I: pbuilder: network access will be disabled during build I: Current time: Sun Dec 8 18:14:19 +14 2024 I: pbuilder-time-stamp: 1733631259 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [python-pyani_0.2.12-3.dsc] I: copying [./python-pyani_0.2.12.orig.tar.gz] I: copying [./python-pyani_0.2.12-3.debian.tar.xz] I: Extracting source gpgv: Signature made Fri Nov 24 20:24:53 2023 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./python-pyani_0.2.12-3.dsc: no acceptable signature found dpkg-source: info: extracting python-pyani in python-pyani-0.2.12 dpkg-source: info: unpacking python-pyani_0.2.12.orig.tar.gz dpkg-source: info: unpacking python-pyani_0.2.12-3.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying pytest.patch dpkg-source: info: applying dataframe_sort.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/17777/tmp/hooks/D01_modify_environment starting debug: Running on ff4a. 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 Dec 8 04:14 /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/17777/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/17777/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]="37" [3]="1" [4]="release" [5]="arm-unknown-linux-gnueabihf") BASH_VERSION='5.2.37(1)-release' BUILDDIR=/build/reproducible-path BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=armhf DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=4 ' DIRSTACK=() DISTRIBUTION=unstable EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=arm HOST_ARCH=armhf IFS=' ' INVOCATION_ID=8fd22b72677f4997b684b5f18f73fbff LANG=C LANGUAGE=it_CH:it LC_ALL=C MACHTYPE=arm-unknown-linux-gnueabihf MAIL=/var/mail/root OPTERR=1 OPTIND=1 OSTYPE=linux-gnueabihf PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path PBCURRENTCOMMANDLINEOPERATION=build PBUILDER_OPERATION=build PBUILDER_PKGDATADIR=/usr/share/pbuilder PBUILDER_PKGLIBDIR=/usr/lib/pbuilder PBUILDER_SYSCONFDIR=/etc PIPESTATUS=([0]="0") POSIXLY_CORRECT=y PPID=17777 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.9PmaPLaJ/pbuilderrc_Nqfc --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.9PmaPLaJ/b2 --logfile b2/build.log python-pyani_0.2.12-3.dsc' SUDO_GID=113 SUDO_UID=107 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://10.0.0.15:3142/ I: uname -a Linux i-capture-the-hostname 6.1.0-28-armmp-lpae #1 SMP Debian 6.1.119-1 (2024-11-22) armv7l GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin I: user script /srv/workspace/pbuilder/17777/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: armhf Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), dh-sequence-python3, python3-all-dev, python3-setuptools, python3-biopython, python3-matplotlib, python3-pandas, python3-scipy, python3-seaborn, mummer, ncbi-blast+, python3-pytest dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19674 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-dev; however: Package python3-all-dev is not installed. pbuilder-satisfydepends-dummy depends on python3-setuptools; however: Package python3-setuptools is not installed. pbuilder-satisfydepends-dummy depends on python3-biopython; however: Package python3-biopython is not installed. pbuilder-satisfydepends-dummy depends on python3-matplotlib; however: Package python3-matplotlib is not installed. pbuilder-satisfydepends-dummy depends on python3-pandas; however: Package python3-pandas is not installed. pbuilder-satisfydepends-dummy depends on python3-scipy; however: Package python3-scipy is not installed. pbuilder-satisfydepends-dummy depends on python3-seaborn; however: Package python3-seaborn is not installed. pbuilder-satisfydepends-dummy depends on mummer; however: Package mummer is not installed. pbuilder-satisfydepends-dummy depends on ncbi-blast+; however: Package ncbi-blast+ is not installed. pbuilder-satisfydepends-dummy depends on python3-pytest; however: Package python3-pytest is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} blt{a} bsdextrautils{a} debhelper{a} dh-autoreconf{a} dh-python{a} dh-strip-nondeterminism{a} dwz{a} file{a} fontconfig-config{a} fonts-dejavu-core{a} fonts-dejavu-mono{a} fonts-lyx{a} fonts-urw-base35{a} gawk{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libblas3{a} libbrotli1{a} libcairo2{a} libcom-err2{a} libdebhelper-perl{a} libdeflate0{a} libelf1t64{a} libexpat1{a} libexpat1-dev{a} libfile-stripnondeterminism-perl{a} libfontconfig1{a} libfontenc1{a} libfreetype6{a} libfribidi0{a} libgfortran5{a} libglib2.0-0t64{a} libgraphite2-3{a} libgssapi-krb5-2{a} libharfbuzz0b{a} libicu72{a} libimagequant0{a} libjbig0{a} libjpeg62-turbo{a} libjs-jquery{a} libjs-jquery-ui{a} libjs-sphinxdoc{a} libjs-underscore{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} liblapack3{a} liblbfgsb0{a} liblcms2-2{a} liblerc4{a} liblmdb0{a} libmagic-mgc{a} libmagic1t64{a} libmbedcrypto16{a} libmbedtls21{a} libmbedx509-7{a} libnghttp2-14{a} libnsl2{a} libopenjp2-7{a} libpipeline1{a} libpixman-1-0{a} libpng16-16t64{a} libpython3-all-dev{a} libpython3-dev{a} libpython3-stdlib{a} libpython3.12-dev{a} libpython3.12-minimal{a} libpython3.12-stdlib{a} libpython3.12t64{a} libpython3.13{a} libpython3.13-dev{a} libpython3.13-minimal{a} libpython3.13-stdlib{a} libqhull-r8.0{a} libraqm0{a} libreadline8t64{a} libsharpyuv0{a} libsigsegv2{a} libtcl8.6{a} libtiff6{a} libtirpc-common{a} libtirpc3t64{a} libtk8.6{a} libtool{a} libuchardet0{a} libuv1t64{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} m4{a} man-db{a} media-types{a} mummer{a} ncbi-blast+{a} ncbi-data{a} netbase{a} po-debconf{a} python-matplotlib-data{a} python3{a} python3-all{a} python3-all-dev{a} python3-appdirs{a} python3-attr{a} python3-autocommand{a} python3-biopython{a} python3-brotli{a} python3-cairo{a} python3-chardet{a} python3-contourpy{a} python3-cycler{a} python3-dateutil{a} python3-decorator{a} python3-dev{a} python3-fonttools{a} python3-freetype{a} python3-fs{a} python3-inflect{a} python3-iniconfig{a} python3-jaraco.context{a} python3-jaraco.functools{a} python3-jaraco.text{a} python3-kiwisolver{a} python3-lxml{a} python3-lz4{a} python3-matplotlib{a} python3-minimal{a} python3-more-itertools{a} python3-mpmath{a} python3-numpy{a} python3-packaging{a} python3-pandas{a} python3-pandas-lib{a} python3-pil{a} python3-pil.imagetk{a} python3-pkg-resources{a} python3-pluggy{a} python3-pyparsing{a} python3-pytest{a} python3-reportlab{a} python3-rlpycairo{a} python3-scipy{a} python3-seaborn{a} python3-setuptools{a} python3-sympy{a} python3-tk{a} python3-typeguard{a} python3-typing-extensions{a} python3-tz{a} python3-ufolib2{a} python3-zipp{a} python3.12{a} python3.12-dev{a} python3.12-minimal{a} python3.12-tk{a} python3.13{a} python3.13-dev{a} python3.13-minimal{a} python3.13-tk{a} readline-common{a} sensible-utils{a} sgml-base{a} tk8.6-blt2.5{a} tzdata{a} unicode-data{a} w3c-sgml-lib{a} x11-common{a} xfonts-encodings{a} xfonts-utils{a} xml-core{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: ca-certificates curl fonts-dejavu-extra isympy-common javascript-common krb5-locales libarchive-cpio-perl libglib2.0-data libltdl-dev libmail-sendmail-perl lynx python-biopython-doc python3-bottleneck python3-bs4 python3-cssselect python3-html5lib python3-jinja2 python3-numexpr python3-odf python3-olefile python3-openpyxl python3-pooch python3-pygments python3-tables shared-mime-info wget xdg-user-dirs 0 packages upgraded, 191 newly installed, 0 to remove and 0 not upgraded. Need to get 152 MB of archives. After unpacking 607 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main armhf readline-common all 8.2-5 [69.3 kB] Get: 2 http://deb.debian.org/debian unstable/main armhf libreadline8t64 armhf 8.2-5 [146 kB] Get: 3 http://deb.debian.org/debian unstable/main armhf libsigsegv2 armhf 2.14-1+b2 [33.6 kB] Get: 4 http://deb.debian.org/debian unstable/main armhf gawk armhf 1:5.2.1-2+b2 [630 kB] Get: 5 http://deb.debian.org/debian unstable/main armhf libpython3.12-minimal armhf 3.12.8-1 [801 kB] Get: 6 http://deb.debian.org/debian unstable/main armhf libexpat1 armhf 2.6.4-1 [83.5 kB] Get: 7 http://deb.debian.org/debian unstable/main armhf python3.12-minimal armhf 3.12.8-1 [1810 kB] Get: 8 http://deb.debian.org/debian unstable/main armhf python3-minimal armhf 3.12.7-1 [26.8 kB] Get: 9 http://deb.debian.org/debian unstable/main armhf media-types all 10.1.0 [26.9 kB] Get: 10 http://deb.debian.org/debian unstable/main armhf netbase all 6.4 [12.8 kB] Get: 11 http://deb.debian.org/debian unstable/main armhf tzdata all 2024b-4 [256 kB] Get: 12 http://deb.debian.org/debian unstable/main armhf libkrb5support0 armhf 1.21.3-3 [30.0 kB] Get: 13 http://deb.debian.org/debian unstable/main armhf libcom-err2 armhf 1.47.2~rc1-2 [22.9 kB] Get: 14 http://deb.debian.org/debian unstable/main armhf libk5crypto3 armhf 1.21.3-3 [75.8 kB] Get: 15 http://deb.debian.org/debian unstable/main armhf libkeyutils1 armhf 1.6.3-4 [8096 B] Get: 16 http://deb.debian.org/debian unstable/main armhf libkrb5-3 armhf 1.21.3-3 [283 kB] Get: 17 http://deb.debian.org/debian unstable/main armhf libgssapi-krb5-2 armhf 1.21.3-3 [114 kB] Get: 18 http://deb.debian.org/debian unstable/main armhf libtirpc-common all 1.3.4+ds-1.3 [10.9 kB] Get: 19 http://deb.debian.org/debian unstable/main armhf libtirpc3t64 armhf 1.3.4+ds-1.3+b1 [71.3 kB] Get: 20 http://deb.debian.org/debian unstable/main armhf libnsl2 armhf 1.3.0-3+b3 [35.0 kB] Get: 21 http://deb.debian.org/debian unstable/main armhf libpython3.12-stdlib armhf 3.12.8-1 [1823 kB] Get: 22 http://deb.debian.org/debian unstable/main armhf python3.12 armhf 3.12.8-1 [677 kB] Get: 23 http://deb.debian.org/debian unstable/main armhf libpython3-stdlib armhf 3.12.7-1 [9712 B] Get: 24 http://deb.debian.org/debian unstable/main armhf python3 armhf 3.12.7-1 [27.8 kB] Get: 25 http://deb.debian.org/debian unstable/main armhf libpython3.13-minimal armhf 3.13.1-1 [843 kB] Get: 26 http://deb.debian.org/debian unstable/main armhf python3.13-minimal armhf 3.13.1-1 [1839 kB] Get: 27 http://deb.debian.org/debian unstable/main armhf sgml-base all 1.31 [15.4 kB] Get: 28 http://deb.debian.org/debian unstable/main armhf sensible-utils all 0.0.24 [24.8 kB] Get: 29 http://deb.debian.org/debian unstable/main armhf libmagic-mgc armhf 1:5.45-3+b1 [314 kB] Get: 30 http://deb.debian.org/debian unstable/main armhf libmagic1t64 armhf 1:5.45-3+b1 [98.5 kB] Get: 31 http://deb.debian.org/debian unstable/main armhf file armhf 1:5.45-3+b1 [42.3 kB] Get: 32 http://deb.debian.org/debian unstable/main armhf gettext-base armhf 0.22.5-2 [195 kB] Get: 33 http://deb.debian.org/debian unstable/main armhf libuchardet0 armhf 0.0.8-1+b2 [65.6 kB] Get: 34 http://deb.debian.org/debian unstable/main armhf groff-base armhf 1.23.0-6 [1091 kB] Get: 35 http://deb.debian.org/debian unstable/main armhf bsdextrautils armhf 2.40.2-12 [83.9 kB] Get: 36 http://deb.debian.org/debian unstable/main armhf libpipeline1 armhf 1.5.8-1 [35.0 kB] Get: 37 http://deb.debian.org/debian unstable/main armhf man-db armhf 2.13.0-1 [1382 kB] Get: 38 http://deb.debian.org/debian unstable/main armhf m4 armhf 1.4.19-4 [264 kB] Get: 39 http://deb.debian.org/debian unstable/main armhf autoconf all 2.72-3 [493 kB] Get: 40 http://deb.debian.org/debian unstable/main armhf autotools-dev all 20220109.1 [51.6 kB] Get: 41 