I: pbuilder: network access will be disabled during build I: Current time: Sun May 14 05:04:47 +14 2023 I: pbuilder-time-stamp: 1683990287 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 [pairtools_1.0.2-2.dsc] I: copying [./pairtools_1.0.2.orig.tar.gz] I: copying [./pairtools_1.0.2-2.debian.tar.xz] I: Extracting source gpgv: Signature made Tue Jan 3 09:23:53 2023 +14 gpgv: using EDDSA key A095B66EE09024BEE6A2F0722A27904BD7243EDA gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./pairtools_1.0.2-2.dsc: no acceptable signature found dpkg-source: info: extracting pairtools in pairtools-1.0.2 dpkg-source: info: unpacking pairtools_1.0.2.orig.tar.gz dpkg-source: info: unpacking pairtools_1.0.2-2.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying makefile dpkg-source: info: applying fix-spelling dpkg-source: info: applying tests-to-python3 dpkg-source: info: applying numpy-1.24.patch dpkg-source: info: applying fix-pysam-ftbfs.patch dpkg-source: info: applying do-not-run-coverage.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/14109/tmp/hooks/D01_modify_environment starting debug: Running on jtx1a. 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 '/bin/sh' -> '/bin/bash' lrwxrwxrwx 1 root root 9 May 14 05:05 /bin/sh -> /bin/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/14109/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/14109/tmp/hooks/D02_print_environment starting I: set BASH=/bin/sh BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath BASH_ALIASES=() BASH_ARGC=() BASH_ARGV=() BASH_CMDS=() BASH_LINENO=([0]="12" [1]="0") BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") BASH_VERSINFO=([0]="5" [1]="2" [2]="15" [3]="1" [4]="release" [5]="arm-unknown-linux-gnueabihf") BASH_VERSION='5.2.15(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=bookworm EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=arm HOST_ARCH=armhf IFS=' ' INVOCATION_ID=11848eda0ad34e3eb37650e452176baa 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=14109 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/r-b-build.Gh1IW9hB/pbuilderrc_J2lx --distribution bookworm --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.Gh1IW9hB/b2 --logfile b2/build.log --extrapackages usrmerge pairtools_1.0.2-2.dsc' SUDO_GID=114 SUDO_UID=108 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://10.0.0.15:3142/ I: uname -a Linux i-capture-the-hostname 5.10.0-22-arm64 #1 SMP Debian 5.10.178-3 (2023-04-22) aarch64 GNU/Linux I: ls -l /bin total 5072 -rwxr-xr-x 1 root root 838488 Apr 24 11:24 bash -rwxr-xr-x 3 root root 67144 Sep 19 2022 bunzip2 -rwxr-xr-x 3 root root 67144 Sep 19 2022 bzcat lrwxrwxrwx 1 root root 6 Sep 19 2022 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2225 Sep 19 2022 bzdiff lrwxrwxrwx 1 root root 6 Sep 19 2022 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4893 Nov 28 2021 bzexe lrwxrwxrwx 1 root root 6 Sep 19 2022 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3775 Sep 19 2022 bzgrep -rwxr-xr-x 3 root root 67144 Sep 19 2022 bzip2 -rwxr-xr-x 1 root root 67112 Sep 19 2022 bzip2recover lrwxrwxrwx 1 root root 6 Sep 19 2022 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Sep 19 2022 bzmore -rwxr-xr-x 1 root root 67632 Sep 21 2022 cat -rwxr-xr-x 1 root root 67676 Sep 21 2022 chgrp -rwxr-xr-x 1 root root 67644 Sep 21 2022 chmod -rwxr-xr-x 1 root root 67684 Sep 21 2022 chown -rwxr-xr-x 1 root root 133532 Sep 21 2022 cp -rwxr-xr-x 1 root root 132868 Jan 6 03:20 dash -rwxr-xr-x 1 root root 133220 Sep 21 2022 date -rwxr-xr-x 1 root root 67732 Sep 21 2022 dd -rwxr-xr-x 1 root root 68104 Sep 21 2022 df -rwxr-xr-x 1 root root 133632 Sep 21 2022 dir -rwxr-xr-x 1 root root 59128 Mar 23 23:02 dmesg lrwxrwxrwx 1 root root 8 Dec 20 03:33 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Dec 20 03:33 domainname -> hostname -rwxr-xr-x 1 root root 67560 Sep 21 2022 echo -rwxr-xr-x 1 root root 41 Jan 25 04:43 egrep -rwxr-xr-x 1 root root 67548 Sep 21 2022 false -rwxr-xr-x 1 root root 41 Jan 25 04:43 fgrep -rwxr-xr-x 1 root root 55748 Mar 23 23:02 findmnt -rwsr-xr-x 1 root root 26208 Mar 23 22:15 fusermount -rwxr-xr-x 1 root root 128608 Jan 25 04:43 grep -rwxr-xr-x 2 root root 2346 Apr 10 2022 gunzip -rwxr-xr-x 1 root root 6447 Apr 10 2022 gzexe -rwxr-xr-x 1 root root 64220 Apr 10 2022 gzip -rwxr-xr-x 1 root root 67032 Dec 20 03:33 hostname -rwxr-xr-x 1 root root 67720 Sep 21 2022 ln -rwxr-xr-x 1 root root 35132 Mar 23 23:51 login -rwxr-xr-x 1 root root 133632 Sep 21 2022 ls -rwxr-xr-x 1 root root 136808 Mar 23 23:02 lsblk -rwxr-xr-x 1 root root 67800 Sep 21 2022 mkdir -rwxr-xr-x 1 root root 67764 Sep 21 2022 mknod -rwxr-xr-x 1 root root 67596 Sep 21 2022 mktemp -rwxr-xr-x 1 root root 38504 Mar 23 23:02 more -rwsr-xr-x 1 root root 38496 Mar 23 23:02 mount -rwxr-xr-x 1 root root 9824 Mar 23 23:02 mountpoint -rwxr-xr-x 1 root root 133532 Sep 21 2022 mv lrwxrwxrwx 1 root root 8 Dec 20 03:33 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Apr 3 20:25 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 67608 Sep 21 2022 pwd lrwxrwxrwx 1 root root 4 Apr 24 11:24 rbash -> bash -rwxr-xr-x 1 root root 67600 Sep 21 2022 readlink -rwxr-xr-x 1 root root 67672 Sep 21 2022 rm -rwxr-xr-x 1 root root 67600 Sep 21 2022 rmdir -rwxr-xr-x 1 root root 67400 Nov 3 2022 run-parts -rwxr-xr-x 1 root root 133372 Jan 6 09:55 sed lrwxrwxrwx 1 root root 9 May 14 05:05 sh -> /bin/bash -rwxr-xr-x 1 root root 67584 Sep 21 2022 sleep -rwxr-xr-x 1 root root 67644 Sep 21 2022 stty -rwsr-xr-x 1 root root 50800 Mar 23 23:02 su -rwxr-xr-x 1 root root 67584 Sep 21 2022 sync -rwxr-xr-x 1 root root 336764 Apr 7 04:25 tar -rwxr-xr-x 1 root root 67144 Nov 3 2022 tempfile -rwxr-xr-x 1 root root 133224 Sep 21 2022 touch -rwxr-xr-x 1 root root 67548 Sep 21 2022 true -rwxr-xr-x 1 root root 9768 Mar 23 22:15 ulockmgr_server -rwsr-xr-x 1 root root 22108 Mar 23 23:02 umount -rwxr-xr-x 1 root root 67572 Sep 21 2022 uname -rwxr-xr-x 2 root root 2346 Apr 10 2022 uncompress -rwxr-xr-x 1 root root 133632 Sep 21 2022 vdir -rwxr-xr-x 1 root root 42608 Mar 23 23:02 wdctl lrwxrwxrwx 1 root root 8 Dec 20 03:33 ypdomainname -> hostname -rwxr-xr-x 1 root root 1984 Apr 10 2022 zcat -rwxr-xr-x 1 root root 1678 Apr 10 2022 zcmp -rwxr-xr-x 1 root root 6460 Apr 10 2022 zdiff -rwxr-xr-x 1 root root 29 Apr 10 2022 zegrep -rwxr-xr-x 1 root root 29 Apr 10 2022 zfgrep -rwxr-xr-x 1 root root 2081 Apr 10 2022 zforce -rwxr-xr-x 1 root root 8103 Apr 10 2022 zgrep -rwxr-xr-x 1 root root 2206 Apr 10 2022 zless -rwxr-xr-x 1 root root 1842 Apr 10 2022 zmore -rwxr-xr-x 1 root root 4577 Apr 10 2022 znew I: user script /srv/workspace/pbuilder/14109/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-compat (= 13), dh-python, python3-all-dev, cython3, python3-setuptools, python3-bioframe, python3-click, python3-exceptiongroup, python3-numpy, python3-pandas, python3-pysam (>= 0.20.0+ds-3~), python3-pytest, python3-scipy, libhts-dev, python3-yaml dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19329 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-all-dev; however: Package python3-all-dev is not installed. pbuilder-satisfydepends-dummy depends on cython3; however: Package cython3 is not installed. pbuilder-satisfydepends-dummy depends on python3-setuptools; however: Package python3-setuptools is not installed. pbuilder-satisfydepends-dummy depends on python3-bioframe; however: Package python3-bioframe is not installed. pbuilder-satisfydepends-dummy depends on python3-click; however: Package python3-click is not installed. pbuilder-satisfydepends-dummy depends on python3-exceptiongroup; however: Package python3-exceptiongroup is not installed. pbuilder-satisfydepends-dummy depends on python3-numpy; however: Package python3-numpy is not installed. pbuilder-satisfydepends-dummy depends on python3-pandas; however: Package python3-pandas is not installed. pbuilder-satisfydepends-dummy depends on python3-pysam (>= 0.20.0+ds-3~); however: Package python3-pysam is not installed. pbuilder-satisfydepends-dummy depends on python3-pytest; however: Package python3-pytest is not installed. pbuilder-satisfydepends-dummy depends on python3-scipy; however: Package python3-scipy is not installed. pbuilder-satisfydepends-dummy depends on libhts-dev; however: Package libhts-dev is not installed. pbuilder-satisfydepends-dummy depends on python3-yaml; however: Package python3-yaml 