I: pbuilder: network access will be disabled during build I: Current time: Sun Jun 1 23:22:32 +14 2025 I: pbuilder-time-stamp: 1748769752 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-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/4036091/tmp/hooks/D01_modify_environment starting debug: Running on codethink01-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 Jun 1 09:22 /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/4036091/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/4036091/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=trixie EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=aarch64 HOST_ARCH=arm64 IFS=' ' INVOCATION_ID=137ce384aaaf4c70b70b7987d1483512 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=4036091 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.dpyyi7cR/pbuilderrc_FjFD --distribution trixie --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.dpyyi7cR/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 6.1.0-20-cloud-arm64 #1 SMP Debian 6.1.85-1 (2024-04-11) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 May 26 17:47 /bin -> usr/bin I: user script /srv/workspace/pbuilder/4036091/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 ... 19940 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} bsdextrautils{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} fontconfig-config{a} fonts-dejavu-core{a} fonts-dejavu-mono{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libbrotli1{a} libbsd0{a} libcairo2{a} libdebhelper-perl{a} libdeflate0{a} libelf1t64{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libfontconfig1{a} libfreetype6{a} libicu72{a} libjbig0{a} libjpeg62-turbo{a} liblcms2-2{a} liblerc4{a} libmagic-mgc{a} libmagic1{a} libnspr4{a} libnss3{a} libopenjp2-7{a} libpipeline1{a} libpixman-1-0{a} libpng16-16t64{a} libpoppler126{a} libsharpyuv0{a} libsub-override-perl{a} libtiff6{a} libtool{a} libuchardet0{a} libwebp7{a} libx11-6{a} libx11-data{a} libxau6{a} libxcb-render0{a} libxcb-shm0{a} libxcb1{a} libxdmcp6{a} libxext6{a} libxml2{a} libxrender1{a} m4{a} man-db{a} po-debconf{a} poppler-utils{a} sensible-utils{a} The following packages are RECOMMENDED but will NOT be installed: curl libarchive-cpio-perl libltdl-dev libmail-sendmail-perl lynx poppler-data wget 0 packages upgraded, 63 newly installed, 0 to remove and 0 not upgraded. Need to get 29.1 MB of archives. After unpacking 105 MB will be used. The following packages have unmet dependencies: pbuilder-satisfydepends-dummy : Depends: dh-sequence-python3 which is a virtual package, provided by: - dh-python (6.20240422), but it is not installable Depends: python3-all but it is not installable Depends: python3-setuptools but it is not installable Depends: pybuild-plugin-pyproject but it is not installable Depends: python3-pytest but it is not installable Depends: python3-pyfaidx but it is not installable Depends: python3-biopython but it is not installable Depends: python3-pandas but it is not installable Depends: python3-numpy but it is not installable Depends: python3-pysam but it is not installable Depends: python3-scipy but it is not installable Depends: python3-matplotlib but it is not installable Depends: python3-pomegranate but it is not installable Depends: r-bioc-dnacopy but it is not installable The following actions will resolve these dependencies: Remove the following packages: 1) libdb5.3 [5.3.28+dfsg2-4+b1 (now)] 2) libssl3 [3.1.5-1 (now)] Install the following packages: 3) blt [2.5.3+dfsg-7 (testing)] 4) ca-certificates [20240203 (testing)] 5) dh-python [6.20240422 (testing)] 6) fontconfig [2.15.0-1.1 (testing)] 7) fonts-lyx [2.4.0~RC3-1 (testing)] 8) fonts-urw-base35 [20200910-8 (testing)] 9) libblis4-serial [0.9.0-1+b2 (testing)] 10) libcurl3t64-gnutls [8.7.1-3 (testing)] 11) libcurl4t64 [8.7.1-3 (testing)] 12) libdatrie1 [0.2.13-3 (testing)] 13) libdb5.3t64 [5.3.28+dfsg2-7 (testing)] 14) libfontenc1 [1:1.1.8-1 (testing)] 15) libfribidi0 [1.0.13-3+b1 (testing)] 16) libgfortran5 [14-20240330-1 (testing)] 17) libglib2.0-0t64 [2.78.4-7 (testing)] 18) libgraphite2-3 [1.3.14-2 (testing)] 19) libharfbuzz0b [8.3.0-2+b1 (testing)] 20) libhts3 [1.19+ds-1 (testing)] 21) libhtscodecs2 [1.6.0-1+b1 (testing)] 22) libice6 [2:1.0.10-1+b1 (testing)] 23) libimagequant0 [2.18.0-1+b1 (testing)] 24) libjs-jquery [3.6.1+dfsg+~3.5.14-1 (testing)] 25) libjs-jquery-ui [1.13.2+dfsg-1 (testing)] 26) libjs-sphinxdoc [7.2.6-6 (testing)] 27) libjs-underscore [1.13.4~dfsg+~1.11.4-3 (testing)] 28) liblapack3 [3.12.0-3 (testing)] 29) liblbfgsb0 [3.0+dfsg.4-1+b1 (testing)] 30) libldap-2.5-0 [2.5.13+dfsg-5+b3 (testing)] 31) libnghttp2-14 [1.59.0-1 (testing)] 32) libpango-1.0-0 [1.52.1+ds-1 (testing)] 33) libpangocairo-1.0-0 [1.52.1+ds-1 (testing)] 34) libpangoft2-1.0-0 [1.52.1+ds-1 (testing)] 35) libpaper-utils [1.1.29+b1 (testing)] 36) libpaper1 [1.1.29+b1 (testing)] 37) libproc2-0 [2:4.0.4-4 (testing)] 38) libpsl5t64 [0.21.2-1.1 (testing)] 39) libpython3-stdlib [3.11.8-1 (testing)] 40) libpython3.11-minimal [3.11.9-1 (testing)] 41) libpython3.11-stdlib [3.11.9-1 (testing)] 42) libpython3.12-minimal [3.12.3-1 (testing)] 43) libpython3.12-stdlib [3.12.3-1 (testing)] 44) libqhull-r8.0 [2020.2-6+b1 (testing)] 45) libraqm0 [0.10.1-1+b1 (testing)] 46) libreadline8t64 [8.2-4 (testing)] 47) librtmp1 [2.4+20151223.gitfa8646d.1-2+b4 (testing)] 48) libsasl2-2 [2.1.28+dfsg1-4+b1 (testing)] 49) libsasl2-modules-db [2.1.28+dfsg1-4+b1 (testing)] 50) libsm6 [2:1.2.3-1+b1 (testing)] 51) libssh2-1t64 [1.11.0-4.1+b2 (testing)] 52) libssl3t64 [3.2.1-3 (testing)] 53) libtcl8.6 [8.6.14+dfsg-1 (testing)] 54) libthai-data [0.1.29-2 (testing)] 55) libthai0 [0.1.29-2 (testing)] 56) libtk8.6 [8.6.14-1 (testing)] 57) libwebpdemux2 [1.3.2-0.4+b1 (testing)] 58) libwebpmux3 [1.3.2-0.4+b1 (testing)] 59) libxft2 [2.3.6-1+b1 (testing)] 60) libxslt1.1 [1.1.35-1+b1 (testing)] 61) libxss1 [1:1.2.3-1+b1 (testing)] 62) libxt6t64 [1:1.2.1-1.2 (testing)] 63) libyaml-0-2 [0.2.5-1+b1 (testing)] 64) media-types [10.1.0 (testing)] 65) netbase [6.4 (testing)] 66) openssl [3.2.1-3 (testing)] 67) procps [2:4.0.4-4 (testing)] 68) pybuild-plugin-pyproject [6.20240422 (testing)] 69) python-matplotlib-data [3.6.3-1 (testing)] 70) python3 [3.11.8-1 (testing)] 71) python3-all [3.11.8-1 (testing)] 72) python3-appdirs [1.4.4-4 (testing)] 73) python3-biopython [1.81+dfsg-3 (testing)] 