I: pbuilder: network access will be disabled during build I: Current time: Mon Sep 15 06:22:47 +14 2025 I: pbuilder-time-stamp: 1757866967 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-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 [cnvkit_0.9.10-2.dsc] I: copying [./cnvkit_0.9.10.orig.tar.gz] I: copying [./cnvkit_0.9.10-2.debian.tar.xz] I: Extracting source gpgv: Signature made Mon Apr 8 08:42:55 2024 gpgv: using RSA key 724D609337113C710550D7473C26763F6C67E6E2 gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./cnvkit_0.9.10-2.dsc: no acceptable signature found dpkg-source: info: extracting cnvkit in cnvkit-0.9.10 dpkg-source: info: unpacking cnvkit_0.9.10.orig.tar.gz dpkg-source: info: unpacking cnvkit_0.9.10-2.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying python3compat.patch dpkg-source: info: applying spelling dpkg-source: info: applying controldir dpkg-source: info: applying ignore-warnings-in-tests.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/1227257/tmp/hooks/D01_modify_environment starting debug: Running on codethink03-arm64. 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 Sep 14 16:23 /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/1227257/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/1227257/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]="21" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu") BASH_VERSION='5.2.21(1)-release' BUILDDIR=/build/reproducible-path BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=arm64 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' DIRSTACK=() DISTRIBUTION=unstable EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=aarch64 HOST_ARCH=arm64 IFS=' ' INVOCATION_ID=e75b5a1360574067baf9b7965321e767 LANG=C LANGUAGE=nl_BE:nl LC_ALL=C MACHTYPE=aarch64-unknown-linux-gnu MAIL=/var/mail/root OPTERR=1 OPTIND=1 OSTYPE=linux-gnu 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=1227257 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.aQTTpheG/pbuilderrc_EHHp --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.aQTTpheG/b2 --logfile b2/build.log cnvkit_0.9.10-2.dsc' SUDO_GID=109 SUDO_UID=104 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://192.168.101.4:3128 I: uname -a Linux i-capture-the-hostname 6.1.0-23-cloud-arm64 #1 SMP Debian 6.1.99-1 (2024-07-15) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 4 2024 /bin -> usr/bin I: user script /srv/workspace/pbuilder/1227257/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-sequence-python3, python3-all, python3-setuptools, pybuild-plugin-pyproject, python3-pytest, python3-pyfaidx, python3-biopython, python3-pandas, python3-numpy, python3-pysam, python3-scipy, python3-matplotlib, python3-pomegranate, r-bioc-dnacopy, poppler-utils dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19840 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-sequence-python3; however: Package dh-sequence-python3 is not installed. pbuilder-satisfydepends-dummy depends on python3-all; however: Package python3-all is not installed. pbuilder-satisfydepends-dummy depends on python3-setuptools; however: Package python3-setuptools is not installed. pbuilder-satisfydepends-dummy depends on pybuild-plugin-pyproject; however: Package pybuild-plugin-pyproject is not installed. pbuilder-satisfydepends-dummy depends on python3-pytest; however: Package python3-pytest is not installed. pbuilder-satisfydepends-dummy depends on python3-pyfaidx; however: Package python3-pyfaidx is not installed. pbuilder-satisfydepends-dummy depends on python3-biopython; however: Package python3-biopython is not installed. pbuilder-satisfydepends-dummy depends on python3-pandas; however: Package python3-pandas is not installed. pbuilder-satisfydepends-dummy depends on python3-numpy; however: Package python3-numpy is not installed. pbuilder-satisfydepends-dummy depends on python3-pysam; however: Package python3-pysam is not installed. pbuilder-satisfydepends-dummy depends on python3-scipy; however: Package python3-scipy is not installed. pbuilder-satisfydepends-dummy depends on python3-matplotlib; however: Package python3-matplotlib is not installed. pbuilder-satisfydepends-dummy depends on python3-pomegranate; however: Package python3-pomegranate is not installed. pbuilder-satisfydepends-dummy depends on r-bioc-dnacopy; however: Package r-bioc-dnacopy is not installed. pbuilder-satisfydepends-dummy depends on poppler-utils; however: Package poppler-utils 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} debhelper{a} dh-autoreconf{a} dh-python{a} dh-strip-nondeterminism{a} dwz{a} file{a} fontconfig{a} fontconfig-config{a} fonts-dejavu-core{a} fonts-dejavu-mono{a} fonts-lyx{a} fonts-urw-base35{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libblas3{a} libbrotli1{a} libcairo2{a} libcom-err2{a} libcurl3t64-gnutls{a} libcurl4t64{a} libdatrie1{a} libdebhelper-perl{a} libdeflate0{a} libelf1t64{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libfontconfig1{a} libfontenc1{a} libfreetype6{a} libfribidi0{a} libgfortran5{a} libglib2.0-0t64{a} libgraphite2-3{a} libgssapi-krb5-2{a} libharfbuzz0b{a} libhts3t64{a} libhtscodecs2{a} libice6{a} libicu72{a} libimagequant0{a} libjbig0{a} libjpeg62-turbo{a} libjs-jquery{a} libjs-jquery-ui{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} liblapack3{a} liblbfgsb0{a} liblcms2-2{a} libldap-2.5-0{a} liblerc4{a} libmagic-mgc{a} libmagic1t64{a} libnghttp2-14{a} libnghttp3-9{a} libngtcp2-16{a} libngtcp2-crypto-gnutls8{a} libnsl2{a} libnspr4{a} libnss3{a} libopenjp2-7{a} libpango-1.0-0{a} libpangocairo-1.0-0{a} libpangoft2-1.0-0{a} libpaper-utils{a} libpaper1{a} libpipeline1{a} libpixman-1-0{a} libpng16-16t64{a} libpoppler134{a} libproc2-0{a} libpsl5t64{a} libpython3-stdlib{a} libpython3.12-minimal{a} libpython3.12-stdlib{a} libqhull-r8.0{a} libraqm0{a} libreadline8t64{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsharpyuv0{a} libsm6{a} libssh2-1t64{a} libtcl8.6{a} libthai-data{a} libthai0{a} libtiff6{a} libtirpc-common{a} libtirpc3t64{a} libtk8.6{a} libtool{a} libuchardet0{a} libwebp7{a} libwebpdemux2{a} libwebpmux3{a} libx11-6{a} libx11-data{a} libxau6{a} libxcb-render0{a} libxcb-shm0{a} libxcb1{a} libxdmcp6{a} libxext6{a} libxft2{a} libxml2{a} libxrender1{a} libxslt1.1{a} libxss1{a} libxt6t64{a} libyaml-0-2{a} m4{a} man-db{a} media-types{a} netbase{a} openssl{a} po-debconf{a} poppler-utils{a} procps{a} pybuild-plugin-pyproject{a} python-matplotlib-data{a} python3{a} python3-all{a} python3-appdirs{a} python3-attr{a} python3-biopython{a} python3-brotli{a} python3-build{a} python3-cairo{a} python3-chardet{a} python3-contourpy{a} python3-cycler{a} python3-dateutil{a} python3-decorator{a} python3-fonttools{a} python3-freetype{a} python3-fs{a} python3-importlib-metadata{a} python3-iniconfig{a} python3-installer{a} python3-joblib{a} python3-kiwisolver{a} python3-lxml{a} python3-lz4{a} python3-matplotlib{a} python3-minimal{a} python3-mpmath{a} python3-networkx{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-pomegranate{a} python3-pyfaidx{a} python3-pyparsing{a} python3-pyproject-hooks{a} python3-pysam{a} python3-pytest{a} python3-reportlab{a} python3-rlpycairo{a} python3-scipy{a} python3-setuptools{a} python3-six{a} python3-sympy{a} python3-tk{a} python3-toml{a} python3-tz{a} python3-ufolib2{a} python3-wheel{a} python3-yaml{a} python3-zipp{a} python3.12{a} python3.12-minimal{a} r-base-core{a} r-bioc-biocgenerics{a} r-bioc-dnacopy{a} readline-common{a} sensible-utils{a} sgml-base{a} tk8.6-blt2.5{a} tzdata{a} ucf{a} unicode-data{a} unzip{a} w3c-sgml-lib{a} x11-common{a} xdg-utils{a} xfonts-encodings{a} xfonts-utils{a} xml-core{a} zip{a} The following packages are RECOMMENDED but will NOT be installed: curl fonts-dejavu-extra isympy-common javascript-common krb5-locales libarchive-cpio-perl libfile-mimeinfo-perl libglib2.0-data libldap-common libltdl-dev libmail-sendmail-perl libnet-dbus-perl libsasl2-modules libx11-protocol-perl linux-sysctl-defaults lynx ncbi-blast+ poppler-data psmisc publicsuffix python-biopython-doc python3-bottleneck python3-bs4 python3-cssselect python3-gdal python3-html5lib python3-jinja2 python3-numexpr python3-odf python3-olefile python3-openpyxl python3-psutil python3-pydot python3-pygments python3-pygraphviz python3-simplejson python3-tables r-base-dev r-doc-html r-recommended shared-mime-info wget x11-utils x11-xserver-utils xdg-user-dirs 0 packages upgraded, 207 newly installed, 0 to remove and 0 not upgraded. Need to get 168 MB of archives. After unpacking 677 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main arm64 libpython3.12-minimal arm64 3.12.5-1 [805 kB] Get: 2 http://deb.debian.org/debian unstable/main arm64 libexpat1 arm64 2.6.2-1 [88.7 kB] Get: 3 http://deb.debian.org/debian unstable/main arm64 python3.12-minimal arm64 3.12.5-1 [1946 kB] Get: 4 http://deb.debian.org/debian unstable/main arm64 python3-minimal arm64 3.12.5-1 [26.7 kB] Get: 5 http://deb.debian.org/debian unstable/main arm64 media-types all 10.1.0 [26.9 kB] Get: 6 http://deb.debian.org/debian unstable/main arm64 netbase all 6.4 [12.8 kB] Get: 7 http://deb.debian.org/debian unstable/main arm64 tzdata all 2024a-4 [255 kB] Get: 8 http://deb.debian.org/debian unstable/main arm64 libkrb5support0 arm64 1.21.3-3 [32.1 kB] Get: 9 http://deb.debian.org/debian unstable/main arm64 libcom-err2 arm64 1.47.1-1 [22.8 kB] Get: 10 http://deb.debian.org/debian unstable/main arm64 libk5crypto3 arm64 1.21.3-3 [80.8 kB] Get: 11 http://deb.debian.org/debian unstable/main arm64 libkeyutils1 arm64 1.6.3-3 [9112 B] Get: 12 http://deb.debian.org/debian unstable/main arm64 libkrb5-3 arm64 1.21.3-3 [310 kB] Get: 13 http://deb.debian.org/debian unstable/main arm64 libgssapi-krb5-2 arm64 1.21.3-3 [126 kB] Get: 14 http://deb.debian.org/debian unstable/main arm64 libtirpc-common all 1.3.4+ds-1.3 [10.9 kB] Get: 15 http://deb.debian.org/debian unstable/main arm64 libtirpc3t64 arm64 1.3.4+ds-1.3 [78.4 kB] Get: 16 http://deb.debian.org/debian unstable/main arm64 libnsl2 arm64 1.3.0-3+b2 [37.7 kB] Get: 17 http://deb.debian.org/debian unstable/main arm64 readline-common all 8.2-4 [69.3 kB] Get: 18 http://deb.debian.org/debian unstable/main arm64 libreadline8t64 arm64 8.2-4 [157 kB] Get: 19 http://deb.debian.org/debian unstable/main arm64 libpython3.12-stdlib arm64 3.12.5-1 [1917 kB] Get: 20 http://deb.debian.org/debian unstable/main arm64 python3.12 arm64 3.12.5-1 [666 kB] Get: 21 http://deb.debian.org/debian unstable/main arm64 libpython3-stdlib arm64 3.12.5-1 [9588 B] Get: 22 http://deb.debian.org/debian unstable/main arm64 python3 arm64 3.12.5-1 [27.6 kB] Get: 23 http://deb.debian.org/debian unstable/main arm64 sgml-base all 1.31 [15.4 kB] Get: 24 http://deb.debian.org/debian unstable/main arm64 libproc2-0 arm64 2:4.0.4-5 [61.3 kB] Get: 25 http://deb.debian.org/debian unstable/main arm64 procps arm64 2:4.0.4-5 [868 kB] Get: 26 http://deb.debian.org/debian unstable/main arm64 sensible-utils all 0.0.24 [24.8 kB] Get: 27 http://deb.debian.org/debian unstable/main arm64 openssl arm64 3.3.1-2 [1346 kB] Get: 28 http://deb.debian.org/debian unstable/main arm64 ca-certificates all 20240203 [158 kB] Get: 29 http://deb.debian.org/debian unstable/main arm64 libmagic-mgc arm64 1:5.45-3 [314 kB] Get: 30 http://deb.debian.org/debian unstable/main arm64 libmagic1t64 arm64 1:5.45-3 [100 kB] Get: 31 http://deb.debian.org/debian unstable/main arm64 file arm64 1:5.45-3 [43.0 kB] Get: 32 http://deb.debian.org/debian unstable/main arm64 gettext-base arm64 0.22.5-2 [198 kB] Get: 33 http://deb.debian.org/debian unstable/main arm64 libuchardet0 arm64 0.0.8-1+b1 [69.0 kB] Get: 34 http://deb.debian.org/debian unstable/main arm64 groff-base arm64 1.23.0-5 [1129 kB] Get: 35 http://deb.debian.org/debian unstable/main arm64 bsdextrautils arm64 2.40.2-6 [96.0 kB] Get: 36 http://deb.debian.org/debian unstable/main arm64 libpipeline1 arm64 1.5.7-2 [36.5 kB] Get: 37 http://deb.debian.org/debian unstable/main arm64 man-db arm64 2.12.1-3 [1397 kB] Get: 38 http://deb.debian.org/debian unstable/main arm64 ucf all 3.0043+nmu1 [55.2 