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} blt{a} bsdextrautils{a} ca-certificates{a} cython3{a} debhelper{a} dh-autoreconf{a} dh-python{a} dh-strip-nondeterminism{a} dwz{a} file{a} fontconfig-config{a} fonts-dejavu-core{a} fonts-lyx{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libblas3{a} libbrotli1{a} libbsd0{a} libcurl3-gnutls{a} libcurl4-gnutls-dev{a} libdebhelper-perl{a} libdeflate-dev{a} libdeflate0{a} libelf1{a} libexpat1{a} libexpat1-dev{a} libfile-stripnondeterminism-perl{a} libfontconfig1{a} libfreetype6{a} libfribidi0{a} libgfortran5{a} libglib2.0-0{a} libgraphite2-3{a} libharfbuzz0b{a} libhts-dev{a} libhts3{a} libhtscodecs2{a} libicu72{a} libimagequant0{a} libjbig0{a} libjpeg62-turbo{a} libjs-jquery{a} libjs-jquery-ui{a} libjs-sphinxdoc{a} libjs-underscore{a} liblapack3{a} liblbfgsb0{a} liblcms2-2{a} libldap-2.5-0{a} liblerc4{a} liblzma-dev{a} libmagic-mgc{a} libmagic1{a} libnghttp2-14{a} libopenjp2-7{a} libpipeline1{a} libpng16-16{a} libpsl5{a} libpython3-all-dev{a} libpython3-dev{a} libpython3-stdlib{a} libpython3.11{a} libpython3.11-dev{a} libpython3.11-minimal{a} libpython3.11-stdlib{a} libqhull-r8.0{a} libraqm0{a} libreadline8{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libssh2-1{a} libsub-override-perl{a} libtcl8.6{a} libtiff6{a} libtk8.6{a} libtool{a} libuchardet0{a} libwebp7{a} libwebpdemux2{a} libwebpmux3{a} libx11-6{a} libx11-data{a} libxau6{a} libxcb1{a} libxdmcp6{a} libxext6{a} libxft2{a} libxml2{a} libxrender1{a} libxslt1.1{a} libxss1{a} libyaml-0-2{a} m4{a} man-db{a} media-types{a} openssl{a} po-debconf{a} python-matplotlib-data{a} python3{a} python3-all{a} python3-all-dev{a} python3-appdirs{a} python3-attr{a} python3-bioframe{a} python3-brotli{a} python3-certifi{a} python3-chardet{a} python3-charset-normalizer{a} python3-click{a} python3-colorama{a} python3-contourpy{a} python3-cycler{a} python3-dateutil{a} python3-decorator{a} python3-dev{a} python3-distutils{a} python3-exceptiongroup{a} python3-fonttools{a} python3-fs{a} python3-idna{a} python3-iniconfig{a} python3-kiwisolver{a} python3-lib2to3{a} python3-lxml{a} python3-lz4{a} python3-matplotlib{a} python3-minimal{a} python3-more-itertools{a} python3-mpmath{a} python3-numpy{a} python3-packaging{a} python3-pandas{a} python3-pandas-lib{a} python3-pil{a} python3-pil.imagetk{a} python3-pkg-resources{a} python3-pluggy{a} python3-py{a} python3-pyparsing{a} python3-pysam{a} python3-pytest{a} python3-requests{a} python3-scipy{a} python3-setuptools{a} python3-six{a} python3-sympy{a} python3-tk{a} python3-tz{a} python3-ufolib2{a} python3-urllib3{a} python3-yaml{a} python3.11{a} python3.11-dev{a} python3.11-minimal{a} readline-common{a} sensible-utils{a} tk8.6-blt2.5{a} unicode-data{a} x11-common{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: curl isympy-common javascript-common libarchive-cpio-perl libglib2.0-data libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules lynx publicsuffix python3-bottleneck python3-bs4 python3-html5lib python3-jinja2 python3-numexpr python3-odf python3-olefile python3-openpyxl python3-pygments python3-tables shared-mime-info wget xdg-user-dirs 0 packages upgraded, 168 newly installed, 0 to remove and 0 not upgraded. Need to get 105 MB of archives. After unpacking 401 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bookworm/main armhf libpython3.11-minimal armhf 3.11.2-6 [798 kB] Get: 2 http://deb.debian.org/debian bookworm/main armhf libexpat1 armhf 2.5.0-1 [79.9 kB] Get: 3 http://deb.debian.org/debian bookworm/main armhf python3.11-minimal armhf 3.11.2-6 [1714 kB] Get: 4 http://deb.debian.org/debian bookworm/main armhf python3-minimal armhf 3.11.2-1+b1 [26.3 kB] Get: 5 http://deb.debian.org/debian bookworm/main armhf media-types all 10.0.0 [26.1 kB] Get: 6 http://deb.debian.org/debian bookworm/main armhf readline-common all 8.2-1.3 [69.0 kB] Get: 7 http://deb.debian.org/debian bookworm/main armhf libreadline8 armhf 8.2-1.3 [144 kB] Get: 8 http://deb.debian.org/debian bookworm/main armhf libpython3.11-stdlib armhf 3.11.2-6 [1678 kB] Get: 9 http://deb.debian.org/debian bookworm/main armhf python3.11 armhf 3.11.2-6 [572 kB] Get: 10 http://deb.debian.org/debian bookworm/main armhf libpython3-stdlib armhf 3.11.2-1+b1 [9296 B] Get: 11 http://deb.debian.org/debian bookworm/main armhf python3 armhf 3.11.2-1+b1 [26.3 kB] Get: 12 http://deb.debian.org/debian bookworm/main armhf sensible-utils all 0.0.17+nmu1 [19.0 kB] Get: 13 http://deb.debian.org/debian bookworm/main armhf openssl armhf 3.0.8-1 [1373 kB] Get: 14 http://deb.debian.org/debian bookworm/main armhf ca-certificates all 20230311 [153 kB] Get: 15 http://deb.debian.org/debian bookworm/main armhf libmagic-mgc armhf 1:5.44-3 [305 kB] Get: 16 http://deb.debian.org/debian bookworm/main armhf libmagic1 armhf 1:5.44-3 [96.5 kB] Get: 17 http://deb.debian.org/debian bookworm/main armhf file armhf 1:5.44-3 [41.6 kB] Get: 18 http://deb.debian.org/debian bookworm/main armhf gettext-base armhf 0.21-12 [157 kB] Get: 19 http://deb.debian.org/debian bookworm/main armhf libuchardet0 armhf 0.0.7-1 [65.0 kB] Get: 20 http://deb.debian.org/debian bookworm/main armhf groff-base armhf 1.22.4-10 [825 kB] Get: 21 http://deb.debian.org/debian bookworm/main armhf bsdextrautils armhf 2.38.1-5+b1 [78.6 kB] Get: 22 http://deb.debian.org/debian bookworm/main armhf libpipeline1 armhf 1.5.7-1 [33.6 kB] Get: 23 http://deb.debian.org/debian bookworm/main armhf man-db armhf 2.11.2-2 [1351 kB] Get: 24 http://deb.debian.org/debian bookworm/main armhf m4 armhf 1.4.19-3 [265 kB] Get: 25 http://deb.debian.org/debian bookworm/main armhf autoconf all 2.71-3 [332 kB] Get: 26 http://deb.debian.org/debian bookworm/main armhf autotools-dev all 20220109.1 [51.6 kB] Get: 27 http://deb.debian.org/debian bookworm/main armhf automake all 1:1.16.5-1.3 [823 kB] Get: 28 http://deb.debian.org/debian bookworm/main armhf autopoint all 0.21-12 [495 kB] Get: 29 http://deb.debian.org/debian bookworm/main armhf libtcl8.6 armhf 8.6.13+dfsg-2 [922 kB] Get: 30 http://deb.debian.org/debian bookworm/main armhf libbrotli1 armhf 1.0.9-2+b6 [271 kB] Get: 31 http://deb.debian.org/debian bookworm/main armhf libpng16-16 armhf 1.6.39-2 [260 kB] Get: 32 http://deb.debian.org/debian bookworm/main armhf libfreetype6 armhf 2.12.1+dfsg-5 [332 kB] Get: 33 http://deb.debian.org/debian bookworm/main armhf fonts-dejavu-core all 2.37-6 [1068 kB] Get: 34 http://deb.debian.org/debian bookworm/main armhf fontconfig-config armhf 2.14.1-4 [315 kB] Get: 35 http://deb.debian.org/debian bookworm/main armhf libfontconfig1 armhf 2.14.1-4 [368 kB] Get: 36 http://deb.debian.org/debian bookworm/main armhf libxau6 armhf 1:1.0.9-1 [19.0 kB] Get: 37 http://deb.debian.org/debian bookworm/main armhf libbsd0 armhf 0.11.7-2 [113 kB] Get: 38 http://deb.debian.org/debian bookworm/main armhf libxdmcp6 armhf 1:1.1.2-3 [24.9 kB] Get: 39 http://deb.debian.org/debian bookworm/main armhf libxcb1 armhf 1.15-1 [140 kB] Get: 40 http://deb.debian.org/debian bookworm/main armhf libx11-data all 2:1.8.4-2 [292 kB] Get: 41 http://deb.debian.org/debian bookworm/main armhf libx11-6 armhf 2:1.8.4-2 [695 kB] Get: 42 http://deb.debian.org/debian bookworm/main armhf libxrender1 armhf 1:0.9.10-1.1 [30.1 kB] Get: 43 http://deb.debian.org/debian bookworm/main armhf libxft2 armhf 2.3.6-1 [53.8 kB] Get: 44 http://deb.debian.org/debian bookworm/main armhf libxext6 armhf 2:1.3.4-1+b1 [47.8 kB] Get: 45 http://deb.debian.org/debian bookworm/main armhf x11-common all 1:7.7+23 [252 kB] Get: 46 http://deb.debian.org/debian bookworm/main armhf libxss1 armhf 1:1.2.3-1 [17.2 kB] Get: 47 http://deb.debian.org/debian bookworm/main armhf libtk8.6 armhf 8.6.13-2 [689 kB] Get: 48 http://deb.debian.org/debian bookworm/main armhf tk8.6-blt2.5 armhf 2.5.3+dfsg-4.1 [489 kB] Get: 49 http://deb.debian.org/debian bookworm/main armhf blt armhf 2.5.3+dfsg-4.1 [14.9 kB] Get: 50 http://deb.debian.org/debian bookworm/main armhf cython3 armhf 0.29.32-2+b1 [1230 kB] Get: 51 http://deb.debian.org/debian bookworm/main armhf libdebhelper-perl all 13.11.4 [81.2 kB] Get: 52 http://deb.debian.org/debian bookworm/main armhf libtool all 2.4.7-5 [517 kB] Get: 53 http://deb.debian.org/debian bookworm/main armhf dh-autoreconf all 20 [17.1 kB] Get: 54 http://deb.debian.org/debian bookworm/main armhf libarchive-zip-perl all 1.68-1 [104 kB] Get: 55 http://deb.debian.org/debian bookworm/main armhf libsub-override-perl all 0.09-4 [9304 B] Get: 56 http://deb.debian.org/debian bookworm/main armhf libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 57 http://deb.debian.org/debian bookworm/main armhf dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 58 http://deb.debian.org/debian bookworm/main armhf libelf1 armhf 0.188-2.1 [170 kB] Get: 59 http://deb.debian.org/debian bookworm/main armhf dwz armhf 0.15-1 [101 kB] Get: 60 http://deb.debian.org/debian bookworm/main armhf libicu72 armhf 72.1-3 [9048 kB] Get: 61 http://deb.debian.org/debian bookworm/main armhf libxml2 armhf 2.9.14+dfsg-1.2 [591 kB] Get: 62 http://deb.debian.org/debian bookworm/main armhf gettext armhf 0.21-12 [1229 kB] Get: 63 http://deb.debian.org/debian bookworm/main armhf intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 64 http://deb.debian.org/debian bookworm/main armhf po-debconf all 1.0.21+nmu1 [248 kB] Get: 65 http://deb.debian.org/debian bookworm/main armhf debhelper all 13.11.4 [942 kB] Get: 66 http://deb.debian.org/debian bookworm/main armhf python3-lib2to3 all 3.11.2-3 [76.3 kB] Get: 67 http://deb.debian.org/debian bookworm/main armhf python3-distutils all 3.11.2-3 [131 kB] Get: 68 http://deb.debian.org/debian bookworm/main armhf dh-python all 5.20230130 [104 kB] Get: 69 http://deb.debian.org/debian bookworm/main armhf fonts-lyx all 2.3.7-1 [186 kB] Get: 70 http://deb.debian.org/debian bookworm/main armhf libblas3 armhf 3.11.0-2 [105 kB] Get: 71 http://deb.debian.org/debian bookworm/main armhf libsasl2-modules-db armhf 2.1.28+dfsg-10 [19.0 kB] Get: 72 http://deb.debian.org/debian bookworm/main armhf libsasl2-2 armhf 2.1.28+dfsg-10 [52.3 kB] Get: 73 http://deb.debian.org/debian bookworm/main armhf libldap-2.5-0 armhf 2.5.13+dfsg-5 [158 kB] Get: 74 http://deb.debian.org/debian bookworm/main armhf libnghttp2-14 armhf 1.52.0-1 [60.8 kB] Get: 75 http://deb.debian.org/debian bookworm/main armhf libpsl5 armhf 0.21.2-1 [57.5 kB] Get: 76 http://deb.debian.org/debian bookworm/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2+b2 [55.2 kB] Get: 77 http://deb.debian.org/debian bookworm/main armhf libssh2-1 armhf 1.10.0-3+b1 [163 kB] Get: 78 http://deb.debian.org/debian bookworm/main armhf libcurl3-gnutls armhf 7.88.1-9 [343 kB] Get: 79 http://deb.debian.org/debian bookworm/main armhf libcurl4-gnutls-dev armhf 7.88.1-9 [448 kB] Get: 80 http://deb.debian.org/debian bookworm/main armhf libdeflate0 armhf 1.14-1 [52.2 kB] Get: 81 http://deb.debian.org/debian bookworm/main armhf libdeflate-dev armhf 1.14-1 [48.7 kB] Get: 82 http://deb.debian.org/debian bookworm/main armhf libexpat1-dev armhf 2.5.0-1 [134 kB] Get: 83 http://deb.debian.org/debian bookworm/main armhf libfribidi0 armhf 1.0.8-2.1 [63.1 kB] Get: 84 