https://launchpad.net/ubuntu/+source/cyvcf2/0.10.0+git20180727-2/+build/15261391 RUN: /usr/share/launchpad-buildd/slavebin/slave-prep Forking launchpad-buildd slave process... Kernel version: Linux bos02-arm64-007 4.4.0-131-generic #157-Ubuntu SMP Thu Jul 12 15:48:43 UTC 2018 aarch64 Buildd toolchain package versions: launchpad-buildd_163 python-lpbuildd_163 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_1:2.7.4-0ubuntu1.4 dpkg-dev_1.18.4ubuntu1.4 python-debian_0.1.27ubuntu2. Syncing the system clock with the buildd NTP service... 14 Aug 17:10:15 ntpdate[1810]: adjust time server 10.211.37.1 offset -0.028641 sec RUN: /usr/share/launchpad-buildd/slavebin/in-target unpack-chroot --backend=chroot --series=cosmic --arch=armhf PACKAGEBUILD-15261391 /home/buildd/filecache-default/fc6c56f66744d62233b3c844f67cb7d83d839bbc Creating target for build PACKAGEBUILD-15261391 RUN: /usr/share/launchpad-buildd/slavebin/in-target mount-chroot --backend=chroot --series=cosmic --arch=armhf PACKAGEBUILD-15261391 Starting target for build PACKAGEBUILD-15261391 RUN: /usr/share/launchpad-buildd/slavebin/in-target override-sources-list --backend=chroot --series=cosmic --arch=armhf PACKAGEBUILD-15261391 'deb http://ftpmaster.internal/ubuntu cosmic main universe' 'deb http://ftpmaster.internal/ubuntu cosmic-security main universe' 'deb http://ftpmaster.internal/ubuntu cosmic-updates main universe' 'deb http://ftpmaster.internal/ubuntu cosmic-proposed main universe' Overriding sources.list in build-PACKAGEBUILD-15261391 RUN: /usr/share/launchpad-buildd/slavebin/in-target update-debian-chroot --backend=chroot --series=cosmic --arch=armhf PACKAGEBUILD-15261391 Updating target for build PACKAGEBUILD-15261391 Get:1 http://ftpmaster.internal/ubuntu cosmic InRelease [242 kB] Get:2 http://ftpmaster.internal/ubuntu cosmic-security InRelease [65.4 kB] Get:3 http://ftpmaster.internal/ubuntu cosmic-updates InRelease [65.4 kB] Get:4 http://ftpmaster.internal/ubuntu cosmic-proposed InRelease [92.5 kB] Get:5 http://ftpmaster.internal/ubuntu cosmic/main armhf Packages [974 kB] Get:6 http://ftpmaster.internal/ubuntu cosmic/main Translation-en [516 kB] Get:7 http://ftpmaster.internal/ubuntu cosmic/universe armhf Packages [8451 kB] Get:8 http://ftpmaster.internal/ubuntu cosmic/universe Translation-en [5052 kB] Get:9 http://ftpmaster.internal/ubuntu cosmic-proposed/main armhf Packages [96.8 kB] Get:10 http://ftpmaster.internal/ubuntu cosmic-proposed/main Translation-en [52.8 kB] Get:11 http://ftpmaster.internal/ubuntu cosmic-proposed/universe armhf Packages [549 kB] Get:12 http://ftpmaster.internal/ubuntu cosmic-proposed/universe Translation-en [292 kB] Fetched 16.4 MB in 16s (1037 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: g++-7 libargon2-0 libncursesw5 libprocps6 libstdc++-7-dev Use 'sudo apt autoremove' to remove them. The following NEW packages will be installed: cpp-8 g++-8 gcc-8 libargon2-1 libasan5 libgcc-8-dev libncurses6 libncursesw6 libprocps7 libstdc++-8-dev libtinfo6 libubsan1 The following packages will be upgraded: adduser apt base-files base-passwd bash binutils binutils-arm-linux-gnueabihf binutils-common bsdutils build-essential cpp cpp-7 debconf debianutils dpkg dpkg-dev e2fslibs e2fsprogs fdisk g++ g++-7 gcc gcc-7 gcc-7-base gcc-8-base gpg gpg-agent gpgconf gpgv init init-system-helpers libapparmor1 libapt-pkg5.0 libargon2-0 libasan4 libatomic1 libaudit-common libaudit1 libbinutils libblkid1 libcap-ng0 libcc1-0 libcilkrts5 libcom-err2 libcomerr2 libcryptsetup12 libdpkg-perl libext2fs2 libfdisk1 libgcc-7-dev libgcc1 libgcrypt20 libgmp10 libgomp1 libgpg-error0 libidn11 libidn2-0 libisl19 libkmod2 liblz4-1 libmount1 libncurses5 libncursesw5 libnpth0 libp11-kit0 libpcre3 libperl5.26 libpng16-16 libreadline7 libseccomp2 libselinux1 libsemanage-common libsemanage1 libsepol1 libslang2 libsmartcols1 libsqlite3-0 libss2 libssl1.1 libstdc++-7-dev libstdc++6 libsystemd0 libtasn1-6 libtinfo5 libubsan0 libudev1 libunistring2 libusb-0.1-4 libuuid1 linux-libc-dev make mount ncurses-base ncurses-bin openssl patch perl perl-base perl-modules-5.26 pinentry-curses pkgbinarymangler procps readline-common sed systemd systemd-sysv tar tzdata util-linux 109 upgraded, 12 newly installed, 0 to remove and 0 not upgraded. Need to get 70.4 MB of archives. After this operation, 68.9 MB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu cosmic/main armhf base-files armhf 10.1ubuntu4 [58.0 kB] Get:2 http://ftpmaster.internal/ubuntu cosmic/main armhf libtinfo6 armhf 6.1+20180210-4ubuntu1 [71.2 kB] Get:3 http://ftpmaster.internal/ubuntu cosmic/main armhf debianutils armhf 4.8.6 [84.4 kB] Get:4 http://ftpmaster.internal/ubuntu cosmic/main armhf bash armhf 4.4.18-2ubuntu2 [552 kB] Get:5 http://ftpmaster.internal/ubuntu cosmic/main armhf bsdutils armhf 1:2.32-0.1ubuntu1 [55.5 kB] Get:6 http://ftpmaster.internal/ubuntu cosmic/main armhf tar armhf 1.30+dfsg-2 [218 kB] Get:7 http://ftpmaster.internal/ubuntu cosmic-proposed/main armhf dpkg armhf 1.19.0.5ubuntu4 [1091 kB] Get:8 http://ftpmaster.internal/ubuntu cosmic/main armhf libext2fs2 armhf 1.44.3-1 [145 kB] Get:9 http://ftpmaster.internal/ubuntu cosmic/main armhf e2fsprogs armhf 1.44.3-1 [375 kB] Get:10 http://ftpmaster.internal/ubuntu cosmic/main armhf ncurses-bin armhf 6.1+20180210-4ubuntu1 [155 kB] Get:11 http://ftpmaster.internal/ubuntu cosmic-proposed/main armhf perl-modules-5.26 all 5.26.2-7 [2764 kB] Get:12 http://ftpmaster.internal/ubuntu cosmic-proposed/main armhf libperl5.26 armhf 5.26.2-7 [2882 kB] Get:13 http://ftpmaster.internal/ubuntu cosmic-proposed/main armhf perl armhf 5.26.2-7 [202 kB] Get:14 http://ftpmaster.internal/ubuntu cosmic-proposed/main armhf perl-base armhf 5.26.2-7 [1296 kB] Get:15 http://ftpmaster.internal/ubuntu cosmic/main armhf sed armhf 4.5-1 [177 kB] Get:16 http://ftpmaster.internal/ubuntu cosmic/main armhf libuuid1 armhf 2.32-0.1ubuntu1 [19.2 kB] Get:17 http://ftpmaster.internal/ubuntu cosmic/main armhf libblkid1 armhf 2.32-0.1ubuntu1 [115 kB] Get:18 http://ftpmaster.internal/ubuntu cosmic/main armhf libfdisk1 armhf 2.32-0.1ubuntu1 [155 kB] Get:19 http://ftpmaster.internal/ubuntu cosmic/main armhf libncursesw6 armhf 6.1+20180210-4ubuntu1 [104 kB] Get:20 http://ftpmaster.internal/ubuntu cosmic/main armhf libpcre3 armhf 2:8.39-11 [207 kB] Get:21 http://ftpmaster.internal/ubuntu cosmic-proposed/main armhf libselinux1 armhf 2.8-1build1 [59.2 kB] Get:22 http://ftpmaster.internal/ubuntu cosmic/main armhf libmount1 armhf 2.32-0.1ubuntu1 [125 kB] Get:23 http://ftpmaster.internal/ubuntu cosmic/main armhf libsmartcols1 armhf 2.32-0.1ubuntu1 [76.2 kB] Get:24 http://ftpmaster.internal/ubuntu cosmic/main armhf fdisk armhf 2.32-0.1ubuntu1 [98.7 kB] Get:25 http://ftpmaster.internal/ubuntu cosmic/main armhf util-linux armhf 2.32-0.1ubuntu1 [858 kB] Get:26 http://ftpmaster.internal/ubuntu cosmic/main armhf base-passwd armhf 3.5.45 [46.0 kB] Get:27 http://ftpmaster.internal/ubuntu cosmic-proposed/main armhf init-system-helpers all 1.52 [38.4 kB] Get:28 http://ftpmaster.internal/ubuntu cosmic/main armhf ncurses-base all 6.1+20180210-4ubuntu1 [18.4 kB] Get:29 http://ftpmaster.internal/ubuntu cosmic-proposed/main armhf libgomp1 armhf 8.2.0-3ubuntu1 [66.6 kB] Get:30 http://ftpmaster.internal/ubuntu cosmic-proposed/main armhf gcc-8-base armhf 8.2.0-3ubuntu1 [18.4 kB] Get:31 http://ftpmaster.internal/ubuntu cosmic-proposed/main armhf libgcc1 armhf 1:8.2.0-3ubuntu1 [37.1 kB] Get:32 http://ftpmaster.internal/ubuntu cosmic-proposed/main armhf libcc1-0 armhf 8.2.0-3ubuntu1 [32.5 kB] Get:33 http://ftpmaster.internal/ubuntu cosmic-proposed/main armhf libatomic1 armhf 8.2.0-3ubuntu1 [7060 B] Get:34 http://ftpmaster.internal/ubuntu cosmic-proposed/main armhf libstdc++6 armhf 8.2.0-3ubuntu1 [350 kB] Get:35 http://ftpmaster.internal/ubuntu cosmic/main armhf liblz4-1 armhf 1.8.2-1ubuntu1 [76.1 kB] Get:36 http://ftpmaster.internal/ubuntu cosmic-proposed/main armhf libudev1 armhf 239-7ubuntu2 [51.0 kB] Get:37 http://ftpmaster.internal/ubuntu cosmic-proposed/main armhf libapt-pkg5.0 armhf 1.7.0~alpha2ubuntu2 [730 kB] Get:38 http://ftpmaster.internal/ubuntu cosmic-proposed/main armhf debconf all 1.5.69 [121 kB] Get:39 http://ftpmaster.internal/ubuntu cosmic/main armhf adduser all 3.117ubuntu1 [163 kB] Get:40 http://ftpmaster.internal/ubuntu cosmic/main armhf libgpg-error0 armhf 1.32-1 [48.4 kB] Get:41 http://ftpmaster.internal/ubuntu cosmic/main armhf libgcrypt20 armhf 1.8.3-1ubuntu1 [364 kB] Get:42 http://ftpmaster.internal/ubuntu cosmic/main armhf gpgv armhf 2.2.8-1ubuntu1 [167 kB] Get:43 http://ftpmaster.internal/ubuntu cosmic/main armhf libseccomp2 armhf 2.3.3-3ubuntu1 [30.4 kB] Get:44 http://ftpmaster.internal/ubuntu cosmic-proposed/main armhf apt armhf 1.7.0~alpha2ubuntu2 [1128 kB] Get:45 http://ftpmaster.internal/ubuntu cosmic/main armhf libapparmor1 armhf 2.12-4ubuntu7 [26.5 kB] Get:46 http://ftpmaster.internal/ubuntu cosmic/main armhf libaudit-common all 1:2.8.3-1ubuntu2 [4064 B] Get:47 http://ftpmaster.internal/ubuntu cosmic/main armhf libcap-ng0 armhf 0.7.9-1 [10.1 kB] Get:48 http://ftpmaster.internal/ubuntu cosmic/main armhf libaudit1 armhf 1:2.8.3-1ubuntu2 [35.5 kB] Get:49 http://ftpmaster.internal/ubuntu cosmic/main armhf libargon2-1 armhf 0~20171227-0.1 [20.7 kB] Get:50 http://ftpmaster.internal/ubuntu cosmic/main armhf libcryptsetup12 armhf 2:2.0.3-6ubuntu1 [123 kB] Get:51 http://ftpmaster.internal/ubuntu cosmic/main armhf libkmod2 armhf 25-1ubuntu1 [35.7 kB] Get:52 http://ftpmaster.internal/ubuntu cosmic/main armhf mount armhf 2.32-0.1ubuntu1 [97.4 kB] Get:53 http://ftpmaster.internal/ubuntu cosmic/main armhf libncurses6 armhf 6.1+20180210-4ubuntu1 [78.5 kB] Get:54 http://ftpmaster.internal/ubuntu cosmic/main armhf libprocps7 armhf 2:3.3.15-2ubuntu1 [29.6 kB] Get:55 http://ftpmaster.internal/ubuntu cosmic/main armhf procps armhf 2:3.3.15-2ubuntu1 [219 kB] Get:56 http://ftpmaster.internal/ubuntu cosmic-proposed/main armhf systemd armhf 239-7ubuntu2 [2802 kB] Get:57 http://ftpmaster.internal/ubuntu cosmic-proposed/main armhf libsystemd0 armhf 239-7ubuntu2 [194 kB] Get:58 http://ftpmaster.internal/ubuntu cosmic-proposed/main armhf init armhf 1.52 [6600 B] Get:59 http://ftpmaster.internal/ubuntu cosmic-proposed/main armhf systemd-sysv armhf 239-7ubuntu2 [14.1 kB] Get:60 http://ftpmaster.internal/ubuntu cosmic/main armhf libcom-err2 armhf 1.44.3-1 [8356 B] Get:61 http://ftpmaster.internal/ubuntu cosmic/main armhf libsepol1 armhf 2.8-1 [219 kB] Get:62 http://ftpmaster.internal/ubuntu cosmic/main armhf libsemanage-common all 2.8-1build1 [7000 B] Get:63 http://ftpmaster.internal/ubuntu cosmic/main armhf libsemanage1 armhf 2.8-1build1 [73.0 kB] Get:64 http://ftpmaster.internal/ubuntu cosmic/main armhf libss2 armhf 1.44.3-1 [9396 B] Get:65 http://ftpmaster.internal/ubuntu cosmic/main armhf libgmp10 armhf 2:6.1.2+dfsg-3 [182 kB] Get:66 http://ftpmaster.internal/ubuntu cosmic/main armhf libunistring2 armhf 0.9.10-1ubuntu1 [350 kB] Get:67 http://ftpmaster.internal/ubuntu cosmic/main armhf libidn2-0 armhf 2.0.4-2.2 [46.0 kB] Get:68 http://ftpmaster.internal/ubuntu cosmic/main armhf libp11-kit0 armhf 0.23.12-2 [163 kB] Get:69 http://ftpmaster.internal/ubuntu cosmic/main armhf libtasn1-6 armhf 4.13-3 [31.1 kB] Get:70 http://ftpmaster.internal/ubuntu cosmic/universe armhf libncurses5 armhf 6.1+20180210-4ubuntu1 [74.9 kB] Get:71 http://ftpmaster.internal/ubuntu cosmic/main armhf libncursesw5 armhf 6.1+20180210-4ubuntu1 [95.3 kB] Get:72 http://ftpmaster.internal/ubuntu cosmic/main armhf libtinfo5 armhf 6.1+20180210-4ubuntu1 [67.6 kB] Get:73 http://ftpmaster.internal/ubuntu cosmic/main armhf libidn11 armhf 1.33-2.2ubuntu1 [43.5 kB] Get:74 http://ftpmaster.internal/ubuntu cosmic/main armhf readline-common all 7.0-5 [52.2 kB] Get:75 http://ftpmaster.internal/ubuntu cosmic/main armhf libreadline7 armhf 7.0-5 [102 kB] Get:76 http://ftpmaster.internal/ubuntu cosmic/main armhf libslang2 armhf 2.3.2-1ubuntu1 [383 kB] Get:77 http://ftpmaster.internal/ubuntu cosmic/main armhf libsqlite3-0 armhf 3.24.0-1 [429 kB] Get:78 http://ftpmaster.internal/ubuntu cosmic/main armhf libssl1.1 armhf 1.1.0g-2ubuntu5 [912 kB] Get:79 http://ftpmaster.internal/ubuntu cosmic/main armhf openssl armhf 1.1.0g-2ubuntu5 [510 kB] Get:80 http://ftpmaster.internal/ubuntu cosmic/main armhf tzdata all 2018e-1 [188 kB] Get:81 http://ftpmaster.internal/ubuntu cosmic-proposed/main armhf libpng16-16 armhf 1.6.34-2 [159 kB] Get:82 http://ftpmaster.internal/ubuntu cosmic-proposed/main armhf libbinutils armhf 2.31.1-3ubuntu1 [309 kB] Get:83 http://ftpmaster.internal/ubuntu cosmic-proposed/main armhf binutils-common armhf 2.31.1-3ubuntu1 [195 kB] Get:84 http://ftpmaster.internal/ubuntu cosmic-proposed/main armhf binutils armhf 2.31.1-3ubuntu1 [3348 B] Get:85 http://ftpmaster.internal/ubuntu cosmic-proposed/main armhf binutils-arm-linux-gnueabihf armhf 2.31.1-3ubuntu1 [2145 kB] Get:86 http://ftpmaster.internal/ubuntu cosmic/main armhf libisl19 armhf 0.20-1 [438 kB] Get:87 http://ftpmaster.internal/ubuntu cosmic-proposed/main armhf cpp-8 armhf 8.2.0-3ubuntu1 [5641 kB] Get:88 http://ftpmaster.internal/ubuntu cosmic/main armhf cpp armhf 4:8.1.0-2ubuntu1 [27.7 kB] Get:89 http://ftpmaster.internal/ubuntu cosmic-proposed/main armhf libasan5 armhf 8.2.0-3ubuntu1 [349 kB] Get:90 http://ftpmaster.internal/ubuntu cosmic-proposed/main armhf libubsan1 armhf 8.2.0-3ubuntu1 [109 kB] Get:91 http://ftpmaster.internal/ubuntu cosmic-proposed/main armhf libgcc-8-dev armhf 8.2.0-3ubuntu1 [632 kB] Get:92 http://ftpmaster.internal/ubuntu cosmic-proposed/main armhf gcc-8 armhf 8.2.0-3ubuntu1 [6342 kB] Get:93 http://ftpmaster.internal/ubuntu cosmic/main armhf gcc armhf 4:8.1.0-2ubuntu1 [5224 B] Get:94 http://ftpmaster.internal/ubuntu cosmic-proposed/main armhf libstdc++-8-dev armhf 8.2.0-3ubuntu1 [1592 kB] Get:95 http://ftpmaster.internal/ubuntu cosmic-proposed/main armhf g++-8 armhf 8.2.0-3ubuntu1 [6424 kB] Get:96 http://ftpmaster.internal/ubuntu cosmic/main armhf g++ armhf 4:8.1.0-2ubuntu1 [1608 B] Get:97 http://ftpmaster.internal/ubuntu cosmic-proposed/main armhf make armhf 4.2.1-1.2 [149 kB] Get:98 http://ftpmaster.internal/ubuntu cosmic-proposed/main armhf dpkg-dev all 1.19.0.5ubuntu4 [607 kB] Get:99 http://ftpmaster.internal/ubuntu cosmic-proposed/main armhf libdpkg-perl all 1.19.0.5ubuntu4 [211 kB] Get:100 http://ftpmaster.internal/ubuntu cosmic/main armhf patch armhf 2.7.6-3 [101 kB] Get:101 http://ftpmaster.internal/ubuntu cosmic/main armhf build-essential armhf 12.5ubuntu2 [4732 B] Get:102 http://ftpmaster.internal/ubuntu cosmic/main armhf libasan4 armhf 7.3.0-27ubuntu1 [327 kB] Get:103 http://ftpmaster.internal/ubuntu cosmic/main armhf libubsan0 armhf 7.3.0-27ubuntu1 [109 kB] Get:104 http://ftpmaster.internal/ubuntu cosmic/main armhf libcilkrts5 armhf 7.3.0-27ubuntu1 [35.9 kB] Get:105 http://ftpmaster.internal/ubuntu cosmic/universe armhf g++-7 armhf 7.3.0-27ubuntu1 [6051 kB] Get:106 http://ftpmaster.internal/ubuntu cosmic/main armhf gcc-7 armhf 7.3.0-27ubuntu1 [5951 kB] Get:107 http://ftpmaster.internal/ubuntu cosmic/main armhf libstdc++-7-dev armhf 7.3.0-27ubuntu1 [1536 kB] Get:108 http://ftpmaster.internal/ubuntu cosmic/main armhf libgcc-7-dev armhf 7.3.0-27ubuntu1 [707 kB] Get:109 http://ftpmaster.internal/ubuntu cosmic/main armhf cpp-7 armhf 7.3.0-27ubuntu1 [5295 kB] Get:110 http://ftpmaster.internal/ubuntu cosmic/main armhf gcc-7-base armhf 7.3.0-27ubuntu1 [18.9 kB] Get:111 http://ftpmaster.internal/ubuntu cosmic/main armhf e2fslibs armhf 1.44.3-1 [2704 B] Get:112 http://ftpmaster.internal/ubuntu cosmic/main armhf pinentry-curses armhf 1.1.0-1build2 [31.4 kB] Get:113 http://ftpmaster.internal/ubuntu cosmic/main armhf libnpth0 armhf 1.6-1 [6624 B] Get:114 http://ftpmaster.internal/ubuntu cosmic/main armhf gpg armhf 2.2.8-1ubuntu1 [411 kB] Get:115 http://ftpmaster.internal/ubuntu cosmic/main armhf gpgconf armhf 2.2.8-1ubuntu1 [105 kB] Get:116 http://ftpmaster.internal/ubuntu cosmic/main armhf gpg-agent armhf 2.2.8-1ubuntu1 [189 kB] Get:117 http://ftpmaster.internal/ubuntu cosmic/universe armhf libargon2-0 armhf 0~20171227-0.1 [4536 B] Get:118 http://ftpmaster.internal/ubuntu cosmic/main armhf libcomerr2 armhf 1.44.3-1 [2704 B] Get:119 http://ftpmaster.internal/ubuntu cosmic/main armhf libusb-0.1-4 armhf 2:0.1.12-32 [15.6 kB] Get:120 http://ftpmaster.internal/ubuntu cosmic-proposed/main armhf linux-libc-dev armhf 4.17.0-7.8 [1002 kB] Get:121 http://ftpmaster.internal/ubuntu cosmic/main armhf pkgbinarymangler all 141 [53.4 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 70.4 MB in 15s (4598 kB/s) (Reading database ... 12378 files and directories currently installed.) Preparing to unpack .../base-files_10.1ubuntu4_armhf.deb ... Unpacking base-files (10.1ubuntu4) over (10.1ubuntu2) ... Setting up base-files (10.1ubuntu4) ... 