kB] Get: 39 http://deb.debian.org/debian unstable/main arm64 m4 arm64 1.4.19-4 [277 kB] Get: 40 http://deb.debian.org/debian unstable/main arm64 autoconf all 2.71-3 [332 kB] Get: 41 http://deb.debian.org/debian unstable/main arm64 autotools-dev all 20220109.1 [51.6 kB] Get: 42 http://deb.debian.org/debian unstable/main arm64 automake all 1:1.16.5-1.3 [823 kB] Get: 43 http://deb.debian.org/debian unstable/main arm64 autopoint all 0.22.5-2 [723 kB] Get: 44 http://deb.debian.org/debian unstable/main arm64 libtcl8.6 arm64 8.6.14+dfsg-1 [975 kB] Get: 45 http://deb.debian.org/debian unstable/main arm64 libbrotli1 arm64 1.1.0-2+b4 [292 kB] Get: 46 http://deb.debian.org/debian unstable/main arm64 libpng16-16t64 arm64 1.6.43-5 [272 kB] Get: 47 http://deb.debian.org/debian unstable/main arm64 libfreetype6 arm64 2.13.2+dfsg-1+b4 [408 kB] Get: 48 http://deb.debian.org/debian unstable/main arm64 fonts-dejavu-mono all 2.37-8 [489 kB] Get: 49 http://deb.debian.org/debian unstable/main arm64 fonts-dejavu-core all 2.37-8 [840 kB] Get: 50 http://deb.debian.org/debian unstable/main arm64 libfontenc1 arm64 1:1.1.8-1 [22.2 kB] Get: 51 http://deb.debian.org/debian unstable/main arm64 x11-common all 1:7.7+23.1 [216 kB] Get: 52 http://deb.debian.org/debian unstable/main arm64 xfonts-encodings all 1:1.0.4-2.2 [577 kB] Get: 53 http://deb.debian.org/debian unstable/main arm64 xfonts-utils arm64 1:7.7+6 [85.6 kB] Get: 54 http://deb.debian.org/debian unstable/main arm64 fonts-urw-base35 all 20200910-8 [10.8 MB] Get: 55 http://deb.debian.org/debian unstable/main arm64 fontconfig-config arm64 2.15.0-1.1 [317 kB] Get: 56 http://deb.debian.org/debian unstable/main arm64 libfontconfig1 arm64 2.15.0-1.1 [385 kB] Get: 57 http://deb.debian.org/debian unstable/main arm64 libxau6 arm64 1:1.0.9-1+b1 [18.1 kB] Get: 58 http://deb.debian.org/debian unstable/main arm64 libxdmcp6 arm64 1:1.1.2-3+b1 [24.3 kB] Get: 59 http://deb.debian.org/debian unstable/main arm64 libxcb1 arm64 1.17.0-2 [143 kB] Get: 60 http://deb.debian.org/debian unstable/main arm64 libx11-data all 2:1.8.7-1 [328 kB] Get: 61 http://deb.debian.org/debian unstable/main arm64 libx11-6 arm64 2:1.8.7-1+b1 [775 kB] Get: 62 http://deb.debian.org/debian unstable/main arm64 libxrender1 arm64 1:0.9.10-1.1+b1 [27.0 kB] Get: 63 http://deb.debian.org/debian unstable/main arm64 libxft2 arm64 2.3.6-1+b1 [51.0 kB] Get: 64 http://deb.debian.org/debian unstable/main arm64 libxext6 arm64 2:1.3.4-1+b1 [51.7 kB] Get: 65 http://deb.debian.org/debian unstable/main arm64 libxss1 arm64 1:1.2.3-1+b1 [17.0 kB] Get: 66 http://deb.debian.org/debian unstable/main arm64 libtk8.6 arm64 8.6.14-1 [732 kB] Get: 67 http://deb.debian.org/debian unstable/main arm64 tk8.6-blt2.5 arm64 2.5.3+dfsg-7 [533 kB] Get: 68 http://deb.debian.org/debian unstable/main arm64 blt arm64 2.5.3+dfsg-7 [6024 B] Get: 69 http://deb.debian.org/debian unstable/main arm64 libdebhelper-perl all 13.16 [88.6 kB] Get: 70 http://deb.debian.org/debian unstable/main arm64 libtool all 2.4.7-7 [517 kB] Get: 71 http://deb.debian.org/debian unstable/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 72 http://deb.debian.org/debian unstable/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 73 http://deb.debian.org/debian unstable/main arm64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 74 http://deb.debian.org/debian unstable/main arm64 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 75 http://deb.debian.org/debian unstable/main arm64 libelf1t64 arm64 0.191-2 [188 kB] Get: 76 http://deb.debian.org/debian unstable/main arm64 dwz arm64 0.15-1+b1 [102 kB] Get: 77 http://deb.debian.org/debian unstable/main arm64 libicu72 arm64 72.1-5 [9224 kB] Get: 78 http://deb.debian.org/debian unstable/main arm64 libxml2 arm64 2.12.7+dfsg-3+b1 [609 kB] Get: 79 http://deb.debian.org/debian unstable/main arm64 gettext arm64 0.22.5-2 [1532 kB] Get: 80 http://deb.debian.org/debian unstable/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 81 http://deb.debian.org/debian unstable/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 82 http://deb.debian.org/debian unstable/main arm64 debhelper all 13.16 [891 kB] Get: 83 http://deb.debian.org/debian unstable/main arm64 python3-pkg-resources all 70.3.0-2 [264 kB] Get: 84 http://deb.debian.org/debian unstable/main arm64 python3-setuptools all 70.3.0-2 [504 kB] Get: 85 http://deb.debian.org/debian unstable/main arm64 dh-python all 6.20240603 [109 kB] Get: 86 http://deb.debian.org/debian unstable/main arm64 fontconfig arm64 2.15.0-1.1 [462 kB] Get: 87 http://deb.debian.org/debian unstable/main arm64 fonts-lyx all 2.4.1-2 [189 kB] Get: 88 http://deb.debian.org/debian unstable/main arm64 libblas3 arm64 3.12.0-3 [91.7 kB] Get: 89 http://deb.debian.org/debian unstable/main arm64 libpixman-1-0 arm64 0.42.2-1+b1 [477 kB] Get: 90 http://deb.debian.org/debian unstable/main arm64 libxcb-render0 arm64 1.17.0-2 [115 kB] Get: 91 http://deb.debian.org/debian unstable/main arm64 libxcb-shm0 arm64 1.17.0-2 [105 kB] Get: 92 http://deb.debian.org/debian unstable/main arm64 libcairo2 arm64 1.18.0-3+b1 [478 kB] Get: 93 http://deb.debian.org/debian unstable/main arm64 libsasl2-modules-db arm64 2.1.28+dfsg1-7 [20.0 kB] Get: 94 http://deb.debian.org/debian unstable/main arm64 libsasl2-2 arm64 2.1.28+dfsg1-7 [55.4 kB] Get: 95 http://deb.debian.org/debian unstable/main arm64 libldap-2.5-0 arm64 2.5.18+dfsg-2 [173 kB] Get: 96 http://deb.debian.org/debian unstable/main arm64 libnghttp2-14 arm64 1.62.1-2 [71.3 kB] Get: 97 http://deb.debian.org/debian unstable/main arm64 libnghttp3-9 arm64 1.4.0-1 [59.5 kB] Get: 98 http://deb.debian.org/debian unstable/main arm64 libngtcp2-16 arm64 1.6.0-1 [112 kB] Get: 99 http://deb.debian.org/debian unstable/main arm64 libngtcp2-crypto-gnutls8 arm64 1.6.0-1 [18.5 kB] Get: 100 http://deb.debian.org/debian unstable/main arm64 libpsl5t64 arm64 0.21.2-1.1 [56.8 kB] Get: 101 http://deb.debian.org/debian unstable/main arm64 librtmp1 arm64 2.4+20151223.gitfa8646d.1-2+b4 [56.7 kB] Get: 102 http://deb.debian.org/debian unstable/main arm64 libssh2-1t64 arm64 1.11.0-7 [208 kB] Get: 103 http://deb.debian.org/debian unstable/main arm64 libcurl3t64-gnutls arm64 8.9.1-2 [441 kB] Get: 104 http://deb.debian.org/debian unstable/main arm64 libcurl4t64 arm64 8.9.1-2 [434 kB] Get: 105 http://deb.debian.org/debian unstable/main arm64 libdatrie1 arm64 0.2.13-3 [37.2 kB] Get: 106 http://deb.debian.org/debian unstable/main arm64 libdeflate0 arm64 1.20-1 [41.5 kB] Get: 107 http://deb.debian.org/debian unstable/main arm64 libfribidi0 arm64 1.0.15-1 [71.8 kB] Get: 108 http://deb.debian.org/debian unstable/main arm64 libgfortran5 arm64 14.2.0-2 [361 kB] Get: 109 http://deb.debian.org/debian unstable/main arm64 libglib2.0-0t64 arm64 2.81.1-3 [1406 kB] Get: 110 http://deb.debian.org/debian unstable/main arm64 libgraphite2-3 arm64 1.3.14-2 [69.2 kB] Get: 111 http://deb.debian.org/debian unstable/main arm64 libharfbuzz0b arm64 8.3.0-2+b1 [2178 kB] Get: 112 http://deb.debian.org/debian unstable/main arm64 libhtscodecs2 arm64 1.6.0-1+b1 [71.6 kB] Get: 113 http://deb.debian.org/debian unstable/main arm64 libhts3t64 arm64 1.20+ds-1 [416 kB] Get: 114 http://deb.debian.org/debian unstable/main arm64 libice6 arm64 2:1.0.10-1+b1 [53.7 kB] Get: 115 http://deb.debian.org/debian unstable/main arm64 libimagequant0 arm64 2.18.0-1+b1 [34.6 kB] Get: 116 http://deb.debian.org/debian unstable/main arm64 libjbig0 arm64 2.1-6.1+b1 [30.4 kB] Get: 117 http://deb.debian.org/debian unstable/main arm64 libjpeg62-turbo arm64 1:2.1.5-3 [172 kB] Get: 118 http://deb.debian.org/debian unstable/main arm64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get: 119 http://deb.debian.org/debian unstable/main arm64 libjs-jquery-ui all 1.13.2+dfsg-1 [250 kB] Get: 120 http://deb.debian.org/debian unstable/main arm64 liblapack3 arm64 3.12.0-3 [1757 kB] Get: 121 http://deb.debian.org/debian unstable/main arm64 liblbfgsb0 arm64 3.0+dfsg.4-1+b1 [25.0 kB] Get: 122 http://deb.debian.org/debian unstable/main arm64 liblcms2-2 arm64 2.14-2+b1 [144 kB] Get: 123 http://deb.debian.org/debian unstable/main arm64 liblerc4 arm64 4.0.0+ds-4+b1 [142 kB] Get: 124 http://deb.debian.org/debian unstable/main arm64 libnspr4 arm64 2:4.35-1.1+b1 [101 kB] Get: 125 http://deb.debian.org/debian unstable/main arm64 libnss3 arm64 2:3.103-1 [1253 kB] Get: 126 http://deb.debian.org/debian unstable/main arm64 libopenjp2-7 arm64 2.5.0-2+b3 [177 kB] Get: 127 http://deb.debian.org/debian unstable/main arm64 libthai-data all 0.1.29-2 [168 kB] Get: 128 http://deb.debian.org/debian unstable/main arm64 libthai0 arm64 0.1.29-2 [48.0 kB] Get: 129 http://deb.debian.org/debian unstable/main arm64 libpango-1.0-0 arm64 1.54.0+ds-1 [207 kB] Get: 130 http://deb.debian.org/debian unstable/main arm64 libpangoft2-1.0-0 arm64 1.54.0+ds-1 [45.4 kB] Get: 131 http://deb.debian.org/debian unstable/main arm64 libpangocairo-1.0-0 arm64 1.54.0+ds-1 [33.1 kB] Get: 132 http://deb.debian.org/debian unstable/main arm64 libpaper1 arm64 1.1.29+b1 [12.9 kB] Get: 133 http://deb.debian.org/debian unstable/main arm64 libpaper-utils arm64 1.1.29+b1 [9068 B] Get: 134 http://deb.debian.org/debian unstable/main arm64 libsharpyuv0 arm64 1.4.0-0.1 [111 kB] Get: 135 http://deb.debian.org/debian unstable/main arm64 libwebp7 arm64 1.4.0-0.1 [267 kB] Get: 136 http://deb.debian.org/debian unstable/main arm64 libtiff6 arm64 4.5.1+git230720-4 [307 kB] Get: 137 http://deb.debian.org/debian unstable/main arm64 libpoppler134 arm64 24.02.0-5+b1 [918 kB] Get: 138 http://deb.debian.org/debian unstable/main arm64 libqhull-r8.0 arm64 2020.2-6+b1 [226 kB] Get: 139 http://deb.debian.org/debian unstable/main arm64 libraqm0 arm64 0.10.1-1+b1 [13.7 kB] Get: 140 http://deb.debian.org/debian unstable/main arm64 libsm6 arm64 2:1.2.3-1+b1 [32.7 kB] Get: 141 http://deb.debian.org/debian unstable/main arm64 libwebpdemux2 arm64 1.4.0-0.1 [110 kB] Get: 142 http://deb.debian.org/debian unstable/main arm64 libwebpmux3 arm64 1.4.0-0.1 [122 kB] Get: 143 http://deb.debian.org/debian unstable/main arm64 libxslt1.1 arm64 1.1.35-1.1 [221 kB] Get: 144 http://deb.debian.org/debian unstable/main arm64 libxt6t64 arm64 1:1.2.1-1.2 [172 kB] Get: 145 http://deb.debian.org/debian unstable/main arm64 libyaml-0-2 arm64 0.2.5-1+b1 [49.0 kB] Get: 146 http://deb.debian.org/debian unstable/main arm64 poppler-utils arm64 24.02.0-5+b1 [183 kB] Get: 147 http://deb.debian.org/debian unstable/main arm64 python3-zipp all 3.19.2-3 [10.3 kB] Get: 148 http://deb.debian.org/debian unstable/main arm64 python3-importlib-metadata all 8.2.0-2 [20.5 kB] Get: 149 http://deb.debian.org/debian unstable/main arm64 python3-packaging all 24.1-1 [45.8 kB] Get: 150 http://deb.debian.org/debian unstable/main arm64 python3-pyproject-hooks all 1.1.0-2 [11.3 kB] Get: 151 http://deb.debian.org/debian unstable/main arm64 python3-toml all 0.10.2-1 [16.2 kB] Get: 152 http://deb.debian.org/debian unstable/main arm64 python3-wheel all 0.43.0-1 [52.5 kB] Get: 153 http://deb.debian.org/debian unstable/main arm64 python3-build all 1.2.1-1 [34.1 kB] Get: 154 http://deb.debian.org/debian unstable/main arm64 python3-installer all 0.7.0+dfsg1-3 [18.6 kB] Get: 155 http://deb.debian.org/debian unstable/main arm64 pybuild-plugin-pyproject all 6.20240603 [11.2 kB] Get: 156 http://deb.debian.org/debian unstable/main arm64 python-matplotlib-data all 3.8.3-3 [2731 kB] Get: 157 http://deb.debian.org/debian unstable/main arm64 python3-all arm64 3.12.5-1 [1044 B] Get: 158 http://deb.debian.org/debian unstable/main arm64 python3-appdirs all 1.4.4-4 [12.5 kB] Get: 159 http://deb.debian.org/debian unstable/main arm64 python3-attr all 23.2.0-2 [65.5 kB] Get: 160 http://deb.debian.org/debian unstable/main arm64 python3-numpy arm64 1:1.26.4+ds-11 [3351 kB] Get: 161 http://deb.debian.org/debian unstable/main arm64 python3-chardet all 5.2.0+dfsg-1 [107 kB] Get: 162 http://deb.debian.org/debian unstable/main arm64 python3-tk arm64 3.12.5-1 [108 kB] Get: 163 http://deb.debian.org/debian unstable/main arm64 python3-pil.imagetk arm64 10.4.0-1 [79.4 kB] Get: 164 http://deb.debian.org/debian