I: pbuilder: network access will be disabled during build I: Current time: Fri Apr 7 09:50:45 -12 2023 I: pbuilder-time-stamp: 1680904245 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bookworm-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. 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 [pyranges_0.0.111+ds-4.dsc] I: copying [./pyranges_0.0.111+ds.orig.tar.xz] I: copying [./pyranges_0.0.111+ds-4.debian.tar.xz] I: Extracting source gpgv: Signature made Sat Jan 14 08:33:17 2023 -12 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./pyranges_0.0.111+ds-4.dsc: no acceptable signature found dpkg-source: info: extracting pyranges in pyranges-0.0.111+ds dpkg-source: info: unpacking pyranges_0.0.111+ds.orig.tar.xz dpkg-source: info: unpacking pyranges_0.0.111+ds-4.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying fix_dtype.patch dpkg-source: info: applying reorder.patch dpkg-source: info: applying numpy_1.24.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/20428/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='arm64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=8' DISTRIBUTION='bookworm' HOME='/var/lib/jenkins' HOST_ARCH='arm64' IFS=' ' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='20428' PS1='# ' PS2='> ' PS4='+ ' PWD='/' SHELL='/bin/bash' SHLVL='2' SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.FMkHsc5X/pbuilderrc_eUjB --distribution bookworm --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.FMkHsc5X/b1 --logfile b1/build.log pyranges_0.0.111+ds-4.dsc' SUDO_GID='117' SUDO_UID='110' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' USERNAME='root' _='/usr/bin/systemd-run' http_proxy='http://192.168.101.16:3128' I: uname -a Linux codethink16-arm64 4.15.0-208-generic #220-Ubuntu SMP Mon Mar 20 14:28:12 UTC 2023 aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Apr 4 22:25 /bin -> usr/bin I: user script /srv/workspace/pbuilder/20428/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: arm64 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-compat (= 13), dh-python, python3-setuptools, python3-all, python3-ncls, python3-pyrle, python3-pytest, python3-pytest-xdist, python3-sorted-nearest, python3-hypothesis, bedtools, samtools dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19616 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-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on dh-python; however: Package dh-python is not installed. pbuilder-satisfydepends-dummy depends on python3-setuptools; however: Package python3-setuptools is not installed. pbuilder-satisfydepends-dummy depends on python3-all; however: Package python3-all is not installed. pbuilder-satisfydepends-dummy depends on python3-ncls; however: Package python3-ncls is not installed. pbuilder-satisfydepends-dummy depends on python3-pyrle; however: Package python3-pyrle is not installed. pbuilder-satisfydepends-dummy depends on python3-pytest; however: Package python3-pytest is not installed. pbuilder-satisfydepends-dummy depends on python3-pytest-xdist; however: Package python3-pytest-xdist is not installed. pbuilder-satisfydepends-dummy depends on python3-sorted-nearest; however: Package python3-sorted-nearest is not installed. pbuilder-satisfydepends-dummy depends on python3-hypothesis; however: Package python3-hypothesis is not installed. pbuilder-satisfydepends-dummy depends on bedtools; however: Package bedtools is not installed. pbuilder-satisfydepends-dummy depends on samtools; however: Package samtools 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} bedtools{a} bsdextrautils{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} libbrotli1{a} libcurl3-gnutls{a} libdebhelper-perl{a} libdeflate0{a} libelf1{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libgfortran5{a} libhts3{a} libhtscodecs2{a} libicu72{a} liblapack3{a} libldap-2.5-0{a} libmagic-mgc{a} libmagic1{a} libncurses6{a} libnghttp2-14{a} libpipeline1{a} libpsl5{a} libpython3-stdlib{a} libpython3.11-minimal{a} libpython3.11-stdlib{a} libreadline8{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libssh2-1{a} libsub-override-perl{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} media-types{a} po-debconf{a} python