http://deb.debian.org/debian unstable/main armhf automake all 1:1.16.5-1.3 [823 kB] Get: 42 http://deb.debian.org/debian unstable/main armhf autopoint all 0.22.5-2 [723 kB] Get: 43 http://deb.debian.org/debian unstable/main armhf libtcl8.6 armhf 8.6.15+dfsg-2 [934 kB] Get: 44 http://deb.debian.org/debian unstable/main armhf libbrotli1 armhf 1.1.0-2+b6 [282 kB] Get: 45 http://deb.debian.org/debian unstable/main armhf libpng16-16t64 armhf 1.6.44-2 [263 kB] Get: 46 http://deb.debian.org/debian unstable/main armhf libfreetype6 armhf 2.13.3+dfsg-1 [385 kB] Get: 47 http://deb.debian.org/debian unstable/main armhf fonts-dejavu-mono all 2.37-8 [489 kB] Get: 48 http://deb.debian.org/debian unstable/main armhf fonts-dejavu-core all 2.37-8 [840 kB] Get: 49 http://deb.debian.org/debian unstable/main armhf libfontenc1 armhf 1:1.1.8-1+b1 [20.8 kB] Get: 50 http://deb.debian.org/debian unstable/main armhf x11-common all 1:7.7+23.1 [216 kB] Get: 51 http://deb.debian.org/debian unstable/main armhf xfonts-encodings all 1:1.0.4-2.2 [577 kB] Get: 52 http://deb.debian.org/debian unstable/main armhf xfonts-utils armhf 1:7.7+7 [84.2 kB] Get: 53 http://deb.debian.org/debian unstable/main armhf fonts-urw-base35 all 20200910-8 [10.8 MB] Get: 54 http://deb.debian.org/debian unstable/main armhf fontconfig-config armhf 2.15.0-1.1+b1 [318 kB] Get: 55 http://deb.debian.org/debian unstable/main armhf libfontconfig1 armhf 2.15.0-1.1+b1 [371 kB] Get: 56 http://deb.debian.org/debian unstable/main armhf libxau6 armhf 1:1.0.11-1 [19.7 kB] Get: 57 http://deb.debian.org/debian unstable/main armhf libxdmcp6 armhf 1:1.1.5-1 [26.4 kB] Get: 58 http://deb.debian.org/debian unstable/main armhf libxcb1 armhf 1.17.0-2+b1 [140 kB] Get: 59 http://deb.debian.org/debian unstable/main armhf libx11-data all 2:1.8.10-2 [337 kB] Get: 60 http://deb.debian.org/debian unstable/main armhf libx11-6 armhf 2:1.8.10-2 [750 kB] Get: 61 http://deb.debian.org/debian unstable/main armhf libxrender1 armhf 1:0.9.10-1.1+b2 [25.0 kB] Get: 62 http://deb.debian.org/debian unstable/main armhf libxft2 armhf 2.3.6-1+b2 [46.5 kB] Get: 63 http://deb.debian.org/debian unstable/main armhf libxext6 armhf 2:1.3.4-1+b2 [45.2 kB] Get: 64 http://deb.debian.org/debian unstable/main armhf libxss1 armhf 1:1.2.3-1+b2 [16.4 kB] Get: 65 http://deb.debian.org/debian unstable/main armhf libtk8.6 armhf 8.6.15-1 [697 kB] Get: 66 http://deb.debian.org/debian unstable/main armhf tk8.6-blt2.5 armhf 2.5.3+dfsg-7 [481 kB] Get: 67 http://deb.debian.org/debian unstable/main armhf blt armhf 2.5.3+dfsg-7 [6024 B] Get: 68 http://deb.debian.org/debian unstable/main armhf libdebhelper-perl all 13.20 [89.7 kB] Get: 69 http://deb.debian.org/debian unstable/main armhf libtool all 2.4.7-8 [517 kB] Get: 70 http://deb.debian.org/debian unstable/main armhf dh-autoreconf all 20 [17.1 kB] Get: 71 http://deb.debian.org/debian unstable/main armhf libarchive-zip-perl all 1.68-1 [104 kB] Get: 72 http://deb.debian.org/debian unstable/main armhf libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 73 http://deb.debian.org/debian unstable/main armhf dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 74 http://deb.debian.org/debian unstable/main armhf libelf1t64 armhf 0.192-4 [184 kB] Get: 75 http://deb.debian.org/debian unstable/main armhf dwz armhf 0.15-1+b2 [106 kB] Get: 76 http://deb.debian.org/debian unstable/main armhf libicu72 armhf 72.1-5+b1 [9088 kB] Get: 77 http://deb.debian.org/debian unstable/main armhf libxml2 armhf 2.12.7+dfsg+really2.9.14-0.2+b1 [605 kB] Get: 78 http://deb.debian.org/debian unstable/main armhf gettext armhf 0.22.5-2 [1485 kB] Get: 79 http://deb.debian.org/debian unstable/main armhf intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 80 http://deb.debian.org/debian unstable/main armhf po-debconf all 1.0.21+nmu1 [248 kB] Get: 81 http://deb.debian.org/debian unstable/main armhf debhelper all 13.20 [915 kB] Get: 82 http://deb.debian.org/debian unstable/main armhf python3-autocommand all 2.2.2-3 [13.6 kB] Get: 83 http://deb.debian.org/debian unstable/main armhf python3-more-itertools all 10.5.0-1 [63.8 kB] Get: 84 http://deb.debian.org/debian unstable/main armhf python3-typing-extensions all 4.12.2-2 [73.0 kB] Get: 85 http://deb.debian.org/debian unstable/main armhf python3-typeguard all 4.4.1-1 [37.0 kB] Get: 86 http://deb.debian.org/debian unstable/main armhf python3-inflect all 7.3.1-2 [32.4 kB] Get: 87 http://deb.debian.org/debian unstable/main armhf python3-jaraco.context all 6.0.0-1 [7984 B] Get: 88 http://deb.debian.org/debian unstable/main armhf python3-jaraco.functools all 4.1.0-1 [12.0 kB] Get: 89 http://deb.debian.org/debian unstable/main armhf python3-pkg-resources all 75.2.0-1 [213 kB] Get: 90 http://deb.debian.org/debian unstable/main armhf python3-jaraco.text all 4.0.0-1 [11.4 kB] Get: 91 http://deb.debian.org/debian unstable/main armhf python3-zipp all 3.21.0-1 [10.6 kB] Get: 92 http://deb.debian.org/debian unstable/main armhf python3-setuptools all 75.2.0-1 [731 kB] Get: 93 http://deb.debian.org/debian unstable/main armhf dh-python all 6.20241024 [109 kB] Get: 94 http://deb.debian.org/debian unstable/main armhf fonts-lyx all 2.4.2.1-1 [190 kB] Get: 95 http://deb.debian.org/debian unstable/main armhf libblas3 armhf 3.12.0-4 [111 kB] Get: 96 http://deb.debian.org/debian unstable/main armhf libpixman-1-0 armhf 0.44.0-3 [164 kB] Get: 97 http://deb.debian.org/debian unstable/main armhf libxcb-render0 armhf 1.17.0-2+b1 [114 kB] Get: 98 http://deb.debian.org/debian unstable/main armhf libxcb-shm0 armhf 1.17.0-2+b1 [105 kB] Get: 99 http://deb.debian.org/debian unstable/main armhf libcairo2 armhf 1.18.2-2 [443 kB] Get: 100 http://deb.debian.org/debian unstable/main armhf libdeflate0 armhf 1.22-1 [36.3 kB] Get: 101 http://deb.debian.org/debian unstable/main armhf libexpat1-dev armhf 2.6.4-1 [140 kB] Get: 102 http://deb.debian.org/debian unstable/main armhf libfribidi0 armhf 1.0.15-1 [70.0 kB] Get: 103 http://deb.debian.org/debian unstable/main armhf libgfortran5 armhf 14.2.0-8 [263 kB] Get: 104 http://deb.debian.org/debian unstable/main armhf libglib2.0-0t64 armhf 2.82.2-3 [1326 kB] Get: 105 http://deb.debian.org/debian unstable/main armhf libgraphite2-3 armhf 1.3.14-2+b1 [63.1 kB] Get: 106 http://deb.debian.org/debian unstable/main armhf libharfbuzz0b armhf 10.1.0-1 [418 kB] Get: 107 http://deb.debian.org/debian unstable/main armhf libimagequant0 armhf 2.18.0-1+b2 [30.5 kB] Get: 108 http://deb.debian.org/debian unstable/main armhf libjbig0 armhf 2.1-6.1+b2 [27.3 kB] Get: 109 http://deb.debian.org/debian unstable/main armhf libjpeg62-turbo armhf 1:2.1.5-3+b1 [145 kB] Get: 110 http://deb.debian.org/debian unstable/main armhf libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get: 111 http://deb.debian.org/debian unstable/main armhf libjs-jquery-ui all 1.13.2+dfsg-1 [250 kB] Get: 112 http://deb.debian.org/debian unstable/main armhf libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB] Get: 113 http://deb.debian.org/debian unstable/main armhf libjs-sphinxdoc all 7.4.7-4 [158 kB] Get: 114 http://deb.debian.org/debian unstable/main armhf liblapack3 armhf 3.12.0-4 [1828 kB] Get: 115 http://deb.debian.org/debian unstable/main armhf liblbfgsb0 armhf 3.0+dfsg.4-1+b2 [25.6 kB] Get: 116 http://deb.debian.org/debian unstable/main armhf liblcms2-2 armhf 2.16-2 [131 kB] Get: 117 http://deb.debian.org/debian unstable/main armhf liblerc4 armhf 4.0.0+ds-5 [146 kB] Get: 118 http://deb.debian.org/debian unstable/main armhf liblmdb0 armhf 0.9.31-1+b2 [38.1 kB] Get: 119 http://deb.debian.org/debian unstable/main armhf libmbedcrypto16 armhf 3.6.2-3 [320 kB] Get: 120 http://deb.debian.org/debian unstable/main armhf libmbedx509-7 armhf 3.6.2-3 [142 kB] Get: 121 http://deb.debian.org/debian unstable/main armhf libmbedtls21 armhf 3.6.2-3 [220 kB] Get: 122 http://deb.debian.org/debian unstable/main armhf libnghttp2-14 armhf 1.64.0-1 [62.9 kB] Get: 123 http://deb.debian.org/debian unstable/main armhf libopenjp2-7 armhf 2.5.0-2+b4 [179 kB] Get: 124 http://deb.debian.org/debian unstable/main armhf libpython3.12t64 armhf 3.12.8-1 [1849 kB] Get: 125 http://deb.debian.org/debian unstable/main armhf zlib1g-dev armhf 1:1.3.dfsg+really1.3.1-1+b1 [905 kB] Get: 126 http://deb.debian.org/debian unstable/main armhf libpython3.12-dev armhf 3.12.8-1 [3829 kB] Get: 127 http://deb.debian.org/debian unstable/main armhf libpython3-dev armhf 3.12.7-1 [9976 B] Get: 128 http://deb.debian.org/debian unstable/main armhf libpython3.13-stdlib armhf 3.13.1-1 [1844 kB] Get: 129 http://deb.debian.org/debian unstable/main armhf libpython3.13 armhf 3.13.1-1 [1868 kB] Get: 130 http://deb.debian.org/debian unstable/main armhf libpython3.13-dev armhf 3.13.1-1 [3799 kB] Get: 131 http://deb.debian.org/debian unstable/main armhf libpython3-all-dev armhf 3.12.7-1 [1072 B] Get: 132 http://deb.debian.org/debian unstable/main armhf libqhull-r8.0 armhf 2020.2-6+b2 [220 kB] Get: 133 http://deb.debian.org/debian unstable/main armhf libraqm0 armhf 0.10.1-1+b2 [11.8 kB] Get: 134 http://deb.debian.org/debian unstable/main armhf libsharpyuv0 armhf 1.4.0-0.1+b1 [111 kB] Get: 135 http://deb.debian.org/debian unstable/main armhf libwebp7 armhf 1.4.0-0.1+b1 [266 kB] Get: 136 http://deb.debian.org/debian unstable/main armhf libtiff6 armhf 4.5.1+git230720-5 [302 kB] Get: 137 http://deb.debian.org/debian unstable/main armhf libuv1t64 armhf 1.48.0-7 [134 kB] Get: 138 http://deb.debian.org/debian unstable/main armhf libwebpdemux2 armhf 1.4.0-0.1+b1 [110 kB] Get: 139 http://deb.debian.org/debian unstable/main armhf libwebpmux3 armhf 1.4.0-0.1+b1 [120 kB] Get: 140 http://deb.debian.org/debian unstable/main armhf libxslt1.1 armhf 1.1.35-1.1+b1 [212 kB] Get: 141 http://deb.debian.org/debian unstable/main armhf mummer armhf 3.23+dfsg-8 [627 kB] Get: 142 http://deb.debian.org/debian unstable/main armhf ncbi-data all 6.1.20170106+dfsg2-5 [3537 kB] Get: 143 http://deb.debian.org/debian unstable/main armhf ncbi-blast+ armhf 2.16.0+ds-6+b1 [13.4 MB] Get: 144 http://deb.debian.org/debian unstable/main armhf python-matplotlib-data all 3.8.3-3 [2731 kB] Get: 145 http://deb.debian.org/debian unstable/main armhf python3.13 armhf 3.13.1-1 [740 kB] Get: 146 http://deb.debian.org/debian unstable/main armhf python3-all armhf 3.12.7-1 [1052 B] Get: 147 http://deb.debian.org/debian unstable/main armhf python3.12-dev armhf 3.12.8-1 [505 kB] Get: 148 http://deb.debian.org/debian unstable/main armhf python3-dev armhf 3.12.7-1 [26.1 kB] Get: 149 http://deb.debian.org/debian unstable/main armhf python3.13-dev armhf 3.13.1-1 [505 kB] Get: 150 http://deb.debian.org/debian unstable/main armhf python3-all-dev armhf 3.12.7-1 [1076 B] Get: 151 http://deb.debian.org/debian unstable/main armhf python3-appdirs all 1.4.4-4 [12.5 kB] Get: 152 http://deb.debian.org/debian unstable/main armhf python3-attr all 24.2.0-1 [68.4 kB] Get: 153 http://deb.debian.org/debian unstable/main armhf python3-numpy armhf 1:1.26.4+ds-12 [3676 kB] Get: 154 http://deb.debian.org/debian unstable/main armhf python3-chardet all 5.2.0+dfsg-1 [107 kB] Get: 155 http://deb.debian.org/debian unstable/main armhf python3.12-tk armhf 3.12.8-1 [109 kB] Get: 156 http://deb.debian.org/debian unstable/main armhf python3.13-tk armhf 3.13.1-1 [99.7 kB] Get: 157 