http://deb.debian.org/debian bookworm/main armhf libgfortran5 armhf 12.2.0-14 [246 kB] Get: 85 http://deb.debian.org/debian bookworm/main armhf libglib2.0-0 armhf 2.74.6-2 [1227 kB] Get: 86 http://deb.debian.org/debian bookworm/main armhf libgraphite2-3 armhf 1.3.14-1 [70.5 kB] Get: 87 http://deb.debian.org/debian bookworm/main armhf libharfbuzz0b armhf 6.0.0+dfsg-3 [1893 kB] Get: 88 http://deb.debian.org/debian bookworm/main armhf libhtscodecs2 armhf 1.3.0-4 [60.4 kB] Get: 89 http://deb.debian.org/debian bookworm/main armhf libhts3 armhf 1.16+ds-3 [375 kB] Get: 90 http://deb.debian.org/debian bookworm/main armhf liblzma-dev armhf 5.4.1-0.2 [248 kB] Get: 91 http://deb.debian.org/debian bookworm/main armhf zlib1g-dev armhf 1:1.2.13.dfsg-1 [902 kB] Get: 92 http://deb.debian.org/debian bookworm/main armhf libhts-dev armhf 1.16+ds-3 [1517 kB] Get: 93 http://deb.debian.org/debian bookworm/main armhf libimagequant0 armhf 2.17.0-1 [27.9 kB] Get: 94 http://deb.debian.org/debian bookworm/main armhf libjbig0 armhf 2.1-6.1 [27.1 kB] Get: 95 http://deb.debian.org/debian bookworm/main armhf libjpeg62-turbo armhf 1:2.1.5-2 [143 kB] Get: 96 http://deb.debian.org/debian bookworm/main armhf libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get: 97 http://deb.debian.org/debian bookworm/main armhf libjs-jquery-ui all 1.13.2+dfsg-1 [250 kB] Get: 98 http://deb.debian.org/debian bookworm/main armhf libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB] Get: 99 http://deb.debian.org/debian bookworm/main armhf libjs-sphinxdoc all 5.3.0-4 [130 kB] Get: 100 http://deb.debian.org/debian bookworm/main armhf liblapack3 armhf 3.11.0-2 [1724 kB] Get: 101 http://deb.debian.org/debian bookworm/main armhf liblbfgsb0 armhf 3.0+dfsg.4-1 [25.0 kB] Get: 102 http://deb.debian.org/debian bookworm/main armhf liblcms2-2 armhf 2.14-2 [125 kB] Get: 103 http://deb.debian.org/debian bookworm/main armhf liblerc4 armhf 4.0.0+ds-2 [137 kB] Get: 104 http://deb.debian.org/debian bookworm/main armhf libopenjp2-7 armhf 2.5.0-1+b1 [170 kB] Get: 105 http://deb.debian.org/debian bookworm/main armhf libpython3.11 armhf 3.11.2-6 [1710 kB] Get: 106 http://deb.debian.org/debian bookworm/main armhf libpython3.11-dev armhf 3.11.2-6 [3518 kB] Get: 107 http://deb.debian.org/debian bookworm/main armhf libpython3-dev armhf 3.11.2-1+b1 [9556 B] Get: 108 http://deb.debian.org/debian bookworm/main armhf libpython3-all-dev armhf 3.11.2-1+b1 [1068 B] Get: 109 http://deb.debian.org/debian bookworm/main armhf libqhull-r8.0 armhf 2020.2-5 [224 kB] Get: 110 http://deb.debian.org/debian bookworm/main armhf libraqm0 armhf 0.7.0-4.1 [9116 B] Get: 111 http://deb.debian.org/debian bookworm/main armhf libwebp7 armhf 1.2.4-0.1 [242 kB] Get: 112 http://deb.debian.org/debian bookworm/main armhf libtiff6 armhf 4.5.0-5 [295 kB] Get: 113 http://deb.debian.org/debian bookworm/main armhf libwebpdemux2 armhf 1.2.4-0.1 [98.2 kB] Get: 114 http://deb.debian.org/debian bookworm/main armhf libwebpmux3 armhf 1.2.4-0.1 [105 kB] Get: 115 http://deb.debian.org/debian bookworm/main armhf libxslt1.1 armhf 1.1.35-1 [223 kB] Get: 116 http://deb.debian.org/debian bookworm/main armhf libyaml-0-2 armhf 0.2.5-1 [46.8 kB] Get: 117 http://deb.debian.org/debian bookworm/main armhf python-matplotlib-data all 3.6.3-1 [2744 kB] Get: 118 http://deb.debian.org/debian bookworm/main armhf python3-all armhf 3.11.2-1+b1 [1060 B] Get: 119 http://deb.debian.org/debian bookworm/main armhf python3.11-dev armhf 3.11.2-6 [615 kB] Get: 120 http://deb.debian.org/debian bookworm/main armhf python3-dev armhf 3.11.2-1+b1 [26.2 kB] Get: 121 http://deb.debian.org/debian bookworm/main armhf python3-all-dev armhf 3.11.2-1+b1 [1076 B] Get: 122 http://deb.debian.org/debian bookworm/main armhf python3-appdirs all 1.4.4-3 [13.0 kB] Get: 123 http://deb.debian.org/debian bookworm/main armhf python3-attr all 22.2.0-1 [65.4 kB] Get: 124 http://deb.debian.org/debian bookworm/main armhf python3-six all 1.16.0-4 [17.5 kB] Get: 125 http://deb.debian.org/debian bookworm/main armhf python3-dateutil all 2.8.2-2 [78.3 kB] Get: 126 http://deb.debian.org/debian bookworm/main armhf python3-pil armhf 9.4.0-1.1+b1 [438 kB] Get: 127 http://deb.debian.org/debian bookworm/main armhf python3-tk armhf 3.11.2-3 [95.4 kB] Get: 128 http://deb.debian.org/debian bookworm/main armhf python3-pil.imagetk armhf 9.4.0-1.1+b1 [73.9 kB] Get: 129 http://deb.debian.org/debian bookworm/main armhf python3-pyparsing all 3.0.9-1 [138 kB] Get: 130 http://deb.debian.org/debian bookworm/main armhf python3-pkg-resources all 66.1.1-1 [296 kB] Get: 131 http://deb.debian.org/debian bookworm/main armhf python3-numpy armhf 1:1.24.2-1 [4165 kB] Get: 132 http://deb.debian.org/debian bookworm/main armhf python3-contourpy armhf 1.0.7-1+b1 [146 kB] Get: 133 http://deb.debian.org/debian bookworm/main armhf python3-cycler all 0.11.0-1 [8020 B] Get: 134 http://deb.debian.org/debian bookworm/main armhf python3-brotli armhf 1.0.9-2+b6 [274 kB] Get: 135 http://deb.debian.org/debian bookworm/main armhf python3-decorator all 5.1.1-3 [14.9 kB] Get: 136 http://deb.debian.org/debian bookworm/main armhf python3-scipy armhf 1.10.1-2 [13.8 MB] Get: 137 http://deb.debian.org/debian bookworm/main armhf python3-ufolib2 all 0.14.0+dfsg1-1 [34.3 kB] Get: 138 http://deb.debian.org/debian bookworm/main armhf python3-mpmath all 1.2.1-2 [418 kB] Get: 139 http://deb.debian.org/debian bookworm/main armhf python3-sympy all 1.11.1-1 [4358 kB] Get: 140 http://deb.debian.org/debian bookworm/main armhf python3-tz all 2022.7.1-3 [30.1 kB] Get: 141 http://deb.debian.org/debian bookworm/main armhf python3-fs all 2.4.16-2 [95.2 kB] Get: 142 http://deb.debian.org/debian bookworm/main armhf python3-lxml armhf 4.9.2-1+b1 [1082 kB] Get: 143 http://deb.debian.org/debian bookworm/main armhf python3-lz4 armhf 4.0.2+dfsg-1+b2 [23.3 kB] Get: 144 http://deb.debian.org/debian bookworm/main armhf unicode-data all 15.0.0-1 [7984 kB] Get: 145 http://deb.debian.org/debian bookworm/main armhf python3-fonttools armhf 4.38.0-1+b1 [989 kB] Get: 146 http://deb.debian.org/debian bookworm/main armhf python3-kiwisolver armhf 1.4.4-1+b1 [50.7 kB] Get: 147 http://deb.debian.org/debian bookworm/main armhf python3-packaging all 23.0-1 [32.5 kB] Get: 148 http://deb.debian.org/debian bookworm/main armhf python3-matplotlib armhf 3.6.3-1+b1 [6784 kB] Get: 149 http://deb.debian.org/debian bookworm/main armhf python3-pandas-lib armhf 1.5.3+dfsg-2 [3167 kB] Get: 150 http://deb.debian.org/debian bookworm/main armhf python3-pandas all 1.5.3+dfsg-2 [2885 kB] Get: 151 http://deb.debian.org/debian bookworm/main armhf python3-certifi all 2022.9.24-1 [153 kB] Get: 152 http://deb.debian.org/debian bookworm/main armhf python3-charset-normalizer all 3.0.1-2 [49.3 kB] Get: 153 http://deb.debian.org/debian bookworm/main armhf python3-idna all 3.3-1 [39.4 kB] Get: 154 http://deb.debian.org/debian bookworm/main armhf python3-urllib3 all 1.26.12-1 [117 kB] Get: 155 http://deb.debian.org/debian bookworm/main armhf python3-chardet all 5.1.0+dfsg-2 [110 kB] Get: 156 http://deb.debian.org/debian bookworm/main armhf python3-requests all 2.28.1+dfsg-1 [67.9 kB] Get: 157 http://deb.debian.org/debian bookworm/main armhf python3-bioframe all 0.3.3-2 [69.9 kB] Get: 158 http://deb.debian.org/debian bookworm/main armhf python3-colorama all 0.4.6-2 [36.8 kB] Get: 159 http://deb.debian.org/debian bookworm/main armhf python3-click all 8.1.3-2 [92.2 kB] Get: 160 http://deb.debian.org/debian bookworm/main armhf python3-exceptiongroup all 1.1.0-1 [17.4 kB] Get: 161 http://deb.debian.org/debian bookworm/main armhf python3-iniconfig all 1.1.1-2 [6396 B] Get: 162 http://deb.debian.org/debian bookworm/main armhf python3-more-itertools all 8.10.0-2 [53.0 kB] Get: 163 http://deb.debian.org/debian bookworm/main armhf python3-pluggy all 1.0.0+repack-1 [19.7 kB] Get: 164 http://deb.debian.org/debian bookworm/main armhf python3-py all 1.11.0-1 [89.2 kB] Get: 165 http://deb.debian.org/debian bookworm/main armhf python3-pysam armhf 0.20.0+ds-3+b1 [1484 kB] Get: 166 http://deb.debian.org/debian bookworm/main armhf python3-pytest all 7.2.1-2 [236 kB] Get: 167 http://deb.debian.org/debian bookworm/main armhf python3-setuptools all 66.1.1-1 [521 kB] Get: 168 http://deb.debian.org/debian bookworm/main armhf python3-yaml armhf 6.0-3+b2 [111 kB] Fetched 105 MB in 25s (4195 kB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.11-minimal: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 ... 19329 files and directories currently installed.) Preparing to unpack .../libpython3.11-minimal_3.11.2-6_armhf.deb ... Unpacking libpython3.11-minimal:armhf (3.11.2-6) ... Selecting previously unselected package libexpat1:armhf. Preparing to unpack .../libexpat1_2.5.0-1_armhf.deb ... Unpacking libexpat1:armhf (2.5.0-1) ... Selecting previously unselected package python3.11-minimal. Preparing to unpack .../python3.11-minimal_3.11.2-6_armhf.deb ... Unpacking python3.11-minimal (3.11.2-6) ... Setting up libpython3.11-minimal:armhf (3.11.2-6) ... Setting up libexpat1:armhf (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 ... 19645 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.11.2-1+b1_armhf.deb ... Unpacking python3-minimal (3.11.2-1+b1) ... 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:armhf. Preparing to unpack .../3-libreadline8_8.2-1.3_armhf.deb ... Unpacking libreadline8:armhf (8.2-1.3) ... Selecting previously unselected package libpython3.11-stdlib:armhf. Preparing to unpack .../4-libpython3.11-stdlib_3.11.2-6_armhf.deb ... Unpacking libpython3.11-stdlib:armhf (3.11.2-6) ... Selecting previously unselected package python3.11. Preparing to unpack .../5-python3.11_3.11.2-6_armhf.deb ... Unpacking python3.11 (3.11.2-6) ... Selecting previously unselected package libpython3-stdlib:armhf. Preparing to unpack .../6-libpython3-stdlib_3.11.2-1+b1_armhf.deb ... Unpacking libpython3-stdlib:armhf (3.11.2-1+b1) ... Setting up python3-minimal (3.11.2-1+b1) ... 