74) python3-brotli [1.1.0-2+b3 (testing)] 75) python3-build [1.1.1-1 (testing)] 76) python3-cairo [1.26.0-1 (testing)] 77) python3-chardet [5.2.0+dfsg-1 (testing)] 78) python3-contourpy [1.0.7-3 (testing)] 79) python3-cycler [0.12.1-1 (testing)] 80) python3-dateutil [2.9.0-2 (testing)] 81) python3-decorator [5.1.1-5 (testing)] 82) python3-defcon [0.10.3-3 (testing)] 83) python3-distutils [3.12.3-1 (testing)] 84) python3-fonttools [4.46.0-1 (testing)] 85) python3-freetype [2.4.0-1 (testing)] 86) python3-fs [2.4.16-4 (testing)] 87) python3-importlib-metadata [4.12.0-1 (testing)] 88) python3-iniconfig [1.1.1-2 (testing)] 89) python3-installer [0.7.0+dfsg1-3 (testing)] 90) python3-joblib [1.3.2-2 (testing)] 91) python3-kiwisolver [1.4.5-1 (testing)] 92) python3-lib2to3 [3.12.3-1 (testing)] 93) python3-lxml [5.1.0-1 (testing)] 94) python3-lz4 [4.0.2+dfsg-1+b3 (testing)] 95) python3-matplotlib [3.6.3-1+b2 (testing)] 96) python3-minimal [3.11.8-1 (testing)] 97) python3-more-itertools [10.2.0-1 (testing)] 98) python3-mpmath [1.3.0-1 (testing)] 99) python3-networkx [2.8.8-2 (testing)] 100) python3-numpy [1:1.24.2-2 (testing)] 101) python3-packaging [24.0-1 (testing)] 102) python3-pandas [2.1.4+dfsg-5 (testing)] 103) python3-pandas-lib [2.1.4+dfsg-5 (testing)] 104) python3-pil [10.3.0-2 (testing)] 105) python3-pil.imagetk [10.3.0-2 (testing)] 106) python3-pkg-resources [68.1.2-2 (testing)] 107) python3-pluggy [1.5.0-1 (testing)] 108) python3-pomegranate [0.14.8-4 (testing)] 109) python3-pyfaidx [0.8.1.1-2 (testing)] 110) python3-pyparsing [3.1.2-1 (testing)] 111) python3-pyproject-hooks [1.0.0-2 (testing)] 112) python3-pysam [0.22.0+ds-1+b1 (testing)] 113) python3-pytest [7.4.4-3 (testing)] 114) python3-reportlab [4.1.0-4 (testing)] 115) python3-rlpycairo [0.3.0-3 (testing)] 116) python3-scipy [1.11.4-6 (testing)] 117) python3-setuptools [68.1.2-2 (testing)] 118) python3-six [1.16.0-6 (testing)] 119) python3-sympy [1.12-7 (testing)] 120) python3-tk [3.12.3-1 (testing)] 121) python3-toml [0.10.2-1 (testing)] 122) python3-tz [2024.1-2 (testing)] 123) python3-wheel [0.43.0-1 (testing)] 124) python3-yaml [6.0.1-2 (testing)] 125) python3-zipp [1.0.0-6 (testing)] 126) python3.11 [3.11.9-1 (testing)] 127) python3.11-minimal [3.11.9-1 (testing)] 128) python3.12 [3.12.3-1 (testing)] 129) python3.12-minimal [3.12.3-1 (testing)] 130) r-base-core [4.3.2-1 (testing)] 131) r-bioc-biocgenerics [0.48.1-2 (testing)] 132) r-bioc-dnacopy [1.76.0-1 (testing)] 133) readline-common [8.2-4 (testing)] 134) sgml-base [1.31 (testing)] 135) tk8.6-blt2.5 [2.5.3+dfsg-7 (testing)] 136) tzdata [2024a-3 (testing)] 137) ucf [3.0043+nmu1 (testing)] 138) unicode-data [15.1.0-1 (testing)] 139) unzip [6.0-28 (testing)] 140) w3c-sgml-lib [1.3-3 (testing)] 141) x11-common [1:7.7+23 (testing)] 142) xdg-utils [1.1.3-4.1 (testing)] 143) xfonts-encodings [1:1.0.4-2.2 (testing)] 144) xfonts-utils [1:7.7+6 (testing)] 145) xml-core [0.19 (testing)] 146) zip [3.0-13 (testing)] 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} libblis4-serial{a} libbrotli1{a} libbsd0{a} libcairo2{a} libcurl3t64-gnutls{a} libcurl4t64{a} libdatrie1{a} libdb5.3t64{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} libharfbuzz0b{a} libhts3{a} libhtscodecs2{a} libice6{a} libicu72{a} libimagequant0{a} libjbig0{a} libjpeg62-turbo{a} libjs-jquery{a} libjs-jquery-ui{a} libjs-sphinxdoc{a} libjs-underscore{a} liblapack3{a} liblbfgsb0{a} liblcms2-2{a} libldap-2.5-0{a} liblerc4{a} libmagic-mgc{a} libmagic1{a} libnghttp2-14{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} libpoppler126{a} libproc2-0{a} libpsl5t64{a} libpython3-stdlib{a} libpython3.11-minimal{a} libpython3.11-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} libssl3t64{a} libsub-override-perl{a} libtcl8.6{a} libthai-data{a} libthai0{a} libtiff6{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-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-defcon{a} python3-distutils{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-lib2to3{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-tz{a} python3-wheel{a} python3-yaml{a} python3-zipp{a} python3.11{a} python3.11-minimal{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 will be REMOVED: libdb5.3{a} libssl3{a} The following packages are RECOMMENDED but will NOT be installed: curl fonts-dejavu-extra isympy-common javascript-common libarchive-cpio-perl libfile-mimeinfo-perl libglib2.0-data libldap-common libltdl-dev libmail-sendmail-perl libnet-dbus-perl libsasl2-modules libx11-protocol-perl lynx ncbi-blast+ poppler-data psmisc publicsuffix python-biopython-doc python3-bottleneck python3-bs4 python3-cssselect python3-fontpens 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, 2 to remove and 0 not upgraded. Need to get 173 MB of archives. After unpacking 722 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main arm64 libdb5.3t64 arm64 5.3.28+dfsg2-7 [625 kB] Get: 2 http://deb.debian.org/debian trixie/main arm64 libssl3t64 arm64 3.2.1-3 [2537 kB] Get: 3 http://deb.debian.org/debian trixie/main arm64 libpython3.11-minimal arm64 3.11.9-1 [813 kB] Get: 4 http://deb.debian.org/debian trixie/main arm64 libexpat1 arm64 2.6.2-1 [88.7 kB] Get: 5 http://deb.debian.org/debian trixie/main arm64 python3.11-minimal arm64 3.11.9-1 [1767 kB] Get: 6 http://deb.debian.org/debian trixie/main arm64 python3-minimal arm64 3.11.8-1 [26.3 kB] Get: 7 http://deb.debian.org/debian trixie/main arm64 media-types all 10.1.0 [26.9 kB] Get: 8 http://deb.debian.org/debian trixie/main arm64 netbase all 6.4 [12.8 kB] Get: 9 http://deb.debian.org/debian trixie/main arm64 tzdata all 2024a-3 [255 kB] Get: 10 http://deb.debian.org/debian trixie/main arm64 readline-common all 8.2-4 [69.3 kB] Get: 11 http://deb.debian.org/debian trixie/main arm64 libreadline8t64 arm64 8.2-4 [157 kB] Get: 12 http://deb.debian.org/debian trixie/main arm64 libpython3.11-stdlib arm64 3.11.9-1 [1775 kB] Get: 13 http://deb.debian.org/debian trixie/main arm64 python3.11 arm64 3.11.9-1 [602 kB] Get: 14 http://deb.debian.org/debian trixie/main arm64 libpython3-stdlib arm64 3.11.8-1 [9332 B] Get: 15 http://deb.debian.org/debian trixie/main arm64 python3 arm64 3.11.8-1 [27.4 kB] Get: 16 http://deb.debian.org/debian trixie/main arm64 libpython3.12-minimal arm64 3.12.3-1 [802 kB] Get: 17 http://deb.debian.org/debian trixie/main arm64 python3.12-minimal arm64 3.12.3-1 [1931 kB] Get: 