http://deb.debian.org/debian unstable/main armhf python3-tk armhf 3.12.7-1 [9444 B] Get: 158 http://deb.debian.org/debian unstable/main armhf python3-pil.imagetk armhf 10.4.0-1+b1 [79.3 kB] Get: 159 http://deb.debian.org/debian unstable/main armhf python3-pil armhf 10.4.0-1+b1 [478 kB] Get: 160 http://deb.debian.org/debian unstable/main armhf python3-cairo armhf 1.26.1-2+b1 [120 kB] Get: 161 http://deb.debian.org/debian unstable/main armhf python3-freetype all 2.5.1-1 [89.3 kB] Get: 162 http://deb.debian.org/debian unstable/main armhf python3-rlpycairo all 0.3.0-3 [9904 B] Get: 163 http://deb.debian.org/debian unstable/main armhf python3-reportlab all 4.2.5-1 [1117 kB] Get: 164 http://deb.debian.org/debian unstable/main armhf xml-core all 0.19 [20.1 kB] Get: 165 http://deb.debian.org/debian unstable/main armhf w3c-sgml-lib all 1.3-3 [273 kB] Get: 166 http://deb.debian.org/debian unstable/main armhf python3-biopython armhf 1.84+dfsg-4+b1 [1625 kB] Get: 167 http://deb.debian.org/debian unstable/main armhf python3-brotli armhf 1.1.0-2+b6 [302 kB] Get: 168 http://deb.debian.org/debian unstable/main armhf python3-contourpy armhf 1.3.1-1 [217 kB] Get: 169 http://deb.debian.org/debian unstable/main armhf python3-cycler all 0.12.1-1 [9496 B] Get: 170 http://deb.debian.org/debian unstable/main armhf python3-dateutil all 2.9.0-3 [79.3 kB] Get: 171 http://deb.debian.org/debian unstable/main armhf python3-decorator all 5.1.1-5 [15.1 kB] Get: 172 http://deb.debian.org/debian unstable/main armhf python3-tz all 2024.1-2 [30.9 kB] Get: 173 http://deb.debian.org/debian unstable/main armhf python3-fs all 2.4.16-5 [95.1 kB] Get: 174 http://deb.debian.org/debian unstable/main armhf python3-lxml armhf 5.3.0-1+b1 [1468 kB] Get: 175 http://deb.debian.org/debian unstable/main armhf python3-lz4 armhf 4.4.0+dfsg-1 [23.9 kB] Get: 176 http://deb.debian.org/debian unstable/main armhf python3-scipy armhf 1.14.1-3 [17.8 MB] Get: 177 http://deb.debian.org/debian unstable/main armhf python3-mpmath all 1.3.0-1 [419 kB] Get: 178 http://deb.debian.org/debian unstable/main armhf python3-sympy all 1.13.3-1 [4147 kB] Get: 179 http://deb.debian.org/debian unstable/main armhf python3-ufolib2 all 0.17.0+dfsg1-1 [33.0 kB] Get: 180 http://deb.debian.org/debian unstable/main armhf unicode-data all 15.1.0-1 [8547 kB] Get: 181 http://deb.debian.org/debian unstable/main armhf python3-fonttools armhf 4.55.0-3 [1529 kB] Get: 182 http://deb.debian.org/debian unstable/main armhf python3-iniconfig all 1.1.1-2 [6396 B] Get: 183 http://deb.debian.org/debian unstable/main armhf python3-kiwisolver armhf 1.4.7-2+b1 [64.9 kB] Get: 184 http://deb.debian.org/debian unstable/main armhf python3-pyparsing all 3.1.2-1 [146 kB] Get: 185 http://deb.debian.org/debian unstable/main armhf python3-packaging all 24.2-1 [55.3 kB] Get: 186 http://deb.debian.org/debian unstable/main armhf python3-matplotlib armhf 3.8.3-3+b1 [5579 kB] Get: 187 http://deb.debian.org/debian unstable/main armhf python3-pandas-lib armhf 2.2.3+dfsg-5+b1 [6440 kB] Get: 188 http://deb.debian.org/debian unstable/main armhf python3-pandas all 2.2.3+dfsg-5 [3096 kB] Get: 189 http://deb.debian.org/debian unstable/main armhf python3-pluggy all 1.5.0-1 [26.9 kB] Get: 190 http://deb.debian.org/debian unstable/main armhf python3-pytest all 8.3.4-1 [250 kB] Get: 191 http://deb.debian.org/debian unstable/main armhf python3-seaborn all 0.13.2-4 [215 kB] Fetched 152 MB in 11s (14.1 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package readline-common. (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 ... 19674 files and directories currently installed.) Preparing to unpack .../readline-common_8.2-5_all.deb ... Unpacking readline-common (8.2-5) ... Selecting previously unselected package libreadline8t64:armhf. Preparing to unpack .../libreadline8t64_8.2-5_armhf.deb ... Adding 'diversion of /lib/arm-linux-gnueabihf/libhistory.so.8 to /lib/arm-linux-gnueabihf/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/arm-linux-gnueabihf/libhistory.so.8.2 to /lib/arm-linux-gnueabihf/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/arm-linux-gnueabihf/libreadline.so.8 to /lib/arm-linux-gnueabihf/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/arm-linux-gnueabihf/libreadline.so.8.2 to /lib/arm-linux-gnueabihf/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:armhf (8.2-5) ... Selecting previously unselected package libsigsegv2:armhf. Preparing to unpack .../libsigsegv2_2.14-1+b2_armhf.deb ... Unpacking libsigsegv2:armhf (2.14-1+b2) ... Setting up readline-common (8.2-5) ... Setting up libreadline8t64:armhf (8.2-5) ... Setting up libsigsegv2:armhf (2.14-1+b2) ... Selecting previously unselected package gawk. (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 ... 19716 files and directories currently installed.) Preparing to unpack .../gawk_1%3a5.2.1-2+b2_armhf.deb ... Unpacking gawk (1:5.2.1-2+b2) ... Selecting previously unselected package libpython3.12-minimal:armhf. Preparing to unpack .../libpython3.12-minimal_3.12.8-1_armhf.deb ... Unpacking libpython3.12-minimal:armhf (3.12.8-1) ... Selecting previously unselected package libexpat1:armhf. Preparing to unpack .../libexpat1_2.6.4-1_armhf.deb ... Unpacking libexpat1:armhf (2.6.4-1) ... Selecting previously unselected package python3.12-minimal. Preparing to unpack .../python3.12-minimal_3.12.8-1_armhf.deb ... Unpacking python3.12-minimal (3.12.8-1) ... Setting up libpython3.12-minimal:armhf (3.12.8-1) ... Setting up libexpat1:armhf (2.6.4-1) ... Setting up python3.12-minimal (3.12.8-1) ... 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 ... 20225 files and directories currently installed.) Preparing to unpack .../00-python3-minimal_3.12.7-1_armhf.deb ... Unpacking python3-minimal (3.12.7-1) ... Selecting previously unselected package media-types. Preparing to unpack .../01-media-types_10.1.0_all.deb ... Unpacking media-types (10.1.0) ... Selecting previously unselected package netbase. Preparing to unpack .../02-netbase_6.4_all.deb ... Unpacking netbase (6.4) ... Selecting previously unselected package tzdata. Preparing to unpack .../03-tzdata_2024b-4_all.deb ... Unpacking tzdata (2024b-4) ... Selecting previously unselected package libkrb5support0:armhf. Preparing to unpack .../04-libkrb5support0_1.21.3-3_armhf.deb ... Unpacking libkrb5support0:armhf (1.21.3-3) ... Selecting previously unselected package libcom-err2:armhf. Preparing to unpack .../05-libcom-err2_1.47.2~rc1-2_armhf.deb ... Unpacking libcom-err2:armhf (1.47.2~rc1-2) ... Selecting previously unselected package libk5crypto3:armhf. Preparing to unpack .../06-libk5crypto3_1.21.3-3_armhf.deb ... Unpacking libk5crypto3:armhf (1.21.3-3) ... Selecting previously unselected package libkeyutils1:armhf. Preparing to unpack .../07-libkeyutils1_1.6.3-4_armhf.deb ... Unpacking libkeyutils1:armhf (1.6.3-4) ... Selecting previously unselected package libkrb5-3:armhf. Preparing to unpack .../08-libkrb5-3_1.21.3-3_armhf.deb ... Unpacking libkrb5-3:armhf (1.21.3-3) ... Selecting previously unselected package libgssapi-krb5-2:armhf. Preparing to unpack .../09-libgssapi-krb5-2_1.21.3-3_armhf.deb ... Unpacking libgssapi-krb5-2:armhf (1.21.3-3) ... Selecting previously unselected package libtirpc-common. Preparing to unpack .../10-libtirpc-common_1.3.4+ds-1.3_all.deb ... Unpacking libtirpc-common (1.3.4+ds-1.3) ... Selecting previously unselected package libtirpc3t64:armhf. Preparing to unpack .../11-libtirpc3t64_1.3.4+ds-1.3+b1_armhf.deb ... Adding 'diversion of /lib/arm-linux-gnueabihf/libtirpc.so.3 to /lib/arm-linux-gnueabihf/libtirpc.so.3.usr-is-merged by libtirpc3t64' Adding 'diversion of /lib/arm-linux-gnueabihf/libtirpc.so.3.0.0 to /lib/arm-linux-gnueabihf/libtirpc.so.3.0.0.usr-is-merged by libtirpc3t64' Unpacking libtirpc3t64:armhf (1.3.4+ds-1.3+b1) ... Selecting previously unselected package libnsl2:armhf. Preparing to unpack .../12-libnsl2_1.3.0-3+b3_armhf.deb ... Unpacking libnsl2:armhf (1.3.0-3+b3) ... Selecting previously unselected package libpython3.12-stdlib:armhf. Preparing to unpack .../13-libpython3.12-stdlib_3.12.8-1_armhf.deb ... Unpacking libpython3.12-stdlib:armhf (3.12.8-1) ... Selecting previously unselected package python3.12. Preparing to unpack .../14-python3.12_3.12.8-1_armhf.deb ... Unpacking python3.12 (3.12.8-1) ... Selecting previously unselected package libpython3-stdlib:armhf. Preparing to unpack .../15-libpython3-stdlib_3.12.7-1_armhf.deb ... Unpacking libpython3-stdlib:armhf (3.12.7-1) ... Setting up python3-minimal (3.12.7-1) ... 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 ... 21256 files and directories currently installed.) Preparing to unpack .../000-python3_3.12.7-1_armhf.deb ... Unpacking python3 (3.12.7-1) ... Selecting previously unselected package libpython3.13-minimal:armhf. Preparing to unpack .../001-libpython3.13-minimal_3.13.1-1_armhf.deb ... Unpacking libpython3.13-minimal:armhf (3.13.1-1) ... Selecting previously unselected package python3.13-minimal. Preparing to unpack .../002-python3.13-minimal_3.13.1-1_armhf.deb ... Unpacking python3.13-minimal (3.13.1-1) ... 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 sensible-utils. Preparing to unpack .../004-sensible-utils_0.0.24_all.deb ... Unpacking sensible-utils (0.0.24) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../005-libmagic-mgc_1%3a5.45-3+b1_armhf.deb ... Unpacking libmagic-mgc (1:5.45-3+b1) ... Selecting previously unselected package libmagic1t64:armhf. Preparing to unpack .../006-libmagic1t64_1%3a5.45-3+b1_armhf.deb ... Unpacking libmagic1t64:armhf (1:5.45-3+b1) ... Selecting previously unselected package file. Preparing to unpack .../007-file_1%3a5.45-3+b1_armhf.deb ... Unpacking file (1:5.45-3+b1) ... Selecting previously unselected package gettext-base. 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Setting up sgml-base (1.31) ... Setting up libkrb5-3:armhf (1.21.3-3) ... Setting up libmbedcrypto16:armhf (3.6.2-3) ... Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Setting up python-matplotlib-data (3.8.3-3) ... Setting up libwebpmux3:armhf (1.4.0-0.1+b1) ... Setting up libpython3.13-stdlib:armhf (3.13.1-1) ... Setting up libxml2:armhf (2.12.7+dfsg+really2.9.14-0.2+b1) ... Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... Setting up libpython3.13:armhf (3.13.1-1) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.14.0-1) ... Setting up liblapack3:armhf (3.12.0-4) ... update-alternatives: using /usr/lib/arm-linux-gnueabihf/lapack/liblapack.so.3 to provide /usr/lib/arm-linux-gnueabihf/liblapack.so.3 (liblapack.so.3-arm-linux-gnueabihf) in auto mode Setting up gettext (0.22.5-2) ... Setting up libxrender1:armhf (1:0.9.10-1.1+b2) ... Setting up libtool (2.4.7-8) ... Setting up python3.13 (3.13.1-1) ... Setting up fontconfig-config (2.15.0-1.1+b1) ... Setting up libwebpdemux2:armhf (1.4.0-0.1+b1) ... Setting up libxext6:armhf (2:1.3.4-1+b2) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up libmbedx509-7:armhf (3.6.2-3) ... Setting up libjs-jquery-ui (1.13.2+dfsg-1) ... Setting up libfreetype6:armhf (2.13.3+dfsg-1) ... Setting up libpython3.13-dev:armhf (3.13.1-1) ... Setting up libgssapi-krb5-2:armhf (1.21.3-3) ... Setting up libjs-sphinxdoc (7.4.7-4) ... Setting up libmbedtls21:armhf (3.6.2-3) ... Setting up dh-strip-nondeterminism (1.14.0-1) ... Setting up groff-base (1.23.0-6) ... Setting up xml-core (0.19) ... Setting up libxslt1.1:armhf (1.1.35-1.1+b1) ... Setting up libharfbuzz0b:armhf (10.1.0-1) ... Setting up libxss1:armhf (1:1.2.3-1+b2) ... Setting up libfontconfig1:armhf (2.15.0-1.1+b1) ... Setting up liblbfgsb0:armhf (3.0+dfsg.4-1+b2) ... Setting up libxft2:armhf (2.3.6-1+b2) ... Setting up libtirpc3t64:armhf (1.3.4+ds-1.3+b1) ... Setting up python3.13-dev (3.13.1-1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libtk8.6:armhf (8.6.15-1) ... Setting up python3.12-tk (3.12.8-1) ... Setting up xfonts-utils (1:7.7+7) ... Setting up man-db (2.13.0-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libcairo2:armhf (1.18.2-2) ... Setting up python3.13-tk (3.13.1-1) ... Setting up libraqm0:armhf (0.10.1-1+b2) ... Setting up libnsl2:armhf (1.3.0-3+b3) ... Setting up tk8.6-blt2.5 (2.5.3+dfsg-7) ... Setting up libpython3.12-stdlib:armhf (3.12.8-1) ... Setting up blt (2.5.3+dfsg-7) ... Setting up python3.12 (3.12.8-1) ... Setting up debhelper (13.20) ... Setting up fonts-urw-base35 (20200910-8) ... Setting up libpython3.12t64:armhf (3.12.8-1) ... Setting up libpython3-stdlib:armhf (3.12.7-1) ... Setting up python3 (3.12.7-1) ... Setting up libpython3.12-dev:armhf (3.12.8-1) ... Setting up python3-zipp (3.21.0-1) ... Setting up python3-freetype (2.5.1-1) ... Setting up python3-autocommand (2.2.2-3) ... Setting up python3-tz (2024.1-2) ... Setting up ncbi-blast+ (2.16.0+ds-6+b1) ... Setting up python3-pil:armhf (10.4.0-1+b1) ... Setting up python3-decorator (5.1.1-5) ... Setting up python3-packaging (24.2-1) ... Setting up python3-pyparsing (3.1.2-1) ... Setting up python3-brotli (1.1.0-2+b6) ... Setting up python3-cycler (0.12.1-1) ... Setting up python3-kiwisolver (1.4.7-2+b1) ... Setting up python3.12-dev (3.12.8-1) ... Setting up python3-typing-extensions (4.12.2-2) ... Setting up python3-pluggy (1.5.0-1) ... Setting up python3-lxml:armhf (5.3.0-1+b1) ... Setting up python3-dateutil (2.9.0-3) ... Setting up python3-mpmath (1.3.0-1) ... Setting up python3-appdirs (1.4.4-4) ... Setting up python3-more-itertools (10.5.0-1) ... Setting up python3-iniconfig (1.1.1-2) ... Setting up python3-sympy (1.13.3-1) ... Setting up python3-attr (24.2.0-1) ... Setting up libpython3-dev:armhf (3.12.7-1) ... Setting up python3-cairo (1.26.1-2+b1) ... Setting up python3-jaraco.functools (4.1.0-1) ... Setting up python3-jaraco.context (6.0.0-1) ... Setting up python3-lz4 (4.4.0+dfsg-1) ... Setting up python3-pytest (8.3.4-1) ... Setting up python3-typeguard (4.4.1-1) ... Setting up python3-all (3.12.7-1) ... Setting up python3-tk:armhf (3.12.7-1) ... Setting up python3-inflect (7.3.1-2) ... Setting up python3-pil.imagetk:armhf (10.4.0-1+b1) ... Setting up python3-rlpycairo (0.3.0-3) ... Setting up libpython3-all-dev:armhf (3.12.7-1) ... Setting up python3-jaraco.text (4.0.0-1) ... Setting up python3-dev (3.12.7-1) ... Setting up python3-pkg-resources (75.2.0-1) ... Setting up python3-all-dev (3.12.7-1) ... Setting up python3-setuptools (75.2.0-1) ... Setting up python3-fs (2.4.16-5) ... Setting up python3-chardet (5.2.0+dfsg-1) ... Setting up python3-numpy (1:1.26.4+ds-12) ... Setting up python3-reportlab (4.2.5-1) ... Setting up python3-contourpy (1.3.1-1) ... Setting up dh-python (6.20241024) ... Setting up python3-scipy (1.14.1-3) ... Setting up python3-pandas-lib:armhf (2.2.3+dfsg-5+b1) ... Setting up python3-pandas (2.2.3+dfsg-5) ... Setting up python3-fonttools (4.55.0-3) ... Setting up python3-ufolib2 (0.17.0+dfsg1-1) ... Setting up python3-matplotlib (3.8.3-3+b1) ... Setting up python3-seaborn (0.13.2-4) ... Processing triggers for libc-bin (2.40-4) ... Processing triggers for sgml-base (1.31) ... Setting up w3c-sgml-lib (1.3-3) ... Setting up python3-biopython (1.84+dfsg-4+b1) ... 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/17777/tmp/hooks/A99_set_merged_usr starting Not re-configuring usrmerge for unstable I: user script /srv/workspace/pbuilder/17777/tmp/hooks/A99_set_merged_usr finished hostname: Name or service not known I: Running cd /build/reproducible-path/python-pyani-0.2.12/ && 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 > ../python-pyani_0.2.12-3_source.changes dpkg-buildpackage: info: source package python-pyani dpkg-buildpackage: info: source version 0.2.12-3 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Ananthu C V dpkg-source --before-build . dpkg-buildpackage: info: host architecture armhf debian/rules clean dh clean --buildsystem=pybuild debian/rules override_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/python-pyani-0.2.12' dh_auto_clean I: pybuild base:311: python3.13 setup.py clean /usr/lib/python3/dist-packages/setuptools/dist.py:491: SetuptoolsDeprecationWarning: Invalid dash-separated options !! ******************************************************************************** Usage of dash-separated 'description-file' will not be supported in future versions. Please use the underscore name 'description_file' instead. By 2025-Mar-03, you need to update your project and remove deprecated calls or your builds will no longer be supported. See https://setuptools.pypa.io/en/latest/userguide/declarative_config.html for details. ******************************************************************************** !! opt = self.warn_dash_deprecation(opt, section) running clean removing '/build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.13_pyani/build' (and everything under it) 'build/bdist.linux-armv7l' does not exist -- can't clean it 'build/scripts-3.13' does not exist -- can't clean it I: pybuild base:311: python3.12 setup.py clean /usr/lib/python3/dist-packages/setuptools/dist.py:491: SetuptoolsDeprecationWarning: Invalid dash-separated options !! ******************************************************************************** Usage of dash-separated 'description-file' will not be supported in future versions. Please use the underscore name 'description_file' instead. By 2025-Mar-03, you need to update your project and remove deprecated calls or your builds will no longer be supported. See https://setuptools.pypa.io/en/latest/userguide/declarative_config.html for details. ******************************************************************************** !! opt = self.warn_dash_deprecation(opt, section) running clean removing '/build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.12_pyani/build' (and everything under it) 'build/bdist.linux-armv7l' does not exist -- can't clean it 'build/scripts-3.12' does not exist -- can't clean it rm -f pyani.egg-info/PKG-INFO pyani.egg-info/SOURCES.txt pyani.egg-info/dependency_links.txt pyani.egg-info/requires.txt pyani.egg-info/top_level.txt make[1]: Leaving directory '/build/reproducible-path/python-pyani-0.2.12' 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 I: pybuild base:311: python3.13 setup.py config /usr/lib/python3/dist-packages/setuptools/dist.py:491: SetuptoolsDeprecationWarning: Invalid dash-separated options !! ******************************************************************************** Usage of dash-separated 'description-file' will not be supported in future versions. Please use the underscore name 'description_file' instead. By 2025-Mar-03, you need to update your project and remove deprecated calls or your builds will no longer be supported. See https://setuptools.pypa.io/en/latest/userguide/declarative_config.html for details. ******************************************************************************** !! opt = self.warn_dash_deprecation(opt, section) running config I: pybuild base:311: python3.12 setup.py config /usr/lib/python3/dist-packages/setuptools/dist.py:491: SetuptoolsDeprecationWarning: Invalid dash-separated options !! ******************************************************************************** Usage of dash-separated 'description-file' will not be supported in future versions. Please use the underscore name 'description_file' instead. By 2025-Mar-03, you need to update your project and remove deprecated calls or your builds will no longer be supported. See https://setuptools.pypa.io/en/latest/userguide/declarative_config.html for details. ******************************************************************************** !! opt = self.warn_dash_deprecation(opt, section) running config dh_auto_build -O--buildsystem=pybuild I: pybuild base:311: /usr/bin/python3.13 setup.py build /usr/lib/python3/dist-packages/setuptools/dist.py:491: SetuptoolsDeprecationWarning: Invalid dash-separated options !! ******************************************************************************** Usage of dash-separated 'description-file' will not be supported in future versions. Please use the underscore name 'description_file' instead. By 2025-Mar-03, you need to update your project and remove deprecated calls or your builds will no longer be supported. See https://setuptools.pypa.io/en/latest/userguide/declarative_config.html for details. ******************************************************************************** !! opt = self.warn_dash_deprecation(opt, section) running build running build_py creating /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.13_pyani/build/pyani copying pyani/anim.py -> /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.13_pyani/build/pyani copying pyani/tetra.py -> /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.13_pyani/build/pyani copying pyani/run_multiprocessing.py -> /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.13_pyani/build/pyani copying pyani/pyani_tools.py -> /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.13_pyani/build/pyani copying pyani/__init__.py -> /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.13_pyani/build/pyani copying pyani/pyani_files.py -> /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.13_pyani/build/pyani copying pyani/pyani_config.py -> /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.13_pyani/build/pyani copying pyani/anib.py -> /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.13_pyani/build/pyani copying pyani/run_sge.py -> /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.13_pyani/build/pyani copying pyani/pyani_graphics.py -> /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.13_pyani/build/pyani copying pyani/pyani_jobs.py -> /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.13_pyani/build/pyani running egg_info creating pyani.egg-info writing pyani.egg-info/PKG-INFO writing dependency_links to pyani.egg-info/dependency_links.txt writing requirements to pyani.egg-info/requires.txt writing top-level names to pyani.egg-info/top_level.txt writing manifest file 'pyani.egg-info/SOURCES.txt' reading manifest file 'pyani.