3{a} python3-all{a} python3-attr{a} python3-dateutil{a} python3-distutils{a} python3-execnet{a} python3-hypothesis{a} python3-iniconfig{a} python3-lib2to3{a} python3-minimal{a} python3-more-itertools{a} python3-natsort{a} python3-ncls{a} python3-numpy{a} python3-packaging{a} python3-pandas{a} python3-pandas-lib{a} python3-pkg-resources{a} python3-pluggy{a} python3-py{a} python3-pyrle{a} python3-pytest{a} python3-pytest-xdist{a} python3-setuptools{a} python3-six{a} python3-sorted-nearest{a} python3-sortedcontainers{a} python3-tabulate{a} python3-tz{a} python3.11{a} python3.11-minimal{a} readline-common{a} samtools{a} sensible-utils{a} The following packages are RECOMMENDED but will NOT be installed: ca-certificates curl libarchive-cpio-perl libgpm2 libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules lynx publicsuffix python3-bottleneck python3-bs4 python3-click python3-dev python3-html5lib python3-jinja2 python3-lxml python3-matplotlib python3-numexpr python3-odf python3-openpyxl python3-pygments python3-scipy python3-tables wget 0 packages upgraded, 88 newly installed, 0 to remove and 0 not upgraded. Need to get 43.9 MB of archives. After unpacking 217 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bookworm/main arm64 libpython3.11-minimal arm64 3.11.2-6 [806 kB] Get: 2 http://deb.debian.org/debian bookworm/main arm64 libexpat1 arm64 2.5.0-1 [84.8 kB] Get: 3 http://deb.debian.org/debian bookworm/main arm64 python3.11-minimal arm64 3.11.2-6 [1858 kB] Get: 4 http://deb.debian.org/debian bookworm/main arm64 python3-minimal arm64 3.11.2-1 [26.0 kB] Get: 5 http://deb.debian.org/debian bookworm/main arm64 media-types all 10.0.0 [26.1 kB] Get: 6 http://deb.debian.org/debian bookworm/main arm64 readline-common all 8.2-1.3 [69.0 kB] Get: 7 http://deb.debian.org/debian bookworm/main arm64 libreadline8 arm64 8.2-1.3 [155 kB] Get: 8 http://deb.debian.org/debian bookworm/main arm64 libpython3.11-stdlib arm64 3.11.2-6 [1747 kB] Get: 9 http://deb.debian.org/debian bookworm/main arm64 python3.11 arm64 3.11.2-6 [572 kB] Get: 10 http://deb.debian.org/debian bookworm/main arm64 libpython3-stdlib arm64 3.11.2-1 [9012 B] Get: 11 http://deb.debian.org/debian bookworm/main arm64 python3 arm64 3.11.2-1 [26.0 kB] Get: 12 http://deb.debian.org/debian bookworm/main arm64 sensible-utils all 0.0.17+nmu1 [19.0 kB] Get: 13 http://deb.debian.org/debian bookworm/main arm64 libmagic-mgc arm64 1:5.44-3 [305 kB] Get: 14 http://deb.debian.org/debian bookworm/main arm64 libmagic1 arm64 1:5.44-3 [98.5 kB] Get: 15 http://deb.debian.org/debian bookworm/main arm64 file arm64 1:5.44-3 [42.5 kB] Get: 16 http://deb.debian.org/debian bookworm/main arm64 gettext-base arm64 0.21-12 [159 kB] Get: 17 http://deb.debian.org/debian bookworm/main arm64 libuchardet0 arm64 0.0.7-1 [67.9 kB] Get: 18 http://deb.debian.org/debian bookworm/main arm64 groff-base arm64 1.22.4-10 [861 kB] Get: 19 http://deb.debian.org/debian bookworm/main arm64 bsdextrautils arm64 2.38.1-5+b1 [86.9 kB] Get: 20 http://deb.debian.org/debian bookworm/main arm64 libpipeline1 arm64 1.5.7-1 [36.4 kB] Get: 21 http://deb.debian.org/debian bookworm/main arm64 man-db arm64 2.11.2-2 [1369 kB] Get: 22 http://deb.debian.org/debian bookworm/main arm64 m4 arm64 1.4.19-3 [276 kB] Get: 23 http://deb.debian.org/debian bookworm/main arm64 autoconf all 2.71-3 [332 kB] Get: 24 http://deb.debian.org/debian bookworm/main arm64 autotools-dev all 20220109.1 [51.6 kB] Get: 25 http://deb.debian.org/debian bookworm/main arm64 automake all 1:1.16.5-1.3 [823 kB] Get: 26 http://deb.debian.org/debian bookworm/main arm64 autopoint all 0.21-12 [495 kB] Get: 27 http://deb.debian.org/debian bookworm/main arm64 bedtools arm64 2.30.0+dfsg-2 [579 kB] Get: 28 http://deb.debian.org/debian bookworm/main arm64 cython3 arm64 0.29.32-2+b1 [1223 kB] Get: 29 http://deb.debian.org/debian bookworm/main arm64 libdebhelper-perl all 13.11.4 [81.2 kB] Get: 30 http://deb.debian.org/debian bookworm/main arm64 libtool all 2.4.7-5 [517 kB] Get: 31 http://deb.debian.org/debian bookworm/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 32 http://deb.debian.org/debian bookworm/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 33 http://deb.debian.org/debian