18 http://deb.debian.org/debian trixie/main arm64 sgml-base all 1.31 [15.4 kB] Get: 19 http://deb.debian.org/debian trixie/main arm64 libproc2-0 arm64 2:4.0.4-4 [61.7 kB] Get: 20 http://deb.debian.org/debian trixie/main arm64 procps arm64 2:4.0.4-4 [869 kB] Get: 21 http://deb.debian.org/debian trixie/main arm64 sensible-utils all 0.0.22 [22.4 kB] Get: 22 http://deb.debian.org/debian trixie/main arm64 openssl arm64 3.2.1-3 [1324 kB] Get: 23 http://deb.debian.org/debian trixie/main arm64 ca-certificates all 20240203 [158 kB] Get: 24 http://deb.debian.org/debian trixie/main arm64 libmagic-mgc arm64 1:5.45-2+b1 [314 kB] Get: 25 http://deb.debian.org/debian trixie/main arm64 libmagic1 arm64 1:5.45-2+b1 [100 kB] Get: 26 http://deb.debian.org/debian trixie/main arm64 file arm64 1:5.45-2+b1 [43.2 kB] Get: 27 http://deb.debian.org/debian trixie/main arm64 gettext-base arm64 0.21-14+b1 [160 kB] Get: 28 http://deb.debian.org/debian trixie/main arm64 libuchardet0 arm64 0.0.8-1+b1 [69.0 kB] Get: 29 http://deb.debian.org/debian trixie/main arm64 groff-base arm64 1.23.0-3+b1 [1126 kB] Get: 30 http://deb.debian.org/debian trixie/main arm64 bsdextrautils arm64 2.39.3-6 [90.0 kB] Get: 31 http://deb.debian.org/debian trixie/main arm64 libpipeline1 arm64 1.5.7-2 [36.5 kB] Get: 32 http://deb.debian.org/debian trixie/main arm64 man-db arm64 2.12.0-3 [1385 kB] Get: 33 http://deb.debian.org/debian trixie/main arm64 ucf all 3.0043+nmu1 [55.2 kB] Get: 34 http://deb.debian.org/debian trixie/main arm64 m4 arm64 1.4.19-4 [277 kB] Get: 35 http://deb.debian.org/debian trixie/main arm64 autoconf all 2.71-3 [332 kB] Get: 36 http://deb.debian.org/debian trixie/main arm64 autotools-dev all 20220109.1 [51.6 kB] Get: 37 http://deb.debian.org/debian trixie/main arm64 automake all 1:1.16.5-1.3 [823 kB] Get: 38 http://deb.debian.org/debian trixie/main arm64 autopoint all 0.21-14 [496 kB] Get: 39 http://deb.debian.org/debian trixie/main arm64 libtcl8.6 arm64 8.6.14+dfsg-1 [975 kB] Get: 40 http://deb.debian.org/debian trixie/main arm64 libbrotli1 arm64 1.1.0-2+b3 [295 kB] Get: 41 http://deb.debian.org/debian trixie/main arm64 libpng16-16t64 arm64 1.6.43-5 [272 kB] Get: 42 http://deb.debian.org/debian trixie/main arm64 libfreetype6 arm64 2.13.2+dfsg-1+b4 [408 kB] Get: 43 http://deb.debian.org/debian trixie/main arm64 fonts-dejavu-mono all 2.37-8 [489 kB] Get: 44 http://deb.debian.org/debian trixie/main arm64 fonts-dejavu-core all 2.37-8 [840 kB] Get: 45 http://deb.debian.org/debian trixie/main arm64 libfontenc1 arm64 1:1.1.8-1 [22.2 kB] Get: 46 http://deb.debian.org/debian trixie/main arm64 x11-common all 1:7.7+23 [252 kB] Get: 47 http://deb.debian.org/debian trixie/main arm64 xfonts-encodings all 1:1.0.4-2.2 [577 kB] Get: 48 http://deb.debian.org/debian trixie/main arm64 xfonts-utils arm64 1:7.7+6 [85.6 kB] Get: 49 http://deb.debian.org/debian trixie/main arm64 fonts-urw-base35 all 20200910-8 [10.8 MB] Get: 50 http://deb.debian.org/debian trixie/main arm64 fontconfig-config arm64 2.15.0-1.1 [317 kB] Get: 51 http://deb.debian.org/debian trixie/main arm64 libfontconfig1 arm64 2.15.0-1.1 [385 kB] Get: 52 http://deb.debian.org/debian trixie/main arm64 libxau6 arm64 1:1.0.9-1+b1 [18.1 kB] Get: 53 http://deb.debian.org/debian trixie/main arm64 libbsd0 arm64 0.12.2-1 [129 kB] Get: 54 http://deb.debian.org/debian trixie/main arm64 libxdmcp6 arm64 1:1.1.2-3+b1 [24.3 kB] Get: 55 http://deb.debian.org/debian trixie/main arm64 libxcb1 arm64 1.15-1 [143 kB] Get: 56 http://deb.debian.org/debian trixie/main arm64 libx11-data all 2:1.8.7-1 [328 kB] Get: 57 http://deb.debian.org/debian trixie/main arm64 libx11-6 arm64 2:1.8.7-1+b1 [775 kB] Get: 58 http://deb.debian.org/debian trixie/main arm64 libxrender1 arm64 1:0.9.10-1.1+b1 [27.0 kB] Get: 59 http://deb.debian.org/debian trixie/main arm64 libxft2 arm64 2.3.6-1+b1 [51.0 kB] Get: 60 http://deb.debian.org/debian trixie/main arm64 libxext6 arm64 2:1.3.4-1+b1 [51.7 kB] Get: 61 http://deb.debian.org/debian trixie/main arm64 libxss1 arm64 1:1.2.3-1+b1 [17.0 kB] Get: 62 http://deb.debian.org/debian trixie/main arm64 libtk8.6 arm64 8.6.14-1 [732 kB] Get: 63 http://deb.debian.org/debian trixie/main arm64 tk8.6-blt2.5 arm64 2.5.3+dfsg-7 [533 kB] Get: 64 http://deb.debian.org/debian trixie/main arm64 blt arm64 2.5.3+dfsg-7 [6024 B] Get: 65 http://deb.debian.org/debian trixie/main arm64 libdebhelper-perl all 13.15.3 [88.0 kB] Get: 66 http://deb.debian.org/debian trixie/main arm64 libtool all 2.4.7-7 [517 kB] Get: 67 http://deb.debian.org/debian trixie/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 68 http://deb.debian.org/debian trixie/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 69 http://deb.debian.org/debian trixie/main arm64 libsub-override-perl all 0.10-1 [10.6 kB] Get: 70 http://deb.debian.org/debian trixie/main arm64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 71 http://deb.debian.org/debian trixie/main arm64 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 72 http://deb.debian.org/debian trixie/main arm64 libelf1t64 arm64 0.191-1+b1 [187 kB] Get: 73 http://deb.debian.org/debian trixie/main arm64 dwz arm64 0.15-1+b1 [102 kB] Get: 74 http://deb.debian.org/debian trixie/main arm64 libicu72 arm64 72.1-4+b1 [9224 kB] Get: 75 http://deb.debian.org/debian trixie/main arm64 libxml2 arm64 2.9.14+dfsg-1.3+b3 [624 kB] Get: 76 http://deb.debian.org/debian trixie/main arm64 gettext arm64 0.21-14+b1 [1249 kB] Get: 77 http://deb.debian.org/debian trixie/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 78 http://deb.debian.org/debian trixie/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 79 http://deb.debian.org/debian trixie/main arm64 debhelper all 13.15.3 [901 kB] Get: 80 http://deb.debian.org/debian trixie/main arm64 python3-pkg-resources all 68.1.2-2 [241 kB] Get: 81 http://deb.debian.org/debian trixie/main arm64 python3-lib2to3 all 3.12.3-1 [77.6 kB] Get: 82 http://deb.debian.org/debian trixie/main arm64 python3-distutils all 3.12.3-1 [131 kB] Get: 83 http://deb.debian.org/debian trixie/main arm64 python3-setuptools all 68.1.2-2 [468 kB] Get: 84 http://deb.debian.org/debian trixie/main arm64 dh-python all 6.20240422 [107 kB] Get: 85 http://deb.debian.org/debian trixie/main arm64 fontconfig arm64 2.15.0-1.1 [462 kB] Get: 86 http://deb.debian.org/debian trixie/main arm64 fonts-lyx all 2.4.0~RC3-1 [189 kB] Get: 87 http://deb.debian.org/debian trixie/main