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 ... Selecting previously unselected package libtinfo6:armhf. (Reading database ... 12378 files and directories currently installed.) Preparing to unpack .../libtinfo6_6.1+20180210-4ubuntu1_armhf.deb ... Unpacking libtinfo6:armhf (6.1+20180210-4ubuntu1) ... Setting up libtinfo6:armhf (6.1+20180210-4ubuntu1) ... (Reading database ... 12387 files and directories currently installed.) Preparing to unpack .../debianutils_4.8.6_armhf.deb ... Unpacking debianutils (4.8.6) over (4.8.4) ... Setting up debianutils (4.8.6) ... (Reading database ... 12387 files and directories currently installed.) Preparing to unpack .../bash_4.4.18-2ubuntu2_armhf.deb ... Unpacking bash (4.4.18-2ubuntu2) over (4.4.18-2ubuntu1) ... Setting up bash (4.4.18-2ubuntu2) ... update-alternatives: using /usr/share/man/man7/bash-builtins.7.gz to provide /usr/share/man/man7/builtins.7.gz (builtins.7.gz) in auto mode (Reading database ... 12387 files and directories currently installed.) Preparing to unpack .../bsdutils_1%3a2.32-0.1ubuntu1_armhf.deb ... Unpacking bsdutils (1:2.32-0.1ubuntu1) over (1:2.31.1-0.4ubuntu3) ... Setting up bsdutils (1:2.32-0.1ubuntu1) ... (Reading database ... 12387 files and directories currently installed.) Preparing to unpack .../tar_1.30+dfsg-2_armhf.deb ... Unpacking tar (1.30+dfsg-2) over (1.29b-2) ... Setting up tar (1.30+dfsg-2) ... (Reading database ... 12387 files and directories currently installed.) Preparing to unpack .../dpkg_1.19.0.5ubuntu4_armhf.deb ... Unpacking dpkg (1.19.0.5ubuntu4) over (1.19.0.5ubuntu2) ... Setting up dpkg (1.19.0.5ubuntu4) ... (Reading database ... 12387 files and directories currently installed.) 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Setting up libnpth0:armhf (1.6-1) ... Setting up libncurses5:armhf (6.1+20180210-4ubuntu1) ... Setting up libgomp1:armhf (8.2.0-3ubuntu1) ... Setting up libatomic1:armhf (8.2.0-3ubuntu1) ... Setting up readline-common (7.0-5) ... Setting up libcc1-0:armhf (8.2.0-3ubuntu1) ... Setting up make (4.2.1-1.2) ... Setting up pkgbinarymangler (141) ... Setting up e2fslibs:armhf (1.44.3-1) ... Setting up libpng16-16:armhf (1.6.34-2) ... Setting up libncursesw5:armhf (6.1+20180210-4ubuntu1) ... Setting up libreadline7:armhf (7.0-5) ... Setting up tzdata (2018e-1) ... Current default time zone: 'Etc/UTC' Local time is now: Tue Aug 14 17:11:27 UTC 2018. Universal Time is now: Tue Aug 14 17:11:27 UTC 2018. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up systemd-sysv (239-7ubuntu2) ... Setting up gpgconf (2.2.8-1ubuntu1) ... Setting up linux-libc-dev:armhf (4.17.0-7.8) ... Setting up perl-modules-5.26 (5.26.2-7) ... Setting up libargon2-0 (0~20171227-0.1) ... 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Setting up init (1.52) ... Setting up libubsan0:armhf (7.3.0-27ubuntu1) ... Setting up binutils-arm-linux-gnueabihf (2.31.1-3ubuntu1) ... Setting up gpg-agent (2.2.8-1ubuntu1) ... Setting up libgcc-7-dev:armhf (7.3.0-27ubuntu1) ... Setting up cpp-7 (7.3.0-27ubuntu1) ... Setting up libstdc++-7-dev:armhf (7.3.0-27ubuntu1) ... Setting up perl (5.26.2-7) ... Setting up libgcc-8-dev:armhf (8.2.0-3ubuntu1) ... Setting up binutils (2.31.1-3ubuntu1) ... Setting up libstdc++-8-dev:armhf (8.2.0-3ubuntu1) ... Setting up gcc-7 (7.3.0-27ubuntu1) ... Setting up g++-7 (7.3.0-27ubuntu1) ... Setting up libdpkg-perl (1.19.0.5ubuntu4) ... Setting up gcc-8 (8.2.0-3ubuntu1) ... Setting up g++-8 (8.2.0-3ubuntu1) ... Setting up dpkg-dev (1.19.0.5ubuntu4) ... Setting up gcc (4:8.1.0-2ubuntu1) ... Setting up g++ (4:8.1.0-2ubuntu1) ... Setting up build-essential (12.5ubuntu2) ... Processing triggers for libc-bin (2.27-3ubuntu1) ... RUN: /usr/share/launchpad-buildd/slavebin/sbuild-package PACKAGEBUILD-15261391 armhf cosmic-proposed -c chroot:build-PACKAGEBUILD-15261391 --arch=armhf --dist=cosmic-proposed --nolog cyvcf2_0.10.0+git20180727-2.dsc Initiating build PACKAGEBUILD-15261391 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 4.4.0-131-generic #157-Ubuntu SMP Thu Jul 12 15:48:43 UTC 2018 armv7l sbuild (Debian sbuild) 0.67.0 (26 Dec 2015) on bos02-arm64-007.buildd +==============================================================================+ | cyvcf2 0.10.0+git20180727-2 (armhf) 14 Aug 2018 17:11 | +==============================================================================+ Package: cyvcf2 Version: 0.10.0+git20180727-2 Source Version: 0.10.0+git20180727-2 Distribution: cosmic-proposed Machine Architecture: arm64 Host Architecture: armhf Build Architecture: armhf I: NOTICE: Log filtering will replace 'build/cyvcf2-uVL8dc/cyvcf2-0.10.0+git20180727' with '<>' I: NOTICE: Log filtering will replace 'build/cyvcf2-uVL8dc' with '<>' I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-15261391/chroot-autobuild' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- cyvcf2_0.10.0+git20180727-2.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-xsoIg2/apt_archive/sbuild-build-depends-core-dummy.deb'. Ign:1 copy:/<>/resolver-xsoIg2/apt_archive ./ InRelease Get:2 copy:/<>/resolver-xsoIg2/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-xsoIg2/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-xsoIg2/apt_archive ./ Sources [214 B] Get:5 copy:/<>/resolver-xsoIg2/apt_archive ./ Packages [526 B] Fetched 2859 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: g++-7 libargon2-0 libncursesw5 libprocps6 libstdc++-7-dev 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-xsoIg2/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 ... 13382 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), dh-python, zlib1g-dev, cython, cython3, python-all, python-setuptools, python3-all, python3-setuptools, libpython-dev, libpython3-dev, 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 Filtered Build-Depends: debhelper (>= 10), dh-python, zlib1g-dev, cython, cython3, python-all, python-setuptools, python3-all, python3-setuptools, libpython-dev, libpython3-dev, 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 dpkg-deb: building package 'sbuild-build-depends-cyvcf2-dummy' in '/<>/resolver-48yJcA/apt_archive/sbuild-build-depends-cyvcf2-dummy.deb'. Ign:1 copy:/<>/resolver-48yJcA/apt_archive ./ InRelease Get:2 copy:/<>/resolver-48yJcA/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-48yJcA/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-48yJcA/apt_archive ./ Sources [325 B] Get:5 copy:/<>/resolver-48yJcA/apt_archive ./ Packages [649 B] Fetched 3093 B in 49710d 6h 28min 15s (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: g++-7 libargon2-0 libncursesw5 libprocps6 libstdc++-7-dev 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 libcroco3 libcurl3-gnutls libcurl4-gnutls-dev libelf1 libexpat1 libexpat1-dev libfile-stripnondeterminism-perl libgfortran5 libglib2.0-0 libgssapi-krb5-2 libgssapi3-heimdal libhcrypto4-heimdal libheimbase1-heimdal libheimntlm0-heimdal libhx509-5-heimdal libicu60 libk5crypto3 libkeyutils1 libkrb5-26-heimdal libkrb5-3 libkrb5support0 liblapack3 libldap-2.4-2 libldap-common libmagic-mgc libmagic1 libmpdec2 libnghttp2-14 libpipeline1 libpsl5 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 libpython3.6 libpython3.6-dev libpython3.6-minimal libpython3.6-stdlib libpython3.7 libpython3.7-dev libpython3.7-minimal libpython3.7-stdlib libroken18-heimdal librtmp1 libsasl2-2 libsasl2-modules-db libsigsegv2 libssl-dev libtimedate-perl libtool libwind0-heimdal libxml2 m4 man-db mime-support po-debconf python python-all python-click python-colorama python-coloredlogs python-humanfriendly python-minimal python-monotonic python-nose python-numpy python-pkg-resources python-setuptools python2 python2-minimal python2.7 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 python3.6 python3.6-dev python3.6-minimal 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 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-dev python-numpy-dbg python-numpy-doc python-setuptools-doc python2-doc python2.7-doc binfmt-support python3-doc python3-tk python3-venv python3-numpy-dbg python3.6-venv python3.6-doc python3.7-venv python3.7-doc Recommended packages: python-dev curl | wget | lynx libarchive-cpio-perl libglib2.0-data shared-mime-info xdg-user-dirs krb5-locales publicsuffix libsasl2-modules libssl-doc 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 libcroco3 libcurl3-gnutls libcurl4-gnutls-dev libelf1 libexpat1 libexpat1-dev libfile-stripnondeterminism-perl libgfortran5 libglib2.0-0 libgssapi-krb5-2 libgssapi3-heimdal libhcrypto4-heimdal libheimbase1-heimdal libheimntlm0-heimdal libhx509-5-heimdal libicu60 libk5crypto3 libkeyutils1 libkrb5-26-heimdal libkrb5-3 libkrb5support0 liblapack3 libldap-2.4-2 libldap-common libmagic-mgc libmagic1 libmpdec2 libnghttp2-14 libpipeline1 libpsl5 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 libpython3.6 libpython3.6-dev libpython3.6-minimal libpython3.6-stdlib libpython3.7 libpython3.7-dev libpython3.7-minimal libpython3.7-stdlib libroken18-heimdal librtmp1 libsasl2-2 libsasl2-modules-db libsigsegv2 libssl-dev libtimedate-perl libtool libwind0-heimdal libxml2 m4 man-db mime-support po-debconf python python-all python-click python-colorama python-coloredlogs python-humanfriendly python-minimal python-monotonic python-nose python-numpy python-pkg-resources python-setuptools python2 python2-minimal python2.7 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 python3.6 python3.6-dev python3.6-minimal python3.7 python3.7-dev python3.7-minimal sbuild-build-depends-cyvcf2-dummy zlib1g-dev 0 upgraded, 123 newly installed, 0 to remove and 0 not upgraded. Need to get 169 MB of archives. After this operation, 365 MB of additional disk space will be used. Get:1 copy:/<>/resolver-48yJcA/apt_archive ./ sbuild-build-depends-cyvcf2-dummy 0.invalid.0 [976 B] Get:2 http://ftpmaster.internal/ubuntu cosmic/main armhf libpython3.6-minimal armhf 3.6.6-1 [522 kB] Get:3 http://ftpmaster.internal/ubuntu cosmic/main armhf libexpat1 armhf 2.2.5-3 [59.7 kB] Get:4 http://ftpmaster.internal/ubuntu cosmic/main armhf python3.6-minimal armhf 3.6.6-1 [1340 kB] Get:5 http://ftpmaster.internal/ubuntu cosmic/main armhf python3-minimal armhf 3.6.6-1 [23.6 kB] Get:6 http://ftpmaster.internal/ubuntu cosmic/main armhf mime-support all 3.60ubuntu1 [30.1 kB] Get:7 http://ftpmaster.internal/ubuntu cosmic/main armhf libmpdec2 armhf 2.4.2-2 [66.4 kB] Get:8 http://ftpmaster.internal/ubuntu cosmic/main armhf libpython3.6-stdlib armhf 3.6.6-1 [1632 kB] Get:9 http://ftpmaster.internal/ubuntu cosmic/main armhf python3.6 armhf 3.6.6-1 [190 kB] Get:10 http://ftpmaster.internal/ubuntu cosmic/main armhf libpython3-stdlib armhf 3.6.6-1 [7144 B] Get:11 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http://ftpmaster.internal/ubuntu cosmic-proposed/main armhf libpython2.7-stdlib armhf 2.7.15-3 [1832 kB] Get:22 http://ftpmaster.internal/ubuntu cosmic-proposed/main armhf python2.7 armhf 2.7.15-3 [239 kB] Get:23 http://ftpmaster.internal/ubuntu cosmic/main armhf libpython2-stdlib armhf 2.7.15-3 [7728 B] Get:24 http://ftpmaster.internal/ubuntu cosmic/main armhf libpython-stdlib armhf 2.7.15-3 [5824 B] Get:25 http://ftpmaster.internal/ubuntu cosmic/main armhf python2 armhf 2.7.15-3 [26.5 kB] Get:26 http://ftpmaster.internal/ubuntu cosmic/main armhf python armhf 2.7.15-3 [7828 B] Get:27 http://ftpmaster.internal/ubuntu cosmic/main armhf libpython3.7-minimal armhf 3.7.0-4 [538 kB] Get:28 http://ftpmaster.internal/ubuntu cosmic/main armhf python3.7-minimal armhf 3.7.0-4 [1410 kB] Get:29 http://ftpmaster.internal/ubuntu cosmic-proposed/main armhf libmagic-mgc armhf 1:5.34-2 [197 kB] Get:30 http://ftpmaster.internal/ubuntu cosmic-proposed/main armhf libmagic1 armhf 1:5.34-2 [65.3 kB] Get:31 http://ftpmaster.internal/ubuntu cosmic-proposed/main armhf file armhf 1:5.34-2 [21.9 kB] Get:32 http://ftpmaster.internal/ubuntu cosmic/main armhf libelf1 armhf 0.170-0.5 [42.2 kB] Get:33 http://ftpmaster.internal/ubuntu cosmic/main armhf libglib2.0-0 armhf 2.57.2-1 [1018 kB] Get:34 http://ftpmaster.internal/ubuntu cosmic/main armhf libicu60 armhf 60.2-6ubuntu1 [7801 kB] Get:35 http://ftpmaster.internal/ubuntu cosmic-proposed/main armhf libxml2 armhf 2.9.4+dfsg1-7build1 [568 kB] Get:36 http://ftpmaster.internal/ubuntu cosmic/main armhf gettext-base armhf 0.19.8.1-7 [46.2 kB] Get:37 http://ftpmaster.internal/ubuntu cosmic/main armhf libkrb5support0 armhf 1.16-2build1 [27.5 kB] Get:38 http://ftpmaster.internal/ubuntu cosmic/main armhf libk5crypto3 armhf 1.16-2build1 [83.2 kB] Get:39 http://ftpmaster.internal/ubuntu cosmic/main armhf libkeyutils1 armhf 1.5.9-9.3 [8660 B] Get:40 http://ftpmaster.internal/ubuntu cosmic/main armhf libkrb5-3 armhf 1.16-2build1 [233 kB] Get:41 http://ftpmaster.internal/ubuntu cosmic/main armhf libgssapi-krb5-2 armhf 1.16-2build1 [101 kB] Get:42 http://ftpmaster.internal/ubuntu cosmic/main armhf libpsl5 armhf 0.20.2-1 [48.0 kB] Get:43 http://ftpmaster.internal/ubuntu cosmic/main armhf libsigsegv2 armhf 2.12-2 [13.1 kB] Get:44 http://ftpmaster.internal/ubuntu cosmic/main armhf m4 armhf 1.4.18-1 [181 kB] Get:45 http://ftpmaster.internal/ubuntu cosmic/main armhf autoconf all 2.69-11 [322 kB] Get:46 http://ftpmaster.internal/ubuntu cosmic/main armhf autotools-dev all 20180224.1 [39.6 kB] Get:47 http://ftpmaster.internal/ubuntu cosmic/main armhf automake all 1:1.15.1-3ubuntu2 [509 kB] Get:48 http://ftpmaster.internal/ubuntu cosmic/main armhf autopoint all 0.19.8.1-7 [412 kB] Get:49 http://ftpmaster.internal/ubuntu cosmic/universe armhf cython armhf 0.28.4-1 [1978 kB] Get:50 http://ftpmaster.internal/ubuntu cosmic/universe armhf cython3 armhf 0.28.4-1 [2849 kB] Get:51 http://ftpmaster.internal/ubuntu cosmic/main armhf libtool all 2.4.6-2.1build1 [196 kB] Get:52 http://ftpmaster.internal/ubuntu cosmic/main armhf dh-autoreconf all 19 [16.1 kB] Get:53 http://ftpmaster.internal/ubuntu cosmic/main armhf libarchive-zip-perl all 1.60-1ubuntu1 [84.6 kB] Get:54 http://ftpmaster.internal/ubuntu cosmic/main armhf libfile-stripnondeterminism-perl all 0.042-1 [15.2 kB] Get:55 http://ftpmaster.internal/ubuntu cosmic/main armhf libtimedate-perl all 2.3000-2 [37.5 kB] Get:56 http://ftpmaster.internal/ubuntu cosmic/main armhf dh-strip-nondeterminism all 0.042-1 [5188 B] Get:57 http://ftpmaster.internal/ubuntu cosmic/main armhf dwz armhf 0.12-2 [72.0 kB] Get:58 http://ftpmaster.internal/ubuntu cosmic/main armhf libcroco3 armhf 0.6.12-2 [69.4 kB] Get:59 http://ftpmaster.internal/ubuntu cosmic/main armhf gettext armhf 0.19.8.1-7 [833 kB] Get:60 http://ftpmaster.internal/ubuntu cosmic/main armhf intltool-debian all 0.35.0+20060710.4 [24.9 kB] Get:61 http://ftpmaster.internal/ubuntu cosmic/main armhf po-debconf all 1.0.20 [232 kB] Get:62 http://ftpmaster.internal/ubuntu cosmic/main armhf debhelper all 11.3.2ubuntu1 [883 kB] Get:63 http://ftpmaster.internal/ubuntu cosmic/main armhf python3-lib2to3 all 3.6.6-1 [76.9 kB] Get:64 http://ftpmaster.internal/ubuntu cosmic/main armhf python3-distutils all 3.6.6-1 [141 kB] Get:65 http://ftpmaster.internal/ubuntu cosmic/main armhf dh-python all 3.20180723 [90.2 kB] Get:66 http://ftpmaster.internal/ubuntu cosmic/main armhf libroken18-heimdal armhf 7.5.0+dfsg-2 [34.3 kB] Get:67 http://ftpmaster.internal/ubuntu cosmic/main armhf libasn1-8-heimdal armhf 7.5.0+dfsg-2 [136 kB] Get:68 http://ftpmaster.internal/ubuntu cosmic-proposed/main armhf libblas3 armhf 3.8.0-1build1 [98.5 kB] Get:69 http://ftpmaster.internal/ubuntu cosmic/main armhf libheimbase1-heimdal armhf 7.5.0+dfsg-2 [24.1 kB] Get:70 http://ftpmaster.internal/ubuntu cosmic/main armhf libhcrypto4-heimdal armhf 7.5.0+dfsg-2 [76.5 kB] Get:71 http://ftpmaster.internal/ubuntu cosmic/main armhf libwind0-heimdal armhf 7.5.0+dfsg-2 [47.2 kB] Get:72 http://ftpmaster.internal/ubuntu cosmic/main armhf libhx509-5-heimdal armhf 7.5.0+dfsg-2 [88.0 kB] Get:73 http://ftpmaster.internal/ubuntu cosmic/main armhf libkrb5-26-heimdal armhf 7.5.0+dfsg-2 [168 kB] Get:74 http://ftpmaster.internal/ubuntu cosmic/main armhf libheimntlm0-heimdal armhf 7.5.0+dfsg-2 [13.1 kB] Get:75 http://ftpmaster.internal/ubuntu cosmic/main armhf libgssapi3-heimdal armhf 7.5.0+dfsg-2 [79.0 kB] Get:76 http://ftpmaster.internal/ubuntu cosmic/main armhf libsasl2-modules-db armhf 2.1.27~101-g0780600+dfsg-3ubuntu2 [13.0 kB] Get:77 http://ftpmaster.internal/ubuntu cosmic/main armhf libsasl2-2 armhf 2.1.27~101-g0780600+dfsg-3ubuntu2 [42.0 kB] Get:78 http://ftpmaster.internal/ubuntu cosmic/main armhf libldap-common all 2.4.46+dfsg-5ubuntu1 [16.6 kB] Get:79 http://ftpmaster.internal/ubuntu cosmic/main armhf libldap-2.4-2 armhf 2.4.46+dfsg-5ubuntu1 [131 kB] Get:80 http://ftpmaster.internal/ubuntu