bookworm/main arm64 libsub-override-perl all 0.09-4 [9304 B] Get: 34 http://deb.debian.org/debian bookworm/main arm64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 35 http://deb.debian.org/debian bookworm/main arm64 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 36 http://deb.debian.org/debian bookworm/main arm64 libelf1 arm64 0.188-2.1 [173 kB] Get: 37 http://deb.debian.org/debian bookworm/main arm64 dwz arm64 0.15-1 [101 kB] Get: 38 http://deb.debian.org/debian bookworm/main arm64 libicu72 arm64 72.1-3 [9204 kB] Get: 39 http://deb.debian.org/debian bookworm/main arm64 libxml2 arm64 2.9.14+dfsg-1.1+b3 [619 kB] Get: 40 http://deb.debian.org/debian bookworm/main arm64 gettext arm64 0.21-12 [1248 kB] Get: 41 http://deb.debian.org/debian bookworm/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 42 http://deb.debian.org/debian bookworm/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 43 http://deb.debian.org/debian bookworm/main arm64 debhelper all 13.11.4 [942 kB] Get: 44 http://deb.debian.org/debian bookworm/main arm64 python3-lib2to3 all 3.11.2-2 [76.2 kB] Get: 45 http://deb.debian.org/debian bookworm/main arm64 python3-distutils all 3.11.2-2 [131 kB] Get: 46 http://deb.debian.org/debian bookworm/main arm64 dh-python all 5.20230130 [104 kB] Get: 47 http://deb.debian.org/debian bookworm/main arm64 libblas3 arm64 3.11.0-2 [91.4 kB] Get: 48 http://deb.debian.org/debian bookworm/main arm64 libbrotli1 arm64 1.0.9-2+b6 [269 kB] Get: 49 http://deb.debian.org/debian bookworm/main arm64 libsasl2-modules-db arm64 2.1.28+dfsg-10 [20.8 kB] Get: 50 http://deb.debian.org/debian bookworm/main arm64 libsasl2-2 arm64 2.1.28+dfsg-10 [58.0 kB] Get: 51 http://deb.debian.org/debian bookworm/main arm64 libldap-2.5-0 arm64 2.5.13+dfsg-5 [171 kB] Get: 52 http://deb.debian.org/debian bookworm/main arm64 libnghttp2-14 arm64 1.52.0-1 [67.9 kB] Get: 53 http://deb.debian.org/debian bookworm/main arm64 libpsl5 arm64 0.21.2-1 [58.6 kB] Get: 54 http://deb.debian.org/debian bookworm/main arm64 librtmp1 arm64 2.4+20151223.gitfa8646d.1-2+b2 [59.4 kB] Get: 55 http://deb.debian.org/debian bookworm/main arm64 libssh2-1 arm64 1.10.0-3+b1 [172 kB] Get: 56 http://deb.debian.org/debian bookworm/main arm64 libcurl3-gnutls arm64 7.88.1-7 [356 kB] Get: 57 http://deb.debian.org/debian bookworm/main arm64 libdeflate0 arm64 1.14-1 [54.3 kB] Get: 58 http://deb.debian.org/debian bookworm/main arm64 libgfortran5 arm64 12.2.0-14 [340 kB] Get: 59 http://deb.debian.org/debian bookworm/main arm64 libhtscodecs2 arm64 1.3.0-4 [70.5 kB] Get: 60 http://deb.debian.org/debian bookworm/main arm64 libhts3 arm64 1.16+ds-3 [392 kB] Get: 61 http://deb.debian.org/debian bookworm/main arm64 liblapack3 arm64 3.11.0-2 [1664 kB] Get: 62 http://deb.debian.org/debian bookworm/main arm64 libncurses6 arm64 6.4-2 [94.0 kB] Get: 63 http://deb.debian.org/debian bookworm/main arm64 python3-all arm64 3.11.2-1 [1060 B] Get: 64 http://deb.debian.org/debian bookworm/main arm64 python3-attr all 22.2.0-1 [65.4 kB] Get: 65 http://deb.debian.org/debian bookworm/main arm64 python3-six all 1.16.0-4 [17.5 kB] Get: 66 http://deb.debian.org/debian bookworm/main arm64 python3-dateutil all 2.8.2-2 [78.3 kB] Get: 67 http://deb.debian.org/debian bookworm/main arm64 python3-execnet all 1.9.0-1 [41.5 kB] Get: 68 http://deb.debian.org/debian bookworm/main arm64 python3-sortedcontainers all 2.4.0-2 [31.9 kB] Get: 69 http://deb.debian.org/debian bookworm/main arm64 python3-hypothesis all 6.67.1-1 [270 kB] Get: 70 http://deb.debian.org/debian bookworm/main arm64 python3-iniconfig all 1.1.1-2 [6396 B] Get: 71 http://deb.debian.org/debian bookworm/main arm64 python3-more-itertools all 8.10.0-2 [53.0 kB] Get: 72 http://deb.debian.org/debian bookworm/main arm64 python3-natsort all 8.0.2-2 [39.0 kB] Get: 73 http://deb.debian.org/debian bookworm/main arm64 python3-pkg-resources all 66.1.1-1 [296 kB] Get: 74 http://deb.debian.org/debian bookworm/main arm64 python3-numpy arm64 1:1.24.2-1 [4751 kB] Get: 75 http://deb.debian.org/debian bookworm/main arm64 python3-ncls arm64 0.0.63-hotfix+ds-1+b3 [306 kB] Get: 76 http://deb.debian.org/debian bookworm/main arm64 python3-packaging all 23.0-1 [32.5 kB] Get: 77 http://deb.debian.org/debian