Sun Oct 6 23:19:16 UTC 2024 I: starting to build cnvkit/experimental/arm64 on jenkins on '2024-10-06 23:19' Sun Oct 6 23:19:16 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/arm64_5/62384/console.log Sun Oct 6 23:19:16 UTC 2024 I: Downloading source for experimental/cnvkit=0.9.10-3~0exp0 --2024-10-06 23:19:17-- http://cdn-fastly.deb.debian.org/debian/pool/main/c/cnvkit/cnvkit_0.9.10-3%7e0exp0.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2485 (2.4K) [text/prs.lines.tag] Saving to: ‘cnvkit_0.9.10-3~0exp0.dsc’ 0K .. 100% 288M=0s 2024-10-06 23:19:17 (288 MB/s) - ‘cnvkit_0.9.10-3~0exp0.dsc’ saved [2485/2485] Sun Oct 6 23:19:17 UTC 2024 I: cnvkit_0.9.10-3~0exp0.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: cnvkit Binary: cnvkit Architecture: all Version: 0.9.10-3~0exp0 Maintainer: Debian Med Packaging Team Uploaders: Michael R. Crusoe , Steffen Moeller , Olivier Sallou Homepage: https://cnvkit.readthedocs.org Standards-Version: 4.6.2 Vcs-Browser: https://salsa.debian.org/med-team/cnvkit Vcs-Git: https://salsa.debian.org/med-team/cnvkit.git Testsuite: autopkgtest, autopkgtest-pkg-pybuild Testsuite-Triggers: poppler-utils Build-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 (>= 1.78.0) , poppler-utils Package-List: cnvkit deb science optional arch=all Checksums-Sha1: 98f56ef2f4c5258ceef043d0ad0e346993f5931a 23663020 cnvkit_0.9.10.orig.tar.gz f7484c46900519e20a2c8cc3ab1b556cb3019c13 17732 cnvkit_0.9.10-3~0exp0.debian.tar.xz Checksums-Sha256: 56739496f1f59511661107e662d81e5fd8af413571e853b0a1b34d882a19349a 23663020 cnvkit_0.9.10.orig.tar.gz 696ffcc1cc38377e62932d50df600747ab8bbfb7a986ab9f4090d758ca9ff7c0 17732 cnvkit_0.9.10-3~0exp0.debian.tar.xz Files: ac1e8d636fc0fc694d1475a212d0cf98 23663020 cnvkit_0.9.10.orig.tar.gz d6423a6acc31aea516cf9f337be69c58 17732 cnvkit_0.9.10-3~0exp0.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQIzBAEBCgAdFiEEck1gkzcRPHEFUNdHPCZ2P2xn5uIFAmaeeYMACgkQPCZ2P2xn 5uIsABAApF6vdPs8ZTgv6rRnDeFByt1Bt6jMaETnIFx2HuqO10tqhFamBiN9mKS/ 9lK+82hAWBowR/lYaMPZ+W6Ob3C8PzlstbK95+t9kD2rkEECdytLWonyb7BawV/u hIwxZKOxeEAww8/q6vOEom6VCModBQgB5Q57ASUE5TUgfLsKK6m0grKrulP7UOlr WA3xMxgeVPOVabocLqU+7vOT9dMV7tmq3rXLbLgBNkiadMcIljZRFh+a0+9CPvMt M6+2Zy+nJ8TpC5dA8VFles68cdgZpZ8GjDCpc27NKEFMpe4QjL1EEf86QRxCLWJ4 tDFpIYB7xOdi+L/3lp05E48zWruofJa4ovk8hYdxmnpbSHFh1PQp1fy6Pofp8E02 QIt4CM0wYQ/Q4pfOteMzKPVT1wy1ubcxPfnMmiVKWDX9d8BNmtBUjx2/mtBeatO4 q3Mc+sw9xOlAcjGVWyRnDkVkejcIoCdnYvcMzOeRznRSseLhN5WZXItB4SdZde22 /XiW2BR1cdZwmtDzbbqhQvM5tISwkMb0y80RSbJj6XBqlUo5QKDfhM87RT8NkMRL qFLzIzYLXGJkqlD2Kcu01r8ZYjZnPEK7eoyv/cviOHv3nIKKb9d5fgmYjmMY19ZY +E5SAMqVU5ljM/9PLcSgO4KUd4wUmP/JnlqOu3Wl+FJ5Yy/wUes= =aJK8 -----END PGP SIGNATURE----- Sun Oct 6 23:19:17 UTC 2024 I: Checking whether the package is not for us Sun Oct 6 23:19:17 UTC 2024 I: Starting 1st build on remote node codethink03-arm64.debian.net. Sun Oct 6 23:19:17 UTC 2024 I: Preparing to do remote build '1' on codethink03-arm64.debian.net. Sun Oct 6 23:23:36 UTC 2024 I: Deleting $TMPDIR on codethink03-arm64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Sat Nov 8 17:42:19 -12 2025 I: pbuilder-time-stamp: 1762666939 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/experimental-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_0.9.10-3~0exp0.dsc] I: copying [./cnvkit_0.9.10.orig.tar.gz] I: copying [./cnvkit_0.9.10-3~0exp0.debian.tar.xz] I: Extracting source gpgv: Signature made Mon Jul 22 15:23:47 2024 gpgv: using RSA key 724D609337113C710550D7473C26763F6C67E6E2 gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./cnvkit_0.9.10-3~0exp0.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_0.9.10-3~0exp0.