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 ... 20079 files and directories currently installed.) Preparing to unpack .../000-python3_3.11.2-1+b1_armhf.deb ... Unpacking python3 (3.11.2-1+b1) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../001-sensible-utils_0.0.17+nmu1_all.deb ... Unpacking sensible-utils (0.0.17+nmu1) ... Selecting previously unselected package openssl. Preparing to unpack .../002-openssl_3.0.8-1_armhf.deb ... Unpacking openssl (3.0.8-1) ... Selecting previously unselected package ca-certificates. Preparing to unpack .../003-ca-certificates_20230311_all.deb ... Unpacking ca-certificates (20230311) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../004-libmagic-mgc_1%3a5.44-3_armhf.deb ... Unpacking libmagic-mgc (1:5.44-3) ... Selecting previously unselected package libmagic1:armhf. Preparing to unpack .../005-libmagic1_1%3a5.44-3_armhf.deb ... Unpacking libmagic1:armhf (1:5.44-3) ... Selecting previously unselected package file. Preparing to unpack .../006-file_1%3a5.44-3_armhf.deb ... Unpacking file (1:5.44-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../007-gettext-base_0.21-12_armhf.deb ... Unpacking gettext-base (0.21-12) ... Selecting previously unselected package libuchardet0:armhf. Preparing to unpack .../008-libuchardet0_0.0.7-1_armhf.deb ... Unpacking libuchardet0:armhf (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../009-groff-base_1.22.4-10_armhf.deb ... Unpacking groff-base (1.22.4-10) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../010-bsdextrautils_2.38.1-5+b1_armhf.deb ... Unpacking bsdextrautils (2.38.1-5+b1) ... Selecting previously unselected package libpipeline1:armhf. Preparing to unpack .../011-libpipeline1_1.5.7-1_armhf.deb ... Unpacking libpipeline1:armhf (1.5.7-1) ... Selecting previously unselected package man-db. Preparing to unpack .../012-man-db_2.11.2-2_armhf.deb ... Unpacking man-db (2.11.2-2) ... Selecting previously unselected package m4. Preparing to unpack .../013-m4_1.4.19-3_armhf.deb ... Unpacking m4 (1.4.19-3) ... Selecting previously unselected package autoconf. Preparing to unpack .../014-autoconf_2.71-3_all.deb ... Unpacking autoconf (2.71-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../015-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../016-automake_1%3a1.16.5-1.3_all.deb ... Unpacking automake (1:1.16.5-1.3) ... Selecting previously unselected package autopoint. Preparing to unpack .../017-autopoint_0.21-12_all.deb ... Unpacking autopoint (0.21-12) ... Selecting previously unselected package libtcl8.6:armhf. Preparing to unpack .../018-libtcl8.6_8.6.13+dfsg-2_armhf.deb ... Unpacking libtcl8.6:armhf (8.6.13+dfsg-2) ... Selecting previously unselected package libbrotli1:armhf. Preparing to unpack .../019-libbrotli1_1.0.9-2+b6_armhf.deb ... Unpacking libbrotli1:armhf (1.0.9-2+b6) ... Selecting previously unselected package libpng16-16:armhf. Preparing to unpack .../020-libpng16-16_1.6.39-2_armhf.deb ... Unpacking libpng16-16:armhf (1.6.39-2) ... Selecting previously unselected package libfreetype6:armhf. Preparing to unpack .../021-libfreetype6_2.12.1+dfsg-5_armhf.deb ... Unpacking libfreetype6:armhf (2.12.1+dfsg-5) ... Selecting previously unselected package fonts-dejavu-core. Preparing to unpack .../022-fonts-dejavu-core_2.37-6_all.deb ... Unpacking fonts-dejavu-core (2.37-6) ... Selecting previously unselected package fontconfig-config. Preparing to unpack .../023-fontconfig-config_2.14.1-4_armhf.deb ... Unpacking fontconfig-config (2.14.1-4) ... Selecting previously unselected package libfontconfig1:armhf. Preparing to unpack .../024-libfontconfig1_2.14.1-4_armhf.deb ... Unpacking libfontconfig1:armhf (2.14.1-4) ... Selecting previously unselected package libxau6:armhf. Preparing to unpack .../025-libxau6_1%3a1.0.9-1_armhf.deb ... Unpacking libxau6:armhf (1:1.0.9-1) ... 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Setting up libarchive-zip-perl (1.68-1) ... Setting up libyaml-0-2:armhf (0.2.5-1) ... Setting up libglib2.0-0:armhf (2.74.6-2) ... No schema files found: doing nothing. Setting up fonts-lyx (2.3.7-1) ... Setting up libdebhelper-perl (13.11.4) ... Setting up libbrotli1:armhf (1.0.9-2+b6) ... Setting up x11-common (1:7.7+23) ... invoke-rc.d: could not determine current runlevel Setting up X socket directories... /tmp/.X11-unix /tmp/.ICE-unix. Setting up libnghttp2-14:armhf (1.52.0-1) ... Setting up libmagic1:armhf (1:5.44-3) ... Setting up libdeflate0:armhf (1.14-1) ... Setting up gettext-base (0.21-12) ... Setting up m4 (1.4.19-3) ... Setting up libqhull-r8.0:armhf (2020.2-5) ... Setting up file (1:5.44-3) ... Setting up libjbig0:armhf (2.1-6.1) ... Setting up libsasl2-modules-db:armhf (2.1.28+dfsg-10) ... Setting up unicode-data (15.0.0-1) ... Setting up autotools-dev (20220109.1) ... Setting up libblas3:armhf (3.11.0-2) ... 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 libexpat1-dev:armhf (2.5.0-1) ... Setting up libjpeg62-turbo:armhf (1:2.1.5-2) ... Setting up libx11-data (2:1.8.4-2) ... Setting up librtmp1:armhf (2.4+20151223.gitfa8646d.1-2+b2) ... Setting up libfribidi0:armhf (1.0.8-2.1) ... Setting up libimagequant0:armhf (2.17.0-1) ... Setting up libpng16-16:armhf (1.6.39-2) ... Setting up libtcl8.6:armhf (8.6.13+dfsg-2) ... Setting up autopoint (0.21-12) ... Setting up fonts-dejavu-core (2.37-6) ... Setting up libsasl2-2:armhf (2.1.28+dfsg-10) ... Setting up libgfortran5:armhf (12.2.0-14) ... Setting up autoconf (2.71-3) ... Setting up libwebp7:armhf (1.2.4-0.1) ... Setting up liblzma-dev:armhf (5.4.1-0.2) ... Setting up zlib1g-dev:armhf (1:1.2.13.dfsg-1) ... Setting up sensible-utils (0.0.17+nmu1) ... Setting up libtiff6:armhf (4.5.0-5) ... Setting up libuchardet0:armhf (0.0.7-1) ... Setting up libopenjp2-7:armhf (2.5.0-1+b1) ... Setting up libsub-override-perl (0.09-4) ... Setting up libssh2-1:armhf (1.10.0-3+b1) ... Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Setting up python-matplotlib-data (3.6.3-1) ... Setting up openssl (3.0.8-1) ... Setting up libwebpmux3:armhf (1.2.4-0.1) ... Setting up libbsd0:armhf (0.11.7-2) ... Setting up libdeflate-dev:armhf (1.14-1) ... Setting up libelf1:armhf (0.188-2.1) ... Setting up readline-common (8.2-1.3) ... Setting up libxml2:armhf (2.9.14+dfsg-1.2) ... Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 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 libxdmcp6:armhf (1:1.1.2-3) ... Setting up liblapack3:armhf (3.11.0-2) ... 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 libxcb1:armhf (1.15-1) ... Setting up gettext (0.21-12) ... Setting up libtool (2.4.7-5) ... Setting up fontconfig-config (2.14.1-4) ... Setting up libwebpdemux2:armhf (1.2.4-0.1) ... Setting up libreadline8:armhf (8.2-1.3) ... Setting up libldap-2.5-0:armhf (2.5.13+dfsg-5) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up ca-certificates (20230311) ... Updating certificates in /etc/ssl/certs... 140 added, 0 removed; done. Setting up libjs-jquery-ui (1.13.2+dfsg-1) ... Setting up libfreetype6:armhf (2.12.1+dfsg-5) ... Setting up libjs-sphinxdoc (5.3.0-4) ... 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 libxslt1.1:armhf (1.1.35-1) ... Setting up libx11-6:armhf (2:1.8.4-2) ... Setting up libharfbuzz0b:armhf (6.0.0+dfsg-3) ... Setting up libfontconfig1:armhf (2.14.1-4) ... Setting up liblbfgsb0:armhf (3.0+dfsg.4-1) ... Setting up libxrender1:armhf (1:0.9.10-1.1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libpython3.11-stdlib:armhf (3.11.2-6) ... Setting up libxext6:armhf (2:1.3.4-1+b1) ... Setting up libcurl3-gnutls:armhf (7.88.1-9) ... Setting up libcurl4-gnutls-dev:armhf (7.88.1-9) ... Setting up man-db (2.11.2-2) ... Not building database; man-db/auto-update is not 'true'. Setting up libraqm0:armhf (0.7.0-4.1) ... Setting up libxss1:armhf (1:1.2.3-1) ... Setting up libpython3-stdlib:armhf (3.11.2-1+b1) ... Setting up python3.11 (3.11.2-6) ... Setting up libxft2:armhf (2.3.6-1) ... Setting up libhts3:armhf (1.16+ds-3) ... Setting up libpython3.11:armhf (3.11.2-6) ... Setting up libtk8.6:armhf (8.6.13-2) ... Setting up libhts-dev:armhf (1.16+ds-3) ... Setting up debhelper (13.11.4) ... Setting up python3 (3.11.2-1+b1) ... Setting up python3-tz (2022.7.1-3) ... Setting up python3-six (1.16.0-4) ... Setting up python3-decorator (5.1.1-3) ... Setting up python3-packaging (23.0-1) ... Setting up python3-pyparsing (3.0.9-1) ... Setting up python3-certifi (2022.9.24-1) ... Setting up libpython3.11-dev:armhf (3.11.2-6) ... Setting up python3-brotli (1.0.9-2+b6) ... Setting up python3-cycler (0.11.0-1) ... Setting up python3-kiwisolver (1.4.4-1+b1) ... Setting up python3-idna (3.3-1) ... Setting up cython3 (0.29.32-2+b1) ... Setting up python3-urllib3 (1.26.12-1) ... Setting up python3-pluggy (1.0.0+repack-1) ... Setting up python3-lxml:armhf (4.9.2-1+b1) ... Setting up python3-exceptiongroup (1.1.0-1) ... Setting up python3-dateutil (2.8.2-2) ... Setting up python3-mpmath (1.2.1-2) ... Setting up python3-lib2to3 (3.11.2-3) ... Setting up python3-appdirs (1.4.4-3) ... Setting up python3-pkg-resources (66.1.1-1) ... Setting up python3-distutils (3.11.2-3) ... 