I: pbuilder: network access will be disabled during build I: Current time: Tue Nov 10 05:16:51 +14 2020 I: pbuilder-time-stamp: 1604935011 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/buster-reproducible-base.tgz] I: copying local configuration I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [cyvcf2_0.10.4-1.dsc] I: copying [./cyvcf2_0.10.4.orig.tar.gz] I: copying [./cyvcf2_0.10.4-1.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/root/.gnupg/trustedkeys.kbx': General error gpgv: Signature made Sat Jan 12 13:24:22 2019 +14 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./cyvcf2_0.10.4-1.dsc dpkg-source: info: extracting cyvcf2 in cyvcf2-0.10.4 dpkg-source: info: unpacking cyvcf2_0.10.4.orig.tar.gz dpkg-source: info: unpacking cyvcf2_0.10.4-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying add_htslib_link_dependency.patch dpkg-source: info: applying split_format_test.patch I: using fakeroot in build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/11204/tmp/hooks/D01_modify_environment starting debug: Running on wbq0. I: Changing host+domainname to test build reproducibility I: Adding a custom variable just for the fun of it... I: Changing /bin/sh to bash Removing 'diversion of /bin/sh to /bin/sh.distrib by dash' Adding 'diversion of /bin/sh to /bin/sh.distrib by bash' Removing 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by dash' Adding 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by bash' I: Setting pbuilder2's login shell to /bin/bash I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other I: user script /srv/workspace/pbuilder/11204/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/11204/tmp/hooks/D02_print_environment starting I: set BASH=/bin/sh BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:hostcomplete:interactive_comments:progcomp:promptvars:sourcepath BASH_ALIASES=() BASH_ARGC=() BASH_ARGV=() BASH_CMDS=() BASH_LINENO=([0]="12" [1]="0") BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") BASH_VERSINFO=([0]="5" [1]="0" [2]="3" [3]="1" [4]="release" [5]="arm-unknown-linux-gnueabihf") BASH_VERSION='5.0.3(1)-release' BUILDDIR=/build BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=armhf DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=4' DIRSTACK=() DISTRIBUTION= EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=arm HOST_ARCH=armhf IFS=' ' INVOCATION_ID=5295eeba061d44a6a7a954b4aeae4c8f LANG=C LANGUAGE=it_CH:it LC_ALL=C MACHTYPE=arm-unknown-linux-gnueabihf MAIL=/var/mail/root OPTERR=1 OPTIND=1 OSTYPE=linux-gnueabihf PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path PBCURRENTCOMMANDLINEOPERATION=build PBUILDER_OPERATION=build PBUILDER_PKGDATADIR=/usr/share/pbuilder PBUILDER_PKGLIBDIR=/usr/lib/pbuilder PBUILDER_SYSCONFDIR=/etc PIPESTATUS=([0]="0") POSIXLY_CORRECT=y PPID=11204 PS4='+ ' PWD=/ SHELL=/bin/bash SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix SHLVL=3 SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/tmp.YZ6Grjw9WX/pbuilderrc_jaRI --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/buster-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.YZ6Grjw9WX/b2 --logfile b2/build.log cyvcf2_0.10.4-1.dsc' SUDO_GID=115 SUDO_UID=111 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://10.0.0.15:8000/ I: uname -a Linux i-capture-the-hostname 5.8.0-0.bpo.2-armmp #1 SMP Debian 5.8.10-1~bpo10+1 (2020-09-26) armv7l GNU/Linux I: ls -l /bin total 3328 -rwxr-xr-x 1 root root 767656 Apr 18 2019 bash -rwxr-xr-x 3 root root 26052 Jul 11 2019 bunzip2 -rwxr-xr-x 3 root root 26052 Jul 11 2019 bzcat lrwxrwxrwx 1 root root 6 Jul 11 2019 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2227 Jul 11 2019 bzdiff lrwxrwxrwx 1 root root 6 Jul 11 2019 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4877 Jun 25 2019 bzexe lrwxrwxrwx 1 root root 6 Jul 11 2019 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3641 Jul 11 2019 bzgrep -rwxr-xr-x 3 root root 26052 Jul 11 2019 bzip2 -rwxr-xr-x 1 root root 9636 Jul 11 2019 bzip2recover lrwxrwxrwx 1 root root 6 Jul 11 2019 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Jul 11 2019 bzmore -rwxr-xr-x 1 root root 22432 Mar 1 2019 cat -rwxr-xr-x 1 root root 38868 Mar 1 2019 chgrp -rwxr-xr-x 1 root root 38836 Mar 1 2019 chmod -rwxr-xr-x 1 root root 42972 Mar 1 2019 chown -rwxr-xr-x 1 root root 88376 Mar 1 2019 cp -rwxr-xr-x 1 root root 75516 Jan 18 2019 dash -rwxr-xr-x 1 root root 71648 Mar 1 2019 date -rwxr-xr-x 1 root root 51212 Mar 1 2019 dd -rwxr-xr-x 1 root root 55672 Mar 1 2019 df -rwxr-xr-x 1 root root 88444 Mar 1 2019 dir -rwxr-xr-x 1 root root 54872 Jan 10 2019 dmesg lrwxrwxrwx 1 root root 8 Sep 27 2018 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Sep 27 2018 domainname -> hostname -rwxr-xr-x 1 root root 22364 Mar 1 2019 echo -rwxr-xr-x 1 root root 28 Jan 8 2019 egrep -rwxr-xr-x 1 root root 18260 Mar 1 2019 false -rwxr-xr-x 1 root root 28 Jan 8 2019 fgrep -rwxr-xr-x 1 root root 47356 Jan 10 2019 findmnt -rwsr-xr-x 1 root root 21980 Apr 23 2020 fusermount -rwxr-xr-x 1 root root 124508 Jan 8 2019 grep -rwxr-xr-x 2 root root 2345 Jan 6 2019 gunzip -rwxr-xr-x 1 root root 6375 Jan 6 2019 gzexe -rwxr-xr-x 1 root root 64232 Jan 6 2019 gzip -rwxr-xr-x 1 root root 13784 Sep 27 2018 hostname -rwxr-xr-x 1 root root 43044 Mar 1 2019 ln -rwxr-xr-x 1 root root 34932 Jul 27 2018 login -rwxr-xr-x 1 root root 88444 Mar 1 2019 ls -rwxr-xr-x 1 root root 67036 Jan 10 2019 lsblk -rwxr-xr-x 1 root root 47168 Mar 1 2019 mkdir -rwxr-xr-x 1 root root 43040 Mar 1 2019 mknod -rwxr-xr-x 1 root root 26552 Mar 1 2019 mktemp -rwxr-xr-x 1 root root 26024 Jan 10 2019 more -rwsr-xr-x 1 root root 34268 Jan 10 2019 mount -rwxr-xr-x 1 root root 9688 Jan 10 2019 mountpoint -rwxr-xr-x 1 root root 84284 Mar 1 2019 mv lrwxrwxrwx 1 root root 8 Sep 27 2018 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Feb 15 2019 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 22416 Mar 1 2019 pwd lrwxrwxrwx 1 root root 4 Apr 18 2019 rbash -> bash -rwxr-xr-x 1 root root 26504 Mar 1 2019 readlink -rwxr-xr-x 1 root root 42968 Mar 1 2019 rm -rwxr-xr-x 1 root root 26496 Mar 1 2019 rmdir -rwxr-xr-x 1 root root 14136 Jan 22 2019 run-parts -rwxr-xr-x 1 root root 76012 Dec 23 2018 sed lrwxrwxrwx 1 root root 4 Nov 10 05:17 sh -> bash lrwxrwxrwx 1 root root 4 Nov 7 22:28 sh.distrib -> dash -rwxr-xr-x 1 root root 22384 Mar 1 2019 sleep -rwxr-xr-x 1 root root 51124 Mar 1 2019 stty -rwsr-xr-x 1 root root 42472 Jan 10 2019 su -rwxr-xr-x 1 root root 22392 Mar 1 2019 sync -rwxr-xr-x 1 root root 283324 Apr 24 2019 tar -rwxr-xr-x 1 root root 9808 Jan 22 2019 tempfile -rwxr-xr-x 1 root root 63464 Mar 1 2019 touch -rwxr-xr-x 1 root root 18260 Mar 1 2019 true -rwxr-xr-x 1 root root 9636 Apr 23 2020 ulockmgr_server -rwsr-xr-x 1 root root 21976 Jan 10 2019 umount -rwxr-xr-x 1 root root 22380 Mar 1 2019 uname -rwxr-xr-x 2 root root 2345 Jan 6 2019 uncompress -rwxr-xr-x 1 root root 88444 Mar 1 2019 vdir -rwxr-xr-x 1 root root 21980 Jan 10 2019 wdctl -rwxr-xr-x 1 root root 946 Jan 22 2019 which lrwxrwxrwx 1 root root 8 Sep 27 2018 ypdomainname -> hostname -rwxr-xr-x 1 root root 1983 Jan 6 2019 zcat -rwxr-xr-x 1 root root 1677 Jan 6 2019 zcmp -rwxr-xr-x 1 root root 5879 Jan 6 2019 zdiff -rwxr-xr-x 1 root root 29 Jan 6 2019 zegrep -rwxr-xr-x 1 root root 29 Jan 6 2019 zfgrep -rwxr-xr-x 1 root root 2080 Jan 6 2019 zforce -rwxr-xr-x 1 root root 7584 Jan 6 2019 zgrep -rwxr-xr-x 1 root root 2205 Jan 6 2019 zless -rwxr-xr-x 1 root root 1841 Jan 6 2019 zmore -rwxr-xr-x 1 root root 4552 Jan 6 2019 znew I: user script /srv/workspace/pbuilder/11204/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: armhf Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper (>= 12~), dh-python, zlib1g-dev, cython, cython3, python-all-dev, python-setuptools, python3-setuptools, python3-all-dev, python-numpy, python3-numpy, python-coloredlogs, python3-coloredlogs, python-click, python3-click, python-nose, python3-nose, libssl-dev, libcurl4-gnutls-dev | libcurl4-openssl-dev, libhts-dev, libbz2-dev dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 18932 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper (>= 12~); however: Package debhelper is not installed. pbuilder-satisfydepends-dummy depends on dh-python; however: Package dh-python is not installed. pbuilder-satisfydepends-dummy depends on zlib1g-dev; however: Package zlib1g-dev is not installed. pbuilder-satisfydepends-dummy depends on cython; however: Package cython is not installed. pbuilder-satisfydepends-dummy depends on cython3; however: Package cython3 is not installed. pbuilder-satisfydepends-dummy depends on python-all-dev; however: Package python-all-dev is not installed. pbuilder-satisfydepends-dummy depends on python-setuptools; however: Package python-setuptools is not installed. pbuilder-satisfydepends-dummy depends on python3-setuptools; however: Package python3-setuptools is not installed. pbuilder-satisfydepends-dummy depends on python3-all-dev; however: Package python3-all-dev is not installed. pbuilder-satisfydepends-dummy depends on python-numpy; however: Package python-numpy is not installed. pbuilder-satisfydepends-dummy depends on python3-numpy; however: Package python3-numpy is not installed. pbuilder-satisfydepends-dummy depends on python-coloredlogs; however: Package python-coloredlogs is not installed. pbuilder-satisfydepends-dummy depends on python3-coloredlogs; however: Package python3-coloredlogs is not installed. pbuilder-satisfydepends-dummy depends on python-click; however: Package python-click is not installed. pbuilder-satisfydepends-dummy depends on python3-click; however: Package python3-click is not installed. pbuilder-satisfydepends-dummy depends on python-nose; however: Package python-nose is not installed. pbuilder-satisfydepends-dummy depends on python3-nose; however: Package python3-nose is not installed. pbuilder-satisfydepends-dummy depends on libssl-dev; however: Package libssl-dev is not installed. pbuilder-satisfydepends-dummy depends on libcurl4-gnutls-dev | libcurl4-openssl-dev; however: Package libcurl4-gnutls-dev is not installed. Package libcurl4-openssl-dev is not installed. pbuilder-satisfydepends-dummy depends on libhts-dev; however: Package libhts-dev is not installed. pbuilder-satisfydepends-dummy depends on libbz2-dev; however: Package libbz2-dev is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdmainutils{a} cython{a} cython3{a} debhelper{a} dh-autoreconf{a} dh-python{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libblas3{a} libbsd0{a} libbz2-dev{a} libcroco3{a} libcurl3-gnutls{a} libcurl4-gnutls-dev{a} libdeflate0{a} libelf1{a} libexpat1{a} libexpat1-dev{a} libfile-stripnondeterminism-perl{a} libgfortran5{a} libglib2.0-0{a} libgssapi-krb5-2{a} libhts-dev{a} libhts2{a} libicu63{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} liblapack3{a} libldap-2.4-2{a} libldap-common{a} liblzma-dev{a} libmagic-mgc{a} libmagic1{a} libmpdec2{a} libncurses6{a} libnghttp2-14{a} libpipeline1{a} libpsl5{a} libpython-all-dev{a} libpython-dev{a} libpython-stdlib{a} libpython2-dev{a} libpython2-stdlib{a} libpython2.7{a} libpython2.7-dev{a} libpython2.7-minimal{a} libpython2.7-stdlib{a} libpython3-all-dev{a} libpython3-dev{a} libpython3-stdlib{a} libpython3.7{a} libpython3.7-dev{a} libpython3.7-minimal{a} libpython3.7-stdlib{a} libreadline7{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsigsegv2{a} libssh2-1{a} libssl-dev{a} libssl1.1{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} mime-support{a} po-debconf{a} python{a} python-all{a} python-all-dev{a} python-click{a} python-colorama{a} python-coloredlogs{a} python-dev{a} python-humanfriendly{a} python-minimal{a} python-monotonic{a} python-nose{a} python-numpy{a} python-pkg-resources{a} python-setuptools{a} python2{a} python2-dev{a} python2-minimal{a} python2.7{a} python2.7-dev{a} python2.7-minimal{a} python3{a} python3-all{a} python3-all-dev{a} python3-click{a} python3-colorama{a} python3-coloredlogs{a} python3-dev{a} python3-distutils{a} python3-humanfriendly{a} python3-lib2to3{a} python3-minimal{a} python3-nose{a} python3-numpy{a} python3-pkg-resources{a} python3-setuptools{a} python3.7{a} python3.7-dev{a} python3.7-minimal{a} readline-common{a} sensible-utils{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: bzip2-doc ca-certificates curl krb5-locales libarchive-cpio-perl libglib2.0-data libgpm2 libltdl-dev libmail-sendmail-perl libsasl2-modules lynx publicsuffix shared-mime-info wget xdg-user-dirs 0 packages upgraded, 122 newly installed, 0 to remove and 0 not upgraded. Need to get 128 MB of archives. After unpacking 285 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian buster/main armhf libbsd0 armhf 0.9.1-2 [103 kB] Get: 2 http://deb.debian.org/debian buster/main armhf bsdmainutils armhf 11.1.2+b1 [186 kB] Get: 3 http://deb.debian.org/debian buster/main armhf libuchardet0 armhf 0.0.6-3 [62.2 kB] Get: 4 http://deb.debian.org/debian buster/main armhf groff-base armhf 1.22.4-3 [828 kB] Get: 5 http://deb.debian.org/debian buster/main armhf libpipeline1 armhf 1.5.1-2 [26.8 kB] Get: 6 http://deb.debian.org/debian buster/main armhf man-db armhf 2.8.5-2 [1240 kB] Get: 7 http://deb.debian.org/debian buster/main armhf libpython2.7-minimal armhf 2.7.16-2+deb10u1 [395 kB] Get: 8 http://deb.debian.org/debian buster/main armhf python2.7-minimal armhf 2.7.16-2+deb10u1 [1171 kB] Get: 9 http://deb.debian.org/debian buster/main armhf python2-minimal armhf 2.7.16-1 [41.4 kB] Get: 10 http://deb.debian.org/debian buster/main armhf python-minimal armhf 2.7.16-1 [21.0 kB] Get: 11 http://deb.debian.org/debian buster/main armhf libssl1.1 armhf 1.1.1d-0+deb10u3 [1299 kB] Get: 12 http://deb.debian.org/debian buster/main armhf mime-support all 3.62 [37.2 kB] Get: 13 http://deb.debian.org/debian buster/main armhf libexpat1 armhf 2.2.6-2+deb10u1 [78.0 kB] Get: 14 http://deb.debian.org/debian buster/main armhf readline-common all 7.0-5 [70.6 kB] Get: 15 http://deb.debian.org/debian buster/main armhf libreadline7 armhf 7.0-5 [131 kB] Get: 16 http://deb.debian.org/debian buster/main armhf libpython2.7-stdlib armhf 2.7.16-2+deb10u1 [1837 kB] Get: 17 http://deb.debian.org/debian buster/main armhf python2.7 armhf 2.7.16-2+deb10u1 [305 kB] Get: 18 http://deb.debian.org/debian buster/main armhf libpython2-stdlib armhf 2.7.16-1 [20.8 