cosmic/main armhf libnghttp2-14 armhf 1.32.0-1 [67.3 kB] Get:81 http://ftpmaster.internal/ubuntu cosmic/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2 [49.2 kB] Get:82 http://ftpmaster.internal/ubuntu cosmic/main armhf libcurl3-gnutls armhf 7.60.0-2ubuntu1 [183 kB] Get:83 http://ftpmaster.internal/ubuntu cosmic/main armhf libcurl4-gnutls-dev armhf 7.60.0-2ubuntu1 [272 kB] Get:84 http://ftpmaster.internal/ubuntu cosmic/main armhf libexpat1-dev armhf 2.2.5-3 [106 kB] Get:85 http://ftpmaster.internal/ubuntu cosmic-proposed/main armhf libgfortran5 armhf 8.2.0-3ubuntu1 [221 kB] Get:86 http://ftpmaster.internal/ubuntu cosmic-proposed/main armhf liblapack3 armhf 3.8.0-1build1 [1618 kB] Get:87 http://ftpmaster.internal/ubuntu cosmic-proposed/main armhf libpython2.7 armhf 2.7.15-3 [890 kB] Get:88 http://ftpmaster.internal/ubuntu cosmic-proposed/main armhf libpython2.7-dev armhf 2.7.15-3 [30.9 MB] Get:89 http://ftpmaster.internal/ubuntu cosmic/main armhf libpython2-dev armhf 2.7.15-3 [7788 B] Get:90 http://ftpmaster.internal/ubuntu cosmic/main armhf libpython-dev armhf 2.7.15-3 [5888 B] Get:91 http://ftpmaster.internal/ubuntu cosmic/main armhf libpython3.6 armhf 3.6.6-1 [1211 kB] Get:92 http://ftpmaster.internal/ubuntu cosmic/main armhf libpython3.6-dev armhf 3.6.6-1 [43.7 MB] Get:93 http://ftpmaster.internal/ubuntu cosmic/main armhf libpython3-dev armhf 3.6.6-1 [7248 B] Get:94 http://ftpmaster.internal/ubuntu cosmic/main armhf libpython3.7-stdlib armhf 3.7.0-4 [1659 kB] Get:95 http://ftpmaster.internal/ubuntu cosmic/main armhf libpython3.7 armhf 3.7.0-4 [1279 kB] Get:96 http://ftpmaster.internal/ubuntu cosmic/main armhf libpython3.7-dev armhf 3.7.0-4 [47.0 MB] Get:97 http://ftpmaster.internal/ubuntu cosmic/main armhf libpython3-all-dev armhf 3.6.6-1 [1116 B] Get:98 http://ftpmaster.internal/ubuntu cosmic/main armhf libssl-dev armhf 1.1.0g-2ubuntu5 [1183 kB] Get:99 http://ftpmaster.internal/ubuntu cosmic/main armhf python-all armhf 2.7.15-3 [1072 B] Get:100 http://ftpmaster.internal/ubuntu cosmic/main armhf python-colorama all 0.3.7-1 [22.6 kB] Get:101 http://ftpmaster.internal/ubuntu cosmic/main armhf python-click all 6.7-5 [56.5 kB] Get:102 http://ftpmaster.internal/ubuntu cosmic/main armhf python-monotonic all 1.1-2 [5262 B] Get:103 http://ftpmaster.internal/ubuntu cosmic/universe armhf python-humanfriendly all 4.4.1-1 [51.0 kB] Get:104 http://ftpmaster.internal/ubuntu cosmic/universe armhf python-coloredlogs all 7.3-1 [27.7 kB] Get:105 http://ftpmaster.internal/ubuntu cosmic/main armhf python-pkg-resources all 39.2.0-1 [128 kB] Get:106 http://ftpmaster.internal/ubuntu cosmic/universe armhf python-nose all 1.3.7-4 [116 kB] Get:107 http://ftpmaster.internal/ubuntu cosmic-proposed/main armhf python-numpy armhf 1:1.14.5-1ubuntu3 [1803 kB] Get:108 http://ftpmaster.internal/ubuntu cosmic/main armhf python-setuptools all 39.2.0-1 [331 kB] Get:109 http://ftpmaster.internal/ubuntu cosmic/main armhf python3.7 armhf 3.7.0-4 [264 kB] Get:110 http://ftpmaster.internal/ubuntu cosmic/main armhf python3-all armhf 3.6.6-1 [1112 B] Get:111 http://ftpmaster.internal/ubuntu cosmic/main armhf python3.6-dev armhf 3.6.6-1 [508 kB] Get:112 http://ftpmaster.internal/ubuntu cosmic/main armhf python3-dev armhf 3.6.6-1 [1312 B] Get:113 http://ftpmaster.internal/ubuntu cosmic/main armhf python3.7-dev armhf 3.7.0-4 [511 kB] Get:114 http://ftpmaster.internal/ubuntu cosmic/main armhf python3-all-dev armhf 3.6.6-1 [1116 B] Get:115 http://ftpmaster.internal/ubuntu cosmic/main armhf python3-colorama all 0.3.7-1 [14.9 kB] Get:116 http://ftpmaster.internal/ubuntu cosmic/main armhf python3-click all 6.7-5 [56.6 kB] Get:117 http://ftpmaster.internal/ubuntu cosmic/universe armhf python3-humanfriendly all 4.4.1-1 [51.1 kB] Get:118 http://ftpmaster.internal/ubuntu cosmic/universe armhf python3-coloredlogs all 7.3-1 [27.8 kB] Get:119 http://ftpmaster.internal/ubuntu cosmic/main armhf python3-pkg-resources all 39.2.0-1 [98.8 kB] Get:120 http://ftpmaster.internal/ubuntu cosmic/universe armhf python3-nose all 1.3.7-4 [116 kB] Get:121 http://ftpmaster.internal/ubuntu cosmic-proposed/main armhf python3-numpy armhf 1:1.14.5-1ubuntu3 [1971 kB] Get:122 http://ftpmaster.internal/ubuntu cosmic/main armhf python3-setuptools all 39.2.0-1 [248 kB] Get:123 http://ftpmaster.internal/ubuntu cosmic/main armhf zlib1g-dev armhf 1:1.2.11.dfsg-0ubuntu2 [168 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 169 MB in 17s (9832 kB/s) Selecting previously unselected package libpython3.6-minimal:armhf. (Reading database ... 13382 files and directories currently installed.) Preparing to unpack .../libpython3.6-minimal_3.6.6-1_armhf.deb ... Unpacking libpython3.6-minimal:armhf (3.6.6-1) ... Selecting previously unselected package libexpat1:armhf. Preparing to unpack .../libexpat1_2.2.5-3_armhf.deb ... Unpacking libexpat1:armhf (2.2.5-3) ... Selecting previously unselected package python3.6-minimal. Preparing to unpack .../python3.6-minimal_3.6.6-1_armhf.deb ... Unpacking python3.6-minimal (3.6.6-1) ... Setting up libpython3.6-minimal:armhf (3.6.6-1) ... Setting up libexpat1:armhf (2.2.5-3) ... Setting up python3.6-minimal (3.6.6-1) ... Selecting previously unselected package python3-minimal. (Reading database ... 13629 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.6.6-1_armhf.deb ... Unpacking python3-minimal (3.6.6-1) ... Selecting previously unselected package mime-support. Preparing to unpack .../1-mime-support_3.60ubuntu1_all.deb ... 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Setting up libicu60:armhf (60.2-6ubuntu1) ... Setting up libarchive-zip-perl (1.60-1ubuntu1) ... Setting up libnghttp2-14:armhf (1.32.0-1) ... Setting up mime-support (3.60ubuntu1) ... Setting up libtimedate-perl (2.3000-2) ... Setting up libsigsegv2:armhf (2.12-2) ... Setting up libldap-common (2.4.46+dfsg-5ubuntu1) ... Setting up libpsl5:armhf (0.20.2-1) ... Setting up libelf1:armhf (0.170-0.5) ... Setting up libssl-dev:armhf (1.1.0g-2ubuntu5) ... Setting up groff-base (1.22.3-10) ... Setting up libglib2.0-0:armhf (2.57.2-1) ... No schema files found: doing nothing. Setting up libsasl2-modules-db:armhf (2.1.27~101-g0780600+dfsg-3ubuntu2) ... Setting up libsasl2-2:armhf (2.1.27~101-g0780600+dfsg-3ubuntu2) ... Setting up gettext-base (0.19.8.1-7) ... Setting up libpipeline1:armhf (1.5.0-1) ... Setting up libroken18-heimdal:armhf (7.5.0+dfsg-2) ... Setting up librtmp1:armhf (2.4+20151223.gitfa8646d.1-2) ... Setting up m4 (1.4.18-1) ... Setting up libpython3.7-minimal:armhf (3.7.0-4) ... Setting up python3.7-minimal (3.7.0-4) ... Setting up libbsd0:armhf (0.9.1-1) ... Setting up libkrb5support0:armhf (1.16-2build1) ... Setting up libxml2:armhf (2.9.4+dfsg1-7build1) ... Setting up libmagic-mgc (1:5.34-2) ... Setting up libmagic1:armhf (1:5.34-2) ... Setting up libcroco3:armhf (0.6.12-2) ... Setting up libblas3:armhf (3.8.0-1build1) ... update-alternatives: using /usr/lib/arm-linux-gnueabihf/blas/libblas.so.3 to provide /usr/lib/arm-linux-gnueabihf/libblas.so.3 (libblas.so.3-arm-linux-gnueabihf) in auto mode Processing triggers for libc-bin (2.27-3ubuntu1) ... Setting up dwz (0.12-2) ... Setting up autotools-dev (20180224.1) ... Setting up libheimbase1-heimdal:armhf (7.5.0+dfsg-2) ... Setting up libexpat1-dev:armhf (2.2.5-3) ... Setting up libkeyutils1:armhf (1.5.9-9.3) ... Setting up bsdmainutils (11.1.2ubuntu2) ... update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode Setting up libgfortran5:armhf (8.2.0-3ubuntu1) ... Setting up libpython2.7-stdlib:armhf (2.7.15-3) ... Setting up autopoint (0.19.8.1-7) ... Setting up libmpdec2:armhf (2.4.2-2) ... Setting up zlib1g-dev:armhf (1:1.2.11.dfsg-0ubuntu2) ... Setting up libfile-stripnondeterminism-perl (0.042-1) ... Setting up libpython3.6-stdlib:armhf (3.6.6-1) ... Setting up libk5crypto3:armhf (1.16-2build1) ... Setting up libpython3.7-stdlib:armhf (3.7.0-4) ... Setting up python3.6 (3.6.6-1) ... Setting up libwind0-heimdal:armhf (7.5.0+dfsg-2) ... Setting up gettext (0.19.8.1-7) ... Setting up libasn1-8-heimdal:armhf (7.5.0+dfsg-2) ... Setting up liblapack3:armhf (3.8.0-1build1) ... update-alternatives: using /usr/lib/arm-linux-gnueabihf/lapack/liblapack.so.3 to provide /usr/lib/arm-linux-gnueabihf/liblapack.so.3 (liblapack.so.3-arm-linux-gnueabihf) in auto mode Setting up libhcrypto4-heimdal:armhf (7.5.0+dfsg-2) ... Setting up python2.7 (2.7.15-3) ... Setting up python3.7 (3.7.0-4) ... Setting up autoconf (2.69-11) ... Setting up file (1:5.34-2) ... Setting up libhx509-5-heimdal:armhf (7.5.0+dfsg-2) ... Setting up intltool-debian (0.35.0+20060710.4) ... Setting up libpython3.7:armhf (3.7.0-4) ... Setting up libpython2.7:armhf (2.7.15-3) ... 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 libpython3.7-dev:armhf (3.7.0-4) ... Setting up man-db (2.8.4-2) ... Not building database; man-db/auto-update is not 'true'. Setting up libpython2-stdlib:armhf (2.7.15-3) ... Setting up libkrb5-3:armhf (1.16-2build1) ... Setting up libpython2.7-dev:armhf (2.7.15-3) ... Setting up libkrb5-26-heimdal:armhf (7.5.0+dfsg-2) ... Setting up libheimntlm0-heimdal:armhf (7.5.0+dfsg-2) ... Setting up libpython3.6:armhf (3.6.6-1) ... Setting up libtool (2.4.6-2.1build1) ... Setting up libpython3-stdlib:armhf (3.6.6-1) ... Setting up po-debconf (1.0.20) ... Setting up python3 (3.6.6-1) ... Setting up python3-numpy (1:1.14.5-1ubuntu3) ... Setting up python3-colorama (0.3.7-1) ... Setting up python3-pkg-resources (39.2.0-1) ... Setting up python3.7-dev (3.7.0-4) ... Setting up libpython3.6-dev:armhf (3.6.6-1) ... Setting up python3-humanfriendly (4.4.1-1) ... Setting up python2 (2.7.15-3) ... Setting up libgssapi-krb5-2:armhf (1.16-2build1) ... Setting up libpython2-dev:armhf (2.7.15-3) ... Setting up libpython-stdlib:armhf (2.7.15-3) ... Setting up python3-nose (1.3.7-4) ... Setting up cython3 (0.28.4-1) ... Setting up libgssapi3-heimdal:armhf (7.5.0+dfsg-2) ... Setting up python3.6-dev (3.6.6-1) ... Setting up python3-coloredlogs (7.3-1) ... Setting up python3-lib2to3 (3.6.6-1) ... Setting up python3-distutils (3.6.6-1) ... Setting up python (2.7.15-3) ... Setting up libpython3-dev:armhf (3.6.6-1) ... Setting up libpython-dev:armhf (2.7.15-3) ... Setting up python-monotonic (1.1-2) ... Setting up python3-click (6.7-5) ... Setting up python-colorama (0.3.7-1) ... Setting up python-pkg-resources (39.2.0-1) ... Setting up python-numpy (1:1.14.5-1ubuntu3) ... Setting up cython (0.28.4-1) ... Setting up libpython3-all-dev:armhf (3.6.6-1) ... Setting up libldap-2.4-2:armhf (2.4.46+dfsg-5ubuntu1) ... Setting up python3-setuptools (39.2.0-1) ... Setting up dh-python (3.20180723) ... Setting up python-nose (1.3.7-4) ... Setting up python-all (2.7.15-3) ... Setting up python-humanfriendly (4.4.1-1) ... Setting up python-setuptools (39.2.0-1) ... Setting up python-click (6.7-5) ... Setting up libcurl3-gnutls:armhf (7.60.0-2ubuntu1) ... Setting up python3-dev (3.6.6-1) ... Setting up python-coloredlogs (7.3-1) ... Setting up python3-all (3.6.6-1) ... Setting up libcurl4-gnutls-dev:armhf (7.60.0-2ubuntu1) ... Setting up python3-all-dev (3.6.6-1) ... Setting up dh-autoreconf (19) ... Setting up dh-strip-nondeterminism (0.042-1) ... Setting up debhelper (11.3.2ubuntu1) ... Setting up sbuild-build-depends-cyvcf2-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.27-3ubuntu1) ... +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 4.4.0-131-generic arm64 (armv7l) Toolchain package versions: binutils_2.31.1-3ubuntu1 dpkg-dev_1.19.0.5ubuntu4 g++-7_7.3.0-27ubuntu1 g++-8_8.2.0-3ubuntu1 gcc-7_7.3.0-27ubuntu1 gcc-8_8.2.0-3ubuntu1 libc6-dev_2.27-3ubuntu1 libstdc++-7-dev_7.3.0-27ubuntu1 libstdc++-8-dev_8.2.0-3ubuntu1 libstdc++6_8.2.0-3ubuntu1 linux-libc-dev_4.17.0-7.8 Package versions: adduser_3.117ubuntu1 advancecomp_2.1-1 apt_1.7.0~alpha2ubuntu2 autoconf_2.69-11 automake_1:1.15.1-3ubuntu2 autopoint_0.19.8.1-7 autotools-dev_20180224.1 base-files_10.1ubuntu4 base-passwd_3.5.45 bash_4.4.18-2ubuntu2 binutils_2.31.1-3ubuntu1 binutils-arm-linux-gnueabihf_2.31.1-3ubuntu1 binutils-common_2.31.1-3ubuntu1 bsdmainutils_11.1.2ubuntu2 bsdutils_1:2.32-0.1ubuntu1 build-essential_12.5ubuntu2 bzip2_1.0.6-8.1 ca-certificates_20180409 coreutils_8.28-1ubuntu1 cpp_4:8.1.0-2ubuntu1 cpp-7_7.3.0-27ubuntu1 cpp-8_8.2.0-3ubuntu1 cython_0.28.4-1 cython3_0.28.4-1 dash_0.5.8-2.10 debconf_1.5.69 debhelper_11.3.2ubuntu1 debianutils_4.8.6 dh-autoreconf_19 dh-python_3.20180723 dh-strip-nondeterminism_0.042-1 diffutils_1:3.6-1 dmsetup_2:1.02.145-4.1ubuntu3 dpkg_1.19.0.5ubuntu4 dpkg-dev_1.19.0.5ubuntu4 dwz_0.12-2 e2fslibs_1.44.3-1 e2fsprogs_1.44.3-1 fakeroot_1.22-2ubuntu1 fdisk_2.32-0.1ubuntu1 file_1:5.34-2 findutils_4.6.0+git+20170828-2 g++_4:8.1.0-2ubuntu1 g++-7_7.3.0-27ubuntu1 g++-8_8.2.0-3ubuntu1 gcc_4:8.1.0-2ubuntu1 gcc-7_7.3.0-27ubuntu1 gcc-7-base_7.3.0-27ubuntu1 gcc-8_8.2.0-3ubuntu1 gcc-8-base_8.2.0-3ubuntu1 gettext_0.19.8.1-7 gettext-base_0.19.8.1-7 gpg_2.2.8-1ubuntu1 gpg-agent_2.2.8-1ubuntu1 gpgconf_2.2.8-1ubuntu1 gpgv_2.2.8-1ubuntu1 grep_3.1-2 groff-base_1.22.3-10 gzip_1.6-5ubuntu1 hostname_3.20 init_1.52 init-system-helpers_1.52 initscripts_2.88dsf-59.3ubuntu2 insserv_1.14.0-5ubuntu3 intltool-debian_0.35.0+20060710.4 libacl1_2.2.52-3build1 libapparmor1_2.12-4ubuntu7 libapt-pkg5.0_1.7.0~alpha2ubuntu2 libarchive-zip-perl_1.60-1ubuntu1 libargon2-0_0~20171227-0.1 libargon2-1_0~20171227-0.1 libasan4_7.3.0-27ubuntu1 libasan5_8.2.0-3ubuntu1 libasn1-8-heimdal_7.5.0+dfsg-2 libassuan0_2.5.1-2 libatomic1_8.2.0-3ubuntu1 libattr1_1:2.4.47-2build1 libaudit-common_1:2.8.3-1ubuntu2 libaudit1_1:2.8.3-1ubuntu2 libbinutils_2.31.1-3ubuntu1 libblas3_3.8.0-1build1 libblkid1_2.32-0.1ubuntu1 libbsd0_0.9.1-1 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_0.7.9-1 libcap2_1:2.25-1.2 libcc1-0_8.2.0-3ubuntu1 libcilkrts5_7.3.0-27ubuntu1 libcom-err2_1.44.3-1 libcomerr2_1.44.3-1 libcroco3_0.6.12-2 libcryptsetup12_2:2.0.3-6ubuntu1 libcurl3-gnutls_7.60.0-2ubuntu1 libcurl4-gnutls-dev_7.60.0-2ubuntu1 libdb5.3_5.3.28-13.1ubuntu1 libdebconfclient0_0.213ubuntu1 libdevmapper1.02.1_2:1.02.145-4.1ubuntu3 libdpkg-perl_1.19.0.5ubuntu4 libelf1_0.170-0.5 libexpat1_2.2.5-3 libexpat1-dev_2.2.5-3 libext2fs2_1.44.3-1 libfakeroot_1.22-2ubuntu1 libfdisk1_2.32-0.1ubuntu1 libffi6_3.2.1-8 libfile-stripnondeterminism-perl_0.042-1 libgcc-7-dev_7.3.0-27ubuntu1 libgcc-8-dev_8.2.0-3ubuntu1 libgcc1_1:8.2.0-3ubuntu1 libgcrypt20_1.8.3-1ubuntu1 libgdbm-compat4_1.14.1-6 libgdbm5_1.14.1-6 libgfortran5_8.2.0-3ubuntu1 libglib2.0-0_2.57.2-1 libgmp10_2:6.1.2+dfsg-3 libgnutls30_3.5.18-1ubuntu1 libgomp1_8.2.0-3ubuntu1 libgpg-error0_1.32-1 libgssapi-krb5-2_1.16-2build1 libgssapi3-heimdal_7.5.0+dfsg-2 libhcrypto4-heimdal_7.5.0+dfsg-2 libheimbase1-heimdal_7.5.0+dfsg-2 libheimntlm0-heimdal_7.5.0+dfsg-2 libhogweed4_3.4-1 libhx509-5-heimdal_7.5.0+dfsg-2 libicu60_60.2-6ubuntu1 libidn11_1.33-2.2ubuntu1 libidn2-0_2.0.4-2.2 libip4tc0_1.6.1-2ubuntu2 libisl19_0.20-1 libjson-c3_0.12.1-1.3 libk5crypto3_1.16-2build1 libkeyutils1_1.5.9-9.3 libkmod2_25-1ubuntu1 libkrb5-26-heimdal_7.5.0+dfsg-2 libkrb5-3_1.16-2build1 libkrb5support0_1.16-2build1 liblapack3_3.8.0-1build1 libldap-2.4-2_2.4.46+dfsg-5ubuntu1 libldap-common_2.4.46+dfsg-5ubuntu1 liblockfile-bin_1.14-1.1 liblockfile1_1.14-1.1 liblz4-1_1.8.2-1ubuntu1 liblzma5_5.2.2-1.3 libmagic-mgc_1:5.34-2 libmagic1_1:5.34-2 libmount1_2.32-0.1ubuntu1 libmpc3_1.1.0-1 libmpdec2_2.4.2-2 libmpfr6_4.0.1-1 libncurses5_6.1+20180210-4ubuntu1 libncurses6_6.1+20180210-4ubuntu1 libncursesw5_6.1+20180210-4ubuntu1 libncursesw6_6.1+20180210-4ubuntu1 libnettle6_3.4-1 libnghttp2-14_1.32.0-1 libnpth0_1.6-1 libp11-kit0_0.23.12-2 libpam-modules_1.1.8-3.6ubuntu2 libpam-modules-bin_1.1.8-3.6ubuntu2 libpam-runtime_1.1.8-3.6ubuntu2 libpam0g_1.1.8-3.6ubuntu2 libpcre3_2:8.39-11 libperl5.26_5.26.2-7 libpipeline1_1.5.0-1 libpng16-16_1.6.34-2 libprocps6_2:3.3.12-3ubuntu1 libprocps7_2:3.3.15-2ubuntu1 libpsl5_0.20.2-1 libpython-dev_2.7.15-3 libpython-stdlib_2.7.15-3 libpython2-dev_2.7.15-3 libpython2-stdlib_2.7.15-3 libpython2.7_2.7.15-3 libpython2.7-dev_2.7.15-3 libpython2.7-minimal_2.7.15-3 libpython2.7-stdlib_2.7.15-3 libpython3-all-dev_3.6.6-1 libpython3-dev_3.6.6-1 libpython3-stdlib_3.6.6-1 libpython3.6_3.6.6-1 libpython3.6-dev_3.6.6-1 libpython3.6-minimal_3.6.6-1 libpython3.6-stdlib_3.6.6-1 libpython3.7_3.7.0-4 libpython3.7-dev_3.7.0-4 libpython3.7-minimal_3.7.0-4 libpython3.7-stdlib_3.7.0-4 libreadline7_7.0-5 libroken18-heimdal_7.5.0+dfsg-2 librtmp1_2.4+20151223.gitfa8646d.1-2 libsasl2-2_2.1.27~101-g0780600+dfsg-3ubuntu2 libsasl2-modules-db_2.1.27~101-g0780600+dfsg-3ubuntu2 libseccomp2_2.3.3-3ubuntu1 libselinux1_2.8-1build1 libsemanage-common_2.8-1build1 libsemanage1_2.8-1build1 libsepol1_2.8-1 libsigsegv2_2.12-2 libslang2_2.3.2-1ubuntu1 libsmartcols1_2.32-0.1ubuntu1 