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-sympy (1.11.1-1) ... Setting up python3-attr (22.2.0-1) ... Setting up tk8.6-blt2.5 (2.5.3+dfsg-4.1) ... Setting up python3-pysam (0.20.0+ds-3+b1) ... Setting up libpython3-dev:armhf (3.11.2-1+b1) ... Setting up python3-setuptools (66.1.1-1) ... Setting up python3-py (1.11.0-1) ... Setting up python3-colorama (0.4.6-2) ... Setting up python3-lz4 (4.0.2+dfsg-1+b2) ... Setting up python3.11-dev (3.11.2-6) ... Setting up python3-charset-normalizer (3.0.1-2) ... Setting up python3-pytest (7.2.1-2) ... Setting up blt (2.5.3+dfsg-4.1) ... Setting up python3-all (3.11.2-1+b1) ... Setting up python3-yaml (6.0-3+b2) ... Setting up python3-tk:armhf (3.11.2-3) ... Setting up python3-click (8.1.3-2) ... Setting up python3-fs (2.4.16-2) ... Setting up python3-chardet (5.1.0+dfsg-2) ... Setting up libpython3-all-dev:armhf (3.11.2-1+b1) ... Setting up python3-dev (3.11.2-1+b1) ... Setting up python3-requests (2.28.1+dfsg-1) ... Setting up python3-numpy (1:1.24.2-1) ... Setting up python3-contourpy (1.0.7-1+b1) ... Setting up python3-all-dev (3.11.2-1+b1) ... Setting up python3-scipy (1.10.1-2) ... Setting up python3-pandas-lib:armhf (1.5.3+dfsg-2) ... Setting up python3-pandas (1.5.3+dfsg-2) ... Setting up python3-ufolib2 (0.14.0+dfsg1-1) ... Setting up python3-fonttools (4.38.0-1+b1) ... Setting up python3-pil.imagetk:armhf (9.4.0-1.1+b1) ... Setting up python3-pil:armhf (9.4.0-1.1+b1) ... Setting up python3-matplotlib (3.6.3-1+b1) ... Setting up python3-bioframe (0.3.3-2) ... Processing triggers for libc-bin (2.36-9) ... Processing triggers for ca-certificates (20230311) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. 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... usrmerge is already the newest version (35). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package I: user script /srv/workspace/pbuilder/14109/tmp/hooks/A99_set_merged_usr starting Re-configuring usrmerge... removed '/etc/unsupported-skip-usrmerge-conversion' The system has been successfully converted. I: user script /srv/workspace/pbuilder/14109/tmp/hooks/A99_set_merged_usr finished hostname: Name or service not known I: Running cd /build/pairtools-1.0.2/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../pairtools_1.0.2-2_source.changes dpkg-buildpackage: info: source package pairtools dpkg-buildpackage: info: source version 1.0.2-2 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Nilesh Patra dpkg-source --before-build . dpkg-buildpackage: info: host architecture armhf debian/rules clean dh clean --with python3,numpy3 --buildsystem=pybuild debian/rules override_dh_auto_clean make[1]: Entering directory '/build/pairtools-1.0.2' dh_auto_clean I: pybuild base:240: python3.11 setup.py clean /usr/lib/python3/dist-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /build/pairtools-1.0.2/pairtools/lib/dedup_cython.pyx tree = Parsing.p_module(s, pxd, full_module_name) /usr/lib/python3/dist-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /build/pairtools-1.0.2/pairtools/lib/parse_pysam.pxd tree = Parsing.p_module(s, pxd, full_module_name) /usr/lib/python3/dist-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /build/pairtools-1.0.2/pairtools/lib/regions.pyx tree = Parsing.p_module(s, pxd, full_module_name) Compiling /build/pairtools-1.0.2/pairtools/lib/dedup_cython.pyx because it changed. Compiling /build/pairtools-1.0.2/pairtools/lib/parse_pysam.pyx because it changed. Compiling /build/pairtools-1.0.2/pairtools/lib/regions.pyx because it changed. [1/3] Cythonizing /build/pairtools-1.0.2/pairtools/lib/dedup_cython.pyx [2/3] Cythonizing /build/pairtools-1.0.2/pairtools/lib/parse_pysam.pyx [3/3] Cythonizing /build/pairtools-1.0.2/pairtools/lib/regions.pyx running clean removing '/build/pairtools-1.0.2/.pybuild/cpython3_3.11/build' (and everything under it) 'build/bdist.linux-armhf' does not exist -- can't clean it 'build/scripts-3.11' does not exist -- can't clean it rm -f pairtools/lib/*.c pairtools/lib/regions.cpp make[1]: Leaving directory '/build/pairtools-1.0.2' dh_autoreconf_clean -O--buildsystem=pybuild dh_clean -O--buildsystem=pybuild debian/rules binary dh binary --with python3,numpy3 --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 /usr/lib/python3/dist-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /build/pairtools-1.0.2/pairtools/lib/dedup_cython.pyx tree = Parsing.p_module(s, pxd, full_module_name) /usr/lib/python3/dist-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /build/pairtools-1.0.2/pairtools/lib/parse_pysam.pxd tree = Parsing.p_module(s, pxd, full_module_name) /usr/lib/python3/dist-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /build/pairtools-1.0.2/pairtools/lib/regions.pyx tree = Parsing.p_module(s, pxd, full_module_name) Compiling /build/pairtools-1.0.2/pairtools/lib/dedup_cython.pyx because it changed. Compiling /build/pairtools-1.0.2/pairtools/lib/parse_pysam.pyx because it changed. Compiling /build/pairtools-1.0.2/pairtools/lib/regions.pyx because it changed. [1/3] Cythonizing /build/pairtools-1.0.2/pairtools/lib/dedup_cython.pyx [2/3] Cythonizing /build/pairtools-1.0.2/pairtools/lib/parse_pysam.pyx [3/3] Cythonizing /build/pairtools-1.0.2/pairtools/lib/regions.pyx running config dh_auto_build -O--buildsystem=pybuild I: pybuild base:240: /usr/bin/python3 setup.py build running build running build_py creating /build/pairtools-1.0.2/.pybuild/cpython3_3.11/build/pairtools copying pairtools/_logging.py -> /build/pairtools-1.0.2/.pybuild/cpython3_3.11/build/pairtools copying pairtools/__main__.py -> /build/pairtools-1.0.2/.pybuild/cpython3_3.11/build/pairtools copying pairtools/__init__.py -> /build/pairtools-1.0.2/.pybuild/cpython3_3.11/build/pairtools creating /build/pairtools-1.0.2/.pybuild/cpython3_3.11/build/pairtools/cli copying pairtools/cli/select.py -> /build/pairtools-1.0.2/.pybuild/cpython3_3.11/build/pairtools/cli copying pairtools/cli/phase.py -> /build/pairtools-1.0.2/.pybuild/cpython3_3.11/build/pairtools/cli copying pairtools/cli/restrict.py -> /build/pairtools-1.0.2/.pybuild/cpython3_3.11/build/pairtools/cli copying pairtools/cli/sort.py -> /build/pairtools-1.0.2/.pybuild/cpython3_3.11/build/pairtools/cli copying pairtools/cli/filterbycov.py -> /build/pairtools-1.0.2/.pybuild/cpython3_3.11/build/pairtools/cli copying pairtools/cli/header.py -> /build/pairtools-1.0.2/.pybuild/cpython3_3.11/build/pairtools/cli copying pairtools/cli/merge.py -> /build/pairtools-1.0.2/.pybuild/cpython3_3.11/build/pairtools/cli copying pairtools/cli/markasdup.py -> /build/pairtools-1.0.2/.pybuild/cpython3_3.11/build/pairtools/cli copying pairtools/cli/__init__.py -> /build/pairtools-1.0.2/.pybuild/cpython3_3.11/build/pairtools/cli copying pairtools/cli/dedup.py -> /build/pairtools-1.0.2/.pybuild/cpython3_3.11/build/pairtools/cli copying pairtools/cli/sample.py -> /build/pairtools-1.0.2/.pybuild/cpython3_3.11/build/pairtools/cli copying pairtools/cli/parse.py -> /build/pairtools-1.0.2/.pybuild/cpython3_3.11/build/pairtools/cli copying pairtools/cli/scaling.py -> /build/pairtools-1.0.2/.pybuild/cpython3_3.11/build/pairtools/cli copying pairtools/cli/parse2.py -> /build/pairtools-1.0.2/.pybuild/cpython3_3.11/build/pairtools/cli copying pairtools/cli/flip.py -> /build/pairtools-1.0.2/.pybuild/cpython3_3.11/build/pairtools/cli copying pairtools/cli/split.py -> /build/pairtools-1.0.2/.pybuild/cpython3_3.11/build/pairtools/cli copying pairtools/cli/stats.py -> /build/pairtools-1.0.2/.pybuild/cpython3_3.11/build/pairtools/cli creating /build/pairtools-1.0.2/.pybuild/cpython3_3.11/build/pairtools/lib copying pairtools/lib/select.py -> /build/pairtools-1.0.2/.pybuild/cpython3_3.11/build/pairtools/lib copying pairtools/lib/fileio.py -> /build/pairtools-1.0.2/.pybuild/cpython3_3.11/build/pairtools/lib copying pairtools/lib/phase.py -> /build/pairtools-1.0.2/.pybuild/cpython3_3.11/build/pairtools/lib copying pairtools/lib/restrict.py -> /build/pairtools-1.0.2/.pybuild/cpython3_3.11/build/pairtools/lib copying pairtools/lib/filterbycov.py -> /build/pairtools-1.0.2/.pybuild/cpython3_3.11/build/pairtools/lib copying pairtools/lib/__init__.py -> /build/pairtools-1.0.2/.pybuild/cpython3_3.11/build/pairtools/lib copying pairtools/lib/dedup.py -> /build/pairtools-1.0.2/.pybuild/cpython3_3.11/build/pairtools/lib copying pairtools/lib/pairsam_format.py -> /build/pairtools-1.0.2/.pybuild/cpython3_3.11/build/pairtools/lib copying pairtools/lib/parse.py -> /build/pairtools-1.0.2/.pybuild/cpython3_3.11/build/pairtools/lib copying pairtools/lib/headerops.py -> /build/pairtools-1.0.2/.pybuild/cpython3_3.11/build/pairtools/lib copying pairtools/lib/scaling.py -> /build/pairtools-1.0.2/.pybuild/cpython3_3.11/build/pairtools/lib copying pairtools/lib/stats.py -> /build/pairtools-1.0.2/.pybuild/cpython3_3.11/build/pairtools/lib running build_ext building 'pairtools.lib.dedup_cython' extension creating build creating build/temp.linux-armhf-cpython-311 creating build/temp.linux-armhf-cpython-311/build creating build/temp.linux-armhf-cpython-311/build/pairtools-1.0.2 creating build/temp.linux-armhf-cpython-311/build/pairtools-1.0.2/pairtools creating build/temp.linux-armhf-cpython-311/build/pairtools-1.0.2/pairtools/lib arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/pairtools-1.0.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/lib/python3/dist-packages/numpy/core/include -c /build/pairtools-1.0.2/pairtools/lib/dedup_cython.c -o build/temp.linux-armhf-cpython-311/build/pairtools-1.0.2/pairtools/lib/dedup_cython.o In file included from /usr/include/python3.11/numpy/ndarraytypes.h:1940, from /usr/include/python3.11/numpy/ndarrayobject.h:12, from /usr/include/python3.11/numpy/arrayobject.h:5, from /build/pairtools-1.0.2/pairtools/lib/dedup_cython.c:759: /usr/include/python3.11/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] 17 | #warning "Using deprecated NumPy API, disable it with " \ | ^~~~~~~ arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -g -O2 -ffile-prefix-map=/build/pairtools-1.0.