bookworm/main arm64 python3-tz all 2022.7.1-1 [32.1 kB] Get: 78 http://deb.debian.org/debian bookworm/main arm64 python3-pandas-lib arm64 1.5.3+dfsg-2 [3048 kB] Get: 79 http://deb.debian.org/debian bookworm/main arm64 python3-pandas all 1.5.3+dfsg-2 [2885 kB] Get: 80 http://deb.debian.org/debian bookworm/main arm64 python3-pluggy all 1.0.0+repack-1 [19.7 kB] Get: 81 http://deb.debian.org/debian bookworm/main arm64 python3-py all 1.11.0-1 [89.2 kB] Get: 82 http://deb.debian.org/debian bookworm/main arm64 python3-tabulate all 0.8.9-1 [35.2 kB] Get: 83 http://deb.debian.org/debian bookworm/main arm64 python3-pyrle arm64 0.0.33-4+b2 [229 kB] Get: 84 http://deb.debian.org/debian bookworm/main arm64 python3-pytest all 7.2.1-2 [236 kB] Get: 85 http://deb.debian.org/debian bookworm/main arm64 python3-pytest-xdist all 3.1.0-1 [39.6 kB] Get: 86 http://deb.debian.org/debian bookworm/main arm64 python3-setuptools all 66.1.1-1 [521 kB] Get: 87 http://deb.debian.org/debian bookworm/main arm64 python3-sorted-nearest arm64 0.0.38+dfsg-1 [402 kB] Get: 88 http://deb.debian.org/debian bookworm/main arm64 samtools arm64 1.16.1-1 [580 kB] Fetched 43.9 MB in 2s (28.9 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.11-minimal:arm64. (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 ... 19616 files and directories currently installed.) Preparing to unpack .../libpython3.11-minimal_3.11.2-6_arm64.deb ... Unpacking libpython3.11-minimal:arm64 (3.11.2-6) ... Selecting previously unselected package libexpat1:arm64. Preparing to unpack .../libexpat1_2.5.0-1_arm64.deb ... Unpacking libexpat1:arm64 (2.5.0-1) ... Selecting previously unselected package python3.11-minimal. Preparing to unpack .../python3.11-minimal_3.11.2-6_arm64.deb ... Unpacking python3.11-minimal (3.11.2-6) ... Setting up libpython3.11-minimal:arm64 (3.11.2-6) ... Setting up libexpat1:arm64 (2.5.0-1) ... Setting up python3.11-minimal (3.11.2-6) ... 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 ... 19932 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.11.2-1_arm64.deb ... Unpacking python3-minimal (3.11.2-1) ... Selecting previously unselected package media-types. Preparing to unpack .../1-media-types_10.0.0_all.deb ... Unpacking media-types (10.0.0) ... Selecting previously unselected package readline-common. Preparing to unpack .../2-readline-common_8.2-1.3_all.deb ... Unpacking readline-common (8.2-1.3) ... Selecting previously unselected package libreadline8:arm64. Preparing to unpack .../3-libreadline8_8.2-1.3_arm64.deb ... Unpacking libreadline8:arm64 (8.2-1.3) ... Selecting previously unselected package libpython3.11-stdlib:arm64. Preparing to unpack .../4-libpython3.11-stdlib_3.11.2-6_arm64.deb ... Unpacking libpython3.11-stdlib:arm64 (3.11.2-6) ... Selecting previously unselected package python3.11. Preparing to unpack .../5-python3.11_3.11.2-6_arm64.deb ... Unpacking python3.11 (3.11.2-6) ... Selecting previously unselected package libpython3-stdlib:arm64. Preparing to unpack .../6-libpython3-stdlib_3.11.2-1_arm64.deb ... Unpacking libpython3-stdlib:arm64 (3.11.2-1) ... Setting up python3-minimal (3.11.2-1) ... 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 ... 20364 files and directories currently installed.) Preparing to unpack .../00-python3_3.11.2-1_arm64.deb ... Unpacking python3 (3.11.2-1) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../01-sensible-utils_0.0.17+nmu1_all.deb ... 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Setting up libbrotli1:arm64 (1.0.9-2+b6) ... Setting up libnghttp2-14:arm64 (1.52.0-1) ... Setting up libmagic1:arm64 (1:5.44-3) ... Setting up libdeflate0:arm64 (1.14-1) ... Setting up gettext-base (0.21-12) ... Setting up m4 (1.4.19-3) ... Setting up file (1:5.44-3) ... Setting up libsasl2-modules-db:arm64 (2.1.28+dfsg-10) ... Setting up autotools-dev (20220109.1) ... Setting up libblas3:arm64 (3.11.0-2) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/aarch64-linux-gnu/libblas.so.3 (libblas.so.3-aarch64-linux-gnu) in auto mode Setting up librtmp1:arm64 (2.4+20151223.gitfa8646d.1-2+b2) ... Setting up libncurses6:arm64 (6.4-2) ... Setting up autopoint (0.21-12) ... Setting up libsasl2-2:arm64 (2.1.28+dfsg-10) ... Setting