unstable/main arm64 python3-pil arm64 10.4.0-1 [480 kB] Get: 165 http://deb.debian.org/debian unstable/main arm64 python3-cairo arm64 1.26.1-1+b1 [113 kB] Get: 166 http://deb.debian.org/debian unstable/main arm64 python3-freetype all 2.4.0-2 [78.6 kB] Get: 167 http://deb.debian.org/debian unstable/main arm64 python3-rlpycairo all 0.3.0-3 [9904 B] Get: 168 http://deb.debian.org/debian unstable/main arm64 python3-reportlab all 4.2.2-1 [1150 kB] Get: 169 http://deb.debian.org/debian unstable/main arm64 xml-core all 0.19 [20.1 kB] Get: 170 http://deb.debian.org/debian unstable/main arm64 w3c-sgml-lib all 1.3-3 [273 kB] Get: 171 http://deb.debian.org/debian unstable/main arm64 python3-biopython arm64 1.83+dfsg1-3+b1 [1593 kB] Get: 172 http://deb.debian.org/debian unstable/main arm64 python3-brotli arm64 1.1.0-2+b4 [301 kB] Get: 173 http://deb.debian.org/debian unstable/main arm64 python3-contourpy arm64 1.2.1-1 [183 kB] Get: 174 http://deb.debian.org/debian unstable/main arm64 python3-cycler all 0.12.1-1 [9496 B] Get: 175 http://deb.debian.org/debian unstable/main arm64 python3-six all 1.16.0-7 [16.4 kB] Get: 176 http://deb.debian.org/debian unstable/main arm64 python3-dateutil all 2.9.0-2 [79.4 kB] Get: 177 http://deb.debian.org/debian unstable/main arm64 python3-decorator all 5.1.1-5 [15.1 kB] Get: 178 http://deb.debian.org/debian unstable/main arm64 python3-scipy arm64 1.13.1-3 [15.4 MB] Get: 179 http://deb.debian.org/debian unstable/main arm64 python3-ufolib2 all 0.16.0+dfsg1-1 [32.9 kB] Get: 180 http://deb.debian.org/debian unstable/main arm64 python3-mpmath all 1.3.0-1 [419 kB] Get: 181 http://deb.debian.org/debian unstable/main arm64 python3-sympy all 1.13.1-1 [4147 kB] Get: 182 http://deb.debian.org/debian unstable/main arm64 python3-tz all 2024.1-2 [30.9 kB] Get: 183 http://deb.debian.org/debian unstable/main arm64 python3-fs all 2.4.16-4 [95.4 kB] Get: 184 http://deb.debian.org/debian unstable/main arm64 python3-lxml arm64 5.2.2-2 [1096 kB] Get: 185 http://deb.debian.org/debian unstable/main arm64 python3-lz4 arm64 4.0.2+dfsg-1+b4 [25.1 kB] Get: 186 http://deb.debian.org/debian unstable/main arm64 unicode-data all 15.1.0-1 [8547 kB] Get: 187 http://deb.debian.org/debian unstable/main arm64 python3-fonttools arm64 4.46.0-1+b1 [1319 kB] Get: 188 http://deb.debian.org/debian unstable/main arm64 python3-iniconfig all 1.1.1-2 [6396 B] Get: 189 http://deb.debian.org/debian unstable/main arm64 python3-joblib all 1.3.2-2 [218 kB] Get: 190 http://deb.debian.org/debian unstable/main arm64 python3-kiwisolver arm64 1.4.5-1+b1 [55.1 kB] Get: 191 http://deb.debian.org/debian unstable/main arm64 python3-pyparsing all 3.1.2-1 [146 kB] Get: 192 http://deb.debian.org/debian unstable/main arm64 python3-matplotlib arm64 3.8.3-3 [5509 kB] Get: 193 http://deb.debian.org/debian unstable/main arm64 python3-networkx all 3.2.1-4 [14.2 MB] Get: 194 http://deb.debian.org/debian unstable/main arm64 python3-pandas-lib arm64 2.2.2+dfsg-4+b1 [3571 kB] Get: 195 http://deb.debian.org/debian unstable/main arm64 python3-pandas all 2.2.2+dfsg-4 [3095 kB] Get: 196 http://deb.debian.org/debian unstable/main arm64 python3-pluggy all 1.5.0-1 [26.9 kB] Get: 197 http://deb.debian.org/debian unstable/main arm64 python3-yaml arm64 6.0.1-2+b1 [108 kB] Get: 198 http://deb.debian.org/debian unstable/main arm64 python3-pomegranate arm64 0.14.8-6+b1 [2317 kB] Get: 199 http://deb.debian.org/debian unstable/main arm64 python3-pyfaidx all 0.8.1.2-1 [29.0 kB] Get: 200 http://deb.debian.org/debian unstable/main arm64 python3-pysam arm64 0.22.1+ds-2+b1 [3244 kB] Get: 201 http://deb.debian.org/debian unstable/main arm64 python3-pytest all 8.3.2-1 [249 kB] Get: 202 http://deb.debian.org/debian unstable/main arm64 zip arm64 3.0-14 [225 kB] Get: 203 http://deb.debian.org/debian unstable/main arm64 unzip arm64 6.0-28 [157 kB] Get: 204 http://deb.debian.org/debian unstable/main arm64 xdg-utils all 1.1.3-4.1 [75.5 kB] Get: 205 http://deb.debian.org/debian unstable/main arm64 r-base-core arm64 4.4.1-1 [28.0 MB] Get: 206 http://deb.debian.org/debian unstable/main arm64 r-bioc-biocgenerics all 0.48.1-2 [597 kB] Get: 207 http://deb.debian.org/debian unstable/main arm64 r-bioc-dnacopy arm64 1.76.0-1 [377 kB] Fetched 168 MB in 2s (85.4 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.12-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 ... 19840 files and directories currently installed.) Preparing to unpack .../libpython3.12-minimal_3.12.5-1_arm64.deb ... Unpacking libpython3.12-minimal:arm64 (3.12.5-1) ... Selecting previously unselected package libexpat1:arm64. Preparing to unpack .../libexpat1_2.6.2-1_arm64.deb ... Unpacking libexpat1:arm64 (2.6.2-1) ... Selecting previously unselected package python3.12-minimal. Preparing to unpack .../python3.12-minimal_3.12.5-1_arm64.deb ... Unpacking python3.12-minimal (3.12.5-1) ... Setting up libpython3.12-minimal:arm64 (3.12.5-1) ... Setting up libexpat1:arm64 (2.6.2-1) ... Setting up python3.12-minimal (3.12.5-1) ... 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 ... 20160 files and directories currently installed.) Preparing to unpack .../00-python3-minimal_3.12.5-1_arm64.deb ... Unpacking python3-minimal (3.12.5-1) ... Selecting previously unselected package media-types. Preparing to unpack .../01-media-types_10.1.0_all.deb ... Unpacking media-types (10.1.0) ... Selecting previously unselected package netbase. Preparing to unpack .../02-netbase_6.4_all.deb ... Unpacking netbase (6.4) ... Selecting previously unselected package tzdata. Preparing to unpack .../03-tzdata_2024a-4_all.deb ... Unpacking tzdata (2024a-4) ... Selecting previously unselected package libkrb5support0:arm64. Preparing to unpack .../04-libkrb5support0_1.21.3-3_arm64.deb ... Unpacking libkrb5support0:arm64 (1.21.3-3) ... Selecting previously unselected package libcom-err2:arm64. Preparing to unpack .../05-libcom-err2_1.47.1-1_arm64.deb ... Unpacking libcom-err2:arm64 (1.47.1-1) ... Selecting previously unselected package libk5crypto3:arm64. Preparing to unpack .../06-libk5crypto3_1.21.3-3_arm64.deb ... Unpacking libk5crypto3:arm64 (1.21.3-3) ... Selecting previously unselected package libkeyutils1:arm64. Preparing to unpack .../07-libkeyutils1_1.6.3-3_arm64.deb ... Unpacking libkeyutils1:arm64 (1.6.3-3) ... Selecting previously unselected package libkrb5-3:arm64. Preparing to unpack .../08-libkrb5-3_1.21.3-3_arm64.deb ... Unpacking libkrb5-3:arm64 (1.21.3-3) ... Selecting previously unselected package libgssapi-krb5-2:arm64. Preparing to unpack .../09-libgssapi-krb5-2_1.21.3-3_arm64.deb ... Unpacking libgssapi-krb5-2:arm64 (1.21.3-3) ... Selecting previously unselected package libtirpc-common. Preparing to unpack .../10-libtirpc-common_1.3.4+ds-1.3_all.deb ... Unpacking libtirpc-common (1.3.4+ds-1.3) ... Selecting previously unselected package libtirpc3t64:arm64. Preparing to unpack .../11-libtirpc3t64_1.3.4+ds-1.3_arm64.deb ... Adding 'diversion of /lib/aarch64-linux-gnu/libtirpc.so.3 to /lib/aarch64-linux-gnu/libtirpc.so.3.usr-is-merged by libtirpc3t64' Adding 'diversion of /lib/aarch64-linux-gnu/libtirpc.so.3.0.0 to /lib/aarch64-linux-gnu/libtirpc.so.3.0.0.usr-is-merged by libtirpc3t64' Unpacking libtirpc3t64:arm64 (1.3.4+ds-1.3) ... Selecting previously unselected package libnsl2:arm64. Preparing to unpack .../12-libnsl2_1.3.0-3+b2_arm64.deb ... Unpacking libnsl2:arm64 (1.3.0-3+b2) ... Selecting previously unselected package readline-common. Preparing to unpack .../13-readline-common_8.2-4_all.deb ... Unpacking readline-common (8.2-4) ... Selecting previously unselected package libreadline8t64:arm64. Preparing to unpack .../14-libreadline8t64_8.2-4_arm64.deb ... Adding 'diversion of /lib/aarch64-linux-gnu/libhistory.so.8 to /lib/aarch64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libhistory.so.8.2 to /lib/aarch64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libreadline.so.8 to /lib/aarch64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libreadline.so.8.2 to /lib/aarch64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:arm64 (8.2-4) ... Selecting previously unselected package libpython3.12-stdlib:arm64. Preparing to unpack .../15-libpython3.12-stdlib_3.12.5-1_arm64.deb ... Unpacking libpython3.12-stdlib:arm64 (3.12.5-1) ... Selecting previously unselected package python3.12. Preparing to unpack .../16-python3.12_3.12.5-1_arm64.deb ... Unpacking python3.12 (3.12.5-1) ... Selecting previously unselected package libpython3-stdlib:arm64. Preparing to unpack .../17-libpython3-stdlib_3.12.5-1_arm64.deb ... Unpacking libpython3-stdlib:arm64 (3.12.5-1) ... Setting up python3-minimal (3.12.5-1) ... 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 ... 21234 files and directories currently installed.) Preparing to unpack .../000-python3_3.12.5-1_arm64.deb ... Unpacking python3 (3.12.5-1) ... Selecting previously unselected package sgml-base. Preparing to unpack .../001-sgml-base_1.31_all.deb ... Unpacking sgml-base (1.31) ... Selecting previously unselected package libproc2-0:arm64. Preparing to unpack .../002-libproc2-0_2%3a4.0.4-5_arm64.deb ... Unpacking libproc2-0:arm64 (2:4.0.4-5) ... Selecting previously unselected package procps. Preparing to unpack .../003-procps_2%3a4.0.4-5_arm64.deb ... Unpacking procps (2:4.0.4-5) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../004-sensible-utils_0.0.24_all.deb ... Unpacking sensible-utils (0.0.24) ... Selecting previously unselected package openssl. Preparing to unpack .../005-openssl_3.3.1-2_arm64.deb ... Unpacking openssl (3.3.1-2) ... Selecting previously unselected package ca-certificates. Preparing to unpack .../006-ca-certificates_20240203_all.deb ... Unpacking ca-certificates (20240203) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../007-libmagic-mgc_1%3a5.45-3_arm64.deb ... Unpacking libmagic-mgc (1:5.45-3) ... Selecting previously unselected package libmagic1t64:arm64. Preparing to unpack .../008-libmagic1t64_1%3a5.45-3_arm64.deb ... Unpacking libmagic1t64:arm64 (1:5.45-3) ... Selecting previously unselected package file. Preparing to unpack .../009-file_1%3a5.45-3_arm64.deb ... Unpacking file (1:5.45-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../010-gettext-base_0.22.5-2_arm64.deb ... Unpacking gettext-base (0.22.5-2) ... Selecting previously unselected package libuchardet0:arm64. Preparing to unpack .../011-libuchardet0_0.0.8-1+b1_arm64.deb ... Unpacking libuchardet0:arm64 (0.0.8-1+b1) ... Selecting previously unselected package groff-base. Preparing to unpack .../012-groff-base_1.23.0-5_arm64.deb ... Unpacking groff-base (1.23.0-5) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../013-bsdextrautils_2.40.2-6_arm64.deb ... Unpacking bsdextrautils (2.40.2-6) ... Selecting previously unselected package libpipeline1:arm64. Preparing to unpack .../014-libpipeline1_1.5.7-2_arm64.deb ... Unpacking libpipeline1:arm64 (1.5.7-2) ... Selecting previously unselected package man-db. Preparing to unpack .../015-man-db_2.12.1-3_arm64.deb ... Unpacking man-db (2.12.1-3) ... Selecting previously unselected package ucf. Preparing to unpack .../016-ucf_3.0043+nmu1_all.deb ... Moving old data out of the way Unpacking ucf (3.0043+nmu1) ... Selecting previously unselected package m4. Preparing to unpack .../017-m4_1.4.19-4_arm64.deb ... Unpacking m4 (1.4.19-4) ... Selecting previously unselected package autoconf. Preparing to unpack .../018-autoconf_2.71-3_all.deb ... Unpacking autoconf (2.71-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../019-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../020-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 .../021-autopoint_0.22.5-2_all.deb ... Unpacking autopoint (0.22.5-2) ... Selecting previously unselected package libtcl8.6:arm64. Preparing to unpack .../022-libtcl8.6_8.6.14+dfsg-1_arm64.deb ... Unpacking libtcl8.6:arm64 (8.6.14+dfsg-1) ... Selecting previously unselected package libbrotli1:arm64. Preparing to unpack .../023-libbrotli1_1.1.0-2+b4_arm64.deb ... Unpacking libbrotli1:arm64 (1.1.0-2+b4) ... Selecting previously unselected