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' adding license file 'LICENSE' writing manifest file 'pyani.egg-info/SOURCES.txt' running build_scripts creating build/scripts-3.13 copying and adjusting bin/average_nucleotide_identity.py -> build/scripts-3.13 copying and adjusting bin/genbank_get_genomes_by_taxon.py -> build/scripts-3.13 copying and adjusting bin/delta_filter_wrapper.py -> build/scripts-3.13 changing mode of build/scripts-3.13/average_nucleotide_identity.py from 644 to 755 changing mode of build/scripts-3.13/genbank_get_genomes_by_taxon.py from 644 to 755 changing mode of build/scripts-3.13/delta_filter_wrapper.py from 644 to 755 I: pybuild base:311: /usr/bin/python3 setup.py build /usr/lib/python3/dist-packages/setuptools/dist.py:491: SetuptoolsDeprecationWarning: Invalid dash-separated options !! ******************************************************************************** Usage of dash-separated 'description-file' will not be supported in future versions. Please use the underscore name 'description_file' instead. By 2025-Mar-03, you need to update your project and remove deprecated calls or your builds will no longer be supported. See https://setuptools.pypa.io/en/latest/userguide/declarative_config.html for details. ******************************************************************************** !! opt = self.warn_dash_deprecation(opt, section) running build running build_py creating /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.12_pyani/build/pyani copying pyani/anim.py -> /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.12_pyani/build/pyani copying pyani/tetra.py -> /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.12_pyani/build/pyani copying pyani/run_multiprocessing.py -> /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.12_pyani/build/pyani copying pyani/pyani_tools.py -> /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.12_pyani/build/pyani copying pyani/__init__.py -> /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.12_pyani/build/pyani copying pyani/pyani_files.py -> /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.12_pyani/build/pyani copying pyani/pyani_config.py -> /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.12_pyani/build/pyani copying pyani/anib.py -> /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.12_pyani/build/pyani copying pyani/run_sge.py -> /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.12_pyani/build/pyani copying pyani/pyani_graphics.py -> /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.12_pyani/build/pyani copying pyani/pyani_jobs.py -> /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.12_pyani/build/pyani running egg_info writing pyani.egg-info/PKG-INFO writing dependency_links to pyani.egg-info/dependency_links.txt writing requirements to pyani.egg-info/requires.txt writing top-level names to pyani.egg-info/top_level.txt reading manifest file 'pyani.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' adding license file 'LICENSE' writing manifest file 'pyani.egg-info/SOURCES.txt' running build_scripts creating build/scripts-3.12 copying and adjusting bin/average_nucleotide_identity.py -> build/scripts-3.12 copying and adjusting bin/genbank_get_genomes_by_taxon.py -> build/scripts-3.12 copying and adjusting bin/delta_filter_wrapper.py -> build/scripts-3.12 changing mode of build/scripts-3.12/average_nucleotide_identity.py from 644 to 755 changing mode of build/scripts-3.12/genbank_get_genomes_by_taxon.py from 644 to 755 changing mode of build/scripts-3.12/delta_filter_wrapper.py from 644 to 755 dh_auto_test -O--buildsystem=pybuild I: pybuild base:311: cd /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.13_pyani/build; python3.13 -m pytest tests ============================= test session starts ============================== platform linux -- Python 3.13.1, pytest-8.3.4, pluggy-1.5.0 rootdir: /build/reproducible-path/python-pyani-0.2.12 plugins: typeguard-4.4.1 collected 56 items tests/test_anib.py sss.....sss...ss [ 28%] tests/test_anim.py ...... [ 39%] tests/test_concordance.py .s.. [ 46%] tests/test_dependencies.py ......s. [ 60%] tests/test_graphics.py ...... [ 71%] tests/test_jobs.py ......... [ 87%] tests/test_multiprocessing.py ... [ 92%] tests/test_parsing.py . [ 94%] tests/test_tetra.py ... [100%] =============================== warnings summary =============================== pyani/pyani_graphics.py:70 /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.13_pyani/build/pyani/pyani_graphics.py:70: MatplotlibDeprecationWarning: The register_cmap function was deprecated in Matplotlib 3.7 and will be removed two minor releases later. Use ``matplotlib.colormaps.register(name)`` instead. plt.register_cmap(cmap=pyani_config.CMAP_SPBND_BURD) pyani/pyani_graphics.py:71 /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.13_pyani/build/pyani/pyani_graphics.py:71: MatplotlibDeprecationWarning: The register_cmap function was deprecated in Matplotlib 3.7 and will be removed two minor releases later. Use ``matplotlib.colormaps.register(name)`` instead. plt.register_cmap(cmap=pyani_config.CMAP_HADAMARD_BURD) pyani/pyani_graphics.py:72 /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.13_pyani/build/pyani/pyani_graphics.py:72: MatplotlibDeprecationWarning: The register_cmap function was deprecated in Matplotlib 3.7 and will be removed two minor releases later. Use ``matplotlib.colormaps.register(name)`` instead. plt.register_cmap(cmap=pyani_config.CMAP_BURD) .pybuild/cpython3_3.13_pyani/build/tests/test_anib.py::TestParsing::test_blastdir_processing .pybuild/cpython3_3.13_pyani/build/tests/test_concordance.py::TestConcordance::test_anib_concordance /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.13_pyani/build/pyani/anib.py:420: FutureWarning: ChainedAssignmentError: behaviour will change in pandas 3.0! You are setting values through chained assignment. Currently this works in certain cases, but when using Copy-on-Write (which will become the default behaviour in pandas 3.0) this will never work to update the original DataFrame or Series, because the intermediate object on which we are setting values will behave as a copy. A typical example is when you are setting values in a column of a DataFrame, like: df["col"][row_indexer] = value Use `df.loc[row_indexer, "col"] = values` instead, to perform the assignment in a single step and ensure this keeps updating the original `df`. See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy results.alignment_lengths[org][org] = length .pybuild/cpython3_3.13_pyani/build/tests/test_anim.py::TestDeltafileProcessing::test_process_deltadir .pybuild/cpython3_3.13_pyani/build/tests/test_concordance.py::TestConcordance::test_anim_concordance /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.13_pyani/build/pyani/anim.py:195: FutureWarning: ChainedAssignmentError: behaviour will change in pandas 3.0! You are setting values through chained assignment. Currently this works in certain cases, but when using Copy-on-Write (which will become the default behaviour in pandas 3.0) this will never work to update the original DataFrame or Series, because the intermediate object on which we are setting values will behave as a copy. A typical example is when you are setting values in a column of a DataFrame, like: df["col"][row_indexer] = value Use `df.loc[row_indexer, "col"] = values` instead, to perform the assignment in a single step and ensure this keeps updating the original `df`. See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy results.alignment_lengths[org][org] = length .pybuild/cpython3_3.13_pyani/build/tests/test_concordance.py::TestConcordance::test_anib_concordance .pybuild/cpython3_3.13_pyani/build/tests/test_concordance.py::TestConcordance::test_anim_concordance .pybuild/cpython3_3.13_pyani/build/tests/test_concordance.py::TestConcordance::test_tetra_concordance /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.13_pyani/build/tests/test_concordance.py:102: FutureWarning: ChainedAssignmentError: behaviour will change in pandas 3.0! You are setting values through chained assignment. Currently this works in certain cases, but when using Copy-on-Write (which will become the default behaviour in pandas 3.0) this will never work to update the original DataFrame or Series, because the intermediate object on which we are setting values will behave as a copy. A typical example is when you are setting values in a column of a DataFrame, like: df["col"][row_indexer] = value Use `df.loc[row_indexer, "col"] = values` instead, to perform the assignment in a single step and ensure this keeps updating the original `df`. See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy data[columns[idx]][row] = 1.0 .pybuild/cpython3_3.13_pyani/build/tests/test_concordance.py::TestConcordance::test_anib_concordance .pybuild/cpython3_3.13_pyani/build/tests/test_concordance.py::TestConcordance::test_anib_concordance .pybuild/cpython3_3.13_pyani/build/tests/test_concordance.py::TestConcordance::test_anib_concordance .pybuild/cpython3_3.13_pyani/build/tests/test_concordance.py::TestConcordance::test_anim_concordance .pybuild/cpython3_3.13_pyani/build/tests/test_concordance.py::TestConcordance::test_anim_concordance .pybuild/cpython3_3.13_pyani/build/tests/test_concordance.py::TestConcordance::test_anim_concordance .pybuild/cpython3_3.13_pyani/build/tests/test_concordance.py::TestConcordance::test_tetra_concordance .pybuild/cpython3_3.13_pyani/build/tests/test_concordance.py::TestConcordance::test_tetra_concordance .pybuild/cpython3_3.13_pyani/build/tests/test_concordance.py::TestConcordance::test_tetra_concordance /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.13_pyani/build/tests/test_concordance.py:98: FutureWarning: ChainedAssignmentError: behaviour will change in pandas 3.0! You are setting values through chained assignment. Currently this works in certain cases, but when using Copy-on-Write (which will become the default behaviour in pandas 3.0) this will never work to update the original DataFrame or Series, because the intermediate object on which we are setting values will behave as a copy. A typical example is when you are setting values in a column of a DataFrame, like: df["col"][row_indexer] = value Use `df.loc[row_indexer, "col"] = values` instead, to perform the assignment in a single step and ensure this keeps updating the original `df`. See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy data[columns[idx]][row] = float(val) .pybuild/cpython3_3.13_pyani/build/tests/test_concordance.py::TestConcordance::test_anib_concordance .pybuild/cpython3_3.13_pyani/build/tests/test_concordance.py::TestConcordance::test_anib_concordance .pybuild/cpython3_3.13_pyani/build/tests/test_concordance.py::TestConcordance::test_anim_concordance .pybuild/cpython3_3.13_pyani/build/tests/test_concordance.py::TestConcordance::test_anim_concordance .pybuild/cpython3_3.13_pyani/build/tests/test_concordance.py::TestConcordance::test_tetra_concordance .pybuild/cpython3_3.13_pyani/build/tests/test_concordance.py::TestConcordance::test_tetra_concordance /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.13_pyani/build/tests/test_concordance.py:100: FutureWarning: ChainedAssignmentError: behaviour will change in pandas 3.0! You are setting values through chained assignment. Currently this works in certain cases, but when using Copy-on-Write (which will become the default behaviour in pandas 3.0) this will never work to update the original DataFrame or Series, because the intermediate object on which we are setting values will behave as a copy. A typical example is when you are setting values in a column of a DataFrame, like: df["col"][row_indexer] = value Use `df.loc[row_indexer, "col"] = values` instead, to perform the assignment in a single step and ensure this keeps updating the original `df`. See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy data[columns[idx]][row] = 100.0 .pybuild/cpython3_3.13_pyani/build/tests/test_concordance.py::TestConcordance::test_anib_concordance /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.13_pyani/build/tests/test_concordance.py:194: FutureWarning: Downcasting object dtype arrays on .fillna, .ffill, .bfill is deprecated and will change in a future version. Call result.infer_objects(copy=False) instead. To opt-in to the future behavior, set `pd.set_option('future.no_silent_downcasting', True)` lo_target = self.target["ANIb"].mask(self.target["ANIb"] >= 90).fillna(0) .pybuild/cpython3_3.13_pyani/build/tests/test_concordance.py::TestConcordance::test_anib_concordance /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.13_pyani/build/tests/test_concordance.py:195: FutureWarning: Downcasting object dtype arrays on .fillna, .ffill, .bfill is deprecated and will change in a future version. Call result.infer_objects(copy=False) instead. To opt-in to the future behavior, set `pd.set_option('future.no_silent_downcasting', True)` hi_target = self.target["ANIb"].mask(self.target["ANIb"] < 90).fillna(0) .pybuild/cpython3_3.13_pyani/build/tests/test_concordance.py::TestConcordance::test_tetra_concordance .pybuild/cpython3_3.13_pyani/build/tests/test_tetra.py::TestTETRA::test_correlations /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.13_pyani/build/pyani/tetra.py:156: FutureWarning: ChainedAssignmentError: behaviour will change in pandas 3.0! You are setting values through chained assignment. Currently this works in certain cases, but when using Copy-on-Write (which will become the default behaviour in pandas 3.0) this will never work to update the original DataFrame or Series, because the intermediate object on which we are setting values will behave as a copy. A typical example is when you are setting values in a column of a DataFrame, like: df["col"][row_indexer] = value Use `df.loc[row_indexer, "col"] = values` instead, to perform the assignment in a single step and ensure this keeps updating the original `df`. See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy correlations[org1][org2] = diffprods / math.sqrt(zdiffs2[0] * zdiffs2[1]) .pybuild/cpython3_3.13_pyani/build/tests/test_concordance.py::TestConcordance::test_tetra_concordance .pybuild/cpython3_3.13_pyani/build/tests/test_tetra.py::TestTETRA::test_correlations /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.13_pyani/build/pyani/tetra.py:157: FutureWarning: ChainedAssignmentError: behaviour will change in pandas 3.0! You are setting values through chained assignment. Currently this works in certain cases, but when using Copy-on-Write (which will become the default behaviour in pandas 3.0) this will never work to update the original DataFrame or Series, because the intermediate object on which we are setting values will behave as a copy. A typical example is when you are setting values in a column of a DataFrame, like: df["col"][row_indexer] = value Use `df.loc[row_indexer, "col"] = values` instead, to perform the assignment in a single step and ensure this keeps updating the original `df`. See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy correlations[org2][org1] = correlations[org1][org2] -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html =========== 46 passed, 10 skipped, 31 warnings in 598.54s (0:09:58) ============ I: pybuild base:311: cd /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.12_pyani/build; python3.12 -m pytest tests ============================= test session starts ============================== platform linux -- Python 3.12.8, pytest-8.3.4, pluggy-1.5.0 rootdir: /build/reproducible-path/python-pyani-0.2.12 plugins: typeguard-4.4.1 collected 56 items tests/test_anib.py sss.....sss...ss [ 28%] tests/test_anim.py ...... [ 39%] tests/test_concordance.py .s.. [ 46%] tests/test_dependencies.py ......s. [ 60%] tests/test_graphics.py ...... [ 71%] tests/test_jobs.py ......... [ 87%] tests/test_multiprocessing.py ... [ 92%] tests/test_parsing.py . [ 94%] tests/test_tetra.py ... [100%] =============================== warnings summary =============================== pyani/pyani_graphics.py:70 /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.12_pyani/build/pyani/pyani_graphics.py:70: MatplotlibDeprecationWarning: The register_cmap function was deprecated in Matplotlib 3.7 and will be removed two minor releases later. Use ``matplotlib.colormaps.register(name)`` instead. plt.register_cmap(cmap=pyani_config.CMAP_SPBND_BURD) pyani/pyani_graphics.py:71 /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.12_pyani/build/pyani/pyani_graphics.py:71: MatplotlibDeprecationWarning: The register_cmap function was deprecated in Matplotlib 3.7 and will be removed two minor releases later. Use ``matplotlib.colormaps.register(name)`` instead. plt.register_cmap(cmap=pyani_config.CMAP_HADAMARD_BURD) pyani/pyani_graphics.py:72 /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.12_pyani/build/pyani/pyani_graphics.py:72: MatplotlibDeprecationWarning: The register_cmap function was deprecated in Matplotlib 3.7 and will be removed two minor releases later. Use ``matplotlib.colormaps.register(name)`` instead. plt.register_cmap(cmap=pyani_config.CMAP_BURD) .pybuild/cpython3_3.12_pyani/build/tests/test_anib.py::TestParsing::test_blastdir_processing .pybuild/cpython3_3.12_pyani/build/tests/test_concordance.py::TestConcordance::test_anib_concordance /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.12_pyani/build/pyani/anib.py:420: FutureWarning: ChainedAssignmentError: behaviour will change in pandas 3.0! You are setting values through chained assignment. Currently this works in certain cases, but when using Copy-on-Write (which will become the default behaviour in pandas 3.0) this will never work to update the original DataFrame or Series, because the intermediate object on which we are setting values will behave as a copy. A typical example is when you are setting values in a column of a DataFrame, like: df["col"][row_indexer] = value Use `df.loc[row_indexer, "col"] = values` instead, to perform the assignment in a single step and ensure this keeps updating the original `df`. See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy results.alignment_lengths[org][org] = length .pybuild/cpython3_3.12_pyani/build/tests/test_anim.py::TestDeltafileProcessing::test_process_deltadir .pybuild/cpython3_3.12_pyani/build/tests/test_concordance.py::TestConcordance::test_anim_concordance /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.12_pyani/build/pyani/anim.py:195: FutureWarning: ChainedAssignmentError: behaviour will change in pandas 3.0! You are setting values through chained assignment. Currently this works in certain cases, but when using Copy-on-Write (which will become the default behaviour in pandas 3.0) this will never work to update the original DataFrame or Series, because the intermediate object on which we are setting values will behave as a copy. A typical example is when you are setting values in a column of a DataFrame, like: df["col"][row_indexer] = value Use `df.loc[row_indexer, "col"] = values` instead, to perform the assignment in a single step and ensure this keeps updating the original `df`. See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy results.alignment_lengths[org][org] = length .pybuild/cpython3_3.12_pyani/build/tests/test_concordance.py::TestConcordance::test_anib_concordance .pybuild/cpython3_3.12_pyani/build/tests/test_concordance.py::TestConcordance::test_anim_concordance .pybuild/cpython3_3.12_pyani/build/tests/test_concordance.py::TestConcordance::test_tetra_concordance /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.12_pyani/build/tests/test_concordance.py:102: FutureWarning: ChainedAssignmentError: behaviour will change in pandas 3.0! You are setting values through chained assignment. Currently this works in certain cases, but when using Copy-on-Write (which will become the default behaviour in pandas 3.0) this will never work to update the original DataFrame or Series, because the intermediate object on which we are setting values will behave as a copy. A typical example is when you are setting values in a column of a DataFrame, like: df["col"][row_indexer] = value Use `df.loc[row_indexer, "col"] = values` instead, to perform the assignment in a single step and ensure this keeps updating the original `df`. See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy data[columns[idx]][row] = 1.0 .pybuild/cpython3_3.12_pyani/build/tests/test_concordance.py::TestConcordance::test_anib_concordance .pybuild/cpython3_3.12_pyani/build/tests/test_concordance.py::TestConcordance::test_anib_concordance .pybuild/cpython3_3.12_pyani/build/tests/test_concordance.py::TestConcordance::test_anib_concordance .pybuild/cpython3_3.12_pyani/build/tests/test_concordance.py::TestConcordance::test_anim_concordance .pybuild/cpython3_3.12_pyani/build/tests/test_concordance.py::TestConcordance::test_anim_concordance .pybuild/cpython3_3.12_pyani/build/tests/test_concordance.py::TestConcordance::test_anim_concordance .pybuild/cpython3_3.12_pyani/build/tests/test_concordance.py::TestConcordance::test_tetra_concordance .pybuild/cpython3_3.12_pyani/build/tests/test_concordance.py::TestConcordance::test_tetra_concordance .pybuild/cpython3_3.12_pyani/build/tests/test_concordance.py::TestConcordance::test_tetra_concordance /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.12_pyani/build/tests/test_concordance.py:98: FutureWarning: ChainedAssignmentError: behaviour will change in pandas 3.0! You are setting values through chained assignment. Currently this works in certain cases, but when using Copy-on-Write (which will become the default behaviour in pandas 3.0) this will never work to update the original DataFrame or Series, because the intermediate object on which we are setting values will behave as a copy. A typical example is when you are setting values in a column of a DataFrame, like: df["col"][row_indexer] = value Use `df.loc[row_indexer, "col"] = values` instead, to perform the assignment in a single step and ensure this keeps updating the original `df`. See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy data[columns[idx]][row] = float(val) .pybuild/cpython3_3.12_pyani/build/tests/test_concordance.py::TestConcordance::test_anib_concordance .pybuild/cpython3_3.12_pyani/build/tests/test_concordance.py::TestConcordance::test_anib_concordance .pybuild/cpython3_3.12_pyani/build/tests/test_concordance.py::TestConcordance::test_anim_concordance .pybuild/cpython3_3.12_pyani/build/tests/test_concordance.py::TestConcordance::test_anim_concordance .pybuild/cpython3_3.12_pyani/build/tests/test_concordance.py::TestConcordance::test_tetra_concordance .pybuild/cpython3_3.12_pyani/build/tests/test_concordance.py::TestConcordance::test_tetra_concordance /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.12_pyani/build/tests/test_concordance.py:100: FutureWarning: ChainedAssignmentError: behaviour will change in pandas 