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/367751/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='arm64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' DISTRIBUTION='experimental' HOME='/root' HOST_ARCH='arm64' IFS=' ' INVOCATION_ID='8b1f0dcb1f464e9280f28f81a7f32ca5' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='367751' PS1='# ' PS2='> ' PS4='+ ' PWD='/' SHELL='/bin/bash' SHLVL='2' SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.M5ynHTct/pbuilderrc_CrkT --distribution experimental --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/experimental-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.M5ynHTct/b1 --logfile b1/build.log cnvkit_0.9.10-3~0exp0.dsc' SUDO_GID='109' SUDO_UID='104' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://192.168.101.4:3128' I: uname -a Linux codethink03-arm64 6.1.0-26-cloud-arm64 #1 SMP Debian 6.1.112-1 (2024-09-30) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 4 2024 /bin -> usr/bin I: user script /srv/workspace/pbuilder/367751/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 (>= 1.78.0), 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 ... 19895 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 (>= 1.78.0); 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} libpoppler140{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-autocommand{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-inflect{a} python3-iniconfig{a} python3-installer{a} python3-jaraco.context{a} python3-jaraco.functools{a} python3-joblib{a} python3-kiwisolver{a} python3-lxml{a} python3-lz4{a} python3-matplotlib{a} python3-minimal{a} python3-more-itertools{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-typeguard{a} python3-typing-extensions{a} python3-tz{a} python3-ufolib2{a} python3-wheel{a} python3-yaml{a} python3-zipp{a} python3.12{a} python3.12-minimal{a} python3.12-tk{a} python3.13-tk{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, 216 newly installed, 0 to remove and 0 not upgraded. Need to get 168 MB of archives. After unpacking 681 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main arm64 libpython3.12-minimal arm64 3.12.7-1 [807 kB] Get: 2 http://deb.debian.org/debian unstable/main arm64 libexpat1 arm64 2.6.3-1 [90.2 kB] Get: 3 http://deb.debian.org/debian unstable/main arm64 python3.12-minimal arm64 3.12.7-1 [1941 kB] Get: 4 http://deb.debian.org/debian unstable/main arm64 python3-minimal arm64 3.12.6-1 [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 2024b-2 [256 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 8.2-5 [69.3 kB] Get: 18 http://deb.debian.org/debian unstable/main arm64 libreadline8t64 arm64 8.2-5 [159 kB] Get: 19 http://deb.debian.org/debian unstable/main arm64 libpython3.12-stdlib arm64 3.12.7-1 [1901 kB] Get: 20 http://deb.debian.org/debian unstable/main arm64 python3.12 arm64 3.12.7-1 [671 kB] Get: 21 http://deb.debian.org/debian unstable/main arm64 libpython3-stdlib arm64 3.12.6-1 [9692 B] Get: 22 http://deb.debian.org/debian unstable/main arm64 python3 arm64 3.12.6-1 [27.8 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 2:4.0.4-6 [62.3 kB] Get: 25 http://deb.debian.org/debian unstable/main arm64 procps arm64 2:4.0.4-6 [872 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 3.3.2-1 [1348 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 2.40.2-9 [96.6 kB] Get: 36 http://deb.debian.org/debian unstable/main arm64 libpipeline1 arm64 1.5.8-1 [40.2 kB] Get: 37 http://deb.debian.org/debian unstable/main arm64 man-db arm64 2.13.0-1 [1404 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 2.72-3 [493 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 8.6.15+dfsg-2 [982 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 1.6.44-2 [273 kB] Get: 47 http://deb.debian.org/debian unstable/main arm64 libfreetype6 arm64 2.13.3+dfsg-1 [422 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+7 [89.3 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 8.6.15-1 [738 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 13.20 [89.7 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+really2.9.14-0.1 [630 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 