: cyvcf2_0.10.8-1.dsc Machine Architecture: s390x Package: cyvcf2 Package-Time: 66 Source-Version: 0.10.8-1 Space: 35364 Status: attempted Version: 0.10.8-1 -------------------------------------------------------------------------------- Finished at 20190622-2009 Build needed 00:01:06, 35364k disc space RUN: /usr/share/launchpad-buildd/bin/in-target scan-for-processes --backend=chroot --series=eoan --arch=s390x PACKAGEBUILD-16961252 Scanning for processes to kill in build PACKAGEBUILD-16961252