kB] Get: 19 http://deb.debian.org/debian buster/main armhf libpython-stdlib armhf 2.7.16-1 [20.8 kB] Get: 20 http://deb.debian.org/debian buster/main armhf python2 armhf 2.7.16-1 [41.6 kB] Get: 21 http://deb.debian.org/debian buster/main armhf python armhf 2.7.16-1 [22.8 kB] Get: 22 http://deb.debian.org/debian buster/main armhf libpython3.7-minimal armhf 3.7.3-2+deb10u2 [582 kB] Get: 23 http://deb.debian.org/debian buster/main armhf python3.7-minimal armhf 3.7.3-2+deb10u2 [1466 kB] Get: 24 http://deb.debian.org/debian buster/main armhf python3-minimal armhf 3.7.3-1 [36.6 kB] Get: 25 http://deb.debian.org/debian buster/main armhf libmpdec2 armhf 2.4.2-2 [69.3 kB] Get: 26 http://deb.debian.org/debian buster/main armhf libpython3.7-stdlib armhf 3.7.3-2+deb10u2 [1660 kB] Get: 27 http://deb.debian.org/debian buster/main armhf python3.7 armhf 3.7.3-2+deb10u2 [330 kB] Get: 28 http://deb.debian.org/debian buster/main armhf libpython3-stdlib armhf 3.7.3-1 [20.0 kB] Get: 29 http://deb.debian.org/debian buster/main armhf python3 armhf 3.7.3-1 [61.5 kB] Get: 30 http://deb.debian.org/debian buster/main armhf sensible-utils all 0.0.12 [15.8 kB] Get: 31 http://deb.debian.org/debian buster/main armhf libmagic-mgc armhf 1:5.35-4+deb10u1 [242 kB] Get: 32 http://deb.debian.org/debian buster/main armhf libmagic1 armhf 1:5.35-4+deb10u1 [110 kB] Get: 33 http://deb.debian.org/debian buster/main armhf file armhf 1:5.35-4+deb10u1 [65.5 kB] Get: 34 http://deb.debian.org/debian buster/main armhf gettext-base armhf 0.19.8.1-9 [118 kB] Get: 35 http://deb.debian.org/debian buster/main armhf libsigsegv2 armhf 2.12-2 [32.1 kB] Get: 36 http://deb.debian.org/debian buster/main armhf m4 armhf 1.4.18-2 [190 kB] Get: 37 http://deb.debian.org/debian buster/main armhf autoconf all 2.69-11 [341 kB] Get: 38 http://deb.debian.org/debian buster/main armhf autotools-dev all 20180224.1 [77.0 kB] Get: 39 http://deb.debian.org/debian buster/main armhf automake all 1:1.16.1-4 [771 kB] Get: 40 http://deb.debian.org/debian buster/main armhf autopoint all 0.19.8.1-9 [434 kB] Get: 41 http://deb.debian.org/debian buster/main armhf cython armhf 0.29.2-2 [1306 kB] Get: 42 http://deb.debian.org/debian buster/main armhf cython3 armhf 0.29.2-2 [1330 kB] Get: 43 http://deb.debian.org/debian buster/main armhf libtool all 2.4.6-9 [547 kB] Get: 44 http://deb.debian.org/debian buster/main armhf dh-autoreconf all 19 [16.9 kB] Get: 45 http://deb.debian.org/debian buster/main armhf libarchive-zip-perl all 1.64-1 [96.8 kB] Get: 46 http://deb.debian.org/debian buster/main armhf libfile-stripnondeterminism-perl all 1.1.2-1 [19.8 kB] Get: 47 http://deb.debian.org/debian buster/main armhf dh-strip-nondeterminism all 1.1.2-1 [13.0 kB] Get: 48 http://deb.debian.org/debian buster/main armhf libelf1 armhf 0.176-1.1 [158 kB] Get: 49 http://deb.debian.org/debian buster/main armhf dwz armhf 0.12-3 [72.0 kB] Get: 50 http://deb.debian.org/debian buster/main armhf libglib2.0-0 armhf 2.58.3-2+deb10u2 [1101 kB] Get: 51 http://deb.debian.org/debian buster/main armhf libicu63 armhf 63.1-6+deb10u1 [8005 kB] Get: 52 http://deb.debian.org/debian buster/main armhf libxml2 armhf 2.9.4+dfsg1-7+b3 [595 kB] Get: 53 http://deb.debian.org/debian buster/main armhf libcroco3 armhf 0.6.12-3 [133 kB] Get: 54 http://deb.debian.org/debian buster/main armhf libncurses6 armhf 6.1+20181013-2+deb10u2 [79.8 kB] Get: 55 http://deb.debian.org/debian buster/main armhf gettext armhf 0.19.8.1-9 [1242 kB] Get: 56 http://deb.debian.org/debian buster/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 57 http://deb.debian.org/debian buster/main armhf po-debconf all 1.0.21 [248 kB] Get: 58 http://deb.debian.org/debian buster/main armhf debhelper all 12.1.1 [1016 kB] Get: 59 http://deb.debian.org/debian buster/main armhf python3-lib2to3 all 3.7.3-1 [76.7 kB] Get: 60 http://deb.debian.org/debian buster/main armhf python3-distutils all 3.7.3-1 [142 kB] Get: 61 http://deb.debian.org/debian buster/main armhf dh-python all 3.20190308 [99.3 kB] Get: 62 http://deb.debian.org/debian buster/main armhf libgfortran5 armhf 8.3.0-6 [213 kB] Get: 63 http://deb.debian.org/debian buster/main armhf libblas3 armhf 3.8.0-2 [109 kB] Get: 64 http://deb.debian.org/debian buster/main armhf libbz2-dev armhf 1.0.6-9.2~deb10u1 [28.8 kB] Get: 65 http://deb.debian.org/debian buster/main armhf libkeyutils1 armhf 1.6-6 [13.9 kB] Get: 66 http://deb.debian.org/debian buster/main armhf libkrb5support0 armhf 1.17-3 [62.3 kB] Get: 67 http://deb.debian.org/debian buster/main armhf libk5crypto3 armhf 1.17-3 [119 kB] Get: 68 http://deb.debian.org/debian buster/main armhf libkrb5-3 armhf 1.17-3 [323 kB] Get: 69 http://deb.debian.org/debian buster/main armhf libgssapi-krb5-2 armhf 1.17-3 [137 kB] Get: 70 http://deb.debian.org/debian buster/main armhf libsasl2-modules-db armhf 2.1.27+dfsg-1+deb10u1 [67.4 kB] Get: 71 http://deb.debian.org/debian buster/main armhf libsasl2-2 armhf 2.1.27+dfsg-1+deb10u1 [98.9 kB] Get: 72 http://deb.debian.org/debian buster/main armhf libldap-common all 2.4.47+dfsg-3+deb10u2 [89.7 kB] Get: 73 http://deb.debian.org/debian buster/main armhf libldap-2.4-2 armhf 2.4.47+dfsg-3+deb10u2 [202 kB] Get: 74 http://deb.debian.org/debian buster/main armhf libnghttp2-14 armhf 1.36.0-2+deb10u1 [74.4 kB] Get: 75 http://deb.debian.org/debian buster/main armhf libpsl5 armhf 0.20.2-2 [52.4 kB] Get: 76 http://deb.debian.org/debian buster/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2 [54.9 kB] Get: 77 http://deb.debian.org/debian buster/main armhf libssh2-1 armhf 1.8.0-2.1 [129 kB] Get: 78 http://deb.debian.org/debian buster/main armhf libcurl3-gnutls armhf 7.64.0-4+deb10u1 [295 kB] Get: 79 http://deb.debian.org/debian buster/main armhf libcurl4-gnutls-dev armhf 7.64.0-4+deb10u1 [389 kB] Get: 80 http://deb.debian.org/debian buster/main armhf libdeflate0 armhf 1.2-1 [46.4 kB] Get: 81 http://deb.debian.org/debian buster/main armhf libexpat1-dev armhf 2.2.6-2+deb10u1 [126 kB] Get: 82 http://deb.debian.org/debian buster/main armhf libhts2 armhf 1.9-11 [261 kB] Get: 83 http://deb.debian.org/debian buster/main armhf liblzma-dev armhf 5.2.4-1 [204 kB] Get: 84 http://deb.debian.org/debian buster/main armhf zlib1g-dev armhf 1:1.2.11.dfsg-1 [207 kB] Get: 85 http://deb.debian.org/debian buster/main armhf libhts-dev armhf 1.9-11 [4289 kB] Get: 86 http://deb.debian.org/debian buster/main armhf liblapack3 armhf 3.8.0-2 [1631 kB] Get: 87 http://deb.debian.org/debian buster/main armhf libpython2.7 armhf 2.7.16-2+deb10u1 [892 kB] Get: 88 http://deb.debian.org/debian buster/main armhf libpython2.7-dev armhf 2.7.16-2+deb10u1 [31.0 MB] Get: 89 http://deb.debian.org/debian buster/main armhf libpython2-dev armhf 2.7.16-1 [20.9 kB] Get: 90 http://deb.debian.org/debian buster/main armhf libpython-dev armhf 2.7.16-1 [20.9 kB] Get: 91 http://deb.debian.org/debian buster/main armhf libpython-all-dev armhf 2.7.16-1 [1064 B] Get: 92 http://deb.debian.org/debian buster/main armhf libpython3.7 armhf 3.7.3-2+deb10u2 [1281 kB] Get: 93 http://deb.debian.org/debian buster/main armhf libpython3.7-dev armhf 3.7.3-2+deb10u2 [47.2 MB] Get: 94 http://deb.debian.org/debian buster/main armhf libpython3-dev armhf 3.7.3-1 [20.1 kB] Get: 95 http://deb.debian.org/debian buster/main armhf libpython3-all-dev armhf 3.7.3-1 [1068 B] Get: 96 http://deb.debian.org/debian buster/main armhf libssl-dev armhf 1.1.1d-0+deb10u3 [1597 kB] Get: 97 http://deb.debian.org/debian buster/main armhf python-all armhf 2.7.16-1 [1044 B] Get: 98 http://deb.debian.org/debian buster/main armhf python2.7-dev armhf 2.7.16-2+deb10u1 [291 kB] Get: 99 http://deb.debian.org/debian buster/main armhf python2-dev armhf 2.7.16-1 [1216 B] Get: 100 http://deb.debian.org/debian buster/main armhf python-dev armhf 2.7.16-1 [1192 B] Get: 101 http://deb.debian.org/debian buster/main armhf python-all-dev armhf 2.7.16-1 [1068 B] Get: 102 http://deb.debian.org/debian buster/main armhf python-colorama all 0.3.7-1 [25.7 kB] Get: 103 http://deb.debian.org/debian buster/main armhf python-click all 7.0-1 [73.5 kB] Get: 104 http://deb.debian.org/debian buster/main armhf python-monotonic all 1.1-2 [5210 B] Get: 105 http://deb.debian.org/debian buster/main armhf python-humanfriendly all 4.18-1 [71.1 kB] Get: 106 http://deb.debian.org/debian buster/main armhf python-coloredlogs all 7.3-1 [27.7 kB] Get: 107 http://deb.debian.org/debian buster/main armhf python-pkg-resources all 40.8.0-1 [182 kB] Get: 108 http://deb.debian.org/debian buster/main armhf python-nose all 1.3.7-4 [132 kB] Get: 109 http://deb.debian.org/debian buster/main armhf python-numpy armhf 1:1.16.2-1 [1885 kB] Get: 110 http://deb.debian.org/debian buster/main armhf python-setuptools all 40.8.0-1 [382 kB] Get: 111 http://deb.debian.org/debian buster/main armhf python3-all armhf 3.7.3-1 [1068 B] Get: 112 http://deb.debian.org/debian buster/main armhf python3.7-dev armhf 3.7.3-2+deb10u2 [509 kB] Get: 113 http://deb.debian.org/debian buster/main armhf python3-dev armhf 3.7.3-1 [1264 B] Get: 114 http://deb.debian.org/debian buster/main armhf python3-all-dev armhf 3.7.3-1 [1064 B] Get: 115 http://deb.debian.org/debian buster/main armhf python3-colorama all 0.3.7-1 [18.1 kB] Get: 116 http://deb.debian.org/debian buster/main armhf python3-click all 7.0-1 [73.6 kB] Get: 117 http://deb.debian.org/debian buster/main armhf python3-humanfriendly all 4.18-1 [71.2 kB] Get: 118 http://deb.debian.org/debian buster/main armhf python3-coloredlogs all 7.3-1 [27.8 kB] Get: 119 http://deb.debian.org/debian buster/main armhf python3-pkg-resources all 40.8.0-1 [153 kB] Get: 120 http://deb.debian.org/debian buster/main armhf python3-nose all 1.3.7-4 [132 kB] Get: 121 http://deb.debian.org/debian buster/main armhf python3-numpy armhf 1:1.16.2-1 [1903 kB] Get: 122 http://deb.debian.org/debian buster/main armhf python3-setuptools all 40.8.0-1 [306 kB] Fetched 128 MB in 15s (8401 kB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libbsd0:armhf. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 18932 files and directories currently installed.) Preparing to unpack .../00-libbsd0_0.9.1-2_armhf.deb ... Unpacking libbsd0:armhf (0.9.1-2) ... Selecting previously unselected package bsdmainutils. Preparing to unpack .../01-bsdmainutils_11.1.2+b1_armhf.deb ... Unpacking bsdmainutils (11.1.2+b1) ... Selecting previously unselected package libuchardet0:armhf. Preparing to unpack .../02-libuchardet0_0.0.6-3_armhf.deb ... Unpacking libuchardet0:armhf (0.0.6-3) ... Selecting previously unselected package groff-base. Preparing to unpack .../03-groff-base_1.22.4-3_armhf.deb ... Unpacking groff-base (1.22.4-3) ... Selecting previously unselected package libpipeline1:armhf. Preparing to unpack .../04-libpipeline1_1.5.1-2_armhf.deb ... Unpacking libpipeline1:armhf (1.5.1-2) ... Selecting previously unselected package man-db. Preparing to unpack .../05-man-db_2.8.5-2_armhf.deb ... Unpacking man-db (2.8.5-2) ... Selecting previously unselected package libpython2.7-minimal:armhf. Preparing to unpack .../06-libpython2.7-minimal_2.7.16-2+deb10u1_armhf.deb ... Unpacking libpython2.7-minimal:armhf (2.7.16-2+deb10u1) ... Selecting previously unselected package python2.7-minimal. Preparing to unpack .../07-python2.7-minimal_2.7.16-2+deb10u1_armhf.deb ... Unpacking python2.7-minimal (2.7.16-2+deb10u1) ... Selecting previously unselected package python2-minimal. Preparing to unpack .../08-python2-minimal_2.7.16-1_armhf.deb ... Unpacking python2-minimal (2.7.16-1) ... Selecting previously unselected package python-minimal. Preparing to unpack .../09-python-minimal_2.7.16-1_armhf.deb ... Unpacking python-minimal (2.7.16-1) ... Selecting previously unselected package libssl1.1:armhf. Preparing to unpack .../10-libssl1.1_1.1.1d-0+deb10u3_armhf.deb ... Unpacking libssl1.1:armhf (1.1.1d-0+deb10u3) ... Selecting previously unselected package mime-support. Preparing to unpack .../11-mime-support_3.62_all.deb ... Unpacking mime-support (3.62) ... Selecting previously unselected package libexpat1:armhf. Preparing to unpack .../12-libexpat1_2.2.6-2+deb10u1_armhf.deb ... Unpacking libexpat1:armhf (2.2.6-2+deb10u1) ... Selecting previously unselected package readline-common. Preparing to unpack .../13-readline-common_7.0-5_all.deb ... Unpacking readline-common (7.0-5) ... Selecting previously unselected package libreadline7:armhf. Preparing to unpack .../14-libreadline7_7.0-5_armhf.deb ... Unpacking libreadline7:armhf (7.0-5) ... Selecting previously unselected package libpython2.7-stdlib:armhf. Preparing to unpack .../15-libpython2.7-stdlib_2.7.16-2+deb10u1_armhf.deb ... Unpacking libpython2.7-stdlib:armhf (2.7.16-2+deb10u1) ... Selecting previously unselected package python2.7. Preparing to unpack .../16-python2.7_2.7.16-2+deb10u1_armhf.deb ... Unpacking python2.7 (2.7.16-2+deb10u1) ... Selecting previously unselected package libpython2-stdlib:armhf. Preparing to unpack .../17-libpython2-stdlib_2.7.16-1_armhf.deb ... Unpacking libpython2-stdlib:armhf (2.7.16-1) ... Selecting previously unselected package libpython-stdlib:armhf. Preparing to unpack .../18-libpython-stdlib_2.7.16-1_armhf.deb ... Unpacking libpython-stdlib:armhf (2.7.16-1) ... Setting up libpython2.7-minimal:armhf (2.7.16-2+deb10u1) ... Setting up python2.7-minimal (2.7.16-2+deb10u1) ... Setting up python2-minimal (2.7.16-1) ... Selecting previously unselected package python2. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 20397 files and directories currently installed.) Preparing to unpack .../python2_2.7.16-1_armhf.deb ... Unpacking python2 (2.7.16-1) ... Setting up python-minimal (2.7.16-1) ... Selecting previously unselected package python. (Reading database ... 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Preparing to unpack .../python3.7-minimal_3.7.3-2+deb10u2_armhf.deb ... Unpacking python3.7-minimal (3.7.3-2+deb10u2) ... Setting up libssl1.1:armhf (1.1.1d-0+deb10u3) ... Setting up libpython3.7-minimal:armhf (3.7.3-2+deb10u2) ... Setting up libexpat1:armhf (2.2.6-2+deb10u1) ... Setting up python3.7-minimal (3.7.3-2+deb10u2) ... Selecting previously unselected package python3-minimal. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 20684 files and directories currently installed.) Preparing to unpack .../python3-minimal_3.7.3-1_armhf.deb ... Unpacking python3-minimal (3.7.3-1) ... Selecting previously unselected package libmpdec2:armhf. Preparing to unpack .../libmpdec2_2.4.2-2_armhf.deb ... Unpacking libmpdec2:armhf (2.4.2-2) ... Selecting previously unselected package libpython3.7-stdlib:armhf. Preparing to unpack .../libpython3.7-stdlib_3.7.3-2+deb10u2_armhf.deb ... Unpacking libpython3.7-stdlib:armhf (3.7.3-2+deb10u2) ... Selecting previously unselected package python3.7. Preparing to unpack .../python3.7_3.7.3-2+deb10u2_armhf.deb ... Unpacking python3.7 (3.7.3-2+deb10u2) ... Selecting previously unselected package libpython3-stdlib:armhf. Preparing to unpack .../libpython3-stdlib_3.7.3-1_armhf.deb ... Unpacking libpython3-stdlib:armhf (3.7.3-1) ... Setting up python3-minimal (3.7.3-1) ... Selecting previously unselected package python3. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 21096 files and directories currently installed.) Preparing to unpack .../00-python3_3.7.3-1_armhf.deb ... Unpacking python3 (3.7.3-1) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../01-sensible-utils_0.0.12_all.deb ... Unpacking sensible-utils (0.0.12) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../02-libmagic-mgc_1%3a5.35-4+deb10u1_armhf.deb ... Unpacking libmagic-mgc (1:5.35-4+deb10u1) ... Selecting previously unselected package libmagic1:armhf. Preparing to unpack .../03-libmagic1_1%3a5.35-4+deb10u1_armhf.deb ... Unpacking libmagic1:armhf (1:5.35-4+deb10u1) ... Selecting previously unselected package file. Preparing to unpack .../04-file_1%3a5.35-4+deb10u1_armhf.deb ... Unpacking file (1:5.35-4+deb10u1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../05-gettext-base_0.19.8.1-9_armhf.deb ... Unpacking gettext-base (0.19.8.1-9) ... Selecting previously unselected package libsigsegv2:armhf. Preparing to unpack .../06-libsigsegv2_2.12-2_armhf.deb ... Unpacking libsigsegv2:armhf (2.12-2) ... Selecting previously unselected package m4. Preparing to unpack .../07-m4_1.4.18-2_armhf.deb ... Unpacking m4 (1.4.18-2) ... Selecting previously unselected package autoconf. Preparing to unpack .../08-autoconf_2.69-11_all.deb ... Unpacking autoconf (2.69-11) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../09-autotools-dev_20180224.1_all.deb ... Unpacking autotools-dev (20180224.1) ... Selecting previously unselected package automake. Preparing to unpack .../10-automake_1%3a1.16.1-4_all.deb ... Unpacking automake (1:1.16.1-4) ... Selecting previously unselected package autopoint. Preparing to unpack .../11-autopoint_0.19.8.1-9_all.deb ... Unpacking autopoint (0.19.8.1-9) ... Selecting previously unselected package cython. Preparing to unpack .../12-cython_0.29.2-2_armhf.deb ... Unpacking cython (0.29.2-2) ... Selecting previously unselected package cython3. Preparing to unpack .../13-cython3_0.29.2-2_armhf.deb ... Unpacking cython3 (0.29.2-2) ... Selecting previously unselected package libtool. Preparing to unpack .../14-libtool_2.4.6-9_all.deb ... Unpacking libtool (2.4.6-9) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../15-dh-autoreconf_19_all.deb ... Unpacking dh-autoreconf (19) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../16-libarchive-zip-perl_1.64-1_all.deb ... Unpacking libarchive-zip-perl (1.64-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../17-libfile-stripnondeterminism-perl_1.1.2-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.1.2-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../18-dh-strip-nondeterminism_1.1.2-1_all.deb ... Unpacking dh-strip-nondeterminism (1.1.2-1) ... Selecting previously unselected package libelf1:armhf. Preparing to unpack .../19-libelf1_0.176-1.1_armhf.deb ... Unpacking libelf1:armhf (0.176-1.1) ... Selecting previously unselected package dwz. Preparing to unpack .../20-dwz_0.12-3_armhf.deb ... Unpacking dwz (0.12-3) ... Selecting previously unselected package libglib2.0-0:armhf. Preparing to unpack .../21-libglib2.0-0_2.58.3-2+deb10u2_armhf.deb ... Unpacking libglib2.0-0:armhf (2.58.3-2+deb10u2) ... Selecting previously unselected package libicu63:armhf. Preparing to unpack .../22-libicu63_63.1-6+deb10u1_armhf.deb ... Unpacking libicu63:armhf (63.1-6+deb10u1) ... Selecting previously unselected package libxml2:armhf. Preparing to unpack .../23-libxml2_2.9.4+dfsg1-7+b3_armhf.deb ... Unpacking libxml2:armhf (2.9.4+dfsg1-7+b3) ... Selecting previously unselected package libcroco3:armhf. Preparing to unpack .../24-libcroco3_0.6.12-3_armhf.deb ... Unpacking libcroco3:armhf (0.6.12-3) ... Selecting previously unselected package libncurses6:armhf. Preparing to unpack .../25-libncurses6_6.1+20181013-2+deb10u2_armhf.deb ... Unpacking libncurses6:armhf (6.1+20181013-2+deb10u2) ... Selecting previously unselected package gettext. Preparing to unpack .../26-gettext_0.19.8.1-9_armhf.deb ... Unpacking gettext (0.19.8.1-9) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../27-intltool-debian_0.35.0+20060710.5_all.deb ... Unpacking intltool-debian (0.35.0+20060710.5) ... Selecting previously unselected package po-debconf. Preparing to unpack .../28-po-debconf_1.0.21_all.deb ... Unpacking po-debconf (1.0.21) ... Selecting previously unselected package debhelper. Preparing to unpack .../29-debhelper_12.1.1_all.deb ... Unpacking debhelper (12.1.1) ... Selecting previously unselected package python3-lib2to3. Preparing to unpack .../30-python3-lib2to3_3.7.3-1_all.deb ... Unpacking python3-lib2to3 (3.7.3-1) ... Selecting previously unselected package python3-distutils. Preparing to unpack .../31-python3-distutils_3.7.3-1_all.deb ... Unpacking python3-distutils (3.7.3-1) ... Selecting previously unselected package dh-python. Preparing to unpack .../32-dh-python_3.20190308_all.deb ... Unpacking dh-python (3.20190308) ... Selecting previously unselected package libgfortran5:armhf. 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Setting up gettext-base (0.19.8.1-9) ... Setting up file (1:5.35-4+deb10u1) ... Setting up libldap-common (2.4.47+dfsg-3+deb10u2) ... Setting up libicu63:armhf (63.1-6+deb10u1) ... Setting up libkrb5support0:armhf (1.17-3) ... Setting up libsasl2-modules-db:armhf (2.1.27+dfsg-1+deb10u1) ... Setting up autotools-dev (20180224.1) ... Setting up libexpat1-dev:armhf (2.2.6-2+deb10u1) ... Setting up librtmp1:armhf (2.4+20151223.gitfa8646d.1-2) ... Setting up libncurses6:armhf (6.1+20181013-2+deb10u2) ... Setting up libsigsegv2:armhf (2.12-2) ... Setting up libssl-dev:armhf (1.1.1d-0+deb10u3) ... Setting up autopoint (0.19.8.1-9) ... Setting up libk5crypto3:armhf (1.17-3) ... Setting up libsasl2-2:armhf (2.1.27+dfsg-1+deb10u1) ... Setting up libgfortran5:armhf (8.3.0-6) ... Setting up liblzma-dev:armhf (5.2.4-1) ... Setting up zlib1g-dev:armhf (1:1.2.11.dfsg-1) ... Setting up sensible-utils (0.0.12) ... Setting up libuchardet0:armhf (0.0.6-3) ... Setting up libssh2-1:armhf (1.8.0-2.1) ... Setting up libkrb5-3:armhf (1.17-3) ... Setting up libmpdec2:armhf (2.4.2-2) ... Setting up libbsd0:armhf (0.9.1-2) ... Setting up libelf1:armhf (0.176-1.1) ... Setting up readline-common (7.0-5) ... Setting up libxml2:armhf (2.9.4+dfsg1-7+b3) ... Setting up libreadline7:armhf (7.0-5) ... Setting up libbz2-dev:armhf (1.0.6-9.2~deb10u1) ... Setting up libfile-stripnondeterminism-perl (1.1.2-1) ... Setting up libpython3.7-stdlib:armhf (3.7.3-2+deb10u2) ... Setting up libpython3.7:armhf (3.7.3-2+deb10u2) ... Setting up libtool (2.4.6-9) ... Setting up libpython3.7-dev:armhf (3.7.3-2+deb10u2) ... Setting up libldap-2.4-2:armhf (2.4.47+dfsg-3+deb10u2) ... Setting up m4 (1.4.18-2) ... Setting up libpython2.7-stdlib:armhf (2.7.16-2+deb10u1) ... Setting up libblas3:armhf (3.8.0-2) ... 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 Setting up bsdmainutils (11.1.2+b1) ... update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode Setting up libgssapi-krb5-2:armhf (1.17-3) ... Setting up libcroco3:armhf (0.6.12-3) ... Setting up autoconf (2.69-11) ... Setting up dwz (0.12-3) ... Setting up groff-base (1.22.4-3) ... Setting up libpython3-stdlib:armhf (3.7.3-1) ... Setting up automake (1:1.16.1-4) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up python3.7 (3.7.3-2+deb10u2) ... Setting up libpython2.7:armhf (2.7.16-2+deb10u1) ... Setting up liblapack3:armhf (3.8.0-2) ... 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 libpython2.7-dev:armhf (2.7.16-2+deb10u1) ... Setting up gettext (0.19.8.1-9) ... Setting up libpython3-dev:armhf (3.7.3-1) ... Setting up python2.7 (2.7.16-2+deb10u1) ... Setting up libpython2-stdlib:armhf (2.7.16-1) ... Setting up libcurl3-gnutls:armhf (7.64.0-4+deb10u1) ... Setting up python3 (3.7.3-1) ... Setting up libcurl4-gnutls-dev:armhf (7.64.0-4+deb10u1) ... Setting up man-db (2.8.5-2) ... Not building database; man-db/auto-update is not 'true'. Setting up python2 (2.7.16-1) ... Setting up python3.7-dev (3.7.3-2+deb10u2) ... Setting up intltool-debian (0.35.0+20060710.5) ... Setting up libpython-stdlib:armhf (2.7.16-1) ... Setting up python3-humanfriendly (4.18-1) ... Setting up libpython3-all-dev:armhf (3.7.3-1) ... Setting up cython3 (0.29.2-2) ... Setting up libpython2-dev:armhf (2.7.16-1) ... Setting up python3-lib2to3 (3.7.3-1) ... Setting up python3-coloredlogs (7.3-1) ... Setting up python (2.7.16-1) ... Setting up python-monotonic (1.1-2) ... Setting up python2.7-dev (2.7.16-2+deb10u1) ... Setting up python3-pkg-resources (40.8.0-1) ... Setting up python3-distutils (3.7.3-1) ... Setting up dh-python (3.20190308) ... Setting up cython (0.29.2-2) ... Setting up python-colorama (0.3.7-1) ... Setting up python2-dev (2.7.16-1) ... Setting up python3-setuptools (40.8.0-1) ... Setting up libhts2:armhf (1.9-11) ... Setting up python3-colorama (0.3.7-1) ... Setting up python-pkg-resources (40.8.0-1) ... Setting up po-debconf (1.0.21) ... Setting up libhts-dev:armhf (1.9-11) ... Setting up python3-all (3.7.3-1) ... Setting up python-all (2.7.16-1) ... Setting up python3-click (7.0-1) ... Setting up python3-nose (1.3.7-4) ... Setting up libpython-dev:armhf (2.7.16-1) ... Setting up python-humanfriendly (4.18-1) ... Setting up python-click (7.0-1) ... Setting up python3-dev (3.7.3-1) ... Setting up python-setuptools (40.8.0-1) ... Setting up python3-numpy (1:1.16.2-1) ... Setting up python-coloredlogs (7.3-1) ... Setting up python-dev (2.7.16-1) ... Setting up python3-all-dev (3.7.3-1) ... Setting up libpython-all-dev:armhf (2.7.16-1) ... Setting up python-numpy (1:1.16.2-1) ... Setting up python-nose (1.3.7-4) ... Setting up python-all-dev (2.7.16-1) ... Setting up debhelper (12.1.1) ... Setting up dh-autoreconf (19) ... Setting up dh-strip-nondeterminism (1.1.2-1) ... Processing triggers for libc-bin (2.28-10) ... Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps Reading package lists... Building dependency tree... Reading state information... fakeroot is already the newest version (1.23-1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package I: Running cd /build/cyvcf2-0.10.4/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b dpkg-buildpackage: info: source package cyvcf2 dpkg-buildpackage: info: source version 0.10.4-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture armhf dpkg-source: info: using options from cyvcf2-0.10.4/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 '/build/cyvcf2-0.10.4/.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 '/build/cyvcf2-0.10.4/.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 dh_autoreconf_clean -O--buildsystem=pybuild debian/rules override_dh_clean make[1]: ingresso nella directory "/build/cyvcf2-0.10.4" dh_clean rm -rf cyvcf2.egg-info cyvcf2/cyvcf2.c __o.vcf find . -name "*.so" -delete make[1]: uscita dalla directory "/build/cyvcf2-0.10.4" debian/rules build dh build --with python2,python3 --buildsystem=pybuild dh_update_autotools_config -O--buildsystem=pybuild dh_autoreconf -O--buildsystem=pybuild dh_auto_configure -O--buildsystem=pybuild I: pybuild base:217: python2.7 setup.py config running config I: pybuild base:217: python3.7 setup.py config running config dh_auto_build -O--buildsystem=pybuild I: pybuild base:217: /usr/bin/python setup.py build running build running build_py creating /build/cyvcf2-0.10.4/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2 copying cyvcf2/__init__.py -> /build/cyvcf2-0.10.4/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2 copying cyvcf2/__main__.py -> /build/cyvcf2-0.10.4/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2 copying cyvcf2/cli.py -> /build/cyvcf2-0.10.4/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2 creating /build/cyvcf2-0.10.4/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/test_hemi.py -> /build/cyvcf2-0.10.4/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/test_reader.py -> /build/cyvcf2-0.10.4/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/__init__.py -> /build/cyvcf2-0.10.4/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/test_cli.py -> /build/cyvcf2-0.10.4/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2/tests running egg_info creating cyvcf2.egg-info writing requirements to cyvcf2.egg-info/requires.txt writing cyvcf2.egg-info/PKG-INFO writing top-level names to cyvcf2.egg-info/top_level.txt writing dependency_links to cyvcf2.egg-info/dependency_links.txt writing entry points to cyvcf2.egg-info/entry_points.txt writing manifest file 'cyvcf2.egg-info/SOURCES.txt' reading manifest file 'cyvcf2.