arm64 libblis4-serial arm64 0.9.0-1+b2 [791 kB] Get: 88 http://deb.debian.org/debian trixie/main arm64 libpixman-1-0 arm64 0.42.2-1+b1 [477 kB] Get: 89 http://deb.debian.org/debian trixie/main arm64 libxcb-render0 arm64 1.15-1 [115 kB] Get: 90 http://deb.debian.org/debian trixie/main arm64 libxcb-shm0 arm64 1.15-1 [106 kB] Get: 91 http://deb.debian.org/debian trixie/main arm64 libcairo2 arm64 1.18.0-1+b1 [478 kB] Get: 92 http://deb.debian.org/debian trixie/main arm64 libsasl2-modules-db arm64 2.1.28+dfsg1-4+b1 [20.2 kB] Get: 93 http://deb.debian.org/debian trixie/main arm64 libsasl2-2 arm64 2.1.28+dfsg1-4+b1 [55.5 kB] Get: 94 http://deb.debian.org/debian trixie/main arm64 libldap-2.5-0 arm64 2.5.13+dfsg-5+b3 [172 kB] Get: 95 http://deb.debian.org/debian trixie/main arm64 libnghttp2-14 arm64 1.59.0-1 [70.2 kB] Get: 96 http://deb.debian.org/debian trixie/main arm64 libpsl5t64 arm64 0.21.2-1.1 [56.8 kB] Get: 97 http://deb.debian.org/debian trixie/main arm64 librtmp1 arm64 2.4+20151223.gitfa8646d.1-2+b4 [56.7 kB] Get: 98 http://deb.debian.org/debian trixie/main arm64 libssh2-1t64 arm64 1.11.0-4.1+b2 [207 kB] Get: 99 http://deb.debian.org/debian trixie/main arm64 libcurl3t64-gnutls arm64 8.7.1-3 [405 kB] Get: 100 http://deb.debian.org/debian trixie/main arm64 libcurl4t64 arm64 8.7.1-3 [412 kB] Get: 101 http://deb.debian.org/debian trixie/main arm64 libdatrie1 arm64 0.2.13-3 [37.2 kB] Get: 102 http://deb.debian.org/debian trixie/main arm64 libdeflate0 arm64 1.20-1 [41.5 kB] Get: 103 http://deb.debian.org/debian trixie/main arm64 libfribidi0 arm64 1.0.13-3+b1 [71.3 kB] Get: 104 http://deb.debian.org/debian trixie/main arm64 libgfortran5 arm64 14-20240330-1 [361 kB] Get: 105 http://deb.debian.org/debian trixie/main arm64 libglib2.0-0t64 arm64 2.78.4-7 [1364 kB] Get: 106 http://deb.debian.org/debian trixie/main arm64 libgraphite2-3 arm64 1.3.14-2 [69.2 kB] Get: 107 http://deb.debian.org/debian trixie/main arm64 libharfbuzz0b arm64 8.3.0-2+b1 [2178 kB] Get: 108 http://deb.debian.org/debian trixie/main arm64 libhtscodecs2 arm64 1.6.0-1+b1 [71.6 kB] Get: 109 http://deb.debian.org/debian trixie/main arm64 libhts3 arm64 1.19+ds-1 [412 kB] Get: 110 http://deb.debian.org/debian trixie/main arm64 libice6 arm64 2:1.0.10-1+b1 [53.7 kB] Get: 111 http://deb.debian.org/debian trixie/main arm64 libimagequant0 arm64 2.18.0-1+b1 [34.6 kB] Get: 112 http://deb.debian.org/debian trixie/main arm64 libjbig0 arm64 2.1-6.1+b1 [30.4 kB] Get: 113 http://deb.debian.org/debian trixie/main arm64 libjpeg62-turbo arm64 1:2.1.5-2+b2 [172 kB] Get: 114 http://deb.debian.org/debian trixie/main arm64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get: 115 http://deb.debian.org/debian trixie/main arm64 libjs-jquery-ui all 1.13.2+dfsg-1 [250 kB] Get: 116 http://deb.debian.org/debian trixie/main arm64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB] Get: 117 http://deb.debian.org/debian trixie/main arm64 libjs-sphinxdoc all 7.2.6-6 [150 kB] Get: 118 http://deb.debian.org/debian trixie/main arm64 liblapack3 arm64 3.12.0-3 [1757 kB] Get: 119 http://deb.debian.org/debian trixie/main arm64 liblbfgsb0 arm64 3.0+dfsg.4-1+b1 [25.0 kB] Get: 120 http://deb.debian.org/debian trixie/main arm64 liblcms2-2 arm64 2.14-2+b1 [144 kB] Get: 121 http://deb.debian.org/debian trixie/main arm64 liblerc4 arm64 4.0.0+ds-4+b1 [142 kB] Get: 122 http://deb.debian.org/debian trixie/main arm64 libnspr4 arm64 2:4.35-1.1+b1 [101 kB] Get: 123 http://deb.debian.org/debian trixie/main arm64 libnss3 arm64 2:3.99-1 [1293 kB] Get: 124 http://deb.debian.org/debian trixie/main arm64 libopenjp2-7 arm64 2.5.0-2+b3 [177 kB] Get: 125 http://deb.debian.org/debian trixie/main arm64 libthai-data all 0.1.29-2 [168 kB] Get: 126 http://deb.debian.org/debian trixie/main arm64 libthai0 arm64 0.1.29-2 [48.0 kB] Get: 127 http://deb.debian.org/debian trixie/main arm64 libpango-1.0-0 arm64 1.52.1+ds-1 [204 kB] Get: 128 http://deb.debian.org/debian trixie/main arm64 libpangoft2-1.0-0 arm64 1.52.1+ds-1 [45.4 kB] Get: 129 http://deb.debian.org/debian trixie/main arm64 libpangocairo-1.0-0 arm64 1.52.1+ds-1 [33.1 kB] Get: 130 http://deb.debian.org/debian trixie/main arm64 libpaper1 arm64 1.1.29+b1 [12.9 kB] Get: 131 http://deb.debian.org/debian trixie/main arm64 libpaper-utils arm64 1.1.29+b1 [9068 B] Get: 132 http://deb.debian.org/debian trixie/main arm64 libsharpyuv0 arm64 1.3.2-0.4+b1 [107 kB] Get: 133 http://deb.debian.org/debian trixie/main arm64 libwebp7 arm64 1.3.2-0.4+b1 [263 kB] Get: 134 http://deb.debian.org/debian trixie/main arm64 libtiff6 arm64 4.5.1+git230720-4 [307 kB] Get: 135 http://deb.debian.org/debian trixie/main arm64 libpoppler126 arm64 22.12.0-2+b1 [1754 kB] Get: 136 http://deb.debian.org/debian trixie/main arm64 libpython3.12-stdlib arm64 3.12.3-1 [1889 kB] Get: 137 http://deb.debian.org/debian trixie/main arm64 libqhull-r8.0 arm64 2020.2-6+b1 [226 kB] Get: 138 http://deb.debian.org/debian trixie/main arm64 libraqm0 arm64 0.10.1-1+b1 [13.7 kB] Get: 139 http://deb.debian.org/debian trixie/main arm64 libsm6 arm64 2:1.2.3-1+b1 [32.7 kB] Get: 140 http://deb.debian.org/debian trixie/main arm64 libwebpdemux2 arm64 1.3.2-0.4+b1 [107 kB] Get: 141 http://deb.debian.org/debian trixie/main arm64 libwebpmux3 arm64 1.3.2-0.4+b1 [119 kB] Get: 142 http://deb.debian.org/debian trixie/main arm64 libxslt1.1 arm64 1.1.35-1+b1 [221 kB] Get: 143 http://deb.debian.org/debian trixie/main arm64 libxt6t64 arm64 1:1.2.1-1.2 [172 kB] Get: 144 http://deb.debian.org/debian trixie/main arm64 libyaml-0-2 arm64 0.2.5-1+b1 [49.0 kB] Get: 145 http://deb.debian.org/debian trixie/main arm64 poppler-utils arm64 22.12.0-2+b1 [177 kB] Get: 146 http://deb.debian.org/debian trixie/main arm64 python3-more-itertools all 10.2.0-1 [59.9 kB] Get: 147 http://deb.debian.org/debian trixie/main arm64 python3-zipp all 1.0.0-6 [6696 B] Get: 148 http://deb.debian.org/debian trixie/main arm64 python3-importlib-metadata all 4.12.0-1 [24.9 kB] Get: 149 http://deb.debian.org/debian trixie/main arm64 python3-packaging all 24.0-1 [45.5 kB] Get: 150 http://deb.debian.org/debian trixie/main arm64 python3-pyproject-hooks all 1.0.0-2 [10.6 kB] Get: 151 http://deb.debian.org/debian trixie/main arm64 python3-toml all 0.10.2-1 [16.2 kB] Get: 152 http://deb.debian.org/debian trixie/main arm64 python3-wheel all 0.43.0-1 [52.5 kB] Get: 153 http://deb.debian.org/debian trixie/main arm64 python3-build