13.20 [915 kB] Get: 83 http://deb.debian.org/debian unstable/main arm64 python3-autocommand all 2.2.2-3 [13.6 kB] Get: 84 http://deb.debian.org/debian unstable/main arm64 python3-more-itertools all 10.5.0-1 [63.8 kB] Get: 85 http://deb.debian.org/debian unstable/main arm64 python3-typing-extensions all 4.12.2-2 [73.0 kB] Get: 86 http://deb.debian.org/debian unstable/main arm64 python3-zipp all 3.20.2-1 [10.3 kB] Get: 87 http://deb.debian.org/debian unstable/main arm64 python3-importlib-metadata all 8.5.0-1 [21.0 kB] Get: 88 http://deb.debian.org/debian unstable/main arm64 python3-typeguard all 4.3.0-1 [36.5 kB] Get: 89 http://deb.debian.org/debian unstable/main arm64 python3-inflect all 7.3.1-2 [32.4 kB] Get: 90 http://deb.debian.org/debian unstable/main arm64 python3-jaraco.context all 6.0.0-1 [7984 B] Get: 91 http://deb.debian.org/debian unstable/main arm64 python3-jaraco.functools all 4.1.0-1 [12.0 kB] Get: 92 http://deb.debian.org/debian unstable/main arm64 python3-pkg-resources all 74.1.2-2 [213 kB] Get: 93 http://deb.debian.org/debian unstable/main arm64 python3-setuptools all 74.1.2-2 [736 kB] Get: 94 http://deb.debian.org/debian unstable/main arm64 dh-python all 6.20240824 [109 kB] Get: 95 http://deb.debian.org/debian unstable/main arm64 fontconfig arm64 2.15.0-1.1 [462 kB] Get: 96 http://deb.debian.org/debian unstable/main arm64 fonts-lyx all 2.4.2.1-1 [190 kB] Get: 97 http://deb.debian.org/debian unstable/main arm64 libblas3 arm64 3.12.0-3 [91.7 kB] Get: 98 http://deb.debian.org/debian unstable/main arm64 libpixman-1-0 arm64 0.42.2-1+b1 [477 kB] Get: 99 http://deb.debian.org/debian unstable/main arm64 libxcb-render0 arm64 1.17.0-2 [115 kB] Get: 100 http://deb.debian.org/debian unstable/main arm64 libxcb-shm0 arm64 1.17.0-2 [105 kB] Get: 101 http://deb.debian.org/debian unstable/main arm64 libcairo2 arm64 1.18.2-2 [483 kB] Get: 102 http://deb.debian.org/debian unstable/main arm64 libsasl2-modules-db arm64 2.1.28+dfsg1-8 [20.0 kB] Get: 103 http://deb.debian.org/debian unstable/main arm64 libsasl2-2 arm64 2.1.28+dfsg1-8 [55.4 kB] Get: 104 http://deb.debian.org/debian unstable/main arm64 libldap-2.5-0 arm64 2.5.18+dfsg-3 [174 kB] Get: 105 http://deb.debian.org/debian unstable/main arm64 libnghttp2-14 arm64 1.63.0-1 [71.2 kB] Get: 106 http://deb.debian.org/debian unstable/main arm64 libnghttp3-9 arm64 1.4.0-1 [59.5 kB] Get: 107 http://deb.debian.org/debian unstable/main arm64 libngtcp2-16 arm64 1.6.0-1 [112 kB] Get: 108 http://deb.debian.org/debian unstable/main arm64 libngtcp2-crypto-gnutls8 arm64 1.6.0-1 [18.5 kB] Get: 109 http://deb.debian.org/debian unstable/main arm64 libpsl5t64 arm64 0.21.2-1.1 [56.8 kB] Get: 110 http://deb.debian.org/debian unstable/main arm64 librtmp1 arm64 2.4+20151223.gitfa8646d.1-2+b4 [56.7 kB] Get: 111 http://deb.debian.org/debian unstable/main arm64 libssh2-1t64 arm64 1.11.0-7 [208 kB] Get: 112 http://deb.debian.org/debian unstable/main arm64 libcurl3t64-gnutls arm64 8.10.1-1 [329 kB] Get: 113 http://deb.debian.org/debian unstable/main arm64 libcurl4t64 arm64 8.10.1-1 [322 kB] Get: 114 http://deb.debian.org/debian unstable/main arm64 libdatrie1 arm64 0.2.13-3 [37.2 kB] Get: 115 http://deb.debian.org/debian unstable/main arm64 libdeflate0 arm64 1.21-1 [42.2 kB] Get: 116 http://deb.debian.org/debian unstable/main arm64 libfribidi0 arm64 1.0.15-1 [71.8 kB] Get: 117 http://deb.debian.org/debian unstable/main arm64 libgfortran5 arm64 14.2.0-6 [361 kB] Get: 118 http://deb.debian.org/debian unstable/main arm64 libglib2.0-0t64 arm64 2.82.1-1 [1410 kB] Get: 119 http://deb.debian.org/debian unstable/main arm64 libgraphite2-3 arm64 1.3.14-2 [69.2 kB] Get: 120 http://deb.debian.org/debian unstable/main arm64 libharfbuzz0b arm64 9.0.0-1 [441 kB] Get: 121 http://deb.debian.org/debian unstable/main arm64 libhtscodecs2 arm64 1.6.1-1 [74.6 kB] Get: 122 http://deb.debian.org/debian