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-cpython-311/build/pairtools-1.0.2/pairtools/lib/dedup_cython.o -L/usr/lib/arm-linux-gnueabihf -o /build/pairtools-1.0.2/.pybuild/cpython3_3.11/build/pairtools/lib/dedup_cython.cpython-311-arm-linux-gnueabihf.so building 'pairtools.lib.parse_pysam' extension arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/pairtools-1.0.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipairtools/lib -I/usr/lib/python3/dist-packages/pysam -I/usr/lib/python3/dist-packages/pysam/include/samtools -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/lib/python3/dist-packages/numpy/core/include -c /build/pairtools-1.0.2/pairtools/lib/parse_pysam.c -o build/temp.linux-armhf-cpython-311/build/pairtools-1.0.2/pairtools/lib/parse_pysam.o arm-linux-gnueabihf-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -g -O2 -ffile-prefix-map=/build/pairtools-1.0.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-cpython-311/build/pairtools-1.0.2/pairtools/lib/parse_pysam.o -L/usr/lib/arm-linux-gnueabihf -o /build/pairtools-1.0.2/.pybuild/cpython3_3.11/build/pairtools/lib/parse_pysam.cpython-311-arm-linux-gnueabihf.so /usr/lib/python3/dist-packages/pysam/libctabixproxies.cpython-311-arm-linux-gnueabihf.so /usr/lib/python3/dist-packages/pysam/libcfaidx.cpython-311-arm-linux-gnueabihf.so /usr/lib/python3/dist-packages/pysam/libcsamfile.cpython-311-arm-linux-gnueabihf.so /usr/lib/python3/dist-packages/pysam/libcvcf.cpython-311-arm-linux-gnueabihf.so /usr/lib/python3/dist-packages/pysam/libcbcf.cpython-311-arm-linux-gnueabihf.so /usr/lib/python3/dist-packages/pysam/libctabix.cpython-311-arm-linux-gnueabihf.so building 'pairtools.lib.regions' extension arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/pairtools-1.0.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/lib/python3/dist-packages/numpy/core/include -c /build/pairtools-1.0.2/pairtools/lib/regions.cpp -o build/temp.linux-armhf-cpython-311/build/pairtools-1.0.2/pairtools/lib/regions.o In file included from /usr/include/python3.11/numpy/ndarraytypes.h:1940, from /usr/include/python3.11/numpy/ndarrayobject.h:12, from /usr/include/python3.11/numpy/arrayobject.h:5, from /build/pairtools-1.0.2/pairtools/lib/regions.cpp:796: /usr/include/python3.11/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] 17 | #warning "Using deprecated NumPy API, disable it with " \ | ^~~~~~~ arm-linux-gnueabihf-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -g -O2 -ffile-prefix-map=/build/pairtools-1.0.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armhf-cpython-311/build/pairtools-1.0.2/pairtools/lib/regions.o -L/usr/lib/arm-linux-gnueabihf -o /build/pairtools-1.0.2/.pybuild/cpython3_3.11/build/pairtools/lib/regions.cpython-311-arm-linux-gnueabihf.so debian/rules override_dh_auto_test make[1]: Entering directory '/build/pairtools-1.0.2' dh_auto_test -- --system=custom --test-args="export CURPY={interpreter}; \ cd {build_dir} && {interpreter} -m pytest -v" I: pybuild base:240: export CURPY=python3.11; cd /build/pairtools-1.0.2/.pybuild/cpython3_3.11/build && python3.11 -m pytest -v ============================= test session starts ============================== platform linux -- Python 3.11.2, pytest-7.2.1, pluggy-1.0.0+repack -- /usr/bin/python3.11 cachedir: .pytest_cache rootdir: /build/pairtools-1.0.2, configfile: pytest.ini collecting ... collected 31 items tests/test_dedup.py::test_mock_pairsam PASSED [ 3%] tests/test_filterbycov.py::test_mock_pairs PASSED [ 6%] tests/test_flip.py::test_flip PASSED [ 9%] tests/test_header.py::test_generate PASSED [ 12%] tests/test_headerops.py::test_make_standard_header PASSED [ 16%] tests/test_headerops.py::test_samheaderops PASSED [ 19%] tests/test_headerops.py::test_merge_pairheaders PASSED [ 22%] tests/test_headerops.py::test_merge_different_pairheaders PASSED [ 25%] tests/test_headerops.py::test_force_merge_pairheaders PASSED [ 29%] tests/test_headerops.py::test_merge_samheaders PASSED [ 32%] tests/test_headerops.py::test_merge_headers PASSED [ 35%] tests/test_markasdup.py::test_mock_pairsam PASSED [ 38%] tests/test_merge.py::test_mock_pairsam PASSED [ 41%] tests/test_parse.py::test_python_version PASSED [ 45%] tests/test_parse.py::test_mock_pysam PASSED [ 48%] tests/test_parse.py::test_mock_pysam_parse_all PASSED [ 51%] tests/test_parse2.py::test_mock_pysam_parse2_read PASSED [ 54%] tests/test_parse2.py::test_mock_pysam_parse2_pair PASSED [ 58%] tests/test_restrict.py::test_restrict PASSED [ 61%] tests/test_scaling.py::test_scaling PASSED [ 64%] tests/test_select.py::test_preserve PASSED [ 67%] tests/test_select.py::test_equal PASSED [ 70%] tests/test_select.py::test_csv PASSED [ 74%] tests/test_select.py::test_wildcard PASSED [ 77%] tests/test_select.py::test_regex PASSED [ 80%] tests/test_select.py::test_chrom_subset PASSED [ 83%] tests/test_select.py::test_remove_columns PASSED [ 87%] tests/test_sort.py::test_mock_pairsam PASSED [ 90%] tests/test_split.py::test_split PASSED [ 93%] tests/test_stats.py::test_mock_pairsam PASSED [ 96%] tests/test_stats.py::test_merge_stats PASSED [100%] =============================== warnings summary =============================== pairtools/lib/fileio.py:2 /build/pairtools-1.0.2/.pybuild/cpython3_3.11/build/pairtools/lib/fileio.py:2: DeprecationWarning: 'pipes' is deprecated and slated for removal in Python 3.13 import pipes pairtools/lib/stats.py:928 /build/pairtools-1.0.2/.pybuild/cpython3_3.11/build/pairtools/lib/stats.py:928: DeprecationWarning: invalid escape sequence '\w' """Extract the name of the tile for each read name in the series -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html ================== 31 passed, 2 warnings in 113.11s (0:01:53) ================== make[1]: Leaving directory '/build/pairtools-1.0.2' create-stamp debian/debhelper-build-stamp dh_testroot -O--buildsystem=pybuild dh_prep -O--buildsystem=pybuild dh_auto_install -O--buildsystem=pybuild I: pybuild base:240: /usr/bin/python3 setup.py install --root /build/pairtools-1.0.2/debian/python3-pairtools running install /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( running build running build_py running build_ext running install_lib creating /build/pairtools-1.0.2/debian/python3-pairtools creating /build/pairtools-1.0.2/debian/python3-pairtools/usr creating /build/pairtools-1.0.2/debian/python3-pairtools/usr/lib creating /build/pairtools-1.0.2/debian/python3-pairtools/usr/lib/python3.11 creating /build/pairtools-1.0.2/debian/python3-pairtools/usr/lib/python3.11/dist-packages copying /build/pairtools-1.0.2/.pybuild/cpython3_3.11/build/mock.no_chromsizes.stats -> /build/pairtools-1.0.2/debian/python3-pairtools/usr/lib/python3.11/dist-packages copying /build/pairtools-1.0.2/.pybuild/cpython3_3.11/build/mock.stats -> /build/pairtools-1.0.2/debian/python3-pairtools/usr/lib/python3.11/dist-packages copying /build/pairtools-1.0.2/.pybuild/cpython3_3.11/build/mock.merged_no_chromsizes.stats -> /build/pairtools-1.0.2/debian/python3-pairtools/usr/lib/python3.11/dist-packages copying /build/pairtools-1.0.2/.pybuild/cpython3_3.11/build/mock.merged_chromsizes.stats -> /build/pairtools-1.0.2/debian/python3-pairtools/usr/lib/python3.11/dist-packages creating /build/pairtools-1.0.2/debian/python3-pairtools/usr/lib/python3.11/dist-packages/pairtools creating /build/pairtools-1.0.2/debian/python3-pairtools/usr/lib/python3.11/dist-packages/pairtools/cli copying /build/pairtools-1.0.2/.pybuild/cpython3_3.11/build/pairtools/cli/select.py -> /build/pairtools-1.0.2/debian/python3-pairtools/usr/lib/python3.11/dist-packages/pairtools/cli copying /build/pairtools-1.0.2/.pybuild/cpython3_3.11/build/pairtools/cli/phase.py -> /build/pairtools-1.0.2/debian/python3-pairtools/usr/lib/python3.11/dist-packages/pairtools/cli copying /build/pairtools-1.0.2/.pybuild/cpython3_3.11/build/pairtools/cli/restrict.py -> /build/pairtools-1.0.2/debian/python3-pairtools/usr/lib/python3.11/dist-packages/pairtools/cli copying /build/pairtools-1.0.2/.pybuild/cpython3_3.11/build/pairtools/cli/sort.py -> /build/pairtools-1.0.2/debian/python3-pairtools/usr/lib/python3.11/dist-packages/pairtools/cli copying /build/pairtools-1.0.2/.pybuild/cpython3_3.11/build/pairtools/cli/filterbycov.py -> /build/pairtools-1.0.2/debian/python3-pairtools/usr/lib/python3.11/dist-packages/pairtools/cli copying /build/pairtools-1.0.2/.pybuild/cpython3_3.11/build/pairtools/cli/header.py -> /build/pairtools-1.0.2/debian/python3-pairtools/usr/lib/python3.11/dist-packages/pairtools/cli copying /build/pairtools-1.0.2/.pybuild/cpython3_3.11/build/pairtools/cli/merge.py -> /build/pairtools-1.0.2/debian/python3-pairtools/usr/lib/python3.11/dist-packages/pairtools/cli copying /build/pairtools-1.0.2/.pybuild/cpython3_3.11/build/pairtools/cli/markasdup.py -> /build/pairtools-1.0.2/debian/python3-pairtools/usr/lib/python3.11/dist-packages/pairtools/cli copying /build/pairtools-1.0.2/.pybuild/cpython3_3.11/build/pairtools/cli/__init__.py -> /build/pairtools-1.0.2/debian/python3-pairtools/usr/lib/python3.11/dist-packages/pairtools/cli copying /build/pairtools-1.0.2/.pybuild/cpython3_3.11/build/pairtools/cli/dedup.py -> /build/pairtools-1.0.2/debian/python3-pairtools/usr/lib/python3.11/dist-packages/pairtools/cli copying /build/pairtools-1.0.2/.pybuild/cpython3_3.11/build/pairtools/cli/sample.py -> /build/pairtools-1.0.2/debian/python3-pairtools/usr/lib/python3.11/dist-packages/pairtools/cli copying /build/pairtools-1.0.2/.pybuild/cpython3_3.11/build/pairtools/cli/parse.py -> /build/pairtools-1.0.2/debian/python3-pairtools/usr/lib/python3.11/dist-packages/pairtools/cli copying /build/pairtools-1.0.2/.pybuild/cpython3_3.11/build/pairtools/cli/scaling.py -> /build/pairtools-1.0.2/debian/python3-pairtools/usr/lib/python3.11/dist-packages/pairtools/cli copying /build/pairtools-1.0.2/.pybuild/cpython3_3.11/build/pairtools/cli/parse2.py -> /build/pairtools-1.0.2/debian/python3-pairtools/usr/lib/python3.11/dist-packages/pairtools/cli