up libgfortran5:arm64 (12.2.0-14) ... Setting up autoconf (2.71-3) ... Setting up sensible-utils (0.0.17+nmu1) ... Setting up libuchardet0:arm64 (0.0.7-1) ... Setting up libsub-override-perl (0.09-4) ... Setting up libssh2-1:arm64 (1.10.0-3+b1) ... Setting up libelf1:arm64 (0.188-2.1) ... Setting up readline-common (8.2-1.3) ... Setting up libxml2:arm64 (2.9.14+dfsg-1.1+b3) ... Setting up bedtools (2.30.0+dfsg-2) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.13.1-1) ... Setting up liblapack3:arm64 (3.11.0-2) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/aarch64-linux-gnu/liblapack.so.3 (liblapack.so.3-aarch64-linux-gnu) in auto mode Setting up gettext (0.21-12) ... Setting up libtool (2.4.7-5) ... Setting up libreadline8:arm64 (8.2-1.3) ... Setting up libldap-2.5-0:arm64 (2.5.13+dfsg-5) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up dwz (0.15-1) ... Setting up groff-base (1.22.4-10) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libpython3.11-stdlib:arm64 (3.11.2-6) ... Setting up libcurl3-gnutls:arm64 (7.88.1-7) ... Setting up man-db (2.11.2-2) ... Not building database; man-db/auto-update is not 'true'. Setting up libpython3-stdlib:arm64 (3.11.2-1) ... Setting up python3.11 (3.11.2-6) ... Setting up libhts3:arm64 (1.16+ds-3) ... Setting up debhelper (13.11.4) ... Setting up python3 (3.11.2-1) ... Setting up python3-sortedcontainers (2.4.0-2) ... Setting up python3-tz (2022.7.1-1) ... Setting up python3-natsort (8.0.2-2) ... Setting up samtools (1.16.1-1) ... Setting up python3-six (1.16.0-4) ... Setting up python3-packaging (23.0-1) ... Setting up cython3 (0.29.32-2+b1) ... Setting up python3-pluggy (1.0.0+repack-1) ... Setting up python3-dateutil (2.8.2-2) ... Setting up python3-execnet (1.9.0-1) ... Setting up python3-lib2to3 (3.11.2-2) ... Setting up python3-pkg-resources (66.1.1-1) ... Setting up python3-distutils (3.11.2-2) ... Setting up dh-python (5.20230130) ... Setting up python3-more-itertools (8.10.0-2) ... Setting up python3-iniconfig (1.1.1-2) ... Setting up python3-attr (22.2.0-1) ... Setting up python3-setuptools (66.1.1-1) ... Setting up python3-py (1.11.0-1) ... Setting up python3-pytest (7.2.1-2) ... Setting up python3-hypothesis (6.67.1-1) ... Setting up python3-tabulate (0.8.9-1) ... Setting up python3-all (3.11.2-1) ... Setting up python3-numpy (1:1.24.2-1) ... Setting up python3-ncls (0.0.63-hotfix+ds-1+b3) ... Setting up python3-pytest-xdist (3.1.0-1) ... Setting up python3-pandas-lib:arm64 (1.5.3+dfsg-2) ... Setting up python3-sorted-nearest (0.0.38+dfsg-1) ... Setting up python3-pandas (1.5.3+dfsg-2) ... Setting up python3-pyrle (0.0.33-4+b2) ... Processing triggers for libc-bin (2.36-8) ... 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 I: Building the package I: Running cd /build/pyranges-0.0.111+ds/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../pyranges_0.0.111+ds-4_source.changes dpkg-buildpackage: info: source package pyranges dpkg-buildpackage: info: source version 0.0.111+ds-4 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 dpkg-source: info: using options from pyranges-0.0.111+ds/debian/source/options: --extend-diff-ignore=^[^/]*[.]egg-info/ debian/rules clean dh clean --with python3 --buildsystem=pybuild dh_auto_clean -O--buildsystem=pybuild I: pybuild base:240: python3.11 setup.py clean 'build/bdist.linux-arm64' does not exist -- can't clean it 'build/scripts-3.11' does not exist -- can't clean it dh_autoreconf_clean -O--buildsystem=pybuild dh_clean -O--buildsystem=pybuild debian/rules binary dh binary --with python3 --buildsystem=pybuild dh_update_autotools_config -O--buildsystem=pybuild dh_autoreconf -O--buildsystem=pybuild dh_auto_configure -O--buildsystem=pybuild I: pybuild base:240: python3.11 setup.py config debian/rules override_dh_auto_build make[1]: Entering directory '/build/pyranges-0.0.111+ds' dh_auto_build I: pybuild base:240: /usr/bin/python3 setup.py build echo 'Generating corresponding files ...' Generating corresponding files ... cat debian/missing-sources/test_sorted.sam| samtools view -Sb - > tests/test_data/test_sorted.bam cat debian/missing-sources/control.sam| samtools view -Sb - > pyranges/example_data/control.bam samtools index