libsqlite3-0_3.24.0-1 libss2_1.44.3-1 libssl-dev_1.1.0g-2ubuntu5 libssl1.1_1.1.0g-2ubuntu5 libstdc++-7-dev_7.3.0-27ubuntu1 libstdc++-8-dev_8.2.0-3ubuntu1 libstdc++6_8.2.0-3ubuntu1 libsystemd0_239-7ubuntu2 libtasn1-6_4.13-3 libtimedate-perl_2.3000-2 libtinfo5_6.1+20180210-4ubuntu1 libtinfo6_6.1+20180210-4ubuntu1 libtool_2.4.6-2.1build1 libubsan0_7.3.0-27ubuntu1 libubsan1_8.2.0-3ubuntu1 libudev1_239-7ubuntu2 libunistring2_0.9.10-1ubuntu1 libusb-0.1-4_2:0.1.12-32 libuuid1_2.32-0.1ubuntu1 libwind0-heimdal_7.5.0+dfsg-2 libxml2_2.9.4+dfsg1-7build1 libzstd1_1.3.3+dfsg-2ubuntu1 linux-libc-dev_4.17.0-7.8 lockfile-progs_0.1.17build1 login_1:4.5-1ubuntu1 lsb-base_9.20170808ubuntu1 m4_1.4.18-1 make_4.2.1-1.2 man-db_2.8.4-2 mawk_1.3.3-17ubuntu3 mime-support_3.60ubuntu1 mount_2.32-0.1ubuntu1 multiarch-support_2.27-3ubuntu1 ncurses-base_6.1+20180210-4ubuntu1 ncurses-bin_6.1+20180210-4ubuntu1 openssl_1.1.0g-2ubuntu5 optipng_0.7.6-1.1 passwd_1:4.5-1ubuntu1 patch_2.7.6-3 perl_5.26.2-7 perl-base_5.26.2-7 perl-modules-5.26_5.26.2-7 pinentry-curses_1.1.0-1build2 pkgbinarymangler_141 po-debconf_1.0.20 policyrcd-script-zg2_0.1-3 procps_2:3.3.15-2ubuntu1 python_2.7.15-3 python-all_2.7.15-3 python-click_6.7-5 python-colorama_0.3.7-1 python-coloredlogs_7.3-1 python-humanfriendly_4.4.1-1 python-minimal_2.7.15-3 python-monotonic_1.1-2 python-nose_1.3.7-4 python-numpy_1:1.14.5-1ubuntu3 python-pkg-resources_39.2.0-1 python-setuptools_39.2.0-1 python2_2.7.15-3 python2-minimal_2.7.15-3 python2.7_2.7.15-3 python2.7-minimal_2.7.15-3 python3_3.6.6-1 python3-all_3.6.6-1 python3-all-dev_3.6.6-1 python3-click_6.7-5 python3-colorama_0.3.7-1 python3-coloredlogs_7.3-1 python3-dev_3.6.6-1 python3-distutils_3.6.6-1 python3-humanfriendly_4.4.1-1 python3-lib2to3_3.6.6-1 python3-minimal_3.6.6-1 python3-nose_1.3.7-4 python3-numpy_1:1.14.5-1ubuntu3 python3-pkg-resources_39.2.0-1 python3-setuptools_39.2.0-1 python3.6_3.6.6-1 python3.6-dev_3.6.6-1 python3.6-minimal_3.6.6-1 python3.7_3.7.0-4 python3.7-dev_3.7.0-4 python3.7-minimal_3.7.0-4 readline-common_7.0-5 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-cyvcf2-dummy_0.invalid.0 sed_4.5-1 sensible-utils_0.0.12 systemd_239-7ubuntu2 systemd-sysv_239-7ubuntu2 sysv-rc_2.88dsf-59.3ubuntu2 sysvinit-utils_2.88dsf-59.10ubuntu1 tar_1.30+dfsg-2 tzdata_2018e-1 ubuntu-keyring_2018.02.28 util-linux_2.32-0.1ubuntu1 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 Aug 14 10:58:25 2018 UTC gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tillea@rki.de" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./cyvcf2_0.10.0+git20180727-2.dsc dpkg-source: info: extracting cyvcf2 in cyvcf2-0.10.0+git20180727 dpkg-source: info: unpacking cyvcf2_0.10.0+git20180727.orig.tar.gz dpkg-source: info: unpacking cyvcf2_0.10.0+git20180727-2.debian.tar.xz Check disc space ---------------- Sufficient free space for build User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf DEB_BUILD_OPTIONS=parallel=4 HOME=/sbuild-nonexistent LANG=C.UTF-8 LC_ALL=C.UTF-8 LOGNAME=buildd PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games SCHROOT_ALIAS_NAME=build-PACKAGEBUILD-15261391 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-15261391 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-15261391 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 0.10.0+git20180727-2 dpkg-buildpackage: info: source distribution unstable dpkg-source --before-build cyvcf2-0.10.0+git20180727 dpkg-buildpackage: info: host architecture armhf dpkg-source: info: using options from cyvcf2-0.10.0+git20180727/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 '/<>/cyvcf2-0.10.0+git20180727/.pybuild/cpython2_2.7_cyvcf2/build' (and everything under it) 'build/bdist.linux-armhf' 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 '/<>/cyvcf2-0.10.0+git20180727/.pybuild/cpython3_3.7_cyvcf2/build' (and everything under it) 'build/bdist.linux-armhf' does not exist -- can't clean it 'build/scripts-3.7' does not exist -- can't clean it I: pybuild base:217: python3.6 setup.py clean running clean removing '/<>/cyvcf2-0.10.0+git20180727/.pybuild/cpython3_3.6_cyvcf2/build' (and everything under it) 'build/bdist.linux-armhf' does not exist -- can't clean it 'build/scripts-3.6' does not exist -- can't clean it debian/rules override_dh_clean make[1]: Entering directory '/<>/cyvcf2-0.10.0+git20180727' dh_clean rm -rf cyvcf2.egg-info cyvcf2/cyvcf2.c __o.vcf find . -name "*.so" -delete make[1]: Leaving directory '/<>/cyvcf2-0.10.0+git20180727' 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 I: pybuild base:217: python3.6 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 /<>/cyvcf2-0.10.0+git20180727/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2 copying cyvcf2/__init__.py -> /<>/cyvcf2-0.10.0+git20180727/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2 copying cyvcf2/cli.py -> /<>/cyvcf2-0.10.0+git20180727/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2 copying cyvcf2/__main__.py -> /<>/cyvcf2-0.10.0+git20180727/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2 creating /<>/cyvcf2-0.10.0+git20180727/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/__init__.py -> /<>/cyvcf2-0.10.0+git20180727/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/test_hemi.py -> /<>/cyvcf2-0.10.0+git20180727/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/test_cli.py -> /<>/cyvcf2-0.10.0+git20180727/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/test_reader.py -> /<>/cyvcf2-0.10.0+git20180727/.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' writing manifest file 'cyvcf2.egg-info/SOURCES.txt' copying cyvcf2/cyvcf2.pxd -> /<>/cyvcf2-0.10.0+git20180727/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2 copying cyvcf2/cyvcf2.pyx -> /<>/cyvcf2-0.10.0+git20180727/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2 copying cyvcf2/helpers.c -> /<>/cyvcf2-0.10.0+git20180727/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2 copying cyvcf2/helpers.h -> /<>/cyvcf2-0.10.0+git20180727/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2 copying cyvcf2/relatedness.h -> /<>/cyvcf2-0.10.0+git20180727/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2 copying cyvcf2/tests/bug.vcf.gz -> /<>/cyvcf2-0.10.0+git20180727/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/decomposed.vcf -> /<>/cyvcf2-0.10.0+git20180727/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/empty.vcf -> /<>/cyvcf2-0.10.0+git20180727/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/issue_44.vcf -> /<>/cyvcf2-0.10.0+git20180727/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/o.vcf.gz -> /<>/cyvcf2-0.10.0+git20180727/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/seg.vcf.gz -> /<>/cyvcf2-0.10.0+git20180727/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/test-alt-repr.vcf -> /<>/cyvcf2-0.10.0+git20180727/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/test-format-string.vcf -> /<>/cyvcf2-0.10.0+git20180727/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/test-haploidX.vcf -> /<>/cyvcf2-0.10.0+git20180727/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/test-hemi.vcf -> /<>/cyvcf2-0.10.0+git20180727/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/test-multiallelic-homozygous-alt.vcf.gz -> /<>/cyvcf2-0.10.0+git20180727/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/test-multiallelic-homozygous-alt.vcf.gz.tbi -> /<>/cyvcf2-0.10.0+git20180727/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/test-strict-gt-option-flag.vcf.gz -> /<>/cyvcf2-0.10.0+git20180727/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/test-strict-gt-option-flag.vcf.gz.tbi -> /<>/cyvcf2-0.10.0+git20180727/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/test.comp_het.3.vcf -> /<>/cyvcf2-0.10.0+git20180727/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/test.snpeff.bcf -> /<>/cyvcf2-0.10.0+git20180727/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/test.snpeff.bcf.csi -> /<>/cyvcf2-0.10.0+git20180727/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/test.snpeff.vcf -> /<>/cyvcf2-0.10.0+git20180727/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/test.vcf.gz -> /<>/cyvcf2-0.10.0+git20180727/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/test.vcf.gz.tbi -> /<>/cyvcf2-0.10.0+git20180727/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/test_gt_alt_freqs.vcf -> /<>/cyvcf2-0.10.0+git20180727/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/test_gt_bases.vcf.gz -> /<>/cyvcf2-0.10.0+git20180727/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2/tests running build_ext cythoning cyvcf2/cyvcf2.pyx to cyvcf2/cyvcf2.c 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:274:30: Declarations should not be declared inline. building 'cyvcf2.cyvcf2' extension creating build creating build/temp.linux-armhf-2.7 creating build/temp.linux-armhf-2.7/cyvcf2 creating build/temp.linux-armhf-2.7/htslib creating build/temp.linux-armhf-2.7/htslib/cram arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/cyvcf2-0.10.0+git20180727=. -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-armhf-2.7/cyvcf2/cyvcf2.o In file included from /usr/lib/python2.7/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1816, from /usr/lib/python2.7/dist-packages/numpy/core/include/numpy/ndarrayobject.h:18, from /usr/lib/python2.7/dist-packages/numpy/core/include/numpy/arrayobject.h:4, from cyvcf2/cyvcf2.c:568: /usr/lib/python2.7/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2: warning: #warning "Using deprecated NumPy API, disable it by " "#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] #warning "Using deprecated NumPy API, disable it by " \ ^~~~~~~ In file included from htslib/htslib/hts.h:35, from htslib/htslib/vcf.h:39, from cyvcf2/helpers.h:1, from cyvcf2/cyvcf2.c:571: htslib/htslib/hts_log.h:52:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes] enum htsLogLevel hts_get_log_level(); ^~~~~~~~~~~ cyvcf2/cyvcf2.c: In function ‘__pyx_pf_6cyvcf2_6cyvcf2_3VCF_4add_to_header’: cyvcf2/cyvcf2.c:8230:44: 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:571: htslib/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:8272:42: 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:571: htslib/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:8881:49: 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:571: htslib/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:9155:44: 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:571: htslib/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:9208:42: 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:571: htslib/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:9418:115: 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); htslib/htslib/vcf.h:796:103: note: in definition of macro ‘bcf_itr_querys’ #define bcf_itr_querys(idx, hdr, s) hts_itr_querys((idx), (s), (hts_name2id_f)(bcf_hdr_name2id), (hdr), hts_itr_query, bcf_readrec) ^~~ In file included from htslib/htslib/vcf.h:39, from cyvcf2/helpers.h:1, from cyvcf2/cyvcf2.c:571: htslib/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:10841:163: 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, 411, __pyx_L1_error) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ cyvcf2/cyvcf2.c:2810:61: 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:12508:33: 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:571: htslib/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:12992:3: 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:571: htslib/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:13245:18: 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:571: cyvcf2/cyvcf2.c:13372:75: 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)); htslib/htslib/vcf.h:799:112: note: in definition of macro ‘bcf_index_seqnames’ #define bcf_index_seqnames(idx, hdr, nptr) hts_idx_seqnames((idx),(nptr),(hts_id2name_f)(bcf_hdr_id2name),(hdr)) ^~~ In file included from htslib/htslib/vcf.h:39, from cyvcf2/helpers.h:1, from cyvcf2/cyvcf2.c:571: htslib/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:13372:22: 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:13605:22: 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:25742:17: 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:35677:13: warning: assignment discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] __pyx_v_h = __pyx_t_5; ^ cyvcf2/cyvcf2.c: In function ‘__pyx_pf_6cyvcf2_6cyvcf2_4INFO_12__next__’: cyvcf2/cyvcf2.c:38663:16: 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:39646:18: 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:40228:35: 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:571: htslib/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:40256:47: 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:571: htslib/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:40322:78: 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:571: htslib/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:40497:60: 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:571: htslib/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:40535:49: 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:571: htslib/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:40594:100: 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, 2073, __pyx_L1_error) ~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from cyvcf2/helpers.h:1, from cyvcf2/cyvcf2.c:571: htslib/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:6771:18: warning: ‘__pyx_f_6cyvcf2_6cyvcf2_xstr’ defined but not used [-Wunused-function] static PyObject *__pyx_f_6cyvcf2_6cyvcf2_xstr(PyObject *__pyx_v_s) { ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/cyvcf2-0.10.0+git20180727=. -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 htslib/hfile_net.c -o build/temp.linux-armhf-2.7/htslib/hfile_net.o In file included from htslib/hfile_internal.h:32, from htslib/hfile_net.c:30: htslib/textutils_internal.h:68:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] hts_json_token * hts_json_alloc_token(); ^~~~~~~~~~~~~~ arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/cyvcf2-0.10.0+git20180727=. -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 htslib/vcf.c -o build/temp.linux-armhf-2.7/htslib/vcf.o In file included from htslib/htslib/hts.h:35, from htslib/htslib/vcf.h:39, from htslib/vcf.c:38: htslib/htslib/hts_log.h:52:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes] enum htsLogLevel hts_get_log_level(); ^~~~~~~~~~~ In file included from htslib/hts_internal.h:31, from htslib/vcf.c:42: htslib/textutils_internal.h:68:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] hts_json_token * hts_json_alloc_token(); ^~~~~~~~~~~~~~ arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/cyvcf2-0.10.0+git20180727=. -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 htslib/regidx.c -o build/temp.linux-armhf-2.7/htslib/regidx.o In file included from htslib/htslib/hts.h:35, from htslib/regidx.c:28: htslib/htslib/hts_log.h:52:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes] enum htsLogLevel hts_get_log_level(); ^~~~~~~~~~~ In file included from htslib/hts_internal.h:31, from htslib/regidx.c:33: htslib/textutils_internal.h:68:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] hts_json_token * hts_json_alloc_token(); ^~~~~~~~~~~~~~ arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/cyvcf2-0.10.0+git20180727=. -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 htslib/synced_bcf_reader.c -o build/temp.linux-armhf-2.7/htslib/synced_bcf_reader.o In file included from htslib/htslib/hts.h:35, from htslib/htslib/synced_bcf_reader.h:59, from htslib/synced_bcf_reader.c:34: htslib/htslib/hts_log.h:52:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes] enum htsLogLevel hts_get_log_level(); ^~~~~~~~~~~ arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/cyvcf2-0.10.0+git20180727=. -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 htslib/hfile_libcurl.c -o build/temp.linux-armhf-2.7/htslib/hfile_libcurl.o In file included from htslib/hfile_internal.h:32, from htslib/hfile_libcurl.c:37: htslib/textutils_internal.h:68:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] hts_json_token * hts_json_alloc_token(); ^~~~~~~~~~~~~~ In file included from htslib/htslib/hts.h:35, from htslib/hfile_libcurl.c:41: htslib/htslib/hts_log.h:52:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes] enum htsLogLevel hts_get_log_level(); ^~~~~~~~~~~ htslib/hfile_libcurl.c:265:13: warning: function declaration isn’t a prototype [-Wstrict-prototypes] static void libcurl_exit() ^~~~~~~~~~~~ arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/cyvcf2-0.10.0+git20180727=. -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 