unstable/main arm64 libhts3t64 arm64 1.20+ds-1 [416 kB] Get: 123 http://deb.debian.org/debian unstable/main arm64 libice6 arm64 2:1.0.10-1+b1 [53.7 kB] Get: 124 http://deb.debian.org/debian unstable/main arm64 libimagequant0 arm64 2.18.0-1+b1 [34.6 kB] Get: 125 http://deb.debian.org/debian unstable/main arm64 libjbig0 arm64 2.1-6.1+b1 [30.4 kB] Get: 126 http://deb.debian.org/debian unstable/main arm64 libjpeg62-turbo arm64 1:2.1.5-3 [172 kB] Get: 127 http://deb.debian.org/debian unstable/main arm64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get: 128 http://deb.debian.org/debian unstable/main arm64 libjs-jquery-ui all 1.13.2+dfsg-1 [250 kB] Get: 129 http://deb.debian.org/debian unstable/main arm64 liblapack3 arm64 3.12.0-3 [1757 kB] Get: 130 http://deb.debian.org/debian unstable/main arm64 liblbfgsb0 arm64 3.0+dfsg.4-1+b1 [25.0 kB] Get: 131 http://deb.debian.org/debian unstable/main arm64 liblcms2-2 arm64 2.14-2+b1 [144 kB] Get: 132 http://deb.debian.org/debian unstable/main arm64 liblerc4 arm64 4.0.0+ds-4+b1 [142 kB] Get: 133 http://deb.debian.org/debian unstable/main arm64 libnspr4 arm64 2:4.35-1.1+b1 [101 kB] Get: 134 http://deb.debian.org/debian unstable/main arm64 libnss3 arm64 2:3.105-2 [1292 kB] Get: 135 http://deb.debian.org/debian unstable/main arm64 libopenjp2-7 arm64 2.5.0-2+b3 [177 kB] Get: 136 http://deb.debian.org/debian unstable/main arm64 libthai-data all 0.1.29-2 [168 kB] Get: 137 http://deb.debian.org/debian unstable/main arm64 libthai0 arm64 0.1.29-2 [48.0 kB] Get: 138 http://deb.debian.org/debian unstable/main arm64 libpango-1.0-0 arm64 1.54.0+ds-2 [210 kB] Get: 139 http://deb.debian.org/debian unstable/main arm64 libpangoft2-1.0-0 arm64 1.54.0+ds-2 [51.8 kB] Get: 140 http://deb.debian.org/debian unstable/main arm64 libpangocairo-1.0-0 arm64 1.54.0+ds-2 [33.4 kB] Get: 141 http://deb.debian.org/debian unstable/main arm64 libpaper1 arm64 1.1.29+b1 [12.9 kB] Get: 142 http://deb.debian.org/debian unstable/main arm64 libpaper-utils arm64 1.1.29+b1 [9068 B] Get: 143 http://deb.debian.org/debian unstable/main arm64 libsharpyuv0 arm64 1.4.0-0.1 [111 kB] Get: 144 http://deb.debian.org/debian unstable/main arm64 libwebp7 arm64 1.4.0-0.1 [267 kB] Get: 145 http://deb.debian.org/debian unstable/main arm64 libtiff6 arm64 4.5.1+git230720-5 [309 kB] Get: 146 http://deb.debian.org/debian unstable/main arm64 libpoppler140 arm64 24.08.0-2 [1842 kB] Get: 147 http://deb.debian.org/debian unstable/main arm64 libqhull-r8.0 arm64 2020.2-6+b1 [226 kB] Get: 148 http://deb.debian.org/debian unstable/main arm64 libraqm0 arm64 0.10.1-1+b1 [13.7 kB] Get: 149 http://deb.debian.org/debian unstable/main arm64 libsm6 arm64 2:1.2.3-1+b1 [32.7 kB] Get: 150 http://deb.debian.org/debian unstable/main arm64 libwebpdemux2 arm64 1.4.0-0.1 [110 kB] Get: 151 http://deb.debian.org/debian unstable/main arm64 libwebpmux3 arm64 1.4.0-0.1 [122 kB] Get: 152 http://deb.debian.org/debian unstable/main arm64 libxslt1.1 arm64 1.1.35-1.1 [221 kB] Get: 153 http://deb.debian.org/debian unstable/main arm64 libxt6t64 arm64 1:1.2.1-1.2 [172 kB] Get: 154 http://deb.debian.org/debian unstable/main arm64 libyaml-0-2 arm64 0.2.5-1+b1 [49.0 kB] Get: 155 http://deb.debian.org/debian unstable/main arm64 poppler-utils arm64 24.08.0-2 [192 kB] Get: 156 http://deb.debian.org/debian unstable/main arm64 python3-packaging all 24.1-1 [45.8 kB] Get: 157 http://deb.debian.org/debian unstable/main arm64 python3-pyproject-hooks all 1.1.0-2 [11.3 kB] Get: 158 http://deb.debian.org/debian unstable/main arm64 python3-toml all 0.10.2-1 [16.2 kB] Get: 159 http://deb.debian.org/debian unstable/main arm64 python3-wheel all 0.44.0-2 [53.4 kB] Get: 160 http://deb.debian.org/debian unstable/main arm64 python3-build all 1.2.2-1 [36.0 kB] Get: 161 http://deb.debian.org/debian unstable/main arm64 python3-installer all 0.7.0+dfsg1-3 [18.6 kB] Get: 162 http://deb.debian.org/debian