tests/test_data/test_sorted.bam tests/test_data/test_sorted.bam.bai samtools index pyranges/example_data/control.bam pyranges/example_data/control.bam.bai make[1]: Leaving directory '/build/pyranges-0.0.111+ds' dh_auto_test -O--buildsystem=pybuild I: pybuild pybuild:307: cp -av /build/pyranges-0.0.111+ds/tests/*.bed /build/pyranges-0.0.111+ds/.pybuild/cpython3_3.11_pyranges/build/tests && cp -av /build/pyranges-0.0.111+ds/tests/test_data /build/pyranges-0.0.111+ds/.pybuild/cpython3_3.11_pyranges/build/tests && cp -av /build/pyranges-0.0.111+ds/tests/data /build/pyranges-0.0.111+ds/.pybuild/cpython3_3.11_pyranges/build/tests && cp -av /build/pyranges-0.0.111+ds/pyranges/example_data /build/pyranges-0.0.111+ds/.pybuild/cpython3_3.11_pyranges/build/pyranges '/build/pyranges-0.0.111+ds/tests/chip_10.bed' -> '/build/pyranges-0.0.111+ds/.pybuild/cpython3_3.11_pyranges/build/tests/chip_10.bed' '/build/pyranges-0.0.111+ds/tests/f1.bed' -> '/build/pyranges-0.0.111+ds/.pybuild/cpython3_3.11_pyranges/build/tests/f1.bed' '/build/pyranges-0.0.111+ds/tests/f2.bed' -> '/build/pyranges-0.0.111+ds/.pybuild/cpython3_3.11_pyranges/build/tests/f2.bed' '/build/pyranges-0.0.111+ds/tests/test_data' -> '/build/pyranges-0.0.111+ds/.pybuild/cpython3_3.11_pyranges/build/tests/test_data' '/build/pyranges-0.0.111+ds/tests/test_data/test_sorted.bam' -> '/build/pyranges-0.0.111+ds/.pybuild/cpython3_3.11_pyranges/build/tests/test_data/test_sorted.bam' '/build/pyranges-0.0.111+ds/tests/test_data/test_sorted.bam.bai' -> '/build/pyranges-0.0.111+ds/.pybuild/cpython3_3.11_pyranges/build/tests/test_data/test_sorted.bam.bai' '/build/pyranges-0.0.111+ds/tests/test_data/ensembl.gtf' -> '/build/pyranges-0.0.111+ds/.pybuild/cpython3_3.11_pyranges/build/tests/test_data/ensembl.gtf' '/build/pyranges-0.0.111+ds/tests/test_data/gencode.gff3' -> '/build/pyranges-0.0.111+ds/.pybuild/cpython3_3.11_pyranges/build/tests/test_data/gencode.gff3' '/build/pyranges-0.0.111+ds/tests/test_data/ucsc_df_to_parse.txt' -> '/build/pyranges-0.0.111+ds/.pybuild/cpython3_3.11_pyranges/build/tests/test_data/ucsc_df_to_parse.txt' '/build/pyranges-0.0.111+ds/tests/data' -> '/build/pyranges-0.0.111+ds/.pybuild/cpython3_3.11_pyranges/build/tests/data' '/build/pyranges-0.0.111+ds/tests/data/test_data.py' -> '/build/pyranges-0.0.111+ds/.pybuild/cpython3_3.11_pyranges/build/tests/data/test_data.py' '/build/pyranges-0.0.111+ds/pyranges/example_data/control.bam' -> '/build/pyranges-0.0.111+ds/.pybuild/cpython3_3.11_pyranges/build/pyranges/example_data/control.bam' '/build/pyranges-0.0.111+ds/pyranges/example_data/control.bam.bai' -> '/build/pyranges-0.0.111+ds/.pybuild/cpython3_3.11_pyranges/build/pyranges/example_data/control.bam.bai' '/build/pyranges-0.0.111+ds/pyranges/example_data/exons.bed' -> '/build/pyranges-0.0.111+ds/.pybuild/cpython3_3.11_pyranges/build/pyranges/example_data/exons.bed' '/build/pyranges-0.0.111+ds/pyranges/example_data/ensembl.gtf' -> '/build/pyranges-0.0.111+ds/.pybuild/cpython3_3.11_pyranges/build/pyranges/example_data/ensembl.gtf' '/build/pyranges-0.0.111+ds/pyranges/example_data/ucsc_human.bed.gz' -> '/build/pyranges-0.0.111+ds/.pybuild/cpython3_3.11_pyranges/build/pyranges/example_data/ucsc_human.bed.gz' '/build/pyranges-0.0.111+ds/pyranges/example_data/chipseq_background.bed' -> '/build/pyranges-0.0.111+ds/.pybuild/cpython3_3.11_pyranges/build/pyranges/example_data/chipseq_background.bed' '/build/pyranges-0.0.111+ds/pyranges/example_data/f2.bed' -> '/build/pyranges-0.0.111+ds/.pybuild/cpython3_3.11_pyranges/build/pyranges/example_data/f2.bed' '/build/pyranges-0.0.111+ds/pyranges/example_data/bw.bw' -> '/build/pyranges-0.0.111+ds/.pybuild/cpython3_3.11_pyranges/build/pyranges/example_data/bw.bw' '/build/pyranges-0.0.111+ds/pyranges/example_data/f1.bed' -> '/build/pyranges-0.0.111+ds/.pybuild/cpython3_3.11_pyranges/build/pyranges/example_data/f1.bed' '/build/pyranges-0.0.111+ds/pyranges/example_data/cpg.bed' -> '/build/pyranges-0.0.111+ds/.pybuild/cpython3_3.11_pyranges/build/pyranges/example_data/cpg.bed' '/build/pyranges-0.0.111+ds/pyranges/example_data/lamina.bed' -> '/build/pyranges-0.0.111+ds/.pybuild/cpython3_3.11_pyranges/build/pyranges/example_data/lamina.bed' '/build/pyranges-0.0.111+ds/