htslib/bgzf.c -o build/temp.linux-armhf-2.7/htslib/bgzf.o In file included from htslib/htslib/hts.h:35, from htslib/bgzf.c:42: htslib/htslib/hts_log.h:52:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes] enum htsLogLevel hts_get_log_level(); ^~~~~~~~~~~ arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/cyvcf2-0.10.0+git20180727=. -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 htslib/t.c -o build/temp.linux-armhf-2.7/htslib/t.o In file included from htslib/htslib/hts.h:35, from htslib/t.c:1: htslib/htslib/hts_log.h:52:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes] enum htsLogLevel hts_get_log_level(); ^~~~~~~~~~~ htslib/t.c:4:5: warning: function declaration isn’t a prototype [-Wstrict-prototypes] int main() { ^~~~ arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/cyvcf2-0.10.0+git20180727=. -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 htslib/vcfutils.c -o build/temp.linux-armhf-2.7/htslib/vcfutils.o In file included from htslib/htslib/hts.h:35, from htslib/htslib/vcf.h:39, from htslib/htslib/vcfutils.h:29, from htslib/vcfutils.c:27: htslib/htslib/hts_log.h:52:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes] enum htsLogLevel hts_get_log_level(); ^~~~~~~~~~~ arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/cyvcf2-0.10.0+git20180727=. -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 htslib/tbx.c -o build/temp.linux-armhf-2.7/htslib/tbx.o In file included from htslib/htslib/hts.h:35, from htslib/htslib/tbx.h:30, from htslib/tbx.c:33: htslib/htslib/hts_log.h:52:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes] enum htsLogLevel hts_get_log_level(); ^~~~~~~~~~~ In file included from htslib/hts_internal.h:31, from htslib/tbx.c:36: htslib/textutils_internal.h:68:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] hts_json_token * hts_json_alloc_token(); ^~~~~~~~~~~~~~ arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/cyvcf2-0.10.0+git20180727=. -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 htslib/knetfile.c -o build/temp.linux-armhf-2.7/htslib/knetfile.o In file included from htslib/knetfile.c:50: htslib/htslib/hts_log.h:52:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes] enum htsLogLevel hts_get_log_level(); ^~~~~~~~~~~ arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/cyvcf2-0.10.0+git20180727=. -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 htslib/hfile_s3.c -o build/temp.linux-armhf-2.7/htslib/hfile_s3.o In file included from htslib/hfile_internal.h:32, from htslib/hfile_s3.c:33: htslib/textutils_internal.h:68:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] hts_json_token * hts_json_alloc_token(); ^~~~~~~~~~~~~~ In file included from htslib/htslib/hts.h:35, from htslib/hfile_s3.c:37: htslib/htslib/hts_log.h:52:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes] enum htsLogLevel hts_get_log_level(); ^~~~~~~~~~~ arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/cyvcf2-0.10.0+git20180727=. -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 htslib/errmod.c -o build/temp.linux-armhf-2.7/htslib/errmod.o In file included from htslib/htslib/hts.h:35, from htslib/errmod.c:29: htslib/htslib/hts_log.h:52:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes] enum htsLogLevel hts_get_log_level(); ^~~~~~~~~~~ arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/cyvcf2-0.10.0+git20180727=. -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 htslib/kfunc.c -o build/temp.linux-armhf-2.7/htslib/kfunc.o arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/cyvcf2-0.10.0+git20180727=. -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 htslib/multipart.c -o build/temp.linux-armhf-2.7/htslib/multipart.o In file included from htslib/htslib/hts.h:35, from htslib/hts_internal.h:29, from htslib/multipart.c:33: htslib/htslib/hts_log.h:52:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes] enum htsLogLevel hts_get_log_level(); ^~~~~~~~~~~ In file included from htslib/hts_internal.h:31, from htslib/multipart.c:33: htslib/textutils_internal.h:68:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] hts_json_token * hts_json_alloc_token(); ^~~~~~~~~~~~~~ arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/cyvcf2-0.10.0+git20180727=. -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 htslib/bcf_sr_sort.c -o build/temp.linux-armhf-2.7/htslib/bcf_sr_sort.o In file included from htslib/htslib/hts.h:35, from htslib/htslib/synced_bcf_reader.h:59, from htslib/bcf_sr_sort.h:37, from htslib/bcf_sr_sort.c:27: htslib/htslib/hts_log.h:52:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes] enum htsLogLevel hts_get_log_level(); ^~~~~~~~~~~ arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/cyvcf2-0.10.0+git20180727=. -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 htslib/probaln.c -o build/temp.linux-armhf-2.7/htslib/probaln.o In file included from htslib/htslib/hts.h:35, from htslib/probaln.c:35: htslib/htslib/hts_log.h:52:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes] enum htsLogLevel hts_get_log_level(); ^~~~~~~~~~~ arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/cyvcf2-0.10.0+git20180727=. -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 htslib/vcf_sweep.c -o build/temp.linux-armhf-2.7/htslib/vcf_sweep.o In file included from htslib/htslib/hts.h:35, from htslib/htslib/vcf_sweep.h:29, from htslib/vcf_sweep.c:27: htslib/htslib/hts_log.h:52:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes] enum htsLogLevel hts_get_log_level(); ^~~~~~~~~~~ arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/cyvcf2-0.10.0+git20180727=. -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 htslib/realn.c -o build/temp.linux-armhf-2.7/htslib/realn.o In file included from htslib/htslib/hts.h:35, from htslib/realn.c:35: htslib/htslib/hts_log.h:52:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes] enum htsLogLevel hts_get_log_level(); ^~~~~~~~~~~ arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/cyvcf2-0.10.0+git20180727=. -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 htslib/sam.c -o build/temp.linux-armhf-2.7/htslib/sam.o In file included from htslib/htslib/hts.h:35, from htslib/htslib/sam.h:31, from htslib/sam.c:35: htslib/htslib/hts_log.h:52:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes] enum htsLogLevel hts_get_log_level(); ^~~~~~~~~~~ In file included from htslib/hts_internal.h:31, from htslib/sam.c:38: htslib/textutils_internal.h:68:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] hts_json_token * hts_json_alloc_token(); ^~~~~~~~~~~~~~ arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/cyvcf2-0.10.0+git20180727=. -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 htslib/kstring.c -o build/temp.linux-armhf-2.7/htslib/kstring.o arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/cyvcf2-0.10.0+git20180727=. -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 htslib/thread_pool.c -o build/temp.linux-armhf-2.7/htslib/thread_pool.o arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/cyvcf2-0.10.0+git20180727=. -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 htslib/hfile_gcs.c -o build/temp.linux-armhf-2.7/htslib/hfile_gcs.o In file included from htslib/htslib/hts.h:35, from htslib/hfile_gcs.c:33: htslib/htslib/hts_log.h:52:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes] enum htsLogLevel hts_get_log_level(); ^~~~~~~~~~~ In file included from htslib/hfile_internal.h:32, from htslib/hfile_gcs.c:35: htslib/textutils_internal.h:68:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] hts_json_token * hts_json_alloc_token(); ^~~~~~~~~~~~~~ arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/cyvcf2-0.10.0+git20180727=. -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 htslib/md5.c -o build/temp.linux-armhf-2.7/htslib/md5.o In file included from htslib/htslib/hts.h:35, from htslib/md5.c:52: htslib/htslib/hts_log.h:52:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes] enum htsLogLevel hts_get_log_level(); ^~~~~~~~~~~ arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/cyvcf2-0.10.0+git20180727=. -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 htslib/hts_os.c -o build/temp.linux-armhf-2.7/htslib/hts_os.o arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/cyvcf2-0.10.0+git20180727=. -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 htslib/faidx.c -o build/temp.linux-armhf-2.7/htslib/faidx.o In file included from htslib/htslib/hts.h:35, from htslib/hts_internal.h:29, from htslib/faidx.c:43: htslib/htslib/hts_log.h:52:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes] enum htsLogLevel hts_get_log_level(); ^~~~~~~~~~~ In file included from htslib/hts_internal.h:31, from htslib/faidx.c:43: htslib/textutils_internal.h:68:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] hts_json_token * hts_json_alloc_token(); ^~~~~~~~~~~~~~ arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/cyvcf2-0.10.0+git20180727=. -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 htslib/hfile.c -o build/temp.linux-armhf-2.7/htslib/hfile.o In file included from htslib/hfile_internal.h:32, from htslib/hfile.c:37: htslib/textutils_internal.h:68:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] hts_json_token * hts_json_alloc_token(); ^~~~~~~~~~~~~~ In file included from htslib/htslib/hts.h:35, from htslib/hts_internal.h:29, from htslib/hfile.c:737: htslib/htslib/hts_log.h:52:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes] enum htsLogLevel hts_get_log_level(); ^~~~~~~~~~~ htslib/hfile.c:874:13: warning: function declaration isn’t a prototype [-Wstrict-prototypes] static void hfile_exit() ^~~~~~~~~~ htslib/hfile.c:934:13: warning: function declaration isn’t a prototype [-Wstrict-prototypes] static void load_hfile_plugins() ^~~~~~~~~~~~~~~~~~ arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/cyvcf2-0.10.0+git20180727=. -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 htslib/hts.c -o build/temp.linux-armhf-2.7/htslib/hts.o In file included from htslib/htslib/hts.h:35, from htslib/hts.c:39: htslib/htslib/hts_log.h:52:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes] enum htsLogLevel hts_get_log_level(); ^~~~~~~~~~~ In file included from htslib/hts_internal.h:31, from htslib/hts.c:45: htslib/textutils_internal.h:68:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] hts_json_token * hts_json_alloc_token(); ^~~~~~~~~~~~~~ htslib/hts.c:2939:18: warning: function declaration isn’t a prototype [-Wstrict-prototypes] enum htsLogLevel hts_get_log_level() ^~~~~~~~~~~~~~~~~ arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/cyvcf2-0.10.0+git20180727=. -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 htslib/textutils.c -o build/temp.linux-armhf-2.7/htslib/textutils.o In file included from htslib/htslib/hts.h:35, from htslib/hts_internal.h:29, from htslib/textutils.c:33: htslib/htslib/hts_log.h:52:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes] enum htsLogLevel hts_get_log_level(); ^~~~~~~~~~~ In file included from htslib/hts_internal.h:31, from htslib/textutils.c:33: htslib/textutils_internal.h:68:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] hts_json_token * hts_json_alloc_token(); ^~~~~~~~~~~~~~ htslib/textutils.c:218:18: warning: function declaration isn’t a prototype [-Wstrict-prototypes] hts_json_token * hts_json_alloc_token() { ^~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/cyvcf2-0.10.0+git20180727=. -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 htslib/cram/open_trace_file.c -o build/temp.linux-armhf-2.7/htslib/cram/open_trace_file.o In file included from htslib/cram/open_trace_file.c:82: htslib/htslib/hts_log.h:52:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes] enum htsLogLevel hts_get_log_level(); ^~~~~~~~~~~ arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/cyvcf2-0.10.0+git20180727=. -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 htslib/cram/cram_external.c -o build/temp.linux-armhf-2.7/htslib/cram/cram_external.o In file included from htslib/htslib/hts.h:35, from htslib/htslib/sam.h:31, from htslib/cram/cram_samtools.h:61, from htslib/cram/cram.h:45, from htslib/cram/cram_external.c:44: htslib/htslib/hts_log.h:52:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes] enum htsLogLevel hts_get_log_level(); ^~~~~~~~~~~ arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/cyvcf2-0.10.0+git20180727=. -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 htslib/cram/cram_samtools.c -o build/temp.linux-armhf-2.7/htslib/cram/cram_samtools.o In file included from htslib/htslib/hts.h:35, from htslib/htslib/sam.h:31, from htslib/cram/cram_samtools.h:61, from htslib/cram/cram.h:45, from htslib/cram/cram_samtools.c:37: htslib/htslib/hts_log.h:52:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes] enum htsLogLevel hts_get_log_level(); ^~~~~~~~~~~ arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/cyvcf2-0.10.0+git20180727=. -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 htslib/cram/files.c -o build/temp.linux-armhf-2.7/htslib/cram/files.o arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/cyvcf2-0.10.0+git20180727=. -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 htslib/cram/cram_stats.c -o build/temp.linux-armhf-2.7/htslib/cram/cram_stats.o In file included from htslib/htslib/hts.h:35, from htslib/htslib/sam.h:31, from htslib/cram/cram_samtools.h:61, from htslib/cram/cram.h:45, from htslib/cram/cram_stats.c:43: htslib/htslib/hts_log.h:52:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes] enum htsLogLevel hts_get_log_level(); ^~~~~~~~~~~ arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/cyvcf2-0.10.0+git20180727=. -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 htslib/cram/cram_decode.c -o build/temp.linux-armhf-2.7/htslib/cram/cram_decode.o In file included from htslib/htslib/hts.h:35, from htslib/htslib/sam.h:31, from htslib/cram/cram_samtools.h:61, from htslib/cram/cram.h:45, from htslib/cram/cram_decode.c:49: htslib/htslib/hts_log.h:52:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes] enum htsLogLevel hts_get_log_level(); ^~~~~~~~~~~ arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/cyvcf2-0.10.0+git20180727=. -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 htslib/cram/sam_header.c -o build/temp.linux-armhf-2.7/htslib/cram/sam_header.o In file included from htslib/htslib/hts.h:35, from htslib/hts_internal.h:29, from htslib/cram/sam_header.c:36: htslib/htslib/hts_log.h:52:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes] enum htsLogLevel hts_get_log_level(); ^~~~~~~~~~~ In file included from htslib/hts_internal.h:31, from htslib/cram/sam_header.c:36: htslib/textutils_internal.h:68:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] hts_json_token * hts_json_alloc_token(); ^~~~~~~~~~~~~~ arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/cyvcf2-0.10.0+git20180727=. -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 htslib/cram/cram_io.c -o build/temp.linux-armhf-2.7/htslib/cram/cram_io.o In file included from htslib/htslib/hts.h:35, from htslib/htslib/sam.h:31, from htslib/cram/cram_samtools.h:61, from htslib/cram/cram.h:45, from htslib/cram/cram_io.c:77: htslib/htslib/hts_log.h:52:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes] enum htsLogLevel hts_get_log_level(); ^~~~~~~~~~~ In file included from htslib/hts_internal.h:31, from htslib/cram/cram_io.c:97: htslib/textutils_internal.h:68:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] hts_json_token * hts_json_alloc_token(); ^~~~~~~~~~~~~~ htslib/cram/cram_io.c:2027:17: warning: function declaration isn’t a prototype [-Wstrict-prototypes] static unsigned get_int_threadid() { ^~~~~~~~~~~~~~~~ arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/cyvcf2-0.10.0+git20180727=. -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 htslib/cram/mFILE.c -o build/temp.linux-armhf-2.7/htslib/cram/mFILE.o In file included from htslib/htslib/hts.h:35, from htslib/hts_internal.h:29, from htslib/cram/mFILE.c:43: htslib/htslib/hts_log.h:52:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes] enum htsLogLevel hts_get_log_level(); ^~~~~~~~~~~ In file included from htslib/hts_internal.h:31, from htslib/cram/mFILE.c:43: htslib/textutils_internal.h:68:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] hts_json_token * hts_json_alloc_token(); ^~~~~~~~~~~~~~ arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/cyvcf2-0.10.0+git20180727=. -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 htslib/cram/cram_encode.c -o build/temp.linux-armhf-2.7/htslib/cram/cram_encode.o In file included from htslib/htslib/hts.h:35, from htslib/htslib/sam.h:31, from htslib/cram/cram_samtools.h:61, from htslib/cram/cram.h:45, from