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no files found matching 'htslib/*.c' warning: no files found matching 'htslib/*.h' warning: no files found matching 'htslib/htslib/*.h' warning: no files found matching 'htslib/cram/*.c' warning: no files found matching 'htslib/cram/*.h' writing manifest file 'cyvcf2.egg-info/SOURCES.txt' copying cyvcf2/cyvcf2.pxd -> /build/cyvcf2-0.10.4/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2 copying cyvcf2/cyvcf2.pyx -> /build/cyvcf2-0.10.4/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2 copying cyvcf2/helpers.c -> /build/cyvcf2-0.10.4/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2 copying cyvcf2/helpers.h -> /build/cyvcf2-0.10.4/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2 copying cyvcf2/relatedness.h -> /build/cyvcf2-0.10.4/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2 copying cyvcf2/tests/bug.vcf.gz -> /build/cyvcf2-0.10.4/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/decomposed.vcf -> /build/cyvcf2-0.10.4/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/empty.vcf -> /build/cyvcf2-0.10.4/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/issue_44.vcf -> /build/cyvcf2-0.10.4/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/o.vcf.gz -> /build/cyvcf2-0.10.4/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/seg.vcf.gz -> /build/cyvcf2-0.10.4/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/test-alt-repr.vcf -> /build/cyvcf2-0.10.4/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/test-format-string.vcf -> /build/cyvcf2-0.10.4/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/test-haploidX.vcf -> /build/cyvcf2-0.10.4/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/test-hemi.vcf -> /build/cyvcf2-0.10.4/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/test-multiallelic-homozygous-alt.vcf.gz -> /build/cyvcf2-0.10.4/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/test-multiallelic-homozygous-alt.vcf.gz.tbi -> /build/cyvcf2-0.10.4/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/test-strict-gt-option-flag.vcf.gz -> /build/cyvcf2-0.10.4/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/test-strict-gt-option-flag.vcf.gz.tbi -> /build/cyvcf2-0.10.4/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/test.comp_het.3.vcf -> /build/cyvcf2-0.10.4/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/test.snpeff.bcf -> /build/cyvcf2-0.10.4/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/test.snpeff.bcf.csi -> /build/cyvcf2-0.10.4/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/test.snpeff.vcf -> /build/cyvcf2-0.10.4/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/test.vcf.gz -> /build/cyvcf2-0.10.4/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/test.vcf.gz.tbi -> /build/cyvcf2-0.10.4/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/test_gt_alt_freqs.vcf -> /build/cyvcf2-0.10.4/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/test_gt_bases.vcf.gz -> /build/cyvcf2-0.10.4/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2/tests running build_ext cythoning cyvcf2/cyvcf2.pyx to cyvcf2/cyvcf2.c /usr/lib/python2.7/dist-packages/Cython/Compiler/Main.py:367: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /build/cyvcf2-0.10.4/cyvcf2/cyvcf2.pxd tree = Parsing.p_module(s, pxd, full_module_name) warning: cyvcf2/cyvcf2.pxd:26:16: Declarations should not be declared inline. warning: cyvcf2/cyvcf2.pxd:188:14: 'BCF_HT_FLAG' redeclared warning: cyvcf2/cyvcf2.pxd:279:30: Declarations should not be declared inline. building 'cyvcf2.cyvcf2' extension creating build creating build/temp.linux-armhf-2.7 creating build/temp.linux-armhf-2.7/cyvcf2 arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -ffile-prefix-map=/build/cyvcf2-0.10.4=. -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:1822, from /usr/lib/python2.7/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /usr/lib/python2.7/dist-packages/numpy/core/include/numpy/arrayobject.h:4, from cyvcf2/cyvcf2.c:614: /usr/lib/python2.7/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] #warning "Using deprecated NumPy API, disable it with " \ ^~~~~~~ cyvcf2/cyvcf2.c: In function ‘__pyx_pf_6cyvcf2_6cyvcf2_3VCF_4add_to_header’: cyvcf2/cyvcf2.c:7926:44: warning: passing argument 1 of ‘bcf_hdr_append’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] __pyx_v_ret = bcf_hdr_append(__pyx_v_self->hdr, __pyx_t_2); ~~~~~~~~~~~~^~~~~ In file included from cyvcf2/helpers.h:1, from cyvcf2/cyvcf2.c:617: /usr/include/htslib/vcf.h:443:35: note: expected ‘bcf_hdr_t *’ {aka ‘struct *’} but argument is of type ‘const bcf_hdr_t *’ {aka ‘const struct *’} int bcf_hdr_append(bcf_hdr_t *h, const char *line); ~~~~~~~~~~~^ cyvcf2/cyvcf2.c:7968:42: warning: passing argument 1 of ‘bcf_hdr_sync’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] __pyx_v_ret = bcf_hdr_sync(__pyx_v_self->hdr); ~~~~~~~~~~~~^~~~~ In file included from cyvcf2/helpers.h:1, from cyvcf2/cyvcf2.c:617: /usr/include/htslib/vcf.h:479:33: note: expected ‘bcf_hdr_t *’ {aka ‘struct *’} but argument is of type ‘const bcf_hdr_t *’ {aka ‘const struct *’} int bcf_hdr_sync(bcf_hdr_t *h); ~~~~~~~~~~~^ cyvcf2/cyvcf2.c: In function ‘__pyx_pf_6cyvcf2_6cyvcf2_3VCF_12set_samples’: cyvcf2/cyvcf2.c:8484:49: warning: passing argument 1 of ‘bcf_hdr_set_samples’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] __pyx_v_ret = bcf_hdr_set_samples(__pyx_v_self->hdr, ((char const *)__pyx_t_6), 0); ~~~~~~~~~~~~^~~~~ In file included from cyvcf2/helpers.h:1, from cyvcf2/cyvcf2.c:617: /usr/include/htslib/vcf.h:315:40: note: expected ‘bcf_hdr_t *’ {aka ‘struct *’} but argument is of type ‘const bcf_hdr_t *’ {aka ‘const struct *’} int bcf_hdr_set_samples(bcf_hdr_t *hdr, const char *samples, int is_file); ~~~~~~~~~~~^~~ cyvcf2/cyvcf2.c: In function ‘__pyx_pf_6cyvcf2_6cyvcf2_3VCF_14update’: cyvcf2/cyvcf2.c:8782:44: warning: passing argument 1 of ‘bcf_hdr_append’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] __pyx_v_ret = bcf_hdr_append(__pyx_v_self->hdr, __pyx_t_4); ~~~~~~~~~~~~^~~~~ In file included from cyvcf2/helpers.h:1, from cyvcf2/cyvcf2.c:617: /usr/include/htslib/vcf.h:443:35: note: expected ‘bcf_hdr_t *’ {aka ‘struct *’} but argument is of type ‘const bcf_hdr_t *’ {aka ‘const struct *’} int bcf_hdr_append(bcf_hdr_t *h, const char *line); ~~~~~~~~~~~^ cyvcf2/cyvcf2.c:8835:42: warning: passing argument 1 of ‘bcf_hdr_sync’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] __pyx_v_ret = bcf_hdr_sync(__pyx_v_self->hdr); ~~~~~~~~~~~~^~~~~ In file included from cyvcf2/helpers.h:1, from cyvcf2/cyvcf2.c:617: /usr/include/htslib/vcf.h:479:33: note: expected ‘bcf_hdr_t *’ {aka ‘struct *’} but argument is of type ‘const bcf_hdr_t *’ {aka ‘const struct *’} int bcf_hdr_sync(bcf_hdr_t *h); ~~~~~~~~~~~^ cyvcf2/cyvcf2.c: In function ‘__pyx_gb_6cyvcf2_6cyvcf2_3VCF_18generator’: cyvcf2/cyvcf2.c:9044:115: warning: passing argument 4 of ‘hts_itr_querys’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] __pyx_cur_scope->__pyx_v_itr = bcf_itr_querys(__pyx_cur_scope->__pyx_v_self->hidx, __pyx_cur_scope->__pyx_v_self->hdr, __pyx_t_2); ^ In file included from /usr/include/htslib/vcf.h:39, from cyvcf2/helpers.h:1, from cyvcf2/cyvcf2.c:617: /usr/include/htslib/hts.h:675:16: note: expected ‘void *’ but argument is of type ‘const bcf_hdr_t *’ {aka ‘const struct *’} hts_itr_t *hts_itr_querys(const hts_idx_t *idx, const char *reg, hts_name2id_f getid, void *hdr, hts_itr_query_func *itr_query, hts_readrec_func *readrec); ^~~~~~~~~~~~~~ cyvcf2/cyvcf2.c: In function ‘__pyx_gb_6cyvcf2_6cyvcf2_3VCF_24generator2’: cyvcf2/cyvcf2.c:10252:163: 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, 407, __pyx_L1_error) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ cyvcf2/cyvcf2.c:2943:61: 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:11909:33: warning: passing argument 1 of ‘bcf_hdr_destroy’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] bcf_hdr_destroy(__pyx_v_self->hdr); ~~~~~~~~~~~~^~~~~ In file included from cyvcf2/helpers.h:1, from cyvcf2/cyvcf2.c:617: /usr/include/htslib/vcf.h:261:37: note: expected ‘bcf_hdr_t *’ {aka ‘struct *’} but argument is of type ‘const bcf_hdr_t *’ {aka ‘const struct *’} void bcf_hdr_destroy(bcf_hdr_t *h); ~~~~~~~~~~~^ cyvcf2/cyvcf2.c: In function ‘__pyx_pf_6cyvcf2_6cyvcf2_3VCF_10raw_header___get__’: cyvcf2/cyvcf2.c:12390:3: warning: ‘bcf_hdr_fmt_text’ is deprecated: use bcf_hdr_format() instead [-Wdeprecated-declarations] __pyx_v_s = bcf_hdr_fmt_text(__pyx_v_self->hdr, 0, (&__pyx_v_hlen)); ^~~~~~~~~ In file included from cyvcf2/helpers.h:1, from cyvcf2/cyvcf2.c:617: /usr/include/htslib/vcf.h:439:11: note: declared here char *bcf_hdr_fmt_text(const bcf_hdr_t *hdr, int is_bcf, int *len) ^~~~~~~~~~~~~~~~ cyvcf2/cyvcf2.c: In function ‘__pyx_pf_6cyvcf2_6cyvcf2_3VCF_8seqnames___get__’: cyvcf2/cyvcf2.c:12643:18: warning: assignment to ‘char **’ from incompatible pointer type ‘const char **’ [-Wincompatible-pointer-types] __pyx_v_cnames = bcf_hdr_seqnames(__pyx_v_self->hdr, (&__pyx_v_n)); ^ In file included from cyvcf2/helpers.h:1, from cyvcf2/cyvcf2.c:617: cyvcf2/cyvcf2.c:12752:75: warning: passing argument 4 of ‘hts_idx_seqnames’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] __pyx_v_cnames = bcf_index_seqnames(__pyx_v_self->hidx, __pyx_v_self->hdr, (&__pyx_v_n)); ^ In file included from /usr/include/htslib/vcf.h:39, from cyvcf2/helpers.h:1, from cyvcf2/cyvcf2.c:617: /usr/include/htslib/hts.h:677:18: note: expected ‘void *’ but argument is of type ‘const bcf_hdr_t *’ {aka ‘const struct *’} const char **hts_idx_seqnames(const hts_idx_t *idx, int *n, hts_id2name_f getid, void *hdr); // free only the array, not the values ^~~~~~~~~~~~~~~~ cyvcf2/cyvcf2.c:12752:22: 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:12835:22: 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:24593:17: 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:34655:13: warning: assignment discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] __pyx_v_h = __pyx_t_6; ^ cyvcf2/cyvcf2.c: In function ‘__pyx_pf_6cyvcf2_6cyvcf2_4INFO_12__next__’: cyvcf2/cyvcf2.c:37698:16: 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:38681:18: 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:39335:35: warning: passing argument 1 of ‘bcf_hdr_sync’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] (void)(bcf_hdr_sync(__pyx_v_tmpl->hdr)); ~~~~~~~~~~~~^~~~~ In file included from cyvcf2/helpers.h:1, from cyvcf2/cyvcf2.c:617: /usr/include/htslib/vcf.h:479:33: note: expected ‘bcf_hdr_t *’ {aka ‘struct *’} but argument is of type ‘const bcf_hdr_t *’ {aka ‘const struct *’} int bcf_hdr_sync(bcf_hdr_t *h); ~~~~~~~~~~~^ cyvcf2/cyvcf2.c:39363:47: warning: passing argument 1 of ‘bcf_hdr_sync’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] (void)(bcf_hdr_sync(__pyx_v_self->__pyx_base.hdr)); ~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from cyvcf2/helpers.h:1, from cyvcf2/cyvcf2.c:617: /usr/include/htslib/vcf.h:479:33: note: expected ‘bcf_hdr_t *’ {aka ‘struct *’} but argument is of type ‘const bcf_hdr_t *’ {aka ‘const struct *’} int bcf_hdr_sync(bcf_hdr_t *h); ~~~~~~~~~~~^ cyvcf2/cyvcf2.c: In function ‘__pyx_pf_6cyvcf2_6cyvcf2_6Writer_2write_header’: cyvcf2/cyvcf2.c:39431:78: warning: passing argument 2 of ‘bcf_hdr_write’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] (void)(bcf_hdr_write(__pyx_v_self->__pyx_base.hts, __pyx_v_self->__pyx_base.hdr)); ~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from cyvcf2/helpers.h:1, from cyvcf2/cyvcf2.c:617: /usr/include/htslib/vcf.h:320:47: note: expected ‘bcf_hdr_t *’ {aka ‘struct *’} but argument is of type ‘const bcf_hdr_t *’ {aka ‘const struct *’} int bcf_hdr_write(htsFile *fp, bcf_hdr_t *h); ~~~~~~~~~~~^ cyvcf2/cyvcf2.c: In function ‘__pyx_pf_6cyvcf2_6cyvcf2_6Writer_4write_record’: cyvcf2/cyvcf2.c:39603:60: warning: passing argument 1 of ‘bcf_hdr_add_hrec’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] __pyx_t_1 = ((bcf_hdr_add_hrec(__pyx_v_self->__pyx_base.hdr, __pyx_v_h) < 0) != 0); ~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from cyvcf2/helpers.h:1, from cyvcf2/cyvcf2.c:617: /usr/include/htslib/vcf.h:482:37: note: expected ‘bcf_hdr_t *’ {aka ‘struct *’} but argument is of type ‘const bcf_hdr_t *’ {aka ‘const struct *’} int bcf_hdr_add_hrec(bcf_hdr_t *hdr, bcf_hrec_t *hrec); ~~~~~~~~~~~^~~ cyvcf2/cyvcf2.c:39641:49: warning: passing argument 1 of ‘bcf_hdr_sync’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] (void)(bcf_hdr_sync(__pyx_v_self->__pyx_base.hdr)); ~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from cyvcf2/helpers.h:1, from cyvcf2/cyvcf2.c:617: /usr/include/htslib/vcf.h:479:33: note: expected ‘bcf_hdr_t *’ {aka ‘struct *’} but argument is of type ‘const bcf_hdr_t *’ {aka ‘const struct *’} int bcf_hdr_sync(bcf_hdr_t *h); ~~~~~~~~~~~^ cyvcf2/cyvcf2.c:39700:100: 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, 2088, __pyx_L1_error) ~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from cyvcf2/helpers.h:1, from cyvcf2/cyvcf2.c:617: /usr/include/htslib/vcf.h:370:43: note: expected ‘bcf_hdr_t *’ {aka ‘struct *’} but argument is of type ‘const bcf_hdr_t *’ {aka ‘const struct *’} int bcf_write(htsFile *fp, bcf_hdr_t *h, bcf1_t *v); ~~~~~~~~~~~^ At top level: cyvcf2/cyvcf2.c:6610:18: 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 -ffile-prefix-map=/build/cyvcf2-0.10.4=. -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 arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -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-RT6aMn/python2.7-2.7.16=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/cyvcf2-0.10.4=. -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/cyvcf2/helpers.o -lz -lbz2 -llzma -lcurl -lssl -lhts -lcrypt -o /build/cyvcf2-0.10.4/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2/cyvcf2.so I: pybuild base:217: /usr/bin/python3 setup.py build running build running build_py creating /build/cyvcf2-0.10.4/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2 copying cyvcf2/__init__.py -> /build/cyvcf2-0.10.4/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2 copying cyvcf2/__main__.py -> /build/cyvcf2-0.10.4/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2 copying cyvcf2/cli.py -> /build/cyvcf2-0.10.4/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2 creating /build/cyvcf2-0.10.4/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/test_hemi.py -> /build/cyvcf2-0.10.4/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/test_reader.py -> /build/cyvcf2-0.10.4/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/__init__.py -> /build/cyvcf2-0.10.4/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/test_cli.py -> /build/cyvcf2-0.10.4/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2/tests running egg_info writing cyvcf2.egg-info/PKG-INFO writing dependency_links to cyvcf2.egg-info/dependency_links.txt writing entry points to cyvcf2.egg-info/entry_points.txt writing requirements to cyvcf2.egg-info/requires.txt writing top-level names to cyvcf2.egg-info/top_level.txt reading manifest file 'cyvcf2.