package libpng16-16t64:arm64. Preparing to unpack .../024-libpng16-16t64_1.6.43-5_arm64.deb ... Unpacking libpng16-16t64:arm64 (1.6.43-5) ... Selecting previously unselected package libfreetype6:arm64. Preparing to unpack .../025-libfreetype6_2.13.2+dfsg-1+b4_arm64.deb ... Unpacking libfreetype6:arm64 (2.13.2+dfsg-1+b4) ... Selecting previously unselected package fonts-dejavu-mono. Preparing to unpack .../026-fonts-dejavu-mono_2.37-8_all.deb ... Unpacking fonts-dejavu-mono (2.37-8) ... Selecting previously unselected package fonts-dejavu-core. Preparing to unpack .../027-fonts-dejavu-core_2.37-8_all.deb ... Unpacking fonts-dejavu-core (2.37-8) ... Selecting previously unselected package libfontenc1:arm64. Preparing to unpack .../028-libfontenc1_1%3a1.1.8-1_arm64.deb ... Unpacking libfontenc1:arm64 (1:1.1.8-1) ... Selecting previously unselected package x11-common. Preparing to unpack .../029-x11-common_1%3a7.7+23.1_all.deb ... Unpacking x11-common (1:7.7+23.1) ... Selecting previously unselected package xfonts-encodings. Preparing to unpack .../030-xfonts-encodings_1%3a1.0.4-2.2_all.deb ... Unpacking xfonts-encodings (1:1.0.4-2.2) ... Selecting previously unselected package xfonts-utils. Preparing to unpack .../031-xfonts-utils_1%3a7.7+6_arm64.deb ... Unpacking xfonts-utils (1:7.7+6) ... Selecting previously unselected package fonts-urw-base35. Preparing to unpack .../032-fonts-urw-base35_20200910-8_all.deb ... Unpacking fonts-urw-base35 (20200910-8) ... Selecting previously unselected package fontconfig-config. Preparing to unpack .../033-fontconfig-config_2.15.0-1.1_arm64.deb ... Unpacking fontconfig-config (2.15.0-1.1) ... Selecting previously unselected package libfontconfig1:arm64. Preparing to unpack .../034-libfontconfig1_2.15.0-1.1_arm64.deb ... Unpacking libfontconfig1:arm64 (2.15.0-1.1) ... Selecting previously unselected package libxau6:arm64. Preparing to unpack .../035-libxau6_1%3a1.0.9-1+b1_arm64.deb ... Unpacking libxau6:arm64 (1:1.0.9-1+b1) ... Selecting previously unselected package libxdmcp6:arm64. Preparing to unpack .../036-libxdmcp6_1%3a1.1.2-3+b1_arm64.deb ... Unpacking libxdmcp6:arm64 (1:1.1.2-3+b1) ... Selecting previously unselected package libxcb1:arm64. Preparing to unpack .../037-libxcb1_1.17.0-2_arm64.deb ... Unpacking libxcb1:arm64 (1.17.0-2) ... Selecting previously unselected package libx11-data. Preparing to unpack .../038-libx11-data_2%3a1.8.7-1_all.deb ... Unpacking libx11-data (2:1.8.7-1) ... Selecting previously unselected package libx11-6:arm64. Preparing to unpack .../039-libx11-6_2%3a1.8.7-1+b1_arm64.deb ... Unpacking libx11-6:arm64 (2:1.8.7-1+b1) ... Selecting previously unselected package libxrender1:arm64. Preparing to unpack .../040-libxrender1_1%3a0.9.10-1.1+b1_arm64.deb ... Unpacking libxrender1:arm64 (1:0.9.10-1.1+b1) ... Selecting previously unselected package libxft2:arm64. Preparing to unpack .../041-libxft2_2.3.6-1+b1_arm64.deb ... Unpacking libxft2:arm64 (2.3.6-1+b1) ... Selecting previously unselected package libxext6:arm64. Preparing to unpack .../042-libxext6_2%3a1.3.4-1+b1_arm64.deb ... Unpacking libxext6:arm64 (2:1.3.4-1+b1) ... Selecting previously unselected package libxss1:arm64. Preparing to unpack .../043-libxss1_1%3a1.2.3-1+b1_arm64.deb ... Unpacking libxss1:arm64 (1:1.2.3-1+b1) ... Selecting previously unselected package libtk8.6:arm64. Preparing to unpack .../044-libtk8.6_8.6.14-1_arm64.deb ... Unpacking libtk8.6:arm64 (8.6.14-1) ... Selecting previously unselected package tk8.6-blt2.5. Preparing to unpack .../045-tk8.6-blt2.5_2.5.3+dfsg-7_arm64.deb ... Unpacking tk8.6-blt2.5 (2.5.3+dfsg-7) ... Selecting previously unselected package blt. Preparing to unpack .../046-blt_2.5.3+dfsg-7_arm64.deb ... Unpacking blt (2.5.3+dfsg-7) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../047-libdebhelper-perl_13.16_all.deb ... Unpacking libdebhelper-perl (13.16) ... Selecting previously unselected package libtool. Preparing to unpack .../048-libtool_2.4.7-7_all.deb ... Unpacking libtool (2.4.7-7) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../049-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../050-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../051-libfile-stripnondeterminism-perl_1.14.0-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.14.0-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../052-dh-strip-nondeterminism_1.14.0-1_all.deb ... Unpacking dh-strip-nondeterminism (1.14.0-1) ... Selecting previously unselected package libelf1t64:arm64. Preparing to unpack .../053-libelf1t64_0.191-2_arm64.deb ... Unpacking libelf1t64:arm64 (0.191-2) ... Selecting previously unselected package dwz. Preparing to unpack .../054-dwz_0.15-1+b1_arm64.deb ... Unpacking dwz (0.15-1+b1) ... Selecting previously unselected package libicu72:arm64. Preparing to unpack .../055-libicu72_72.1-5_arm64.deb ... Unpacking libicu72:arm64 (72.1-5) ... Selecting previously unselected package libxml2:arm64. Preparing to unpack .../056-libxml2_2.12.7+dfsg-3+b1_arm64.deb ... Unpacking libxml2:arm64 (2.12.7+dfsg-3+b1) ... Selecting previously unselected package gettext. Preparing to unpack .../057-gettext_0.22.5-2_arm64.deb ... Unpacking gettext (0.22.5-2) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../058-intltool-debian_0.35.0+20060710.6_all.deb ... Unpacking intltool-debian (0.35.0+20060710.6) ... Selecting previously unselected package po-debconf. Preparing to unpack .../059-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../060-debhelper_13.16_all.deb ... Unpacking debhelper (13.16) ... Selecting previously unselected package python3-pkg-resources. Preparing to unpack .../061-python3-pkg-resources_70.3.0-2_all.deb ... Unpacking python3-pkg-resources (70.3.0-2) ... Selecting previously unselected package python3-setuptools. Preparing to unpack .../062-python3-setuptools_70.3.0-2_all.deb ... Unpacking python3-setuptools (70.3.0-2) ... Selecting previously unselected package dh-python. Preparing to unpack .../063-dh-python_6.20240603_all.deb ... Unpacking dh-python (6.20240603) ... Selecting previously unselected package fontconfig. Preparing to unpack .../064-fontconfig_2.15.0-1.1_arm64.deb ... Unpacking fontconfig (2.15.0-1.1) ... Selecting previously unselected package fonts-lyx. Preparing to unpack .../065-fonts-lyx_2.4.1-2_all.deb ... Unpacking fonts-lyx (2.4.1-2) ... Selecting previously unselected package libblas3:arm64. Preparing to unpack .../066-libblas3_3.12.0-3_arm64.deb ... Unpacking libblas3:arm64 (3.12.0-3) ... Selecting previously unselected package libpixman-1-0:arm64. Preparing to unpack .../067-libpixman-1-0_0.42.2-1+b1_arm64.deb ... Unpacking libpixman-1-0:arm64 (0.42.2-1+b1) ... Selecting previously unselected package libxcb-render0:arm64. Preparing to unpack .../068-libxcb-render0_1.17.0-2_arm64.deb ... Unpacking libxcb-render0:arm64 (1.17.0-2) ... Selecting previously unselected package libxcb-shm0:arm64. Preparing to unpack .../069-libxcb-shm0_1.17.0-2_arm64.deb ... Unpacking libxcb-shm0:arm64 (1.17.0-2) ... Selecting previously unselected package libcairo2:arm64. Preparing to unpack .../070-libcairo2_1.18.0-3+b1_arm64.deb ... Unpacking libcairo2:arm64 (1.18.0-3+b1) ... Selecting previously unselected package libsasl2-modules-db:arm64. Preparing to unpack .../071-libsasl2-modules-db_2.1.28+dfsg1-7_arm64.deb ... Unpacking libsasl2-modules-db:arm64 (2.1.28+dfsg1-7) ... Selecting previously unselected package libsasl2-2:arm64. Preparing to unpack .../072-libsasl2-2_2.1.28+dfsg1-7_arm64.deb ... Unpacking libsasl2-2:arm64 (2.1.28+dfsg1-7) ... Selecting previously unselected package libldap-2.5-0:arm64. Preparing to unpack .../073-libldap-2.5-0_2.5.18+dfsg-2_arm64.deb ... Unpacking libldap-2.5-0:arm64 (2.5.18+dfsg-2) ... Selecting previously unselected package libnghttp2-14:arm64. Preparing to unpack .../074-libnghttp2-14_1.62.1-2_arm64.deb ... Unpacking libnghttp2-14:arm64 (1.62.1-2) ... Selecting previously unselected package libnghttp3-9:arm64. Preparing to unpack .../075-libnghttp3-9_1.4.0-1_arm64.deb ... Unpacking libnghttp3-9:arm64 (1.4.0-1) ... Selecting previously unselected package libngtcp2-16:arm64. Preparing to unpack .../076-libngtcp2-16_1.6.0-1_arm64.deb ... Unpacking libngtcp2-16:arm64 (1.6.0-1) ... Selecting previously unselected package libngtcp2-crypto-gnutls8:arm64. Preparing to unpack .../077-libngtcp2-crypto-gnutls8_1.6.0-1_arm64.deb ... Unpacking libngtcp2-crypto-gnutls8:arm64 (1.6.0-1) ... Selecting previously unselected package libpsl5t64:arm64. Preparing to unpack .../078-libpsl5t64_0.21.2-1.1_arm64.deb ... Unpacking libpsl5t64:arm64 (0.21.2-1.1) ... Selecting previously unselected package librtmp1:arm64. Preparing to unpack .../079-librtmp1_2.4+20151223.gitfa8646d.1-2+b4_arm64.deb ... Unpacking librtmp1:arm64 (2.4+20151223.gitfa8646d.1-2+b4) ... Selecting previously unselected package libssh2-1t64:arm64. Preparing to unpack .../080-libssh2-1t64_1.11.0-7_arm64.deb ... Unpacking libssh2-1t64:arm64 (1.11.0-7) ... Selecting previously unselected package libcurl3t64-gnutls:arm64. Preparing to unpack .../081-libcurl3t64-gnutls_8.9.1-2_arm64.deb ... Unpacking libcurl3t64-gnutls:arm64 (8.9.1-2) ... Selecting previously unselected package libcurl4t64:arm64. Preparing to unpack .../082-libcurl4t64_8.9.1-2_arm64.deb ... Unpacking libcurl4t64:arm64 (8.9.1-2) ... Selecting previously unselected package libdatrie1:arm64. Preparing to unpack .../083-libdatrie1_0.2.13-3_arm64.deb ... Unpacking libdatrie1:arm64 (0.2.13-3) ... Selecting previously unselected package libdeflate0:arm64. Preparing to unpack .../084-libdeflate0_1.20-1_arm64.deb ... Unpacking libdeflate0:arm64 (1.20-1) ... Selecting previously unselected package libfribidi0:arm64. Preparing to unpack .../085-libfribidi0_1.0.15-1_arm64.deb ... Unpacking libfribidi0:arm64 (1.0.15-1) ... Selecting previously unselected package libgfortran5:arm64. Preparing to unpack .../086-libgfortran5_14.2.0-2_arm64.deb ... Unpacking libgfortran5:arm64 (14.2.0-2) ... Selecting previously unselected package libglib2.0-0t64:arm64. Preparing to unpack .../087-libglib2.0-0t64_2.81.1-3_arm64.deb ... Unpacking libglib2.0-0t64:arm64 (2.81.1-3) ... Selecting previously unselected package libgraphite2-3:arm64. Preparing to unpack .../088-libgraphite2-3_1.3.14-2_arm64.deb ... Unpacking libgraphite2-3:arm64 (1.3.14-2) ... Selecting previously unselected package libharfbuzz0b:arm64. Preparing to unpack .../089-libharfbuzz0b_8.3.0-2+b1_arm64.deb ... Unpacking libharfbuzz0b:arm64 (8.3.0-2+b1) ... Selecting previously unselected package libhtscodecs2:arm64. Preparing to unpack .../090-libhtscodecs2_1.6.0-1+b1_arm64.deb ... Unpacking libhtscodecs2:arm64 (1.6.0-1+b1) ... Selecting previously unselected package libhts3t64:arm64. Preparing to unpack .../091-libhts3t64_1.20+ds-1_arm64.deb ... Unpacking libhts3t64:arm64 (1.20+ds-1) ... Selecting previously unselected package libice6:arm64. Preparing to unpack .../092-libice6_2%3a1.0.10-1+b1_arm64.deb ... Unpacking libice6:arm64 (2:1.0.10-1+b1) ... Selecting previously unselected package libimagequant0:arm64. Preparing to unpack .../093-libimagequant0_2.18.0-1+b1_arm64.deb ... Unpacking libimagequant0:arm64 (2.18.0-1+b1) ... Selecting previously unselected package libjbig0:arm64. Preparing to unpack .../094-libjbig0_2.1-6.1+b1_arm64.deb ... Unpacking libjbig0:arm64 (2.1-6.1+b1) ... Selecting previously unselected package libjpeg62-turbo:arm64. Preparing to unpack .../095-libjpeg62-turbo_1%3a2.1.5-3_arm64.deb ... Unpacking libjpeg62-turbo:arm64 (1:2.1.5-3) ... Selecting previously unselected package libjs-jquery. Preparing to unpack .../096-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Selecting previously unselected package libjs-jquery-ui. Preparing to unpack .../097-libjs-jquery-ui_1.13.2+dfsg-1_all.deb ... Unpacking libjs-jquery-ui (1.13.2+dfsg-1) ... Selecting previously unselected package liblapack3:arm64. Preparing to unpack .../098-liblapack3_3.12.0-3_arm64.deb ... Unpacking liblapack3:arm64 (3.12.0-3) ... Selecting previously unselected package liblbfgsb0:arm64. Preparing