all 1.1.1-1 [32.5 kB] Get: 154 http://deb.debian.org/debian trixie/main arm64 python3-installer all 0.7.0+dfsg1-3 [18.6 kB] Get: 155 http://deb.debian.org/debian trixie/main arm64 pybuild-plugin-pyproject all 6.20240422 [11.1 kB] Get: 156 http://deb.debian.org/debian trixie/main arm64 python-matplotlib-data all 3.6.3-1 [2744 kB] Get: 157 http://deb.debian.org/debian trixie/main arm64 python3.12 arm64 3.12.3-1 [659 kB] Get: 158 http://deb.debian.org/debian trixie/main arm64 python3-all arm64 3.11.8-1 [1056 B] Get: 159 http://deb.debian.org/debian trixie/main arm64 python3-appdirs all 1.4.4-4 [12.5 kB] Get: 160 http://deb.debian.org/debian trixie/main arm64 python3-numpy arm64 1:1.24.2-2 [4122 kB] Get: 161 http://deb.debian.org/debian trixie/main arm64 python3-chardet all 5.2.0+dfsg-1 [107 kB] Get: 162 http://deb.debian.org/debian trixie/main arm64 python3-tk arm64 3.12.3-1 [110 kB] Get: 163 http://deb.debian.org/debian trixie/main arm64 python3-pil.imagetk arm64 10.3.0-2 [80.0 kB] Get: 164 http://deb.debian.org/debian trixie/main arm64 python3-pil arm64 10.3.0-2 [552 kB] Get: 165 http://deb.debian.org/debian trixie/main arm64 python3-cairo arm64 1.26.0-1 [139 kB] Get: 166 http://deb.debian.org/debian trixie/main arm64 python3-freetype all 2.4.0-1 [80.3 kB] Get: 167 http://deb.debian.org/debian trixie/main arm64 python3-rlpycairo all 0.3.0-3 [9904 B] Get: 168 http://deb.debian.org/debian trixie/main arm64 python3-reportlab all 4.1.0-4 [1113 kB] Get: 169 http://deb.debian.org/debian trixie/main arm64 xml-core all 0.19 [20.1 kB] Get: 170 http://deb.debian.org/debian trixie/main arm64 w3c-sgml-lib all 1.3-3 [273 kB] Get: 171 http://deb.debian.org/debian trixie/main arm64 python3-biopython arm64 1.81+dfsg-3 [1611 kB] Get: 172 http://deb.debian.org/debian trixie/main arm64 python3-brotli arm64 1.1.0-2+b3 [316 kB] Get: 173 http://deb.debian.org/debian trixie/main arm64 python3-contourpy arm64 1.0.7-3 [247 kB] Get: 174 http://deb.debian.org/debian trixie/main arm64 python3-cycler all 0.12.1-1 [9496 B] Get: 175 http://deb.debian.org/debian trixie/main arm64 python3-six all 1.16.0-6 [16.3 kB] Get: 176 http://deb.debian.org/debian trixie/main arm64 python3-dateutil all 2.9.0-2 [79.4 kB] Get: 177 http://deb.debian.org/debian trixie/main arm64 python3-decorator all 5.1.1-5 [15.1 kB] Get: 178 http://deb.debian.org/debian trixie/main arm64 python3-scipy arm64 1.11.4-6 [17.5 MB] Get: 179 http://deb.debian.org/debian trixie/main arm64 python3-mpmath all 1.3.0-1 [419 kB] Get: 180 http://deb.debian.org/debian trixie/main arm64 python3-sympy all 1.12-7 [3869 kB] Get: 181 http://deb.debian.org/debian trixie/main arm64 python3-tz all 2024.1-2 [30.9 kB] Get: 182 http://deb.debian.org/debian trixie/main arm64 python3-fs all 2.4.16-4 [95.4 kB] Get: 183 http://deb.debian.org/debian trixie/main arm64 python3-lxml arm64 5.1.0-1 [1810 kB] Get: 184 http://deb.debian.org/debian trixie/main arm64 python3-lz4 arm64 4.0.2+dfsg-1+b3 [26.6 kB] Get: 185 http://deb.debian.org/debian trixie/main arm64 unicode-data all 15.1.0-1 [8547 kB] Get: 186 http://deb.debian.org/debian trixie/main arm64 python3-fonttools arm64 4.46.0-1 [1510 kB] Get: 187 http://deb.debian.org/debian trixie/main arm64 python3-defcon all 0.10.3-3 [189 kB] Get: 188 http://deb.debian.org/debian trixie/main arm64 python3-iniconfig all 1.1.1-2 [6396 B] Get: 189 http://deb.debian.org/debian trixie/main arm64 python3-joblib all 1.3.2-2 [218 kB] Get: 190 http://deb.debian.org/debian trixie/main arm64 python3-kiwisolver arm64 1.4.5-1 [75.0 kB] Get: 191 http://deb.debian.org/debian trixie/main arm64 python3-pyparsing all 3.1.2-1 [146 kB] Get: 192 http://deb.debian.org/debian trixie/main arm64 python3-matplotlib arm64 3.6.3-1+b2 [7970 kB] Get: 193 http://deb.debian.org/debian trixie/main arm64 python3-networkx all 2.8.8-2 [1425 kB] Get: 194 http://deb.debian.org/debian trixie/main arm64 python3-pandas-lib arm64 2.1.4+dfsg-5 [6620 kB] Get: 195 http://deb.debian.org/debian trixie/main arm64 python3-pandas all 2.1.4+dfsg-5 [3015 kB] Get: 196 http://deb.debian.org/debian trixie/main arm64 python3-pluggy all 1.5.0-1 [26.9 kB] Get: 197 http://deb.debian.org/debian trixie/main arm64 python3-yaml arm64 6.0.1-2 [153 kB] Get: 198 http://deb.debian.org/debian trixie/main arm64 python3-pomegranate arm64 0.14.8-4 [3577 kB] Get: 199 http://deb.debian.org/debian trixie/main arm64 python3-pyfaidx all 0.8.1.1-2 [29.0 kB] Get: 200 http://deb.debian.org/debian trixie/main arm64 python3-pysam arm64 0.22.0+ds-1+b1 [3765 kB] Get: 201 http://deb.debian.org/debian trixie/main arm64 python3-pytest all 7.4.4-3 [239 kB] Get: 202 http://deb.debian.org/debian trixie/main arm64 zip arm64 3.0-13 [223 kB] Get: 203 http://deb.debian.org/debian trixie/main arm64 unzip arm64 6.0-28 [157 kB] Get: 204 http://deb.debian.org/debian trixie/main arm64 xdg-utils all 1.1.3-4.1 [75.5 kB] Get: 205 http://deb.debian.org/debian trixie/main arm64 r-base-core arm64 4.3.2-1 [26.5 MB] Get: 206 http://deb.debian.org/debian trixie/main arm64 r-bioc-biocgenerics all 0.48.1-2 [597 kB] Get: 207 http://deb.debian.org/debian trixie/main arm64 r-bioc-dnacopy arm64 1.76.0-1 [377 kB] Fetched 173 MB in 1s (256 MB/s) debconf: delaying package configuration, since apt-utils is not installed dpkg: libdb5.3:arm64: dependency problems, but removing anyway as you requested: libperl5.38:arm64 depends on libdb5.3. libpam-modules:arm64 depends on libdb5.3. (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 ... 19940 files and directories currently installed.) Removing libdb5.3:arm64 (5.3.28+dfsg2-4+b1) ... Selecting previously unselected package libdb5.3t64: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 ... 19933 files and directories currently installed.) Preparing to unpack .../libdb5.3t64_5.3.28+dfsg2-7_arm64.deb ... Unpacking libdb5.3t64:arm64 (5.3.28+dfsg2-7) ... Setting up libdb5.3t64:arm64 (5.3.28+dfsg2-7) ... dpkg: libssl3:arm64: dependency problems, but removing anyway as you requested: libkrb5-3:arm64 depends on libssl3 (>= 3.0.0). coreutils depends on libssl3 (>= 3.0.0). (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 ... 19939 files and directories currently installed.) Removing libssl3:arm64 (3.1.5-1) ... Selecting previously unselected package libssl3t64: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 ... 