3.0! You are setting values through chained assignment. Currently this works in certain cases, but when using Copy-on-Write (which will become the default behaviour in pandas 3.0) this will never work to update the original DataFrame or Series, because the intermediate object on which we are setting values will behave as a copy. A typical example is when you are setting values in a column of a DataFrame, like: df["col"][row_indexer] = value Use `df.loc[row_indexer, "col"] = values` instead, to perform the assignment in a single step and ensure this keeps updating the original `df`. See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy data[columns[idx]][row] = 100.0 .pybuild/cpython3_3.12_pyani/build/tests/test_concordance.py::TestConcordance::test_anib_concordance /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.12_pyani/build/tests/test_concordance.py:194: FutureWarning: Downcasting object dtype arrays on .fillna, .ffill, .bfill is deprecated and will change in a future version. Call result.infer_objects(copy=False) instead. To opt-in to the future behavior, set `pd.set_option('future.no_silent_downcasting', True)` lo_target = self.target["ANIb"].mask(self.target["ANIb"] >= 90).fillna(0) .pybuild/cpython3_3.12_pyani/build/tests/test_concordance.py::TestConcordance::test_anib_concordance /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.12_pyani/build/tests/test_concordance.py:195: FutureWarning: Downcasting object dtype arrays on .fillna, .ffill, .bfill is deprecated and will change in a future version. Call result.infer_objects(copy=False) instead. To opt-in to the future behavior, set `pd.set_option('future.no_silent_downcasting', True)` hi_target = self.target["ANIb"].mask(self.target["ANIb"] < 90).fillna(0) .pybuild/cpython3_3.12_pyani/build/tests/test_concordance.py::TestConcordance::test_tetra_concordance .pybuild/cpython3_3.12_pyani/build/tests/test_tetra.py::TestTETRA::test_correlations /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.12_pyani/build/pyani/tetra.py:156: FutureWarning: ChainedAssignmentError: behaviour will change in pandas 3.0! You are setting values through chained assignment. Currently this works in certain cases, but when using Copy-on-Write (which will become the default behaviour in pandas 3.0) this will never work to update the original DataFrame or Series, because the intermediate object on which we are setting values will behave as a copy. A typical example is when you are setting values in a column of a DataFrame, like: df["col"][row_indexer] = value Use `df.loc[row_indexer, "col"] = values` instead, to perform the assignment in a single step and ensure this keeps updating the original `df`. See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy correlations[org1][org2] = diffprods / math.sqrt(zdiffs2[0] * zdiffs2[1]) .pybuild/cpython3_3.12_pyani/build/tests/test_concordance.py::TestConcordance::test_tetra_concordance .pybuild/cpython3_3.12_pyani/build/tests/test_tetra.py::TestTETRA::test_correlations /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.12_pyani/build/pyani/tetra.py:157: FutureWarning: ChainedAssignmentError: behaviour will change in pandas 3.0! You are setting values through chained assignment. Currently this works in certain cases, but when using Copy-on-Write (which will become the default behaviour in pandas 3.0) this will never work to update the original DataFrame or Series, because the intermediate object on which we are setting values will behave as a copy. A typical example is when you are setting values in a column of a DataFrame, like: df["col"][row_indexer] = value Use `df.loc[row_indexer, "col"] = values` instead, to perform the assignment in a single step and ensure this keeps updating the original `df`. See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy correlations[org2][org1] = correlations[org1][org2] -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html =========== 46 passed, 10 skipped, 31 warnings in 718.86s (0:11:58) ============ create-stamp debian/debhelper-build-stamp dh_testroot -O--buildsystem=pybuild dh_prep -O--buildsystem=pybuild dh_auto_install --destdir=debian/python3-pyani/ -O--buildsystem=pybuild I: pybuild base:311: /usr/bin/python3.13 setup.py install --root /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani /usr/lib/python3/dist-packages/setuptools/dist.py:491: SetuptoolsDeprecationWarning: Invalid dash-separated options !! ******************************************************************************** Usage of dash-separated 'description-file' will not be supported in future versions. Please use the underscore name 'description_file' instead. By 2025-Mar-03, you need to update your project and remove deprecated calls or your builds will no longer be supported. See https://setuptools.pypa.io/en/latest/userguide/declarative_config.html for details. ******************************************************************************** !! opt = self.warn_dash_deprecation(opt, section) running install /usr/lib/python3/dist-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated. !! ******************************************************************************** Please avoid running ``setup.py`` directly. Instead, use pypa/build, pypa/installer or other standards-based tools. See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. ******************************************************************************** !! self.initialize_options() running build running build_py running egg_info writing pyani.egg-info/PKG-INFO writing dependency_links to pyani.egg-info/dependency_links.txt writing requirements to pyani.egg-info/requires.txt writing top-level names to pyani.egg-info/top_level.txt reading manifest file 'pyani.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' adding license file 'LICENSE' writing manifest file 'pyani.egg-info/SOURCES.txt' running build_scripts running install_lib creating /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.13/dist-packages creating /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.13/dist-packages/pyani copying /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.13_pyani/build/pyani/anim.py -> /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.13/dist-packages/pyani copying /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.13_pyani/build/pyani/tetra.py -> /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.13/dist-packages/pyani copying /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.13_pyani/build/pyani/run_multiprocessing.py -> /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.13/dist-packages/pyani copying /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.13_pyani/build/pyani/pyani_tools.py -> /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.13/dist-packages/pyani copying /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.13_pyani/build/pyani/__init__.py -> /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.13/dist-packages/pyani copying /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.13_pyani/build/pyani/pyani_files.py -> /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.13/dist-packages/pyani copying /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.13_pyani/build/pyani/pyani_config.py -> /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.13/dist-packages/pyani copying /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.13_pyani/build/pyani/anib.py -> /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.13/dist-packages/pyani copying /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.13_pyani/build/pyani/run_sge.py -> /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.13/dist-packages/pyani creating /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.13/dist-packages/pyani/__pycache__ copying /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.13_pyani/build/pyani/__pycache__/tetra.cpython-313.pyc -> /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.13/dist-packages/pyani/__pycache__ copying /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.13_pyani/build/pyani/__pycache__/pyani_tools.cpython-313.pyc -> /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.13/dist-packages/pyani/__pycache__ copying /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.13_pyani/build/pyani/__pycache__/pyani_files.cpython-313.pyc -> /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.13/dist-packages/pyani/__pycache__ copying /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.13_pyani/build/pyani/__pycache__/__init__.cpython-313.pyc -> /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.13/dist-packages/pyani/__pycache__ copying /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.13_pyani/build/pyani/__pycache__/run_multiprocessing.cpython-313.pyc -> /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.13/dist-packages/pyani/__pycache__ copying /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.13_pyani/build/pyani/__pycache__/pyani_config.cpython-313.pyc -> /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.13/dist-packages/pyani/__pycache__ copying /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.13_pyani/build/pyani/__pycache__/pyani_graphics.cpython-313.pyc -> /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.13/dist-packages/pyani/__pycache__ copying /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.13_pyani/build/pyani/__pycache__/anim.cpython-313.pyc -> /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.13/dist-packages/pyani/__pycache__ copying /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.13_pyani/build/pyani/__pycache__/pyani_jobs.cpython-313.pyc -> /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.13/dist-packages/pyani/__pycache__ copying /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.13_pyani/build/pyani/__pycache__/anib.cpython-313.pyc -> /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.13/dist-packages/pyani/__pycache__ copying /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.13_pyani/build/pyani/pyani_graphics.py -> /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.13/dist-packages/pyani copying /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.13_pyani/build/pyani/pyani_jobs.py -> /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.13/dist-packages/pyani byte-compiling /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.13/dist-packages/pyani/anim.py to anim.cpython-313.pyc byte-compiling /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.13/dist-packages/pyani/tetra.py to tetra.cpython-313.pyc byte-compiling /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.13/dist-packages/pyani/run_multiprocessing.py to run_multiprocessing.cpython-313.pyc byte-compiling /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.13/dist-packages/pyani/pyani_tools.py to pyani_tools.cpython-313.pyc byte-compiling /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.13/dist-packages/pyani/__init__.py to __init__.cpython-313.pyc byte-compiling /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.13/dist-packages/pyani/pyani_files.py to pyani_files.cpython-313.pyc byte-compiling /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.13/dist-packages/pyani/pyani_config.py to