to unpack .../099-liblbfgsb0_3.0+dfsg.4-1+b1_arm64.deb ... Unpacking liblbfgsb0:arm64 (3.0+dfsg.4-1+b1) ... Selecting previously unselected package liblcms2-2:arm64. Preparing to unpack .../100-liblcms2-2_2.14-2+b1_arm64.deb ... Unpacking liblcms2-2:arm64 (2.14-2+b1) ... Selecting previously unselected package liblerc4:arm64. Preparing to unpack .../101-liblerc4_4.0.0+ds-4+b1_arm64.deb ... Unpacking liblerc4:arm64 (4.0.0+ds-4+b1) ... Selecting previously unselected package libnspr4:arm64. Preparing to unpack .../102-libnspr4_2%3a4.35-1.1+b1_arm64.deb ... Unpacking libnspr4:arm64 (2:4.35-1.1+b1) ... Selecting previously unselected package libnss3:arm64. Preparing to unpack .../103-libnss3_2%3a3.103-1_arm64.deb ... Unpacking libnss3:arm64 (2:3.103-1) ... Selecting previously unselected package libopenjp2-7:arm64. Preparing to unpack .../104-libopenjp2-7_2.5.0-2+b3_arm64.deb ... Unpacking libopenjp2-7:arm64 (2.5.0-2+b3) ... Selecting previously unselected package libthai-data. Preparing to unpack .../105-libthai-data_0.1.29-2_all.deb ... Unpacking libthai-data (0.1.29-2) ... Selecting previously unselected package libthai0:arm64. Preparing to unpack .../106-libthai0_0.1.29-2_arm64.deb ... Unpacking libthai0:arm64 (0.1.29-2) ... Selecting previously unselected package libpango-1.0-0:arm64. Preparing to unpack .../107-libpango-1.0-0_1.54.0+ds-1_arm64.deb ... Unpacking libpango-1.0-0:arm64 (1.54.0+ds-1) ... Selecting previously unselected package libpangoft2-1.0-0:arm64. Preparing to unpack .../108-libpangoft2-1.0-0_1.54.0+ds-1_arm64.deb ... Unpacking libpangoft2-1.0-0:arm64 (1.54.0+ds-1) ... Selecting previously unselected package libpangocairo-1.0-0:arm64. Preparing to unpack .../109-libpangocairo-1.0-0_1.54.0+ds-1_arm64.deb ... Unpacking libpangocairo-1.0-0:arm64 (1.54.0+ds-1) ... Selecting previously unselected package libpaper1:arm64. Preparing to unpack .../110-libpaper1_1.1.29+b1_arm64.deb ... Unpacking libpaper1:arm64 (1.1.29+b1) ... Selecting previously unselected package libpaper-utils. Preparing to unpack .../111-libpaper-utils_1.1.29+b1_arm64.deb ... Unpacking libpaper-utils (1.1.29+b1) ... Selecting previously unselected package libsharpyuv0:arm64. Preparing to unpack .../112-libsharpyuv0_1.4.0-0.1_arm64.deb ... Unpacking libsharpyuv0:arm64 (1.4.0-0.1) ... Selecting previously unselected package libwebp7:arm64. Preparing to unpack .../113-libwebp7_1.4.0-0.1_arm64.deb ... Unpacking libwebp7:arm64 (1.4.0-0.1) ... Selecting previously unselected package libtiff6:arm64. Preparing to unpack .../114-libtiff6_4.5.1+git230720-4_arm64.deb ... Unpacking libtiff6:arm64 (4.5.1+git230720-4) ... Selecting previously unselected package libpoppler134:arm64. Preparing to unpack .../115-libpoppler134_24.02.0-5+b1_arm64.deb ... Unpacking libpoppler134:arm64 (24.02.0-5+b1) ... Selecting previously unselected package libqhull-r8.0:arm64. Preparing to unpack .../116-libqhull-r8.0_2020.2-6+b1_arm64.deb ... Unpacking libqhull-r8.0:arm64 (2020.2-6+b1) ... Selecting previously unselected package libraqm0:arm64. Preparing to unpack .../117-libraqm0_0.10.1-1+b1_arm64.deb ... Unpacking libraqm0:arm64 (0.10.1-1+b1) ... Selecting previously unselected package libsm6:arm64. Preparing to unpack .../118-libsm6_2%3a1.2.3-1+b1_arm64.deb ... Unpacking libsm6:arm64 (2:1.2.3-1+b1) ... Selecting previously unselected package libwebpdemux2:arm64. Preparing to unpack .../119-libwebpdemux2_1.4.0-0.1_arm64.deb ... Unpacking libwebpdemux2:arm64 (1.4.0-0.1) ... Selecting previously unselected package libwebpmux3:arm64. Preparing to unpack .../120-libwebpmux3_1.4.0-0.1_arm64.deb ... Unpacking libwebpmux3:arm64 (1.4.0-0.1) ... Selecting previously unselected package libxslt1.1:arm64. Preparing to unpack .../121-libxslt1.1_1.1.35-1.1_arm64.deb ... Unpacking libxslt1.1:arm64 (1.1.35-1.1) ... Selecting previously unselected package libxt6t64:arm64. Preparing to unpack .../122-libxt6t64_1%3a1.2.1-1.2_arm64.deb ... Unpacking libxt6t64:arm64 (1:1.2.1-1.2) ... Selecting previously unselected package libyaml-0-2:arm64. Preparing to unpack .../123-libyaml-0-2_0.2.5-1+b1_arm64.deb ... Unpacking libyaml-0-2:arm64 (0.2.5-1+b1) ... Selecting previously unselected package poppler-utils. Preparing to unpack .../124-poppler-utils_24.02.0-5+b1_arm64.deb ... Unpacking poppler-utils (24.02.0-5+b1) ... Selecting previously unselected package python3-zipp. Preparing to unpack .../125-python3-zipp_3.19.2-3_all.deb ... Unpacking python3-zipp (3.19.2-3) ... Selecting previously unselected package python3-importlib-metadata. Preparing to unpack .../126-python3-importlib-metadata_8.2.0-2_all.deb ... Unpacking python3-importlib-metadata (8.2.0-2) ... Selecting previously unselected package python3-packaging. Preparing to unpack .../127-python3-packaging_24.1-1_all.deb ... Unpacking python3-packaging (24.1-1) ... Selecting previously unselected package python3-pyproject-hooks. Preparing to unpack .../128-python3-pyproject-hooks_1.1.0-2_all.deb ... Unpacking python3-pyproject-hooks (1.1.0-2) ... Selecting previously unselected package python3-toml. Preparing to unpack .../129-python3-toml_0.10.2-1_all.deb ... Unpacking python3-toml (0.10.2-1) ... Selecting previously unselected package python3-wheel. Preparing to unpack .../130-python3-wheel_0.43.0-1_all.deb ... Unpacking python3-wheel (0.43.0-1) ... Selecting previously unselected package python3-build. Preparing to unpack .../131-python3-build_1.2.1-1_all.deb ... Unpacking python3-build (1.2.1-1) ... Selecting previously unselected package python3-installer. Preparing to unpack .../132-python3-installer_0.7.0+dfsg1-3_all.deb ... Unpacking python3-installer (0.7.0+dfsg1-3) ... Selecting previously unselected package pybuild-plugin-pyproject. Preparing to unpack .../133-pybuild-plugin-pyproject_6.20240603_all.deb ... Unpacking pybuild-plugin-pyproject (6.20240603) ... Selecting previously unselected package python-matplotlib-data. Preparing to unpack .../134-python-matplotlib-data_3.8.3-3_all.deb ... Unpacking python-matplotlib-data (3.8.3-3) ... Selecting previously unselected package python3-all. Preparing to unpack .../135-python3-all_3.12.5-1_arm64.deb ... Unpacking python3-all (3.12.5-1) ... Selecting previously unselected package python3-appdirs. Preparing to unpack .../136-python3-appdirs_1.4.4-4_all.deb ... Unpacking python3-appdirs (1.4.4-4) ... Selecting previously unselected package python3-attr. Preparing to unpack .../137-python3-attr_23.2.0-2_all.deb ... Unpacking python3-attr (23.2.0-2) ... Selecting previously unselected package python3-numpy. Preparing to unpack .../138-python3-numpy_1%3a1.26.4+ds-11_arm64.deb ... Unpacking python3-numpy (1:1.26.4+ds-11) ... Selecting previously unselected package python3-chardet. Preparing to unpack .../139-python3-chardet_5.2.0+dfsg-1_all.deb ... Unpacking python3-chardet (5.2.0+dfsg-1) ... Selecting previously unselected package python3-tk:arm64. Preparing to unpack .../140-python3-tk_3.12.5-1_arm64.deb ... Unpacking python3-tk:arm64 (3.12.5-1) ... Selecting previously unselected package python3-pil.imagetk:arm64. Preparing to unpack .../141-python3-pil.imagetk_10.4.0-1_arm64.deb ... Unpacking python3-pil.imagetk:arm64 (10.4.0-1) ... Selecting previously unselected package python3-pil:arm64. Preparing to unpack .../142-python3-pil_10.4.0-1_arm64.deb ... Unpacking python3-pil:arm64 (10.4.0-1) ... Selecting previously unselected package python3-cairo. Preparing to unpack .../143-python3-cairo_1.26.1-1+b1_arm64.deb ... Unpacking python3-cairo (1.26.1-1+b1) ... Selecting previously unselected package python3-freetype. Preparing to unpack .../144-python3-freetype_2.4.0-2_all.deb ... Unpacking python3-freetype (2.4.0-2) ... Selecting previously unselected package python3-rlpycairo. Preparing to unpack .../145-python3-rlpycairo_0.3.0-3_all.deb ... Unpacking python3-rlpycairo (0.3.0-3) ... Selecting previously unselected package python3-reportlab. Preparing to unpack .../146-python3-reportlab_4.2.2-1_all.deb ... Unpacking python3-reportlab (4.2.2-1) ... Selecting previously unselected package xml-core. Preparing to unpack .../147-xml-core_0.19_all.deb ... Unpacking xml-core (0.19) ... Selecting previously unselected package w3c-sgml-lib. Preparing to unpack .../148-w3c-sgml-lib_1.3-3_all.deb ... Unpacking w3c-sgml-lib (1.3-3) ... Selecting previously unselected package python3-biopython. Preparing to unpack .../149-python3-biopython_1.83+dfsg1-3+b1_arm64.deb ... Unpacking python3-biopython (1.83+dfsg1-3+b1) ... Selecting previously unselected package python3-brotli. Preparing to unpack .../150-python3-brotli_1.1.0-2+b4_arm64.deb ... Unpacking python3-brotli (1.1.0-2+b4) ... Selecting previously unselected package python3-contourpy. Preparing to unpack .../151-python3-contourpy_1.2.1-1_arm64.deb ... Unpacking python3-contourpy (1.2.1-1) ... Selecting previously unselected package python3-cycler. Preparing to unpack .../152-python3-cycler_0.12.1-1_all.deb ... Unpacking python3-cycler (0.12.1-1) ... Selecting previously unselected package python3-six. Preparing to unpack .../153-python3-six_1.16.0-7_all.deb ... Unpacking python3-six (1.16.0-7) ... Selecting previously unselected package python3-dateutil. Preparing to unpack .../154-python3-dateutil_2.9.0-2_all.deb ... Unpacking python3-dateutil (2.9.0-2) ... Selecting previously unselected package python3-decorator. Preparing to unpack .../155-python3-decorator_5.1.1-5_all.deb ... Unpacking python3-decorator (5.1.1-5) ... Selecting previously unselected package python3-scipy. Preparing to unpack .../156-python3-scipy_1.13.1-3_arm64.deb ... Unpacking python3-scipy (1.13.1-3) ... Selecting previously unselected package python3-ufolib2. Preparing to unpack .../157-python3-ufolib2_0.16.0+dfsg1-1_all.deb ... Unpacking python3-ufolib2 (0.16.0+dfsg1-1) ... Selecting previously unselected package python3-mpmath. Preparing to unpack .../158-python3-mpmath_1.3.0-1_all.deb ... Unpacking python3-mpmath (1.3.0-1) ... Selecting previously unselected package python3-sympy. Preparing to unpack .../159-python3-sympy_1.13.1-1_all.deb ... Unpacking python3-sympy (1.13.1-1) ... Selecting previously unselected package python3-tz. Preparing to unpack .../160-python3-tz_2024.1-2_all.deb ... Unpacking python3-tz (2024.1-2) ... Selecting previously unselected package python3-fs. Preparing to unpack .../161-python3-fs_2.4.16-4_all.deb ... Unpacking python3-fs (2.4.16-4) ... Selecting previously unselected package python3-lxml:arm64. Preparing to unpack .../162-python3-lxml_5.2.2-2_arm64.deb ... Unpacking python3-lxml:arm64 (5.2.2-2) ... Selecting previously unselected package python3-lz4. Preparing to unpack .../163-python3-lz4_4.0.2+dfsg-1+b4_arm64.deb ... Unpacking python3-lz4 (4.0.2+dfsg-1+b4) ... Selecting previously unselected package unicode-data. Preparing to unpack .../164-unicode-data_15.1.0-1_all.deb ... Unpacking unicode-data (15.1.0-1) ... Selecting previously unselected package python3-fonttools. Preparing to unpack .../165-python3-fonttools_4.46.0-1+b1_arm64.deb ... Unpacking python3-fonttools (4.46.0-1+b1) ... Selecting previously unselected package python3-iniconfig. Preparing to unpack .../166-python3-iniconfig_1.1.1-2_all.deb ... Unpacking python3-iniconfig (1.1.1-2) ... Selecting previously unselected package python3-joblib. Preparing to unpack .../167-python3-joblib_1.3.2-2_all.deb ... Unpacking python3-joblib (1.3.2-2) ... Selecting previously unselected package python3-kiwisolver. Preparing to unpack .../168-python3-kiwisolver_1.4.5-1+b1_arm64.deb ... Unpacking python3-kiwisolver (1.4.5-1+b1) ... Selecting previously unselected package python3-pyparsing. Preparing to unpack .../169-python3-pyparsing_3.1.2-1_all.deb ... Unpacking python3-pyparsing (3.1.2-1) ... Selecting previously unselected package python3-matplotlib. Preparing to unpack .../170-python3-matplotlib_3.8.3-3_arm64.deb ... Unpacking python3-matplotlib (3.8.3-3) ... Selecting previously unselected package python3-networkx. Preparing to unpack .../171-python3-networkx_3.2.1-4_all.deb ... Unpacking python3-networkx (3.2.1-4) ... Selecting previously unselected package python3-pandas-lib:arm64. Preparing to unpack .../172-python3-pandas-lib_2.2.2+dfsg-4+b1_arm64.deb ... Unpacking python3-pandas-lib:arm64 (2.2.2+dfsg-4+b1) ... Selecting previously unselected package python3-pandas. Preparing to unpack .../173-python3-pandas_2.2.2+dfsg-4_all.deb ... Unpacking python3-pandas (2.2.2+dfsg-4) ... Selecting previously unselected package python3-pluggy. Preparing to unpack .../174-python3-pluggy_1.5.0-1_all.deb ... Unpacking python3-pluggy (1.5.0-1) ... Selecting previously unselected package python3-yaml. Preparing to unpack .../175-python3-yaml_6.0.1-2+b1_arm64.deb ... Unpacking python3-yaml (6.0.1-2+b1) ... Selecting previously unselected package python3-pomegranate. Preparing to unpack .../176-python3-pomegranate_0.14.8-6+b1_arm64.deb ... Unpacking python3-pomegranate (0.14.8-6+b1) ... Selecting previously unselected package python3-pyfaidx. Preparing to unpack .../177-python3-pyfaidx_0.8.1.2-1_all.deb ... Unpacking python3-pyfaidx (0.8.1.2-1) ... Selecting previously unselected package python3-pysam. Preparing to unpack .../178-python3-pysam_0.22.1+ds-2+b1_arm64.deb ... Unpacking python3-pysam (0.22.1+ds-2+b1) ... Selecting previously unselected package python3-pytest. Preparing to unpack .../179-python3-pytest_8.3.2-1_all.deb ... Unpacking python3-pytest (8.3.2-1) ... Selecting previously unselected package zip. Preparing to unpack .../180-zip_3.0-14_arm64.deb ... Unpacking zip (3.0-14) ... Selecting previously unselected package unzip. Preparing to unpack .../181-unzip_6.0-28_arm64.deb ... Unpacking unzip (6.0-28) ... Selecting previously unselected package xdg-utils. Preparing to unpack .../182-xdg-utils_1.1.3-4.1_all.deb ... Unpacking xdg-utils (1.1.3-4.1) ... Selecting previously unselected package r-base-core. Preparing to unpack .../183-r-base-core_4.4.1-1_arm64.deb ... Unpacking r-base-core (4.4.1-1) ... Selecting previously unselected package r-bioc-biocgenerics. Preparing to unpack .../184-r-bioc-biocgenerics_0.48.1-2_all.deb ... Unpacking r-bioc-biocgenerics (0.48.1-2) ... Selecting previously unselected package r-bioc-dnacopy. Preparing to unpack .../185-r-bioc-dnacopy_1.76.0-1_arm64.deb ... Unpacking r-bioc-dnacopy (1.76.0-1) ... Setting up libhtscodecs2:arm64 (1.6.0-1+b1) ... Setting up media-types (10.1.0) ... Setting up libpipeline1:arm64 (1.5.7-2) ... Setting up libgraphite2-3:arm64 (1.3.14-2) ... Setting up liblcms2-2:arm64 (2.14-2+b1) ... Setting up libpixman-1-0:arm64 (0.42.2-1+b1) ... Setting up libsharpyuv0:arm64 (1.4.0-0.1) ... Setting up libxau6:arm64 (1:1.0.9-1+b1) ... Setting up libxdmcp6:arm64 (1:1.1.2-3+b1) ... Setting up libkeyutils1:arm64 (1.6.3-3) ... Setting up libxcb1:arm64 (1.17.0-2) ... Setting up libicu72:arm64 (72.1-5) ... Setting up liblerc4:arm64 (4.0.0+ds-4+b1) ... Setting up bsdextrautils (2.40.2-6) ... Setting up libdatrie1:arm64 (0.2.13-3) ... Setting up libmagic-mgc (1:5.45-3) ... Setting up libxcb-render0:arm64 (1.17.0-2) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libyaml-0-2:arm64 (0.2.5-1+b1) ... Setting up libtirpc-common (1.3.4+ds-1.3) ... Setting up fonts-lyx (2.4.1-2) ... Setting up unzip (6.0-28) ... Setting up libdebhelper-perl (13.16) ... Setting up libbrotli1:arm64 (1.1.0-2+b4) ... Setting up libmagic1t64:arm64 (1:5.45-3) ... Setting up x11-common (1:7.7+23.1) ... invoke-rc.d: could not determine current runlevel Setting up X socket directories... /tmp/.X11-unix /tmp/.ICE-unix. Setting up libpsl5t64:arm64 (0.21.2-1.1) ... Setting up libnghttp2-14:arm64 (1.62.1-2) ... Setting up libdeflate0:arm64 (1.20-1) ... Setting up gettext-base (0.22.5-2) ... Setting up m4 (1.4.19-4) ... Setting up libqhull-r8.0:arm64 (2020.2-6+b1) ... Setting up libxcb-shm0:arm64 (1.17.0-2) ... Setting up libcom-err2:arm64 (1.47.1-1) ... Setting up file (1:5.45-3) ... Setting up libjbig0:arm64 (2.1-6.1+b1) ... Setting up libelf1t64:arm64 (0.191-2) ... Setting up libkrb5support0:arm64 (1.21.3-3) ... Setting up libsasl2-modules-db:arm64 (2.1.28+dfsg1-7) ... Setting up tzdata (2024a-4) ... Current default time zone: 'Etc/UTC' Local time is now: Sun Sep 14 16:24:37 UTC 2025. Universal Time is now: Sun Sep 14 16:24:37 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up unicode-data (15.1.0-1) ... Setting up zip (3.0-14) ... Setting up libfontenc1:arm64 (1:1.1.8-1) ... Setting up autotools-dev (20220109.1) ... Setting up libglib2.0-0t64:arm64 (2.81.1-3) ... No schema files found: doing nothing. Setting up libblas3:arm64 (3.12.0-3) ... 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 libjpeg62-turbo:arm64 (1:2.1.5-3) ... Setting up libx11-data (2:1.8.7-1) ... Setting up libnspr4:arm64 (2:4.35-1.1+b1) ... Setting up librtmp1:arm64 (2.4+20151223.gitfa8646d.1-2+b4) ... Setting up xfonts-encodings (1:1.0.4-2.2) ... Setting up libfribidi0:arm64 (1.0.15-1) ... Setting up libimagequant0:arm64 (2.18.0-1+b1) ... Setting up libproc2-0:arm64 (2:4.0.4-5) ... Setting up fonts-dejavu-mono (2.37-8) ... Setting up libpng16-16t64:arm64 (1.6.43-5) ... Setting up libtcl8.6:arm64 (8.6.14+dfsg-1) ... Setting up autopoint (0.22.5-2) ... Setting up fonts-dejavu-core (2.37-8) ... Setting up libk5crypto3:arm64 (1.21.3-3) ... Setting up libsasl2-2:arm64 (2.1.28+dfsg1-7) ... Setting up libgfortran5:arm64 (14.2.0-2) ... Setting up autoconf (2.71-3) ... Setting up libnghttp3-9:arm64 (1.4.0-1) ... Setting up libwebp7:arm64 (1.4.0-0.1) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.24) ... Setting up libtiff6:arm64 (4.5.1+git230720-4) ... Setting up libuchardet0:arm64 (0.0.8-1+b1) ... Setting up procps (2:4.0.4-5) ... Setting up libopenjp2-7:arm64 (2.5.0-2+b3) ... Setting up libx11-6:arm64 (2:1.8.7-1+b1) ... Setting up libthai-data (0.1.29-2) ... Setting up netbase (6.4) ... Setting up libngtcp2-16:arm64 (1.6.0-1) ... Setting up sgml-base (1.31) ... Setting up libkrb5-3:arm64 (1.21.3-3) ... Setting up libssh2-1t64:arm64 (1.11.0-7) ... Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Setting up python-matplotlib-data (3.8.3-3) ... Setting up openssl (3.3.1-2) ... Setting up libwebpmux3:arm64 (1.4.0-0.1) ... Setting up readline-common (8.2-4) ... Setting up libxml2:arm64 (2.12.7+dfsg-3+b1) ... Setting up xdg-utils (1.1.3-4.1) ... update-alternatives: using /usr/bin/xdg-open to provide /usr/bin/open (open) in auto mode Setting up libngtcp2-crypto-gnutls8:arm64 (1.6.0-1) ... 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 (1.14.0-1) ... Setting up libice6:arm64 (2:1.0.10-1+b1) ... Setting up liblapack3:arm64 (3.12.0-3) ... 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 (0.22.5-2) ... Setting up libxrender1:arm64 (1:0.9.10-1.1+b1) ... Setting up libtool (2.4.7-7) ... Setting up fontconfig-config (2.15.0-1.1) ... Setting up libwebpdemux2:arm64 (1.4.0-0.1) ... Setting up libxext6:arm64 (2:1.3.4-1+b1) ... Setting up libnss3:arm64 (2:3.103-1) ... Setting up libldap-2.5-0:arm64 (2.5.18+dfsg-2) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up libthai0:arm64 (0.1.29-2) ... Setting up ca-certificates (20240203) ... Updating certificates in /etc/ssl/certs... 146 added, 0 removed; done. Setting up libjs-jquery-ui (1.13.2+dfsg-1) ... Setting up libfreetype6:arm64 (2.13.2+dfsg-1+b4) ... Setting up libgssapi-krb5-2:arm64 (1.21.3-3) ... Setting up ucf (3.0043+nmu1) ... Setting up libreadline8t64:arm64 (8.2-4) ... Setting up dh-strip-nondeterminism (1.14.0-1) ... Setting up groff-base (1.23.0-5) ... Setting up xml-core (0.19) ... Setting up libxslt1.1:arm64 (1.1.35-1.1) ... Setting up libharfbuzz0b:arm64 (8.3.0-2+b1) ... Setting up libxss1:arm64 (1:1.2.3-1+b1) ... Setting up libfontconfig1:arm64 (2.15.0-1.1) ... Setting up libsm6:arm64 (2:1.2.3-1+b1) ... Setting up liblbfgsb0:arm64 (3.0+dfsg.4-1+b1) ... Setting up libpaper1:arm64 (1.1.29+b1) ... Creating config file /etc/papersize with new version Setting up fontconfig (2.15.0-1.1) ... Regenerating fonts cache... done. Setting up libxft2:arm64 (2.3.6-1+b1) ... Setting up libcurl4t64:arm64 (8.9.1-2) ... Setting up libtirpc3t64:arm64 (1.3.4+ds-1.3) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libtk8.6:arm64 (8.6.14-1) ... Setting up libpango-1.0-0:arm64 (1.54.0+ds-1) ... Setting up libcurl3t64-gnutls:arm64 (8.9.1-2) ... Setting up libpaper-utils (1.1.29+b1) ... Setting up xfonts-utils (1:7.7+6) ... Setting up man-db (2.12.1-3) ... Not building database; man-db/auto-update is not 'true'. Setting up libcairo2:arm64 (1.18.0-3+b1) ... Setting up libraqm0:arm64 (0.10.1-1+b1) ... Setting up libxt6t64:arm64 (1:1.2.1-1.2) ... Setting up libnsl2:arm64 (1.3.0-3+b2) ... Setting up libhts3t64:arm64 (1.20+ds-1) ... Setting up libpangoft2-1.0-0:arm64 (1.54.0+ds-1) ... Setting up libpangocairo-1.0-0:arm64 (1.54.0+ds-1) ... Setting up tk8.6-blt2.5 (2.5.3+dfsg-7) ... Setting up libpython3.12-stdlib:arm64 (3.12.5-1) ... Setting up libpoppler134:arm64 (24.02.0-5+b1) ... Setting up blt (2.5.3+dfsg-7) ... Setting up python3.12 (3.12.5-1) ... Setting up debhelper (13.16) ... Setting up fonts-urw-base35 (20200910-8) ... Setting up r-base-core (4.4.1-1) ... Creating config file /etc/R/Renviron with new version Setting up poppler-utils (24.02.0-5+b1) ... Setting up libpython3-stdlib:arm64 (3.12.5-1) ... Setting up r-bioc-biocgenerics (0.48.1-2) ... Setting up python3 (3.12.5-1) ... Setting up python3-zipp (3.19.2-3) ... Setting up python3-freetype (2.4.0-2) ... Setting up python3-wheel (0.43.0-1) ... Setting up python3-tz (2024.1-2) ... Setting up python3-six (1.16.0-7) ... Setting up python3-pil:arm64 (10.4.0-1) ... Setting up python3-decorator (5.1.1-5) ... Setting up python3-packaging (24.1-1) ... Setting up python3-pyproject-hooks (1.1.0-2) ... Setting up python3-pyparsing (3.1.2-1) ... Setting up python3-brotli (1.1.0-2+b4) ... Setting up python3-cycler (0.12.1-1) ... Setting up python3-kiwisolver (1.4.5-1+b1) ... Setting up python3-toml (0.10.2-1) ... Setting up python3-installer (0.7.0+dfsg1-3) ... Setting up python3-pluggy (1.5.0-1) ... Setting up r-bioc-dnacopy (1.76.0-1) ... Setting up python3-lxml:arm64 (5.2.2-2) ... Setting up python3-dateutil (2.9.0-2) ... Setting up python3-mpmath (1.3.0-1) ... Setting up python3-build (1.2.1-1) ... Setting up python3-appdirs (1.4.4-4) ... Setting up python3-pkg-resources (70.3.0-2) ... Setting up python3-iniconfig (1.1.1-2) ... Setting up python3-sympy (1.13.1-1) ... Setting up python3-attr (23.2.0-2) ... Setting up python3-pysam (0.22.1+ds-2+b1) ... Setting up python3-cairo (1.26.1-1+b1) ... Setting up python3-importlib-metadata (8.2.0-2) ... Setting up python3-setuptools (70.3.0-2) ... Setting up python3-joblib (1.3.2-2) ... Setting up python3-lz4 (4.0.2+dfsg-1+b4) ... Setting up python3-pytest (8.3.2-1) ... Setting up python3-all (3.12.5-1) ... Setting up python3-yaml (6.0.1-2+b1) ... Setting up python3-tk:arm64 (3.12.5-1) ... Setting up python3-networkx (3.2.1-4) ... Setting up python3-fs (2.4.16-4) ... Setting up python3-chardet (5.2.0+dfsg-1) ... Setting up python3-pil.imagetk:arm64 (10.4.0-1) ... Setting up python3-rlpycairo (0.3.0-3) ... Setting up python3-numpy (1:1.26.4+ds-11) ... Setting up python3-reportlab (4.2.2-1) ... Setting up python3-contourpy (1.2.1-1) ... Setting up dh-python (6.20240603) ... Setting up python3-pyfaidx (0.8.1.2-1) ... Setting up python3-scipy (1.13.1-3) ... Setting up pybuild-plugin-pyproject (6.20240603) ... Setting up python3-pomegranate (0.14.8-6+b1) ... Setting up python3-pandas-lib:arm64 (2.2.2+dfsg-4+b1) ... Setting up python3-pandas (2.2.2+dfsg-4) ... Setting up python3-fonttools (4.46.0-1+b1) ... Setting up python3-ufolib2 (0.16.0+dfsg1-1) ... Setting up python3-matplotlib (3.8.3-3) ... Processing triggers for libc-bin (2.39-6) ... Processing triggers for sgml-base (1.31) ... Setting up w3c-sgml-lib (1.3-3) ... Setting up python3-biopython (1.83+dfsg1-3+b1) ... Processing triggers for ca-certificates (20240203) ... 