unstable/main arm64 pybuild-plugin-pyproject all 6.20240824 [11.2 kB] Get: 163 http://deb.debian.org/debian unstable/main arm64 python-matplotlib-data all 3.8.3-3 [2731 kB] Get: 164 http://deb.debian.org/debian unstable/main arm64 python3-all arm64 3.12.6-1 [1040 B] Get: 165 http://deb.debian.org/debian unstable/main arm64 python3-appdirs all 1.4.4-4 [12.5 kB] Get: 166 http://deb.debian.org/debian unstable/main arm64 python3-attr all 24.2.0-1 [68.4 kB] Get: 167 http://deb.debian.org/debian unstable/main arm64 python3-numpy arm64 1:1.26.4+ds-11 [3351 kB] Get: 168 http://deb.debian.org/debian unstable/main arm64 python3-chardet all 5.2.0+dfsg-1 [107 kB] Get: 169 http://deb.debian.org/debian unstable/main arm64 python3.12-tk arm64 3.12.7-1 [110 kB] Get: 170 http://deb.debian.org/debian unstable/main arm64 python3.13-tk arm64 3.13.0~rc3-1 [101 kB] Get: 171 http://deb.debian.org/debian unstable/main arm64 python3-tk arm64 3.12.6-1 [9428 B] Get: 172 http://deb.debian.org/debian unstable/main arm64 python3-pil.imagetk arm64 10.4.0-1 [79.4 kB] Get: 173 http://deb.debian.org/debian unstable/main arm64 python3-pil arm64 10.4.0-1 [480 kB] Get: 174 http://deb.debian.org/debian unstable/main arm64 python3-cairo arm64 1.26.1-2 [113 kB] Get: 175 http://deb.debian.org/debian unstable/main arm64 python3-freetype all 2.5.1-1 [89.3 kB] Get: 176 http://deb.debian.org/debian unstable/main arm64 python3-rlpycairo all 0.3.0-3 [9904 B] Get: 177 http://deb.debian.org/debian unstable/main arm64 python3-reportlab all 4.2.5-1 [1117 kB] Get: 178 http://deb.debian.org/debian unstable/main arm64 xml-core all 0.19 [20.1 kB] Get: 179 http://deb.debian.org/debian unstable/main arm64 w3c-sgml-lib all 1.3-3 [273 kB] Get: 180 http://deb.debian.org/debian unstable/main arm64 python3-biopython arm64 1.84+dfsg-2 [1635 kB] Get: 181 http://deb.debian.org/debian unstable/main arm64 python3-brotli arm64 1.1.0-2+b4 [301 kB] Get: 182 http://deb.debian.org/debian unstable/main arm64 python3-contourpy arm64 1.3.0-2 [191 kB] Get: 183 http://deb.debian.org/debian unstable/main arm64 python3-cycler all 0.12.1-1 [9496 B] Get: 184 http://deb.debian.org/debian unstable/main arm64 python3-dateutil all 2.9.0-3 [79.3 kB] Get: 185 http://deb.debian.org/debian unstable/main arm64 python3-decorator all 5.1.1-5 [15.1 kB] Get: 186 http://deb.debian.org/debian unstable/main arm64 python3-scipy arm64 1.13.1-5 [15.4 MB] Get: 187 http://deb.debian.org/debian unstable/main arm64 python3-ufolib2 all 0.16.0+dfsg1-1 [32.9 kB] Get: 188 http://deb.debian.org/debian unstable/main arm64 python3-mpmath all 1.3.0-1 [419 kB] Get: 189 http://deb.debian.org/debian unstable/main arm64 python3-sympy all 1.13.3-1 [4147 kB] Get: 190 http://deb.debian.org/debian unstable/main arm64 python3-tz all 2024.1-2 [30.9 kB] Get: 191 http://deb.debian.org/debian unstable/main arm64 python3-six all 1.16.0-7 [16.4 kB] Get: 192 http://deb.debian.org/debian unstable/main arm64 python3-fs all 2.4.16-4 [95.4 kB] Get: 193 http://deb.debian.org/debian unstable/main arm64 python3-lxml arm64 5.3.0-1 [1096 kB] Get: 194 http://deb.debian.org/debian unstable/main arm64 python3-lz4 arm64 4.0.2+dfsg-1+b4 [25.1 kB] Get: 195 http://deb.debian.org/debian unstable/main arm64 unicode-data all 15.1.0-1 [8547 kB] Get: 196 http://deb.debian.org/debian unstable/main arm64 python3-fonttools arm64 4.46.0-1+b1 [1319 kB] Get: 197 http://deb.debian.org/debian unstable/main arm64 python3-iniconfig all 1.1.1-2 [6396 B] Get: 198 http://deb.debian.org/debian unstable/main arm64 python3-joblib all 1.3.2-3 [216 kB] Get: 199 http://deb.debian.org/debian unstable/main arm64 python3-kiwisolver arm64 1.4.7-1 [55.4 kB] Get: 200 http://deb.debian.org/debian unstable/main arm64 python3-pyparsing all 3.1.2-1 [146 kB] Get: 201 http://deb.debian.org/debian unstable/main arm64 python3-matplotlib arm64 3.8.3-3 [5509 kB] Get: 202 http://deb.debian.org/debian unstable/main