Sat Apr 8 11:08:40 UTC 2023 I: starting to build paleomix/bookworm/arm64 on jenkins on '2023-04-08 11:08' Sat Apr 8 11:08:40 UTC 2023 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/arm64_16/21733/console.log Sat Apr 8 11:08:40 UTC 2023 I: Downloading source for bookworm/paleomix=1.3.7-3 --2023-04-08 11:08:41-- http://cdn-fastly.deb.debian.org/debian/pool/main/p/paleomix/paleomix_1.3.7-3.dsc Connecting to 78.137.99.97:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2466 (2.4K) [text/prs.lines.tag] Saving to: ‘paleomix_1.3.7-3.dsc’ 0K .. 100% 142M=0s 2023-04-08 11:08:41 (142 MB/s) - ‘paleomix_1.3.7-3.dsc’ saved [2466/2466] Sat Apr 8 11:08:41 UTC 2023 I: paleomix_1.3.7-3.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: paleomix Binary: paleomix Architecture: any Version: 1.3.7-3 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille , Étienne Mollier Homepage: https://geogenetics.ku.dk/publications/paleomix Standards-Version: 4.6.2 Vcs-Browser: https://salsa.debian.org/med-team/paleomix Vcs-Git: https://salsa.debian.org/med-team/paleomix.git Testsuite: autopkgtest Testsuite-Triggers: python3-pytest Build-Depends: debhelper-compat (= 13), dh-python, python3, python3-setuptools, python3-pytest , python3-coloredlogs , python3-configargparse , python3-ruamel.yaml , python3-pysam , python3-setproctitle , default-jre-headless , bowtie2, rsync, examl, picard-tools Package-List: paleomix deb science optional arch=any Checksums-Sha1: 0143623f4bc3c6ffe5a3ff3332099cad28788052 1137101 paleomix_1.3.7.orig.tar.gz 8047d477cc6e851ab02d60459de1463939302f32 10940 paleomix_1.3.7-3.debian.tar.xz Checksums-Sha256: 63c03e8b0d9938714836862c3c98763aefd18b4c13730d713713a0045e18c088 1137101 paleomix_1.3.7.orig.tar.gz c0c37149ff9c29ec9e8fc49039a859eac0538a58ed1f03cb64586b1db53aaf9f 10940 paleomix_1.3.7-3.debian.tar.xz Files: 9af2d5ef609ff5e13255d282931a1b7f 1137101 paleomix_1.3.7.orig.tar.gz e8a35d561a8d97e38da9b80e8c813729 10940 paleomix_1.3.7-3.debian.tar.xz Dgit: f9da09b9236faae94d9d197b58d6dd95e7c9e889 debian archive/debian/1.3.7-3 https://git.dgit.debian.org/paleomix -----BEGIN PGP SIGNATURE----- iQJIBAEBCgAyFiEEj5GyJ8fW8rGUjII2eTz2fo8NEdoFAmPC/UIUHGVtb2xsaWVy QGRlYmlhbi5vcmcACgkQeTz2fo8NEdrLABAAgm0EXCuX9kmdDh0/vI9uMj8ZIytY Nk3hyL+yqlAlqC/nkkyT3BGMKtoCzaIfAOl9D0l+Buq3/t9BQ/w1zOYTW65qWDWA QKaX0zCc/cWVNCDUSCGiOndTI4+gUaCjZUCW+L62qj336lMxHausFoybN7MYDnYb SRMipSavnRPW68dMy/mcOIgd4OkCk0yg7Gy/hCzZwVbVUTS48DkjPWzTmW1SNp98 8W4sujkqz3kcbAs8dWcamwSXH5DFacky8kYSnh3GPDP/i5mG4fKwWnYDM2DhviBX UBddXjM5q00OIqk7Rc0JaBRH0VSeYeuTMA26lIfb+zFrQA7l4rlDx1K09VENEBxF VdFR3rTH1uK1T6zUUxEYhQQmj6WXsRcY5AWlAm8tPWg15Uh38nE9ix9sWTutY7Qg gi/4WOKHm5a0X4rRwkYGjFK7ffbf8b5L+pt4KuqrSvxNqoW4Mw4qLr54kuY1/EGb DIGE4RasBeWNT6mkEPB93ps4efVvs1IK6Ima50geT6nhLHLBMn4z0Wy7QzkoSkVX b5D2zUbbpuABOwU4dBHW64RQuqdX+FWzm+gQ9odu64+HcieFHqD2zCuHRMIsmrrT zJ+TZbI4clp3sBv6c30Y8VEIcSz2s+gw9xcEavh9KUMwnbS4a21MHKndx+59qSBo z1GNzda3/b8erVY= =fGnh -----END PGP SIGNATURE----- Sat Apr 8 11:08:41 UTC 2023 I: Checking whether the package is not for us Sat Apr 8 11:08:41 UTC 2023 I: Starting 1st build on remote node codethink12-arm64.debian.net. Sat Apr 8 11:08:41 UTC 2023 I: Preparing to do remote build '1' on codethink12-arm64.debian.net. Sat Apr 8 11:12:01 UTC 2023 I: Deleting $TMPDIR on codethink12-arm64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Fri Apr 7 23:08:44 -12 2023 I: pbuilder-time-stamp: 1680952124 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bookworm-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [paleomix_1.3.7-3.dsc] I: copying [./paleomix_1.3.7.orig.tar.gz] I: copying [./paleomix_1.3.7-3.debian.tar.xz] I: Extracting source gpgv: Signature made Sat Jan 14 07:06:42 2023 -12 gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA gpgv: issuer "emollier@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./paleomix_1.3.7-3.dsc: no acceptable signature found dpkg-source: info: extracting paleomix in paleomix-1.3.7 dpkg-source: info: unpacking paleomix_1.3.7.orig.tar.gz dpkg-source: info: unpacking paleomix_1.3.7-3.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying xfail_command_tests.patch dpkg-source: info: applying python3.11.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/10559/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='arm64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=8' DISTRIBUTION='bookworm' HOME='/var/lib/jenkins' HOST_ARCH='arm64' IFS=' ' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='10559' PS1='# ' PS2='> ' PS4='+ ' PWD='/' SHELL='/bin/bash' SHLVL='2' SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.kAw6y1MW/pbuilderrc_hdCx --distribution bookworm --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.kAw6y1MW/b1 --logfile b1/build.log paleomix_1.3.7-3.dsc' SUDO_GID='117' SUDO_UID='110' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' USERNAME='root' _='/usr/bin/systemd-run' http_proxy='http://192.168.101.16:3128' I: uname -a Linux codethink12-arm64 4.15.0-208-generic #220-Ubuntu SMP Mon Mar 20 14:28:12 UTC 2023 aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Apr 5 22:25 /bin -> usr/bin I: user script /srv/workspace/pbuilder/10559/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: arm64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), dh-python, python3, python3-setuptools, python3-pytest, python3-coloredlogs, python3-configargparse, python3-ruamel.yaml, python3-pysam, python3-setproctitle, default-jre-headless, bowtie2, rsync, examl, picard-tools dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19616 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on dh-python; however: Package dh-python is not installed. pbuilder-satisfydepends-dummy depends on python3; however: Package python3 is not installed. pbuilder-satisfydepends-dummy depends on python3-setuptools; however: Package python3-setuptools is not installed. pbuilder-satisfydepends-dummy depends on python3-pytest; however: Package python3-pytest is not installed. pbuilder-satisfydepends-dummy depends on python3-coloredlogs; however: Package python3-coloredlogs is not installed. pbuilder-satisfydepends-dummy depends on python3-configargparse; however: Package python3-configargparse is not installed. pbuilder-satisfydepends-dummy depends on python3-ruamel.yaml; however: Package python3-ruamel.yaml is not installed. pbuilder-satisfydepends-dummy depends on python3-pysam; however: Package python3-pysam is not installed. pbuilder-satisfydepends-dummy depends on python3-setproctitle; however: Package python3-setproctitle is not installed. pbuilder-satisfydepends-dummy depends on default-jre-headless; however: Package default-jre-headless is not installed. pbuilder-satisfydepends-dummy depends on bowtie2; however: Package bowtie2 is not installed. pbuilder-satisfydepends-dummy depends on rsync; however: Package rsync is not installed. pbuilder-satisfydepends-dummy depends on examl; however: Package examl is not installed. pbuilder-satisfydepends-dummy depends on picard-tools; however: Package picard-tools 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: adwaita-icon-theme{a} at-spi2-common{a} autoconf{a} automake{a} autopoint{a} autotools-dev{a} bowtie2{a} bsdextrautils{a} ca-certificates{a} ca-certificates-java{a} debhelper{a} default-jre{a} default-jre-headless{a} dh-autoreconf{a} dh-python{a} dh-strip-nondeterminism{a} dwz{a} examl{a} file{a} fontconfig{a} fontconfig-config{a} fonts-dejavu-core{a} gettext{a} gettext-base{a} groff-base{a} gtk-update-icon-cache{a} hicolor-icon-theme{a} ibverbs-providers{a} intltool-debian{a} java-common{a} libapache-pom-java{a} libarchive-zip-perl{a} libasound2{a} libasound2-data{a} libatk1.0-0{a} libavahi-client3{a} libavahi-common-data{a} libavahi-common3{a} libbarclay-java{a} libbrotli1{a} libbsd0{a} libcairo2{a} libcbor0.8{a} libcommons-codec-java{a} libcommons-compress-java{a} libcommons-io-java{a} libcommons-jexl2-java{a} libcommons-lang3-java{a} libcommons-logging-java{a} libcommons-math3-java{a} libcommons-parent-java{a} libcups2{a} libcurl3-gnutls{a} libdatrie1{a} libdbus-1-3{a} libdebhelper-perl{a} libdeflate0{a} libdrm-amdgpu1{a} libdrm-common{a} libdrm-nouveau2{a} libdrm-radeon1{a} libdrm2{a} libedit2{a} libelf1{a} libevent-core-2.1-7{a} libevent-pthreads-2.1-7{a} libexpat1{a} libfabric1{a} libfido2-1{a} libfile-stripnondeterminism-perl{a} libfontconfig1{a} libfreemarker-java{a} libfreetype6{a} libfribidi0{a} libgatk-native-bindings-java{a} libgdk-pixbuf-2.0-0{a} libgdk-pixbuf2.0-common{a} libgif7{a} libgkl-java{a} libgl1{a} libgl1-mesa-dri{a} libglapi-mesa{a} libglib2.0-0{a} libglvnd0{a} libglx-mesa0{a} libglx0{a} libgoogle-gson-java{a} libgraphite2-3{a} libgtk2.0-0{a} libgtk2.0-common{a} libharfbuzz0b{a} libhts3{a} libhtscodecs2{a} libhtsjdk-java{a} libhttpclient-java{a} libhttpcore-java{a} libhwloc-plugins{a} libhwloc15{a} libibverbs1{a} libicu72{a} libjbig0{a} libjoptsimple-java{a} libjpeg62-turbo{a} liblcms2-2{a} libldap-2.5-0{a} liblerc4{a} liblightcouch-java{a} libllvm15{a} liblog4j2-java{a} libmagic-mgc{a} libmagic1{a} libmbedcrypto7{a} libmbedtls14{a} libmbedx509-1{a} libmjson-java{a} libmongodb-java{a} libmunge2{a} libncbi-ngs3{a} libncbi-vdb3{a} libnghttp2-14{a} libngs-java{a} libngs-jni{a} libnl-3-200{a} libnl-route-3-200{a} libnspr4{a} libnss3{a} libnuma1{a} libopenmpi3{a} libpango-1.0-0{a} libpangocairo-1.0-0{a} libpangoft2-1.0-0{a} libpciaccess0{a} libpcsclite1{a} libpicard-java{a} libpipeline1{a} libpixman-1-0{a} libpmix2{a} libpng16-16{a} libpopt0{a} libpsl5{a} libpython3-stdlib{a} libpython3.11-minimal{a} libpython3.11-stdlib{a} librdmacm1{a} libreadline8{a} librhino-java{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsensors-config{a} libsensors5{a} libslf4j-java{a} libsnappy-java{a} libsnappy-jni{a} libsnappy1v5{a} libssh2-1{a} libsub-override-perl{a} libthai-data{a} libthai0{a} libtiff6{a} libtool{a} libuchardet0{a} libucx0{a} libwebp7{a} libx11-6{a} libx11-data{a} libx11-xcb1{a} libxau6{a} libxcb-dri2-0{a} libxcb-dri3-0{a} libxcb-glx0{a} libxcb-present0{a} libxcb-randr0{a} libxcb-render0{a} libxcb-shm0{a} libxcb-sync1{a} libxcb-xfixes0{a} libxcb1{a} libxcomposite1{a} libxcursor1{a} libxdamage1{a} libxdmcp6{a} libxext6{a} libxfixes3{a} libxi6{a} libxinerama1{a} libxml2{a} libxnvctrl0{a} libxrandr2{a} libxrender1{a} libxshmfence1{a} libxtst6{a} libxxf86vm1{a} libz3-4{a} m4{a} man-db{a} media-types{a} ncbi-vdb-data{a} ocl-icd-libopencl1{a} openjdk-17-jre{a} openjdk-17-jre-headless{a} openmpi-bin{a} openmpi-common{a} openssh-client{a} openssl{a} picard-tools{a} po-debconf{a} python3{a} python3-attr{a} python3-coloredlogs{a} python3-configargparse{a} python3-distutils{a} python3-humanfriendly{a} python3-iniconfig{a} python3-lib2to3{a} python3-minimal{a} python3-more-itertools{a} python3-packaging{a} python3-pkg-resources{a} python3-pluggy{a} python3-py{a} python3-pysam{a} python3-pytest{a} python3-ruamel.yaml{a} python3-ruamel.yaml.clib{a} python3-setproctitle{a} python3-setuptools{a} python3.11{a} python3.11-minimal{a} readline-common{a} rsync{a} sensible-utils{a} shared-mime-info{a} x11-common{a} The following packages are RECOMMENDED but will NOT be installed: alsa-topology-conf alsa-ucm-conf curl dbus fonts-dejavu-extra libarchive-cpio-perl libatk-wrapper-java-jni libgail-common libgdk-pixbuf2.0-bin libglib2.0-data libgtk2.0-bin libldap-common libltdl-dev libmail-sendmail-perl librsvg2-common libsasl2-modules lynx publicsuffix python3-pygments r-base-core wget xauth xdg-user-dirs 0 packages upgraded, 234 newly installed, 0 to remove and 0 not upgraded. Need to get 161 MB of archives. After unpacking 644 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bookworm/main arm64 libpython3.11-minimal arm64 3.11.2-6 [806 kB] Get: 2 http://deb.debian.org/debian bookworm/main arm64 libexpat1 arm64 2.5.0-1 [84.8 kB] Get: 3 http://deb.debian.org/debian bookworm/main arm64 python3.11-minimal arm64 3.11.2-6 [1858 kB] Get: 4 http://deb.debian.org/debian bookworm/main arm64 python3-minimal arm64 3.11.2-1 [26.0 kB] Get: 5 http://deb.debian.org/debian bookworm/main arm64 media-types all 10.0.0 [26.1 kB] Get: 6 http://deb.debian.org/debian bookworm/main arm64 readline-common all 8.2-1.3 [69.0 kB] Get: 7 http://deb.debian.org/debian bookworm/main arm64 libreadline8 arm64 8.2-1.3 [155 kB] Get: 8 http://deb.debian.org/debian bookworm/main arm64 libpython3.11-stdlib arm64 3.11.2-6 [1747 kB] Get: 9 http://deb.debian.org/debian bookworm/main arm64 python3.11 arm64 3.11.2-6 [572 kB] Get: 10 http://deb.debian.org/debian bookworm/main arm64 libpython3-stdlib arm64 3.11.2-1 [9012 B] Get: 11 http://deb.debian.org/debian bookworm/main arm64 python3 arm64 3.11.2-1 [26.0 kB] Get: 12 http://deb.debian.org/debian bookworm/main arm64 libpopt0 arm64 1.19+dfsg-1 [42.0 kB] Get: 13 http://deb.debian.org/debian bookworm/main arm64 rsync arm64 3.2.7-1 [399 kB] Get: 14 http://deb.debian.org/debian bookworm/main arm64 sensible-utils all 0.0.17+nmu1 [19.0 kB] Get: 15 http://deb.debian.org/debian bookworm/main arm64 openssl arm64 3.0.8-1 [1373 kB] Get: 16 http://deb.debian.org/debian bookworm/main arm64 ca-certificates all 20230311 [153 kB] Get: 17 http://deb.debian.org/debian bookworm/main arm64 libmagic-mgc arm64 1:5.44-3 [305 kB] Get: 18 http://deb.debian.org/debian bookworm/main arm64 libmagic1 arm64 1:5.44-3 [98.5 kB] Get: 19 http://deb.debian.org/debian bookworm/main arm64 file arm64 1:5.44-3 [42.5 kB] Get: 20 http://deb.debian.org/debian bookworm/main arm64 gettext-base arm64 0.21-12 [159 kB] Get: 21 http://deb.debian.org/debian bookworm/main arm64 libuchardet0 arm64 0.0.7-1 [67.9 kB] Get: 22 http://deb.debian.org/debian bookworm/main arm64 groff-base arm64 1.22.4-10 [861 kB] Get: 23 http://deb.debian.org/debian bookworm/main arm64 bsdextrautils arm64 2.38.1-5+b1 [86.9 kB] Get: 24 http://deb.debian.org/debian bookworm/main arm64 libpipeline1 arm64 1.5.7-1 [36.4 kB] Get: 25 http://deb.debian.org/debian bookworm/main arm64 man-db arm64 2.11.2-2 [1369 kB] Get: 26 http://deb.debian.org/debian bookworm/main arm64 libbsd0 arm64 0.11.7-2 [115 kB] Get: 27 http://deb.debian.org/debian bookworm/main arm64 libedit2 arm64 3.1-20221030-2 [88.1 kB] Get: 28 http://deb.debian.org/debian bookworm/main arm64 libcbor0.8 arm64 0.8.0-2+b1 [26.0 kB] Get: 29 http://deb.debian.org/debian bookworm/main arm64 libfido2-1 arm64 1.12.0-2+b1 [72.6 kB] Get: 30 http://deb.debian.org/debian bookworm/main arm64 openssh-client arm64 1:9.2p1-2 [931 kB] Get: 31 http://deb.debian.org/debian bookworm/main arm64 hicolor-icon-theme all 0.17-2 [11.4 kB] Get: 32 http://deb.debian.org/debian bookworm/main arm64 libgdk-pixbuf2.0-common all 2.42.10+dfsg-1 [306 kB] Get: 33 http://deb.debian.org/debian bookworm/main arm64 libglib2.0-0 arm64 2.74.6-1 [1311 kB] Get: 34 http://deb.debian.org/debian bookworm/main arm64 libicu72 arm64 72.1-3 [9204 kB] Get: 35 http://deb.debian.org/debian bookworm/main arm64 libxml2 arm64 2.9.14+dfsg-1.1+b3 [619 kB] Get: 36 http://deb.debian.org/debian bookworm/main arm64 shared-mime-info arm64 2.2-1 [727 kB] Get: 37 http://deb.debian.org/debian bookworm/main arm64 libjpeg62-turbo arm64 1:2.1.5-2 [171 kB] Get: 38 http://deb.debian.org/debian bookworm/main arm64 libpng16-16 arm64 1.6.39-2 [269 kB] Get: 39 http://deb.debian.org/debian bookworm/main arm64 libdeflate0 arm64 1.14-1 [54.3 kB] Get: 40 http://deb.debian.org/debian bookworm/main arm64 libjbig0 arm64 2.1-6.1 [30.0 kB] Get: 41 http://deb.debian.org/debian bookworm/main arm64 liblerc4 arm64 4.0.0+ds-2 [138 kB] Get: 42 http://deb.debian.org/debian bookworm/main arm64 libwebp7 arm64 1.2.4-0.1 [259 kB] Get: 43 http://deb.debian.org/debian bookworm/main arm64 libtiff6 arm64 4.5.0-5 [300 kB] Get: 44 http://deb.debian.org/debian bookworm/main arm64 libgdk-pixbuf-2.0-0 arm64 2.42.10+dfsg-1+b1 [130 kB] Get: 45 http://deb.debian.org/debian bookworm/main arm64 gtk-update-icon-cache arm64 3.24.37-2 [42.7 kB] Get: 46 http://deb.debian.org/debian bookworm/main arm64 adwaita-icon-theme all 43-1 [5124 kB] Get: 47 http://deb.debian.org/debian bookworm/main arm64 at-spi2-common all 2.46.0-5 [162 kB] Get: 48 http://deb.debian.org/debian bookworm/main arm64 m4 arm64 1.4.19-3 [276 kB] Get: 49 http://deb.debian.org/debian bookworm/main arm64 autoconf all 2.71-3 [332 kB] Get: 50 http://deb.debian.org/debian bookworm/main arm64 autotools-dev all 20220109.1 [51.6 kB] Get: 51 http://deb.debian.org/debian bookworm/main arm64 automake all 1:1.16.5-1.3 [823 kB] Get: 52 http://deb.debian.org/debian bookworm/main arm64 autopoint all 0.21-12 [495 kB] Get: 53 http://deb.debian.org/debian bookworm/main arm64 bowtie2 arm64 2.5.0-3+b2 [1295 kB] Get: 54 http://deb.debian.org/debian bookworm/main arm64 java-common all 0.74 [6388 B] Get: 55 http://deb.debian.org/debian bookworm/main arm64 libavahi-common-data arm64 0.8-9 [107 kB] Get: 56 http://deb.debian.org/debian bookworm/main arm64 libavahi-common3 arm64 0.8-9 [40.3 kB] Get: 57 http://deb.debian.org/debian bookworm/main arm64 libdbus-1-3 arm64 1.14.6-1 [191 kB] Get: 58 http://deb.debian.org/debian bookworm/main arm64 libavahi-client3 arm64 0.8-9 [43.7 kB] Get: 59 http://deb.debian.org/debian bookworm/main arm64 libcups2 arm64 2.4.2-2 [228 kB] Get: 60 http://deb.debian.org/debian bookworm/main arm64 liblcms2-2 arm64 2.14-2 [143 kB] Get: 61 http://deb.debian.org/debian bookworm/main arm64 libbrotli1 arm64 1.0.9-2+b6 [269 kB] Get: 62 http://deb.debian.org/debian bookworm/main arm64 libfreetype6 arm64 2.12.1+dfsg-4 [369 kB] Get: 63 http://deb.debian.org/debian bookworm/main arm64 fonts-dejavu-core all 2.37-6 [1068 kB] Get: 64 http://deb.debian.org/debian bookworm/main arm64 fontconfig-config arm64 2.14.1-4 [315 kB] Get: 65 http://deb.debian.org/debian bookworm/main arm64 libfontconfig1 arm64 2.14.1-4 [381 kB] Get: 66 http://deb.debian.org/debian bookworm/main arm64 libnspr4 arm64 2:4.35-1 [105 kB] Get: 67 http://deb.debian.org/debian bookworm/main arm64 libnss3 arm64 2:3.87.1-1 [1218 kB] Get: 68 http://deb.debian.org/debian bookworm/main arm64 libasound2-data all 1.2.8-1 [20.5 kB] Get: 69 http://deb.debian.org/debian bookworm/main arm64 libasound2 arm64 1.2.8-1+b1 [327 kB] Get: 70 http://deb.debian.org/debian bookworm/main arm64 libgraphite2-3 arm64 1.3.14-1 [75.6 kB] Get: 71 http://deb.debian.org/debian bookworm/main arm64 libharfbuzz0b arm64 6.0.0+dfsg-3 [1914 kB] Get: 72 http://deb.debian.org/debian bookworm/main arm64 libpcsclite1 arm64 1.9.9-1 [60.4 kB] Get: 73 http://deb.debian.org/debian bookworm/main arm64 openjdk-17-jre-headless arm64 17.0.6+10-1 [42.5 MB] Get: 74 http://deb.debian.org/debian bookworm/main arm64 default-jre-headless arm64 2:1.17-74 [2932 B] Get: 75 http://deb.debian.org/debian bookworm/main arm64 ca-certificates-java all 20230103 [11.4 kB] Get: 76 http://deb.debian.org/debian bookworm/main arm64 libdebhelper-perl all 13.11.4 [81.2 kB] Get: 77 http://deb.debian.org/debian bookworm/main arm64 libtool all 2.4.7-5 [517 kB] Get: 78 http://deb.debian.org/debian bookworm/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 79 http://deb.debian.org/debian bookworm/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 80 http://deb.debian.org/debian bookworm/main arm64 libsub-override-perl all 0.09-4 [9304 B] Get: 81 http://deb.debian.org/debian bookworm/main arm64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 82 http://deb.debian.org/debian bookworm/main arm64 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 83 http://deb.debian.org/debian bookworm/main arm64 libelf1 arm64 0.188-2.1 [173 kB] Get: 84 http://deb.debian.org/debian bookworm/main arm64 dwz arm64 0.15-1 [101 kB] Get: 85 http://deb.debian.org/debian bookworm/main arm64 gettext arm64 0.21-12 [1248 kB] Get: 86 http://deb.debian.org/debian bookworm/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 87 http://deb.debian.org/debian bookworm/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 88 http://deb.debian.org/debian bookworm/main arm64 debhelper all 13.11.4 [942 kB] Get: 89 http://deb.debian.org/debian bookworm/main arm64 libgtk2.0-common all 2.24.33-2 [2700 kB] Get: 90 http://deb.debian.org/debian bookworm/main arm64 libatk1.0-0 arm64 2.46.0-5 [47.4 kB] Get: 91 http://deb.debian.org/debian bookworm/main arm64 libpixman-1-0 arm64 0.42.2-1 [470 kB] Get: 92 http://deb.debian.org/debian bookworm/main arm64 libxau6 arm64 1:1.0.9-1 [19.7 kB] Get: 93 http://deb.debian.org/debian bookworm/main arm64 libxdmcp6 arm64 1:1.1.2-3 [25.4 kB] Get: 94 http://deb.debian.org/debian bookworm/main arm64 libxcb1 arm64 1.15-1 [143 kB] Get: 95 http://deb.debian.org/debian bookworm/main arm64 libx11-data all 2:1.8.4-2 [292 kB] Get: 96 http://deb.debian.org/debian bookworm/main arm64 libx11-6 arm64 2:1.8.4-2 [736 kB] Get: 97 http://deb.debian.org/debian bookworm/main arm64 libxcb-render0 arm64 1.15-1 [115 kB] Get: 98 http://deb.debian.org/debian bookworm/main arm64 libxcb-shm0 arm64 1.15-1 [106 kB] Get: 99 http://deb.debian.org/debian bookworm/main arm64 libxext6 arm64 2:1.3.4-1+b1 [51.7 kB] Get: 100 http://deb.debian.org/debian bookworm/main arm64 libxrender1 arm64 1:0.9.10-1.1 [32.0 kB] Get: 101 http://deb.debian.org/debian bookworm/main arm64 libcairo2 arm64 1.16.0-7 [527 kB] Get: 102 http://deb.debian.org/debian bookworm/main arm64 fontconfig arm64 2.14.1-4 [449 kB] Get: 103 http://deb.debian.org/debian bookworm/main arm64 libfribidi0 arm64 1.0.8-2.1 [64.9 kB] Get: 104 http://deb.debian.org/debian bookworm/main arm64 libthai-data all 0.1.29-1 [176 kB] Get: 105 http://deb.debian.org/debian bookworm/main arm64 libdatrie1 arm64 0.2.13-2+b1 [42.6 kB] Get: 106 http://deb.debian.org/debian bookworm/main arm64 libthai0 arm64 0.1.29-1 [56.2 kB] Get: 107 http://deb.debian.org/debian bookworm/main arm64 libpango-1.0-0 arm64 1.50.12+ds-1 [200 kB] Get: 108 http://deb.debian.org/debian bookworm/main arm64 libpangoft2-1.0-0 arm64 1.50.12+ds-1 [44.5 kB] Get: 109 http://deb.debian.org/debian bookworm/main arm64 libpangocairo-1.0-0 arm64 1.50.12+ds-1 [32.0 kB] Get: 110 http://deb.debian.org/debian bookworm/main arm64 libxcomposite1 arm64 1:0.4.5-1 [16.6 kB] Get: 111 http://deb.debian.org/debian