19926 files and directories currently installed.) Preparing to unpack .../libssl3t64_3.2.1-3_arm64.deb ... Unpacking libssl3t64:arm64 (3.2.1-3) ... Setting up libssl3t64:arm64 (3.2.1-3) ... Selecting previously unselected package libpython3.11-minimal:arm64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19941 files and directories currently installed.) Preparing to unpack .../libpython3.11-minimal_3.11.9-1_arm64.deb ... Unpacking libpython3.11-minimal:arm64 (3.11.9-1) ... 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 python3.11-minimal. Preparing to unpack .../python3.11-minimal_3.11.9-1_arm64.deb ... Unpacking python3.11-minimal (3.11.9-1) ... Setting up libpython3.11-minimal:arm64 (3.11.9-1) ... Setting up libexpat1:arm64 (2.6.2-1) ... Setting up python3.11-minimal (3.11.9-1) ... 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 ... 20257 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.11.8-1_arm64.deb ... Unpacking python3-minimal (3.11.8-1) ... Selecting previously unselected package media-types. Preparing to unpack .../1-media-types_10.1.0_all.deb ... Unpacking media-types (10.1.0) ... Selecting previously unselected package netbase. Preparing to unpack .../2-netbase_6.4_all.deb ... Unpacking netbase (6.4) ... Selecting previously unselected package tzdata. Preparing to unpack .../3-tzdata_2024a-3_all.deb ... Unpacking tzdata (2024a-3) ... Selecting previously unselected package readline-common. Preparing to unpack .../4-readline-common_8.2-4_all.deb ... Unpacking readline-common (8.2-4) ... Selecting previously unselected package libreadline8t64:arm64. Preparing to unpack .../5-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 libpython3.11-stdlib:arm64. Preparing to unpack .../6-libpython3.11-stdlib_3.11.9-1_arm64.deb ... Unpacking libpython3.11-stdlib:arm64 (3.11.9-1) ... Selecting previously unselected package python3.11. Preparing to unpack .../7-python3.11_3.11.9-1_arm64.deb ... Unpacking python3.11 (3.11.9-1) ... Selecting previously unselected package libpython3-stdlib:arm64. Preparing to unpack .../8-libpython3-stdlib_3.11.8-1_arm64.deb ... Unpacking libpython3-stdlib:arm64 (3.11.8-1) ... Setting up python3-minimal (3.11.8-1) ... 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 ... 21249 files and directories currently installed.) Preparing to unpack .../000-python3_3.11.8-1_arm64.deb ... Unpacking python3 (3.11.8-1) ... Selecting previously unselected package libpython3.12-minimal:arm64. Preparing to unpack .../001-libpython3.12-minimal_3.12.3-1_arm64.deb ... Unpacking libpython3.12-minimal:arm64 (3.12.3-1) ... Selecting previously unselected package python3.12-minimal. Preparing to unpack .../002-python3.12-minimal_3.12.3-1_arm64.deb ... Unpacking python3.12-minimal (3.12.3-1) ... Selecting previously unselected package sgml-base. Preparing to unpack .../003-sgml-base_1.31_all.deb ... Unpacking sgml-base (1.31) ... Selecting previously unselected package libproc2-0:arm64. Preparing to unpack .../004-libproc2-0_2%3a4.0.4-4_arm64.deb ... Unpacking libproc2-0:arm64 (2:4.0.4-4) ... Selecting previously unselected package procps. Preparing to unpack .../005-procps_2%3a4.0.4-4_arm64.deb ... Unpacking procps (2:4.0.4-4) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../006-sensible-utils_0.0.22_all.deb ... Unpacking sensible-utils (0.0.22) ... Selecting previously unselected package openssl. Preparing to unpack .../007-openssl_3.2.1-3_arm64.deb ... Unpacking openssl (3.2.1-3) ... Selecting previously unselected package ca-certificates. Preparing to unpack .../008-ca-certificates_20240203_all.deb ... Unpacking ca-certificates (20240203) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../009-libmagic-mgc_1%3a5.45-2+b1_arm64.deb ... Unpacking libmagic-mgc (1:5.45-2+b1) ... Selecting previously unselected package libmagic1:arm64. Preparing to unpack .../010-libmagic1_1%3a5.45-2+b1_arm64.deb ... Unpacking libmagic1:arm64 (1:5.45-2+b1) ... Selecting previously unselected package file. Preparing to unpack .../011-file_1%3a5.45-2+b1_arm64.deb ... Unpacking file (1:5.45-2+b1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../012-gettext-base_0.21-14+b1_arm64.deb ... Unpacking gettext-base (0.21-14+b1) ... Selecting previously unselected package libuchardet0:arm64. Preparing to unpack .../013-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 .../014-groff-base_1.23.0-3+b1_arm64.deb ... Unpacking groff-base (1.23.0-3+b1) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../015-bsdextrautils_2.39.3-6_arm64.deb ... Unpacking bsdextrautils (2.39.3-6) ... Selecting previously unselected package libpipeline1:arm64. Preparing to unpack .../016-libpipeline1_1.5.7-2_arm64.deb ... Unpacking libpipeline1:arm64 (1.5.7-2) ... Selecting previously unselected package man-db. Preparing to unpack .../017-man-db_2.12.0-3_arm64.deb ... Unpacking man-db (2.12.0-3) ... Selecting previously unselected package ucf. Preparing to unpack .../018-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 .../019-m4_1.4.19-4_arm64.deb ... Unpacking m4 (1.4.19-4) ... Selecting previously unselected package autoconf. Preparing to unpack .../020-autoconf_2.71-3_all.deb ... Unpacking autoconf (2.71-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../021-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../022-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 .../023-autopoint_0.21-14_all.deb ... Unpacking autopoint (0.21-14) ... Selecting previously unselected package libtcl8.6:arm64. Preparing to unpack .../024-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 .../025-libbrotli1_1.1.0-2+b3_arm64.deb ... Unpacking libbrotli1:arm64 (1.1.0-2+b3) ... Selecting previously unselected package libpng16-16t64:arm64. Preparing to unpack .../026-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 .../027-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 .../028-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 .../029-fonts-dejavu-core_2.37-8_all.deb ... Unpacking fonts-dejavu-core (2.37-8) ... Selecting previously unselected package libfontenc1:arm64. Preparing to unpack .../030-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 .../031-x11-common_1%3a7.7+23_all.deb ... Unpacking x11-common (1:7.7+23) ... Selecting previously unselected package xfonts-encodings. Preparing to unpack .../032-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 .../033-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 .../034-fonts-urw-base35_20200910-8_all.deb ... Unpacking fonts-urw-base35 (20200910-8) ... Selecting previously unselected package fontconfig-config. Preparing to unpack .../035-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 .../036-libfontconfig1_2.15.0-1.1_arm64.deb ... Unpacking libfontconfig1:arm64 (2.15.0-1.1) ... Selecting previously unselected package libxau6:arm64. 