pyranges/example_data/gencode_human.gtf.gz' -> '/build/pyranges-0.0.111+ds/.pybuild/cpython3_3.11_pyranges/build/pyranges/example_data/gencode_human.gtf.gz' '/build/pyranges-0.0.111+ds/pyranges/example_data/chipseq.bed' -> '/build/pyranges-0.0.111+ds/.pybuild/cpython3_3.11_pyranges/build/pyranges/example_data/chipseq.bed' '/build/pyranges-0.0.111+ds/pyranges/example_data/aorta.bed' -> '/build/pyranges-0.0.111+ds/.pybuild/cpython3_3.11_pyranges/build/pyranges/example_data/aorta.bed' '/build/pyranges-0.0.111+ds/pyranges/example_data/ensembl_human.gtf.gz' -> '/build/pyranges-0.0.111+ds/.pybuild/cpython3_3.11_pyranges/build/pyranges/example_data/ensembl_human.gtf.gz' '/build/pyranges-0.0.111+ds/pyranges/example_data/chromsizes.bed' -> '/build/pyranges-0.0.111+ds/.pybuild/cpython3_3.11_pyranges/build/pyranges/example_data/chromsizes.bed' '/build/pyranges-0.0.111+ds/pyranges/example_data/aorta2.bed' -> '/build/pyranges-0.0.111+ds/.pybuild/cpython3_3.11_pyranges/build/pyranges/example_data/aorta2.bed' I: pybuild base:240: cd /build/pyranges-0.0.111+ds/.pybuild/cpython3_3.11_pyranges/build; python3.11 -m pytest -n 8 ============================= test session starts ============================== platform linux -- Python 3.11.2, pytest-7.2.1, pluggy-1.0.0+repack rootdir: /build/pyranges-0.0.111+ds plugins: xdist-3.1.0, hypothesis-6.67.1 gw0 I / gw1 I / gw2 I / gw3 I / gw4 I / gw5 I / gw6 I / gw7 I gw0 [531] / gw1 [531] / gw2 [531] / gw3 [531] / gw4 [531] / gw5 [531] / gw6 [531] / gw7 [531] ........................................................................ [ 13%] ........................................................................ [ 27%] ........................................................................ [ 40%] ........................................................................ [ 54%] ........................................................................ [ 67%] ........................................................................ [ 81%] ........................................................................ [ 94%] ........................... [100%] =============================== warnings summary =============================== tests/conftest.py:83 /build/pyranges-0.0.111+ds/.pybuild/cpython3_3.11_pyranges/build/tests/conftest.py:83: DeprecationWarning: invalid escape sequence '\s' sep="\s+", .pybuild/cpython3_3.11_pyranges/build/tests/test_binary.py: 18000 warnings /build/pyranges-0.0.111+ds/.pybuild/cpython3_3.11_pyranges/build/tests/test_binary.py:349: FutureWarning: In a future version of pandas all arguments of DataFrame.drop except for the argument 'labels' will be keyword-only. bedtools_df = bedtools_df.drop("Chromosome2", 1) .pybuild/cpython3_3.11_pyranges/build/tests/test_binary.py: 18000 warnings /build/pyranges-0.0.111+ds/.pybuild/cpython3_3.11_pyranges/build/tests/test_binary.py:544: FutureWarning: In a future version of pandas all arguments of DataFrame.drop except for the argument 'labels' will be keyword-only. bedtools_df = bedtools_df.drop("Chromosome2", 1) .pybuild/cpython3_3.11_pyranges/build/tests/test_binary.py: 12096 warnings /build/pyranges-0.0.111+ds/.pybuild/cpython3_3.11_pyranges/build/pyranges/pyranges.py:2503: FutureWarning: is_monotonic is deprecated and will be removed in a future version. Use is_monotonic_increasing instead. if not result.__IX__.is_monotonic: .pybuild/cpython3_3.11_pyranges/build/tests/test_genomicfeatures.py: 119 warnings /build/pyranges-0.0.111+ds/.pybuild/cpython3_3.11_pyranges/build/tests/test_genomicfeatures.py:40: DeprecationWarning: In a future version, `df.iloc[:, i] = newvals` will attempt to set the values inplace instead of always setting a new array. To retain the old behavior, use either `df[df.columns[i]] = newvals` or, if columns are non-unique, `df.isetitem(i, newvals)` x.loc[:, "Start"] = x.Start.astype(int) .pybuild/cpython3_3.11_pyranges/build/tests/test_unary.py: 2000 warnings /build/pyranges-0.0.111+ds/.pybuild/cpython3_3.11_pyranges/build/tests/test_unary.py:119: FutureWarning: The squeeze argument has been deprecated and will be removed in a future version. Append .squeeze("columns") to the call to squeeze. bedtools_df = pd.read_csv( .pybuild/cpython3_3.11_pyranges/build/tests/test_unary.py: 