htslib/cram/cram_encode.c:43: htslib/htslib/hts_log.h:52:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes] enum htsLogLevel hts_get_log_level(); ^~~~~~~~~~~ htslib/cram/cram_encode.c: In function ‘process_one_read’: htslib/cram/cram_encode.c:2834:17: warning: unused variable ‘brg’ [-Wunused-variable] SAM_RG *brg = sam_hdr_find_rg(fd->header, "UNKNOWN"); ^~~ arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/cyvcf2-0.10.0+git20180727=. -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 htslib/cram/cram_index.c -o build/temp.linux-armhf-2.7/htslib/cram/cram_index.o In file included from htslib/htslib/hts.h:35, from htslib/hts_internal.h:29, from htslib/cram/cram_index.c:65: htslib/htslib/hts_log.h:52:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes] enum htsLogLevel hts_get_log_level(); ^~~~~~~~~~~ In file included from htslib/hts_internal.h:31, from htslib/cram/cram_index.c:65: htslib/textutils_internal.h:68:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes] hts_json_token * hts_json_alloc_token(); ^~~~~~~~~~~~~~ htslib/cram/cram_index.c: In function ‘cram_index_build’: htslib/cram/cram_index.c:587:23: warning: variable ‘hpos’ set but not used [-Wunused-but-set-variable] off_t cpos, spos, hpos; ^~~~ arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/cyvcf2-0.10.0+git20180727=. -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 htslib/cram/string_alloc.c -o build/temp.linux-armhf-2.7/htslib/cram/string_alloc.o arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/cyvcf2-0.10.0+git20180727=. -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 htslib/cram/pooled_alloc.c -o build/temp.linux-armhf-2.7/htslib/cram/pooled_alloc.o arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/cyvcf2-0.10.0+git20180727=. -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 htslib/cram/cram_codecs.c -o build/temp.linux-armhf-2.7/htslib/cram/cram_codecs.o In file included from htslib/htslib/hts.h:35, from htslib/htslib/sam.h:31, from htslib/cram/cram_samtools.h:61, from htslib/cram/cram.h:45, from htslib/cram/cram_codecs.c:45: htslib/htslib/hts_log.h:52:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes] enum htsLogLevel hts_get_log_level(); ^~~~~~~~~~~ arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/cyvcf2-0.10.0+git20180727=. -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 htslib/cram/rANS_static.c -o build/temp.linux-armhf-2.7/htslib/cram/rANS_static.o arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/<>/cyvcf2-0.10.0+git20180727=. -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-armhf-2.7/cyvcf2/helpers.o In file included from htslib/htslib/hts.h:35, from htslib/htslib/vcf.h:39, from cyvcf2/helpers.h:1, from cyvcf2/helpers.c:1: htslib/htslib/hts_log.h:52:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes] enum htsLogLevel hts_get_log_level(); ^~~~~~~~~~~ arm-linux-gnueabihf-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/python2.7-0W6d3z/python2.7-2.7.15=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/cyvcf2-0.10.0+git20180727=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-2.7/cyvcf2/cyvcf2.o build/temp.linux-armhf-2.7/htslib/hfile_net.o build/temp.linux-armhf-2.7/htslib/vcf.o build/temp.linux-armhf-2.7/htslib/regidx.o build/temp.linux-armhf-2.7/htslib/synced_bcf_reader.o build/temp.linux-armhf-2.7/htslib/hfile_libcurl.o build/temp.linux-armhf-2.7/htslib/bgzf.o build/temp.linux-armhf-2.7/htslib/t.o build/temp.linux-armhf-2.7/htslib/vcfutils.o build/temp.linux-armhf-2.7/htslib/tbx.o build/temp.linux-armhf-2.7/htslib/knetfile.o build/temp.linux-armhf-2.7/htslib/hfile_s3.o build/temp.linux-armhf-2.7/htslib/errmod.o build/temp.linux-armhf-2.7/htslib/kfunc.o build/temp.linux-armhf-2.7/htslib/multipart.o build/temp.linux-armhf-2.7/htslib/bcf_sr_sort.o build/temp.linux-armhf-2.7/htslib/probaln.o build/temp.linux-armhf-2.7/htslib/vcf_sweep.o build/temp.linux-armhf-2.7/htslib/realn.o build/temp.linux-armhf-2.7/htslib/sam.o build/temp.linux-armhf-2.7/htslib/kstring.o build/temp.linux-armhf-2.7/htslib/thread_pool.o build/temp.linux-armhf-2.7/htslib/hfile_gcs.o build/temp.linux-armhf-2.7/htslib/md5.o build/temp.linux-armhf-2.7/htslib/hts_os.o build/temp.linux-armhf-2.7/htslib/faidx.o build/temp.linux-armhf-2.7/htslib/hfile.o build/temp.linux-armhf-2.7/htslib/hts.o build/temp.linux-armhf-2.7/htslib/textutils.o build/temp.linux-armhf-2.7/htslib/cram/open_trace_file.o build/temp.linux-armhf-2.7/htslib/cram/cram_external.o build/temp.linux-armhf-2.7/htslib/cram/cram_samtools.o build/temp.linux-armhf-2.7/htslib/cram/files.o build/temp.linux-armhf-2.7/htslib/cram/cram_stats.o build/temp.linux-armhf-2.7/htslib/cram/cram_decode.o build/temp.linux-armhf-2.7/htslib/cram/sam_header.o build/temp.linux-armhf-2.7/htslib/cram/cram_io.o build/temp.linux-armhf-2.7/htslib/cram/mFILE.o build/temp.linux-armhf-2.7/htslib/cram/cram_encode.o build/temp.linux-armhf-2.7/htslib/cram/cram_index.o build/temp.linux-armhf-2.7/htslib/cram/string_alloc.o build/temp.linux-armhf-2.7/htslib/cram/pooled_alloc.o build/temp.linux-armhf-2.7/htslib/cram/cram_codecs.o build/temp.linux-armhf-2.7/htslib/cram/rANS_static.o build/temp.linux-armhf-2.7/cyvcf2/helpers.o -lz -lcurl -lssl -lcrypt -o /<>/cyvcf2-0.10.0+git20180727/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2/cyvcf2.so I: pybuild base:217: /usr/bin/python3.7 setup.py build running build running build_py creating /<>/cyvcf2-0.10.0+git20180727/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2 copying cyvcf2/__init__.py -> /<>/cyvcf2-0.10.0+git20180727/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2 copying cyvcf2/cli.py -> /<>/cyvcf2-0.10.0+git20180727/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2 copying cyvcf2/__main__.py -> /<>/cyvcf2-0.10.0+git20180727/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2 creating /<>/cyvcf2-0.10.0+git20180727/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/__init__.py -> /<>/cyvcf2-0.10.0+git20180727/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/test_hemi.py -> /<>/cyvcf2-0.10.0+git20180727/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/test_cli.py -> /<>/cyvcf2-0.10.0+git20180727/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/test_reader.py -> /<>/cyvcf2-0.10.0+git20180727/.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' writing manifest file 'cyvcf2.egg-info/SOURCES.txt' copying cyvcf2/cyvcf2.c -> /<>/cyvcf2-0.10.0+git20180727/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2 copying cyvcf2/cyvcf2.pxd -> /<>/cyvcf2-0.10.0+git20180727/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2 copying cyvcf2/cyvcf2.pyx -> /<>/cyvcf2-0.10.0+git20180727/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2 copying cyvcf2/helpers.c -> /<>/cyvcf2-0.10.0+git20180727/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2 copying cyvcf2/helpers.h -> /<>/cyvcf2-0.10.0+git20180727/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2 copying cyvcf2/relatedness.h -> /<>/cyvcf2-0.10.0+git20180727/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2 copying cyvcf2/tests/bug.vcf.gz -> /<>/cyvcf2-0.10.0+git20180727/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/decomposed.vcf -> /<>/cyvcf2-0.10.0+git20180727/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/empty.vcf -> /<>/cyvcf2-0.10.0+git20180727/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/issue_44.vcf -> /<>/cyvcf2-0.10.0+git20180727/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/o.vcf.gz -> /<>/cyvcf2-0.10.0+git20180727/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/seg.vcf.gz -> /<>/cyvcf2-0.10.0+git20180727/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/test-alt-repr.vcf -> /<>/cyvcf2-0.10.0+git20180727/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/test-format-string.vcf -> /<>/cyvcf2-0.10.0+git20180727/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/test-haploidX.vcf -> /<>/cyvcf2-0.10.0+git20180727/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/test-hemi.vcf -> /<>/cyvcf2-0.10.0+git20180727/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/test-multiallelic-homozygous-alt.vcf.gz -> /<>/cyvcf2-0.10.0+git20180727/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/test-multiallelic-homozygous-alt.vcf.gz.tbi -> /<>/cyvcf2-0.10.0+git20180727/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/test-strict-gt-option-flag.vcf.gz -> /<>/cyvcf2-0.10.0+git20180727/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/test-strict-gt-option-flag.vcf.gz.tbi -> /<>/cyvcf2-0.10.0+git20180727/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/test.comp_het.3.vcf -> /<>/cyvcf2-0.10.0+git20180727/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/test.snpeff.bcf -> /<>/cyvcf2-0.10.0+git20180727/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/test.snpeff.bcf.csi -> /<>/cyvcf2-0.10.0+git20180727/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/test.snpeff.vcf -> /<>/cyvcf2-0.10.0+git20180727/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/test.vcf.gz -> /<>/cyvcf2-0.10.0+git20180727/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/test.vcf.gz.tbi -> /<>/cyvcf2-0.10.0+git20180727/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/test_gt_alt_freqs.vcf -> /<>/cyvcf2-0.10.0+git20180727/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/test_gt_bases.vcf.gz -> /<>/cyvcf2-0.10.0+git20180727/.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-armhf-3.7 creating build/temp.linux-armhf-3.7/cyvcf2 creating build/temp.linux-armhf-3.7/htslib creating build/temp.linux-armhf-3.7/htslib/cram arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<>/cyvcf2-0.10.0+git20180727=. -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-armhf-3.7/cyvcf2/cyvcf2.o In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1816, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:18, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:4, from cyvcf2/cyvcf2.c:568: /usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2: warning: #warning "Using deprecated NumPy API, disable it by " "#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] #warning "Using deprecated NumPy API, disable it by " \ ^~~~~~~ cyvcf2/cyvcf2.c: In function ‘__pyx_pf_6cyvcf2_6cyvcf2_3VCF_4add_to_header’: cyvcf2/cyvcf2.c:8230:44: 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:571: htslib/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:8272:42: 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:571: htslib/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:8881:49: 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:571: htslib/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:9155:44: 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:571: htslib/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:9208:42: 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:571: htslib/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:9418:115: 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); htslib/htslib/vcf.h:796:103: note: in definition of macro ‘bcf_itr_querys’ #define bcf_itr_querys(idx, hdr, s) hts_itr_querys((idx), (s), (hts_name2id_f)(bcf_hdr_name2id), (hdr), hts_itr_query, bcf_readrec) ^~~ In file included from htslib/htslib/vcf.h:39, from cyvcf2/helpers.h:1, from cyvcf2/cyvcf2.c:571: htslib/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:10841:163: 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, 411, __pyx_L1_error) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ cyvcf2/cyvcf2.c:2810:61: 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:12508:33: 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:571: htslib/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:12992:3: 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:571: htslib/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:13245:18: 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:571: cyvcf2/cyvcf2.c:13372:75: 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)); htslib/htslib/vcf.h:799:112: note: in definition of macro ‘bcf_index_seqnames’ #define bcf_index_seqnames(idx, hdr, nptr) hts_idx_seqnames((idx),(nptr),(hts_id2name_f)(bcf_hdr_id2name),(hdr)) ^~~ In file included from htslib/htslib/vcf.h:39, from cyvcf2/helpers.h:1, from cyvcf2/cyvcf2.c:571: htslib/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:13372:22: 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:13605:22: 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:25742:17: 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:35677:13: warning: assignment discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] __pyx_v_h = __pyx_t_5; ^ cyvcf2/cyvcf2.c: In function ‘__pyx_pf_6cyvcf2_6cyvcf2_4INFO_12__next__’: cyvcf2/cyvcf2.c:38663:16: 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:39646:18: 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:40228:35: 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:571: htslib/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:40256:47: 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:571: htslib/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:40322:78: 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:571: htslib/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:40497:60: 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:571: htslib/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:40535:49: 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:571: htslib/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:40594:100: 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, 2073, __pyx_L1_error) ~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from cyvcf2/helpers.h:1, from cyvcf2/cyvcf2.c:571: htslib/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:6771:18: warning: ‘__pyx_f_6cyvcf2_6cyvcf2_xstr’ defined but not used [-Wunused-function] static PyObject *__pyx_f_6cyvcf2_6cyvcf2_xstr(PyObject *__pyx_v_s) { ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<>/cyvcf2-0.10.0+git20180727=. -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 htslib/hfile_net.c -o build/temp.linux-armhf-3.7/htslib/hfile_net.o arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<>/cyvcf2-0.10.0+git20180727=. -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 htslib/vcf.c -o build/temp.linux-armhf-3.7/htslib/vcf.o arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<>/cyvcf2-0.10.0+git20180727=. -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 htslib/regidx.c -o build/temp.linux-armhf-3.7/htslib/regidx.o arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<>/cyvcf2-0.10.0+git20180727=. -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 htslib/synced_bcf_reader.c -o build/temp.linux-armhf-3.7/htslib/synced_bcf_reader.o arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<>/cyvcf2-0.10.0+git20180727=. -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 htslib/hfile_libcurl.c -o build/temp.linux-armhf-3.7/htslib/hfile_libcurl.o arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<>/cyvcf2-0.10.0+git20180727=. -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 htslib/bgzf.c -o build/temp.linux-armhf-3.7/htslib/bgzf.o arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<>/cyvcf2-0.10.0+git20180727=. -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 htslib/t.c -o build/temp.linux-armhf-3.7/htslib/t.o arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<>/cyvcf2-0.10.0+git20180727=. -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 htslib/vcfutils.c -o build/temp.linux-armhf-3.7/htslib/vcfutils.o arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<>/cyvcf2-0.10.0+git20180727=. -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 htslib/tbx.c -o build/temp.linux-armhf-3.7/htslib/tbx.o arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<>/cyvcf2-0.10.0+git20180727=. -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 htslib/knetfile.c -o build/temp.linux-armhf-3.7/htslib/knetfile.o arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<>/cyvcf2-0.10.0+git20180727=. -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 htslib/hfile_s3.c -o build/temp.linux-armhf-3.7/htslib/hfile_s3.o arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<>/cyvcf2-0.10.0+git20180727=. -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 htslib/errmod.c -o build/temp.linux-armhf-3.7/htslib/errmod.o arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<>/cyvcf2-0.10.0+git20180727=. -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 htslib/kfunc.c -o build/temp.linux-armhf-3.7/htslib/kfunc.o arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<>/cyvcf2-0.10.0+git20180727=. -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 