arm64 python3-networkx all 3.2.1-4 [14.2 MB] Get: 203 http://deb.debian.org/debian unstable/main arm64 python3-pandas-lib arm64 2.2.3+dfsg-1 [3743 kB] Get: 204 http://deb.debian.org/debian unstable/main arm64 python3-pandas all 2.2.3+dfsg-1 [3096 kB] Get: 205 http://deb.debian.org/debian unstable/main arm64 python3-pluggy all 1.5.0-1 [26.9 kB] Get: 206 http://deb.debian.org/debian unstable/main arm64 python3-yaml arm64 6.0.2-1 [119 kB] Get: 207 http://deb.debian.org/debian unstable/main arm64 python3-pomegranate arm64 0.14.8-6+b1 [2317 kB] Get: 208 http://deb.debian.org/debian unstable/main arm64 python3-pyfaidx all 0.8.1.2-1 [29.0 kB] Get: 209 http://deb.debian.org/debian unstable/main arm64 python3-pysam arm64 0.22.1+ds-2+b1 [3244 kB] Get: 210 http://deb.debian.org/debian unstable/main arm64 python3-pytest all 8.3.3-1 [249 kB] Get: 211 http://deb.debian.org/debian unstable/main arm64 zip arm64 3.0-14 [225 kB] Get: 212 http://deb.debian.org/debian unstable/main arm64 unzip arm64 6.0-28 [157 kB] Get: 213 http://deb.debian.org/debian unstable/main arm64 xdg-utils all 1.1.3-4.1 [75.5 kB] Get: 214 http://deb.debian.org/debian unstable/main arm64 r-base-core arm64 4.4.1-3 [28.0 MB] Get: 215 http://deb.debian.org/debian unstable/main arm64 r-bioc-biocgenerics all 0.50.0-2 [607 kB] Get: 216 http://deb.debian.org/debian unstable/main arm64 r-bioc-dnacopy arm64 1.78.0-1 [376 kB] Fetched 168 MB in 1s (230 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 ... 19895 files and directories currently installed.) Preparing to unpack .../libpython3.12-minimal_3.12.7-1_arm64.deb ... Unpacking libpython3.12-minimal:arm64 (3.12.7-1) ... Selecting previously unselected package libexpat1:arm64. Preparing to unpack .../libexpat1_2.6.3-1_arm64.deb ... Unpacking libexpat1:arm64 (2.6.3-1) ... Selecting previously unselected package python3.12-minimal. Preparing to unpack .../python3.12-minimal_3.12.7-1_arm64.deb ... Unpacking python3.12-minimal (3.12.7-1) ... Setting up libpython3.12-minimal:arm64 (3.12.7-1) ... Setting up libexpat1:arm64 (2.6.3-1) ... Setting up python3.12-minimal (3.12.7-1) ... 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 ... 20215 files and directories currently installed.) Preparing to unpack .../00-python3-minimal_3.12.6-1_arm64.deb ... Unpacking python3-minimal (3.12.6-1) ... 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_2024b-2_all.deb ... Unpacking tzdata (2024b-2) ... 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) ... 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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 (1.63.0-1) ... Setting up libdeflate0:arm64 (1.21-1) ... 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+dfsg1-8) ... Setting up tzdata (2024b-2) ... Current default time zone: 'Etc/UTC' Local time is now: Sun Nov 9 05:42:56 UTC 2025. Universal Time is now: Sun Nov 9 05:42:56 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 (2.82.1-1) ... 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 (2:4.0.4-6) ... Setting up fonts-dejavu-mono (2.37-8) ... Setting up libpng16-16t64:arm64 (1.6.44-2) ... Setting up libtcl8.6:arm64 (8.6.15+dfsg-2) ... Setting up autopoint (0.22.5-2) ... 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Setting up libwebpmux3:arm64 (1.4.0-0.1) ... Setting up readline-common (8.2-5) ... Setting up libxml2:arm64 (2.12.7+dfsg+really2.9.14-0.1) ... 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 (2:3.105-2) ... Setting up libldap-2.5-0:arm64 (2.5.18+dfsg-3) ... 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 (2.13.3+dfsg-1) ... Setting up libgssapi-krb5-2:arm64 (1.21.3-3) ... Setting up ucf (3.0043+nmu1) ... Setting up libreadline8t64:arm64 (8.2-5) ... 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 (9.0.0-1) ... 