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 I: Building the package I: user script /srv/workspace/pbuilder/1227257/tmp/hooks/A99_set_merged_usr starting Not re-configuring usrmerge for unstable I: user script /srv/workspace/pbuilder/1227257/tmp/hooks/A99_set_merged_usr finished hostname: Name or service not known I: Running cd /build/reproducible-path/cnvkit-0.9.10/ && 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 > ../cnvkit_0.9.10-2_source.changes dpkg-buildpackage: info: source package cnvkit dpkg-buildpackage: info: source version 0.9.10-2 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Michael R. Crusoe dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 debian/rules clean dh clean --buildsystem=pybuild debian/rules override_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/cnvkit-0.9.10' cd test && /usr/bin/make clean || /bin/true make[2]: Entering directory '/build/reproducible-path/cnvkit-0.9.10/test' # Picard rm -rf build/p*targetcoverage.cnn build/reference-picard.cnn build/p2-5_5.cnr build/p2-9_2.cnr build/p2-20_1.cnr build/p2-20_2.cnr build/p2-20_3.cnr build/p2-20_4.cnr build/p2-20_5.cnr build/p2-5_5.cns build/p2-9_2.cns build/p2-20_1.cns build/p2-20_2.cns build/p2-20_3.cns build/p2-20_4.cns build/p2-20_5.cns all-scatters.pdf all-diagrams.pdf heatmap-picard.pdf p2-9_2-breaks.txt p2-9_2-genemetrics.txt gender-picard.txt p2-all.cdt p2-all-jtv.txt p2-all.seg p2-9_2.nexus p2-9_2.nexus-ogt p2-all.bed p2-9_2.vcf p2-9_2.theta2.input p2-9_2-segmetrics.cns p2-5_5-segmetrics.cns p*-scatter.pdf p*-diagram.pdf make[2]: Leaving directory '/build/reproducible-path/cnvkit-0.9.10/test' dh_auto_clean make[1]: Leaving directory '/build/reproducible-path/cnvkit-0.9.10' dh_autoreconf_clean -O--buildsystem=pybuild dh_clean -O--buildsystem=pybuild debian/rules binary dh binary --buildsystem=pybuild dh_update_autotools_config -O--buildsystem=pybuild dh_autoreconf -O--buildsystem=pybuild dh_auto_configure -O--buildsystem=pybuild dh_auto_build -O--buildsystem=pybuild I: pybuild plugin_pyproject:129: Building wheel for python3.12 with "build" module I: pybuild base:311: python3.12 -m build --skip-dependency-check --no-isolation --wheel --outdir /build/reproducible-path/cnvkit-0.9.10/.pybuild/cpython3_3.12_cnvkit * Building wheel... running bdist_wheel running build running build_py creating build creating build/lib creating build/lib/cnvlib copying cnvlib/commands.py -> build/lib/cnvlib copying cnvlib/vary.py -> build/lib/cnvlib copying cnvlib/target.py -> build/lib/cnvlib copying cnvlib/smoothing.py -> build/lib/cnvlib copying cnvlib/segmetrics.py -> build/lib/cnvlib copying cnvlib/segfilters.py -> build/lib/cnvlib copying cnvlib/scatter.py -> build/lib/cnvlib copying cnvlib/samutil.py -> build/lib/cnvlib copying cnvlib/rna.py -> build/lib/cnvlib copying cnvlib/reports.py -> build/lib/cnvlib copying cnvlib/reference.py -> build/lib/cnvlib copying cnvlib/plots.py -> build/lib/cnvlib copying cnvlib/params.py -> build/lib/cnvlib copying cnvlib/parallel.py -> build/lib/cnvlib copying cnvlib/metrics.py -> build/lib/cnvlib copying cnvlib/importers.py -> build/lib/cnvlib copying cnvlib/import_rna.py -> build/lib/cnvlib copying cnvlib/heatmap.py -> build/lib/cnvlib copying cnvlib/fix.py -> build/lib/cnvlib copying cnvlib/export.py -> build/lib/cnvlib copying cnvlib/diagram.py -> build/lib/cnvlib copying cnvlib/descriptives.py -> build/lib/cnvlib copying cnvlib/coverage.py -> build/lib/cnvlib copying cnvlib/core.py -> build/lib/cnvlib copying cnvlib/cnvkit.py -> build/lib/cnvlib copying cnvlib/cnary.py -> build/lib/cnvlib copying cnvlib/cmdutil.py -> build/lib/cnvlib copying cnvlib/cluster.py -> build/lib/cnvlib copying cnvlib/call.py -> build/lib/cnvlib copying cnvlib/bintest.py -> build/lib/cnvlib copying cnvlib/batch.py -> build/lib/cnvlib copying cnvlib/autobin.py -> build/lib/cnvlib copying cnvlib/antitarget.py -> build/lib/cnvlib copying cnvlib/access.py -> build/lib/cnvlib copying cnvlib/_version.py -> build/lib/cnvlib copying cnvlib/__init__.py -> build/lib/cnvlib creating build/lib/cnvlib/segmentation copying cnvlib/segmentation/none.py -> build/lib/cnvlib/segmentation copying cnvlib/segmentation/hmm.py -> build/lib/cnvlib/segmentation copying cnvlib/segmentation/haar.py -> build/lib/cnvlib/segmentation copying cnvlib/segmentation/flasso.py -> build/lib/cnvlib/segmentation copying cnvlib/segmentation/cbs.py -> build/lib/cnvlib/segmentation copying cnvlib/segmentation/__init__.py -> build/lib/cnvlib/segmentation creating build/lib/skgenome copying skgenome/subtract.py -> build/lib/skgenome copying skgenome/subdivide.py -> build/lib/skgenome copying skgenome/rangelabel.py -> build/lib/skgenome copying skgenome/merge.py -> build/lib/skgenome copying skgenome/intersect.py -> build/lib/skgenome copying skgenome/gary.py -> build/lib/skgenome copying skgenome/combiners.py -> build/lib/skgenome copying skgenome/chromsort.py -> build/lib/skgenome copying skgenome/__init__.py -> build/lib/skgenome creating build/lib/skgenome/tabio copying skgenome/tabio/vcfsimple.py -> build/lib/skgenome/tabio copying skgenome/tabio/vcfio.py -> build/lib/skgenome/tabio copying skgenome/tabio/util.py -> build/lib/skgenome/tabio copying skgenome/tabio/textcoord.py -> build/lib/skgenome/tabio copying skgenome/tabio/tab.py -> build/lib/skgenome/tabio copying skgenome/tabio/seqdict.py -> build/lib/skgenome/tabio copying skgenome/tabio/seg.py -> build/lib/skgenome/tabio copying skgenome/tabio/picard.py -> build/lib/skgenome/tabio copying skgenome/tabio/gff.py -> build/lib/skgenome/tabio copying skgenome/tabio/genepred.py -> build/lib/skgenome/tabio copying skgenome/tabio/bedio.py -> build/lib/skgenome/tabio copying skgenome/tabio/__init__.py -> build/lib/skgenome/tabio running egg_info creating CNVkit.egg-info writing CNVkit.egg-info/PKG-INFO writing dependency_links to CNVkit.egg-info/dependency_links.txt writing entry points to CNVkit.egg-info/entry_points.txt writing requirements to CNVkit.egg-info/requires.txt writing top-level names to CNVkit.egg-info/top_level.txt writing manifest file 'CNVkit.egg-info/SOURCES.txt' reading manifest file 'CNVkit.egg-info/SOURCES.txt' adding license file 'LICENSE' writing manifest file 'CNVkit.egg-info/SOURCES.txt' installing to build/bdist.linux-aarch64/wheel running install running install_lib creating build/bdist.linux-aarch64 creating build/bdist.linux-aarch64/wheel creating build/bdist.linux-aarch64/wheel/skgenome creating build/bdist.linux-aarch64/wheel/skgenome/tabio copying build/lib/skgenome/tabio/__init__.py -> build/bdist.linux-aarch64/wheel/skgenome/tabio copying build/lib/skgenome/tabio/bedio.py -> build/bdist.linux-aarch64/wheel/skgenome/tabio copying build/lib/skgenome/tabio/genepred.py -> build/bdist.linux-aarch64/wheel/skgenome/tabio copying build/lib/skgenome/tabio/gff.py -> build/bdist.linux-aarch64/wheel/skgenome/tabio copying build/lib/skgenome/tabio/picard.py -> build/bdist.linux-aarch64/wheel/skgenome/tabio copying build/lib/skgenome/tabio/seg.py -> build/bdist.linux-aarch64/wheel/skgenome/tabio copying build/lib/skgenome/tabio/seqdict.py -> build/bdist.linux-aarch64/wheel/skgenome/tabio copying build/lib/skgenome/tabio/tab.py -> build/bdist.linux-aarch64/wheel/skgenome/tabio copying build/lib/skgenome/tabio/textcoord.py -> build/bdist.linux-aarch64/wheel/skgenome/tabio copying build/lib/skgenome/tabio/util.py -> build/bdist.linux-aarch64/wheel/skgenome/tabio copying build/lib/skgenome/tabio/vcfio.py -> build/bdist.linux-aarch64/wheel/skgenome/tabio copying build/lib/skgenome/tabio/vcfsimple.py -> build/bdist.linux-aarch64/wheel/skgenome/tabio copying build/lib/skgenome/__init__.py -> build/bdist.linux-aarch64/wheel/skgenome copying build/lib/skgenome/chromsort.py -> build/bdist.linux-aarch64/wheel/skgenome copying build/lib/skgenome/combiners.py -> build/bdist.linux-aarch64/wheel/skgenome copying build/lib/skgenome/gary.py -> build/bdist.linux-aarch64/wheel/skgenome copying build/lib/skgenome/intersect.py -> build/bdist.linux-aarch64/wheel/skgenome copying build/lib/skgenome/merge.py -> build/bdist.linux-aarch64/wheel/skgenome copying build/lib/skgenome/rangelabel.py -> build/bdist.linux-aarch64/wheel/skgenome copying build/lib/skgenome/subdivide.py -> build/bdist.linux-aarch64/wheel/skgenome copying build/lib/skgenome/subtract.py -> build/bdist.linux-aarch64/wheel/skgenome creating build/bdist.linux-aarch64/wheel/cnvlib creating build/bdist.linux-aarch64/wheel/cnvlib/segmentation copying build/lib/cnvlib/segmentation/__init__.py -> build/bdist.linux-aarch64/wheel/cnvlib/segmentation copying build/lib/cnvlib/segmentation/cbs.py -> build/bdist.linux-aarch64/wheel/cnvlib/segmentation copying build/lib/cnvlib/segmentation/flasso.py -> build/bdist.linux-aarch64/wheel/cnvlib/segmentation copying build/lib/cnvlib/segmentation/haar.py -> build/bdist.linux-aarch64/wheel/cnvlib/segmentation copying build/lib/cnvlib/segmentation/hmm.py -> build/bdist.linux-aarch64/wheel/cnvlib/segmentation copying build/lib/cnvlib/segmentation/none.py -> build/bdist.linux-aarch64/wheel/cnvlib/segmentation copying build/lib/cnvlib/__init__.py -> build/bdist.linux-aarch64/wheel/cnvlib copying build/lib/cnvlib/_version.py -> build/bdist.linux-aarch64/wheel/cnvlib copying build/lib/cnvlib/access.py -> build/bdist.linux-aarch64/wheel/cnvlib copying build/lib/cnvlib/antitarget.py -> build/bdist.linux-aarch64/wheel/cnvlib copying build/lib/cnvlib/autobin.py -> build/bdist.linux-aarch64/wheel/cnvlib copying build/lib/cnvlib/batch.py -> build/bdist.linux-aarch64/wheel/cnvlib copying build/lib/cnvlib/bintest.py -> build/bdist.linux-aarch64/wheel/cnvlib copying build/lib/cnvlib/call.py -> build/bdist.linux-aarch64/wheel/cnvlib copying build/lib/cnvlib/cluster.py -> build/bdist.linux-aarch64/wheel/cnvlib copying build/lib/cnvlib/cmdutil.py -> build/bdist.linux-aarch64/wheel/cnvlib copying build/lib/cnvlib/cnary.py -> build/bdist.linux-aarch64/wheel/cnvlib copying build/lib/cnvlib/cnvkit.py -> build/bdist.linux-aarch64/wheel/cnvlib copying build/lib/cnvlib/core.py -> build/bdist.linux-aarch64/wheel/cnvlib copying build/lib/cnvlib/coverage.py -> build/bdist.linux-aarch64/wheel/cnvlib copying build/lib/cnvlib/descriptives.py -> build/bdist.linux-aarch64/wheel/cnvlib copying build/lib/cnvlib/diagram.py -> build/bdist.linux-aarch64/wheel/cnvlib copying build/lib/cnvlib/export.py -> build/bdist.linux-aarch64/wheel/cnvlib copying build/lib/cnvlib/fix.py -> build/bdist.linux-aarch64/wheel/cnvlib copying build/lib/cnvlib/heatmap.py -> build/bdist.linux-aarch64/wheel/cnvlib copying build/lib/cnvlib/import_rna.py -> build/bdist.linux-aarch64/wheel/cnvlib copying build/lib/cnvlib/importers.py -> build/bdist.linux-aarch64/wheel/cnvlib copying build/lib/cnvlib/metrics.py -> build/bdist.linux-aarch64/wheel/cnvlib copying build/lib/cnvlib/parallel.py -> build/bdist.linux-aarch64/wheel/cnvlib copying build/lib/cnvlib/params.py -> build/bdist.linux-aarch64/wheel/cnvlib copying build/lib/cnvlib/plots.py -> build/bdist.linux-aarch64/wheel/cnvlib copying build/lib/cnvlib/reference.py -> build/bdist.linux-aarch64/wheel/cnvlib copying build/lib/cnvlib/reports.py -> build/bdist.linux-aarch64/wheel/cnvlib copying build/lib/cnvlib/rna.py -> build/bdist.linux-aarch64/wheel/cnvlib copying build/lib/cnvlib/samutil.py -> build/bdist.linux-aarch64/wheel/cnvlib copying build/lib/cnvlib/scatter.py -> build/bdist.linux-aarch64/wheel/cnvlib copying build/lib/cnvlib/segfilters.py -> build/bdist.linux-aarch64/wheel/cnvlib copying build/lib/cnvlib/segmetrics.py -> build/bdist.linux-aarch64/wheel/cnvlib copying build/lib/cnvlib/smoothing.py -> build/bdist.linux-aarch64/wheel/cnvlib copying build/lib/cnvlib/target.py -> build/bdist.linux-aarch64/wheel/cnvlib copying build/lib/cnvlib/vary.py -> build/bdist.linux-aarch64/wheel/cnvlib copying build/lib/cnvlib/commands.py -> build/bdist.linux-aarch64/wheel/cnvlib running install_egg_info Copying CNVkit.egg-info to build/bdist.linux-aarch64/wheel/CNVkit-0.9.10.egg-info running install_scripts creating build/bdist.linux-aarch64/wheel/CNVkit-0.9.10.dist-info/WHEEL creating '/build/reproducible-path/cnvkit-0.9.10/.pybuild/cpython3_3.12_cnvkit/.tmp-crcv3f96/CNVkit-0.9.10-py3-none-any.whl' and adding 'build/bdist.linux-aarch64/wheel' to it adding 