2000 warnings /build/pyranges-0.0.111+ds/.pybuild/cpython3_3.11_pyranges/build/tests/test_unary.py:193: DeprecationWarning: In a future version, `df.iloc[:, i] = newvals` will attempt to set the values inplace instead of always setting a new array. To retain the old behavior, use either `df[df.columns[i]] = newvals` or, if columns are non-unique, `df.isetitem(i, newvals)` expected.loc[:, "Cluster"] = expected.Cluster.astype(np.int32) .pybuild/cpython3_3.11_pyranges/build/tests/test_unary.py: 1000 warnings /build/pyranges-0.0.111+ds/.pybuild/cpython3_3.11_pyranges/build/tests/test_unary.py:251: FutureWarning: The squeeze argument has been deprecated and will be removed in a future version. Append .squeeze("columns") to the call to squeeze. bedtools_df = pd.read_csv( .pybuild/cpython3_3.11_pyranges/build/tests/test_concat.py::test_concat_stranded_unstranded .pybuild/cpython3_3.11_pyranges/build/tests/test_concat.py::test_concat_unstranded_stranded /build/pyranges-0.0.111+ds/.pybuild/cpython3_3.11_pyranges/build/pyranges/methods/concat.py:47: DeprecationWarning: In a future version, `df.iloc[:, i] = newvals` will attempt to set the values inplace instead of always setting a new array. To retain the old behavior, use either `df[df.columns[i]] = newvals` or, if columns are non-unique, `df.isetitem(i, newvals)` v.loc[:, "Strand"] = type_v.cat.add_categories(["."]) .pybuild/cpython3_3.11_pyranges/build/tests/test_count_overlaps.py::test_strand_vs_strand_same .pybuild/cpython3_3.11_pyranges/build/tests/test_count_overlaps.py::test_strand_vs_strand_same .pybuild/cpython3_3.11_pyranges/build/tests/test_count_overlaps.py::test_strand_vs_strand_same .pybuild/cpython3_3.11_pyranges/build/tests/test_count_overlaps.py::test_strand_vs_strand_same .pybuild/cpython3_3.11_pyranges/build/tests/test_count_overlaps.py::test_strand_vs_strand_same .pybuild/cpython3_3.11_pyranges/build/tests/test_count_overlaps.py::test_strand_vs_strand_same /build/pyranges-0.0.111+ds/.pybuild/cpython3_3.11_pyranges/build/pyranges/multioverlap.py:155: DeprecationWarning: In a future version, `df.iloc[:, i] = newvals` will attempt to set the values inplace instead of always setting a new array. To retain the old behavior, use either `df[df.columns[i]] = newvals` or, if columns are non-unique, `df.isetitem(i, newvals)` df.loc[:, names] = df[names].astype(np.int32) -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html ============== 531 passed, 53224 warnings in 13695.50s (3:48:15) =============== create-stamp debian/debhelper-build-stamp dh_testroot -O--buildsystem=pybuild dh_prep -O--buildsystem=pybuild dh_auto_install --destdir=debian/python3-pyranges/ -O--buildsystem=pybuild I: pybuild base:240: /usr/bin/python3 setup.py install --root /build/pyranges-0.0.111+ds/debian/python3-pyranges /usr/lib/python3/dist-packages/setuptools/command/install.py:34: SetuptoolsDeprecationWarning: setup.py install is deprecated. Use build and pip and other standards-based tools. warnings.warn( debian/rules override_dh_install make[1]: Entering directory '/build/pyranges-0.0.111+ds' dh_install find debian/ -name *.bam* | xargs rm -rf find debian/ -name 'hi' | xargs rm -rf find debian/ -name '.hypothesis' | xargs rm -rf make[1]: Leaving directory '/build/pyranges-0.0.111+ds' dh_installdocs -O--buildsystem=pybuild dh_installchangelogs -O--buildsystem=pybuild dh_python3 -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_installdeb -O--buildsystem=pybuild dh_gencontrol -O--buildsystem=pybuild dh_md5sums -O--buildsystem=pybuild dh_builddeb -O--buildsystem=pybuild dpkg-deb: building package 'python3-pyranges' in '../python3-pyranges_0.0.111+ds-4_all.deb'. dpkg-genbuildinfo --build=binary -O../pyranges_0.0.111+ds-4_arm64.buildinfo dpkg-genchanges --build=binary -O../pyranges_0.0.111+ds-4_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-source: info: using options from pyranges-0.0.111+ds/debian/source/options: --extend-diff-ignore=^[^/]*[.]egg-info/ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration 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/20428 and its subdirectories I: Current time: Fri Apr 7 13:40:36 -12 2023 I: pbuilder-time-stamp: 1680918036