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 (8.10.1-1) ... Setting up libtirpc3t64:arm64 (1.3.4+ds-1.3) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libtk8.6:arm64 (8.6.15-1) ... Setting up libpango-1.0-0:arm64 (1.54.0+ds-2) ... Setting up python3.12-tk (3.12.7-1) ... Setting up libcurl3t64-gnutls:arm64 (8.10.1-1) ... Setting up libpaper-utils (1.1.29+b1) ... Setting up xfonts-utils (1:7.7+7) ... Setting up man-db (2.13.0-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libcairo2:arm64 (1.18.2-2) ... Setting up python3.13-tk (3.13.0~rc3-1) ... 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 libpoppler140:arm64 (24.08.0-2) ... Setting up libhts3t64:arm64 (1.20+ds-1) ... Setting up poppler-utils (24.08.0-2) ... Setting up libpangoft2-1.0-0:arm64 (1.54.0+ds-2) ... Setting up libpangocairo-1.0-0:arm64 (1.54.0+ds-2) ... Setting up tk8.6-blt2.5 (2.5.3+dfsg-7) ... Setting up libpython3.12-stdlib:arm64 (3.12.7-1) ... Setting up blt (2.5.3+dfsg-7) ... Setting up python3.12 (3.12.7-1) ... Setting up debhelper (13.20) ... Setting up fonts-urw-base35 (20200910-8) ... Setting up r-base-core (4.4.1-3) ... Creating config file /etc/R/Renviron with new version Setting up libpython3-stdlib:arm64 (3.12.6-1) ... Setting up r-bioc-biocgenerics (0.50.0-2) ... Setting up python3 (3.12.6-1) ... Setting up python3-zipp (3.20.2-1) ... Setting up python3-freetype (2.5.1-1) ... Setting up python3-autocommand (2.2.2-3) ... Setting up python3-wheel (0.44.0-2) ... 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 (1.4.7-1) ... Setting up python3-typing-extensions (4.12.2-2) ... 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 (1.78.0-1) ... Setting up python3-lxml:arm64 (5.3.0-1) ... Setting up python3-dateutil (2.9.0-3) ... Setting up python3-mpmath (1.3.0-1) ... Setting up python3-build (1.2.2-1) ... Setting up python3-appdirs (1.4.4-4) ... Setting up python3-more-itertools (10.5.0-1) ... Setting up python3-iniconfig (1.1.1-2) ... Setting up python3-sympy (1.13.3-1) ... Setting up python3-attr (24.2.0-1) ... Setting up python3-pysam (0.22.1+ds-2+b1) ... Setting up python3-cairo (1.26.1-2) ... Setting up python3-importlib-metadata (8.5.0-1) ... Setting up python3-jaraco.functools (4.1.0-1) ... Setting up python3-jaraco.context (6.0.0-1) ... Setting up python3-lz4 (4.0.2+dfsg-1+b4) ... Setting up python3-pytest (8.3.3-1) ... Setting up python3-typeguard (4.3.0-1) ... Setting up python3-all (3.12.6-1) ... Setting up python3-yaml (6.0.2-1) ... Setting up python3-tk:arm64 (3.12.6-1) ... Setting up python3-inflect (7.3.1-2) ... Setting up python3-pil.imagetk:arm64 (10.4.0-1) ... Setting up python3-rlpycairo (0.3.0-3) ... Setting up python3-pkg-resources (74.1.2-2) ... Setting up python3-pyfaidx (0.8.1.2-1) ... Setting up python3-setuptools (74.1.2-2) ... Setting up python3-joblib (1.3.2-3) ... 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-numpy (1:1.26.4+ds-11) ... Setting up python3-reportlab (4.2.5-1) ... Setting up python3-contourpy (1.3.0-2) ... Setting up dh-python (6.20240824) ... Setting up python3-scipy (1.13.1-5) ... Setting up pybuild-plugin-pyproject (6.20240824) ... Setting up python3-pomegranate (0.14.8-6+b1) ... Setting up python3-pandas-lib:arm64 (2.2.3+dfsg-1) ... Setting up python3-pandas (2.2.3+dfsg-1) ... 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 (2.40-3) ... Processing triggers for sgml-base (1.31) ... Setting up w3c-sgml-lib (1.3-3) ... Setting up python3-biopython (1.84+dfsg-2) ... 