bookworm/main arm64 libxfixes3 arm64 1:6.0.0-2 [22.9 kB] Get: 112 http://deb.debian.org/debian bookworm/main arm64 libxcursor1 arm64 1:1.2.1-1 [40.2 kB] Get: 113 http://deb.debian.org/debian bookworm/main arm64 libxdamage1 arm64 1:1.1.6-1 [15.2 kB] Get: 114 http://deb.debian.org/debian bookworm/main arm64 libxi6 arm64 2:1.8-1+b1 [82.3 kB] Get: 115 http://deb.debian.org/debian bookworm/main arm64 libxinerama1 arm64 2:1.1.4-3 [17.8 kB] Get: 116 http://deb.debian.org/debian bookworm/main arm64 libxrandr2 arm64 2:1.5.2-2+b1 [38.4 kB] Get: 117 http://deb.debian.org/debian bookworm/main arm64 libgtk2.0-0 arm64 2.24.33-2 [1704 kB] Get: 118 http://deb.debian.org/debian bookworm/main arm64 libglvnd0 arm64 1.6.0-1 [41.4 kB] Get: 119 http://deb.debian.org/debian bookworm/main arm64 libdrm-common all 2.4.114-1 [7112 B] Get: 120 http://deb.debian.org/debian bookworm/main arm64 libdrm2 arm64 2.4.114-1+b1 [36.7 kB] Get: 121 http://deb.debian.org/debian bookworm/main arm64 libglapi-mesa arm64 22.3.6-1+deb12u1 [44.7 kB] Get: 122 http://deb.debian.org/debian bookworm/main arm64 libx11-xcb1 arm64 2:1.8.4-2 [192 kB] Get: 123 http://deb.debian.org/debian bookworm/main arm64 libxcb-dri2-0 arm64 1.15-1 [107 kB] Get: 124 http://deb.debian.org/debian bookworm/main arm64 libxcb-dri3-0 arm64 1.15-1 [107 kB] Get: 125 http://deb.debian.org/debian bookworm/main arm64 libxcb-glx0 arm64 1.15-1 [123 kB] Get: 126 http://deb.debian.org/debian bookworm/main arm64 libxcb-present0 arm64 1.15-1 [106 kB] Get: 127 http://deb.debian.org/debian bookworm/main arm64 libxcb-randr0 arm64 1.15-1 [117 kB] Get: 128 http://deb.debian.org/debian bookworm/main arm64 libxcb-sync1 arm64 1.15-1 [109 kB] Get: 129 http://deb.debian.org/debian bookworm/main arm64 libxcb-xfixes0 arm64 1.15-1 [110 kB] Get: 130 http://deb.debian.org/debian bookworm/main arm64 libxshmfence1 arm64 1.3-1 [8712 B] Get: 131 http://deb.debian.org/debian bookworm/main arm64 libxxf86vm1 arm64 1:1.1.4-1+b2 [20.1 kB] Get: 132 http://deb.debian.org/debian bookworm/main arm64 libdrm-amdgpu1 arm64 2.4.114-1+b1 [20.4 kB] Get: 133 http://deb.debian.org/debian bookworm/main arm64 libdrm-nouveau2 arm64 2.4.114-1+b1 [18.4 kB] Get: 134 http://deb.debian.org/debian bookworm/main arm64 libdrm-radeon1 arm64 2.4.114-1+b1 [20.9 kB] Get: 135 http://deb.debian.org/debian bookworm/main arm64 libz3-4 arm64 4.8.12-3.1 [6282 kB] Get: 136 http://deb.debian.org/debian bookworm/main arm64 libllvm15 arm64 1:15.0.6-4+b1 [20.7 MB] Get: 137 http://deb.debian.org/debian bookworm/main arm64 libsensors-config all 1:3.6.0-7.1 [14.3 kB] Get: 138 http://deb.debian.org/debian bookworm/main arm64 libsensors5 arm64 1:3.6.0-7.1 [33.3 kB] Get: 139 http://deb.debian.org/debian bookworm/main arm64 libgl1-mesa-dri arm64 22.3.6-1+deb12u1 [6278 kB] Get: 140 http://deb.debian.org/debian bookworm/main arm64 libglx-mesa0 arm64 22.3.6-1+deb12u1 [146 kB] Get: 141 http://deb.debian.org/debian bookworm/main arm64 libglx0 arm64 1.6.0-1 [30.8 kB] Get: 142 http://deb.debian.org/debian bookworm/main arm64 libgl1 arm64 1.6.0-1 [90.2 kB] Get: 143 http://deb.debian.org/debian bookworm/main arm64 libgif7 arm64 5.2.1-2.5 [46.7 kB] Get: 144 http://deb.debian.org/debian bookworm/main arm64 x11-common all 1:7.7+23 [252 kB] Get: 145 http://deb.debian.org/debian bookworm/main arm64 libxtst6 arm64 2:1.2.3-1.1 [27.8 kB] Get: 146 http://deb.debian.org/debian bookworm/main arm64 openjdk-17-jre arm64 17.0.6+10-1 [156 kB] Get: 147 http://deb.debian.org/debian bookworm/main arm64 default-jre arm64 2:1.17-74 [1056 B] Get: 148 http://deb.debian.org/debian bookworm/main arm64 python3-lib2to3 all 3.11.2-2 [76.2 kB] Get: 149 http://deb.debian.org/debian bookworm/main arm64 python3-distutils all 3.11.2-2 [131 kB] Get: 150 http://deb.debian.org/debian bookworm/main arm64 dh-python all 5.20230130 [104 kB] Get: 151 http://deb.debian.org/debian bookworm/main arm64 libevent-core-2.1-7 arm64 2.1.12-stable-8 [124 kB] Get: 152 http://deb.debian.org/debian bookworm/main arm64 libevent-pthreads-2.1-7 arm64 2.1.12-stable-8 [53.7 kB] Get: 153 http://deb.debian.org/debian bookworm/main arm64 libnl-3-200 arm64 3.7.0-0.2+b1 [60.2 kB] Get: 154 http://deb.debian.org/debian bookworm/main arm64 libnl-route-3-200 arm64 3.7.0-0.2+b1 [168 kB] Get: 155 http://deb.debian.org/debian bookworm/main arm64 libibverbs1 arm64 44.0-2 [56.8 kB] Get: 156 http://deb.debian.org/debian bookworm/main arm64 ibverbs-providers arm64 44.0-2 [306 kB] Get: 157 http://deb.debian.org/debian bookworm/main arm64 librdmacm1 arm64 44.0-2 [64.9 kB] Get: 158 http://deb.debian.org/debian bookworm/main arm64 libfabric1 arm64 1.17.0-3 [476 kB] Get: 159 http://deb.debian.org/debian bookworm/main arm64 libhwloc15 arm64 2.9.0-1 [133 kB] Get: 160 http://deb.debian.org/debian bookworm/main arm64 libmunge2 arm64 0.5.15-2 [18.8 kB] Get: 161 http://deb.debian.org/debian bookworm/main arm64 libpciaccess0 arm64 0.17-2 [50.4 kB] Get: 162 http://deb.debian.org/debian bookworm/main arm64 libxnvctrl0 arm64 525.85.05-1 [13.3 kB] Get: 163 http://deb.debian.org/debian bookworm/main arm64 ocl-icd-libopencl1 arm64 2.3.1-1 [42.1 kB] Get: 164 http://deb.debian.org/debian bookworm/main arm64 libhwloc-plugins arm64 2.9.0-1 [17.2 kB] Get: 165 http://deb.debian.org/debian bookworm/main arm64 libpmix2 arm64 4.2.2-1+b1 [554 kB] Get: 166 http://deb.debian.org/debian bookworm/main arm64 libnuma1 arm64 2.0.16-1 [20.3 kB] Get: 167 http://deb.debian.org/debian bookworm/main arm64 libucx0 arm64 1.13.1-1 [734 kB] Get: 168 http://deb.debian.org/debian bookworm/main arm64 libopenmpi3 arm64 4.1.4-3+b1 [2161 kB] Get: 169 http://deb.debian.org/debian bookworm/main arm64 openmpi-common all 4.1.4-3 [167 kB] Get: 170 http://deb.debian.org/debian bookworm/main arm64 openmpi-bin arm64 4.1.4-3+b1 [225 kB] Get: 171 http://deb.debian.org/debian bookworm/main arm64 examl arm64 3.0.22-3+b2 [799 kB] Get: 172 http://deb.debian.org/debian bookworm/main arm64 libapache-pom-java all 29-2 [5276 B] Get: 173 http://deb.debian.org/debian bookworm/main arm64 libcommons-parent-java all 56-1 [10.8 kB] Get: 174 http://deb.debian.org/debian bookworm/main arm64 libcommons-lang3-java all 3.12.0-2 [561 kB] Get: 175 http://deb.debian.org/debian bookworm/main arm64 libfreemarker-java all 2.3.31-2 [1528 kB] Get: 176 http://deb.debian.org/debian bookworm/main arm64 libgoogle-gson-java all 2.10-1 [261 kB] Get: 177 http://deb.debian.org/debian bookworm/main arm64 libjoptsimple-java all 5.0.4-4 [73.1 kB] Get: 178 http://deb.debian.org/debian bookworm/main arm64 libcommons-codec-java all 1.15-1 [292 kB] Get: 179 http://deb.debian.org/debian bookworm/main arm64 libcommons-logging-java all 1.2-3 [62.4 kB] Get: 180 http://deb.debian.org/debian bookworm/main arm64 libhttpcore-java all 4.4.16-1 [636 kB] Get: 181 http://deb.debian.org/debian bookworm/main arm64 libhttpclient-java all 4.5.14-1 [1247 kB] Get: 182 http://deb.debian.org/debian bookworm/main arm64 liblightcouch-java all 0.2.0-1 [75.0 kB] Get: 183 http://deb.debian.org/debian bookworm/main arm64 libmongodb-java all 3.6.3-2 [1901 kB] Get: 184 http://deb.debian.org/debian bookworm/main arm64 libslf4j-java all 1.7.32-1 [144 kB] Get: 185 http://deb.debian.org/debian bookworm/main arm64 liblog4j2-java all 2.19.0-2 [2310 kB] Get: 186 http://deb.debian.org/debian bookworm/main arm64 libbarclay-java all 4.1.0+dfsg-1 [103 kB] Get: 187 http://deb.debian.org/debian bookworm/main arm64 libcommons-compress-java all 1.22-1 [615 kB] Get: 188 http://deb.debian.org/debian bookworm/main arm64 libcommons-io-java all 2.11.0-2 [319 kB] Get: 189 http://deb.debian.org/debian bookworm/main arm64 libcommons-jexl2-java all 2.1.1-6 [256 kB] Get: 190 http://deb.debian.org/debian bookworm/main arm64 libcommons-math3-java all 3.6.1-3 [2018 kB] Get: 191 http://deb.debian.org/debian bookworm/main arm64 libsasl2-modules-db arm64 2.1.28+dfsg-10 [20.8 kB] Get: 192 http://deb.debian.org/debian bookworm/main arm64 libsasl2-2 arm64 2.1.28+dfsg-10 [58.0 kB] Get: 193 http://deb.debian.org/debian bookworm/main arm64 libldap-2.5-0 arm64 2.5.13+dfsg-5 [171 kB] Get: 194 http://deb.debian.org/debian bookworm/main arm64 libnghttp2-14 arm64 1.52.0-1 [67.9 kB] Get: 195 http://deb.debian.org/debian bookworm/main arm64 libpsl5 arm64 0.21.2-1 [58.6 kB] Get: 196 http://deb.debian.org/debian bookworm/main arm64 librtmp1 arm64 2.4+20151223.gitfa8646d.1-2+b2 [59.4 kB] Get: 197 http://deb.debian.org/debian bookworm/main arm64 libssh2-1 arm64 1.10.0-3+b1 [172 kB] Get: 198 http://deb.debian.org/debian bookworm/main arm64 libcurl3-gnutls arm64 7.88.1-7 [356 kB] Get: 199 http://deb.debian.org/debian bookworm/main arm64 libgatk-native-bindings-java all 1.0.0+dfsg-2 [8024 B] Get: 200 http://deb.debian.org/debian bookworm/main arm64 libmjson-java all 1.4.0-3 [60.4 kB] Get: 201 http://deb.debian.org/debian bookworm/main arm64 libmbedcrypto7 arm64 2.28.2-1 [261 kB] Get: 202 http://deb.debian.org/debian bookworm/main arm64 libmbedx509-1 arm64 2.28.2-1 [126 kB] Get: 203 http://deb.debian.org/debian bookworm/main arm64 libmbedtls14 arm64 2.28.2-1 [155 kB] Get: 204 http://deb.debian.org/debian bookworm/main arm64 ncbi-vdb-data all 3.0.2+dfsg-2 [73.3 kB] Get: 205 http://deb.debian.org/debian bookworm/main arm64 libncbi-vdb3 arm64 3.0.2+dfsg-2 [977 kB] Get: 206 http://deb.debian.org/debian bookworm/main arm64 libncbi-ngs3 arm64 3.0.3+dfsg-5 [141 kB] Get: 207 http://deb.debian.org/debian bookworm/main arm64 libngs-jni arm64 3.0.3+dfsg-5 [23.4 kB] Get: 208 http://deb.debian.org/debian bookworm/main arm64 libngs-java arm64 3.0.3+dfsg-5 [110 kB] Get: 209 http://deb.debian.org/debian bookworm/main arm64 librhino-java all 1.7.7.2-3 [1200 kB] Get: 210 http://deb.debian.org/debian bookworm/main arm64 libsnappy1v5 arm64 1.1.9-3 [25.4 kB] Get: 211 http://deb.debian.org/debian bookworm/main arm64 libsnappy-jni arm64 1.1.8.3-1 [7056 B] Get: 212 http://deb.debian.org/debian bookworm/main arm64 libsnappy-java all 1.1.8.3-1 [98.9 kB] Get: 213 http://deb.debian.org/debian bookworm/main arm64 libhtsjdk-java all 3.0.4+dfsg-2 [1813 kB] Get: 214 http://deb.debian.org/debian bookworm/main arm64 libgkl-java all 0.8.10+dfsg-3 [25.0 kB] Get: 215 http://deb.debian.org/debian bookworm/main arm64 libhtscodecs2 arm64 1.3.0-4 [70.5 kB] Get: 216 http://deb.debian.org/debian bookworm/main arm64 libhts3 arm64 1.16+ds-3 [392 kB] Get: 217 http://deb.debian.org/debian bookworm/main arm64 libpicard-java all 2.27.5+dfsg-2 [1725 kB] Get: 218 http://deb.debian.org/debian bookworm/main arm64 picard-tools all 2.27.5+dfsg-2 [311 kB] Get: 219 http://deb.debian.org/debian bookworm/main arm64 python3-attr all 22.2.0-1 [65.4 kB] Get: 220 http://deb.debian.org/debian bookworm/main arm64 python3-humanfriendly all 10.0-3 [85.2 kB] Get: 221 http://deb.debian.org/debian bookworm/main arm64 python3-coloredlogs all 15.0.1-1 [47.4 kB] Get: 222 http://deb.debian.org/debian bookworm/main arm64 python3-configargparse all 1.5.3-1 [26.1 kB] Get: 223 http://deb.debian.org/debian bookworm/main arm64 python3-iniconfig all 1.1.1-2 [6396 B] Get: 224 http://deb.debian.org/debian bookworm/main arm64 python3-more-itertools all 8.10.0-2 [53.0 kB] Get: 225 http://deb.debian.org/debian bookworm/main arm64 python3-packaging all 23.0-1 [32.5 kB] Get: 226 http://deb.debian.org/debian bookworm/main arm64 python3-pkg-resources all 66.1.1-1 [296 kB] Get: 227 http://deb.debian.org/debian bookworm/main arm64 python3-pluggy all 1.0.0+repack-1 [19.7 kB] Get: 228 http://deb.debian.org/debian bookworm/main arm64 python3-py all 1.11.0-1 [89.2 kB] Get: 229 http://deb.debian.org/debian bookworm/main arm64 python3-pysam arm64 0.20.0+ds-3+b1 [1493 kB] Get: 230 http://deb.debian.org/debian bookworm/main arm64 python3-pytest all 7.2.1-2 [236 kB] Get: 231 http://deb.debian.org/debian bookworm/main arm64 python3-ruamel.yaml.clib arm64 0.2.7-1+b2 [98.1 kB] Get: 232 http://deb.debian.org/debian bookworm/main arm64 python3-ruamel.yaml all 0.17.21-1 [103 kB] Get: 233 http://deb.debian.org/debian bookworm/main arm64 python3-setproctitle arm64 1.3.1-1+b2 [17.8 kB] Get: 234 http://deb.debian.org/debian bookworm/main arm64 python3-setuptools all 66.1.1-1 [521 kB] Fetched 161 MB in 6s (26.8 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.11-minimal:arm64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19616 files and directories currently installed.) Preparing to unpack .../libpython3.11-minimal_3.11.2-6_arm64.deb ... Unpacking libpython3.11-minimal:arm64 (3.11.2-6) ... Selecting previously unselected package libexpat1:arm64. Preparing to unpack .../libexpat1_2.5.0-1_arm64.deb ... Unpacking libexpat1:arm64 (2.5.0-1) ... Selecting previously unselected package python3.11-minimal. 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Unpacking libpython3-stdlib:arm64 (3.11.2-1) ... Setting up python3-minimal (3.11.2-1) ... 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 ... 20364 files and directories currently installed.) Preparing to unpack .../000-python3_3.11.2-1_arm64.deb ... Unpacking python3 (3.11.2-1) ... Selecting previously unselected package libpopt0:arm64. Preparing to unpack .../001-libpopt0_1.19+dfsg-1_arm64.deb ... 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Setting up libgatk-native-bindings-java (1.0.0+dfsg-2) ... Setting up java-common (0.74) ... Setting up libdatrie1:arm64 (0.2.13-2+b1) ... Setting up libmagic-mgc (1:5.44-3) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libglib2.0-0:arm64 (2.74.6-1) ... No schema files found: doing nothing. Setting up libglvnd0:arm64 (1.6.0-1) ... Setting up libgoogle-gson-java (2.10-1) ... Setting up libmjson-java (1.4.0-3) ... Setting up libcbor0.8:arm64 (0.8.0-2+b1) ... Setting up libdebhelper-perl (13.11.4) ... Setting up libbrotli1:arm64 (1.0.9-2+b6) ... Setting up libgdk-pixbuf2.0-common (2.42.10+dfsg-1) ... Setting up x11-common (1:7.7+23) ... invoke-rc.d: could not determine current runlevel Setting up X socket directories... /tmp/.X11-unix /tmp/.ICE-unix. Setting up libsensors-config (1:3.6.0-7.1) ... Setting up libnghttp2-14:arm64 (1.52.0-1) ... Setting up libmagic1:arm64 (1:5.44-3) ... Setting up libdeflate0:arm64 (1.14-1) ... Setting up gettext-base (0.21-12) ... Setting up m4 (1.4.19-3) ... Setting up file (1:5.44-3) ... Setting up libjbig0:arm64 (2.1-6.1) ... Setting up libsnappy1v5:arm64 (1.1.9-3) ... Setting up libsasl2-modules-db:arm64 (2.1.28+dfsg-10) ... Setting up libasound2-data (1.2.8-1) ... Setting up librhino-java (1.7.7.2-3) ... Setting up autotools-dev (20220109.1) ... Setting up libz3-4:arm64 (4.8.12-3.1) ... Setting up libmunge2 (0.5.15-2) ... Setting up libjpeg62-turbo:arm64 (1:2.1.5-2) ... Setting up libmbedcrypto7:arm64 (2.28.2-1) ... Setting up libx11-data (2:1.8.4-2) ... Setting up libnspr4:arm64 (2:4.35-1) ... Setting up librtmp1:arm64 (2.4+20151223.gitfa8646d.1-2+b2) ... Setting up libapache-pom-java (29-2) ... Setting up libavahi-common-data:arm64 (0.8-9) ... Setting up libdbus-1-3:arm64 (1.14.6-1) ... Setting up libfribidi0:arm64 (1.0.8-2.1) ... Setting up libpng16-16:arm64 (1.6.39-2) ... Setting up libhwloc15:arm64 (2.9.0-1) ... Setting up libevent-core-2.1-7:arm64 (2.1.12-stable-8) ... Setting up autopoint (0.21-12) ... Setting up fonts-dejavu-core (2.37-6) ... Setting up libpcsclite1:arm64 (1.9.9-1) ... Setting up libsensors5:arm64 (1:3.6.0-7.1) ... Setting up libmongodb-java (3.6.3-2) ... Setting up libglapi-mesa:arm64 (22.3.6-1+deb12u1) ... Setting up libsasl2-2:arm64 (2.1.28+dfsg-10) ... Setting up autoconf (2.71-3) ... Setting up libwebp7:arm64 (1.2.4-0.1) ... Setting up libgif7:arm64 (5.2.1-2.5) ... Setting up libnuma1:arm64 (2.0.16-1) ... Setting up libfreemarker-java (2.3.31-2) ... Setting up sensible-utils (0.0.17+nmu1) ... Setting up ocl-icd-libopencl1:arm64 (2.3.1-1) ... Setting up libxshmfence1:arm64 (1.3-1) ... Setting up at-spi2-common (2.46.0-5) ... Setting up libtiff6:arm64 (4.5.0-5) ... Setting up libuchardet0:arm64 (0.0.7-1) ... Setting up libasound2:arm64 (1.2.8-1+b1) ... Setting up libnl-3-200:arm64 (3.7.0-0.2+b1) ... Setting up openmpi-common (4.1.4-3) ... Setting up libsub-override-perl (0.09-4) ... Setting up ncbi-vdb-data (3.0.2+dfsg-2) ... Setting up libthai-data (0.1.29-1) ... Setting up libssh2-1:arm64 (1.10.0-3+b1) ... Setting up libcommons-math3-java (3.6.1-3) ... Setting up libgtk2.0-common (2.24.33-2) ... Setting up libatk1.0-0:arm64 (2.46.0-5) ... Setting up libhttpcore-java (4.4.16-1) ... Setting up libjoptsimple-java (5.0.4-4) ... Setting up libfido2-1:arm64 (1.12.0-2+b1) ... Setting up openssl (3.0.8-1) ... Setting up libbsd0:arm64 (0.11.7-2) ... Setting up libdrm-common (2.4.114-1) ... Setting up libelf1:arm64 (0.188-2.1) ... Setting up libsnappy-jni (1.1.8.3-1) ... Setting up readline-common (8.2-1.3) ... Setting up libxml2:arm64 (2.9.14+dfsg-1.1+b3) ... Setting up libpopt0:arm64 (1.19+dfsg-1) ... Setting up libevent-pthreads-2.1-7:arm64 (2.1.12-stable-8) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.13.1-1) ... Setting up libxdmcp6:arm64 (1:1.1.2-3) ... Setting up libxcb1:arm64 (1.15-1) ... Setting up gettext (0.21-12) ... Setting up libxcb-xfixes0:arm64 (1.15-1) ... Setting up libmbedx509-1:arm64 (2.28.2-1) ... Setting up libmbedtls14:arm64 (2.28.2-1) ... Setting up libtool (2.4.7-5) ... Setting up libxcb-render0:arm64 (1.15-1) ... Setting up fontconfig-config (2.14.1-4) ... Setting up libxcb-glx0:arm64 (1.15-1) ... Setting up libedit2:arm64 (3.1-20221030-2) ... Setting up libreadline8:arm64 (8.2-1.3) ... Setting up libcommons-parent-java (56-1) ... Setting up libavahi-common3:arm64 (0.8-9) ... Setting up libncbi-vdb3:arm64 (3.0.2+dfsg-2) ... Setting up libcommons-logging-java (1.2-3) ... Setting up libnss3:arm64 (2:3.87.1-1) ... Setting up libxcb-shm0:arm64 (1.15-1) ... Setting up libldap-2.5-0:arm64 (2.5.13+dfsg-5) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up libnl-route-3-200:arm64 (3.7.0-0.2+b1) ... Setting up libxcb-present0:arm64 (1.15-1) ... Setting up dh-autoreconf (20) ... Setting up libcommons-jexl2-java (2.1.1-6) ... Setting up libthai0:arm64 (0.1.29-1) ... Setting up ca-certificates (20230311) ... Updating certificates in /etc/ssl/certs... 140 added, 0 removed; done. Setting up libfreetype6:arm64 (2.12.1+dfsg-4) ... Setting up libxcb-sync1:arm64 (1.15-1) ... Setting up shared-mime-info (2.2-1) ... Setting up libcommons-lang3-java (3.12.0-2) ... Setting up libxcb-dri2-0:arm64 (1.15-1) ... Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up libdrm2:arm64 (2.4.114-1+b1) ... Setting up dwz (0.15-1) ... Setting up groff-base (1.22.4-10) ... Setting up libxcb-randr0:arm64 (1.15-1) ... Setting up libllvm15:arm64 (1:15.0.6-4+b1) ... Setting up libx11-6:arm64 (2:1.8.4-2) ... Setting up libharfbuzz0b:arm64 (6.0.0+dfsg-3) ... Setting up libgdk-pixbuf-2.0-0:arm64 (2.42.10+dfsg-1+b1) ... Setting up libsnappy-java (1.1.8.3-1) ... Setting up libfontconfig1:arm64 (2.14.1-4) ... Setting up libcommons-codec-java (1.15-1) ... Setting up libxcomposite1:arm64 (1:0.4.5-1) ... Setting up libavahi-client3:arm64 (0.8-9) ... Setting up rsync (3.2.7-1) ... invoke-rc.d: could not determine current runlevel invoke-rc.d: policy-rc.d denied execution of start. Setting up libdrm-amdgpu1:arm64 (2.4.114-1+b1) ... Setting up libncbi-ngs3:arm64 (3.0.3+dfsg-5) ... Setting up libxcb-dri3-0:arm64 (1.15-1) ... Setting up gtk-update-icon-cache (3.24.37-2) ... Setting up libx11-xcb1:arm64 (2:1.8.4-2) ... Setting up libibverbs1:arm64 (44.0-2) ... Setting up fontconfig (2.14.1-4) ... Regenerating fonts cache... done. Setting up libngs-jni:arm64 (3.0.3+dfsg-5) ... Setting up libdrm-nouveau2:arm64 (2.4.114-1+b1) ... Setting up libxdamage1:arm64 (1:1.1.6-1) ... Setting up libxrender1:arm64 (1:0.9.10-1.1) ... Setting up libcommons-compress-java (1.22-1) ... Setting up ibverbs-providers:arm64 (44.0-2) ... Setting up libcommons-io-java (2.11.0-2) ... Setting up libdrm-radeon1:arm64 (2.4.114-1+b1) ... Setting up openssh-client (1:9.2p1-2) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libpython3.11-stdlib:arm64 (3.11.2-6) ... Setting up libpango-1.0-0:arm64 (1.50.12+ds-1) ... Setting up libgl1-mesa-dri:arm64 (22.3.6-1+deb12u1) ... Setting up libxext6:arm64 (2:1.3.4-1+b1) ... Setting up libcurl3-gnutls:arm64 (7.88.1-7) ... Setting up man-db (2.11.2-2) ... Not building database; man-db/auto-update is not 'true'. Setting up libcairo2:arm64 (1.16.0-7) ... Setting up libxxf86vm1:arm64 (1:1.1.4-1+b2) ... Setting up libxnvctrl0:arm64 (525.85.05-1) ... Setting up adwaita-icon-theme (43-1) ... update-alternatives: using /usr/share/icons/Adwaita/cursor.theme to provide /usr/share/icons/default/index.theme (x-cursor-theme) in auto mode Setting up libxfixes3:arm64 (1:6.0.0-2) ... Setting up libxinerama1:arm64 (2:1.1.4-3) ... Setting up libxrandr2:arm64 (2:1.5.2-2+b1) ... Setting up libcups2:arm64 (2.4.2-2) ... Setting up libhttpclient-java (4.5.14-1) ... Setting up liblightcouch-java (0.2.0-1) ... Setting up libngs-java:arm64 (3.0.3+dfsg-5) ... Setting up libpangoft2-1.0-0:arm64 (1.50.12+ds-1) ... Setting up libhtsjdk-java (3.0.4+dfsg-2) ... Setting up libpangocairo-1.0-0:arm64 (1.50.12+ds-1) ... Setting up libpython3-stdlib:arm64 (3.11.2-1) ... Setting up librdmacm1:arm64 (44.0-2) ... Setting up python3.11 (3.11.2-6) ... Setting up libucx0:arm64 (1.13.1-1) ... Setting up libhts3:arm64 (1.16+ds-3) ... Setting up libglx-mesa0:arm64 (22.3.6-1+deb12u1) ... Setting up libxi6:arm64 (2:1.8-1+b1) ... Setting up libglx0:arm64 (1.6.0-1) ... Setting up libxtst6:arm64 (2:1.2.3-1.1) ... Setting up liblog4j2-java (2.19.0-2) ... Setting up libxcursor1:arm64 (1:1.2.1-1) ... Setting up debhelper (13.11.4) ... Setting up python3 (3.11.2-1) ... Setting up libhwloc-plugins:arm64 (2.9.0-1) ... Setting up bowtie2 (2.5.0-3+b2) ... Setting up python3-packaging (23.0-1) ... Setting up libgl1:arm64 (1.6.0-1) ... Setting up python3-humanfriendly (10.0-3) ... Setting up python3-setproctitle:arm64 (1.3.1-1+b2) ... Setting up python3-pluggy (1.0.0+repack-1) ... Setting up python3-lib2to3 (3.11.2-2) ... Setting up python3-coloredlogs (15.0.1-1) ... Setting up libbarclay-java (4.1.0+dfsg-1) ... Setting up python3-pkg-resources (66.1.1-1) ... Setting up python3-distutils (3.11.2-2) ... Setting up dh-python (5.20230130) ... Setting up python3-more-itertools (8.10.0-2) ... Setting up python3-configargparse (1.5.3-1) ... Setting up libfabric1:arm64 (1.17.0-3) ... Setting up python3-iniconfig (1.1.1-2) ... Setting up python3-attr (22.2.0-1) ... Setting up python3-pysam (0.20.0+ds-3+b1) ... Setting up python3-setuptools (66.1.1-1) ... Setting up python3-py (1.11.0-1) ... Setting up libpmix2:arm64 (4.2.2-1+b1) ... Setting up libgkl-java (0.8.10+dfsg-3) ... Setting up python3-pytest (7.2.1-2) ... Setting up libgtk2.0-0:arm64 (2.24.33-2) ... Setting up libopenmpi3:arm64 (4.1.4-3+b1) ... Setting up python3-ruamel.yaml.clib:arm64 (0.2.7-1+b2) ... Setting up libpicard-java (2.27.5+dfsg-2) ... Setting up python3-ruamel.yaml (0.17.21-1) ... Setting up openmpi-bin (4.1.4-3+b1) ... update-alternatives: using /usr/bin/mpirun.openmpi to provide /usr/bin/mpirun (mpirun) in auto mode update-alternatives: using /usr/bin/mpicc.openmpi to provide /usr/bin/mpicc (mpi) in auto mode Setting up examl (3.0.22-3+b2) ... Setting up default-jre-headless (2:1.17-74) ... Setting up openjdk-17-jre-headless:arm64 (17.0.6+10-1) ... update-alternatives: using /usr/lib/jvm/java-17-openjdk-arm64/bin/java to provide /usr/bin/java (java) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-arm64/bin/jpackage to provide /usr/bin/jpackage (jpackage) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-arm64/bin/keytool to provide /usr/bin/keytool (keytool) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-arm64/bin/rmiregistry to provide /usr/bin/rmiregistry (rmiregistry) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-arm64/lib/jexec to provide /usr/bin/jexec (jexec) in auto mode Setting up ca-certificates-java (20230103) ... Adding debian:ACCVRAIZ1.pem Adding debian:AC_RAIZ_FNMT-RCM.pem Adding debian:AC_RAIZ_FNMT-RCM_SERVIDORES_SEGUROS.pem Adding debian:ANF_Secure_Server_Root_CA.pem Adding debian:Actalis_Authentication_Root_CA.pem Adding debian:AffirmTrust_Commercial.pem Adding debian:AffirmTrust_Networking.pem Adding debian:AffirmTrust_Premium.pem Adding debian:AffirmTrust_Premium_ECC.pem Adding debian:Amazon_Root_CA_1.pem Adding debian:Amazon_Root_CA_2.pem Adding debian:Amazon_Root_CA_3.pem Adding debian:Amazon_Root_CA_4.pem Adding debian:Atos_TrustedRoot_2011.pem Adding debian:Autoridad_de_Certificacion_Firmaprofesional_CIF_A62634068.pem Adding debian:Autoridad_de_Certificacion_Firmaprofesional_CIF_A62634068_2.pem Adding debian:Baltimore_CyberTrust_Root.pem Adding debian:Buypass_Class_2_Root_CA.pem Adding debian:Buypass_Class_3_Root_CA.pem Adding debian:CA_Disig_Root_R2.pem Adding debian:CFCA_EV_ROOT.pem Adding debian:COMODO_Certification_Authority.pem Adding debian:COMODO_ECC_Certification_Authority.pem Adding debian:COMODO_RSA_Certification_Authority.pem Adding debian:Certainly_Root_E1.pem Adding debian:Certainly_Root_R1.pem Adding debian:Certigna.pem Adding debian:Certigna_Root_CA.pem Adding debian:Certum_EC-384_CA.pem Adding debian:Certum_Trusted_Network_CA.pem Adding debian:Certum_Trusted_Network_CA_2.pem Adding debian:Certum_Trusted_Root_CA.pem Adding debian:Comodo_AAA_Services_root.pem Adding debian:D-TRUST_BR_Root_CA_1_2020.pem Adding debian:D-TRUST_EV_Root_CA_1_2020.pem Adding debian:D-TRUST_Root_Class_3_CA_2_2009.pem Adding debian:D-TRUST_Root_Class_3_CA_2_EV_2009.pem Adding debian:DigiCert_Assured_ID_Root_CA.pem Adding debian:DigiCert_Assured_ID_Root_G2.pem Adding debian:DigiCert_Assured_ID_Root_G3.pem Adding debian:DigiCert_Global_Root_CA.pem Adding debian:DigiCert_Global_Root_G2.pem Adding debian:DigiCert_Global_Root_G3.pem Adding debian:DigiCert_High_Assurance_EV_Root_CA.pem Adding debian:DigiCert_TLS_ECC_P384_Root_G5.pem Adding debian:DigiCert_TLS_RSA4096_Root_G5.pem Adding debian:DigiCert_Trusted_Root_G4.pem Adding debian:E-Tugra_Certification_Authority.pem Adding debian:E-Tugra_Global_Root_CA_ECC_v3.pem Adding debian:E-Tugra_Global_Root_CA_RSA_v3.pem Adding debian:Entrust.net_Premium_2048_Secure_Server_CA.pem Adding debian:Entrust_Root_Certification_Authority.pem Adding debian:Entrust_Root_Certification_Authority_-_EC1.pem Adding debian:Entrust_Root_Certification_Authority_-_G2.pem Adding debian:Entrust_Root_Certification_Authority_-_G4.pem Adding debian:GDCA_TrustAUTH_R5_ROOT.pem Adding debian:GLOBALTRUST_2020.pem Adding debian:GTS_Root_R1.pem Adding debian:GTS_Root_R2.pem Adding debian:GTS_Root_R3.pem Adding debian:GTS_Root_R4.pem Adding debian:GlobalSign_ECC_Root_CA_-_R4.pem Adding debian:GlobalSign_ECC_Root_CA_-_R5.pem Adding debian:GlobalSign_Root_CA.pem Adding debian:GlobalSign_Root_CA_-_R3.pem Adding debian:GlobalSign_Root_CA_-_R6.pem Adding debian:GlobalSign_Root_E46.pem Adding debian:GlobalSign_Root_R46.pem Adding debian:Go_Daddy_Class_2_CA.pem Adding debian:Go_Daddy_Root_Certificate_Authority_-_G2.pem Adding debian:HARICA_TLS_ECC_Root_CA_2021.pem Adding debian:HARICA_TLS_RSA_Root_CA_2021.pem Adding debian:Hellenic_Academic_and_Research_Institutions_ECC_RootCA_2015.pem Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2015.pem Adding debian:HiPKI_Root_CA_-_G1.pem Adding debian:Hongkong_Post_Root_CA_1.pem Adding debian:Hongkong_Post_Root_CA_3.pem Adding debian:ISRG_Root_X1.pem Adding debian:ISRG_Root_X2.pem Adding debian:IdenTrust_Commercial_Root_CA_1.pem Adding debian:IdenTrust_Public_Sector_Root_CA_1.pem Adding debian:Izenpe.com.pem Adding debian:Microsec_e-Szigno_Root_CA_2009.pem Adding debian:Microsoft_ECC_Root_Certificate_Authority_2017.pem Adding debian:Microsoft_RSA_Root_Certificate_Authority_2017.pem Adding debian:NAVER_Global_Root_Certification_Authority.pem Adding debian:NetLock_Arany_=Class_Gold=_Főtanúsítvány.pem Adding debian:OISTE_WISeKey_Global_Root_GB_CA.pem Adding debian:OISTE_WISeKey_Global_Root_GC_CA.pem Adding debian:QuoVadis_Root_CA_1_G3.pem Adding debian:QuoVadis_Root_CA_2.pem Adding debian:QuoVadis_Root_CA_2_G3.pem Adding debian:QuoVadis_Root_CA_3.pem Adding debian:QuoVadis_Root_CA_3_G3.pem Adding debian:SSL.com_EV_Root_Certification_Authority_ECC.pem Adding debian:SSL.com_EV_Root_Certification_Authority_RSA_R2.pem Adding debian:SSL.com_Root_Certification_Authority_ECC.pem Adding debian:SSL.com_Root_Certification_Authority_RSA.pem Adding debian:SZAFIR_ROOT_CA2.pem Adding debian:SecureSign_RootCA11.pem Adding debian:SecureTrust_CA.pem Adding debian:Secure_Global_CA.pem Adding debian:Security_Communication_ECC_RootCA1.pem Adding debian:Security_Communication_RootCA2.pem Adding debian:Security_Communication_RootCA3.pem Adding debian:Security_Communication_Root_CA.pem Adding debian:Starfield_Class_2_CA.pem Adding debian:Starfield_Root_Certificate_Authority_-_G2.pem Adding debian:Starfield_Services_Root_Certificate_Authority_-_G2.pem Adding debian:SwissSign_Gold_CA_-_G2.pem Adding debian:SwissSign_Silver_CA_-_G2.pem Adding debian:T-TeleSec_GlobalRoot_Class_2.pem Adding debian:T-TeleSec_GlobalRoot_Class_3.pem Adding debian:TUBITAK_Kamu_SM_SSL_Kok_Sertifikasi_-_Surum_1.pem Adding debian:TWCA_Global_Root_CA.pem Adding debian:TWCA_Root_Certification_Authority.pem Adding debian:TeliaSonera_Root_CA_v1.pem Adding debian:Telia_Root_CA_v2.pem Adding debian:TrustCor_ECA-1.pem Adding debian:TrustCor_RootCert_CA-1.pem Adding debian:TrustCor_RootCert_CA-2.pem Adding debian:Trustwave_Global_Certification_Authority.pem Adding debian:Trustwave_Global_ECC_P256_Certification_Authority.pem Adding debian:Trustwave_Global_ECC_P384_Certification_Authority.pem Adding debian:TunTrust_Root_CA.pem Adding debian:UCA_Extended_Validation_Root.pem Adding debian:UCA_Global_G2_Root.pem Adding debian:USERTrust_ECC_Certification_Authority.pem Adding debian:USERTrust_RSA_Certification_Authority.pem Adding debian:XRamp_Global_CA_Root.pem Adding debian:certSIGN_ROOT_CA.pem Adding debian:certSIGN_Root_CA_G2.pem Adding debian:e-Szigno_Root_CA_2017.pem Adding debian:ePKI_Root_Certification_Authority.pem Adding debian:emSign_ECC_Root_CA_-_C3.pem Adding debian:emSign_ECC_Root_CA_-_G3.pem Adding debian:emSign_Root_CA_-_C1.pem Adding debian:emSign_Root_CA_-_G1.pem Adding debian:vTrus_ECC_Root_CA.pem Adding debian:vTrus_Root_CA.pem done. Setting up openjdk-17-jre:arm64 (17.0.6+10-1) ... Setting up default-jre (2:1.17-74) ... Setting up picard-tools (2.27.5+dfsg-2) ... Processing triggers for libc-bin (2.36-8) ... Processing triggers for ca-certificates (20230311) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. Processing triggers for ca-certificates-java (20230103) ... done. Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/paleomix-1.3.7/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../paleomix_1.3.7-3_source.changes dpkg-buildpackage: info: source package paleomix dpkg-buildpackage: info: source version 1.3.7-3 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Étienne Mollier dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 debian/rules clean dh clean --with python3 --buildsystem=pybuild dh_auto_clean -O--buildsystem=pybuild I: pybuild base:240: python3.11 setup.py clean running clean removing '/build/paleomix-1.3.7/.pybuild/cpython3_3.11/build' (and everything under it) 'build/bdist.linux-arm64' does not exist -- can't clean it 'build/scripts-3.11' does not exist -- can't clean it dh_autoreconf_clean -O--buildsystem=pybuild dh_clean -O--buildsystem=pybuild debian/rules binary dh binary --with python3 --buildsystem=pybuild dh_update_autotools_config -O--buildsystem=pybuild dh_autoreconf -O--buildsystem=pybuild dh_auto_configure -O--buildsystem=pybuild I: pybuild base:240: python3.11 setup.py config running config dh_auto_build -O--buildsystem=pybuild I: pybuild base:240: /usr/bin/python3 setup.py build running build running build_py creating /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix copying paleomix/yaml.py -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix copying paleomix/pipeline.py -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix copying paleomix/nodegraph.py -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix copying paleomix/node.py -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix copying paleomix/main.py -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix copying paleomix/__init__.py -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix creating /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/tools copying paleomix/tools/vcf_to_fasta.py -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/tools copying paleomix/tools/vcf_filter.py -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/tools copying paleomix/tools/validate_fastq.py -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/tools copying paleomix/tools/rmdup_collapsed.py -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/tools copying paleomix/tools/gtf_to_bed.py -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/tools copying paleomix/tools/factory.py -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/tools copying paleomix/tools/dupcheck.py -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/tools copying paleomix/tools/depths.py -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/tools copying paleomix/tools/coverage.py -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/tools copying paleomix/tools/cleanup.py -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/tools copying paleomix/tools/__init__.py -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/tools creating /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/resources copying paleomix/resources/__init__.py -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/resources creating /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines copying paleomix/pipelines/__init__.py -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines creating /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/nodes copying paleomix/nodes/validation.py -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/nodes copying paleomix/nodes/sequences.py -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/nodes copying paleomix/nodes/samtools.py -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/nodes copying paleomix/nodes/raxml.py -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/nodes copying paleomix/nodes/picard.py -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/nodes copying paleomix/nodes/phylip.py -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/nodes copying paleomix/nodes/newick.py -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/nodes copying paleomix/nodes/mapdamage.py -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/nodes copying paleomix/nodes/mafft.py -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/nodes copying paleomix/nodes/formats.py -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/nodes copying paleomix/nodes/examl.py -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/nodes copying paleomix/nodes/commands.py -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/nodes copying paleomix/nodes/bwa.py -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/nodes copying paleomix/nodes/bowtie2.py -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/nodes copying paleomix/nodes/bedtools.py -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/nodes copying paleomix/nodes/adapterremoval.py -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/nodes copying paleomix/nodes/__init__.py -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/nodes creating /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/common copying paleomix/common/versions.py -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/common copying paleomix/common/vcfwrap.py -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/common copying paleomix/common/vcffilter.py -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/common copying paleomix/common/utilities.py -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/common copying paleomix/common/timer.py -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/common copying paleomix/common/text.py -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/common copying paleomix/common/testing.py -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/common copying paleomix/common/system.py -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/common copying paleomix/common/sequences.py -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/common copying paleomix/common/sampling.py -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/common copying paleomix/common/rtools.py -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/common copying paleomix/common/procs.py -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/common copying paleomix/common/makefile.py -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/common copying paleomix/common/logging.py -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/common copying paleomix/common/fileutils.py -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/common copying paleomix/common/bedtools.py -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/common copying paleomix/common/bamfiles.py -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/common copying paleomix/common/argparse.py -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/common copying paleomix/common/__init__.py -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/common creating /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/atomiccmd copying paleomix/atomiccmd/sets.py -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/atomiccmd copying paleomix/atomiccmd/pprint.py -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/atomiccmd copying paleomix/atomiccmd/command.py -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/atomiccmd copying paleomix/atomiccmd/builder.py -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/atomiccmd copying paleomix/atomiccmd/__init__.py -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/atomiccmd creating /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/tools/bam_stats copying paleomix/tools/bam_stats/coverage.py -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/tools/bam_stats copying paleomix/tools/bam_stats/common.py -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/tools/bam_stats copying paleomix/tools/bam_stats/__init__.py -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/tools/bam_stats creating /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/zonkey copying paleomix/pipelines/zonkey/pipeline.py -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/zonkey copying paleomix/pipelines/zonkey/database.py -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/zonkey copying paleomix/pipelines/zonkey/config.py -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/zonkey copying paleomix/pipelines/zonkey/common.py -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/zonkey copying paleomix/pipelines/zonkey/build_tped.py -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/zonkey copying paleomix/pipelines/zonkey/build_mito.py -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/zonkey copying paleomix/pipelines/zonkey/build_db.py -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/zonkey copying paleomix/pipelines/zonkey/__init__.py -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/zonkey creating /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/phylo copying paleomix/pipelines/phylo/pipeline.py -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/phylo copying paleomix/pipelines/phylo/mkfile.py -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/phylo copying paleomix/pipelines/phylo/makefile.py -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/phylo copying paleomix/pipelines/phylo/example.py -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/phylo copying paleomix/pipelines/phylo/config.py -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/phylo copying paleomix/pipelines/phylo/__init__.py -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/phylo creating /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/bam copying paleomix/pipelines/bam/trim_pipeline.py -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/bam copying paleomix/pipelines/bam/pipeline.py -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/bam copying paleomix/pipelines/bam/paths.py -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/bam copying paleomix/pipelines/bam/nodes.py -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/bam copying paleomix/pipelines/bam/mkfile.py -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/bam copying paleomix/pipelines/bam/makefile.py -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/bam copying paleomix/pipelines/bam/config.py -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/bam copying paleomix/pipelines/bam/__init__.py -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/bam creating /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/zonkey/parts copying paleomix/pipelines/zonkey/parts/summary.py -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/zonkey/parts copying paleomix/pipelines/zonkey/parts/report.py -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/zonkey/parts copying paleomix/pipelines/zonkey/parts/nuclear.py -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/zonkey/parts copying paleomix/pipelines/zonkey/parts/mitochondria.py -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/zonkey/parts copying paleomix/pipelines/zonkey/parts/common.py -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/zonkey/parts copying paleomix/pipelines/zonkey/parts/admixture.py -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/zonkey/parts copying paleomix/pipelines/zonkey/parts/__init__.py -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/zonkey/parts creating /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/phylo/parts copying paleomix/pipelines/phylo/parts/phylo.py -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/phylo/parts copying paleomix/pipelines/phylo/parts/msa.py -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/phylo/parts copying paleomix/pipelines/phylo/parts/genotype.py -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/phylo/parts copying paleomix/pipelines/phylo/parts/__init__.py -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/phylo/parts creating /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/bam/parts copying paleomix/pipelines/bam/parts/target.py -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/bam/parts copying paleomix/pipelines/bam/parts/summary.py -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/bam/parts copying paleomix/pipelines/bam/parts/statistics.py -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/bam/parts copying paleomix/pipelines/bam/parts/sample.py -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/bam/parts copying paleomix/pipelines/bam/parts/reads.py -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/bam/parts copying paleomix/pipelines/bam/parts/prefix.py -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/bam/parts copying paleomix/pipelines/bam/parts/library.py -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/bam/parts copying paleomix/pipelines/bam/parts/lane.py -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/bam/parts copying paleomix/pipelines/bam/parts/__init__.py -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/bam/parts creating /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/common/formats copying paleomix/common/formats/phylip.py -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/common/formats copying paleomix/common/formats/newick.py -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/common/formats copying paleomix/common/formats/msa.py -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/common/formats copying paleomix/common/formats/fastq.py -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/common/formats copying paleomix/common/formats/fasta.py -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/common/formats copying paleomix/common/formats/_graph.py -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/common/formats copying paleomix/common/formats/_common.py -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/common/formats copying paleomix/common/formats/__init__.py -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/common/formats running egg_info creating paleomix.egg-info writing paleomix.egg-info/PKG-INFO writing dependency_links to paleomix.egg-info/dependency_links.txt writing entry points to paleomix.egg-info/entry_points.txt writing requirements to paleomix.egg-info/requires.txt writing top-level names to paleomix.egg-info/top_level.txt writing manifest file 'paleomix.egg-info/SOURCES.txt' reading manifest file 'paleomix.