'cnvlib/__init__.py' adding 'cnvlib/_version.py' adding 'cnvlib/access.py' adding 'cnvlib/antitarget.py' adding 'cnvlib/autobin.py' adding 'cnvlib/batch.py' adding 'cnvlib/bintest.py' adding 'cnvlib/call.py' adding 'cnvlib/cluster.py' adding 'cnvlib/cmdutil.py' adding 'cnvlib/cnary.py' adding 'cnvlib/cnvkit.py' adding 'cnvlib/commands.py' adding 'cnvlib/core.py' adding 'cnvlib/coverage.py' adding 'cnvlib/descriptives.py' adding 'cnvlib/diagram.py' adding 'cnvlib/export.py' adding 'cnvlib/fix.py' adding 'cnvlib/heatmap.py' adding 'cnvlib/import_rna.py' adding 'cnvlib/importers.py' adding 'cnvlib/metrics.py' adding 'cnvlib/parallel.py' adding 'cnvlib/params.py' adding 'cnvlib/plots.py' adding 'cnvlib/reference.py' adding 'cnvlib/reports.py' adding 'cnvlib/rna.py' adding 'cnvlib/samutil.py' adding 'cnvlib/scatter.py' adding 'cnvlib/segfilters.py' adding 'cnvlib/segmetrics.py' adding 'cnvlib/smoothing.py' adding 'cnvlib/target.py' adding 'cnvlib/vary.py' adding 'cnvlib/segmentation/__init__.py' adding 'cnvlib/segmentation/cbs.py' adding 'cnvlib/segmentation/flasso.py' adding 'cnvlib/segmentation/haar.py' adding 'cnvlib/segmentation/hmm.py' adding 'cnvlib/segmentation/none.py' adding 'skgenome/__init__.py' adding 'skgenome/chromsort.py' adding 'skgenome/combiners.py' adding 'skgenome/gary.py' adding 'skgenome/intersect.py' adding 'skgenome/merge.py' adding 'skgenome/rangelabel.py' adding 'skgenome/subdivide.py' adding 'skgenome/subtract.py' adding 'skgenome/tabio/__init__.py' adding 'skgenome/tabio/bedio.py' adding 'skgenome/tabio/genepred.py' adding 'skgenome/tabio/gff.py' adding 'skgenome/tabio/picard.py' adding 'skgenome/tabio/seg.py' adding 'skgenome/tabio/seqdict.py' adding 'skgenome/tabio/tab.py' adding 'skgenome/tabio/textcoord.py' adding 'skgenome/tabio/util.py' adding 'skgenome/tabio/vcfio.py' adding 'skgenome/tabio/vcfsimple.py' adding 'CNVkit-0.9.10.dist-info/LICENSE' adding 'CNVkit-0.9.10.dist-info/METADATA' adding 'CNVkit-0.9.10.dist-info/WHEEL' adding 'CNVkit-0.9.10.dist-info/entry_points.txt' adding 'CNVkit-0.9.10.dist-info/top_level.txt' adding 'CNVkit-0.9.10.dist-info/RECORD' removing build/bdist.linux-aarch64/wheel Successfully built CNVkit-0.9.10-py3-none-any.whl I: pybuild plugin_pyproject:144: Unpacking wheel built for python3.12 with "installer" module dh_auto_test -O--buildsystem=pybuild I: pybuild pybuild:308: ln -s /build/reproducible-path/cnvkit-0.9.10/data /build/reproducible-path/cnvkit-0.9.10/.pybuild/cpython3_3.12_cnvkit/build/data; I: pybuild base:311: cd /build/reproducible-path/cnvkit-0.9.10/.pybuild/cpython3_3.12_cnvkit/build; python3.12 -m pytest test ============================= test session starts ============================== platform linux -- Python 3.12.5, pytest-8.3.2, pluggy-1.5.0 rootdir: /build/reproducible-path/cnvkit-0.9.10/.pybuild/cpython3_3.12_cnvkit/build configfile: pyproject.toml collected 64 items test/test_cnvlib.py ......... [ 14%] test/test_commands.py ......................... [ 53%] test/test_genome.py ................... [ 82%] test/test_io.py .......... [ 98%] test/test_r.py . [100%] =============================== warnings summary =============================== test/test_commands.py::CommandTests::test_antitarget test/test_commands.py::CommandTests::test_target test/test_genome.py::GaryTests::test_ranges_resize test/test_io.py::IOTests::test_empty test/test_io.py::IOTests::test_read_auto test/test_io.py::IOTests::test_read_auto test/test_io.py::IOTests::test_read_ilist /build/reproducible-path/cnvkit-0.9.10/.pybuild/cpython3_3.12_cnvkit/build/skgenome/tabio/picard.py:27: FutureWarning: A value is trying to be set on a copy of a DataFrame or Series through chained assignment using an inplace method. The behavior will change in pandas 3.0. This inplace method will never work because the intermediate object on which we are setting values always behaves as a copy. For example, when doing 'df[col].method(value, inplace=True)', try using 'df.method({col: value}, inplace=True)' or df[col] = df[col].method(value) instead, to perform the operation inplace on the original object. dframe["gene"].fillna("-", inplace=True) test/test_commands.py: 11 warnings test/test_genome.py: 6 warnings /build/reproducible-path/cnvkit-0.9.10/.pybuild/cpython3_3.12_cnvkit/build/skgenome/merge.py:149: DeprecationWarning: DataFrameGroupBy.apply operated on the grouping columns. This behavior is deprecated, and in a future version of pandas the grouping columns will be excluded from the operation. Either pass `include_groups=False` to exclude the groupings or explicitly select the grouping columns after groupby to silence this warning. .apply(_merge_overlapping, bp, cmb) test/test_commands.py::CommandTests::test_batch /build/reproducible-path/cnvkit-0.9.10/.pybuild/cpython3_3.12_cnvkit/build/cnvlib/coverage.py:198: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise an error in a future version of pandas. Value '[0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 1.20240481 0.31062124 0.89178357 0. 0. 0. 1.20240481 0.4 0.2004008 0. 0.4008016 0.4 0.4008016 0. 0. 0. 0.4008016 0. 1.20240481 0. 0. 0. 0. 0.4 ]' has dtype incompatible with int64, please explicitly cast to a compatible dtype first. table.loc[ok_idx, "depth"] = table.loc[ok_idx, "basecount"] / spans[ok_idx] test/test_commands.py::CommandTests::test_batch test/test_commands.py::CommandTests::test_batch /build/reproducible-path/cnvkit-0.9.10/.pybuild/cpython3_3.12_cnvkit/build/cnvlib/reference.py:187: FutureWarning: The behavior of DataFrame concatenation with empty or all-NA entries is deprecated. In a future version, this will no longer exclude empty or all-NA columns when determining the result dtypes. To retain the old behavior, exclude the relevant entries before the concat operation. ref_df = pd.concat([ref_df, anti_ref_df], ignore_index=True) test/test_commands.py::CommandTests::test_batch test/test_commands.py::CommandTests::test_batch /build/reproducible-path/cnvkit-0.9.10/.pybuild/cpython3_3.12_cnvkit/build/cnvlib/coverage.py:198: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise an error in a future version of pandas. Value '[ 3. 3. 3. 3.09090909 4. 4. 3.77777778 4. 91.75 81.66666667 75.11111111]' has dtype incompatible with int64, please explicitly cast to a compatible dtype first. table.loc[ok_idx, "depth"] = table.loc[ok_idx, "basecount"] / spans[ok_idx] test/test_commands.py: 19 warnings /build/reproducible-path/cnvkit-0.9.10/.pybuild/cpython3_3.12_cnvkit/build/cnvlib/segfilters.py:72: DeprecationWarning: DataFrameGroupBy.apply operated on the grouping columns. This behavior is deprecated, and in a future version of pandas the grouping columns will be excluded from the operation. Either pass `include_groups=False` to exclude the groupings or explicitly select the grouping columns after groupby to silence this warning. .apply(squash_region) test/test_commands.py: 10 warnings /build/reproducible-path/cnvkit-0.9.10/.pybuild/cpython3_3.12_cnvkit/build/cnvlib/segfilters.py:59: FutureWarning: Downcasting behavior in `replace` is deprecated and will be removed in a future version. To retain the old behavior, explicitly call `result.infer_objects(copy=False)`. To opt-in to the future behavior, set `pd.set_option('future.no_silent_downcasting', True)` chrom_col = cnarr["chromosome"].replace( test/test_commands.py::CommandTests::test_coverage test/test_commands.py::CommandTests::test_coverage test/test_commands.py::CommandTests::test_coverage test/test_commands.py::CommandTests::test_coverage /build/reproducible-path/cnvkit-0.9.10/.pybuild/cpython3_3.12_cnvkit/build/cnvlib/coverage.py:198: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise an error in a future version of pandas. Value '[82.5 3.02325581 4. 3.88888889]' has dtype incompatible with int64, please explicitly cast to a compatible dtype first. table.loc[ok_idx, "depth"] = table.loc[ok_idx, "basecount"] / spans[ok_idx] test/test_commands.py::CommandTests::test_export_theta test/test_commands.py::CommandTests::test_export_theta /build/reproducible-path/cnvkit-0.9.10/.pybuild/cpython3_3.12_cnvkit/build/cnvlib/export.py:489: FutureWarning: Downcasting behavior in `replace` is deprecated and will be removed in a future version. To retain the old behavior, explicitly call `result.infer_objects(copy=False)`. To opt-in to the future behavior, set `pd.set_option('future.no_silent_downcasting', True)` table["chrm"] = tumor_segs.chromosome.replace(chr2idx) test/test_commands.py: 8 warnings test/test_genome.py: 21 warnings /build/reproducible-path/cnvkit-0.9.10/.pybuild/cpython3_3.12_cnvkit/build/skgenome/gary.py:90: FutureWarning: Passing a DataFrame to DataFrame.from_records is deprecated. Use set_index and/or drop to modify the DataFrame instead. table = pd.DataFrame.from_records(rows, columns=columns) test/test_commands.py::CommandTests::test_target test/test_commands.py::CommandTests::test_target test/test_commands.py::CommandTests::test_target test/test_commands.py::CommandTests::test_target test/test_commands.py::CommandTests::test_target test/test_commands.py::CommandTests::test_target test/test_genome.py::GaryTests::test_total_range_size test/test_genome.py::GaryTests::test_total_range_size /build/reproducible-path/cnvkit-0.9.10/.pybuild/cpython3_3.12_cnvkit/build/skgenome/combiners.py:53: FutureWarning: unique with argument that is not not a Series, Index, ExtensionArray, or np.ndarray is deprecated and will raise in a future version. return sep.join(pd.unique(elems)) test/test_genome.py::GaryTests::test_ranges_resize /build/reproducible-path/cnvkit-0.9.10/.pybuild/cpython3_3.12_cnvkit/build/skgenome/gary.py:669: FutureWarning: Downcasting behavior in `replace` is deprecated and will be removed in a future version. To retain the old behavior, explicitly call `result.infer_objects(copy=False)`. To opt-in to the future behavior, set `pd.set_option('future.no_silent_downcasting', True)` limits["upper"] = self.chromosome.replace(chrom_sizes) test/test_genome.py::IntervalTests::test_flatten test/test_genome.py::IntervalTests::test_flatten /build/reproducible-path/cnvkit-0.9.10/.pybuild/cpython3_3.12_cnvkit/build/skgenome/merge.py:29: DeprecationWarning: DataFrameGroupBy.apply operated on the grouping columns. This behavior is deprecated, and in a future version of pandas the grouping columns will be excluded from the operation. Either pass `include_groups=False` to exclude the groupings or explicitly select the grouping columns after groupby to silence this warning. .apply(_flatten_overlapping, cmb, split_columns) -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html ================= 64 passed, 104 warnings in 177.00s (0:02:56) ================= create-stamp debian/debhelper-build-stamp dh_testroot -O--buildsystem=pybuild dh_prep -O--buildsystem=pybuild debian/rules override_dh_auto_install make[1]: Entering directory '/build/reproducible-path/cnvkit-0.9.10' for script in `find scripts -name "*.py"` ; do \ dh_install ${script} /usr/bin; \ done dh_auto_install I: pybuild plugin_pyproject:178: Copying package built for python3.12 to destdir make[1]: Leaving directory '/build/reproducible-path/cnvkit-0.9.10' dh_install -O--buildsystem=pybuild dh_installdocs -O--buildsystem=pybuild dh_installchangelogs -O--buildsystem=pybuild dh_installexamples -O--buildsystem=pybuild dh_installman -O--buildsystem=pybuild dh_python3 -O--buildsystem=pybuild I: dh_python3 tools:113: replacing shebang in debian/cnvkit/usr/bin/genome_instability_index.py dh_installsystemduser -O--buildsystem=pybuild dh_lintian -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 'cnvkit' in '../cnvkit_0.9.10-2_all.deb'. dpkg-genbuildinfo --build=binary -O../cnvkit_0.9.10-2_arm64.buildinfo dpkg-genchanges --build=binary -O../cnvkit_0.9.10-2_arm64.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/1227257/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/1227257/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/1227257 and its subdirectories I: Current time: Mon Sep 15 06:33:55 +14 2025 I: pbuilder-time-stamp: 1757867635