pyani_config.cpython-313.pyc byte-compiling /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.13/dist-packages/pyani/anib.py to anib.cpython-313.pyc byte-compiling /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.13/dist-packages/pyani/run_sge.py to run_sge.cpython-313.pyc byte-compiling /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.13/dist-packages/pyani/pyani_graphics.py to pyani_graphics.cpython-313.pyc byte-compiling /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.13/dist-packages/pyani/pyani_jobs.py to pyani_jobs.cpython-313.pyc running install_egg_info Copying pyani.egg-info to /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.13/dist-packages/pyani-0.2.12.egg-info Skipping SOURCES.txt running install_scripts creating /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/bin copying build/scripts-3.13/average_nucleotide_identity.py -> /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/bin copying build/scripts-3.13/delta_filter_wrapper.py -> /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/bin copying build/scripts-3.13/genbank_get_genomes_by_taxon.py -> /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/bin changing mode of /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/bin/average_nucleotide_identity.py to 755 changing mode of /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/bin/delta_filter_wrapper.py to 755 changing mode of /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/bin/genbank_get_genomes_by_taxon.py to 755 I: pybuild base:311: /usr/bin/python3 setup.py install --root /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani /usr/lib/python3/dist-packages/setuptools/dist.py:491: SetuptoolsDeprecationWarning: Invalid dash-separated options !! ******************************************************************************** Usage of dash-separated 'description-file' will not be supported in future versions. Please use the underscore name 'description_file' instead. By 2025-Mar-03, you need to update your project and remove deprecated calls or your builds will no longer be supported. See https://setuptools.pypa.io/en/latest/userguide/declarative_config.html for details. ******************************************************************************** !! opt = self.warn_dash_deprecation(opt, section) running install /usr/lib/python3/dist-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated. !! ******************************************************************************** Please avoid running ``setup.py`` directly. Instead, use pypa/build, pypa/installer or other standards-based tools. See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. ******************************************************************************** !! self.initialize_options() running build running build_py running egg_info writing pyani.egg-info/PKG-INFO writing dependency_links to pyani.egg-info/dependency_links.txt writing requirements to pyani.egg-info/requires.txt writing top-level names to pyani.egg-info/top_level.txt reading manifest file 'pyani.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' adding license file 'LICENSE' writing manifest file 'pyani.egg-info/SOURCES.txt' running build_scripts running install_lib creating /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.12/dist-packages creating /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.12/dist-packages/pyani copying /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.12_pyani/build/pyani/anim.py -> /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.12/dist-packages/pyani copying /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.12_pyani/build/pyani/tetra.py -> /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.12/dist-packages/pyani copying /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.12_pyani/build/pyani/run_multiprocessing.py -> /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.12/dist-packages/pyani copying /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.12_pyani/build/pyani/pyani_tools.py -> /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.12/dist-packages/pyani copying /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.12_pyani/build/pyani/__init__.py -> /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.12/dist-packages/pyani copying /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.12_pyani/build/pyani/pyani_files.py -> /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.12/dist-packages/pyani copying /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.12_pyani/build/pyani/pyani_config.py -> /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.12/dist-packages/pyani copying /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.12_pyani/build/pyani/anib.py -> /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.12/dist-packages/pyani copying /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.12_pyani/build/pyani/run_sge.py -> /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.12/dist-packages/pyani creating /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.12/dist-packages/pyani/__pycache__ copying /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.12_pyani/build/pyani/__pycache__/anim.cpython-312.pyc -> /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.12/dist-packages/pyani/__pycache__ copying /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.12_pyani/build/pyani/__pycache__/pyani_files.cpython-312.pyc -> /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.12/dist-packages/pyani/__pycache__ copying /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.12_pyani/build/pyani/__pycache__/pyani_graphics.cpython-312.pyc -> /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.12/dist-packages/pyani/__pycache__ copying /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.12_pyani/build/pyani/__pycache__/pyani_jobs.cpython-312.pyc -> /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.12/dist-packages/pyani/__pycache__ copying /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.12_pyani/build/pyani/__pycache__/tetra.cpython-312.pyc -> /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.12/dist-packages/pyani/__pycache__ copying /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.12_pyani/build/pyani/__pycache__/pyani_config.cpython-312.pyc -> /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.12/dist-packages/pyani/__pycache__ copying /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.12_pyani/build/pyani/__pycache__/run_multiprocessing.cpython-312.pyc -> /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.12/dist-packages/pyani/__pycache__ copying /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.12_pyani/build/pyani/__pycache__/anib.cpython-312.pyc -> /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.12/dist-packages/pyani/__pycache__ copying /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.12_pyani/build/pyani/__pycache__/__init__.cpython-312.pyc -> /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.12/dist-packages/pyani/__pycache__ copying /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.12_pyani/build/pyani/__pycache__/pyani_tools.cpython-312.pyc -> /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.12/dist-packages/pyani/__pycache__ copying /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.12_pyani/build/pyani/pyani_graphics.py -> /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.12/dist-packages/pyani copying /build/reproducible-path/python-pyani-0.2.12/.pybuild/cpython3_3.12_pyani/build/pyani/pyani_jobs.py -> /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.12/dist-packages/pyani byte-compiling /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.12/dist-packages/pyani/anim.py to anim.cpython-312.pyc byte-compiling /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.12/dist-packages/pyani/tetra.py to tetra.cpython-312.pyc byte-compiling /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.12/dist-packages/pyani/run_multiprocessing.py to run_multiprocessing.cpython-312.pyc byte-compiling /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.12/dist-packages/pyani/pyani_tools.py to pyani_tools.cpython-312.pyc byte-compiling /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.12/dist-packages/pyani/__init__.py to __init__.cpython-312.pyc byte-compiling /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.12/dist-packages/pyani/pyani_files.py to pyani_files.cpython-312.pyc byte-compiling /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.12/dist-packages/pyani/pyani_config.py to pyani_config.cpython-312.pyc byte-compiling /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.12/dist-packages/pyani/anib.py to anib.cpython-312.pyc byte-compiling /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.12/dist-packages/pyani/run_sge.py to run_sge.cpython-312.pyc byte-compiling /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.12/dist-packages/pyani/pyani_graphics.py to pyani_graphics.cpython-312.pyc byte-compiling /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.12/dist-packages/pyani/pyani_jobs.py to pyani_jobs.cpython-312.pyc running install_egg_info Copying pyani.egg-info to /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/lib/python3.12/dist-packages/pyani-0.2.12.egg-info Skipping SOURCES.txt running install_scripts copying build/scripts-3.12/average_nucleotide_identity.py -> /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/bin copying build/scripts-3.12/delta_filter_wrapper.py -> /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/bin copying build/scripts-3.12/genbank_get_genomes_by_taxon.py -> /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/bin changing mode of /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/bin/average_nucleotide_identity.py to 755 changing mode of /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/bin/delta_filter_wrapper.py to 755 changing mode of /build/reproducible-path/python-pyani-0.2.12/debian/python3-pyani/usr/bin/genbank_get_genomes_by_taxon.py to 755 dh_installdocs -O--buildsystem=pybuild dh_installchangelogs -O--buildsystem=pybuild debian/rules override_dh_installman make[1]: Entering directory '/build/reproducible-path/python-pyani-0.2.12' dh_installman --language=C make[1]: Leaving directory '/build/reproducible-path/python-pyani-0.2.12' dh_python3 -O--buildsystem=pybuild 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_dwz -a -O--buildsystem=pybuild dh_strip -a -O--buildsystem=pybuild dh_makeshlibs -a -O--buildsystem=pybuild dh_shlibdeps -a -O--buildsystem=pybuild dh_installdeb -O--buildsystem=pybuild dh_gencontrol -O--buildsystem=pybuild dh_md5sums -O--buildsystem=pybuild dh_builddeb -O--buildsystem=pybuild dpkg-deb: building package 'python3-pyani' in '../python3-pyani_0.2.12-3_armhf.deb'. dpkg-genbuildinfo --build=binary -O../python-pyani_0.2.12-3_armhf.buildinfo dpkg-genchanges --build=binary -O../python-pyani_0.2.12-3_armhf.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: user script /srv/workspace/pbuilder/17777/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/17777/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/17777 and its subdirectories I: Current time: Sun Dec 8 18:45:41 +14 2024 I: pbuilder-time-stamp: 1733633141