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no files found matching 'paleomix/yaml/CHANGES' warning: no files found matching 'paleomix/yaml/LICENSE' warning: no files found matching 'paleomix/yaml/PKG-INFO' warning: no files found matching 'paleomix/yaml/README' warning: no files found matching 'pylint.conf' adding license file 'LICENSE' writing manifest file 'paleomix.egg-info/SOURCES.txt' /usr/lib/python3/dist-packages/setuptools/command/build_py.py:202: SetuptoolsDeprecationWarning: Installing 'paleomix.resources.examples.bam_pipeline' as data is deprecated, please list it in `packages`. !! ############################ # Package would be ignored # ############################ Python recognizes 'paleomix.resources.examples.bam_pipeline' as an importable package, but it is not listed in the `packages` configuration of setuptools. 'paleomix.resources.examples.bam_pipeline' has been automatically added to the distribution only because it may contain data files, but this behavior is likely to change in future versions of setuptools (and therefore is considered deprecated). Please make sure that 'paleomix.resources.examples.bam_pipeline' is included as a package by using the `packages` configuration field or the proper discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" and "data files" on setuptools documentation page. !! check.warn(importable) /usr/lib/python3/dist-packages/setuptools/command/build_py.py:202: SetuptoolsDeprecationWarning: Installing 'paleomix.resources.examples.bam_pipeline.data' as data is deprecated, please list it in `packages`. !! ############################ # Package would be ignored # ############################ Python recognizes 'paleomix.resources.examples.bam_pipeline.data' as an importable package, but it is not listed in the `packages` configuration of setuptools. 'paleomix.resources.examples.bam_pipeline.data' has been automatically added to the distribution only because it may contain data files, but this behavior is likely to change in future versions of setuptools (and therefore is considered deprecated). Please make sure that 'paleomix.resources.examples.bam_pipeline.data' is included as a package by using the `packages` configuration field or the proper discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" and "data files" on setuptools documentation page. !! check.warn(importable) /usr/lib/python3/dist-packages/setuptools/command/build_py.py:202: SetuptoolsDeprecationWarning: Installing 'paleomix.resources.examples.bam_pipeline.data.ACGATA_L2' as data is deprecated, please list it in `packages`. !! ############################ # Package would be ignored # ############################ Python recognizes 'paleomix.resources.examples.bam_pipeline.data.ACGATA_L2' as an importable package, but it is not listed in the `packages` configuration of setuptools. 'paleomix.resources.examples.bam_pipeline.data.ACGATA_L2' has been automatically added to the distribution only because it may contain data files, but this behavior is likely to change in future versions of setuptools (and therefore is considered deprecated). Please make sure that 'paleomix.resources.examples.bam_pipeline.data.ACGATA_L2' is included as a package by using the `packages` configuration field or the proper discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" and "data files" on setuptools documentation page. !! check.warn(importable) /usr/lib/python3/dist-packages/setuptools/command/build_py.py:202: SetuptoolsDeprecationWarning: Installing 'paleomix.resources.examples.bam_pipeline.prefixes' as data is deprecated, please list it in `packages`. !! ############################ # Package would be ignored # ############################ Python recognizes 'paleomix.resources.examples.bam_pipeline.prefixes' as an importable package, but it is not listed in the `packages` configuration of setuptools. 'paleomix.resources.examples.bam_pipeline.prefixes' has been automatically added to the distribution only because it may contain data files, but this behavior is likely to change in future versions of setuptools (and therefore is considered deprecated). Please make sure that 'paleomix.resources.examples.bam_pipeline.prefixes' is included as a package by using the `packages` configuration field or the proper discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" and "data files" on setuptools documentation page. !! check.warn(importable) /usr/lib/python3/dist-packages/setuptools/command/build_py.py:202: SetuptoolsDeprecationWarning: Installing 'paleomix.resources.examples.phylo_pipeline' as data is deprecated, please list it in `packages`. !! ############################ # Package would be ignored # ############################ Python recognizes 'paleomix.resources.examples.phylo_pipeline' as an importable package, but it is not listed in the `packages` configuration of setuptools. 'paleomix.resources.examples.phylo_pipeline' has been automatically added to the distribution only because it may contain data files, but this behavior is likely to change in future versions of setuptools (and therefore is considered deprecated). Please make sure that 'paleomix.resources.examples.phylo_pipeline' is included as a package by using the `packages` configuration field or the proper discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" and "data files" on setuptools documentation page. !! check.warn(importable) /usr/lib/python3/dist-packages/setuptools/command/build_py.py:202: SetuptoolsDeprecationWarning: Installing 'paleomix.resources.examples.phylo_pipeline.alignment' as data is deprecated, please list it in `packages`. !! ############################ # Package would be ignored # ############################ Python recognizes 'paleomix.resources.examples.phylo_pipeline.alignment' as an importable package, but it is not listed in the `packages` configuration of setuptools. 'paleomix.resources.examples.phylo_pipeline.alignment' has been automatically added to the distribution only because it may contain data files, but this behavior is likely to change in future versions of setuptools (and therefore is considered deprecated). Please make sure that 'paleomix.resources.examples.phylo_pipeline.alignment' is included as a package by using the `packages` configuration field or the proper discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" and "data files" on setuptools documentation page. !! check.warn(importable) /usr/lib/python3/dist-packages/setuptools/command/build_py.py:202: SetuptoolsDeprecationWarning: Installing 'paleomix.resources.examples.phylo_pipeline.alignment.prefixes' as data is deprecated, please list it in `packages`. !! ############################ # Package would be ignored # ############################ Python recognizes 'paleomix.resources.examples.phylo_pipeline.alignment.prefixes' as an importable package, but it is not listed in the `packages` configuration of setuptools. 'paleomix.resources.examples.phylo_pipeline.alignment.prefixes' has been automatically added to the distribution only because it may contain data files, but this behavior is likely to change in future versions of setuptools (and therefore is considered deprecated). Please make sure that 'paleomix.resources.examples.phylo_pipeline.alignment.prefixes' is included as a package by using the `packages` configuration field or the proper discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" and "data files" on setuptools documentation page. !! check.warn(importable) /usr/lib/python3/dist-packages/setuptools/command/build_py.py:202: SetuptoolsDeprecationWarning: Installing 'paleomix.resources.examples.phylo_pipeline.phylogeny' as data is deprecated, please list it in `packages`. !! ############################ # Package would be ignored # ############################ Python recognizes 'paleomix.resources.examples.phylo_pipeline.phylogeny' as an importable package, but it is not listed in the `packages` configuration of setuptools. 'paleomix.resources.examples.phylo_pipeline.phylogeny' has been automatically added to the distribution only because it may contain data files, but this behavior is likely to change in future versions of setuptools (and therefore is considered deprecated). Please make sure that 'paleomix.resources.examples.phylo_pipeline.phylogeny' is included as a package by using the `packages` configuration field or the proper discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" and "data files" on setuptools documentation page. !! check.warn(importable) /usr/lib/python3/dist-packages/setuptools/command/build_py.py:202: SetuptoolsDeprecationWarning: Installing 'paleomix.resources.examples.phylo_pipeline.phylogeny.data.regions' as data is deprecated, please list it in `packages`. !! ############################ # Package would be ignored # ############################ Python recognizes 'paleomix.resources.examples.phylo_pipeline.phylogeny.data.regions' as an importable package, but it is not listed in the `packages` configuration of setuptools. 'paleomix.resources.examples.phylo_pipeline.phylogeny.data.regions' has been automatically added to the distribution only because it may contain data files, but this behavior is likely to change in future versions of setuptools (and therefore is considered deprecated). Please make sure that 'paleomix.resources.examples.phylo_pipeline.phylogeny.data.regions' is included as a package by using the `packages` configuration field or the proper discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" and "data files" on setuptools documentation page. !! check.warn(importable) /usr/lib/python3/dist-packages/setuptools/command/build_py.py:202: SetuptoolsDeprecationWarning: Installing 'paleomix.resources.reports.zonkey' as data is deprecated, please list it in `packages`. !! ############################ # Package would be ignored # ############################ Python recognizes 'paleomix.resources.reports.zonkey' as an importable package, but it is not listed in the `packages` configuration of setuptools. 'paleomix.resources.reports.zonkey' has been automatically added to the distribution only because it may contain data files, but this behavior is likely to change in future versions of setuptools (and therefore is considered deprecated). Please make sure that 'paleomix.resources.reports.zonkey' is included as a package by using the `packages` configuration field or the proper discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" and "data files" on setuptools documentation page. !! check.warn(importable) /usr/lib/python3/dist-packages/setuptools/command/build_py.py:202: SetuptoolsDeprecationWarning: Installing 'paleomix.resources.rscripts.common' as data is deprecated, please list it in `packages`. !! ############################ # Package would be ignored # ############################ Python recognizes 'paleomix.resources.rscripts.common' as an importable package, but it is not listed in the `packages` configuration of setuptools. 'paleomix.resources.rscripts.common' has been automatically added to the distribution only because it may contain data files, but this behavior is likely to change in future versions of setuptools (and therefore is considered deprecated). Please make sure that 'paleomix.resources.rscripts.common' is included as a package by using the `packages` configuration field or the proper discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" and "data files" on setuptools documentation page. !! check.warn(importable) /usr/lib/python3/dist-packages/setuptools/command/build_py.py:202: SetuptoolsDeprecationWarning: Installing 'paleomix.resources.rscripts.zonkey' as data is deprecated, please list it in `packages`. !! ############################ # Package would be ignored # ############################ Python recognizes 'paleomix.resources.rscripts.zonkey' as an importable package, but it is not listed in the `packages` configuration of setuptools. 'paleomix.resources.rscripts.zonkey' has been automatically added to the distribution only because it may contain data files, but this behavior is likely to change in future versions of setuptools (and therefore is considered deprecated). Please make sure that 'paleomix.resources.rscripts.zonkey' is included as a package by using the `packages` configuration field or the proper discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" and "data files" on setuptools documentation page. !! check.warn(importable) creating /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/resources/examples creating /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/resources/examples/bam_pipeline copying paleomix/resources/examples/bam_pipeline/makefile.yaml -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/resources/examples/bam_pipeline creating /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/resources/examples/bam_pipeline/data copying paleomix/resources/examples/bam_pipeline/data/ACGATA_L1_R1_01.fastq.gz -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/resources/examples/bam_pipeline/data copying paleomix/resources/examples/bam_pipeline/data/ACGATA_L1_R1_02.fastq.gz -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/resources/examples/bam_pipeline/data copying paleomix/resources/examples/bam_pipeline/data/ACGATA_L1_R1_03.fastq.gz -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/resources/examples/bam_pipeline/data copying paleomix/resources/examples/bam_pipeline/data/ACGATA_L1_R1_04.fastq.gz -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/resources/examples/bam_pipeline/data copying paleomix/resources/examples/bam_pipeline/data/ACGATA_L1_R2_01.fastq.gz -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/resources/examples/bam_pipeline/data copying paleomix/resources/examples/bam_pipeline/data/ACGATA_L1_R2_02.fastq.gz -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/resources/examples/bam_pipeline/data copying paleomix/resources/examples/bam_pipeline/data/ACGATA_L1_R2_03.fastq.gz -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/resources/examples/bam_pipeline/data copying paleomix/resources/examples/bam_pipeline/data/ACGATA_L1_R2_04.fastq.gz -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/resources/examples/bam_pipeline/data copying paleomix/resources/examples/bam_pipeline/data/GCTCTG_L1_R1_01.fastq.gz -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/resources/examples/bam_pipeline/data copying paleomix/resources/examples/bam_pipeline/data/GCTCTG_L1_R1_02.fastq.gz -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/resources/examples/bam_pipeline/data copying paleomix/resources/examples/bam_pipeline/data/GCTCTG_L1_R1_03.fastq.gz -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/resources/examples/bam_pipeline/data copying paleomix/resources/examples/bam_pipeline/data/TGCTCA_L1_R1_01.fastq.gz -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/resources/examples/bam_pipeline/data copying paleomix/resources/examples/bam_pipeline/data/TGCTCA_L1_R1_02.fastq.gz -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/resources/examples/bam_pipeline/data copying paleomix/resources/examples/bam_pipeline/data/TGCTCA_L1_R1_03.fastq.gz -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/resources/examples/bam_pipeline/data copying paleomix/resources/examples/bam_pipeline/data/TGCTCA_L2_R1_01.fastq.gz -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/resources/examples/bam_pipeline/data copying paleomix/resources/examples/bam_pipeline/data/TGCTCA_L2_R1_02.fastq.gz -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/resources/examples/bam_pipeline/data copying paleomix/resources/examples/bam_pipeline/data/TGCTCA_L2_R1_03.fastq.gz -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/resources/examples/bam_pipeline/data copying paleomix/resources/examples/bam_pipeline/data/TGCTCA_L2_R2_01.fastq.gz -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/resources/examples/bam_pipeline/data copying paleomix/resources/examples/bam_pipeline/data/TGCTCA_L2_R2_02.fastq.gz -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/resources/examples/bam_pipeline/data copying paleomix/resources/examples/bam_pipeline/data/TGCTCA_L2_R2_03.fastq.gz -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/resources/examples/bam_pipeline/data creating /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/resources/examples/bam_pipeline/data/ACGATA_L2 copying paleomix/resources/examples/bam_pipeline/data/ACGATA_L2/reads.collapsed.gz -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/resources/examples/bam_pipeline/data/ACGATA_L2 copying paleomix/resources/examples/bam_pipeline/data/ACGATA_L2/reads.collapsed.truncated.gz -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/resources/examples/bam_pipeline/data/ACGATA_L2 copying paleomix/resources/examples/bam_pipeline/data/ACGATA_L2/reads.singleton.truncated.gz -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/resources/examples/bam_pipeline/data/ACGATA_L2 creating /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/resources/examples/bam_pipeline/prefixes copying paleomix/resources/examples/bam_pipeline/prefixes/rCRS.fasta -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/resources/examples/bam_pipeline/prefixes creating /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/resources/examples/phylo_pipeline copying paleomix/resources/examples/phylo_pipeline/setup.sh -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/resources/examples/phylo_pipeline copying paleomix/resources/examples/phylo_pipeline/synthesize_reads.py -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/resources/examples/phylo_pipeline creating /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/resources/examples/phylo_pipeline/alignment copying paleomix/resources/examples/phylo_pipeline/alignment/makefile.yaml -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/resources/examples/phylo_pipeline/alignment copying paleomix/resources/examples/phylo_pipeline/alignment/setup.sh -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/resources/examples/phylo_pipeline/alignment creating /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/resources/examples/phylo_pipeline/alignment/prefixes copying paleomix/resources/examples/phylo_pipeline/alignment/prefixes/bonobo.fasta -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/resources/examples/phylo_pipeline/alignment/prefixes copying paleomix/resources/examples/phylo_pipeline/alignment/prefixes/chimpanzee.fasta -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/resources/examples/phylo_pipeline/alignment/prefixes copying paleomix/resources/examples/phylo_pipeline/alignment/prefixes/gorilla.fasta -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/resources/examples/phylo_pipeline/alignment/prefixes copying paleomix/resources/examples/phylo_pipeline/alignment/prefixes/rCRS.fasta -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/resources/examples/phylo_pipeline/alignment/prefixes copying paleomix/resources/examples/phylo_pipeline/alignment/prefixes/rCRS.fasta.fai -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/resources/examples/phylo_pipeline/alignment/prefixes copying paleomix/resources/examples/phylo_pipeline/alignment/prefixes/sumatran_orangutan.fasta -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/resources/examples/phylo_pipeline/alignment/prefixes copying paleomix/resources/examples/phylo_pipeline/alignment/prefixes/white_handed_gibbon.fasta -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/resources/examples/phylo_pipeline/alignment/prefixes creating /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/resources/examples/phylo_pipeline/phylogeny copying paleomix/resources/examples/phylo_pipeline/phylogeny/makefile.yaml -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/resources/examples/phylo_pipeline/phylogeny creating /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/resources/examples/phylo_pipeline/phylogeny/data creating /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/resources/examples/phylo_pipeline/phylogeny/data/regions copying paleomix/resources/examples/phylo_pipeline/phylogeny/data/regions/rCRS.non_coding.bed -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/resources/examples/phylo_pipeline/phylogeny/data/regions copying paleomix/resources/examples/phylo_pipeline/phylogeny/data/regions/rCRS.protein_coding.CDS.bed -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/resources/examples/phylo_pipeline/phylogeny/data/regions creating /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/resources/reports creating /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/resources/reports/zonkey copying paleomix/resources/reports/zonkey/report.css -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/resources/reports/zonkey creating /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/resources/rscripts creating /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/resources/rscripts/common copying paleomix/resources/rscripts/common/requires.r -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/resources/rscripts/common creating /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/resources/rscripts/zonkey copying paleomix/resources/rscripts/zonkey/admixture.r -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/resources/rscripts/zonkey copying paleomix/resources/rscripts/zonkey/coverage.r -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/resources/rscripts/zonkey copying paleomix/resources/rscripts/zonkey/pca.r -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/resources/rscripts/zonkey copying paleomix/resources/rscripts/zonkey/tinytree.r -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/resources/rscripts/zonkey copying paleomix/resources/rscripts/zonkey/treemix.r -> /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/resources/rscripts/zonkey debian/rules override_dh_auto_test make[1]: Entering directory '/build/paleomix-1.3.7' PATH=/build/paleomix-1.3.7/bin/:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games dh_auto_test I: pybuild pybuild:307: cp -a README.rst /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build; I: pybuild base:240: cd /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build; python3.11 -m pytest tests ============================= test session starts ============================== platform linux -- Python 3.11.2, pytest-7.2.1, pluggy-1.0.0+repack rootdir: /build/paleomix-1.3.7, configfile: setup.cfg collected 1494 items tests/node_test.py ..................................................... [ 3%] ......................................... [ 6%] tests/nodegraph_test.py ......... [ 6%] tests/atomiccmd_test/builder_test.py ................................... [ 9%] ...................................................... [ 12%] tests/atomiccmd_test/command_test.py ................................... [ 15%] ........................................................................ [ 20%] ................ [ 21%] tests/atomiccmd_test/pprint_test.py .................................... [ 23%] .. [ 23%] tests/atomiccmd_test/sets_test.py ...................................... [ 26%] ............ [ 26%] tests/common_tests/bedtools_test.py ............................... [ 29%] tests/common_tests/fileutils_test.py ................................... [ 31%] ...................................................................... [ 36%] tests/common_tests/makefile_test.py .................................... [ 38%] ........................................................................ [ 43%] ........................................................................ [ 48%] ........................................................................ [ 52%] ........................................................................ [ 57%] ............................... [ 59%] tests/common_tests/sampling_test.py ........................ [ 61%] tests/common_tests/sequences_test.py ................................... [ 63%] ............... [ 64%] tests/common_tests/text_test.py ....................................... [ 67%] tests/common_tests/utilities_test.py ................................... [ 69%] ........................................................................ [ 74%] .. [ 74%] tests/common_tests/versions_test.py .................................... [ 77%] ............................................................ [ 81%] tests/common_tests/formats_tests/fasta_test.py ......................... [ 82%] ............. [ 83%] tests/common_tests/formats_tests/fastq_test.py ......................... [ 85%] ........... [ 86%] tests/common_tests/formats_tests/msa_test.py ........................... [ 87%] ................... [ 89%] tests/common_tests/formats_tests/newick_test.py ........................ [ 90%] ........................................................................ [ 95%] ...... [ 95%] tests/common_tests/formats_tests/phylip_test.py ........ [ 96%] tests/tools_test/factory_test.py xXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX [ 99%] XXXXXXXXXXXXX [100%] =============================== warnings summary =============================== paleomix/atomiccmd/pprint.py:24 /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/atomiccmd/pprint.py:24: DeprecationWarning: 'pipes' is deprecated and slated for removal in Python 3.13 import pipes .pybuild/cpython3_3.11/build/tests/node_test.py::test_dir /usr/lib/python3/dist-packages/_pytest/python.py:199: PytestReturnNotNoneWarning: Expected None, but .pybuild/cpython3_3.11/build/tests/node_test.py::test_dir returned '/build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/tests', which will be an error in a future version of pytest. Did you mean to use `assert` instead of `return`? warnings.warn( .pybuild/cpython3_3.11/build/tests/node_test.py::test_file /usr/lib/python3/dist-packages/_pytest/python.py:199: PytestReturnNotNoneWarning: Expected None, but .pybuild/cpython3_3.11/build/tests/node_test.py::test_file returned '/build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/tests/data', which will be an error in a future version of pytest. Did you mean to use `assert` instead of `return`? warnings.warn( -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html =========== 1442 passed, 1 xfailed, 51 xpassed, 3 warnings in 46.58s =========== make[1]: Leaving directory '/build/paleomix-1.3.7' create-stamp debian/debhelper-build-stamp dh_testroot -O--buildsystem=pybuild dh_prep -O--buildsystem=pybuild dh_auto_install --destdir=debian/paleomix/ -O--buildsystem=pybuild I: pybuild base:240: /usr/bin/python3 setup.py install --root /build/paleomix-1.3.7/debian/paleomix running install /usr/lib/python3/dist-packages/setuptools/command/install.py:34: SetuptoolsDeprecationWarning: setup.py install is deprecated. Use build and pip and other standards-based tools. warnings.warn( running build running build_py running egg_info writing paleomix.egg-info/PKG-INFO writing dependency_links to paleomix.egg-info/dependency_links.txt writing entry points to paleomix.egg-info/entry_points.txt writing requirements to paleomix.egg-info/requires.txt writing top-level names to paleomix.egg-info/top_level.txt reading manifest file 'paleomix.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no files found matching 'paleomix/yaml/CHANGES' warning: no files found matching 'paleomix/yaml/LICENSE' warning: no files found matching 'paleomix/yaml/PKG-INFO' warning: no files found matching 'paleomix/yaml/README' warning: no files found matching 'pylint.conf' adding license file 'LICENSE' writing manifest file 'paleomix.egg-info/SOURCES.txt' /usr/lib/python3/dist-packages/setuptools/command/build_py.py:202: SetuptoolsDeprecationWarning: Installing 'paleomix.resources.examples.bam_pipeline' as data is deprecated, please list it in `packages`. !! ############################ # Package would be ignored # ############################ Python recognizes 'paleomix.resources.examples.bam_pipeline' as an importable package, but it is not listed in the `packages` configuration of setuptools. 'paleomix.resources.examples.bam_pipeline' has been automatically added to the distribution only because it may contain data files, but this behavior is likely to change in future versions of setuptools (and therefore is considered deprecated). Please make sure that 'paleomix.resources.examples.bam_pipeline' is included as a package by using the `packages` configuration field or the proper discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" and "data files" on setuptools documentation page. !! check.warn(importable) /usr/lib/python3/dist-packages/setuptools/command/build_py.py:202: SetuptoolsDeprecationWarning: Installing 'paleomix.resources.examples.bam_pipeline.data' as data is deprecated, please list it in `packages`. !! ############################ # Package would be ignored # ############################ Python recognizes 'paleomix.resources.examples.bam_pipeline.data' as an importable package, but it is not listed in the `packages` configuration of setuptools. 'paleomix.resources.examples.bam_pipeline.data' has been automatically added to the distribution only because it may contain data files, but this behavior is likely to change in future versions of setuptools (and therefore is considered deprecated). Please make sure that 'paleomix.resources.examples.bam_pipeline.data' is included as a package by using the `packages` configuration field or the proper discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" and "data files" on setuptools documentation page. !! check.warn(importable) /usr/lib/python3/dist-packages/setuptools/command/build_py.py:202: SetuptoolsDeprecationWarning: Installing 'paleomix.resources.examples.bam_pipeline.data.ACGATA_L2' as data is deprecated, please list it in `packages`. !! ############################ # Package would be ignored # ############################ Python recognizes 'paleomix.resources.examples.bam_pipeline.data.ACGATA_L2' as an importable package, but it is not listed in the `packages` configuration of setuptools. 'paleomix.resources.examples.bam_pipeline.data.ACGATA_L2' has been automatically added to the distribution only because it may contain data files, but this behavior is likely to change in future versions of setuptools (and therefore is considered deprecated). Please make sure that 'paleomix.resources.examples.bam_pipeline.data.ACGATA_L2' is included as a package by using the `packages` configuration field or the proper discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" and "data files" on setuptools documentation page. !! check.warn(importable) /usr/lib/python3/dist-packages/setuptools/command/build_py.py:202: SetuptoolsDeprecationWarning: Installing 'paleomix.resources.examples.bam_pipeline.prefixes' as data is deprecated, please list it in `packages`. !! ############################ # Package would be ignored # ############################ Python recognizes 'paleomix.resources.examples.bam_pipeline.prefixes' as an importable package, but it is not listed in the `packages` configuration of setuptools. 'paleomix.resources.examples.bam_pipeline.prefixes' has been automatically added to the distribution only because it may contain data files, but this behavior is likely to change in future versions of setuptools (and therefore is considered deprecated). Please make sure that 'paleomix.resources.examples.bam_pipeline.prefixes' is included as a package by using the `packages` configuration field or the proper discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" and "data files" on setuptools documentation page. !! check.warn(importable) /usr/lib/python3/dist-packages/setuptools/command/build_py.py:202: SetuptoolsDeprecationWarning: Installing 'paleomix.resources.examples.phylo_pipeline' as data is deprecated, please list it in `packages`. !! ############################ # Package would be ignored # ############################ Python recognizes 'paleomix.resources.examples.phylo_pipeline' as an importable package, but it is not listed in the `packages` configuration of setuptools. 'paleomix.resources.examples.phylo_pipeline' has been automatically added to the distribution only because it may contain data files, but this behavior is likely to change in future versions of setuptools (and therefore is considered deprecated). Please make sure that 'paleomix.resources.examples.phylo_pipeline' is included as a package by using the `packages` configuration field or the proper discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" and "data files" on setuptools documentation page. !! check.warn(importable) /usr/lib/python3/dist-packages/setuptools/command/build_py.py:202: SetuptoolsDeprecationWarning: Installing 'paleomix.resources.examples.phylo_pipeline.alignment' as data is deprecated, please list it in `packages`. !! ############################ # Package would be ignored # ############################ Python recognizes 'paleomix.resources.examples.phylo_pipeline.alignment' as an importable package, but it is not listed in the `packages` configuration of setuptools. 'paleomix.resources.examples.phylo_pipeline.alignment' has been automatically added to the distribution only because it may contain data files, but this behavior is likely to change in future versions of setuptools (and therefore is considered deprecated). Please make sure that 'paleomix.resources.examples.phylo_pipeline.alignment' is included as a package by using the `packages` configuration field or the proper discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" and "data files" on setuptools documentation page. !! check.warn(importable) /usr/lib/python3/dist-packages/setuptools/command/build_py.py:202: SetuptoolsDeprecationWarning: Installing 'paleomix.resources.examples.phylo_pipeline.alignment.prefixes' as data is deprecated, please list it in `packages`. !! ############################ # Package would be ignored # ############################ Python recognizes 'paleomix.resources.examples.phylo_pipeline.alignment.prefixes' as an importable package, but it is not listed in the `packages` configuration of setuptools. 'paleomix.resources.examples.phylo_pipeline.alignment.prefixes' has been automatically added to the distribution only because it may contain data files, but this behavior is likely to change in future versions of setuptools (and therefore is considered deprecated). Please make sure that 'paleomix.resources.examples.phylo_pipeline.alignment.prefixes' is included as a package by using the `packages` configuration field or the proper discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" and "data files" on setuptools documentation page. !! check.warn(importable) /usr/lib/python3/dist-packages/setuptools/command/build_py.py:202: SetuptoolsDeprecationWarning: Installing 'paleomix.resources.examples.phylo_pipeline.phylogeny' as data is deprecated, please list it in `packages`. !! ############################ # Package would be ignored # ############################ Python recognizes 'paleomix.resources.examples.phylo_pipeline.phylogeny' as an importable package, but it is not listed in the `packages` configuration of setuptools. 'paleomix.resources.examples.phylo_pipeline.phylogeny' has been automatically added to the distribution only because it may contain data files, but this behavior is likely to change in future versions of setuptools (and therefore is considered deprecated). Please make sure that 'paleomix.resources.examples.phylo_pipeline.phylogeny' is included as a package by using the `packages` configuration field or the proper discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" and "data files" on setuptools documentation page. !! check.warn(importable) /usr/lib/python3/dist-packages/setuptools/command/build_py.py:202: SetuptoolsDeprecationWarning: Installing 'paleomix.resources.examples.phylo_pipeline.phylogeny.data.regions' as data is deprecated, please list it in `packages`. !! ############################ # Package would be ignored # ############################ Python recognizes 'paleomix.resources.examples.phylo_pipeline.phylogeny.data.regions' as an importable package, but it is not listed in the `packages` configuration of setuptools. 'paleomix.resources.examples.phylo_pipeline.phylogeny.data.regions' has been automatically added to the distribution only because it may contain data files, but this behavior is likely to change in future versions of setuptools (and therefore is considered deprecated). Please make sure that 'paleomix.resources.examples.phylo_pipeline.phylogeny.data.regions' is included as a package by using the `packages` configuration field or the proper discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" and "data files" on setuptools documentation page. !! check.warn(importable) /usr/lib/python3/dist-packages/setuptools/command/build_py.py:202: SetuptoolsDeprecationWarning: Installing 'paleomix.resources.reports.zonkey' as data is deprecated, please list it in `packages`. !! ############################ # Package would be ignored # ############################ Python recognizes 'paleomix.resources.reports.zonkey' as an importable package, but it is not listed in the `packages` configuration of setuptools. 'paleomix.resources.reports.zonkey' has been automatically added to the distribution only because it may contain data files, but this behavior is likely to change in future versions of setuptools (and therefore is considered deprecated). Please make sure that 'paleomix.resources.reports.zonkey' is included as a package by using the `packages` configuration field or the proper discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" and "data files" on setuptools documentation page. !! check.warn(importable) /usr/lib/python3/dist-packages/setuptools/command/build_py.py:202: SetuptoolsDeprecationWarning: Installing 'paleomix.resources.rscripts.common' as data is deprecated, please list it in `packages`. !! ############################ # Package would be ignored # ############################ Python recognizes 'paleomix.resources.rscripts.common' as an importable package, but it is not listed in the `packages` configuration of setuptools. 'paleomix.resources.rscripts.common' has been automatically added to the distribution only because it may contain data files, but this behavior is likely to change in future versions of setuptools (and therefore is considered deprecated). Please make sure that 'paleomix.resources.rscripts.common' is included as a package by using the `packages` configuration field or the proper discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" and "data files" on setuptools documentation page. !! check.warn(importable) /usr/lib/python3/dist-packages/setuptools/command/build_py.py:202: SetuptoolsDeprecationWarning: Installing 'paleomix.resources.rscripts.zonkey' as data is deprecated, please list it in `packages`. !! ############################ # Package would be ignored # ############################ Python recognizes 'paleomix.resources.rscripts.zonkey' as an importable package, but it is not listed in the `packages` configuration of setuptools. 'paleomix.resources.rscripts.zonkey' has been automatically added to the distribution only because it may contain data files, but this behavior is likely to change in future versions of setuptools (and therefore is considered deprecated). Please make sure that 'paleomix.resources.rscripts.zonkey' is included as a package by using the `packages` configuration field or the proper discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" and "data files" on setuptools documentation page. !! check.warn(importable) running install_lib creating /build/paleomix-1.3.7/debian/paleomix/usr creating /build/paleomix-1.3.7/debian/paleomix/usr/lib creating /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11 creating /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/README.rst -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages creating /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix creating /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/__pycache__ copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/__pycache__/pipeline.cpython-311.pyc -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/__pycache__ copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/__pycache__/main.cpython-311.pyc -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/__pycache__ copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/__pycache__/yaml.cpython-311.pyc -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/__pycache__ copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/__pycache__/nodegraph.cpython-311.pyc -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/__pycache__ copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/__pycache__/node.cpython-311.pyc -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/__pycache__ copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/__pycache__/__init__.cpython-311.pyc -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/__pycache__ creating /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/atomiccmd creating /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/atomiccmd/__pycache__ copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/atomiccmd/__pycache__/sets.cpython-311.pyc -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/atomiccmd/__pycache__ copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/atomiccmd/__pycache__/builder.cpython-311.pyc -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/atomiccmd/__pycache__ copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/atomiccmd/__pycache__/pprint.cpython-311.pyc -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/atomiccmd/__pycache__ copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/atomiccmd/__pycache__/command.cpython-311.pyc -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/atomiccmd/__pycache__ copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/atomiccmd/__pycache__/__init__.cpython-311.pyc -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/atomiccmd/__pycache__ copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/atomiccmd/__init__.py -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/atomiccmd copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/atomiccmd/builder.py -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/atomiccmd copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/atomiccmd/command.py -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/atomiccmd copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/atomiccmd/pprint.py -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/atomiccmd copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/atomiccmd/sets.py -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/atomiccmd creating /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common creating /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common/__pycache__ copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/common/__pycache__/vcfwrap.cpython-311.pyc -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common/__pycache__ copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/common/__pycache__/vcffilter.cpython-311.pyc -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common/__pycache__ copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/common/__pycache__/timer.cpython-311.pyc -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common/__pycache__ copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/common/__pycache__/bamfiles.cpython-311.pyc -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common/__pycache__ copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/common/__pycache__/argparse.cpython-311.pyc -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common/__pycache__ copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/common/__pycache__/rtools.cpython-311.pyc -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common/__pycache__ copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/common/__pycache__/logging.cpython-311.pyc -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common/__pycache__ copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/common/__pycache__/system.cpython-311.pyc -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common/__pycache__ copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/common/__pycache__/text.cpython-311.pyc -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common/__pycache__ copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/common/__pycache__/sequences.cpython-311.pyc -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common/__pycache__ copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/common/__pycache__/sampling.cpython-311.pyc -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common/__pycache__ copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/common/__pycache__/makefile.cpython-311.pyc -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common/__pycache__ copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/common/__pycache__/testing.cpython-311.pyc -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common/__pycache__ copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/common/__pycache__/bedtools.cpython-311.pyc -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common/__pycache__ copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/common/__pycache__/versions.cpython-311.pyc -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common/__pycache__ copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/common/__pycache__/procs.cpython-311.pyc -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common/__pycache__ copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/common/__pycache__/utilities.cpython-311.pyc -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common/__pycache__ copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/common/__pycache__/fileutils.cpython-311.pyc -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common/__pycache__ copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/common/__pycache__/__init__.cpython-311.pyc -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common/__pycache__ creating /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common/formats creating /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common/formats/__pycache__ copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/common/formats/__pycache__/phylip.cpython-311.pyc -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common/formats/__pycache__ copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/common/formats/__pycache__/_graph.cpython-311.pyc -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common/formats/__pycache__ copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/common/formats/__pycache__/newick.cpython-311.pyc -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common/formats/__pycache__ copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/common/formats/__pycache__/msa.cpython-311.pyc -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common/formats/__pycache__ copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/common/formats/__pycache__/fastq.cpython-311.pyc -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common/formats/__pycache__ copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/common/formats/__pycache__/fasta.cpython-311.pyc -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common/formats/__pycache__ copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/common/formats/__pycache__/_common.cpython-311.pyc -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common/formats/__pycache__ copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/common/formats/__pycache__/__init__.cpython-311.pyc -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common/formats/__pycache__ copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/common/formats/__init__.py -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common/formats copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/common/formats/_common.py -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common/formats copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/common/formats/_graph.py -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common/formats copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/common/formats/fasta.py -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common/formats copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/common/formats/fastq.py -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common/formats copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/common/formats/msa.py -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common/formats copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/common/formats/newick.py -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common/formats copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/common/formats/phylip.py -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common/formats copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/common/__init__.py -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/common/argparse.py -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/common/bamfiles.py -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/common/bedtools.py -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/common/fileutils.py -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/common/logging.py -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/common/makefile.py -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/common/procs.py -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/common/rtools.py -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/common/sampling.py -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/common/sequences.py -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/common/system.py -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/common/testing.py -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/common/text.py -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/common/timer.py -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/common/utilities.py -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/common/vcffilter.py -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/common/vcfwrap.py -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/common/versions.py -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common creating /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/nodes creating /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/nodes/__pycache__ copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/nodes/__pycache__/newick.cpython-311.pyc -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/nodes/__pycache__ copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/nodes/__pycache__/examl.cpython-311.pyc -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/nodes/__pycache__ copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/nodes/__pycache__/phylip.cpython-311.pyc -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/nodes/__pycache__ copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/nodes/__pycache__/raxml.cpython-311.pyc -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/nodes/__pycache__ copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/nodes/__pycache__/formats.cpython-311.pyc -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/nodes/__pycache__ copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/nodes/__pycache__/mafft.cpython-311.pyc -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/nodes/__pycache__ copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/nodes/__pycache__/sequences.cpython-311.pyc -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/nodes/__pycache__ copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/nodes/__pycache__/bedtools.cpython-311.pyc -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/nodes/__pycache__ copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/nodes/__pycache__/commands.cpython-311.pyc -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/nodes/__pycache__ copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/nodes/__pycache__/mapdamage.cpython-311.pyc -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/nodes/__pycache__ copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/nodes/__pycache__/picard.cpython-311.pyc -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/nodes/__pycache__ copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/nodes/__pycache__/adapterremoval.cpython-311.pyc -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/nodes/__pycache__ copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/nodes/__pycache__/validation.cpython-311.pyc -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/nodes/__pycache__ copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/nodes/__pycache__/bowtie2.cpython-311.pyc -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/nodes/__pycache__ copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/nodes/__pycache__/bwa.cpython-311.pyc -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/nodes/__pycache__ copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/nodes/__pycache__/samtools.cpython-311.pyc -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/nodes/__pycache__ copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/nodes/__pycache__/__init__.cpython-311.pyc -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/nodes/__pycache__ copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/nodes/__init__.py -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/nodes copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/nodes/adapterremoval.py -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/nodes copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/nodes/bedtools.py -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/nodes copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/nodes/bowtie2.py -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/nodes copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/nodes/bwa.py -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/nodes copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/nodes/commands.py -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/nodes copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/nodes/examl.py -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/nodes copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/nodes/formats.py -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/nodes copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/nodes/mafft.py -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/nodes copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/nodes/mapdamage.py -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/nodes copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/nodes/newick.py -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/nodes copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/nodes/phylip.py -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/nodes copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/nodes/picard.py -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/nodes copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/nodes/raxml.py -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/nodes copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/nodes/samtools.py -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/nodes copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/nodes/sequences.py -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/nodes copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/nodes/validation.py -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/nodes creating /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines creating /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/__pycache__ copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/__pycache__/__init__.cpython-311.pyc -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/__pycache__ creating /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/bam creating /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/bam/__pycache__ copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/bam/__pycache__/trim_pipeline.cpython-311.pyc -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/bam/__pycache__ copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/bam/__pycache__/mkfile.cpython-311.pyc -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/bam/__pycache__ copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/bam/__pycache__/config.cpython-311.pyc -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/bam/__pycache__ copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/bam/__pycache__/nodes.cpython-311.pyc -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/bam/__pycache__ copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/bam/__pycache__/makefile.cpython-311.pyc -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/bam/__pycache__ copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/bam/__pycache__/pipeline.cpython-311.pyc -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/bam/__pycache__ copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/bam/__pycache__/paths.cpython-311.pyc -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/bam/__pycache__ copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/bam/__pycache__/__init__.cpython-311.pyc -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/bam/__pycache__ creating /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/bam/parts creating /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/bam/parts/__pycache__ copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/bam/parts/__pycache__/summary.cpython-311.pyc -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/bam/parts/__pycache__ copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/bam/parts/__pycache__/statistics.cpython-311.pyc -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/bam/parts/__pycache__ copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/bam/parts/__pycache__/target.cpython-311.pyc -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/bam/parts/__pycache__ copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/bam/parts/__pycache__/prefix.cpython-311.pyc -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/bam/parts/__pycache__ copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/bam/parts/__pycache__/sample.cpython-311.pyc -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/bam/parts/__pycache__ copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/bam/parts/__pycache__/library.cpython-311.pyc -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/bam/parts/__pycache__ copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/bam/parts/__pycache__/lane.cpython-311.pyc -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/bam/parts/__pycache__ copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/bam/parts/__pycache__/reads.cpython-311.pyc -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/bam/parts/__pycache__ copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/bam/parts/__pycache__/__init__.cpython-311.pyc -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/bam/parts/__pycache__ copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/bam/parts/__init__.py -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/bam/parts copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/bam/parts/lane.py -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/bam/parts copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/bam/parts/library.py -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/bam/parts copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/bam/parts/prefix.py -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/bam/parts copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/bam/parts/reads.py -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/bam/parts copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/bam/parts/sample.py -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/bam/parts copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/bam/parts/statistics.py -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/bam/parts copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/bam/parts/summary.py -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/bam/parts copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/bam/parts/target.py -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/bam/parts copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/bam/__init__.py -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/bam copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/bam/config.py -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/bam copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/bam/makefile.py -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/bam copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/bam/mkfile.py -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/bam copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/bam/nodes.py -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/bam copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/bam/paths.py -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/bam copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/bam/pipeline.py -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/bam copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/bam/trim_pipeline.py -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/bam creating /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/phylo creating /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/phylo/__pycache__ copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/phylo/__pycache__/makefile.cpython-311.pyc -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/phylo/__pycache__ copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/phylo/__pycache__/config.cpython-311.pyc -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/phylo/__pycache__ copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/phylo/__pycache__/mkfile.cpython-311.pyc -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/phylo/__pycache__ copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/phylo/__pycache__/example.cpython-311.pyc -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/phylo/__pycache__ copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/phylo/__pycache__/pipeline.cpython-311.pyc -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/phylo/__pycache__ copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/phylo/__pycache__/__init__.cpython-311.pyc -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/phylo/__pycache__ creating /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/phylo/parts creating /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/phylo/parts/__pycache__ copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/phylo/parts/__pycache__/phylo.cpython-311.pyc -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/phylo/parts/__pycache__ copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/phylo/parts/__pycache__/msa.cpython-311.pyc -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/phylo/parts/__pycache__ copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/phylo/parts/__pycache__/genotype.cpython-311.pyc -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/phylo/parts/__pycache__ copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/phylo/parts/__pycache__/__init__.cpython-311.pyc -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/phylo/parts/__pycache__ copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/phylo/parts/__init__.py -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/phylo/parts copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/phylo/parts/genotype.py -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/phylo/parts copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/phylo/parts/msa.py -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/phylo/parts copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/phylo/parts/phylo.py -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/phylo/parts copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/phylo/__init__.py -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/phylo copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/phylo/config.py -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/phylo copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/phylo/example.py -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/phylo copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/phylo/makefile.py -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/phylo copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/phylo/mkfile.py -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/phylo copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/phylo/pipeline.py -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/phylo