copying /build/pairtools-1.0.2/.pybuild/cpython3_3.11/build/pairtools/cli/flip.py -> /build/pairtools-1.0.2/debian/python3-pairtools/usr/lib/python3.11/dist-packages/pairtools/cli copying /build/pairtools-1.0.2/.pybuild/cpython3_3.11/build/pairtools/cli/split.py -> /build/pairtools-1.0.2/debian/python3-pairtools/usr/lib/python3.11/dist-packages/pairtools/cli creating /build/pairtools-1.0.2/debian/python3-pairtools/usr/lib/python3.11/dist-packages/pairtools/cli/__pycache__ copying /build/pairtools-1.0.2/.pybuild/cpython3_3.11/build/pairtools/cli/__pycache__/restrict.cpython-311.pyc -> /build/pairtools-1.0.2/debian/python3-pairtools/usr/lib/python3.11/dist-packages/pairtools/cli/__pycache__ copying /build/pairtools-1.0.2/.pybuild/cpython3_3.11/build/pairtools/cli/__pycache__/dedup.cpython-311.pyc -> /build/pairtools-1.0.2/debian/python3-pairtools/usr/lib/python3.11/dist-packages/pairtools/cli/__pycache__ copying /build/pairtools-1.0.2/.pybuild/cpython3_3.11/build/pairtools/cli/__pycache__/merge.cpython-311.pyc -> /build/pairtools-1.0.2/debian/python3-pairtools/usr/lib/python3.11/dist-packages/pairtools/cli/__pycache__ copying /build/pairtools-1.0.2/.pybuild/cpython3_3.11/build/pairtools/cli/__pycache__/phase.cpython-311.pyc -> /build/pairtools-1.0.2/debian/python3-pairtools/usr/lib/python3.11/dist-packages/pairtools/cli/__pycache__ copying /build/pairtools-1.0.2/.pybuild/cpython3_3.11/build/pairtools/cli/__pycache__/select.cpython-311.pyc -> /build/pairtools-1.0.2/debian/python3-pairtools/usr/lib/python3.11/dist-packages/pairtools/cli/__pycache__ copying /build/pairtools-1.0.2/.pybuild/cpython3_3.11/build/pairtools/cli/__pycache__/parse.cpython-311.pyc -> /build/pairtools-1.0.2/debian/python3-pairtools/usr/lib/python3.11/dist-packages/pairtools/cli/__pycache__ copying /build/pairtools-1.0.2/.pybuild/cpython3_3.11/build/pairtools/cli/__pycache__/header.cpython-311.pyc -> /build/pairtools-1.0.2/debian/python3-pairtools/usr/lib/python3.11/dist-packages/pairtools/cli/__pycache__ copying /build/pairtools-1.0.2/.pybuild/cpython3_3.11/build/pairtools/cli/__pycache__/sample.cpython-311.pyc -> /build/pairtools-1.0.2/debian/python3-pairtools/usr/lib/python3.11/dist-packages/pairtools/cli/__pycache__ copying /build/pairtools-1.0.2/.pybuild/cpython3_3.11/build/pairtools/cli/__pycache__/flip.cpython-311.pyc -> /build/pairtools-1.0.2/debian/python3-pairtools/usr/lib/python3.11/dist-packages/pairtools/cli/__pycache__ copying /build/pairtools-1.0.2/.pybuild/cpython3_3.11/build/pairtools/cli/__pycache__/scaling.cpython-311.pyc -> /build/pairtools-1.0.2/debian/python3-pairtools/usr/lib/python3.11/dist-packages/pairtools/cli/__pycache__ copying /build/pairtools-1.0.2/.pybuild/cpython3_3.11/build/pairtools/cli/__pycache__/split.cpython-311.pyc -> /build/pairtools-1.0.2/debian/python3-pairtools/usr/lib/python3.11/dist-packages/pairtools/cli/__pycache__ copying /build/pairtools-1.0.2/.pybuild/cpython3_3.11/build/pairtools/cli/__pycache__/__init__.cpython-311.pyc -> /build/pairtools-1.0.2/debian/python3-pairtools/usr/lib/python3.11/dist-packages/pairtools/cli/__pycache__ copying /build/pairtools-1.0.2/.pybuild/cpython3_3.11/build/pairtools/cli/__pycache__/parse2.cpython-311.pyc -> /build/pairtools-1.0.2/debian/python3-pairtools/usr/lib/python3.11/dist-packages/pairtools/cli/__pycache__ copying /build/pairtools-1.0.2/.pybuild/cpython3_3.11/build/pairtools/cli/__pycache__/markasdup.cpython-311.pyc -> /build/pairtools-1.0.2/debian/python3-pairtools/usr/lib/python3.11/dist-packages/pairtools/cli/__pycache__ copying /build/pairtools-1.0.2/.pybuild/cpython3_3.11/build/pairtools/cli/__pycache__/stats.cpython-311.pyc -> /build/pairtools-1.0.2/debian/python3-pairtools/usr/lib/python3.11/dist-packages/pairtools/cli/__pycache__ copying /build/pairtools-1.0.2/.pybuild/cpython3_3.11/build/pairtools/cli/__pycache__/filterbycov.cpython-311.pyc -> /build/pairtools-1.0.2/debian/python3-pairtools/usr/lib/python3.11/dist-packages/pairtools/cli/__pycache__ copying /build/pairtools-1.0.2/.pybuild/cpython3_3.11/build/pairtools/cli/__pycache__/sort.cpython-311.pyc -> /build/pairtools-1.0.2/debian/python3-pairtools/usr/lib/python3.11/dist-packages/pairtools/cli/__pycache__ copying /build/pairtools-1.0.2/.pybuild/cpython3_3.11/build/pairtools/cli/stats.py -> /build/pairtools-1.0.2/debian/python3-pairtools/usr/lib/python3.11/dist-packages/pairtools/cli creating /build/pairtools-1.0.2/debian/python3-pairtools/usr/lib/python3.11/dist-packages/pairtools/lib copying /build/pairtools-1.0.2/.pybuild/cpython3_3.11/build/pairtools/lib/select.py -> /build/pairtools-1.0.2/debian/python3-pairtools/usr/lib/python3.11/dist-packages/pairtools/lib copying /build/pairtools-1.0.2/.pybuild/cpython3_3.11/build/pairtools/lib/fileio.py -> /build/pairtools-1.0.2/debian/python3-pairtools/usr/lib/python3.11/dist-packages/pairtools/lib copying /build/pairtools-1.0.2/.pybuild/cpython3_3.11/build/pairtools/lib/phase.py -> /build/pairtools-1.0.2/debian/python3-pairtools/usr/lib/python3.11/dist-packages/pairtools/lib copying /build/pairtools-1.0.2/.pybuild/cpython3_3.11/build/pairtools/lib/dedup_cython.cpython-311-arm-linux-gnueabihf.so -> /build/pairtools-1.0.2/debian/python3-pairtools/usr/lib/python3.11/dist-packages/pairtools/lib copying /build/pairtools-1.0.2/.pybuild/cpython3_3.11/build/pairtools/lib/restrict.py -> /build/pairtools-1.0.2/debian/python3-pairtools/usr/lib/python3.11/dist-packages/pairtools/lib copying /build/pairtools-1.0.2/.pybuild/cpython3_3.11/build/pairtools/lib/regions.cpython-311-arm-linux-gnueabihf.so -> /build/pairtools-1.0.2/debian/python3-pairtools/usr/lib/python3.11/dist-packages/pairtools/lib copying /build/pairtools-1.0.2/.pybuild/cpython3_3.11/build/pairtools/lib/filterbycov.py -> /build/pairtools-1.0.2/debian/python3-pairtools/usr/lib/python3.11/dist-packages/pairtools/lib copying /build/pairtools-1.0.2/.pybuild/cpython3_3.11/build/pairtools/lib/parse_pysam.cpython-311-arm-linux-gnueabihf.so -> /build/pairtools-1.0.2/debian/python3-pairtools/usr/lib/python3.11/dist-packages/pairtools/lib copying /build/pairtools-1.0.2/.pybuild/cpython3_3.11/build/pairtools/lib/__init__.py -> /build/pairtools-1.0.2/debian/python3-pairtools/usr/lib/python3.11/dist-packages/pairtools/lib copying /build/pairtools-1.0.2/.pybuild/cpython3_3.11/build/pairtools/lib/dedup.py -> /build/pairtools-1.0.2/debian/python3-pairtools/usr/lib/python3.11/dist-packages/pairtools/lib copying /build/pairtools-1.0.2/.pybuild/cpython3_3.11/build/pairtools/lib/pairsam_format.py -> /build/pairtools-1.0.2/debian/python3-pairtools/usr/lib/python3.11/dist-packages/pairtools/lib copying /build/pairtools-1.0.2/.pybuild/cpython3_3.11/build/pairtools/lib/parse.py -> /build/pairtools-1.0.2/debian/python3-pairtools/usr/lib/python3.11/dist-packages/pairtools/lib copying /build/pairtools-1.0.2/.pybuild/cpython3_3.11/build/pairtools/lib/headerops.py -> /build/pairtools-1.0.2/debian/python3-pairtools/usr/lib/python3.11/dist-packages/pairtools/lib copying /build/pairtools-1.0.2/.pybuild/cpython3_3.11/build/pairtools/lib/scaling.py -> /build/pairtools-1.0.2/debian/python3-pairtools/usr/lib/python3.11/dist-packages/pairtools/lib creating /build/pairtools-1.0.2/debian/python3-pairtools/usr/lib/python3.11/dist-packages/pairtools/lib/__pycache__ copying /build/pairtools-1.0.2/.pybuild/cpython3_3.11/build/pairtools/lib/__pycache__/restrict.cpython-311.pyc -> /build/pairtools-1.0.2/debian/python3-pairtools/usr/lib/python3.11/dist-packages/pairtools/lib/__pycache__ copying /build/pairtools-1.0.2/.pybuild/cpython3_3.11/build/pairtools/lib/__pycache__/dedup.cpython-311.pyc -> /build/pairtools-1.0.2/debian/python3-pairtools/usr/lib/python3.11/dist-packages/pairtools/lib/__pycache__ copying /build/pairtools-1.0.2/.pybuild/cpython3_3.11/build/pairtools/lib/__pycache__/headerops.cpython-311.pyc -> /build/pairtools-1.0.2/debian/python3-pairtools/usr/lib/python3.11/dist-packages/pairtools/lib/__pycache__ copying /build/pairtools-1.0.2/.pybuild/cpython3_3.11/build/pairtools/lib/__pycache__/phase.cpython-311.pyc -> /build/pairtools-1.0.2/debian/python3-pairtools/usr/lib/python3.11/dist-packages/pairtools/lib/__pycache__ copying /build/pairtools-1.0.2/.pybuild/cpython3_3.11/build/pairtools/lib/__pycache__/fileio.cpython-311.pyc -> /build/pairtools-1.0.2/debian/python3-pairtools/usr/lib/python3.11/dist-packages/pairtools/lib/__pycache__ copying /build/pairtools-1.0.2/.pybuild/cpython3_3.11/build/pairtools/lib/__pycache__/pairsam_format.cpython-311.pyc -> /build/pairtools-1.0.2/debian/python3-pairtools/usr/lib/python3.11/dist-packages/pairtools/lib/__pycache__ copying /build/pairtools-1.0.2/.pybuild/cpython3_3.11/build/pairtools/lib/__pycache__/select.cpython-311.pyc -> /build/pairtools-1.0.2/debian/python3-pairtools/usr/lib/python3.11/dist-packages/pairtools/lib/__pycache__ copying /build/pairtools-1.0.2/.pybuild/cpython3_3.11/build/pairtools/lib/__pycache__/parse.cpython-311.pyc -> /build/pairtools-1.0.2/debian/python3-pairtools/usr/lib/python3.11/dist-packages/pairtools/lib/__pycache__ copying /build/pairtools-1.0.2/.pybuild/cpython3_3.11/build/pairtools/lib/__pycache__/scaling.cpython-311.pyc -> /build/pairtools-1.0.2/debian/python3-pairtools/usr/lib/python3.11/dist-packages/pairtools/lib/__pycache__ copying /build/pairtools-1.0.2/.pybuild/cpython3_3.11/build/pairtools/lib/__pycache__/__init__.cpython-311.pyc -> /build/pairtools-1.0.2/debian/python3-pairtools/usr/lib/python3.11/dist-packages/pairtools/lib/__pycache__ copying /build/pairtools-1.0.2/.pybuild/cpython3_3.11/build/pairtools/lib/__pycache__/stats.cpython-311.pyc -> /build/pairtools-1.0.2/debian/python3-pairtools/usr/lib/python3.11/dist-packages/pairtools/lib/__pycache__ copying /build/pairtools-1.0.2/.pybuild/cpython3_3.11/build/pairtools/lib/__pycache__/filterbycov.cpython-311.pyc -> /build/pairtools-1.0.2/debian/python3-pairtools/usr/lib/python3.11/dist-packages/pairtools/lib/__pycache__ copying /build/pairtools-1.0.2/.pybuild/cpython3_3.11/build/pairtools/lib/stats.py -> /build/pairtools-1.0.2/debian/python3-pairtools/usr/lib/python3.11/dist-packages/pairtools/lib copying /build/pairtools-1.0.2/.pybuild/cpython3_3.11/build/pairtools/_logging.py -> /build/pairtools-1.0.2/debian/python3-pairtools/usr/lib/python3.11/dist-packages/pairtools copying /build/pairtools-1.0.2/.pybuild/cpython3_3.11/build/pairtools/__main__.py -> /build/pairtools-1.0.2/debian/python3-pairtools/usr/lib/python3.11/dist-packages/pairtools copying /build/pairtools-1.0.2/.pybuild/cpython3_3.11/build/pairtools/__init__.py -> /build/pairtools-1.0.2/debian/python3-pairtools/usr/lib/python3.11/dist-packages/pairtools creating /build/pairtools-1.0.2/debian/python3-pairtools/usr/lib/python3.11/dist-packages/pairtools/__pycache__ copying /build/pairtools-1.0.2/.pybuild/cpython3_3.11/build/pairtools/__pycache__/__main__.cpython-311.pyc -> /build/pairtools-1.0.2/debian/python3-pairtools/usr/lib/python3.11/dist-packages/pairtools/__pycache__ copying /build/pairtools-1.0.2/.pybuild/cpython3_3.11/build/pairtools/__pycache__/_logging.cpython-311.pyc -> /build/pairtools-1.0.2/debian/python3-pairtools/usr/lib/python3.11/dist-packages/pairtools/__pycache__ copying /build/pairtools-1.0.2/.pybuild/cpython3_3.11/build/pairtools/__pycache__/__init__.cpython-311.pyc -> /build/pairtools-1.0.2/debian/python3-pairtools/usr/lib/python3.11/dist-packages/pairtools/__pycache__ copying /build/pairtools-1.0.2/.pybuild/cpython3_3.11/build/mock.merged_mixed.stats -> /build/pairtools-1.0.2/debian/python3-pairtools/usr/lib/python3.11/dist-packages byte-compiling /build/pairtools-1.0.2/debian/python3-pairtools/usr/lib/python3.11/dist-packages/pairtools/cli/select.py to select.cpython-311.pyc byte-compiling /build/pairtools-1.0.2/debian/python3-pairtools/usr/lib/python3.11/dist-packages/pairtools/cli/phase.py to phase.cpython-311.pyc byte-compiling /build/pairtools-1.0.2/debian/python3-pairtools/usr/lib/python3.11/dist-packages/pairtools/cli/restrict.py to restrict.cpython-311.pyc byte-compiling /build/pairtools-1.0.2/debian/python3-pairtools/usr/lib/python3.11/dist-packages/pairtools/cli/sort.py to sort.cpython-311.pyc byte-compiling /build/pairtools-1.0.2/debian/python3-pairtools/usr/lib/python3.11/dist-packages/pairtools/cli/filterbycov.py to filterbycov.cpython-311.pyc byte-compiling /build/pairtools-1.0.2/debian/python3-pairtools/usr/lib/python3.11/dist-packages/pairtools/cli/header.py to header.cpython-311.pyc byte-compiling /build/pairtools-1.0.2/debian/python3-pairtools/usr/lib/python3.11/dist-packages/pairtools/cli/merge.py to merge.cpython-311.pyc byte-compiling /build/pairtools-1.0.2/debian/python3-pairtools/usr/lib/python3.11/dist-packages/pairtools/cli/markasdup.py to markasdup.cpython-311.pyc byte-compiling /build/pairtools-1.0.2/debian/python3-pairtools/usr/lib/python3.11/dist-packages/pairtools/cli/__init__.py to __init__.cpython-311.pyc byte-compiling /build/pairtools-1.0.2/debian/python3-pairtools/usr/lib/python3.11/dist-packages/pairtools/cli/dedup.py to dedup.cpython-311.pyc byte-compiling /build/pairtools-1.0.2/debian/python3-pairtools/usr/lib/python3.11/dist-packages/pairtools/cli/sample.py to sample.cpython-311.pyc byte-compiling /build/pairtools-1.0.2/debian/python3-pairtools/usr/lib/python3.11/dist-packages/pairtools/cli/parse.py to parse.cpython-311.pyc byte-compiling /build/pairtools-1.0.2/debian/python3-pairtools/usr/lib/python3.11/dist-packages/pairtools/cli/scaling.py to scaling.cpython-311.pyc byte-compiling /build/pairtools-1.0.2/debian/python3-pairtools/usr/lib/python3.11/dist-packages/pairtools/cli/parse2.py to parse2.cpython-311.pyc byte-compiling /build/pairtools-1.0.2/debian/python3-pairtools/usr/lib/python3.11/dist-packages/pairtools/cli/flip.py to flip.cpython-311.pyc byte-compiling /build/pairtools-1.0.2/debian/python3-pairtools/usr/lib/python3.11/dist-packages/pairtools/cli/split.py to split.cpython-311.pyc byte-compiling /build/pairtools-1.0.2/debian/python3-pairtools/usr/lib/python3.11/dist-packages/pairtools/cli/stats.py to stats.cpython-311.pyc byte-compiling /build/pairtools-1.0.2/debian/python3-pairtools/usr/lib/python3.11/dist-packages/pairtools/lib/select.py to select.cpython-311.pyc byte-compiling /build/pairtools-1.0.2/debian/python3-pairtools/usr/lib/python3.11/dist-packages/pairtools/lib/fileio.py to fileio.cpython-311.pyc byte-compiling /build/pairtools-1.0.2/debian/python3-pairtools/usr/lib/python3.11/dist-packages/pairtools/lib/phase.py to phase.cpython-311.pyc byte-compiling /build/pairtools-1.0.2/debian/python3-pairtools/usr/lib/python3.11/dist-packages/pairtools/lib/restrict.py to restrict.cpython-311.pyc byte-compiling /build/pairtools-1.0.2/debian/python3-pairtools/usr/lib/python3.11/dist-packages/pairtools/lib/filterbycov.py to filterbycov.cpython-311.pyc byte-compiling /build/pairtools-1.0.2/debian/python3-pairtools/usr/lib/python3.11/dist-packages/pairtools/lib/__init__.py to __init__.cpython-311.pyc byte-compiling /build/pairtools-1.0.2/debian/python3-pairtools/usr/lib/python3.11/dist-packages/pairtools/lib/dedup.py to dedup.cpython-311.pyc byte-compiling /build/pairtools-1.0.2/debian/python3-pairtools/usr/lib/python3.11/dist-packages/pairtools/lib/pairsam_format.py to pairsam_format.cpython-311.pyc byte-compiling /build/pairtools-1.0.2/debian/python3-pairtools/usr/lib/python3.11/dist-packages/pairtools/lib/parse.py to parse.cpython-311.pyc byte-compiling /build/pairtools-1.0.2/debian/python3-pairtools/usr/lib/python3.11/dist-packages/pairtools/lib/headerops.py to headerops.cpython-311.pyc byte-compiling /build/pairtools-1.0.2/debian/python3-pairtools/usr/lib/python3.11/dist-packages/pairtools/lib/scaling.py to scaling.cpython-311.pyc byte-compiling /build/pairtools-1.0.2/debian/python3-pairtools/usr/lib/python3.11/dist-packages/pairtools/lib/stats.py to stats.cpython-311.pyc byte-compiling /build/pairtools-1.0.2/debian/python3-pairtools/usr/lib/python3.11/dist-packages/pairtools/_logging.py to _logging.cpython-311.pyc byte-compiling /build/pairtools-1.0.2/debian/python3-pairtools/usr/lib/python3.11/dist-packages/pairtools/__main__.py to __main__.cpython-311.pyc byte-compiling /build/pairtools-1.0.2/debian/python3-pairtools/usr/lib/python3.11/dist-packages/pairtools/__init__.py to __init__.cpython-311.pyc running install_egg_info running egg_info creating pairtools.egg-info writing pairtools.egg-info/PKG-INFO writing dependency_links to pairtools.egg-info/dependency_links.txt writing entry points to pairtools.egg-info/entry_points.txt writing requirements to pairtools.egg-info/requires.txt writing top-level names to pairtools.egg-info/top_level.txt writing manifest file 'pairtools.egg-info/SOURCES.txt' reading manifest file 'pairtools.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' no previously-included directories found matching 'doc/_build' no previously-included directories found matching 'doc/_templates' warning: no previously-included files matching '__pycache__/*' found anywhere in distribution warning: no previously-included files matching '*.so' found anywhere in distribution warning: no previously-included files matching '*.pyd' found anywhere in distribution warning: no previously-included files matching '*.pyc' found anywhere in distribution warning: no previously-included files matching '.git*' found anywhere in distribution warning: no previously-included files matching '.deps/*' found anywhere in distribution warning: no previously-included files matching '.DS_Store' found anywhere in distribution adding license file 'LICENSE' writing manifest file 'pairtools.egg-info/SOURCES.txt' Copying pairtools.egg-info to /build/pairtools-1.0.2/debian/python3-pairtools/usr/lib/python3.11/dist-packages/pairtools-1.0.2.egg-info Skipping SOURCES.txt running install_scripts Installing pairtools script to /build/pairtools-1.0.2/debian/python3-pairtools/usr/bin debian/rules execute_after_dh_auto_install make[1]: Entering directory '/build/pairtools-1.0.2' find debian/ -name '*.stats' -delete make[1]: Leaving directory '/build/pairtools-1.0.2' dh_install -O--buildsystem=pybuild 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_dwz -a -O--buildsystem=pybuild dh_strip -a -O--buildsystem=pybuild dh_makeshlibs -a -O--buildsystem=pybuild dh_shlibdeps -a -O--buildsystem=pybuild dh_installdeb -O--buildsystem=pybuild dh_numpy3 -O--buildsystem=pybuild dh_gencontrol -O--buildsystem=pybuild dpkg-gencontrol: warning: Depends field of package python3-pairtools-examples: substitution variable ${shlibs:Depends} used, but is not defined dpkg-gencontrol: warning: package python3-pairtools-examples: substitution variable ${python3:Depends} unused, but is defined dh_md5sums -O--buildsystem=pybuild dh_builddeb -O--buildsystem=pybuild dpkg-deb: building package 'python3-pairtools-examples' in '../python3-pairtools-examples_1.0.2-2_armhf.deb'. dpkg-deb: building package 'python3-pairtools-dbgsym' in '../python3-pairtools-dbgsym_1.0.2-2_armhf.deb'. dpkg-deb: building package 'python3-pairtools' in '../python3-pairtools_1.0.2-2_armhf.deb'. dpkg-genbuildinfo --build=binary -O../pairtools_1.0.2-2_armhf.buildinfo dpkg-genchanges --build=binary -O../pairtools_1.0.2-2_armhf.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: user script /srv/workspace/pbuilder/14109/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/14109/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/14109 and its subdirectories I: Current time: Sun May 14 05:13:16 +14 2023 I: pbuilder-time-stamp: 1683990796