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Setting up libsharpyuv0:arm64 (1.3.2-0.4+b1) ... Setting up libxau6:arm64 (1:1.0.9-1+b1) ... Setting up libicu72:arm64 (72.1-4+b1) ... Setting up liblerc4:arm64 (4.0.0+ds-4+b1) ... Setting up bsdextrautils (2.39.3-6) ... Setting up libdatrie1:arm64 (0.2.13-3) ... Setting up libmagic-mgc (1:5.45-2+b1) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libyaml-0-2:arm64 (0.2.5-1+b1) ... Setting up fonts-lyx (2.4.0~RC3-1) ... Setting up unzip (6.0-28) ... Setting up libdebhelper-perl (13.15.3) ... Setting up libbrotli1:arm64 (1.1.0-2+b3) ... Setting up libpython3.12-minimal:arm64 (3.12.3-1) ... Setting up x11-common (1:7.7+23) ... invoke-rc.d: could not determine current runlevel Setting up X socket directories... /tmp/.X11-unix /tmp/.ICE-unix. Setting up libpsl5t64:arm64 (0.21.2-1.1) ... Setting up libnghttp2-14:arm64 (1.59.0-1) ... Setting up libmagic1:arm64 (1:5.45-2+b1) ... Setting up libdeflate0:arm64 (1.20-1) ... Setting up gettext-base (0.21-14+b1) ... Setting up m4 (1.4.19-4) ... Setting up libqhull-r8.0:arm64 (2020.2-6+b1) ... Setting up libblis4-serial:arm64 (0.9.0-1+b2) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/blis-serial/libblis.so.4 to provide /usr/lib/aarch64-linux-gnu/libblis.so.4 (libblis.so.4-aarch64-linux-gnu) in auto mode update-alternatives: using /usr/lib/aarch64-linux-gnu/blis-serial/libblas.so.3 to provide /usr/lib/aarch64-linux-gnu/libblas.so.3 (libblas.so.3-aarch64-linux-gnu) in auto mode Setting up file (1:5.45-2+b1) ... Setting up libjbig0:arm64 (2.1-6.1+b1) ... Setting up libelf1t64:arm64 (0.191-1+b1) ... Setting up libsasl2-modules-db:arm64 (2.1.28+dfsg1-4+b1) ... Setting up tzdata (2024a-3) ... Current default time zone: 'Etc/UTC' Local time is now: Sun Jun 1 09:23:08 UTC 2025. Universal Time is now: Sun Jun 1 09:23:08 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up unicode-data (15.1.0-1) ... Setting up zip (3.0-13) ... Setting up libfontenc1:arm64 (1:1.1.8-1) ... Setting up autotools-dev (20220109.1) ... Setting up libglib2.0-0t64:arm64 (2.78.4-7) ... No schema files found: doing nothing. Setting up libjpeg62-turbo:arm64 (1:2.1.5-2+b2) ... 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 (1.0.13-3+b1) ... Setting up libimagequant0:arm64 (2.18.0-1+b1) ... Setting up libproc2-0:arm64 (2:4.0.4-4) ... 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 (0.21-14) ... Setting up fonts-dejavu-core (2.37-8) ... Setting up libsasl2-2:arm64 (2.1.28+dfsg1-4+b1) ... Setting up libgfortran5:arm64 (14-20240330-1) ... Setting up autoconf (2.71-3) ... Setting up libwebp7:arm64 (1.3.2-0.4+b1) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.22) ... Setting up libtiff6:arm64 (4.5.1+git230720-4) ... Setting up libuchardet0:arm64 (0.0.8-1+b1) ... Setting up procps (2:4.0.4-4) ... Setting up libopenjp2-7:arm64 (2.5.0-2+b3) ... Setting up libsub-override-perl (0.10-1) ... Setting up libthai-data (0.1.29-2) ... Setting up netbase (6.4) ... Setting up sgml-base (1.31) ... Setting up libssh2-1t64:arm64 (1.11.0-4.1+b2) ... Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Setting up python-matplotlib-data (3.6.3-1) ... Setting up openssl (3.2.1-3) ... Setting up libwebpmux3:arm64 (1.3.2-0.4+b1) ... Setting up libbsd0:arm64 (0.12.2-1) ... Setting up readline-common (8.2-4) ... Setting up libxml2:arm64 (2.9.14+dfsg-1.3+b3) ... 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 libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.13.1-1) ... Setting up python3.12-minimal (3.12.3-1) ... Setting up libice6:arm64 (2:1.0.10-1+b1) ... Setting up libxdmcp6:arm64 (1:1.1.2-3+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 libxcb1:arm64 (1.15-1) ... Setting up gettext (0.21-14+b1) ... Setting up libtool (2.4.7-7) ... Setting up libxcb-render0:arm64 (1.15-1) ... Setting up fontconfig-config (2.15.0-1.1) ... Setting up libwebpdemux2:arm64 (1.3.2-0.4+b1) ... Setting up libnss3:arm64 (2:3.99-1) ... Setting up libxcb-shm0:arm64 (1.15-1) ... Setting up libldap-2.5-0:arm64 (2.5.13+dfsg-5+b3) ... 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 ucf (3.0043+nmu1) ... Setting up libjs-sphinxdoc (7.2.6-6) ... Setting up libreadline8t64:arm64 (8.2-4) ... Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up groff-base (1.23.0-3+b1) ... Setting up xml-core (0.19) ... Setting up libxslt1.1:arm64 (1.1.35-1+b1) ... Setting up libx11-6:arm64 (2:1.8.7-1+b1) ... Setting up libharfbuzz0b:arm64 (8.3.0-2+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 libpython3.12-stdlib:arm64 (3.12.3-1) ... Setting up libxrender1:arm64 (1:0.9.10-1.1+b1) ... Setting up libcurl4t64:arm64 (8.7.1-3) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libpython3.11-stdlib:arm64 (3.11.9-1) ... Setting up python3.12 (3.12.3-1) ... Setting up libpango-1.0-0:arm64 (1.52.1+ds-1) ... Setting up libcurl3t64-gnutls:arm64 (8.7.1-3) ... Setting up libxext6:arm64 (2:1.3.4-1+b1) ... Setting up libpaper-utils (1.1.29+b1) ... Setting up xfonts-utils (1:7.7+6) ... Setting up man-db (2.12.0-3) ... Not building database; man-db/auto-update is not 'true'. Setting up libcairo2:arm64 (1.18.0-1+b1) ... Setting up libraqm0:arm64 (0.10.1-1+b1) ... Setting up libxt6t64:arm64 (1:1.2.1-1.2) ... Setting up libpoppler126:arm64 (22.12.0-2+b1) ... Setting up libxss1:arm64 (1:1.2.3-1+b1) ... Setting up poppler-utils (22.12.0-2+b1) ... Setting up libpangoft2-1.0-0:arm64 (1.52.1+ds-1) ... Setting up libpangocairo-1.0-0:arm64 (1.52.1+ds-1) ... Setting up libpython3-stdlib:arm64 (3.11.8-1) ... Setting up python3.11 (3.11.9-1) ... Setting up libxft2:arm64 (2.3.6-1+b1) ... Setting up libhts3:arm64 (1.19+ds-1) ... Setting up libtk8.6:arm64 (8.6.14-1) ... Setting up debhelper (13.15.3) ... Setting up python3 (3.11.8-1) ... Setting up fonts-urw-base35 (20200910-8) ... Setting up python3-freetype (2.4.0-1) ... Setting up python3-wheel (0.43.0-1) ... Setting up python3-tz (2024.1-2) ... Setting up python3-six (1.16.0-6) ... Setting up python3-pil:arm64 (10.3.0-2) ... Setting up python3-decorator (5.1.1-5) ... Setting up python3-packaging (24.0-1) ... Setting up python3-pyproject-hooks (1.0.0-2) ... Setting up python3-pyparsing (3.1.2-1) ... Setting up python3-brotli (1.1.0-2+b3) ... Setting up python3-cycler (0.12.1-1) ... Setting up r-base-core (4.3.2-1) ... Creating config file /etc/R/Renviron with new version Setting up python3-kiwisolver (1.4.5-1) ... 