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no files found matching 'htslib/*.c' warning: no files found matching 'htslib/*.h' warning: no files found matching 'htslib/htslib/*.h' warning: no files found matching 'htslib/cram/*.c' warning: no files found matching 'htslib/cram/*.h' writing manifest file 'cyvcf2.egg-info/SOURCES.txt' copying cyvcf2/cyvcf2.c -> /build/cyvcf2-0.10.4/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2 copying cyvcf2/cyvcf2.pxd -> /build/cyvcf2-0.10.4/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2 copying cyvcf2/cyvcf2.pyx -> /build/cyvcf2-0.10.4/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2 copying cyvcf2/helpers.c -> /build/cyvcf2-0.10.4/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2 copying cyvcf2/helpers.h -> /build/cyvcf2-0.10.4/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2 copying cyvcf2/relatedness.h -> /build/cyvcf2-0.10.4/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2 copying cyvcf2/tests/bug.vcf.gz -> /build/cyvcf2-0.10.4/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/decomposed.vcf -> /build/cyvcf2-0.10.4/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/empty.vcf -> /build/cyvcf2-0.10.4/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/issue_44.vcf -> /build/cyvcf2-0.10.4/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/o.vcf.gz -> /build/cyvcf2-0.10.4/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/seg.vcf.gz -> /build/cyvcf2-0.10.4/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/test-alt-repr.vcf -> /build/cyvcf2-0.10.4/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/test-format-string.vcf -> /build/cyvcf2-0.10.4/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/test-haploidX.vcf -> /build/cyvcf2-0.10.4/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/test-hemi.vcf -> /build/cyvcf2-0.10.4/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/test-multiallelic-homozygous-alt.vcf.gz -> /build/cyvcf2-0.10.4/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/test-multiallelic-homozygous-alt.vcf.gz.tbi -> /build/cyvcf2-0.10.4/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/test-strict-gt-option-flag.vcf.gz -> /build/cyvcf2-0.10.4/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/test-strict-gt-option-flag.vcf.gz.tbi -> /build/cyvcf2-0.10.4/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/test.comp_het.3.vcf -> /build/cyvcf2-0.10.4/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/test.snpeff.bcf -> /build/cyvcf2-0.10.4/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/test.snpeff.bcf.csi -> /build/cyvcf2-0.10.4/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/test.snpeff.vcf -> /build/cyvcf2-0.10.4/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/test.vcf.gz -> /build/cyvcf2-0.10.4/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/test.vcf.gz.tbi -> /build/cyvcf2-0.10.4/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/test_gt_alt_freqs.vcf -> /build/cyvcf2-0.10.4/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2/tests copying cyvcf2/tests/test_gt_bases.vcf.gz -> /build/cyvcf2-0.10.4/.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 arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -ffile-prefix-map=/build/cyvcf2-0.10.4=. -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:1822, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:4, from cyvcf2/cyvcf2.c:614: /usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] #warning "Using deprecated NumPy API, disable it with " \ ^~~~~~~ cyvcf2/cyvcf2.c: In function ‘__pyx_pf_6cyvcf2_6cyvcf2_3VCF_4add_to_header’: cyvcf2/cyvcf2.c:7926:44: warning: passing argument 1 of ‘bcf_hdr_append’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] __pyx_v_ret = bcf_hdr_append(__pyx_v_self->hdr, __pyx_t_2); ~~~~~~~~~~~~^~~~~ In file included from cyvcf2/helpers.h:1, from cyvcf2/cyvcf2.c:617: /usr/include/htslib/vcf.h:443:35: note: expected ‘bcf_hdr_t *’ {aka ‘struct *’} but argument is of type ‘const bcf_hdr_t *’ {aka ‘const struct *’} int bcf_hdr_append(bcf_hdr_t *h, const char *line); ~~~~~~~~~~~^ cyvcf2/cyvcf2.c:7968:42: warning: passing argument 1 of ‘bcf_hdr_sync’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] __pyx_v_ret = bcf_hdr_sync(__pyx_v_self->hdr); ~~~~~~~~~~~~^~~~~ In file included from cyvcf2/helpers.h:1, from cyvcf2/cyvcf2.c:617: /usr/include/htslib/vcf.h:479:33: note: expected ‘bcf_hdr_t *’ {aka ‘struct *’} but argument is of type ‘const bcf_hdr_t *’ {aka ‘const struct *’} int bcf_hdr_sync(bcf_hdr_t *h); ~~~~~~~~~~~^ cyvcf2/cyvcf2.c: In function ‘__pyx_pf_6cyvcf2_6cyvcf2_3VCF_12set_samples’: cyvcf2/cyvcf2.c:8484:49: warning: passing argument 1 of ‘bcf_hdr_set_samples’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] __pyx_v_ret = bcf_hdr_set_samples(__pyx_v_self->hdr, ((char const *)__pyx_t_6), 0); ~~~~~~~~~~~~^~~~~ In file included from cyvcf2/helpers.h:1, from cyvcf2/cyvcf2.c:617: /usr/include/htslib/vcf.h:315:40: note: expected ‘bcf_hdr_t *’ {aka ‘struct *’} but argument is of type ‘const bcf_hdr_t *’ {aka ‘const struct *’} int bcf_hdr_set_samples(bcf_hdr_t *hdr, const char *samples, int is_file); ~~~~~~~~~~~^~~ cyvcf2/cyvcf2.c: In function ‘__pyx_pf_6cyvcf2_6cyvcf2_3VCF_14update’: cyvcf2/cyvcf2.c:8782:44: warning: passing argument 1 of ‘bcf_hdr_append’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] __pyx_v_ret = bcf_hdr_append(__pyx_v_self->hdr, __pyx_t_4); ~~~~~~~~~~~~^~~~~ In file included from cyvcf2/helpers.h:1, from cyvcf2/cyvcf2.c:617: /usr/include/htslib/vcf.h:443:35: note: expected ‘bcf_hdr_t *’ {aka ‘struct *’} but argument is of type ‘const bcf_hdr_t *’ {aka ‘const struct *’} int bcf_hdr_append(bcf_hdr_t *h, const char *line); ~~~~~~~~~~~^ cyvcf2/cyvcf2.c:8835:42: warning: passing argument 1 of ‘bcf_hdr_sync’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] __pyx_v_ret = bcf_hdr_sync(__pyx_v_self->hdr); ~~~~~~~~~~~~^~~~~ In file included from cyvcf2/helpers.h:1, from cyvcf2/cyvcf2.c:617: /usr/include/htslib/vcf.h:479:33: note: expected ‘bcf_hdr_t *’ {aka ‘struct *’} but argument is of type ‘const bcf_hdr_t *’ {aka ‘const struct *’} int bcf_hdr_sync(bcf_hdr_t *h); ~~~~~~~~~~~^ cyvcf2/cyvcf2.c: In function ‘__pyx_gb_6cyvcf2_6cyvcf2_3VCF_18generator’: cyvcf2/cyvcf2.c:9044:115: warning: passing argument 4 of ‘hts_itr_querys’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] __pyx_cur_scope->__pyx_v_itr = bcf_itr_querys(__pyx_cur_scope->__pyx_v_self->hidx, __pyx_cur_scope->__pyx_v_self->hdr, __pyx_t_2); ^ In file included from /usr/include/htslib/vcf.h:39, from cyvcf2/helpers.h:1, from cyvcf2/cyvcf2.c:617: /usr/include/htslib/hts.h:675:16: note: expected ‘void *’ but argument is of type ‘const bcf_hdr_t *’ {aka ‘const struct *’} hts_itr_t *hts_itr_querys(const hts_idx_t *idx, const char *reg, hts_name2id_f getid, void *hdr, hts_itr_query_func *itr_query, hts_readrec_func *readrec); ^~~~~~~~~~~~~~ cyvcf2/cyvcf2.c: In function ‘__pyx_gb_6cyvcf2_6cyvcf2_3VCF_24generator2’: cyvcf2/cyvcf2.c:10252:163: 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, 407, __pyx_L1_error) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ cyvcf2/cyvcf2.c:2943:61: 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:11909:33: warning: passing argument 1 of ‘bcf_hdr_destroy’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] bcf_hdr_destroy(__pyx_v_self->hdr); ~~~~~~~~~~~~^~~~~ In file included from cyvcf2/helpers.h:1, from cyvcf2/cyvcf2.c:617: /usr/include/htslib/vcf.h:261:37: note: expected ‘bcf_hdr_t *’ {aka ‘struct *’} but argument is of type ‘const bcf_hdr_t *’ {aka ‘const struct *’} void bcf_hdr_destroy(bcf_hdr_t *h); ~~~~~~~~~~~^ cyvcf2/cyvcf2.c: In function ‘__pyx_pf_6cyvcf2_6cyvcf2_3VCF_10raw_header___get__’: cyvcf2/cyvcf2.c:12390:3: warning: ‘bcf_hdr_fmt_text’ is deprecated: use bcf_hdr_format() instead [-Wdeprecated-declarations] __pyx_v_s = bcf_hdr_fmt_text(__pyx_v_self->hdr, 0, (&__pyx_v_hlen)); ^~~~~~~~~ In file included from cyvcf2/helpers.h:1, from cyvcf2/cyvcf2.c:617: /usr/include/htslib/vcf.h:439:11: note: declared here char *bcf_hdr_fmt_text(const bcf_hdr_t *hdr, int is_bcf, int *len) ^~~~~~~~~~~~~~~~ cyvcf2/cyvcf2.c: In function ‘__pyx_pf_6cyvcf2_6cyvcf2_3VCF_8seqnames___get__’: cyvcf2/cyvcf2.c:12643:18: warning: assignment to ‘char **’ from incompatible pointer type ‘const char **’ [-Wincompatible-pointer-types] __pyx_v_cnames = bcf_hdr_seqnames(__pyx_v_self->hdr, (&__pyx_v_n)); ^ In file included from cyvcf2/helpers.h:1, from cyvcf2/cyvcf2.c:617: cyvcf2/cyvcf2.c:12752:75: warning: passing argument 4 of ‘hts_idx_seqnames’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] __pyx_v_cnames = bcf_index_seqnames(__pyx_v_self->hidx, __pyx_v_self->hdr, (&__pyx_v_n)); ^ In file included from /usr/include/htslib/vcf.h:39, from cyvcf2/helpers.h:1, from cyvcf2/cyvcf2.c:617: /usr/include/htslib/hts.h:677:18: note: expected ‘void *’ but argument is of type ‘const bcf_hdr_t *’ {aka ‘const struct *’} const char **hts_idx_seqnames(const hts_idx_t *idx, int *n, hts_id2name_f getid, void *hdr); // free only the array, not the values ^~~~~~~~~~~~~~~~ cyvcf2/cyvcf2.c:12752:22: 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:12835:22: 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:24593:17: 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:34655:13: warning: assignment discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] __pyx_v_h = __pyx_t_6; ^ cyvcf2/cyvcf2.c: In function ‘__pyx_pf_6cyvcf2_6cyvcf2_4INFO_12__next__’: cyvcf2/cyvcf2.c:37698:16: 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:38681:18: 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:39335:35: warning: passing argument 1 of ‘bcf_hdr_sync’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] (void)(bcf_hdr_sync(__pyx_v_tmpl->hdr)); ~~~~~~~~~~~~^~~~~ In file included from cyvcf2/helpers.h:1, from cyvcf2/cyvcf2.c:617: /usr/include/htslib/vcf.h:479:33: note: expected ‘bcf_hdr_t *’ {aka ‘struct *’} but argument is of type ‘const bcf_hdr_t *’ {aka ‘const struct *’} int bcf_hdr_sync(bcf_hdr_t *h); ~~~~~~~~~~~^ cyvcf2/cyvcf2.c:39363:47: warning: passing argument 1 of ‘bcf_hdr_sync’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] (void)(bcf_hdr_sync(__pyx_v_self->__pyx_base.hdr)); ~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from cyvcf2/helpers.h:1, from cyvcf2/cyvcf2.c:617: /usr/include/htslib/vcf.h:479:33: note: expected ‘bcf_hdr_t *’ {aka ‘struct *’} but argument is of type ‘const bcf_hdr_t *’ {aka ‘const struct *’} int bcf_hdr_sync(bcf_hdr_t *h); ~~~~~~~~~~~^ cyvcf2/cyvcf2.c: In function ‘__pyx_pf_6cyvcf2_6cyvcf2_6Writer_2write_header’: cyvcf2/cyvcf2.c:39431:78: warning: passing argument 2 of ‘bcf_hdr_write’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] (void)(bcf_hdr_write(__pyx_v_self->__pyx_base.hts, __pyx_v_self->__pyx_base.hdr)); ~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from cyvcf2/helpers.h:1, from cyvcf2/cyvcf2.c:617: /usr/include/htslib/vcf.h:320:47: note: expected ‘bcf_hdr_t *’ {aka ‘struct *’} but argument is of type ‘const bcf_hdr_t *’ {aka ‘const struct *’} int bcf_hdr_write(htsFile *fp, bcf_hdr_t *h); ~~~~~~~~~~~^ cyvcf2/cyvcf2.c: In function ‘__pyx_pf_6cyvcf2_6cyvcf2_6Writer_4write_record’: cyvcf2/cyvcf2.c:39603:60: warning: passing argument 1 of ‘bcf_hdr_add_hrec’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] __pyx_t_1 = ((bcf_hdr_add_hrec(__pyx_v_self->__pyx_base.hdr, __pyx_v_h) < 0) != 0); ~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from cyvcf2/helpers.h:1, from cyvcf2/cyvcf2.c:617: /usr/include/htslib/vcf.h:482:37: note: expected ‘bcf_hdr_t *’ {aka ‘struct *’} but argument is of type ‘const bcf_hdr_t *’ {aka ‘const struct *’} int bcf_hdr_add_hrec(bcf_hdr_t *hdr, bcf_hrec_t *hrec); ~~~~~~~~~~~^~~ cyvcf2/cyvcf2.c:39641:49: warning: passing argument 1 of ‘bcf_hdr_sync’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] (void)(bcf_hdr_sync(__pyx_v_self->__pyx_base.hdr)); ~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from cyvcf2/helpers.h:1, from cyvcf2/cyvcf2.c:617: /usr/include/htslib/vcf.h:479:33: note: expected ‘bcf_hdr_t *’ {aka ‘struct *’} but argument is of type ‘const bcf_hdr_t *’ {aka ‘const struct *’} int bcf_hdr_sync(bcf_hdr_t *h); ~~~~~~~~~~~^ cyvcf2/cyvcf2.c:39700:100: 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, 2088, __pyx_L1_error) ~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from cyvcf2/helpers.h:1, from cyvcf2/cyvcf2.c:617: /usr/include/htslib/vcf.h:370:43: note: expected ‘bcf_hdr_t *’ {aka ‘struct *’} but argument is of type ‘const bcf_hdr_t *’ {aka ‘const struct *’} int bcf_write(htsFile *fp, bcf_hdr_t *h, bcf1_t *v); ~~~~~~~~~~~^ At top level: cyvcf2/cyvcf2.c:6610:18: 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 -ffile-prefix-map=/build/cyvcf2-0.10.4=. -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,-z,relro -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/cyvcf2-0.10.4=. -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/cyvcf2/helpers.o -lz -lbz2 -llzma -lcurl -lssl -lhts -lcrypt -o /build/cyvcf2-0.10.4/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2/cyvcf2.cpython-37m-arm-linux-gnueabihf.so dh_auto_test -O--buildsystem=pybuild I: pybuild base:217: cd /build/cyvcf2-0.10.4/.pybuild/cpython2_2.7_cyvcf2/build; python2.7 -m nose -v cyvcf2.tests.test_cli.test_version ... ok make sure that we are getting the correct gt_types ... ok cyvcf2.tests.test_reader.test_init ... ok cyvcf2.tests.test_reader.test_type ... ok cyvcf2.tests.test_reader.test_format_str ... [W::vcf_parse] Contig '7' is not defined in the header. (Quick workaround: index the file with tabix.) ok cyvcf2.tests.test_reader.test_missing_samples ... ok cyvcf2.tests.test_reader.test_ibd ... ok cyvcf2.tests.test_reader.test_relatedness ... tested: 44 variants out of 115 ok cyvcf2.tests.test_reader.test_pls ... ok cyvcf2.tests.test_reader.test_gt_alt_freqs ... ok cyvcf2.tests.test_reader.test_str ... ok cyvcf2.tests.test_reader.test_region ... ok cyvcf2.tests.test_reader.test_empty_info ... ok cyvcf2.tests.test_reader.test_phases ... ok cyvcf2.tests.test_reader.test_bad_init ... [E::hts_open_format] Failed to open file XXXXX ok cyvcf2.tests.test_reader.test_samples ... ok cyvcf2.tests.test_reader.test_next ... ok cyvcf2.tests.test_reader.test_variant ... ok cyvcf2.tests.test_reader.test_info_dict ... ok cyvcf2.tests.test_reader.test_attrs ... ok cyvcf2.tests.test_reader.test_empty ... ok cyvcf2.tests.test_reader.test_format_field ... ok cyvcf2.tests.test_reader.test_writer ... ok cyvcf2.tests.test_reader.test_add_info_to_header ... ok