htslib/multipart.c -o build/temp.linux-armhf-3.7/htslib/multipart.o arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<>/cyvcf2-0.10.0+git20180727=. -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 htslib/bcf_sr_sort.c -o build/temp.linux-armhf-3.7/htslib/bcf_sr_sort.o arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<>/cyvcf2-0.10.0+git20180727=. -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 htslib/probaln.c -o build/temp.linux-armhf-3.7/htslib/probaln.o arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<>/cyvcf2-0.10.0+git20180727=. -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 htslib/vcf_sweep.c -o build/temp.linux-armhf-3.7/htslib/vcf_sweep.o arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<>/cyvcf2-0.10.0+git20180727=. -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 htslib/realn.c -o build/temp.linux-armhf-3.7/htslib/realn.o arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<>/cyvcf2-0.10.0+git20180727=. -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 htslib/sam.c -o build/temp.linux-armhf-3.7/htslib/sam.o arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<>/cyvcf2-0.10.0+git20180727=. -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 htslib/kstring.c -o build/temp.linux-armhf-3.7/htslib/kstring.o arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<>/cyvcf2-0.10.0+git20180727=. -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 htslib/thread_pool.c -o build/temp.linux-armhf-3.7/htslib/thread_pool.o arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<>/cyvcf2-0.10.0+git20180727=. -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 htslib/hfile_gcs.c -o build/temp.linux-armhf-3.7/htslib/hfile_gcs.o arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<>/cyvcf2-0.10.0+git20180727=. -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 htslib/md5.c -o build/temp.linux-armhf-3.7/htslib/md5.o arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<>/cyvcf2-0.10.0+git20180727=. -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 htslib/hts_os.c -o build/temp.linux-armhf-3.7/htslib/hts_os.o arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<>/cyvcf2-0.10.0+git20180727=. -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 htslib/faidx.c -o build/temp.linux-armhf-3.7/htslib/faidx.o arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<>/cyvcf2-0.10.0+git20180727=. -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 htslib/hfile.c -o build/temp.linux-armhf-3.7/htslib/hfile.o arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<>/cyvcf2-0.10.0+git20180727=. -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 htslib/hts.c -o build/temp.linux-armhf-3.7/htslib/hts.o arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<>/cyvcf2-0.10.0+git20180727=. -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 htslib/textutils.c -o build/temp.linux-armhf-3.7/htslib/textutils.o arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<>/cyvcf2-0.10.0+git20180727=. -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 htslib/cram/open_trace_file.c -o build/temp.linux-armhf-3.7/htslib/cram/open_trace_file.o arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<>/cyvcf2-0.10.0+git20180727=. -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 htslib/cram/cram_external.c -o build/temp.linux-armhf-3.7/htslib/cram/cram_external.o arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<>/cyvcf2-0.10.0+git20180727=. -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 htslib/cram/cram_samtools.c -o build/temp.linux-armhf-3.7/htslib/cram/cram_samtools.o arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<>/cyvcf2-0.10.0+git20180727=. -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 htslib/cram/files.c -o build/temp.linux-armhf-3.7/htslib/cram/files.o arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<>/cyvcf2-0.10.0+git20180727=. -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 htslib/cram/cram_stats.c -o build/temp.linux-armhf-3.7/htslib/cram/cram_stats.o arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<>/cyvcf2-0.10.0+git20180727=. -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 htslib/cram/cram_decode.c -o build/temp.linux-armhf-3.7/htslib/cram/cram_decode.o arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<>/cyvcf2-0.10.0+git20180727=. -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 htslib/cram/sam_header.c -o build/temp.linux-armhf-3.7/htslib/cram/sam_header.o arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<>/cyvcf2-0.10.0+git20180727=. -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 htslib/cram/cram_io.c -o build/temp.linux-armhf-3.7/htslib/cram/cram_io.o arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<>/cyvcf2-0.10.0+git20180727=. -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 htslib/cram/mFILE.c -o build/temp.linux-armhf-3.7/htslib/cram/mFILE.o arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<>/cyvcf2-0.10.0+git20180727=. -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 htslib/cram/cram_encode.c -o build/temp.linux-armhf-3.7/htslib/cram/cram_encode.o htslib/cram/cram_encode.c: In function ‘process_one_read’: htslib/cram/cram_encode.c:2834:17: warning: unused variable ‘brg’ [-Wunused-variable] SAM_RG *brg = sam_hdr_find_rg(fd->header, "UNKNOWN"); ^~~ arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<>/cyvcf2-0.10.0+git20180727=. -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 htslib/cram/cram_index.c -o build/temp.linux-armhf-3.7/htslib/cram/cram_index.o htslib/cram/cram_index.c: In function ‘cram_index_build’: htslib/cram/cram_index.c:587:23: warning: variable ‘hpos’ set but not used [-Wunused-but-set-variable] off_t cpos, spos, hpos; ^~~~ arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<>/cyvcf2-0.10.0+git20180727=. -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 htslib/cram/string_alloc.c -o build/temp.linux-armhf-3.7/htslib/cram/string_alloc.o arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<>/cyvcf2-0.10.0+git20180727=. -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 htslib/cram/pooled_alloc.c -o build/temp.linux-armhf-3.7/htslib/cram/pooled_alloc.o arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<>/cyvcf2-0.10.0+git20180727=. -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 htslib/cram/cram_codecs.c -o build/temp.linux-armhf-3.7/htslib/cram/cram_codecs.o arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<>/cyvcf2-0.10.0+git20180727=. -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 htslib/cram/rANS_static.c -o build/temp.linux-armhf-3.7/htslib/cram/rANS_static.o arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<>/cyvcf2-0.10.0+git20180727=. -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-armhf-3.7/cyvcf2/helpers.o arm-linux-gnueabihf-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=/<>/cyvcf2-0.10.0+git20180727=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-3.7/cyvcf2/cyvcf2.o build/temp.linux-armhf-3.7/htslib/hfile_net.o build/temp.linux-armhf-3.7/htslib/vcf.o build/temp.linux-armhf-3.7/htslib/regidx.o build/temp.linux-armhf-3.7/htslib/synced_bcf_reader.o build/temp.linux-armhf-3.7/htslib/hfile_libcurl.o build/temp.linux-armhf-3.7/htslib/bgzf.o build/temp.linux-armhf-3.7/htslib/t.o build/temp.linux-armhf-3.7/htslib/vcfutils.o build/temp.linux-armhf-3.7/htslib/tbx.o build/temp.linux-armhf-3.7/htslib/knetfile.o build/temp.linux-armhf-3.7/htslib/hfile_s3.o build/temp.linux-armhf-3.7/htslib/errmod.o build/temp.linux-armhf-3.7/htslib/kfunc.o build/temp.linux-armhf-3.7/htslib/multipart.o build/temp.linux-armhf-3.7/htslib/bcf_sr_sort.o build/temp.linux-armhf-3.7/htslib/probaln.o build/temp.linux-armhf-3.7/htslib/vcf_sweep.o build/temp.linux-armhf-3.7/htslib/realn.o build/temp.linux-armhf-3.7/htslib/sam.o build/temp.linux-armhf-3.7/htslib/kstring.o build/temp.linux-armhf-3.7/htslib/thread_pool.o build/temp.linux-armhf-3.7/htslib/hfile_gcs.o build/temp.linux-armhf-3.7/htslib/md5.o build/temp.linux-armhf-3.7/htslib/hts_os.o build/temp.linux-armhf-3.7/htslib/faidx.o build/temp.linux-armhf-3.7/htslib/hfile.o build/temp.linux-armhf-3.7/htslib/hts.o build/temp.linux-armhf-3.7/htslib/textutils.o build/temp.linux-armhf-3.7/htslib/cram/open_trace_file.o build/temp.linux-armhf-3.7/htslib/cram/cram_external.o build/temp.linux-armhf-3.7/htslib/cram/cram_samtools.o build/temp.linux-armhf-3.7/htslib/cram/files.o build/temp.linux-armhf-3.7/htslib/cram/cram_stats.o build/temp.linux-armhf-3.7/htslib/cram/cram_decode.o build/temp.linux-armhf-3.7/htslib/cram/sam_header.o build/temp.linux-armhf-3.7/htslib/cram/cram_io.o build/temp.linux-armhf-3.7/htslib/cram/mFILE.o build/temp.linux-armhf-3.7/htslib/cram/cram_encode.o build/temp.linux-armhf-3.7/htslib/cram/cram_index.o build/temp.linux-armhf-3.7/htslib/cram/string_alloc.o build/temp.linux-armhf-3.7/htslib/cram/pooled_alloc.o build/temp.linux-armhf-3.7/htslib/cram/cram_codecs.o build/temp.linux-armhf-3.7/htslib/cram/rANS_static.o build/temp.linux-armhf-3.7/cyvcf2/helpers.o -lz -lcurl -lssl -lcrypt -o /<>/cyvcf2-0.10.0+git20180727/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2/cyvcf2.cpython-37m-arm-linux-gnueabihf.so I: pybuild base:217: /usr/bin/python3 setup.py build running build running build_py creating /<>/cyvcf2-0.10.0+git20180727/.pybuild/cpython3_3.6_cyvcf2/build/cyvcf2 copying cyvcf2/__init__.py -> /<>/cyvcf2-0.10.0+git20180727/.pybuild/cpython3_3.6_cyvcf2/build/cyvcf2 copying cyvcf2/cli.py -> /<>/cyvcf2-0.10.0+git20180727/.pybuild/cpython3_3.6_cyvcf2/build/cyvcf2 copying cyvcf2/__main__.py -> /<>/cyvcf2-0.10.0+git20180727/.pybuild/cpython3_3.6_cyvcf2/build/cyvcf2 creating /<>/cyvcf2-0.10.0+git20180727/.pybuild/cpython3_3.6_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/__init__.py -> /<>/cyvcf2-0.10.0+git20180727/.pybuild/cpython3_3.6_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/test_hemi.py -> /<>/cyvcf2-0.10.0+git20180727/.pybuild/cpython3_3.6_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/test_cli.py -> /<>/cyvcf2-0.10.0+git20180727/.pybuild/cpython3_3.6_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/test_reader.py -> /<>/cyvcf2-0.10.0+git20180727/.pybuild/cpython3_3.6_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' writing manifest file 'cyvcf2.egg-info/SOURCES.txt' copying cyvcf2/cyvcf2.c -> /<>/cyvcf2-0.10.0+git20180727/.pybuild/cpython3_3.6_cyvcf2/build/cyvcf2 copying cyvcf2/cyvcf2.pxd -> /<>/cyvcf2-0.10.0+git20180727/.pybuild/cpython3_3.6_cyvcf2/build/cyvcf2 copying cyvcf2/cyvcf2.pyx -> /<>/cyvcf2-0.10.0+git20180727/.pybuild/cpython3_3.6_cyvcf2/build/cyvcf2 copying cyvcf2/helpers.c -> /<>/cyvcf2-0.10.0+git20180727/.pybuild/cpython3_3.6_cyvcf2/build/cyvcf2 copying cyvcf2/helpers.h -> /<>/cyvcf2-0.10.0+git20180727/.pybuild/cpython3_3.6_cyvcf2/build/cyvcf2 copying cyvcf2/relatedness.h -> /<>/cyvcf2-0.10.0+git20180727/.pybuild/cpython3_3.6_cyvcf2/build/cyvcf2 copying cyvcf2/tests/bug.vcf.gz -> /<>/cyvcf2-0.10.0+git20180727/.pybuild/cpython3_3.6_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/decomposed.vcf -> /<>/cyvcf2-0.10.0+git20180727/.pybuild/cpython3_3.6_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/empty.vcf -> /<>/cyvcf2-0.10.0+git20180727/.pybuild/cpython3_3.6_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/issue_44.vcf -> /<>/cyvcf2-0.10.0+git20180727/.pybuild/cpython3_3.6_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/o.vcf.gz -> /<>/cyvcf2-0.10.0+git20180727/.pybuild/cpython3_3.6_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/seg.vcf.gz -> /<>/cyvcf2-0.10.0+git20180727/.pybuild/cpython3_3.6_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/test-alt-repr.vcf -> /<>/cyvcf2-0.10.0+git20180727/.pybuild/cpython3_3.6_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/test-format-string.vcf -> /<>/cyvcf2-0.10.0+git20180727/.pybuild/cpython3_3.6_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/test-haploidX.vcf -> /<>/cyvcf2-0.10.0+git20180727/.pybuild/cpython3_3.6_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/test-hemi.vcf -> /<>/cyvcf2-0.10.0+git20180727/.pybuild/cpython3_3.6_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/test-multiallelic-homozygous-alt.vcf.gz -> /<>/cyvcf2-0.10.0+git20180727/.pybuild/cpython3_3.6_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/test-multiallelic-homozygous-alt.vcf.gz.tbi -> /<>/cyvcf2-0.10.0+git20180727/.pybuild/cpython3_3.6_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/test-strict-gt-option-flag.vcf.gz -> /<>/cyvcf2-0.10.0+git20180727/.pybuild/cpython3_3.6_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/test-strict-gt-option-flag.vcf.gz.tbi -> /<>/cyvcf2-0.10.0+git20180727/.pybuild/cpython3_3.6_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/test.comp_het.3.vcf -> /<>/cyvcf2-0.10.0+git20180727/.pybuild/cpython3_3.6_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/test.snpeff.bcf -> /<>/cyvcf2-0.10.0+git20180727/.pybuild/cpython3_3.6_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/test.snpeff.bcf.csi -> /<>/cyvcf2-0.10.0+git20180727/.pybuild/cpython3_3.6_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/test.snpeff.vcf -> /<>/cyvcf2-0.10.0+git20180727/.pybuild/cpython3_3.6_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/test.vcf.gz -> /<>/cyvcf2-0.10.0+git20180727/.pybuild/cpython3_3.6_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/test.vcf.gz.tbi -> /<>/cyvcf2-0.10.0+git20180727/.pybuild/cpython3_3.6_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/test_gt_alt_freqs.vcf -> /<>/cyvcf2-0.10.0+git20180727/.pybuild/cpython3_3.6_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/test_gt_bases.vcf.gz -> /<>/cyvcf2-0.10.0+git20180727/.pybuild/cpython3_3.6_cyvcf2/build/cyvcf2/tests running build_ext skipping 'cyvcf2/cyvcf2.c' Cython extension (up-to-date) building 'cyvcf2.cyvcf2' extension creating build/temp.linux-armhf-3.6 creating build/temp.linux-armhf-3.6/cyvcf2 creating build/temp.linux-armhf-3.6/htslib creating build/temp.linux-armhf-3.6/htslib/cram arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<>/cyvcf2-0.10.0+git20180727=. -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/python3.6m -c cyvcf2/cyvcf2.c -o build/temp.linux-armhf-3.6/cyvcf2/cyvcf2.o In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1816, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:18, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:4, from cyvcf2/cyvcf2.c:568: /usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2: warning: #warning "Using deprecated NumPy API, disable it by " "#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] #warning "Using deprecated NumPy API, disable it by " \ ^~~~~~~ cyvcf2/cyvcf2.c: In function ‘__pyx_pf_6cyvcf2_6cyvcf2_3VCF_4add_to_header’: cyvcf2/cyvcf2.c:8230:44: 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:571: htslib/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:8272:42: 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:571: htslib/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:8881:49: 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:571: htslib/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:9155:44: 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:571: htslib/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:9208:42: 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:571: htslib/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:9418:115: 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); htslib/htslib/vcf.h:796:103: note: in definition of macro ‘bcf_itr_querys’ #define bcf_itr_querys(idx, hdr, s) hts_itr_querys((idx), (s), (hts_name2id_f)(bcf_hdr_name2id), (hdr), hts_itr_query, bcf_readrec) ^~~ In file included from htslib/htslib/vcf.h:39, from cyvcf2/helpers.h:1, from cyvcf2/cyvcf2.c:571: htslib/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:10841:163: 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, 411, __pyx_L1_error) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ cyvcf2/cyvcf2.c:2810:61: 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:12508:33: 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:571: htslib/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:12992:3: 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:571: htslib/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:13245:18: 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:571: cyvcf2/cyvcf2.c:13372:75: 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)); htslib/htslib/vcf.h:799:112: note: in definition of macro ‘bcf_index_seqnames’ #define bcf_index_seqnames(idx, hdr, nptr) hts_idx_seqnames((idx),(nptr),(hts_id2name_f)(bcf_hdr_id2name),(hdr)) ^~~ In file included from