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 python3-lxml:arm64 (5.1.0-1) ... Setting up python3-dateutil (2.9.0-2) ... Setting up python3-mpmath (1.3.0-1) ... Setting up python3-build (1.1.1-1) ... Setting up python3-lib2to3 (3.12.3-1) ... Setting up python3-appdirs (1.4.4-4) ... Setting up python3-pkg-resources (68.1.2-2) ... Setting up python3-distutils (3.12.3-1) ... python3.12: can't get files for byte-compilation Setting up python3-more-itertools (10.2.0-1) ... Setting up python3-iniconfig (1.1.1-2) ... Setting up python3-sympy (1.12-7) ... Setting up tk8.6-blt2.5 (2.5.3+dfsg-7) ... Setting up r-bioc-biocgenerics (0.48.1-2) ... Setting up python3-pysam (0.22.0+ds-1+b1) ... Setting up python3-cairo (1.26.0-1) ... Setting up python3-setuptools (68.1.2-2) ... Setting up python3-joblib (1.3.2-2) ... Setting up python3-lz4 (4.0.2+dfsg-1+b3) ... Setting up python3-pytest (7.4.4-3) ... Setting up blt (2.5.3+dfsg-7) ... Setting up python3-all (3.11.8-1) ... Setting up python3-yaml (6.0.1-2) ... Setting up python3-tk:arm64 (3.12.3-1) ... Setting up python3-zipp (1.0.0-6) ... Setting up python3-networkx (2.8.8-2) ... /usr/lib/python3/dist-packages/networkx/readwrite/tests/test_gml.py:556: SyntaxWarning: invalid octal escape sequence '\420' "graph [edge [ source u'u\4200' target u'u\4200' ] " /usr/lib/python3/dist-packages/networkx/readwrite/tests/test_gml.py:557: SyntaxWarning: invalid octal escape sequence '\420' + "node [ id u'u\4200' label b ] ]" Setting up python3-fs (2.4.16-4) ... Setting up python3-chardet (5.2.0+dfsg-1) ... Setting up python3-pil.imagetk:arm64 (10.3.0-2) ... Setting up python3-rlpycairo (0.3.0-3) ... Setting up python3-numpy (1:1.24.2-2) ... Setting up python3-reportlab (4.1.0-4) ... Setting up r-bioc-dnacopy (1.76.0-1) ... Setting up python3-contourpy (1.0.7-3) ... Setting up dh-python (6.20240422) ... Setting up python3-scipy (1.11.4-6) ... Setting up python3-importlib-metadata (4.12.0-1) ... Setting up pybuild-plugin-pyproject (6.20240422) ... Setting up python3-pomegranate (0.14.8-4) ... Setting up python3-pandas-lib:arm64 (2.1.4+dfsg-5) ... Setting up python3-pandas (2.1.4+dfsg-5) ... Setting up python3-pyfaidx (0.8.1.1-2) ... Setting up python3-defcon (0.10.3-3) ... Setting up python3-fonttools (4.46.0-1) ... Setting up python3-matplotlib (3.6.3-1+b2) ... Processing triggers for libc-bin (2.37-18) ... Processing triggers for sgml-base (1.31) ... Setting up w3c-sgml-lib (1.3-3) ... Setting up python3-biopython (1.81+dfsg-3) ... 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/4036091/tmp/hooks/A99_set_merged_usr starting Not re-configuring usrmerge for trixie I: user script /srv/workspace/pbuilder/4036091/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-l0oyg8bg/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 I: pybuild plugin_pyproject:129: Building wheel for python3.11 with "build" module I: pybuild base:311: python3.11 -m build --skip-dependency-check --no-isolation --wheel --outdir /build/reproducible-path/cnvkit-0.9.10/.pybuild/cpython3_3.11_cnvkit * Building wheel... running bdist_wheel running build running build_py running 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 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/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_3.11_cnvkit/.tmp-hkhrtn0w/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 python3.11 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 3.12.3, pytest-7.4.4, 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_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 in a future error 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 in a future error 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::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 in a future error 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: 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)) -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html ======================= 64 passed, 46 warnings in 50.06s ======================= I: pybuild pybuild:308: ln -s /build/reproducible-path/cnvkit-0.9.10/data /build/reproducible-path/cnvkit-0.9.10/.pybuild/cpython3_3.11_cnvkit/build/data; I: pybuild base:311: cd /build/reproducible-path/cnvkit-0.9.10/.pybuild/cpython3_3.11_cnvkit/build; python3.11 -m pytest test ============================= test session starts ============================== platform linux -- Python 3.11.9, pytest-7.4.4, pluggy-1.5.0 rootdir: /build/reproducible-path/cnvkit-0.9.10/.pybuild/cpython3_3.11_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_batch /build/reproducible-path/cnvkit-0.9.10/.pybuild/cpython3_3.11_cnvkit/build/cnvlib/coverage.py:198: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error 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_3.11_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_3.11_cnvkit/build/cnvlib/coverage.py:198: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error 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::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_3.11_cnvkit/build/cnvlib/coverage.py:198: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error 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: 8 warnings test/test_genome.py: 21 warnings /build/reproducible-path/cnvkit-0.9.10/.pybuild/cpython3_3.11_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_3.11_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)) -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html ======================= 64 passed, 46 warnings in 51.92s ======================= 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 I: pybuild plugin_pyproject:178: Copying package built for python3.11 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/4036091/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/4036091/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/4036091 and its subdirectories I: Current time: Sun Jun 1 23:27:42 +14 2025 I: pbuilder-time-stamp: 1748770062