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: Running cd /build/reproducible-path/cnvkit-0.9.10/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../cnvkit_0.9.10-3~0exp0_source.changes dpkg-buildpackage: info: source package cnvkit dpkg-buildpackage: info: source version 0.9.10-3~0exp0 dpkg-buildpackage: info: source distribution experimental 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-zoutk64j/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 3.12.7, pytest-8.3.3, pluggy-1.5.0 rootdir: /build/reproducible-path/cnvkit-0.9.10/.pybuild/cpython3_3.12_cnvkit/build configfile: pyproject.toml plugins: typeguard-4.3.0 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 75.31s (0:01:15) ================== 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_0.9.10-3~0exp0_all.deb'. dpkg-genbuildinfo --build=binary -O../cnvkit_0.9.10-3~0exp0_arm64.buildinfo dpkg-genchanges --build=binary -O../cnvkit_0.9.10-3~0exp0_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: 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/367751 and its subdirectories I: Current time: Sat Nov 8 17:46:34 -12 2025 I: pbuilder-time-stamp: 1762667194 Sun Oct 6 23:23:37 UTC 2024 I: 1st build successful. Starting 2nd build on remote node codethink01-arm64.debian.net. Sun Oct 6 23:23:37 UTC 2024 I: Preparing to do remote build '2' on codethink01-arm64.debian.net. Sun Oct 6 23:31:20 UTC 2024 I: Deleting $TMPDIR on codethink01-arm64.debian.net. Sun Oct 6 23:31:21 UTC 2024 I: cnvkit_0.9.10-3~0exp0_arm64.changes: Format: 1.8 Date: Mon, 22 Jul 2024 17:06:49 +0200 Source: cnvkit Binary: cnvkit Architecture: all Version: 0.9.10-3~0exp0 Distribution: experimental Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Michael R. Crusoe Description: cnvkit - Copy number variant detection from targeted DNA sequencing Changes: cnvkit (0.9.10-3~0exp0) experimental; urgency=medium . * Experimental build to confirm bioc-3.19 compat. Checksums-Sha1: 6ae619f17d1ee79e32ceb4c5468dce3d773c794a 19507240 cnvkit_0.9.10-3~0exp0_all.deb 50f3037ec1fdb9a133d5fe7e757420b583a4ee69 10571 cnvkit_0.9.10-3~0exp0_arm64.buildinfo Checksums-Sha256: 8edde45ee99f7c2f7b2869a6fefd23d84736f6ac0247d9241be3749cccdcef3b 19507240 cnvkit_0.9.10-3~0exp0_all.deb de8f8f56aee8b27dac47eaa3d5a7b02251a53bb0027c4788163ff858dc723ac4 10571 cnvkit_0.9.10-3~0exp0_arm64.buildinfo Files: 6450ce7ace4cf9212404712d76ad86ea 19507240 science optional cnvkit_0.9.10-3~0exp0_all.deb 64c5f7812cc052c5c05b274fda899dda 10571 science optional cnvkit_0.9.10-3~0exp0_arm64.buildinfo Sun Oct 6 23:31:21 UTC 2024 I: diffoscope 278 will be used to compare the two builds: Running as unit: rb-diffoscope-arm64_5-62384.service Warning: program compiled against libxml 212 using older 209 # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.M5ynHTct/cnvkit_0.9.10-3~0exp0.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.M5ynHTct/cnvkit_0.9.10-3~0exp0.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.M5ynHTct/cnvkit_0.9.10-3~0exp0.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.M5ynHTct/b1/cnvkit_0.9.10-3~0exp0_arm64.changes /srv/reproducible-results/rbuild-debian/r-b-build.M5ynHTct/b2/cnvkit_0.9.10-3~0exp0_arm64.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call abc.DotChangesFile ## main (total time: 0.723s) 0.723s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.270s) 0.270s 12 calls diffoscope.comparators.binary.FilesystemFile ## specialize (total time: 0.000s) 0.000s 1 call specialize Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 1.105s CPU time consumed: 1.106s Sun Oct 6 23:31:23 UTC 2024 I: diffoscope 278 found no differences in the changes files, and a .buildinfo file also exists. Sun Oct 6 23:31:23 UTC 2024 I: cnvkit from experimental built successfully and reproducibly on arm64. Sun Oct 6 23:31:25 UTC 2024 I: Submitting .buildinfo files to external archives: Sun Oct 6 23:31:25 UTC 2024 I: Submitting 12K b1/cnvkit_0.9.10-3~0exp0_arm64.buildinfo.asc Sun Oct 6 23:31:26 UTC 2024 I: Submitting 12K b2/cnvkit_0.9.10-3~0exp0_arm64.buildinfo.asc Sun Oct 6 23:31:27 UTC 2024 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Sun Oct 6 23:31:27 UTC 2024 I: Done submitting .buildinfo files. Sun Oct 6 23:31:27 UTC 2024 I: Removing signed cnvkit_0.9.10-3~0exp0_arm64.buildinfo.asc files: removed './b1/cnvkit_0.9.10-3~0exp0_arm64.buildinfo.asc' removed './b2/cnvkit_0.9.10-3~0exp0_arm64.buildinfo.asc'