htslib/htslib/vcf.h:39, from cyvcf2/helpers.h:1, from cyvcf2/cyvcf2.c:571: htslib/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:13372:22: 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:13605:22: 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:25742:17: 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:35677:13: warning: assignment discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] __pyx_v_h = __pyx_t_5; ^ cyvcf2/cyvcf2.c: In function ‘__pyx_pf_6cyvcf2_6cyvcf2_4INFO_12__next__’: cyvcf2/cyvcf2.c:38663:16: 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:39646:18: 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:40228:35: 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:571: htslib/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:40256:47: 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:571: htslib/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:40322:78: 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:571: htslib/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:40497:60: 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:571: htslib/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:40535:49: 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:571: htslib/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:40594:100: 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, 2073, __pyx_L1_error) ~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from cyvcf2/helpers.h:1, from cyvcf2/cyvcf2.c:571: htslib/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:6771:18: warning: ‘__pyx_f_6cyvcf2_6cyvcf2_xstr’ defined but not used [-Wunused-function] static PyObject *__pyx_f_6cyvcf2_6cyvcf2_xstr(PyObject *__pyx_v_s) { ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<>/cyvcf2-0.10.0+git20180727=. -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/python3.6m -c htslib/hfile_net.c -o build/temp.linux-armhf-3.6/htslib/hfile_net.o arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<>/cyvcf2-0.10.0+git20180727=. -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/python3.6m -c htslib/vcf.c -o build/temp.linux-armhf-3.6/htslib/vcf.o arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<>/cyvcf2-0.10.0+git20180727=. -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/python3.6m -c htslib/regidx.c -o build/temp.linux-armhf-3.6/htslib/regidx.o arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<>/cyvcf2-0.10.0+git20180727=. -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/python3.6m -c htslib/synced_bcf_reader.c -o build/temp.linux-armhf-3.6/htslib/synced_bcf_reader.o arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<>/cyvcf2-0.10.0+git20180727=. -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/python3.6m -c htslib/hfile_libcurl.c -o build/temp.linux-armhf-3.6/htslib/hfile_libcurl.o arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<>/cyvcf2-0.10.0+git20180727=. -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/python3.6m -c htslib/bgzf.c -o build/temp.linux-armhf-3.6/htslib/bgzf.o arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<>/cyvcf2-0.10.0+git20180727=. -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/python3.6m -c htslib/t.c -o build/temp.linux-armhf-3.6/htslib/t.o arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<>/cyvcf2-0.10.0+git20180727=. -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/python3.6m -c htslib/vcfutils.c -o build/temp.linux-armhf-3.6/htslib/vcfutils.o arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<>/cyvcf2-0.10.0+git20180727=. -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/python3.6m -c htslib/tbx.c -o build/temp.linux-armhf-3.6/htslib/tbx.o arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<>/cyvcf2-0.10.0+git20180727=. -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/python3.6m -c htslib/knetfile.c -o build/temp.linux-armhf-3.6/htslib/knetfile.o arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<>/cyvcf2-0.10.0+git20180727=. -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/python3.6m -c htslib/hfile_s3.c -o build/temp.linux-armhf-3.6/htslib/hfile_s3.o arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<>/cyvcf2-0.10.0+git20180727=. -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/python3.6m -c htslib/errmod.c -o build/temp.linux-armhf-3.6/htslib/errmod.o arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<>/cyvcf2-0.10.0+git20180727=. -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/python3.6m -c htslib/kfunc.c -o build/temp.linux-armhf-3.6/htslib/kfunc.o arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<>/cyvcf2-0.10.0+git20180727=. -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/python3.6m -c htslib/multipart.c -o build/temp.linux-armhf-3.6/htslib/multipart.o arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<>/cyvcf2-0.10.0+git20180727=. -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/python3.6m -c htslib/bcf_sr_sort.c -o build/temp.linux-armhf-3.6/htslib/bcf_sr_sort.o arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<>/cyvcf2-0.10.0+git20180727=. -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/python3.6m -c htslib/probaln.c -o build/temp.linux-armhf-3.6/htslib/probaln.o arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<>/cyvcf2-0.10.0+git20180727=. -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/python3.6m -c htslib/vcf_sweep.c -o build/temp.linux-armhf-3.6/htslib/vcf_sweep.o arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<>/cyvcf2-0.10.0+git20180727=. -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/python3.6m -c htslib/realn.c -o build/temp.linux-armhf-3.6/htslib/realn.o arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<>/cyvcf2-0.10.0+git20180727=. -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/python3.6m -c htslib/sam.c -o build/temp.linux-armhf-3.6/htslib/sam.o arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<>/cyvcf2-0.10.0+git20180727=. -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/python3.6m -c htslib/kstring.c -o build/temp.linux-armhf-3.6/htslib/kstring.o arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<>/cyvcf2-0.10.0+git20180727=. -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/python3.6m -c htslib/thread_pool.c -o build/temp.linux-armhf-3.6/htslib/thread_pool.o arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<>/cyvcf2-0.10.0+git20180727=. -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/python3.6m -c htslib/hfile_gcs.c -o build/temp.linux-armhf-3.6/htslib/hfile_gcs.o arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<>/cyvcf2-0.10.0+git20180727=. -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/python3.6m -c htslib/md5.c -o build/temp.linux-armhf-3.6/htslib/md5.o arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<>/cyvcf2-0.10.0+git20180727=. -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/python3.6m -c htslib/hts_os.c -o build/temp.linux-armhf-3.6/htslib/hts_os.o arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<>/cyvcf2-0.10.0+git20180727=. -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/python3.6m -c htslib/faidx.c -o build/temp.linux-armhf-3.6/htslib/faidx.o arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<>/cyvcf2-0.10.0+git20180727=. -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/python3.6m -c htslib/hfile.c -o build/temp.linux-armhf-3.6/htslib/hfile.o arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<>/cyvcf2-0.10.0+git20180727=. -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/python3.6m -c htslib/hts.c -o build/temp.linux-armhf-3.6/htslib/hts.o arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<>/cyvcf2-0.10.0+git20180727=. -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/python3.6m -c htslib/textutils.c -o build/temp.linux-armhf-3.6/htslib/textutils.o arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<>/cyvcf2-0.10.0+git20180727=. -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/python3.6m -c htslib/cram/open_trace_file.c -o build/temp.linux-armhf-3.6/htslib/cram/open_trace_file.o arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<>/cyvcf2-0.10.0+git20180727=. -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/python3.6m -c htslib/cram/cram_external.c -o build/temp.linux-armhf-3.6/htslib/cram/cram_external.o arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<>/cyvcf2-0.10.0+git20180727=. -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/python3.6m -c htslib/cram/cram_samtools.c -o build/temp.linux-armhf-3.6/htslib/cram/cram_samtools.o arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<>/cyvcf2-0.10.0+git20180727=. -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/python3.6m -c htslib/cram/files.c -o build/temp.linux-armhf-3.6/htslib/cram/files.o arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<>/cyvcf2-0.10.0+git20180727=. -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/python3.6m -c htslib/cram/cram_stats.c -o build/temp.linux-armhf-3.6/htslib/cram/cram_stats.o arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<>/cyvcf2-0.10.0+git20180727=. -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/python3.6m -c htslib/cram/cram_decode.c -o build/temp.linux-armhf-3.6/htslib/cram/cram_decode.o arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<>/cyvcf2-0.10.0+git20180727=. -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/python3.6m -c htslib/cram/sam_header.c -o build/temp.linux-armhf-3.6/htslib/cram/sam_header.o arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<>/cyvcf2-0.10.0+git20180727=. -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/python3.6m -c htslib/cram/cram_io.c -o build/temp.linux-armhf-3.6/htslib/cram/cram_io.o arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<>/cyvcf2-0.10.0+git20180727=. -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/python3.6m -c htslib/cram/mFILE.c -o build/temp.linux-armhf-3.6/htslib/cram/mFILE.o arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<>/cyvcf2-0.10.0+git20180727=. -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/python3.6m -c htslib/cram/cram_encode.c -o build/temp.linux-armhf-3.6/htslib/cram/cram_encode.o htslib/cram/cram_encode.c: In function ‘process_one_read’: htslib/cram/cram_encode.c:2834:17: warning: unused variable ‘brg’ [-Wunused-variable] SAM_RG *brg = sam_hdr_find_rg(fd->header, "UNKNOWN"); ^~~ arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<>/cyvcf2-0.10.0+git20180727=. -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/python3.6m -c htslib/cram/cram_index.c -o build/temp.linux-armhf-3.6/htslib/cram/cram_index.o htslib/cram/cram_index.c: In function ‘cram_index_build’: htslib/cram/cram_index.c:587:23: warning: variable ‘hpos’ set but not used [-Wunused-but-set-variable] off_t cpos, spos, hpos; ^~~~ arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<>/cyvcf2-0.10.0+git20180727=. -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/python3.6m -c htslib/cram/string_alloc.c -o build/temp.linux-armhf-3.6/htslib/cram/string_alloc.o arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<>/cyvcf2-0.10.0+git20180727=. -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/python3.6m -c htslib/cram/pooled_alloc.c -o build/temp.linux-armhf-3.6/htslib/cram/pooled_alloc.o arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<>/cyvcf2-0.10.0+git20180727=. -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/python3.6m -c htslib/cram/cram_codecs.c -o build/temp.linux-armhf-3.6/htslib/cram/cram_codecs.o arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<>/cyvcf2-0.10.0+git20180727=. -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/python3.6m -c htslib/cram/rANS_static.c -o build/temp.linux-armhf-3.6/htslib/cram/rANS_static.o arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -fdebug-prefix-map=/<>/cyvcf2-0.10.0+git20180727=. -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/python3.6m -c cyvcf2/helpers.c -o build/temp.linux-armhf-3.6/cyvcf2/helpers.o arm-linux-gnueabihf-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=/<>/cyvcf2-0.10.0+git20180727=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-3.6/cyvcf2/cyvcf2.o build/temp.linux-armhf-3.6/htslib/hfile_net.o build/temp.linux-armhf-3.6/htslib/vcf.o build/temp.linux-armhf-3.6/htslib/regidx.o build/temp.linux-armhf-3.6/htslib/synced_bcf_reader.o build/temp.linux-armhf-3.6/htslib/hfile_libcurl.o build/temp.linux-armhf-3.6/htslib/bgzf.o build/temp.linux-armhf-3.6/htslib/t.o build/temp.linux-armhf-3.6/htslib/vcfutils.o build/temp.linux-armhf-3.6/htslib/tbx.o build/temp.linux-armhf-3.6/htslib/knetfile.o build/temp.linux-armhf-3.6/htslib/hfile_s3.o build/temp.linux-armhf-3.6/htslib/errmod.o build/temp.linux-armhf-3.6/htslib/kfunc.o build/temp.linux-armhf-3.6/htslib/multipart.o build/temp.linux-armhf-3.6/htslib/bcf_sr_sort.o build/temp.linux-armhf-3.6/htslib/probaln.o build/temp.linux-armhf-3.6/htslib/vcf_sweep.o build/temp.linux-armhf-3.6/htslib/realn.o build/temp.linux-armhf-3.6/htslib/sam.o build/temp.linux-armhf-3.6/htslib/kstring.o build/temp.linux-armhf-3.6/htslib/thread_pool.o build/temp.linux-armhf-3.6/htslib/hfile_gcs.o build/temp.linux-armhf-3.6/htslib/md5.o build/temp.linux-armhf-3.6/htslib/hts_os.o build/temp.linux-armhf-3.6/htslib/faidx.o build/temp.linux-armhf-3.6/htslib/hfile.o build/temp.linux-armhf-3.6/htslib/hts.o build/temp.linux-armhf-3.6/htslib/textutils.o build/temp.linux-armhf-3.6/htslib/cram/open_trace_file.o build/temp.linux-armhf-3.6/htslib/cram/cram_external.o build/temp.linux-armhf-3.6/htslib/cram/cram_samtools.o build/temp.linux-armhf-3.6/htslib/cram/files.o build/temp.linux-armhf-3.6/htslib/cram/cram_stats.o build/temp.linux-armhf-3.6/htslib/cram/cram_decode.o build/temp.linux-armhf-3.6/htslib/cram/sam_header.o build/temp.linux-armhf-3.6/htslib/cram/cram_io.o build/temp.linux-armhf-3.6/htslib/cram/mFILE.o build/temp.linux-armhf-3.6/htslib/cram/cram_encode.o build/temp.linux-armhf-3.6/htslib/cram/cram_index.o build/temp.linux-armhf-3.6/htslib/cram/string_alloc.o build/temp.linux-armhf-3.6/htslib/cram/pooled_alloc.o build/temp.linux-armhf-3.6/htslib/cram/cram_codecs.o build/temp.linux-armhf-3.6/htslib/cram/rANS_static.o build/temp.linux-armhf-3.6/cyvcf2/helpers.o -lz -lcurl -lssl -lcrypt -o /<>/cyvcf2-0.10.0+git20180727/.pybuild/cpython3_3.6_cyvcf2/build/cyvcf2/cyvcf2.cpython-36m-arm-linux-gnueabihf.so dh_auto_test -a -O--buildsystem=pybuild I: pybuild base:217: cd /<>/cyvcf2-0.10.0+git20180727/.pybuild/cpython2_2.7_cyvcf2/build; python2.7 -m nose E ====================================================================== ERROR: Failure: ImportError (/<>/cyvcf2-0.10.0+git20180727/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2/cyvcf2.so: undefined symbol: EVP_sha1) ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/lib/python2.7/dist-packages/nose/loader.py", line 418, in loadTestsFromName addr.filename, addr.module) File "/usr/lib/python2.7/dist-packages/nose/importer.py", line 47, in importFromPath return self.importFromDir(dir_path, fqname) File "/usr/lib/python2.7/dist-packages/nose/importer.py", line 94, in importFromDir mod = load_module(part_fqname, fh, filename, desc) File "/<>/cyvcf2-0.10.0+git20180727/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2/__init__.py", line 1, in from .cyvcf2 import (VCF, Variant, Writer, r_ as r_unphased, par_relatedness, ImportError: /<>/cyvcf2-0.10.0+git20180727/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2/cyvcf2.so: undefined symbol: EVP_sha1 ---------------------------------------------------------------------- Ran 1 test in 0.020s FAILED (errors=1) E: pybuild pybuild:338: test: plugin distutils failed with: exit code=1: cd /<>/cyvcf2-0.10.0+git20180727/.pybuild/cpython2_2.7_cyvcf2/build; python2.7 -m nose 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 20180814-1721 Finished -------- E: Build failure (dpkg-buildpackage died) +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not removing build depends: as requested +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: armhf Build-Space: 53520 Build-Time: 494 Distribution: cosmic-proposed Fail-Stage: build Host Architecture: armhf Install-Time: 88 Job: cyvcf2_0.10.0+git20180727-2.dsc Machine Architecture: arm64 Package: cyvcf2 Package-Time: 583 Source-Version: 0.10.0+git20180727-2 Space: 53520 Status: attempted Version: 0.10.0+git20180727-2 -------------------------------------------------------------------------------- Finished at 20180814-1721 Build needed 00:09:43, 53520k disc space RUN: /usr/share/launchpad-buildd/slavebin/in-target scan-for-processes --backend=chroot --series=cosmic --arch=armhf PACKAGEBUILD-15261391 Scanning for processes to kill in build PACKAGEBUILD-15261391