creating /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/zonkey creating /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/zonkey/__pycache__ copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/zonkey/__pycache__/build_tped.cpython-311.pyc -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/zonkey/__pycache__ copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/zonkey/__pycache__/build_mito.cpython-311.pyc -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/zonkey/__pycache__ copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/zonkey/__pycache__/build_db.cpython-311.pyc -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/zonkey/__pycache__ copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/zonkey/__pycache__/common.cpython-311.pyc -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/zonkey/__pycache__ copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/zonkey/__pycache__/database.cpython-311.pyc -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/zonkey/__pycache__ copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/zonkey/__pycache__/config.cpython-311.pyc -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/zonkey/__pycache__ copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/zonkey/__pycache__/pipeline.cpython-311.pyc -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/zonkey/__pycache__ copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/zonkey/__pycache__/__init__.cpython-311.pyc -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/zonkey/__pycache__ creating /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/zonkey/parts creating /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/zonkey/parts/__pycache__ copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/zonkey/parts/__pycache__/summary.cpython-311.pyc -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/zonkey/parts/__pycache__ copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/zonkey/parts/__pycache__/admixture.cpython-311.pyc -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/zonkey/parts/__pycache__ copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/zonkey/parts/__pycache__/report.cpython-311.pyc -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/zonkey/parts/__pycache__ copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/zonkey/parts/__pycache__/nuclear.cpython-311.pyc -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/zonkey/parts/__pycache__ copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/zonkey/parts/__pycache__/mitochondria.cpython-311.pyc -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/zonkey/parts/__pycache__ copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/zonkey/parts/__pycache__/common.cpython-311.pyc -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/zonkey/parts/__pycache__ copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/zonkey/parts/__pycache__/__init__.cpython-311.pyc -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/zonkey/parts/__pycache__ copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/zonkey/parts/__init__.py -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/zonkey/parts copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/zonkey/parts/admixture.py -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/zonkey/parts copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/zonkey/parts/common.py -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/zonkey/parts copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/zonkey/parts/mitochondria.py -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/zonkey/parts copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/zonkey/parts/nuclear.py -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/zonkey/parts copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/zonkey/parts/report.py -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/zonkey/parts copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/zonkey/parts/summary.py -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/zonkey/parts copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/zonkey/__init__.py -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/zonkey copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/zonkey/build_db.py -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/zonkey copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/zonkey/build_mito.py -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/zonkey copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/zonkey/build_tped.py -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/zonkey copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/zonkey/common.py -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/zonkey copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/zonkey/config.py -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/zonkey copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/zonkey/database.py -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/zonkey copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/zonkey/pipeline.py -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/zonkey copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipelines/__init__.py -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines creating /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/resources creating /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/resources/__pycache__ copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/resources/__pycache__/__init__.cpython-311.pyc -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/resources/__pycache__ creating /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/resources/rscripts creating /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/resources/rscripts/zonkey copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/resources/rscripts/zonkey/treemix.r -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/resources/rscripts/zonkey copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/resources/rscripts/zonkey/tinytree.r -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/resources/rscripts/zonkey copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/resources/rscripts/zonkey/pca.r -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/resources/rscripts/zonkey copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/resources/rscripts/zonkey/coverage.r -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/resources/rscripts/zonkey copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/resources/rscripts/zonkey/admixture.r -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/resources/rscripts/zonkey creating /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/resources/rscripts/common copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/resources/rscripts/common/requires.r -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/resources/rscripts/common creating /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/resources/reports creating /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/resources/reports/zonkey copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/resources/reports/zonkey/report.css -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/resources/reports/zonkey creating /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/resources/examples creating /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/resources/examples/phylo_pipeline creating /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/resources/examples/phylo_pipeline/phylogeny creating /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/resources/examples/phylo_pipeline/phylogeny/data creating /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/resources/examples/phylo_pipeline/phylogeny/data/regions copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/resources/examples/phylo_pipeline/phylogeny/data/regions/rCRS.protein_coding.CDS.bed -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/resources/examples/phylo_pipeline/phylogeny/data/regions copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/resources/examples/phylo_pipeline/phylogeny/data/regions/rCRS.non_coding.bed -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/resources/examples/phylo_pipeline/phylogeny/data/regions copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/resources/examples/phylo_pipeline/phylogeny/makefile.yaml -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/resources/examples/phylo_pipeline/phylogeny creating /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/resources/examples/phylo_pipeline/alignment creating /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/resources/examples/phylo_pipeline/alignment/prefixes copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/resources/examples/phylo_pipeline/alignment/prefixes/white_handed_gibbon.fasta -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/resources/examples/phylo_pipeline/alignment/prefixes copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/resources/examples/phylo_pipeline/alignment/prefixes/sumatran_orangutan.fasta -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/resources/examples/phylo_pipeline/alignment/prefixes copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/resources/examples/phylo_pipeline/alignment/prefixes/rCRS.fasta.fai -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/resources/examples/phylo_pipeline/alignment/prefixes copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/resources/examples/phylo_pipeline/alignment/prefixes/rCRS.fasta -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/resources/examples/phylo_pipeline/alignment/prefixes copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/resources/examples/phylo_pipeline/alignment/prefixes/gorilla.fasta -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/resources/examples/phylo_pipeline/alignment/prefixes copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/resources/examples/phylo_pipeline/alignment/prefixes/chimpanzee.fasta -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/resources/examples/phylo_pipeline/alignment/prefixes copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/resources/examples/phylo_pipeline/alignment/prefixes/bonobo.fasta -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/resources/examples/phylo_pipeline/alignment/prefixes copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/resources/examples/phylo_pipeline/alignment/setup.sh -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/resources/examples/phylo_pipeline/alignment copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/resources/examples/phylo_pipeline/alignment/makefile.yaml -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/resources/examples/phylo_pipeline/alignment copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/resources/examples/phylo_pipeline/synthesize_reads.py -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/resources/examples/phylo_pipeline copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/resources/examples/phylo_pipeline/setup.sh -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/resources/examples/phylo_pipeline creating /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/resources/examples/bam_pipeline creating /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/resources/examples/bam_pipeline/prefixes copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/resources/examples/bam_pipeline/prefixes/rCRS.fasta -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/resources/examples/bam_pipeline/prefixes creating /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/resources/examples/bam_pipeline/data creating /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/resources/examples/bam_pipeline/data/ACGATA_L2 copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/resources/examples/bam_pipeline/data/ACGATA_L2/reads.singleton.truncated.gz -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/resources/examples/bam_pipeline/data/ACGATA_L2 copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/resources/examples/bam_pipeline/data/ACGATA_L2/reads.collapsed.truncated.gz -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/resources/examples/bam_pipeline/data/ACGATA_L2 copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/resources/examples/bam_pipeline/data/ACGATA_L2/reads.collapsed.gz -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/resources/examples/bam_pipeline/data/ACGATA_L2 copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/resources/examples/bam_pipeline/data/TGCTCA_L2_R2_03.fastq.gz -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/resources/examples/bam_pipeline/data copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/resources/examples/bam_pipeline/data/TGCTCA_L2_R2_02.fastq.gz -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/resources/examples/bam_pipeline/data copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/resources/examples/bam_pipeline/data/TGCTCA_L2_R2_01.fastq.gz -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/resources/examples/bam_pipeline/data copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/resources/examples/bam_pipeline/data/TGCTCA_L2_R1_03.fastq.gz -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/resources/examples/bam_pipeline/data copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/resources/examples/bam_pipeline/data/TGCTCA_L2_R1_02.fastq.gz -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/resources/examples/bam_pipeline/data copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/resources/examples/bam_pipeline/data/TGCTCA_L2_R1_01.fastq.gz -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/resources/examples/bam_pipeline/data copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/resources/examples/bam_pipeline/data/TGCTCA_L1_R1_03.fastq.gz -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/resources/examples/bam_pipeline/data copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/resources/examples/bam_pipeline/data/TGCTCA_L1_R1_02.fastq.gz -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/resources/examples/bam_pipeline/data copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/resources/examples/bam_pipeline/data/TGCTCA_L1_R1_01.fastq.gz -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/resources/examples/bam_pipeline/data copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/resources/examples/bam_pipeline/data/GCTCTG_L1_R1_03.fastq.gz -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/resources/examples/bam_pipeline/data copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/resources/examples/bam_pipeline/data/GCTCTG_L1_R1_02.fastq.gz -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/resources/examples/bam_pipeline/data copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/resources/examples/bam_pipeline/data/GCTCTG_L1_R1_01.fastq.gz -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/resources/examples/bam_pipeline/data copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/resources/examples/bam_pipeline/data/ACGATA_L1_R2_04.fastq.gz -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/resources/examples/bam_pipeline/data copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/resources/examples/bam_pipeline/data/ACGATA_L1_R2_03.fastq.gz -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/resources/examples/bam_pipeline/data copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/resources/examples/bam_pipeline/data/ACGATA_L1_R2_02.fastq.gz -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/resources/examples/bam_pipeline/data copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/resources/examples/bam_pipeline/data/ACGATA_L1_R2_01.fastq.gz -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/resources/examples/bam_pipeline/data copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/resources/examples/bam_pipeline/data/ACGATA_L1_R1_04.fastq.gz -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/resources/examples/bam_pipeline/data copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/resources/examples/bam_pipeline/data/ACGATA_L1_R1_03.fastq.gz -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/resources/examples/bam_pipeline/data copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/resources/examples/bam_pipeline/data/ACGATA_L1_R1_02.fastq.gz -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/resources/examples/bam_pipeline/data copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/resources/examples/bam_pipeline/data/ACGATA_L1_R1_01.fastq.gz -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/resources/examples/bam_pipeline/data copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/resources/examples/bam_pipeline/makefile.yaml -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/resources/examples/bam_pipeline copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/resources/__init__.py -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/resources creating /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/tools creating /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/tools/__pycache__ copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/tools/__pycache__/validate_fastq.cpython-311.pyc -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/tools/__pycache__ copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/tools/__pycache__/vcf_to_fasta.cpython-311.pyc -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/tools/__pycache__ copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/tools/__pycache__/vcf_filter.cpython-311.pyc -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/tools/__pycache__ copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/tools/__pycache__/rmdup_collapsed.cpython-311.pyc -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/tools/__pycache__ copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/tools/__pycache__/depths.cpython-311.pyc -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/tools/__pycache__ copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/tools/__pycache__/coverage.cpython-311.pyc -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/tools/__pycache__ copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/tools/__pycache__/cleanup.cpython-311.pyc -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/tools/__pycache__ copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/tools/__pycache__/factory.cpython-311.pyc -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/tools/__pycache__ copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/tools/__pycache__/__init__.cpython-311.pyc -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/tools/__pycache__ creating /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/tools/bam_stats creating /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/tools/bam_stats/__pycache__ copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/tools/bam_stats/__pycache__/common.cpython-311.pyc -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/tools/bam_stats/__pycache__ copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/tools/bam_stats/__pycache__/coverage.cpython-311.pyc -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/tools/bam_stats/__pycache__ copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/tools/bam_stats/__pycache__/__init__.cpython-311.pyc -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/tools/bam_stats/__pycache__ copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/tools/bam_stats/__init__.py -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/tools/bam_stats copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/tools/bam_stats/common.py -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/tools/bam_stats copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/tools/bam_stats/coverage.py -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/tools/bam_stats copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/tools/__init__.py -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/tools copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/tools/cleanup.py -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/tools copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/tools/coverage.py -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/tools copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/tools/depths.py -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/tools copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/tools/dupcheck.py -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/tools copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/tools/factory.py -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/tools copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/tools/gtf_to_bed.py -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/tools copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/tools/rmdup_collapsed.py -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/tools copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/tools/validate_fastq.py -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/tools copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/tools/vcf_filter.py -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/tools copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/tools/vcf_to_fasta.py -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/tools copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/__init__.py -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/main.py -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/node.py -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/nodegraph.py -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/pipeline.py -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix copying /build/paleomix-1.3.7/.pybuild/cpython3_3.11/build/paleomix/yaml.py -> /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix byte-compiling /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/atomiccmd/__init__.py to __init__.cpython-311.pyc byte-compiling /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/atomiccmd/builder.py to builder.cpython-311.pyc byte-compiling /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/atomiccmd/command.py to command.cpython-311.pyc byte-compiling /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/atomiccmd/pprint.py to pprint.cpython-311.pyc byte-compiling /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/atomiccmd/sets.py to sets.cpython-311.pyc byte-compiling /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common/formats/__init__.py to __init__.cpython-311.pyc byte-compiling /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common/formats/_common.py to _common.cpython-311.pyc byte-compiling /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common/formats/_graph.py to _graph.cpython-311.pyc byte-compiling /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common/formats/fasta.py to fasta.cpython-311.pyc byte-compiling /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common/formats/fastq.py to fastq.cpython-311.pyc byte-compiling /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common/formats/msa.py to msa.cpython-311.pyc byte-compiling /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common/formats/newick.py to newick.cpython-311.pyc byte-compiling /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common/formats/phylip.py to phylip.cpython-311.pyc byte-compiling /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common/__init__.py to __init__.cpython-311.pyc byte-compiling /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common/argparse.py to argparse.cpython-311.pyc byte-compiling /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common/bamfiles.py to bamfiles.cpython-311.pyc byte-compiling /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common/bedtools.py to bedtools.cpython-311.pyc byte-compiling /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common/fileutils.py to fileutils.cpython-311.pyc byte-compiling /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common/logging.py to logging.cpython-311.pyc byte-compiling /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common/makefile.py to makefile.cpython-311.pyc byte-compiling /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common/procs.py to procs.cpython-311.pyc byte-compiling /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common/rtools.py to rtools.cpython-311.pyc byte-compiling /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common/sampling.py to sampling.cpython-311.pyc byte-compiling /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common/sequences.py to sequences.cpython-311.pyc byte-compiling /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common/system.py to system.cpython-311.pyc byte-compiling /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common/testing.py to testing.cpython-311.pyc byte-compiling /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common/text.py to text.cpython-311.pyc byte-compiling /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common/timer.py to timer.cpython-311.pyc byte-compiling /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common/utilities.py to utilities.cpython-311.pyc byte-compiling /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common/vcffilter.py to vcffilter.cpython-311.pyc byte-compiling /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common/vcfwrap.py to vcfwrap.cpython-311.pyc byte-compiling /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/common/versions.py to versions.cpython-311.pyc byte-compiling /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/nodes/__init__.py to __init__.cpython-311.pyc byte-compiling /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/nodes/adapterremoval.py to adapterremoval.cpython-311.pyc byte-compiling /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/nodes/bedtools.py to bedtools.cpython-311.pyc byte-compiling /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/nodes/bowtie2.py to bowtie2.cpython-311.pyc byte-compiling /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/nodes/bwa.py to bwa.cpython-311.pyc byte-compiling /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/nodes/commands.py to commands.cpython-311.pyc byte-compiling /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/nodes/examl.py to examl.cpython-311.pyc byte-compiling /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/nodes/formats.py to formats.cpython-311.pyc byte-compiling /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/nodes/mafft.py to mafft.cpython-311.pyc byte-compiling /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/nodes/mapdamage.py to mapdamage.cpython-311.pyc byte-compiling /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/nodes/newick.py to newick.cpython-311.pyc byte-compiling /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/nodes/phylip.py to phylip.cpython-311.pyc byte-compiling /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/nodes/picard.py to picard.cpython-311.pyc byte-compiling /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/nodes/raxml.py to raxml.cpython-311.pyc byte-compiling /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/nodes/samtools.py to samtools.cpython-311.pyc byte-compiling /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/nodes/sequences.py to sequences.cpython-311.pyc byte-compiling /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/nodes/validation.py to validation.cpython-311.pyc byte-compiling /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/bam/parts/__init__.py to __init__.cpython-311.pyc byte-compiling /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/bam/parts/lane.py to lane.cpython-311.pyc byte-compiling /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/bam/parts/library.py to library.cpython-311.pyc byte-compiling /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/bam/parts/prefix.py to prefix.cpython-311.pyc byte-compiling /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/bam/parts/reads.py to reads.cpython-311.pyc byte-compiling /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/bam/parts/sample.py to sample.cpython-311.pyc byte-compiling /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/bam/parts/statistics.py to statistics.cpython-311.pyc byte-compiling /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/bam/parts/summary.py to summary.cpython-311.pyc byte-compiling /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/bam/parts/target.py to target.cpython-311.pyc byte-compiling /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/bam/__init__.py to __init__.cpython-311.pyc byte-compiling /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/bam/config.py to config.cpython-311.pyc byte-compiling /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/bam/makefile.py to makefile.cpython-311.pyc byte-compiling /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/bam/mkfile.py to mkfile.cpython-311.pyc byte-compiling /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/bam/nodes.py to nodes.cpython-311.pyc byte-compiling /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/bam/paths.py to paths.cpython-311.pyc byte-compiling /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/bam/pipeline.py to pipeline.cpython-311.pyc byte-compiling /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/bam/trim_pipeline.py to trim_pipeline.cpython-311.pyc byte-compiling /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/phylo/parts/__init__.py to __init__.cpython-311.pyc byte-compiling /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/phylo/parts/genotype.py to genotype.cpython-311.pyc byte-compiling /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/phylo/parts/msa.py to msa.cpython-311.pyc byte-compiling /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/phylo/parts/phylo.py to phylo.cpython-311.pyc byte-compiling /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/phylo/__init__.py to __init__.cpython-311.pyc byte-compiling /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/phylo/config.py to config.cpython-311.pyc byte-compiling /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/phylo/example.py to example.cpython-311.pyc byte-compiling /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/phylo/makefile.py to makefile.cpython-311.pyc byte-compiling /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/phylo/mkfile.py to mkfile.cpython-311.pyc byte-compiling /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/phylo/pipeline.py to pipeline.cpython-311.pyc byte-compiling /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/zonkey/parts/__init__.py to __init__.cpython-311.pyc byte-compiling /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/zonkey/parts/admixture.py to admixture.cpython-311.pyc byte-compiling /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/zonkey/parts/common.py to common.cpython-311.pyc byte-compiling /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/zonkey/parts/mitochondria.py to mitochondria.cpython-311.pyc byte-compiling /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/zonkey/parts/nuclear.py to nuclear.cpython-311.pyc byte-compiling /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/zonkey/parts/report.py to report.cpython-311.pyc byte-compiling /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/zonkey/parts/summary.py to summary.cpython-311.pyc byte-compiling /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/zonkey/__init__.py to __init__.cpython-311.pyc byte-compiling /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/zonkey/build_db.py to build_db.cpython-311.pyc byte-compiling /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/zonkey/build_mito.py to build_mito.cpython-311.pyc byte-compiling /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/zonkey/build_tped.py to build_tped.cpython-311.pyc byte-compiling /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/zonkey/common.py to common.cpython-311.pyc byte-compiling /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/zonkey/config.py to config.cpython-311.pyc byte-compiling /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/zonkey/database.py to database.cpython-311.pyc byte-compiling /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/zonkey/pipeline.py to pipeline.cpython-311.pyc byte-compiling /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipelines/__init__.py to __init__.cpython-311.pyc byte-compiling /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/resources/examples/phylo_pipeline/synthesize_reads.py to synthesize_reads.cpython-311.pyc byte-compiling /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/resources/__init__.py to __init__.cpython-311.pyc byte-compiling /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/tools/bam_stats/__init__.py to __init__.cpython-311.pyc byte-compiling /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/tools/bam_stats/common.py to common.cpython-311.pyc byte-compiling /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/tools/bam_stats/coverage.py to coverage.cpython-311.pyc byte-compiling /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/tools/__init__.py to __init__.cpython-311.pyc byte-compiling /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/tools/cleanup.py to cleanup.cpython-311.pyc byte-compiling /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/tools/coverage.py to coverage.cpython-311.pyc byte-compiling /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/tools/depths.py to depths.cpython-311.pyc byte-compiling /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/tools/dupcheck.py to dupcheck.cpython-311.pyc byte-compiling /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/tools/factory.py to factory.cpython-311.pyc byte-compiling /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/tools/gtf_to_bed.py to gtf_to_bed.cpython-311.pyc byte-compiling /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/tools/rmdup_collapsed.py to rmdup_collapsed.cpython-311.pyc byte-compiling /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/tools/validate_fastq.py to validate_fastq.cpython-311.pyc byte-compiling /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/tools/vcf_filter.py to vcf_filter.cpython-311.pyc byte-compiling /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/tools/vcf_to_fasta.py to vcf_to_fasta.cpython-311.pyc byte-compiling /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/__init__.py to __init__.cpython-311.pyc byte-compiling /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/main.py to main.cpython-311.pyc byte-compiling /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/node.py to node.cpython-311.pyc byte-compiling /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/nodegraph.py to nodegraph.cpython-311.pyc byte-compiling /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/pipeline.py to pipeline.cpython-311.pyc byte-compiling /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix/yaml.py to yaml.cpython-311.pyc running install_egg_info Copying paleomix.egg-info to /build/paleomix-1.3.7/debian/paleomix/usr/lib/python3.11/dist-packages/paleomix-1.3.7.egg-info Skipping SOURCES.txt running install_scripts Installing paleomix script to /build/paleomix-1.3.7/debian/paleomix/usr/bin debian/rules override_dh_install make[1]: Entering directory '/build/paleomix-1.3.7' dh_install find debian -name LICENSE -delete find debian -name README.rst -delete make[1]: Leaving directory '/build/paleomix-1.3.7' debian/rules override_dh_installdocs make[1]: Entering directory '/build/paleomix-1.3.7' dh_installdocs # since tests dir contains empty files which are used afterwards for # testing and dh_installdocs is ignoring empty files we need to make # sure all files are really copied rsync -a -v tests debian/paleomix/usr/share/doc/paleomix sending incremental file list tests/atomiccmd_test/ tests/common_tests/ tests/common_tests/formats_tests/ tests/data/ tests/data/empty_file_1 tests/data/empty_file_2 sent 950 bytes received 76 bytes 2,052.00 bytes/sec total size is 334,745 speedup is 326.26 # test runner is seeking for paleomix modules in source - we use inside the installed package ### sed -i 's:(find paleomix -mindepth 1:(find /usr/lib/python*/dist-packages/paleomix -mindepth 1:' debian/*/usr/share/doc/*/tests/run #echo "====== Also empty files belong to the docs ======" #find debian -name "empty_file*" #find debian -name "timestamp_*" #echo "====== Hope something was printed between these lines ====" # # This test tries to execute setup.sh which does not work outside source directory find debian/paleomix/usr/share/doc/ -name fileutils_test.py -delete find debian/paleomix/usr/share/doc/ -name setup.h -delete make[1]: Leaving directory '/build/paleomix-1.3.7' dh_installchangelogs -O--buildsystem=pybuild dh_installman -O--buildsystem=pybuild debian/rules override_dh_python3 make[1]: Entering directory '/build/paleomix-1.3.7' dh_python3 --verbose --shebang=/usr/bin/python3 D: dh_python3 dh_python3:179: version: 5.20230130 D: dh_python3 dh_python3:180: argv: ['/usr/bin/dh_python3', '--verbose', '--shebang=/usr/bin/python3'] D: dh_python3 dh_python3:181: options: Namespace(guess_deps=True, skip_private=False, verbose=True, arch=None, package=None, no_package=None, remaining_packages=False, compile_all=False, vrange=None, regexpr=None, accept_upstream_versions=False, depends=None, depends_section=None, recommends=None, recommends_section=None, suggests=None, suggests_section=None, requires=None, shebang='/usr/bin/python3', ignore_shebangs=False, clean_dbg_pkg=True, no_ext_rename=False, no_shebang_rewrite=False, private_dir=None, O=None) D: dh_python3 dh_python3:182: supported Python versions: 3.11 (default=3.11) D: dh_python3 debhelper:183: source=paleomix, binary packages=['paleomix'] D: dh_python3 dh_python3:204: processing package paleomix... D: dh_python3 fs:52: moving files from debian/paleomix/usr/lib/python3.11/dist-packages to debian/paleomix/usr/lib/python3/dist-packages/ I: dh_python3 tools:114: replacing shebang in debian/paleomix/usr/bin/paleomix D: dh_python3 fs:400: package paleomix details = {'requires.txt': {'debian/paleomix/usr/lib/python3/dist-packages/paleomix-1.3.7.egg-info/requires.txt'}, 'egg-info': set(), 'dist-info': set(), 'nsp.txt': set(), 'shebangs': {/usr/bin/python3}, 'public_vers': {Version('3')}, 'private_dirs': {}, 'compile': True, 'ext_vers': set(), 'ext_no_version': set()} D: dh_python3 depends:117: generating dependencies for package paleomix D: dh_python3 pydist:173: trying to find dependency for coloredlogs>=10.0 (python=None) D: dh_python3 pydist:207: dependency: module seems to be installed D: dh_python3 pydist:270: dependency: included in build-deps D: dh_python3 pydist:173: trying to find dependency for configargparse>=0.13.0 (python=None) D: dh_python3 pydist:207: dependency: module seems to be installed D: dh_python3 pydist:270: dependency: included in build-deps D: dh_python3 pydist:173: trying to find dependency for pysam>=0.10.0 (python=None) D: dh_python3 pydist:207: dependency: module seems to be installed D: dh_python3 pydist:270: dependency: included in build-deps D: dh_python3 pydist:173: trying to find dependency for ruamel.yaml>=0.16.0 (python=None) D: dh_python3 pydist:207: dependency: module seems to be installed D: dh_python3 pydist:270: dependency: included in build-deps D: dh_python3 pydist:173: trying to find dependency for setproctitle>=1.1.0 (python=None) D: dh_python3 pydist:207: dependency: module seems to be installed D: dh_python3 pydist:270: dependency: included in build-deps D: dh_python3 depends:281: D={'python3-pysam', 'python3-setproctitle', 'python3-coloredlogs', 'python3:any', 'python3-ruamel.yaml', 'python3-configargparse'}; R=[]; S=[]; E=[], B=[]; RT=[] make[1]: Leaving directory '/build/paleomix-1.3.7' 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 debian/rules override_dh_fixperms make[1]: Entering directory '/build/paleomix-1.3.7' dh_fixperms for rs in `find debian -iname "*.r"` ; do \ if head -n 1 $rs | grep -q '^#!/usr/bin/.*Rscript' ; then \ chmod +x $rs ; \ else \ chmod -x $rs ; \ fi ; \ done make[1]: Leaving directory '/build/paleomix-1.3.7' 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 'paleomix' in '../paleomix_1.3.7-3_arm64.deb'. dpkg-genbuildinfo --build=binary -O../paleomix_1.3.7-3_arm64.buildinfo dpkg-genchanges --build=binary -O../paleomix_1.3.7-3_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/10559 and its subdirectories I: Current time: Fri Apr 7 23:12:00 -12 2023 I: pbuilder-time-stamp: 1680952320 Sat Apr 8 11:12:02 UTC 2023 I: 1st build successful. Starting 2nd build on remote node codethink15-arm64.debian.net. Sat Apr 8 11:12:02 UTC 2023 I: Preparing to do remote build '2' on codethink15-arm64.debian.net. Sat Apr 8 11:14:25 UTC 2023 I: Deleting $TMPDIR on codethink15-arm64.debian.net. Sat Apr 8 11:14:26 UTC 2023 I: paleomix_1.3.7-3_arm64.changes: Format: 1.8 Date: Sat, 14 Jan 2023 19:29:03 +0100 Source: paleomix Binary: paleomix Architecture: arm64 Version: 1.3.7-3 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Étienne Mollier Description: paleomix - pipelines and tools for the processing of ancient and modern HTS Closes: 1028856 Changes: paleomix (1.3.7-3) unstable; urgency=medium . * d/salsa-ci.yml: disable i386 and reprotest; they always failed. * python3.11.patch: add; fix test failure with python3.11. (Closes: #1028856) * d/copyright: bump copyright year. * Standards-Version: 4.6.2 (routine-update) Checksums-Sha1: d1e4d19a9d754b6f6ea6a22d0345b53f5aa14636 11418 paleomix_1.3.7-3_arm64.buildinfo 6f0192e6a7c6b4917f77bb9768f9ffc03fa11c76 983840 paleomix_1.3.7-3_arm64.deb Checksums-Sha256: 61ac8273e93e8bb53b7cae27fecfa56f220a70d4a537daa72bc101c903747800 11418 paleomix_1.3.7-3_arm64.buildinfo a39a3110ece7ab6766427c7d72b34f94adf6ed87500cc962aeaac5d9e2779ea8 983840 paleomix_1.3.7-3_arm64.deb Files: bfe3f32dcdff7597e09f83647dc0f83f 11418 science optional paleomix_1.3.7-3_arm64.buildinfo 1ee7c8ed725cb72bbf4d52e517766838 983840 science optional paleomix_1.3.7-3_arm64.deb Sat Apr 8 11:14:27 UTC 2023 I: diffoscope 240 will be used to compare the two builds: # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.kAw6y1MW/paleomix_1.3.7-3.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.kAw6y1MW/paleomix_1.3.7-3.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.kAw6y1MW/paleomix_1.3.7-3.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.kAw6y1MW/b1/paleomix_1.3.7-3_arm64.changes /srv/reproducible-results/rbuild-debian/r-b-build.kAw6y1MW/b2/paleomix_1.3.7-3_arm64.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call abc.DotChangesFile ## main (total time: 0.290s) 0.290s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.025s) 0.025s 12 calls diffoscope.comparators.binary.FilesystemFile 0.000s 10 calls abc.DotChangesFile ## specialize (total time: 0.000s) 0.000s 1 call specialize Sat Apr 8 11:14:28 UTC 2023 I: diffoscope 240 found no differences in the changes files, and a .buildinfo file also exists. Sat Apr 8 11:14:28 UTC 2023 I: paleomix from bookworm built successfully and reproducibly on arm64. Sat Apr 8 11:14:30 UTC 2023 I: Submitting .buildinfo files to external archives: Sat Apr 8 11:14:30 UTC 2023 I: Submitting 16K b1/paleomix_1.3.7-3_arm64.buildinfo.asc Sat Apr 8 11:14:31 UTC 2023 I: Submitting 16K b2/paleomix_1.3.7-3_arm64.buildinfo.asc Sat Apr 8 11:14:32 UTC 2023 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Sat Apr 8 11:14:32 UTC 2023 I: Done submitting .buildinfo files. Sat Apr 8 11:14:32 UTC 2023 I: Removing signed paleomix_1.3.7-3_arm64.buildinfo.asc files: removed './b1/paleomix_1.3.7-3_arm64.buildinfo.asc' removed './b2/paleomix_1.3.7-3_arm64.buildinfo.asc'