cyvcf2.tests.test_reader.test_read_flag ... ok cyvcf2.tests.test_reader.test_add_flag ... ok cyvcf2.tests.test_reader.test_constants ... ok cyvcf2.tests.test_reader.test_add_filter_to_header ... ok cyvcf2.tests.test_reader.test_seqnames ... ok cyvcf2.tests.test_reader.test_var_type ... ok cyvcf2.tests.test_reader.test_header_info ... ok cyvcf2.tests.test_reader.test_snpeff_header ... ok cyvcf2.tests.test_reader.test_gt_types ... ok cyvcf2.tests.test_reader.test_raw_header ... ok cyvcf2.tests.test_reader.test_iterate ... ok cyvcf2.tests.test_reader.test_empty_call ... ok cyvcf2.tests.test_reader.test_haploid ... ok cyvcf2.tests.test_reader.test_diploid ... ok cyvcf2.tests.test_reader.test_format ... ok cyvcf2.tests.test_reader.test_header_stuff ... ok cyvcf2.tests.test_reader.test_bcf ... OK no intervals found for /build/cyvcf2-0.10.4/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2/tests/test.snpeff.bcf at 1:69260-69438 ok cyvcf2.tests.test_reader.test_issue12 ... [W::vcf_parse] Contig '7' is not defined in the header. (Quick workaround: index the file with tabix.) ok Ensure gt_bases works with more complex base representations. ... ok cyvcf2.tests.test_reader.test_set_format_float ... [W::vcf_parse] Contig '7' is not defined in the header. (Quick workaround: index the file with tabix.) /build/cyvcf2-0.10.4/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2/tests/test_reader.py:567: FutureWarning: Conversion of the second argument of issubdtype from `int` to `np.signedinteger` is deprecated. In future, it will be treated as `np.int32 == np.dtype(int).type`. v.set_format("PS", np.array([0.555, 1.111], dtype=np.float)) /build/cyvcf2-0.10.4/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2/tests/test_reader.py:567: FutureWarning: Conversion of the second argument of issubdtype from `float` to `np.floating` is deprecated. In future, it will be treated as `np.float64 == np.dtype(float).type`. v.set_format("PS", np.array([0.555, 1.111], dtype=np.float)) /build/cyvcf2-0.10.4/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2/tests/test_reader.py:570: FutureWarning: Conversion of the second argument of issubdtype from `int` to `np.signedinteger` is deprecated. In future, it will be treated as `np.int32 == np.dtype(int).type`. v.set_format("PS", np.array([8.555, 11.111], dtype=np.float64)) /build/cyvcf2-0.10.4/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2/tests/test_reader.py:570: FutureWarning: Conversion of the second argument of issubdtype from `float` to `np.floating` is deprecated. In future, it will be treated as `np.float64 == np.dtype(float).type`. v.set_format("PS", np.array([8.555, 11.111], dtype=np.float64)) /build/cyvcf2-0.10.4/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2/tests/test_reader.py:573: FutureWarning: Conversion of the second argument of issubdtype from `int` to `np.signedinteger` is deprecated. In future, it will be treated as `np.int32 == np.dtype(int).type`. v.set_format("PS", np.array([9998.555, 99911.111], dtype=np.float32)) /build/cyvcf2-0.10.4/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2/tests/test_reader.py:573: FutureWarning: Conversion of the second argument of issubdtype from `float` to `np.floating` is deprecated. In future, it will be treated as `np.float64 == np.dtype(float).type`. v.set_format("PS", np.array([9998.555, 99911.111], dtype=np.float32)) ok cyvcf2.tests.test_reader.test_set_format_int_a ... [W::vcf_parse] Contig '7' is not defined in the header. (Quick workaround: index the file with tabix.) /build/cyvcf2-0.10.4/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2/tests/test_reader.py:581: FutureWarning: Conversion of the second argument of issubdtype from `int` to `np.signedinteger` is deprecated. In future, it will be treated as `np.int32 == np.dtype(int).type`. v.set_format("PI", np.array([5, 1], dtype=np.int)) ok cyvcf2.tests.test_reader.test_set_format_int_b ... [W::vcf_parse] Contig '7' is not defined in the header. (Quick workaround: index the file with tabix.) /build/cyvcf2-0.10.4/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2/tests/test_reader.py:589: FutureWarning: Conversion of the second argument of issubdtype from `int` to `np.signedinteger` is deprecated. In future, it will be treated as `np.int32 == np.dtype(int).type`. v.set_format("PI", np.array([855, 11], dtype=np.int64)) ok cyvcf2.tests.test_reader.test_set_format_int_c ... [W::vcf_parse] Contig '7' is not defined in the header. (Quick workaround: index the file with tabix.) /build/cyvcf2-0.10.4/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2/tests/test_reader.py:597: FutureWarning: Conversion of the second argument of issubdtype from `int` to `np.signedinteger` is deprecated. In future, it will be treated as `np.int32 == np.dtype(int).type`. v.set_format("PI", np.array([9998, 99911], dtype=np.int32)) ok test that we can handle multiple (in this case 3) values per sample ... [W::vcf_parse] Contig '7' is not defined in the header. (Quick workaround: index the file with tabix.) /build/cyvcf2-0.10.4/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2/tests/test_reader.py:607: FutureWarning: Conversion of the second argument of issubdtype from `int` to `np.signedinteger` is deprecated. In future, it will be treated as `np.int32 == np.dtype(int).type`. v.set_format("P3", exp) ok cyvcf2.tests.test_reader.test_set_gts ... [W::vcf_parse] Contig '7' is not defined in the header. (Quick workaround: index the file with tabix.) ok cyvcf2.tests.test_reader.test_info_del ... ok cyvcf2.tests.test_reader.test_filter_id ... ok cyvcf2.tests.test_reader.test_access_gts ... [W::vcf_parse] Contig '7' is not defined in the header. (Quick workaround: index the file with tabix.) ok cyvcf2.tests.test_reader.test_alt_homozygous_gt ... ok cyvcf2.tests.test_reader.test_write_missing_contig ... [W::vcf_parse] Contig '1' is not defined in the header. (Quick workaround: index the file with tabix.) ok cyvcf2.tests.test_reader.test_set_samples ... ok cyvcf2.tests.test_reader.test_hrec ... ok cyvcf2.tests.test_reader.test_issue44 ... ok cyvcf2.tests.test_reader.test_id_field_updates ... ok cyvcf2.tests.test_reader.test_set_pos ... ok cyvcf2.tests.test_reader.test_set_qual ... ok cyvcf2.tests.test_reader.test_strict_gt_option_flag ... ok cyvcf2.tests.test_reader.test_alt_repr ... ok cyvcf2.tests.test_reader.test_seqlens ... ok cyvcf2.tests.test_reader.test_closed_iter ... ok cyvcf2.tests.test_reader.test_issue72 ... ok cyvcf2.tests.test_reader.test_is_transition ... ok cyvcf2.tests.test_reader.test_decomposed ... ok cyvcf2.tests.test_reader.test_fd ... ok cyvcf2.tests.test_reader.test_set_reference ... ok cyvcf2.tests.test_reader.test_set_alternates ... ok ---------------------------------------------------------------------- Ran 70 tests in 14.896s OK I: pybuild base:217: cd /build/cyvcf2-0.10.4/.pybuild/cpython3_3.7_cyvcf2/build; python3.7 -m nose -v cyvcf2.tests.test_cli.test_version ... ok make sure that we are getting the correct gt_types ... ok cyvcf2.tests.test_reader.test_init ... ok cyvcf2.tests.test_reader.test_type ... ok cyvcf2.tests.test_reader.test_format_str ... [W::vcf_parse] Contig '7' is not defined in the header. (Quick workaround: index the file with tabix.) ok cyvcf2.tests.test_reader.test_missing_samples ... ok cyvcf2.tests.test_reader.test_ibd ... ok cyvcf2.tests.test_reader.test_relatedness ... tested: 44 variants out of 115 ok cyvcf2.tests.test_reader.test_pls ... ok cyvcf2.tests.test_reader.test_gt_alt_freqs ... ok cyvcf2.tests.test_reader.test_str ... ok cyvcf2.tests.test_reader.test_region ... ok cyvcf2.tests.test_reader.test_empty_info ... ok cyvcf2.tests.test_reader.test_phases ... ok cyvcf2.tests.test_reader.test_bad_init ... [E::hts_open_format] Failed to open file XXXXX ok cyvcf2.tests.test_reader.test_samples ... ok cyvcf2.tests.test_reader.test_next ... ok cyvcf2.tests.test_reader.test_variant ... ok cyvcf2.tests.test_reader.test_info_dict ... ok cyvcf2.tests.test_reader.test_attrs ... ok cyvcf2.tests.test_reader.test_empty ... ok cyvcf2.tests.test_reader.test_format_field ... ok cyvcf2.tests.test_reader.test_writer ... ok cyvcf2.tests.test_reader.test_add_info_to_header ... ok cyvcf2.tests.test_reader.test_read_flag ... ok cyvcf2.tests.test_reader.test_add_flag ... ok cyvcf2.tests.test_reader.test_constants ... ok cyvcf2.tests.test_reader.test_add_filter_to_header ... ok cyvcf2.tests.test_reader.test_seqnames ... ok cyvcf2.tests.test_reader.test_var_type ... ok cyvcf2.tests.test_reader.test_header_info ... ok cyvcf2.tests.test_reader.test_snpeff_header ... ok cyvcf2.tests.test_reader.test_gt_types ... ok cyvcf2.tests.test_reader.test_raw_header ... ok cyvcf2.tests.test_reader.test_iterate ... ok cyvcf2.tests.test_reader.test_empty_call ... ok cyvcf2.tests.test_reader.test_haploid ... ok cyvcf2.tests.test_reader.test_diploid ... ok cyvcf2.tests.test_reader.test_format ... ok cyvcf2.tests.test_reader.test_header_stuff ... ok cyvcf2.tests.test_reader.test_bcf ... OK no intervals found for b'/build/cyvcf2-0.10.4/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2/tests/test.snpeff.bcf' at 1:69260-69438 ok cyvcf2.tests.test_reader.test_issue12 ... [W::vcf_parse] Contig '7' is not defined in the header. (Quick workaround: index the file with tabix.) ok Ensure gt_bases works with more complex base representations. ... ok cyvcf2.tests.test_reader.test_set_format_float ... [W::vcf_parse] Contig '7' is not defined in the header. (Quick workaround: index the file with tabix.) /build/cyvcf2-0.10.4/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2/tests/test_reader.py:567: FutureWarning: Conversion of the second argument of issubdtype from `int` to `np.signedinteger` is deprecated. In future, it will be treated as `np.int32 == np.dtype(int).type`. v.set_format("PS", np.array([0.555, 1.111], dtype=np.float)) /build/cyvcf2-0.10.4/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2/tests/test_reader.py:567: FutureWarning: Conversion of the second argument of issubdtype from `float` to `np.floating` is deprecated. In future, it will be treated as `np.float64 == np.dtype(float).type`. v.set_format("PS", np.array([0.555, 1.111], dtype=np.float)) /build/cyvcf2-0.10.4/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2/tests/test_reader.py:570: FutureWarning: Conversion of the second argument of issubdtype from `int` to `np.signedinteger` is deprecated. In future, it will be treated as `np.int32 == np.dtype(int).type`. v.set_format("PS", np.array([8.555, 11.111], dtype=np.float64)) /build/cyvcf2-0.10.4/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2/tests/test_reader.py:570: FutureWarning: Conversion of the second argument of issubdtype from `float` to `np.floating` is deprecated. In future, it will be treated as `np.float64 == np.dtype(float).type`. v.set_format("PS", np.array([8.555, 11.111], dtype=np.float64)) /build/cyvcf2-0.10.4/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2/tests/test_reader.py:573: FutureWarning: Conversion of the second argument of issubdtype from `int` to `np.signedinteger` is deprecated. In future, it will be treated as `np.int32 == np.dtype(int).type`. v.set_format("PS", np.array([9998.555, 99911.111], dtype=np.float32)) /build/cyvcf2-0.10.4/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2/tests/test_reader.py:573: FutureWarning: Conversion of the second argument of issubdtype from `float` to `np.floating` is deprecated. In future, it will be treated as `np.float64 == np.dtype(float).type`. v.set_format("PS", np.array([9998.555, 99911.111], dtype=np.float32)) ok cyvcf2.tests.test_reader.test_set_format_int_a ... [W::vcf_parse] Contig '7' is not defined in the header. (Quick workaround: index the file with tabix.) /build/cyvcf2-0.10.4/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2/tests/test_reader.py:581: FutureWarning: Conversion of the second argument of issubdtype from `int` to `np.signedinteger` is deprecated. In future, it will be treated as `np.int32 == np.dtype(int).type`. v.set_format("PI", np.array([5, 1], dtype=np.int)) ok cyvcf2.tests.test_reader.test_set_format_int_b ... [W::vcf_parse] Contig '7' is not defined in the header. (Quick workaround: index the file with tabix.) /build/cyvcf2-0.10.4/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2/tests/test_reader.py:589: FutureWarning: Conversion of the second argument of issubdtype from `int` to `np.signedinteger` is deprecated. In future, it will be treated as `np.int32 == np.dtype(int).type`. v.set_format("PI", np.array([855, 11], dtype=np.int64)) ok cyvcf2.tests.test_reader.test_set_format_int_c ... [W::vcf_parse] Contig '7' is not defined in the header. (Quick workaround: index the file with tabix.) /build/cyvcf2-0.10.4/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2/tests/test_reader.py:597: FutureWarning: Conversion of the second argument of issubdtype from `int` to `np.signedinteger` is deprecated. In future, it will be treated as `np.int32 == np.dtype(int).type`. v.set_format("PI", np.array([9998, 99911], dtype=np.int32)) ok test that we can handle multiple (in this case 3) values per sample ... [W::vcf_parse] Contig '7' is not defined in the header. (Quick workaround: index the file with tabix.) /build/cyvcf2-0.10.4/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2/tests/test_reader.py:607: FutureWarning: Conversion of the second argument of issubdtype from `int` to `np.signedinteger` is deprecated. In future, it will be treated as `np.int32 == np.dtype(int).type`. v.set_format("P3", exp) ok cyvcf2.tests.test_reader.test_set_gts ... [W::vcf_parse] Contig '7' is not defined in the header. (Quick workaround: index the file with tabix.) ok cyvcf2.tests.test_reader.test_info_del ... ok cyvcf2.tests.test_reader.test_filter_id ... ok cyvcf2.tests.test_reader.test_access_gts ... [W::vcf_parse] Contig '7' is not defined in the header. (Quick workaround: index the file with tabix.) ok cyvcf2.tests.test_reader.test_alt_homozygous_gt ... ok cyvcf2.tests.test_reader.test_write_missing_contig ... [W::vcf_parse] Contig '1' is not defined in the header. (Quick workaround: index the file with tabix.) ok cyvcf2.tests.test_reader.test_set_samples ... ok cyvcf2.tests.test_reader.test_hrec ... ok cyvcf2.tests.test_reader.test_issue44 ... ok cyvcf2.tests.test_reader.test_id_field_updates ... ok cyvcf2.tests.test_reader.test_set_pos ... ok cyvcf2.tests.test_reader.test_set_qual ... ok cyvcf2.tests.test_reader.test_strict_gt_option_flag ... ok cyvcf2.tests.test_reader.test_alt_repr ... ok cyvcf2.tests.test_reader.test_seqlens ... ok cyvcf2.tests.test_reader.test_closed_iter ... ok cyvcf2.tests.test_reader.test_issue72 ... ok cyvcf2.tests.test_reader.test_is_transition ... ok cyvcf2.tests.test_reader.test_decomposed ... ok cyvcf2.tests.test_reader.test_fd ... ok cyvcf2.tests.test_reader.test_set_reference ... ok cyvcf2.tests.test_reader.test_set_alternates ... ok ---------------------------------------------------------------------- Ran 70 tests in 12.162s OK create-stamp debian/debhelper-build-stamp fakeroot debian/rules binary dh binary --with python2,python3 --buildsystem=pybuild dh_testroot -O--buildsystem=pybuild dh_prep -O--buildsystem=pybuild debian/rules override_dh_auto_install make[1]: ingresso nella directory "/build/cyvcf2-0.10.4" dh_auto_install I: pybuild base:217: /usr/bin/python setup.py install --root /build/cyvcf2-0.10.4/debian/python-cyvcf2 running install running build running build_py running 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 reading manifest file 'cyvcf2.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no files found matching 'htslib/*.c' warning: no files found matching 'htslib/*.h' warning: no files found matching 'htslib/htslib/*.h' warning: no files found matching 'htslib/cram/*.c' warning: no files found matching 'htslib/cram/*.h' writing manifest file 'cyvcf2.egg-info/SOURCES.txt' copying cyvcf2/cyvcf2.c -> /build/cyvcf2-0.10.4/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2 running build_ext skipping 'cyvcf2/cyvcf2.c' Cython extension (up-to-date) running install_lib creating /build/cyvcf2-0.10.4/debian/python-cyvcf2 creating /build/cyvcf2-0.10.4/debian/python-cyvcf2/usr creating /build/cyvcf2-0.10.4/debian/python-cyvcf2/usr/lib creating /build/cyvcf2-0.10.4/debian/python-cyvcf2/usr/lib/python2.7 creating /build/cyvcf2-0.10.4/debian/python-cyvcf2/usr/lib/python2.7/dist-packages creating /build/cyvcf2-0.10.4/debian/python-cyvcf2/usr/lib/python2.7/dist-packages/cyvcf2 copying /build/cyvcf2-0.10.4/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2/__init__.pyc -> /build/cyvcf2-0.10.4/debian/python-cyvcf2/usr/lib/python2.7/dist-packages/cyvcf2 copying /build/cyvcf2-0.10.4/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2/helpers.h -> /build/cyvcf2-0.10.4/debian/python-cyvcf2/usr/lib/python2.7/dist-packages/cyvcf2 copying /build/cyvcf2-0.10.4/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2/relatedness.h -> /build/cyvcf2-0.10.4/debian/python-cyvcf2/usr/lib/python2.7/dist-packages/cyvcf2 copying /build/cyvcf2-0.10.4/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2/cyvcf2.pxd -> /build/cyvcf2-0.10.4/debian/python-cyvcf2/usr/lib/python2.7/dist-packages/cyvcf2 creating /build/cyvcf2-0.10.4/debian/python-cyvcf2/usr/lib/python2.7/dist-packages/cyvcf2/tests copying /build/cyvcf2-0.10.4/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2/tests/decomposed.vcf -> /build/cyvcf2-0.10.4/debian/python-cyvcf2/usr/lib/python2.7/dist-packages/cyvcf2/tests copying /build/cyvcf2-0.10.4/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2/tests/__init__.pyc -> /build/cyvcf2-0.10.4/debian/python-cyvcf2/usr/lib/python2.7/dist-packages/cyvcf2/tests copying /build/cyvcf2-0.10.4/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2/tests/test.snpeff.vcf -> /build/cyvcf2-0.10.4/debian/python-cyvcf2/usr/lib/python2.7/dist-packages/cyvcf2/tests copying /build/cyvcf2-0.10.4/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2/tests/test_hemi.py -> /build/cyvcf2-0.10.4/debian/python-cyvcf2/usr/lib/python2.7/dist-packages/cyvcf2/tests copying /build/cyvcf2-0.10.4/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2/tests/test-multiallelic-homozygous-alt.vcf.gz.tbi -> /build/cyvcf2-0.10.4/debian/python-cyvcf2/usr/lib/python2.7/dist-packages/cyvcf2/tests copying /build/cyvcf2-0.10.4/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2/tests/test-strict-gt-option-flag.vcf.gz.tbi -> /build/cyvcf2-0.10.4/debian/python-cyvcf2/usr/lib/python2.7/dist-packages/cyvcf2/tests copying /build/cyvcf2-0.10.4/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2/tests/test-alt-repr.vcf -> /build/cyvcf2-0.10.4/debian/python-cyvcf2/usr/lib/python2.7/dist-packages/cyvcf2/tests copying /build/cyvcf2-0.10.4/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2/tests/test-format-string.vcf -> /build/cyvcf2-0.10.4/debian/python-cyvcf2/usr/lib/python2.7/dist-packages/cyvcf2/tests copying /build/cyvcf2-0.10.4/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2/tests/test_reader.py -> /build/cyvcf2-0.10.4/debian/python-cyvcf2/usr/lib/python2.7/dist-packages/cyvcf2/tests copying /build/cyvcf2-0.10.4/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2/tests/test.vcf.gz -> /build/cyvcf2-0.10.4/debian/python-cyvcf2/usr/lib/python2.7/dist-packages/cyvcf2/tests copying /build/cyvcf2-0.10.4/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2/tests/test.snpeff.bcf -> /build/cyvcf2-0.10.4/debian/python-cyvcf2/usr/lib/python2.7/dist-packages/cyvcf2/tests copying /build/cyvcf2-0.10.4/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2/tests/empty.vcf -> /build/cyvcf2-0.10.4/debian/python-cyvcf2/usr/lib/python2.7/dist-packages/cyvcf2/tests copying /build/cyvcf2-0.10.4/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2/tests/__init__.py -> /build/cyvcf2-0.10.4/debian/python-cyvcf2/usr/lib/python2.7/dist-packages/cyvcf2/tests copying /build/cyvcf2-0.10.4/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2/tests/test.snpeff.bcf.csi -> /build/cyvcf2-0.10.4/debian/python-cyvcf2/usr/lib/python2.7/dist-packages/cyvcf2/tests copying /build/cyvcf2-0.10.4/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2/tests/test-hemi.vcf -> /build/cyvcf2-0.10.4/debian/python-cyvcf2/usr/lib/python2.7/dist-packages/cyvcf2/tests copying /build/cyvcf2-0.10.4/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2/tests/test.vcf.gz.tbi -> /build/cyvcf2-0.10.4/debian/python-cyvcf2/usr/lib/python2.7/dist-packages/cyvcf2/tests copying /build/cyvcf2-0.10.4/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2/tests/test_reader.pyc -> /build/cyvcf2-0.10.4/debian/python-cyvcf2/usr/lib/python2.7/dist-packages/cyvcf2/tests copying /build/cyvcf2-0.10.4/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2/tests/test.comp_het.3.vcf -> /build/cyvcf2-0.10.4/debian/python-cyvcf2/usr/lib/python2.7/dist-packages/cyvcf2/tests copying /build/cyvcf2-0.10.4/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2/tests/issue_44.vcf -> /build/cyvcf2-0.10.4/debian/python-cyvcf2/usr/lib/python2.7/dist-packages/cyvcf2/tests copying /build/cyvcf2-0.10.4/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2/tests/test-multiallelic-homozygous-alt.vcf.gz -> /build/cyvcf2-0.10.4/debian/python-cyvcf2/usr/lib/python2.7/dist-packages/cyvcf2/tests copying /build/cyvcf2-0.10.4/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2/tests/test-haploidX.vcf -> /build/cyvcf2-0.10.4/debian/python-cyvcf2/usr/lib/python2.7/dist-packages/cyvcf2/tests copying /build/cyvcf2-0.10.4/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2/tests/test_cli.py -> /build/cyvcf2-0.10.4/debian/python-cyvcf2/usr/lib/python2.7/dist-packages/cyvcf2/tests copying /build/cyvcf2-0.10.4/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2/tests/seg.vcf.gz -> /build/cyvcf2-0.10.4/debian/python-cyvcf2/usr/lib/python2.7/dist-packages/cyvcf2/tests copying /build/cyvcf2-0.10.4/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2/tests/test-strict-gt-option-flag.vcf.gz -> /build/cyvcf2-0.10.4/debian/python-cyvcf2/usr/lib/python2.7/dist-packages/cyvcf2/tests copying /build/cyvcf2-0.10.4/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2/tests/test_gt_alt_freqs.vcf -> /build/cyvcf2-0.10.4/debian/python-cyvcf2/usr/lib/python2.7/dist-packages/cyvcf2/tests copying /build/cyvcf2-0.10.4/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2/tests/test_hemi.pyc -> /build/cyvcf2-0.10.4/debian/python-cyvcf2/usr/lib/python2.7/dist-packages/cyvcf2/tests copying /build/cyvcf2-0.10.4/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2/tests/test_gt_bases.vcf.gz -> /build/cyvcf2-0.10.4/debian/python-cyvcf2/usr/lib/python2.7/dist-packages/cyvcf2/tests copying /build/cyvcf2-0.10.4/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2/tests/o.vcf.gz -> /build/cyvcf2-0.10.4/debian/python-cyvcf2/usr/lib/python2.7/dist-packages/cyvcf2/tests copying /build/cyvcf2-0.10.4/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2/tests/test_cli.pyc -> /build/cyvcf2-0.10.4/debian/python-cyvcf2/usr/lib/python2.7/dist-packages/cyvcf2/tests copying /build/cyvcf2-0.10.4/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2/tests/bug.vcf.gz -> /build/cyvcf2-0.10.4/debian/python-cyvcf2/usr/lib/python2.7/dist-packages/cyvcf2/tests copying /build/cyvcf2-0.10.4/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2/__init__.py -> /build/cyvcf2-0.10.4/debian/python-cyvcf2/usr/lib/python2.7/dist-packages/cyvcf2 copying /build/cyvcf2-0.10.4/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2/cyvcf2.c -> /build/cyvcf2-0.10.4/debian/python-cyvcf2/usr/lib/python2.7/dist-packages/cyvcf2 copying /build/cyvcf2-0.10.4/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2/__main__.py -> /build/cyvcf2-0.10.4/debian/python-cyvcf2/usr/lib/python2.7/dist-packages/cyvcf2 copying /build/cyvcf2-0.10.4/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2/cli.pyc -> /build/cyvcf2-0.10.4/debian/python-cyvcf2/usr/lib/python2.7/dist-packages/cyvcf2 copying /build/cyvcf2-0.10.4/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2/cyvcf2.so -> /build/cyvcf2-0.10.4/debian/python-cyvcf2/usr/lib/python2.7/dist-packages/cyvcf2 copying /build/cyvcf2-0.10.4/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2/cli.py -> /build/cyvcf2-0.10.4/debian/python-cyvcf2/usr/lib/python2.7/dist-packages/cyvcf2 copying /build/cyvcf2-0.10.4/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2/helpers.c -> /build/cyvcf2-0.10.4/debian/python-cyvcf2/usr/lib/python2.7/dist-packages/cyvcf2 copying /build/cyvcf2-0.10.4/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2/cyvcf2.pyx -> /build/cyvcf2-0.10.4/debian/python-cyvcf2/usr/lib/python2.7/dist-packages/cyvcf2 byte-compiling /build/cyvcf2-0.10.4/debian/python-cyvcf2/usr/lib/python2.7/dist-packages/cyvcf2/tests/test_hemi.py to test_hemi.pyc byte-compiling /build/cyvcf2-0.10.4/debian/python-cyvcf2/usr/lib/python2.7/dist-packages/cyvcf2/tests/test_reader.py to test_reader.pyc byte-compiling /build/cyvcf2-0.10.4/debian/python-cyvcf2/usr/lib/python2.7/dist-packages/cyvcf2/tests/__init__.py to __init__.pyc byte-compiling /build/cyvcf2-0.10.4/debian/python-cyvcf2/usr/lib/python2.7/dist-packages/cyvcf2/tests/test_cli.py to test_cli.pyc byte-compiling /build/cyvcf2-0.10.4/debian/python-cyvcf2/usr/lib/python2.7/dist-packages/cyvcf2/__init__.py to __init__.pyc byte-compiling /build/cyvcf2-0.10.4/debian/python-cyvcf2/usr/lib/python2.7/dist-packages/cyvcf2/__main__.py to __main__.pyc byte-compiling /build/cyvcf2-0.10.4/debian/python-cyvcf2/usr/lib/python2.7/dist-packages/cyvcf2/cli.py to cli.pyc running install_egg_info Copying cyvcf2.egg-info to /build/cyvcf2-0.10.4/debian/python-cyvcf2/usr/lib/python2.7/dist-packages/cyvcf2-0.10.4.egg-info Skipping SOURCES.txt running install_scripts Installing cyvcf2 script to /build/cyvcf2-0.10.4/debian/python-cyvcf2/usr/bin I: pybuild base:217: /usr/bin/python3 setup.py install --root /build/cyvcf2-0.10.4/debian/python3-cyvcf2 running install running build running build_py running egg_info writing cyvcf2.egg-info/PKG-INFO writing dependency_links to cyvcf2.egg-info/dependency_links.txt writing entry points to cyvcf2.egg-info/entry_points.txt writing requirements to cyvcf2.egg-info/requires.txt writing top-level names to cyvcf2.egg-info/top_level.txt reading manifest file 'cyvcf2.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no files found matching 'htslib/*.c' warning: no files found matching 'htslib/*.h' warning: no files found matching 'htslib/htslib/*.h' warning: no files found matching 'htslib/cram/*.c' warning: no files found matching 'htslib/cram/*.h' writing manifest file 'cyvcf2.egg-info/SOURCES.txt' running build_ext skipping 'cyvcf2/cyvcf2.c' Cython extension (up-to-date) running install_lib creating /build/cyvcf2-0.10.4/debian/python3-cyvcf2 creating /build/cyvcf2-0.10.4/debian/python3-cyvcf2/usr creating /build/cyvcf2-0.10.4/debian/python3-cyvcf2/usr/lib creating /build/cyvcf2-0.10.4/debian/python3-cyvcf2/usr/lib/python3.7 creating /build/cyvcf2-0.10.4/debian/python3-cyvcf2/usr/lib/python3.7/dist-packages creating /build/cyvcf2-0.10.4/debian/python3-cyvcf2/usr/lib/python3.7/dist-packages/cyvcf2 copying /build/cyvcf2-0.10.4/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2/helpers.h -> /build/cyvcf2-0.10.4/debian/python3-cyvcf2/usr/lib/python3.7/dist-packages/cyvcf2 copying /build/cyvcf2-0.10.4/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2/relatedness.h -> /build/cyvcf2-0.10.4/debian/python3-cyvcf2/usr/lib/python3.7/dist-packages/cyvcf2 copying /build/cyvcf2-0.10.4/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2/cyvcf2.pxd -> /build/cyvcf2-0.10.4/debian/python3-cyvcf2/usr/lib/python3.7/dist-packages/cyvcf2 creating /build/cyvcf2-0.10.4/debian/python3-cyvcf2/usr/lib/python3.7/dist-packages/cyvcf2/tests copying /build/cyvcf2-0.10.4/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2/tests/decomposed.vcf -> /build/cyvcf2-0.10.4/debian/python3-cyvcf2/usr/lib/python3.7/dist-packages/cyvcf2/tests copying /build/cyvcf2-0.10.4/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2/tests/test.snpeff.vcf -> /build/cyvcf2-0.10.4/debian/python3-cyvcf2/usr/lib/python3.7/dist-packages/cyvcf2/tests copying /build/cyvcf2-0.10.4/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2/tests/test_hemi.py -> /build/cyvcf2-0.10.4/debian/python3-cyvcf2/usr/lib/python3.7/dist-packages/cyvcf2/tests copying /build/cyvcf2-0.10.4/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2/tests/test-multiallelic-homozygous-alt.vcf.gz.tbi -> /build/cyvcf2-0.10.4/debian/python3-cyvcf2/usr/lib/python3.7/dist-packages/cyvcf2/tests copying /build/cyvcf2-0.10.4/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2/tests/test-strict-gt-option-flag.vcf.gz.tbi -> /build/cyvcf2-0.10.4/debian/python3-cyvcf2/usr/lib/python3.7/dist-packages/cyvcf2/tests copying /build/cyvcf2-0.10.4/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2/tests/test-alt-repr.vcf -> /build/cyvcf2-0.10.4/debian/python3-cyvcf2/usr/lib/python3.7/dist-packages/cyvcf2/tests copying /build/cyvcf2-0.10.4/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2/tests/test-format-string.vcf -> /build/cyvcf2-0.10.4/debian/python3-cyvcf2/usr/lib/python3.7/dist-packages/cyvcf2/tests copying /build/cyvcf2-0.10.4/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2/tests/test_reader.py -> /build/cyvcf2-0.10.4/debian/python3-cyvcf2/usr/lib/python3.7/dist-packages/cyvcf2/tests copying /build/cyvcf2-0.10.4/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2/tests/test.vcf.gz -> /build/cyvcf2-0.10.4/debian/python3-cyvcf2/usr/lib/python3.7/dist-packages/cyvcf2/tests copying /build/cyvcf2-0.10.4/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2/tests/test.snpeff.bcf -> /build/cyvcf2-0.10.4/debian/python3-cyvcf2/usr/lib/python3.7/dist-packages/cyvcf2/tests copying /build/cyvcf2-0.10.4/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2/tests/empty.vcf -> /build/cyvcf2-0.10.4/debian/python3-cyvcf2/usr/lib/python3.7/dist-packages/cyvcf2/tests copying /build/cyvcf2-0.10.4/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2/tests/__init__.py -> /build/cyvcf2-0.10.4/debian/python3-cyvcf2/usr/lib/python3.7/dist-packages/cyvcf2/tests copying /build/cyvcf2-0.10.4/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2/tests/test.snpeff.bcf.csi -> /build/cyvcf2-0.10.4/debian/python3-cyvcf2/usr/lib/python3.7/dist-packages/cyvcf2/tests copying /build/cyvcf2-0.10.4/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2/tests/test-hemi.vcf -> /build/cyvcf2-0.10.4/debian/python3-cyvcf2/usr/lib/python3.7/dist-packages/cyvcf2/tests copying /build/cyvcf2-0.10.4/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2/tests/test.vcf.gz.tbi -> /build/cyvcf2-0.10.4/debian/python3-cyvcf2/usr/lib/python3.7/dist-packages/cyvcf2/tests copying /build/cyvcf2-0.10.4/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2/tests/test.comp_het.3.vcf -> /build/cyvcf2-0.10.4/debian/python3-cyvcf2/usr/lib/python3.7/dist-packages/cyvcf2/tests copying /build/cyvcf2-0.10.4/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2/tests/issue_44.vcf -> /build/cyvcf2-0.10.4/debian/python3-cyvcf2/usr/lib/python3.7/dist-packages/cyvcf2/tests copying /build/cyvcf2-0.10.4/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2/tests/test-multiallelic-homozygous-alt.vcf.gz -> /build/cyvcf2-0.10.4/debian/python3-cyvcf2/usr/lib/python3.7/dist-packages/cyvcf2/tests copying /build/cyvcf2-0.10.4/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2/tests/test-haploidX.vcf -> /build/cyvcf2-0.10.4/debian/python3-cyvcf2/usr/lib/python3.7/dist-packages/cyvcf2/tests copying /build/cyvcf2-0.10.4/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2/tests/test_cli.py -> /build/cyvcf2-0.10.4/debian/python3-cyvcf2/usr/lib/python3.7/dist-packages/cyvcf2/tests copying /build/cyvcf2-0.10.4/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2/tests/seg.vcf.gz -> /build/cyvcf2-0.10.4/debian/python3-cyvcf2/usr/lib/python3.7/dist-packages/cyvcf2/tests copying /build/cyvcf2-0.10.4/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2/tests/test-strict-gt-option-flag.vcf.gz -> /build/cyvcf2-0.10.4/debian/python3-cyvcf2/usr/lib/python3.7/dist-packages/cyvcf2/tests copying /build/cyvcf2-0.10.4/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2/tests/test_gt_alt_freqs.vcf -> /build/cyvcf2-0.10.4/debian/python3-cyvcf2/usr/lib/python3.7/dist-packages/cyvcf2/tests copying /build/cyvcf2-0.10.4/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2/tests/test_gt_bases.vcf.gz -> /build/cyvcf2-0.10.4/debian/python3-cyvcf2/usr/lib/python3.7/dist-packages/cyvcf2/tests creating /build/cyvcf2-0.10.4/debian/python3-cyvcf2/usr/lib/python3.7/dist-packages/cyvcf2/tests/__pycache__ copying /build/cyvcf2-0.10.4/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2/tests/__pycache__/test_reader.cpython-37.pyc -> /build/cyvcf2-0.10.4/debian/python3-cyvcf2/usr/lib/python3.7/dist-packages/cyvcf2/tests/__pycache__ copying /build/cyvcf2-0.10.4/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2/tests/__pycache__/test_cli.cpython-37.pyc -> /build/cyvcf2-0.10.4/debian/python3-cyvcf2/usr/lib/python3.7/dist-packages/cyvcf2/tests/__pycache__ copying /build/cyvcf2-0.10.4/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2/tests/__pycache__/__init__.cpython-37.pyc -> /build/cyvcf2-0.10.4/debian/python3-cyvcf2/usr/lib/python3.7/dist-packages/cyvcf2/tests/__pycache__ copying /build/cyvcf2-0.10.4/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2/tests/__pycache__/test_hemi.cpython-37.pyc -> /build/cyvcf2-0.10.4/debian/python3-cyvcf2/usr/lib/python3.7/dist-packages/cyvcf2/tests/__pycache__ copying /build/cyvcf2-0.10.4/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2/tests/o.vcf.gz -> /build/cyvcf2-0.10.4/debian/python3-cyvcf2/usr/lib/python3.7/dist-packages/cyvcf2/tests copying /build/cyvcf2-0.10.4/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2/tests/bug.vcf.gz -> /build/cyvcf2-0.10.4/debian/python3-cyvcf2/usr/lib/python3.7/dist-packages/cyvcf2/tests copying /build/cyvcf2-0.10.4/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2/cyvcf2.cpython-37m-arm-linux-gnueabihf.so -> /build/cyvcf2-0.10.4/debian/python3-cyvcf2/usr/lib/python3.7/dist-packages/cyvcf2 copying /build/cyvcf2-0.10.4/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2/__init__.py -> /build/cyvcf2-0.10.4/debian/python3-cyvcf2/usr/lib/python3.7/dist-packages/cyvcf2 copying /build/cyvcf2-0.10.4/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2/cyvcf2.c -> /build/cyvcf2-0.10.4/debian/python3-cyvcf2/usr/lib/python3.7/dist-packages/cyvcf2 copying /build/cyvcf2-0.10.4/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2/__main__.py -> /build/cyvcf2-0.10.4/debian/python3-cyvcf2/usr/lib/python3.7/dist-packages/cyvcf2 creating /build/cyvcf2-0.10.4/debian/python3-cyvcf2/usr/lib/python3.7/dist-packages/cyvcf2/__pycache__ copying /build/cyvcf2-0.10.4/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2/__pycache__/cli.cpython-37.pyc -> /build/cyvcf2-0.10.4/debian/python3-cyvcf2/usr/lib/python3.7/dist-packages/cyvcf2/__pycache__ copying /build/cyvcf2-0.10.4/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2/__pycache__/__init__.cpython-37.pyc -> /build/cyvcf2-0.10.4/debian/python3-cyvcf2/usr/lib/python3.7/dist-packages/cyvcf2/__pycache__ copying /build/cyvcf2-0.10.4/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2/cli.py -> /build/cyvcf2-0.10.4/debian/python3-cyvcf2/usr/lib/python3.7/dist-packages/cyvcf2 copying /build/cyvcf2-0.10.4/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2/helpers.c -> /build/cyvcf2-0.10.4/debian/python3-cyvcf2/usr/lib/python3.7/dist-packages/cyvcf2 copying /build/cyvcf2-0.10.4/.pybuild/cpython3_3.7_cyvcf2/build/cyvcf2/cyvcf2.pyx -> /build/cyvcf2-0.10.4/debian/python3-cyvcf2/usr/lib/python3.7/dist-packages/cyvcf2 byte-compiling /build/cyvcf2-0.10.4/debian/python3-cyvcf2/usr/lib/python3.7/dist-packages/cyvcf2/tests/test_hemi.py to test_hemi.cpython-37.pyc byte-compiling /build/cyvcf2-0.10.4/debian/python3-cyvcf2/usr/lib/python3.7/dist-packages/cyvcf2/tests/test_reader.py to test_reader.cpython-37.pyc byte-compiling /build/cyvcf2-0.10.4/debian/python3-cyvcf2/usr/lib/python3.7/dist-packages/cyvcf2/tests/__init__.py to __init__.cpython-37.pyc byte-compiling /build/cyvcf2-0.10.4/debian/python3-cyvcf2/usr/lib/python3.7/dist-packages/cyvcf2/tests/test_cli.py to test_cli.cpython-37.pyc byte-compiling /build/cyvcf2-0.10.4/debian/python3-cyvcf2/usr/lib/python3.7/dist-packages/cyvcf2/__init__.py to __init__.cpython-37.pyc byte-compiling /build/cyvcf2-0.10.4/debian/python3-cyvcf2/usr/lib/python3.7/dist-packages/cyvcf2/__main__.py to __main__.cpython-37.pyc byte-compiling /build/cyvcf2-0.10.4/debian/python3-cyvcf2/usr/lib/python3.7/dist-packages/cyvcf2/cli.py to cli.cpython-37.pyc running install_egg_info Copying cyvcf2.egg-info to /build/cyvcf2-0.10.4/debian/python3-cyvcf2/usr/lib/python3.7/dist-packages/cyvcf2-0.10.4.egg-info Skipping SOURCES.txt running install_scripts Installing cyvcf2 script to /build/cyvcf2-0.10.4/debian/python3-cyvcf2/usr/bin rm -f debian/python-cyvcf2/usr/bin/cyvcf2 make[1]: uscita dalla directory "/build/cyvcf2-0.10.4" debian/rules override_dh_install make[1]: ingresso nella directory "/build/cyvcf2-0.10.4" dh_numpy dh_install make[1]: uscita dalla directory "/build/cyvcf2-0.10.4" dh_installdocs -O--buildsystem=pybuild dh_installchangelogs -O--buildsystem=pybuild dh_python2 -O--buildsystem=pybuild I: dh_python2 fs:343: renaming cyvcf2.so to cyvcf2.arm-linux-gnueabihf.so dh_python3 -O--buildsystem=pybuild dh_installinit -O--buildsystem=pybuild dh_installsystemduser -O--buildsystem=pybuild dh_perl -O--buildsystem=pybuild dh_link -O--buildsystem=pybuild dh_strip_nondeterminism -O--buildsystem=pybuild dh_compress -O--buildsystem=pybuild dh_fixperms -O--buildsystem=pybuild dh_missing -O--buildsystem=pybuild dh_dwz -O--buildsystem=pybuild dh_strip -O--buildsystem=pybuild dh_makeshlibs -O--buildsystem=pybuild dh_shlibdeps -O--buildsystem=pybuild dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/python3-cyvcf2/usr/lib/python3/dist-packages/cyvcf2/cyvcf2.cpython-37m-arm-linux-gnueabihf.so was not linked against libcrypt.so.1 (it uses none of the library's symbols) dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/python3-cyvcf2/usr/lib/python3/dist-packages/cyvcf2/cyvcf2.cpython-37m-arm-linux-gnueabihf.so was not linked against libz.so.1 (it uses none of the library's symbols) dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/python3-cyvcf2/usr/lib/python3/dist-packages/cyvcf2/cyvcf2.cpython-37m-arm-linux-gnueabihf.so was not linked against libssl.so.1.1 (it uses none of the library's symbols) dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/python3-cyvcf2/usr/lib/python3/dist-packages/cyvcf2/cyvcf2.cpython-37m-arm-linux-gnueabihf.so was not linked against libbz2.so.1.0 (it uses none of the library's symbols) dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/python3-cyvcf2/usr/lib/python3/dist-packages/cyvcf2/cyvcf2.cpython-37m-arm-linux-gnueabihf.so was not linked against liblzma.so.5 (it uses none of the library's symbols) dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/python3-cyvcf2/usr/lib/python3/dist-packages/cyvcf2/cyvcf2.cpython-37m-arm-linux-gnueabihf.so was not linked against libcurl-gnutls.so.4 (it uses none of the library's symbols) dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/python-cyvcf2/usr/lib/python2.7/dist-packages/cyvcf2/cyvcf2.arm-linux-gnueabihf.so was not linked against libz.so.1 (it uses none of the library's symbols) dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/python-cyvcf2/usr/lib/python2.7/dist-packages/cyvcf2/cyvcf2.arm-linux-gnueabihf.so was not linked against libcurl-gnutls.so.4 (it uses none of the library's symbols) dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/python-cyvcf2/usr/lib/python2.7/dist-packages/cyvcf2/cyvcf2.arm-linux-gnueabihf.so was not linked against libcrypt.so.1 (it uses none of the library's symbols) dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/python-cyvcf2/usr/lib/python2.7/dist-packages/cyvcf2/cyvcf2.arm-linux-gnueabihf.so was not linked against libssl.so.1.1 (it uses none of the library's symbols) dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/python-cyvcf2/usr/lib/python2.7/dist-packages/cyvcf2/cyvcf2.arm-linux-gnueabihf.so was not linked against liblzma.so.5 (it uses none of the library's symbols) dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/python-cyvcf2/usr/lib/python2.7/dist-packages/cyvcf2/cyvcf2.arm-linux-gnueabihf.so was not linked against libbz2.so.1.0 (it uses none of the library's symbols) dh_installdeb -O--buildsystem=pybuild dh_gencontrol -O--buildsystem=pybuild dpkg-gencontrol: warning: package python-cyvcf2: substitution variable ${python:Provides} unused, but is defined dpkg-gencontrol: warning: package python-cyvcf2: substitution variable ${python:Versions} unused, but is defined dpkg-gencontrol: warning: package python3-cyvcf2: substitution variable ${python3:Provides} unused, but is defined dpkg-gencontrol: warning: package python3-cyvcf2: substitution variable ${python3:Versions} unused, but is defined dpkg-gencontrol: warning: package python3-cyvcf2: substitution variable ${python:Depends} unused, but is defined dpkg-gencontrol: warning: package python-cyvcf2: substitution variable ${python:Provides} unused, but is defined dpkg-gencontrol: warning: package python-cyvcf2: substitution variable ${python:Versions} unused, but is defined dpkg-gencontrol: warning: package python3-cyvcf2: substitution variable ${python3:Provides} unused, but is defined dpkg-gencontrol: warning: package python3-cyvcf2: substitution variable ${python3:Versions} unused, but is defined dpkg-gencontrol: warning: package python3-cyvcf2: substitution variable ${python:Depends} unused, but is defined dh_md5sums -O--buildsystem=pybuild dh_builddeb -O--buildsystem=pybuild dpkg-deb: generazione del pacchetto "python-cyvcf2" in "../python-cyvcf2_0.10.4-1_armhf.deb". dpkg-deb: generazione del pacchetto "python-cyvcf2-dbgsym" in "../python-cyvcf2-dbgsym_0.10.4-1_armhf.deb". dpkg-deb: generazione del pacchetto "python3-cyvcf2-dbgsym" in "../python3-cyvcf2-dbgsym_0.10.4-1_armhf.deb". dpkg-deb: generazione del pacchetto "python3-cyvcf2" in "../python3-cyvcf2_0.10.4-1_armhf.deb". dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../cyvcf2_0.10.4-1_armhf.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-source: info: using options from cyvcf2-0.10.4/debian/source/options: --extend-diff-ignore=^[^/]*[.]egg-info/ dpkg-buildpackage: info: binary-only upload (no source included) I: copying local configuration I: user script /srv/workspace/pbuilder/11204/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/11204/tmp/hooks/B01_cleanup finished I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/11204 and its subdirectories I: Current time: Tue Nov 10 05:30:14 +14 2020 I: pbuilder-time-stamp: 1604935814